524 results on '"Peter Lu"'
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2. Supplementary Tables 1 - 2 from An Evaluation of Novel, Lower-Cost Molecular Screening Tests for Human Papillomavirus in Rural China
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Philip E. Castle, Mark H. Stoler, Feng Chen, Jing Li, Roger Peck, Ping Bai, Marthe Berard-Bergery, Charles Mahoney, Proma Paul, Pooja Bansil, Le-Ni Kang, Xun Zhang, Peter Lu, Melissa Valdez, Wen Chen, Johannes Schweizer, You-Lin Qiao, Jose Jeronimo, and Fang-Hui Zhao
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PDF file - 107K, Supplemental Tables 1A and 1B: Agreement between worst study histopathologic diagnosis. Supplemental Table 2: The relationship of E6 and DNA detection of human papillomavirus (HPV) genotypes 16, 18, and/or 45 (HPV16/18/45) on cervical exfoliated cells with HPV genotypes detected in the tissue of cervical intraepithelial neoplasia grade 2 (CIN2), grade 3 (CIN3), and cervical cancer, overall (all) and by clinical site.
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- 2023
3. Data from An Evaluation of Novel, Lower-Cost Molecular Screening Tests for Human Papillomavirus in Rural China
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Philip E. Castle, Mark H. Stoler, Feng Chen, Jing Li, Roger Peck, Ping Bai, Marthe Berard-Bergery, Charles Mahoney, Proma Paul, Pooja Bansil, Le-Ni Kang, Xun Zhang, Peter Lu, Melissa Valdez, Wen Chen, Johannes Schweizer, You-Lin Qiao, Jose Jeronimo, and Fang-Hui Zhao
- Abstract
New, lower-cost tests that target high-risk human papillomavirus (HR-HPV) have been developed for cervical cancer screening in lower-resource settings but large, population-based screening studies are lacking. Women ages 25 to 65 years and living in rural China (n = 7,543) self-collected a cervicovaginal specimen, had 2 cervical specimens collected by a clinician, and underwent visual inspection after acetic acid (VIA). The self- and one clinician-collected specimens underwent HR-HPV DNA testing by careHPV (QIAGEN) and Hybrid Capture 2 (HC2; QIAGEN) and the other clinician-collected specimen was tested for HPV16, 18, and 45 E6 using OncoE6 (Arbor Vita Corporation). Women who screened positive for any test and a random sample of those negative on all tests underwent colposcopic evaluation. The percent test positive was 1.8% for HPV E6 oncoprotein, between 14% and 18% for HR-HPV DNA testing, and 7.3% for VIA. The sensitivity for cervical intraepithelial neoplasia grade 3 or more severe (CIN3+; n = 99) was 53.5% for OncoE6, 97.0% for both careHPV and HC2 testing of the clinician-collected specimen, 83.8% for careHPV testing and 90.9% for HC2 testing of the self-collected specimen, and 50.5% for VIA. OncoE6 had the greatest positive predictive value (PPV), at 40.8% for CIN3+, compared with the other tests, which had a PPV of less than 10%. OncoE6 tested 70.3% positive for HPV16, 18, or 45-positive CIN3+ and tested negative for all HPV16-, 18-, or 45-negative CIN3+ (P < 0.0001). HPV E6 oncoprotein detection is useful for identifying women who have cervical precancer and cancer. Cancer Prev Res; 6(9); 938–48. ©2013 AACR.
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- 2023
4. Rangers on the frontline of wildlife monitoring: a case study on African lions in Uganda’s Nile Delta
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Alexander R. Braczkowski, Lilian Namukose, Silvan Musobozi, Orin Cornille, Tutilo Mudumba, Gilbert Drileyo, Femke Broekhuis, Sophia Jingo, Brenda Asimwe, Peter Luhonda, Bosco Atukwatse, Christopher J. O’Bryan, Hamish McCallum, Duan Biggs, Luke Gibson, Aggrey Rwetsiba, Arjun M. Gopalaswamy, Peter Lindsey, and Nicholas Elliot
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Biology (General) ,QH301-705.5 - Abstract
Regular population monitoring of imperilled charismatic species such as large carnivores is critical for conservation. However, the role of monitoring in conservation is frequently diminished due to: 1) surveys being implemented in isolation, 2) limited on-ground-capacity leading to infrequent monitoring, and 3) inappropriate methods being applied. Wildlife monitoring is often resource-intensive and the utility and cost of different field protocols is rarely reported. In this study we deployed two standard field protocols aimed at collecting data on African lions within a spatial capture-recapture framework. For our first protocol, we trained Uganda Wildlife Authority rangers in search-encounter techniques, the industry gold standard for monitoring lions. The second protocol involved deploying 32 paired stations of state-of-the-art infra-red camera traps. During the search-encounter protocol, two rangers covered 2939 km in 76 days, recording 102 detections (30 individuals) in a ~ 256 km2 area. The resulting density estimates (13.91 lions/100 km2, posterior SD = 2.34) yielded acceptable precision. Conversely, 64 camera traps over 1601 trap nights yielded two usable lion detections. We argue that where wildlife tourism rangers exist, they could be a powerful addition to future lion and wildlife census attempts across the continent. Our results confirm that the current technology of store-bought infra-red camera traps is not suitable for individual identification of lions, and therefore cannot be applied to analytical models that require unambiguous individual identities. However, we encourage the continued testing and advancement of infra-red camera trap technology since in many instances, this may be preferable to white-flash camera traps, which can yield individual identities for lions. Our study also shows the immense importance of the Nile Delta for African lions in Uganda’s Murchison Falls National Park, a protected area with both oil extraction and high rates of anthropogenic snaring pressure.
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- 2024
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5. Effect of carbohydrate type in silages and concentrates on feed intake, enteric methane, and milk yield from dairy cows
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Giulio Giagnoni, Peter Lund, Marianne Johansen, Anne Louise F. Hellwing, Samantha J. Noel, Julia P.S. Thomsen, Nina A. Poulsen, and Martin R. Weisbjerg
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barley ,beet pulp ,corn ,grass-clover ,Dairy processing. Dairy products ,SF250.5-275 ,Dairying ,SF221-250 - Abstract
ABSTRACT: Dietary carbohydrate manipulation can be used to reduce enteric CH4 emission, but few studies have focused on the interaction of the different types of carbohydrates that can affect feed intake and ruminal fermentation. Understanding this interaction is necessary to make the most out of CH4 mitigation feeding strategies using different dietary carbohydrates. The aim of this study was to test the effect on enteric CH4 emission, feed intake, and milk production response when cows were fed either grass-clover silage (GCS) or corn silage (CS) as the sole forage source (55% of dry matter, DM), in combination with either barley (BAR) or dried beet pulp (DBP) as a concentrate (21.5% of DM). A total of 24 (half first-parity and half second-parity) cows were used in a crossover design with 2 periods of 21 d each, receiving 2 of 4 diets obtained from a 2 × 2 factorial arrangement of the experimental diet. Feed intake, CH4 emission metrics, and milk production were recorded at the end of the experimental periods. The diets had NDF concentrations between 258 and 340 g/kg of DM and starch concentrations between 340 and 7.45 g/kg of DM (CS-BAR and GCS-DBP, respectively). The effects of silage and concentrate on dry matter intake (DMI) were additive, with the highest feed intake in cows fed CS-BAR, followed by cows fed CS-DBP, GCS-BAR, and GCS-DBP (21.2, 19.9, 19.1, and 18.3 kg/d, respectively). Energy corrected milk (ECM) yield was not affected by silage source in first parity cows, but it was higher for cows fed CS than cows fed GCS in second parity. The effects of silage and concentrate on CH4 production (g/d), yield (g/kg of DMI), and intensity (g/kg of ECM) were not additive, as cows fed GCS had similar responses regardless of the concentrate used, but cows fed CS had lower CH4 production, yield, and intensity when fed BAR instead of DBP. The lower CH4 production, yield, and intensity in cows fed CS-BAR compared with other diets could be partially explained by the nonlinear relationship between ruminal VFA and carbohydrates (NDF and starch) concentration reported in the literature; however, we observed a linear relationship between the acetate/propionate ratio and CH4 yield, suggesting possible other effects. The effects of silage and concentrate on the ruminal VFA were additive in first parity cows, but not in second parity cows. The interaction between dietary carbohydrate type and parity might indicate an effect of feed intake or the energy balance of the cow. Feeding cows silage and concentrate both rich in starch can result in the lowest enteric CH4 emission.
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- 2024
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6. Biodiversity of a temperate karst landscape–ice cave collapse doline supports high α-diversity of the soil mesofauna
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Veronika Petrovová, Peter Ľuptáčik, Vladislav Kolarčik, and Ľubomír Kováč
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Medicine ,Science - Abstract
Abstract Caves represent a specific environment with a special microclimate and fauna adapted to it. However, we have still a restricted knowledge on soil fauna communities in an environments with a marked microclimate gradient at the interface between cave and surface habitats. In the present study, we investigated the community patterns of dominant soil microarthropod group, oribatid mites, and their relationship to environmental factors across the microclimate gradient along a transect with seven study sites from cold and wet cave entrance zone to warm and drier deciduous forest. The cold and wet sites showed low oribatid abundances and a high spatial clustering of individuals in comparison to the warm sites. The oribatid mites showed significantly higher abundance and species richness at warm forest sites. Indicator species analysis indicated specific cold-tolerant species that dominated at cold sites of the gradient, but which were absent at the warmest sites. Variance analysis clarified that community composition at sites were significantly driven by environmental factors: temperature, soil moisture, pH and C/N ratio. The study underlines the importance of ice cave entrances as sources of high α-diversity of soil mesofauna and thus the conservation priority of these valuable habitats.
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- 2024
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7. Single-Molecule Human Nucleosome Spontaneously Ruptures under the Stress of Compressive Force: A New Perspective on Gene Stability and Epigenetic Pathways
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Lalita Shahu, S. Roy Chowdhury, and H. Peter Lu
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Materials Chemistry ,Physical and Theoretical Chemistry ,Surfaces, Coatings and Films - Abstract
Force manipulation on the biological entities from living cells to protein molecules has revealed many mechanical details of cell biology from resolving folding and unfolding pathways to finding molecular interaction forces. A nucleosome is the basic repeating unit of chromatin where the histone octamer is wrapped by DNA, important for gene stability and regulation. How the inner side of the DNA gets accessed by other DNA binding molecules has been a puzzle that has been intensively studied and debated, important to epigenetics, gene stability, and regulations. Here we report our observation of spontaneous ruptures of human nucleosomes under pico-Newton (pN) compressive force. The amplitude of the compressive force, a squeezing rather than pulling force, involved in our experiment is tens of pN, which can be thermally available by biological force fluctuation at room temperature and under physiological conditions. This kind of structural rupture can loosen up the DNA around the histone, which in turn makes the DNA accessible to transcription and epigenetic modifications.
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- 2022
8. Effect of Bis-diazirine-Mediated Photo-Crosslinking on Polyvinylcarbazole and Solution-Processed Polymer LEDs
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H. Peter Lu, S. Roy Chowdhury, Kaustav Dey, Joseph Shinar, Ruth Shinar, Pavel Anzenbacher, and Erik Dykstra
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chemistry.chemical_classification ,Materials science ,Polymer ,Photochemistry ,Electronic, Optical and Magnetic Materials ,Solution processed ,law.invention ,chemistry.chemical_compound ,chemistry ,law ,Photo crosslinking ,Diazirine ,Materials Chemistry ,Electrochemistry ,Light-emitting diode - Published
- 2021
9. Unraveling the mechanism of tau protein aggregation in presence of zinc ion: The earliest step of tau aggregation
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S. Roy Chowdhury and H. Peter Lu
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Raman spectroscopic analysis ,Physics and Astronomy (miscellaneous) ,Materials Science (miscellaneous) ,Physics ,QC1-999 ,Biophysics ,Condensed Matter Physics ,Biochemistry ,Atomic and Molecular Physics, and Optics ,Electronic, Optical and Magnetic Materials ,Aggregation ,Chemistry ,Tau protein ,Physical and Theoretical Chemistry ,QD1-999 - Abstract
Recent studies have indicated that tau protein aggregation is closely related to Alzheimer's disease. Though the later stages of the aggregation process are extensively studied, it is still unknown how the aggregation occurs in the earliest stage. It is reported that the presence of low micromolar zinc ions can trigger the aggregation process even without the presence of any cofactors like heparin. The earlier studies have indicated that zinc binds to the tau protein in a tetrahedral geometry, binding to two cysteine and two histidine residues. Nevertheless, the mechanism is still unclear on how the aggregation occurs, especially the early events that lead to the aggregation. Here we have used surface-enhanced Raman spectroscopy to study the aggregation process under the presence of zinc ions. We observed a broadening of the C-S stretching band upon the addition of zinc ions, which indicates a direct involvement of the zinc-binding domain in the aggregation process. We attribute that zinc ion promotes the intermolecular bridging of tau monomers through cysteine and histidine binding, and that triggers the aggregation process. Our finding suggests a plausible mechanism of tau protein aggregation under an imbalance of zinc ions inside the pathological brain.
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- 2022
10. Repeat ablation of atrial fibrillation using electrogram dispersion to identify additional areas of mechanistic significance
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Junaid A.B. Zaman, MA (Oxon), BMBCh, FRCP (Edin), PhD, Abdulhaseeb Khan, MS, Jan Nielsen, MD, PhD, Steen B. Kristiansen, MD, PhD, Mads B. Kronborg, MD, DMSc, PhD, Christoffer T. Witt, MD, PhD, Christian Gerdes, MD, PhD, Jens Kristensen, MD, PhD, Henrik K. Jensen, MD, PhD, Peter Lukac, MD, PhD, and Sharad C. Agarwal, MBBS
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Electrogram ,Dispersion ,Atrial fibrillation ,Mapping ,Termination ,Repeat ablation ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background: Electrogram dispersion identifies putative atrial fibrillation (AF) drivers in first time ablation procedures, with high acute termination rates and long-term outcomes akin to extensive ablation approaches. Its use in a population that had undergone repeat ablation is unknown, particularly where the pulmonary veins are already isolated. Objective: This purpose of this study was to assess electrogram dispersion mapping during repeat ablation procedures for persistent AF. Methods: One hundred sixty-seven patients from the United Kingdom and Denmark, all with persistent AF recurrence after prior ablation procedure(s), were mapped using a five splined catheter for electrogram dispersion before ablation. Areas were manually tagged on biatrial electroanatomic maps and ablated once pulmonary vein isolation was confirmed or reisolated if required. All patients had 12-month continuous monitoring, with most of the cohort having follow-up beyond 24 months. Results: Of the 167 patients [53 (32%) female; mean age 66 ± 8 years; mean left atrial (LA) diameter 4.8 cm; mean ejection fraction 53%], 108 had pulmonary veins already isolated. Dispersion sites occurred in both atria (3.2 LA, 1.4 right atrium). Acute termination to sinus rhythm occurred in 71 (42%) of the cohort patients, with a further 73 (44%) terminating to atrial tachycardia/flutter. At 12-month follow-up, 95% of patients were free of AF, with 74% overall freedom from all atrial arrhythmias. Heart failure and severely enlarged LA predicted recurrence, and termination to sinus improved freedom from all atrial arrhythmias. Conclusion: Dispersion mapping is a promising approach at repeat ablation procedures for persistent AF, with high acute termination rates and good clinical outcomes. Further prospective randomized trials are needed to evaluate this approach in a population that had undergone repeat ablation.
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- 2024
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11. How much can performance measures explain of the between-cow variation in enteric methane?
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Giulio Giagnoni, Nicolas C. Friggens, Marianne Johansen, Morten Maigaard, Wenji Wang, Peter Lund, and Martin R. Weisbjerg
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emission ,PCA ,principal component regression ,residual methane ,CO2 ,Dairy processing. Dairy products ,SF250.5-275 ,Dairying ,SF221-250 - Abstract
ABSTRACT: Enteric CH4 produced from dairy cows contributes to the emission of greenhouse gases from anthropogenic sources. Recent studies have shown that the selection of lower CH4-emitting cows is possible, but doing so would be simpler if performance measures already recorded on farm could be used, instead of measuring gas emissions from individual cows. These performance measures could be used for selection of low emitting cows. The aim of this analysis was to quantify how much of the between-cow variation in CH4 production can be explained by variation in performance measures. A dataset with 3 experiments and a total of 149 lactating dairy cows with repeated measures was used to estimate the between-cow variation (the variation between cow estimates) for performance and gas measures from GreenFeed (C-Lock, Rapid City, SD). The cow estimates were obtained with a linear mixed model with the diet within period effect as a fixed effect and the cow within experiment as a random effect. The cow estimates for CH4 production were first regressed on the performance and gas measures individually, and then performance and CO2 production measures were grouped in 3 subsets for principal component analysis and principal component regression. The variables that explained most of the between-cow variation in CH4 production were DMI (R2 = 0.44), among the performance measures, and CO2 production (R2 = 0.61), among gas measures. Grouping the measures increased the R2 to 0.53 when only performance measures were used, and to 0.66 when CO2 production was added to the significant performance measures. We found the marginal improvement to be insufficient to justify the use of grouped measures rather than an individual measure because the latter simplifies the model and avoids over-fitting. Investigation of other measures that can be explored to increase explanatory power of between-cow variation in CH4 production is briefly discussed. Finally, the use of residual CH4 as a measure for CH4 efficiency could be considered by using either DMI or CO2 production as the sole predicting variables.
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- 2024
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12. Predicting troponin biomarker elevation from electrocardiograms using a deep neural network
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Truls Råmunddal, Erik Andersson, Zacharias Mandalenakis, Kristofer Skoglund, Araz Rawshani, Elmir Omerovic, Jan Borén, Petur Petursson, Aidin Rawshani, Peter Lundgren, Christian Dworeck, Lukas Hilgendorf, Vibha Gupta, Charlotta Ljungman, and Gustav Smith
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Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background Elevated troponin levels are a sensitive biomarker for cardiac injury. The quick and reliable prediction of troponin elevation for patients with chest pain from readily available ECGs may pose a valuable time-saving diagnostic tool during decision-making concerning this patient population.Methods and results The data used included 15 856 ECGs from patients presenting to the emergency rooms with chest pain or dyspnoea at two centres in Sweden from 2015 to June 2023. All patients had high-sensitivity troponin test results within 6 hours after 12-lead ECG. Both troponin I (TnI) and TnT were used, with biomarker-specific cut-offs and sex-specific cut-offs for TnI. On this dataset, a residual convolutional neural network (ResNet) was trained 10 times, each on a unique split of the data. The final model achieved an average area under the curve for the receiver operating characteristic curve of 0.7717 (95% CI±0.0052), calibration curve analysis revealed a mean slope of 1.243 (95% CI±0.075) and intercept of −0.073 (95% CI±0.034), indicating a good correlation between prediction and ground truth. Post-classification, tuned for F1 score, accuracy was 71.43% (95% CI±1.28), with an F1 score of 0.5642 (95% CI±0.0052) and a negative predictive value of 0.8660 (95% CI±0.0048), respectively. The ResNet displayed comparable or surpassing metrics to prior presented models.Conclusion The model exhibited clinically meaningful performance, notably its high negative predictive accuracy. Therefore, clinical use of comparable neural networks in first-line, quick-response triage of patients with chest pain or dyspnoea appears as a valuable option in future medical practice.
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- 2024
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13. Burnout and moral injuries after foreign deployment among medical personnel of the German armed forces: a pre-post study
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Franziska Langner, Anna Katharina Börke, Patric Muschner, Maria Muther, Andreas Reichelt, Gerd-Dieter Willmund, Ulrich Wesemann, Peter Lutz Zimmermann, and Isabel Schönsee
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burnout ,values ,soldiers ,military ,moral injury ,deployment ,Psychiatry ,RC435-571 - Abstract
IntroductionGiven a high amount of workplace stressors, burnout syndrome, as a depression-related syndrome, is highly relevant for medical service soldiers. This study aims to examine their effects with regard to moral injuries and personal values following foreign deployment.Materials and methodsThis longitudinal study included 91 soldiers of the German Armed Forces Medical Service. Participants completed the Maslach Burnout Inventory (MBI) and the Portrait-Value-Questionnaire (PVQ) before and after a foreign deployment as well as the Moral Injury Scale (SMBE) after deployment. Analysis has been conducted using t-tests to assess potential changes in MBI and PVQ scales between pre-test - t1 (2-4 weeks before deployment) and post-test – t2 (up to 6 months after deployment). In addition, correlations were examined between moral injuries (MI) after deployment and MBI scores at t1 and t2 as well as between personal values (PVQ t1) and MBI scores at t1 and t2.ResultsThe MBI subscales showed mild to moderate burnout symptoms at both pre- and post-tests, with a slight deterioration during the study period, albeit not significant. There were no significant mean differences in PVQ between measurement points. Nevertheless, PVQ self-direction and tradition at t1 correlated negatively with MBI INV at t2 (PVQ SD r = -.21, p = .043) and MBI PA at t2 (PVQ TR r = -.23, p = .027). Furthermore, the subscale PVQ power at t1 correlated positively with MBI PA at t2 (PVQ PO r = .28, p = .006), meanwhile PVQ universalism at t1 correlated positively with MBI INV at t1 (PVQ UN r = .25, p = .018). Furthermore, positive correlations were found between moral injuries at t2 (SMBE total score, SMBE_Sub1, SMBE_Sub2) and MBI subscales Emotional Exhaustion (EE; r = -.54, p = .001), Depersonalization (DP; r = .38, p = .001), and Involvement (INV; r = .30, p = .004) before and after the deployment period. No correlation was found between MI and MBI subscale Personal Accomplishment (PA).ConclusionThe results indicate that medical service soldiers exhibit mild to moderate burnout symptoms even before deployment. Significant associations between moral injuries and burnout were found in 3 out of 4 MBI subscales (EE, DP, INV). There was a significant association with a stronger moral injury and higher burnout levels, persisting both before and after the study period. Furthermore, our results suggest that personal value orientations might be meaningful predictors of burnout. Hence, causal questions regarding general work stress among medical service soldiers should be further explored in more detailed studies. Further research could lay the foundation for future approaches in psychotherapy as well as primary and secondary prevention in this field.
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- 2024
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14. Diazirine-based photo-crosslinkers for defect free fabrication of solution processed organic light-emitting diodes
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Pavel Anzenbacher, H. Peter Lu, Erik Dykstra, S. Roy Chowdhury, Kaustav Dey, Ruth Shinar, Aleksandr Koronatov, and Joseph Shinar
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chemistry.chemical_classification ,Materials science ,General Chemistry ,Polymer ,Photochemistry ,Polyfluorene ,chemistry.chemical_compound ,chemistry ,PEDOT:PSS ,Diazirine ,Materials Chemistry ,Surface roughness ,OLED ,Quantum efficiency ,Luminous efficacy - Abstract
The fabrication of solution deposited OLEDs is fraught with difficulties, largely due to the interlayer mixing and surface erosion during sequential deposition of the layers. We demonstrate that these problems can be circumvented by using photopolymerizable diazirine-based cross-linker capable of converting soluble organic materials into highly cross-linked insoluble networks. 3-Trifluoromethyl(aryl)diazirines photolyze readily upon the 10–15 min exposure of 365 nm UV irradiation to generate carbenes, which react with polymers or small molecules via C–H bond insertion producing highly cross-linked materials. This photo-generated cross-linking does not require any catalyst, initiator or short-wavelength UV light and is performed at room temperature, releasing molecular nitrogen as the only byproduct. To show the cross-linked polymer layers do not display inter-layer mixing, we deposited red-emitting regioregular poly(3-hexylthiophene-2,5-diyl) (P3HT) over cross-linked (10% cross-linker) blue emitting dioctyl polyfluorene (PFO) layer. The overlaid layers showed clear and well-defined boundary with no interlayer mixing. The surface morphology of the solution deposited layers was investigated by AFM to show that the cross-linked layers exhibited significant decrease in surface roughness. This is also shown on the example of the hole transporting material 4,4′-bis[N-(1-naphthyl)-N-phenylamino]-biphenyl (NPB) which displayed roughness average to decrease from 6.4 nm to 1.0 nm. The effect of decreased surface roughness on the performance of phosphorescent OLEDs was investigated by fabricating devices with configuration of ITO/PEDOT:PSS/NPB:(0%/5%/10%) cross-linker/MCP:6% Ir(mppy)3/TPBI/CsF/Al. Following the diazirine-mediated cross-linking, the OLEDs displayed a decrease in turn-on voltage from 3.8 V to 3.0 V along with a six-fold enhancement of external quantum efficiency (EQEmax) from 1.1% to 6.8% and maximum luminous efficiency increase from 3.8 cd A−1 to 22.9 cd A−1. These results demonstrate that the simple diazirine mediated photo-cross-linking using mild conditions compatible with organic layers is a promising strategy for improving the performance of the solution-processed OLEDs.
- Published
- 2020
15. Probing functional conformation-state fluctuation dynamics in recognition binding between calmodulin and target peptide
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Yufan He, H. Peter Lu, and Sunidhi Jaiswal
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chemistry.chemical_classification ,Cell signaling ,Binding Sites ,Calmodulin ,biology ,Chemistry ,Protein Conformation ,Spectrum Analysis ,Dynamics (mechanics) ,General Physics and Astronomy ,Target peptide ,Peptide ,Membrane ,Förster resonance energy transfer ,biology.protein ,Biophysics ,Fluorescence Resonance Energy Transfer ,Calcium ,Physical and Theoretical Chemistry ,Spectroscopy ,Protein Binding - Abstract
Conformational dynamics play a crucial role in protein functions. A molecular-level understanding of the conformational transition dynamics of proteins is fundamental for studying protein functions. Here, we report a study of real-time conformational dynamic interaction between calcium-activated calmodulin (CaM) and C28W peptide using single-molecule fluorescence resonance energy transfer (FRET) spectroscopy and imaging. Plasma membrane Ca-ATPase protein interacts with CaM by its peptide segment that contains 28 amino acids (C28W). The interaction between CaM and the Ca-ATPase is essential for cell signaling. However, details about its dynamic interaction are still not clear. In our current study, we used Cyanine3 labeled CaM (N-domain) and Dylight 649 labeled C28W peptide (N-domain) to study the conformational dynamics during their interaction. In this study, the FRET can be measured when the CaM-C28W complex is formed and only be observed when such a complex is formed. By using single-molecule FRET efficiency trajectory and unique statistical approaches, we were able to observe multiple binding steps with detailed dynamic features of loosely bound and tightly bound state fluctuations. The C-domain of CaM tends to bind with C28W first with a higher affinity, followed by the binding of the CaM N-domain. Due to the comparatively high flexibility and low affinity of the N-domain and the presence of multiple anchor hydrophobic residues on the peptide, the N-domain binding may switch between selective and non-selective binding states, while the C-domain remains strongly bound with C28W. The results provide a mechanistic understanding of the CaM signaling interaction and activation of the Ca-ATPase through multiple-state binding to the C28W. The new single-molecule spectroscopic analyses demonstrated in this work can be applied for broad studies of protein functional conformation fluctuation and protein-protein interaction dynamics.
- Published
- 2022
16. A physiologically-based digital twin for alcohol consumption—predicting real-life drinking responses and long-term plasma PEth
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Henrik Podéus, Christian Simonsson, Patrik Nasr, Mattias Ekstedt, Stergios Kechagias, Peter Lundberg, William Lövfors, and Gunnar Cedersund
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Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
Abstract Alcohol consumption is associated with a wide variety of preventable health complications and is a major risk factor for all-cause mortality in the age group 15-47 years. To reduce dangerous drinking behavior, eHealth applications have shown promise. A particularly interesting potential lies in the combination of eHealth apps with mathematical models. However, existing mathematical models do not consider real-life situations, such as combined intake of meals and beverages, and do not connect drinking to clinical markers, such as phosphatidylethanol (PEth). Herein, we present such a model which can simulate real-life situations and connect drinking to long-term markers. The new model can accurately describe both estimation data according to a χ2 -test (187.0
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- 2024
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17. Changes in temperature in preheated crystalloids at ambient temperatures relevant to a prehospital setting: an experimental simulation study with the application of prehospital treatment of trauma patients suffering from accidental hypothermia
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Emil Jensen, Helena Rentzhog, Johan Herlitz, Christer Axelsson, and Peter Lundgren
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Accidental hypothermia ,Advanced trauma life support care ,Resuscitation ,Special situations and conditions ,RC952-1245 ,Medical emergencies. Critical care. Intensive care. First aid ,RC86-88.9 - Abstract
Abstract Background Accidental hypothermia is common in all trauma patients and contributes to the lethal diamond, increasing both morbidity and mortality. In hypotensive shock, fluid resuscitation is recommended using fluids with a temperature of 37–42°, as fluid temperature can decrease the patient’s body temperature. In Sweden, virtually all prehospital services use preheated fluids. The aim of the present study was to investigate how the temperature of preheated infusion fluids is affected by the ambient temperatures and flow rates relevant for prehospital emergency care. Methods In this experimental simulation study, temperature changes in crystalloids preheated to 39 °C were evaluated. The fluid temperature changes were measured both in the infusion bag and at the patient end of the infusion system. Measurements were conducted in conditions relevant to prehospital emergency care, with ambient temperatures varying between − 4 and 28 °C and flow rates of 1000 ml/h and 6000 ml/h, through an uninsulated infusion set at a length of 175 cm. Results The flow rate and ambient temperature affected the temperature in the infusion fluid both in the infusion bag and at the patient end of the system. A lower ambient temperature and lower flow rate were both associated with a greater temperature loss in the infusion fluid. Conclusion This study shows that both a high infusion rate and a high ambient temperature are needed if an infusion fluid preheated to 39 °C is to remain above 37 °C when it reaches the patient using a 175-cm-long uninsulated infusion set. It is apparent that the lower the ambient temperature, the higher the flow rate needs to be to limit temperature loss of the fluid.
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- 2024
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18. Online evolution of a phased array for ultrasonic imaging by a novel adaptive data acquisition method
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Peter Lukacs, Theodosia Stratoudaki, Geo Davis, and Anthony Gachagan
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Medicine ,Science - Abstract
Abstract Ultrasonic imaging, using ultrasonic phased arrays, has an enormous impact in science, medicine and society and is a widely used modality in many application fields. The maximum amount of information which can be captured by an array is provided by the data acquisition method capturing the complete data set of signals from all possible combinations of ultrasonic generation and detection elements of a dense array. However, capturing this complete data set requires long data acquisition time, large number of array elements and transmit channels and produces a large volume of data. All these reasons make such data acquisition unfeasible due to the existing phased array technology or non-applicable to cases requiring fast measurement time. This paper introduces the concept of an adaptive data acquisition process, the Selective Matrix Capture (SMC), which can adapt, dynamically, to specific imaging requirements for efficient ultrasonic imaging. SMC is realised experimentally using Laser Induced Phased Arrays (LIPAs), that use lasers to generate and detect ultrasound. The flexibility and reconfigurability of LIPAs enable the evolution of the array configuration, on-the-fly. The SMC methodology consists of two stages: a stage for detecting and localising regions of interest, by means of iteratively synthesising a sparse array, and a second stage for array optimisation to the region of interest. The delay-and-sum is used as the imaging algorithm and the experimental results are compared to images produced using the complete generation-detection data set. It is shown that SMC, without a priori knowledge of the test sample, is able to achieve comparable results, while preforming $$\sim$$ ∼ 10 times faster data acquisition and achieving $$\sim$$ ∼ 10 times reduction in data size.
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- 2024
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19. Gas exchange, rumen hydrogen sinks, and nutrient digestibility and metabolism in lactating dairy cows fed 3-nitrooxypropanol and cracked rapeseed
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Maria H. Kjeldsen, Martin R. Weisbjerg, Mogens Larsen, Ole Højberg, Christer Ohlsson, Nicola Walker, Anne Louise F. Hellwing, and Peter Lund
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Bovaer ,cattle ,feed additive ,fat ,Dairy processing. Dairy products ,SF250.5-275 ,Dairying ,SF221-250 - Abstract
ABSTRACT: Fat in the form of cracked rapeseed and 3-nitrooxypropanol (3-NOP, market as Bovaer) were fed alone or in combination to 4 Danish Holstein multicannulated dairy cows, with the objective to investigate effects on gas exchange, dry matter intake (DMI), nutrient digestion, and nutrient metabolism. The study design was a 4 × 4 Latin square with a 2 × 2 factorial treatment arrangement with 2 levels of fat supplementation; 33 g of crude fat per kg of dry matter (DM) or 64 g of crude fat per kg of DM for low and high fat diets, respectively, and 2 levels of 3-NOP; 0 mg/kg DM or 80 mg/kg DM. In total, 4 diets were formulated: low fat (LF), high fat (HF), 3-NOP and low fat (3LF), and 3-NOP and high fat (3HF). Cows were fed ad libitum and milked twice daily. The adaptation period lasted 11 d, followed by 5 d with 12 diurnal sampling times of digesta and ruminal fluid. Thereafter, gas exchange was measured for 5 d in respiration chambers. Chromic oxide and titanium dioxide were used as external flow markers to determine intestinal nutrient flow. No interactions between fat supplementation and 3-NOP were observed for methane yield (g/kg DM), total-tract digestibility of nutrients or total volatile fatty acid (VFA) concentration in the rumen. Methane yield (g/kg DMI) was decreased by 24% when cows were fed 3-NOP. In addition, 3-NOP increased carbon dioxide and hydrogen yield (g/kg DM) by 6% and 3,500%, respectively. However, carbon dioxide production was decreased when expressed on a daily basis. Fat supplementation did not affect methane yield but tended to reduce methane in percent of gross energy intake. A decrease (11%) in DMI was observed, when cows were fed 3-NOP. Likely, the lower DMI mediated a lower passage rate causing the tendency to higher rumen and total-tract neutral detergent fiber digestibility, when the cows were fed 3-NOP. Total VFA concentrations in the rumen were negatively affected both by 3-NOP and fat supplementation. Furthermore, 3-NOP caused a shift in the VFA fermentation profile, with decreased acetate proportion and increased butyrate proportion, whereas propionate proportion was unaffected. Increased concentrations of the alcohols methanol, ethanol, propanol, butanol, and 2-butanol were observed in the ruminal fluid when cows were fed 3-NOP. These changes in rumen metabolites indicate partial re-direction of hydrogen into other hydrogen sinks, when methanogenesis is inhibited by 3-NOP. In conclusion, fat supplementation did not reduce methane yield, whereas 3-NOP reduced methane yield, irrespective of fat level. However, the concentration of 3-NOP and diet composition and resulting desired mitigation effect must be considered before implementation. The observed reduction in DMI with 80 mg 3-NOP/kg DM was intriguing and may indicate that a lower dose should be applied in a Northern European context; however, the mechanism behind needs further investigation.
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- 2024
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20. Prognosis versus Actual Outcomes in Stereotactic Radiosurgery of Brain Metastases: Reliability of Common Prognostic Parameters and Indices
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Julian Mangesius, Thomas Seppi, Christoph Reinhold Arnold, Stephanie Mangesius, Johannes Kerschbaumer, Matthias Demetz, Danijela Minasch, Samuel Moritz Vorbach, Manuel Sarcletti, Peter Lukas, Meinhard Nevinny-Stickel, and Ute Ganswindt
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radiosurgery ,brain metastases ,prognosis ,prognostic scores ,outcome ,sex differences ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
This study aims to evaluate the clinical outcome of stereotactic radiosurgery as the sole treatment for brain metastases and to assess prognostic factors influencing survival. A total of 108 consecutive patients with 213 metastases were retrospectively analyzed. Treatment was determined with close-meshed MRI follow-up. Various prognostic factors were assessed, and several prognostic indices were compared regarding their reliability to estimate overall survival. Median overall survival was 15 months; one-year overall survival was 50.5%. Both one- and two-year local controls were 90.9%. The rate of new metastases after SRS was 49.1%. Multivariate analysis of prognostic factors revealed that the presence of extracranial metastases, male sex, lower KPI, and progressive extracranial disease were significant risk factors for decreased survival. Of all evaluated prognostic indices, the Basic Score for Brain Metastases (BSBMs) showed the best correlation with overall survival. A substantial survival advantage was found for female patients after SRS when compared to male patients (18 versus 9 months, p = 0.003). SRS of brain metastasis is a safe and effective treatment option when frequent monitoring for new metastases with MRI is performed. Common prognostic scores lack reliable estimation of survival times. Female sex should be considered as an additional independent positive prognostic factor influencing survival.
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- 2024
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21. More than double the fun with two-photon excitation microscopy
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Peter Luu, Scott E. Fraser, and Falk Schneider
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Biology (General) ,QH301-705.5 - Abstract
Abstract For generations researchers have been observing the dynamic processes of life through the lens of a microscope. This has offered tremendous insights into biological phenomena that span multiple orders of time- and length-scales ranging from the pure magic of molecular reorganization at the membrane of immune cells, to cell migration and differentiation during development or wound healing. Standard fluorescence microscopy techniques offer glimpses at such processes in vitro, however, when applied in intact systems, they are challenged by reduced signal strengths and signal-to-noise ratios that result from deeper imaging. As a remedy, two-photon excitation (TPE) microscopy takes a special place, because it allows us to investigate processes in vivo, in their natural environment, even in a living animal. Here, we review the fundamental principles underlying TPE aimed at basic and advanced microscopy users interested in adopting TPE for intravital imaging. We focus on applications in neurobiology, present current trends towards faster, wider and deeper imaging, discuss the combination with photon counting technologies for metabolic imaging and spectroscopy, as well as highlight outstanding issues and drawbacks in development and application of these methodologies.
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- 2024
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22. Conformational states and fluctuations in endothelial nitric oxide synthase under calmodulin regulation
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H. Peter Lu, Yufan He, Dennis J. Stuehr, and Mohammad Mahfuzul Haque
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chemistry.chemical_classification ,biology ,Calmodulin ,Endothelial nitric oxide synthase ,Nitric Oxide Synthase Type III ,Biophysics ,Heme ,Nitric Oxide Synthase Type I ,Articles ,Endothelial NOS ,Nitric Oxide ,Nitric oxide synthase ,Electron Transport ,chemistry.chemical_compound ,Electron transfer ,Enzyme ,Förster resonance energy transfer ,chemistry ,biology.protein ,Nitric Oxide Synthase - Abstract
Mechanisms that regulate nitric oxide synthase enzymes (NOS) are of interest in biology and medicine. Although NOS catalysis relies on domain motions and is activated by calmodulin (CaM) binding, the relationships are unclear. We used single-molecule fluorescence resonance energy transfer (FRET) spectroscopy to elucidate the conformational states distribution and associated conformational fluctuation dynamics of the two NOS electron transfer domains in an FRET dye-labeled endothelial NOS reductase domain (eNOSr) and to understand how CaM affects the dynamics to regulate catalysis by shaping the spatial and temporal conformational behaviors of eNOSr. In addition, we developed and applied a new imaging approach capable of recording three-dimensional FRET efficiency versus time images to characterize the impact on dynamic conformal states of the eNOSr enzyme by the binding of CaM, which identifies clearly that CaM binding generates an extra new open state of eNOSr, resolving more detailed NOS conformational states and their fluctuation dynamics. We identified a new output state that has an extra open conformation that is only populated in the CaM-bound eNOSr. This may reveal the critical role of CaM in triggering NOS activity as it gives conformational flexibility for eNOSr to assume the electron transfer output FMN-heme state. Our results provide a dynamic link to recently reported EM static structure analyses and demonstrate a capable approach in probing and simultaneously analyzing all of the conformational states, their fluctuations, and the fluctuation dynamics for understanding the mechanism of NOS electron transfer, involving electron transfer among FAD, FMN, and heme domains, during nitric oxide synthesis.
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- 2021
23. Emerging semiconductor ionic materials tailored by mixed ionic-electronic conductors for advanced fuel cells
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Bushra Bibi, Atif Nazar, Bin Zhu, Fan Yang, Muhammad Yousaf, Rizwan Raza, M.A.K. Yousaf Shah, Jung-Sik Kim, Muhammad Afzal, Yongpeng Lei, Yifu Jing, Peter Lund, and Sining Yun
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MIEC ,SIM ,e-i coupling ,SIMFC ,TCO ,Surface and interface ,Mining engineering. Metallurgy ,TN1-997 - Abstract
Mixed ionic-electronic conductors (MIECs) play a crucial role in the landscape of energy conversion and storage technologies, with a pronounced focus on electrode materials’ application in solid oxide fuel cells (SOFCs) and proton-conducting ceramic fuel cells (PCFCs). In parallel, the emergence of semiconductor ionic materials (SIMs) has introduced a new paradigm in the field of functional materials, particularly for both electrode and electrolyte development for low-temperature, 300–550 °C, SOFCs, and PCFCs. This review article critically delves into the intricate mechanisms underpinning the synergistic relationship between MIECs and SIMs, with a particular emphasis on elucidating the fundamental working principles of semiconductor ionic membrane fuel cells (SIMFCs). By exploring critical facets such as ion-coupled electron transfer/transport, junction effect, energy bands alignment, and theoretical computations, it casts an illuminating spotlight on the transformative potential of MIECs, also involving triple charge conducting oxides (TCOs) in the context of SIMs and advanced fuel cells (FCs). The insights and findings articulated herein contribute substantially to the advancement of SIMs and SIMFCs by tailoring MIECs (TCOs) as promising avenues toward the emergence of high-performance SIMFCs. This scientific quest not only addresses the insistent challenges surrounding efficient charge transfer, ionic transport and power output but also unlocks the profound potential for the widespread commercialization of FC technology.
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- 2024
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24. P‐79: Evaluation of Diffraction Induced Background Image Quality Degradation through Transparent OLED Display
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Wen Tsan Lin, Chi Jui Cheng, Cheng Chih Hsieh, Tzu Chin Huang, Peter Lu, Hoang Yan Lin, and Peng Yu Chen
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Diffraction ,Quality (physics) ,Materials science ,business.industry ,OLED ,Optoelectronics ,business ,Background image ,Degradation (telecommunications) - Published
- 2019
25. Association of pre-existing cardiovascular disease with administration of fluoropyrimidine chemotherapy in patients with gastrointestinal malignancies
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Chris Gale, Li Wei, Adam Timmis, Michael D Peake, Lucy Elliss-Brookes, Peter Ludman, Alison Fielding, David Adlam, Francis Murgatroyd, Clive Weston, Theresa McDonagh, Lizz Paley, Alistair Ring, Charlotte Manisty, Mike Hawkins, Raoul Reulen, Abbas Khushnood, Sally Vernon, John Deanfield, Nadeem Fazal, Jem Rashbass, Andrew Goodwin, Chengsheng Ju, Sarah Slater, Brian Shand, Mark De Belder, Paul Lambert, Catherine A Welch, Andrew Harrison, Michael Sweeting, Jennifer Lai, Mick Peake, Paul C Lambert, Mark de Belder, Paul Charlton, Alexander Lyon, Sarah Darby, Freya Tyrer, Mark Rutherford, Aderonke Temilade Abiodun, Pinkie Chambers, Kai Keen Shiu, Sally Jeans, Andy Deutsch, James Chal, Akosua Donkor, and Anil Gunesh
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Objective Fluoropyrimidine chemotherapy is a first-line treatment for many gastrointestinal (GI) cancers, however, cardiotoxicity concerns may limit administration in patients with pre-existing cardiovascular disease (CVD). This study investigated the association of pre-existing CVD with use of fluoropyrimidine chemotherapy in tumour-eligible GI cancer patients.Methods and analysis National cancer registry data from the Virtual Cardio-Oncology Research Initiative from England between 2014 and 2018 was used to identify GI cancer patients eligible to receive fluoropyrimidine chemotherapy. Linkage to Hospital Episode Statistics and CVD registry data were used to ascertain prior CVD and outcomes. Primary outcome was first administration of fluoropyrimidine chemotherapy following cancer diagnosis. Cox proportional hazard models determined HR and 95% CIs for the association between initiation of fluoropyrimidine treatment and prior CVD.Results 112 726 eligible patients were identified (median age 71 years (IQR 62–80), 39.7% female). 33 026 (29.3%) had pre-existing CVD. 73 392 (65.1%) patients had a diagnosis of colorectal, 23 208 (20.6%) oesophageal, 14 788 (13.1%) gastric and 1338 (1.2%) small bowel cancer. Individuals with pre-existing CVD had a 27% reduced rate of receiving fluoropyrimidine chemotherapy (HR, 0.73; 95% CI 0.70 to 0.75) on multivariable analysis. Significantly reduced rates of fluoropyrimidine administration were found across all subtypes of pre-existing CVD.Conclusions GI cancer patients with all types of pre-existing CVD are less likely to receive fluoropyrimidine chemotherapy despite eligibility. This suggests widespread caution regarding administration of fluoropyrimidines across this population; further research is needed to assess whether such conservatism is justified.
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- 2024
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26. An indicator framework to guide food system sustainability transition – The case of Sweden
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Helena Hansson, Sarah Säll, Assem Abouhatab, Serina Ahlgren, Åsa Berggren, Elinor Hallström, Peter Lundqvist, U. Martin Persson, Lotta Rydhmer, Elin Röös, Pernilla Tidåker, Anna Winkvist, and Li-hua Zhu
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Consumption ,Food policy ,Indicators ,Monitoring ,Production ,Environmental sciences ,GE1-350 - Abstract
Well-aligned food policies are needed at both national and international level to guide food system transformation towards sustainability. Rigorous indicator frameworks are essential in order to facilitate discussion of priorities, enable comparisons, assessment and progress monitoring, and ensure accountability. In this study, we develop a national framework for a sustainable food system, using Sweden as a case. Our framework, the Food System Sustainability House, advances the literature on sustainable food system frameworks in three distinct ways. Firstly, it is tailored to a specific national context (Sweden in our case); secondly, it distinguishes between impacts of domestic production arising within territorial boundaries and impacts related to Swedish consumption independent of country of origin; and thirdly, to facilitate policy priorities, it suggests how different dimensions of sustainability are interlinked at a conceptual level. From a scientific perspective, the Food System Sustainability House postulates the interlinkages between the societal objectives of the food system, the environmental foundations on which production takes place, and the economic system and governance which in the framework are suggested to function as enablers for an overall sustainable system. From a policy perspective, the framework provides a much-needed basis for assessing food system sustainability by suggesting indicators within a comprehensive set of sustainability themes at national level for monitoring distinct perspectives. It also provides the necessary basis for a discussion on how sustainability dimensions are interlinked.
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- 2024
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27. Hospitalized patients’ attitudes towards participating in a randomized control trial in case of a cardiac arrest
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Malin Albert, Marie Thonander, Sune Forsberg, Frida Lindgren, Meena Thuccani, Annika Odell, Kristofer Skoglund, Niklas Bergh, Jacob Hollenberg, Mattias Ringh, Martin Jonsson, Per Nordberg, and Peter Lundgren
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Informed consent ,Waiver informed consent ,Cardiac arrest ,Specialties of internal medicine ,RC581-951 - Abstract
Background: No previous study has evaluated patients attitudes towards inclusion in an ongoing cardiac arrest clinical trial. The aim of this study was to assess patientś willingness and motives to participate in the ongoing randomized controlled drug trial “Vasopressin and Steroids in addition to Adrenaline in cardiac arrest” (VAST-A trial) in case of an in-hospital cardiac arrest (IHCA). Objectives: Hospitalized patients, men ≥ 18 and women ≥ 50 years, were asked for informed consent for inclusion in the VAST-A trial in case of an IHCA, the reason for approving or declining inclusion in the trial and baseline characteristics. Methods: Patients admitted to hospital were asked to give informed consent of inclusion in VAST-A in case of an IHCA during their hospital stay. Patients were also asked why they approved or declined inclusion as well as baseline characteristics questions. Results: 1,064 patients were asked about willingness to participate in the VAST-A trial, of these 902 (84.8%) patients approved inclusion. A subgroup of 411 patients were, except willingness, also asked about motives to participate or not and basic characteristics. The main reason for approving inclusion was to contribute to research (n = 328, 83.9%). The main reason for declining inclusion was concerns regarding testing the drug treatment (n = 6, 30%). Conclusion: Among hospitalized patients the vast majority gave informed consent to inclusion in an ongoing randomized cardiac arrest drug trial. The main reason for approving inclusion was to contribute to research.
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- 2024
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28. Study protocol for the Screen-Free Time with Friends Feasibility Trial
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Sarah Overgaard Sørensen, Kristian Traberg Larsen, Teresa Victoria Høy, Anders Blædel Gottlieb Hansen, Russell Jago, Peter Lund Kristensen, Mette Toftager, Anders Grøntved, and Anne Kær Gejl
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Screen time ,Time with friends ,Feasibility ,Acceptability ,Compliance ,Medicine (General) ,R5-920 - Abstract
Abstract Background Children are spending less leisure time with their friends in person and an increasing amount of time with digital screens. These changes may negatively affect children’s physical and mental health. The Screen-Free Time with Friends Feasibility Trial will test the feasibility, including acceptability and compliance, of an intervention designed to reduce screen media usage and encourage physical interaction with friends during leisure time in 9–11-year-old children. Methods A non-randomized single-group feasibility trial will be conducted from March to October 2023 including approximately 75 children (aged 9–11 years) and 75 parents (at least 1 per child) from 3 different schools recruited from 3 different municipalities in Denmark. The Screen-Free Time with Friends intervention is a multicomponent intervention targeting families, afterschool clubs, and local communities. It has been developed using a systematic process guided by the Medical Research Council UK’s framework for developing and evaluating complex interventions. With a systems perspective in mind, the intervention and implementation approach has been designed to facilitate adaptation to the specific needs of diverse local communities while maintaining the core components of the intervention. Feasibility and acceptability of the intervention will be assessed during the intervention using process evaluation inspired by the RE-AIM framework including questionnaires and interviews with the municipality project managers, research team members, local ambassadors and stakeholders, parents and school, and afterschool club personnel. In addition, participation, recruitment, retention rate, and compliance to the outcome measurements will be investigated and presented. Discussion The trial will investigate the feasibility and acceptability of the Screen-Free Time with Friends intervention, the recruitment strategy, and the planned outcome measurements. This feasibility study will investigate necessary refinements before the implementation of the intervention program in a larger cluster randomized controlled trial to evaluate its impact. Trial registration. ClinicalTrials.gov, ID: NCT05480085. Registered 29 July 2022. https://clinicaltrials.gov/ct2/show/NCT05480085?cond=Screen+free+time+with+friends&draw=2&rank=1
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- 2024
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29. Low-dose acetylsalicylic acid reduces local inflammation and tissue perfusion in dense breast tissue in postmenopausal women
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Peter Lundberg, Annelie Abrahamsson, Johan Kihlberg, Jens Tellman, Ieva Tomkeviciene, Anette Karlsson, Maria Kristoffersen Wiberg, Marcel Warntjes, and Charlotta Dabrosin
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Randomized trial ,MRI ,Mammography ,Inflammation ,Microdialysis ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Purpose One major risk factor for breast cancer is high mammographic density. It has been estimated that dense breast tissue contributes to ~ 30% of all breast cancer. Prevention targeting dense breast tissue has the potential to improve breast cancer mortality and morbidity. Anti-estrogens, which may be associated with severe side-effects, can be used for prevention of breast cancer in women with high risk of the disease per se. However, no preventive therapy targeting dense breasts is currently available. Inflammation is a hallmark of cancer. Although the biological mechanisms involved in the increased risk of cancer in dense breasts is not yet fully understood, high mammographic density has been associated with increased inflammation. We investigated whether low-dose acetylsalicylic acid (ASA) affects local breast tissue inflammation and/or structural and dynamic changes in dense breasts. Methods Postmenopausal women with mammographic dense breasts on their regular mammography screen were identified. A total of 53 women were randomized to receive ASA 160 mg/day or no treatment for 6 months. Magnetic resonance imaging (MRI) was performed before and after 6 months for a sophisticated and continuous measure breast density by calculating lean tissue fraction (LTF). Additionally, dynamic quantifications including tissue perfusion were performed. Microdialysis for sampling of proteins in vivo from breasts and abdominal subcutaneous fat, as a measure of systemic effects, before and after 6 months were performed. A panel of 92 inflammatory proteins were quantified in the microdialysates using proximity extension assay. Results After correction for false discovery rate, 20 of the 92 inflammatory proteins were significantly decreased in breast tissue after ASA treatment, whereas no systemic effects were detected. In the no-treatment group, protein levels were unaffected. Breast density, measured by LTF on MRI, were unaffected in both groups. ASA significantly decreased the perfusion rate. The perfusion rate correlated positively with local breast tissue concentration of VEGF. Conclusions ASA may shape the local breast tissue microenvironment into an anti-tumorigenic state. Trials investigating the effects of low-dose ASA and risk of primary breast cancer among postmenopausal women with maintained high mammographic density are warranted. Trial registration EudraCT: 2017-000317-22.
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- 2024
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30. Effects of dietary fat, nitrate, and 3-nitrooxypropanol and their combinations on methane emission, feed intake, and milk production in dairy cows
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Morten Maigaard, Martin R. Weisbjerg, Marianne Johansen, Nicola Walker, Christer Ohlsson, and Peter Lund
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feed additive ,eating behavior ,combined effect ,3-NOP ,methanogen inhibitor ,Dairy processing. Dairy products ,SF250.5-275 ,Dairying ,SF221-250 - Abstract
ABSTRACT: The objective of the present study was to investigate the effect of individual and combined use of dietary fat, nitrate, and 3-nitrooxypropanol (3-NOP) on dairy cows' enteric methane (CH4) emission and production performance. Twenty-four primiparous and 24 multiparous Danish Holstein cows (111 ± 44.6 d in milk; mean ± standard deviation) were included in an incomplete 8 × 8 Latin square design with six 21-d periods. Dietary treatments were organized in a 2 × 2 × 2 factorial arrangement aiming for 2 levels of FAT (30 or 63 g of crude fat/kg of dry matter [DM]; LF or HF, respectively), 2 levels of NITRATE (0 or 10 g of nitrate/kg of DM; UREA or NIT, respectively), and 2 levels of 3-NOP (0 or 80 mg/kg DM; BLANK or NOP, respectively). Treatments were included in ad libitum-fed partial mixed rations in bins that automatically measured feed intake and eating behavior. Additional concentrate was offered as bait in GreenFeed units used for measurement of gas emission. For total DM intake (DMI), a FAT × NITRATE interaction showed that DMI, across parities and levels of 3-NOP, was unaffected by separate fat supplementation, but reduced by nitrate with 4.6% and synergistically decreased (significant 2-way interaction) with 13.0% when fat and nitrate were combined. Additionally, 3-NOP decreased DMI by 13.4% and the combination of 3-NOP with fat and nitrate decreased DMI in an additive way (no significant 3-way interaction). The decreasing effects on DMI were more pronounced in multiparous cows than in primiparous cows. For treatments with largest reductions in DMI, eating behavior was altered toward more frequent, but smaller meals, a slower eating rate and increased attempts to visit unassigned feed bins. Energy-corrected milk (ECM) yield increased by 6.3% with fat supplementation, whereas ECM yield did not differ among diets including nitrate (FAT × NITRATE interaction). Cows supplemented with 3-NOP had 9.0% lower ECM yield than cows fed no 3-NOP. Based on three 2-way interactions including FAT, NITRATE, and 3-NOP, the combined use of the additives resulted in antagonistic effects on CH4 reduction. A 6% to 7% reduction in CH4 yield (CH4/kg of DMI) could be ascribed to the effect of fat, a 12% to 13% reduction could be ascribed to the effect of nitrate and an 18% to 23% reduction could be ascribed to the effect of 3-NOP. Hence, no combinations of additives resulted in CH4 yield-reductions that were greater than what was obtained by separate supplementation of the most potent additive within the combination. The CH4 yield reduction potential of additives was similar between parities. Increased apparent total-tract digestibility of organic matter (OM) in cows fed combinations including nitrate or 3-NOP was a result of a NITRATE × 3-NOP interaction. Apparent total-tract digestibility of OM was also increased by fat supplementation. These increases reflected observed decreases in DMI. In conclusion, combined use of fat, nitrate, and 3-NOP in all combinations did not result in CH4 reductions that were greater than separate supplementation of the most potent additive within the combination (3-NOP > nitrate > fat). Additionally, separate supplementation of some additives and combined use of all additives reduced DMI.
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- 2024
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31. A rapid, non-invasive, clinical surveillance for CachExia, sarcopenia, portal hypertension, and hepatocellular carcinoma in end-stage liver disease: the ACCESS-ESLD study protocol
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Patrik Nasr, Mikael Forsgren, Wile Balkhed, Cecilia Jönsson, Nils Dahlström, Christian Simonsson, Shan Cai, Anna Cederborg, Martin Henriksson, Henrik Stjernman, Martin Rejler, Daniel Sjögren, Gunnar Cedersund, Wolf Bartholomä, Ingvar Rydén, Peter Lundberg, Stergios Kechagias, Olof Dahlqvist Leinhard, and Mattias Ekstedt
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Liver cirrhosis ,Hepatocellular carcinoma ,Portal hypertension ,Sarcopenia ,Biomarkers ,Abbreviated MRI ,Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Abstract Background Liver cirrhosis, the advanced stage of many chronic liver diseases, is associated with escalated risks of liver-related complications like decompensation and hepatocellular carcinoma (HCC). Morbidity and mortality in cirrhosis patients are linked to portal hypertension, sarcopenia, and hepatocellular carcinoma. Although conventional cirrhosis management centered on treating complications, contemporary approaches prioritize preemptive measures. This study aims to formulate novel blood- and imaging-centric methodologies for monitoring liver cirrhosis patients. Methods In this prospective study, 150 liver cirrhosis patients will be enrolled from three Swedish liver clinics. Their conditions will be assessed through extensive blood-based markers and magnetic resonance imaging (MRI). The MRI protocol encompasses body composition profile with Muscle Assement Score, portal flow assessment, magnet resonance elastography, and a abbreviated MRI for HCC screening. Evaluation of lifestyle, muscular strength, physical performance, body composition, and quality of life will be conducted. Additionally, DNA, serum, and plasma biobanking will facilitate future investigations. Discussion The anticipated outcomes involve the identification and validation of non-invasive blood- and imaging-oriented biomarkers, enhancing the care paradigm for liver cirrhosis patients. Notably, the temporal evolution of these biomarkers will be crucial for understanding dynamic changes. Trial registration Clinicaltrials.gov, registration identifier NCT05502198. Registered on 16 August 2022. Link: https://classic.clinicaltrials.gov/ct2/show/NCT05502198 .
- Published
- 2023
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32. An Evaluation of Kant’s Transcendental Idealism Using the Inversion Theory of Truth
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Peter Lugten
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inversion theory of truth ,active subjectivism ,essential falsehood ,representational inexactitude ,falsifiability ,transcendental idealism ,categorical imperative ,Philosophy (General) ,B1-5802 - Abstract
This paper examines the work of Immanuel Kant in the light of a new theory on the nature of truth, knowledge and falsehood (the Inversion Theory of Truth). Kant’s idea that knowledge could be absolutely certain, and that its truth must correspond with reality, is discredited by a dissection of the Correspondence Theory of Truth. This examination of the nature of truth, as well as knowledge and falsehood, is conducted with reference to Sir Karl Popper’s writings on regulative ideas, the criterion of demarcation and the principle of falsifiability. It is argued that if truth is to be regarded as certain, it should be used to describe objects and events in the objective (noumenal) state, and that subjective knowledge must contain (and is improved by) falsehood. Perceptions and knowledge are obtained by the biological and evolutionary process of Active Subjectivism. Ideas we have knowledge of can be metaphysical or scientific, according to Popper’s Criterion of Demarcation. Kant’s “Copernican revolution” claim that our intellect imposes absolutely true laws on nature could not allow for the possibility that ideas might be constructed from fallible perceptions, and hence that all knowledge is uncertain. Instead, he developed a Critique of Practical Reason in which religion, though not provable through logical reasoning, could be proved by our innate moral sense, giving us a Categorical Imperative that could lead to perverse results. By rejecting the absolute certainty of a priori knowledge, and admitting a degree of essential falsehood, we arrive at a more reasonable grounding for moral behavior.
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- 2023
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33. High-throughput ligand profile characterization in novel cell lines expressing seven heterologous insect olfactory receptors for the detection of volatile plant biomarkers
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Katalin Zboray, Adam V. Toth, Tímea D. Miskolczi, Krisztina Pesti, Emilio Casanova, Emanuel Kreidl, Arpad Mike, Áron Szenes, László Sági, and Peter Lukacs
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Medicine ,Science - Abstract
Abstract Agriculturally important crop plants emit a multitude of volatile organic compounds (VOCs), which are excellent indicators of their health status and their interactions with pathogens and pests. In this study, we have developed a novel cellular olfactory panel for detecting fungal pathogen-related VOCs we had identified in the field, as well as during controlled inoculations of several crop plants. The olfactory panel consists of seven stable HEK293 cell lines each expressing a functional Drosophila olfactory receptor as a biosensing element along with GCaMP6, a fluorescent calcium indicator protein. An automated 384-well microplate reader was used to characterize the olfactory receptor cell lines for their sensitivity to reference VOCs. Subsequently, we profiled a set of 66 VOCs on all cell lines, covering a concentration range from 1 to 100 μM. Results showed that 49 VOCs (74.2%) elicited a response in at least one olfactory receptor cell line. Some VOCs activated the cell lines even at nanomolar (ppb) concentrations. The interaction profiles obtained here will support the development of biosensors for agricultural applications. Additionally, the olfactory receptor proteins can be purified from these cell lines with sufficient yields for further processing, such as structure determination or integration with sensor devices.
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- 2023
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34. Nutrient deprivation alters the rate of COPII subunit recruitment at ER subdomains to tune secretory protein transport
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William Kasberg, Peter Luong, Kevin A. Swift, and Anjon Audhya
- Subjects
Science - Abstract
Abstract Co-assembly of the multilayered coat protein complex II (COPII) with the Sar1 GTPase at subdomains of the endoplasmic reticulum (ER) enables secretory cargoes to be concentrated efficiently within nascent transport intermediates, which subsequently deliver their contents to ER-Golgi intermediate compartments. Here, we define the spatiotemporal accumulation of native COPII subunits and secretory cargoes at ER subdomains under differing nutrient availability conditions using a combination of CRISPR/Cas9-mediated genome editing and live cell imaging. Our findings demonstrate that the rate of inner COPII coat recruitment serves as a determinant for the pace of cargo export, irrespective of COPII subunit expression levels. Moreover, increasing inner COPII coat recruitment kinetics is sufficient to rescue cargo trafficking deficits caused by acute nutrient limitation. Our findings are consistent with a model in which the rate of inner COPII coat addition acts as an important control point to regulate cargo export from the ER.
- Published
- 2023
- Full Text
- View/download PDF
35. A multi-scale digital twin for adiposity-driven insulin resistance in humans: diet and drug effects
- Author
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Tilda Herrgårdh, Christian Simonsson, Mattias Ekstedt, Peter Lundberg, Karin G. Stenkula, Elin Nyman, Peter Gennemark, and Gunnar Cedersund
- Subjects
Digital twin ,Mathematical modelling ,Insulin resistance ,Nutritional diseases. Deficiency diseases ,RC620-627 - Abstract
Abstract Background The increased prevalence of insulin resistance is one of the major health risks in society today. Insulin resistance involves both short-term dynamics, such as altered meal responses, and long-term dynamics, such as the development of type 2 diabetes. Insulin resistance also occurs on different physiological levels, ranging from disease phenotypes to organ-organ communication and intracellular signaling. To better understand the progression of insulin resistance, an analysis method is needed that can combine different timescales and physiological levels. One such method is digital twins, consisting of combined mechanistic mathematical models. We have previously developed a model for short-term glucose homeostasis and intracellular insulin signaling, and there exist long-term weight regulation models. Herein, we combine these models into a first interconnected digital twin for the progression of insulin resistance in humans. Methods The model is based on ordinary differential equations representing biochemical and physiological processes, in which unknown parameters were fitted to data using a MATLAB toolbox. Results The interconnected twin correctly predicts independent data from a weight increase study, both for weight-changes, fasting plasma insulin and glucose levels, and intracellular insulin signaling. Similarly, the model can predict independent weight-change data in a weight loss study with the weight loss drug topiramate. The model can also predict non-measured variables. Conclusions The model presented herein constitutes the basis for a new digital twin technology, which in the future could be used to aid medical pedagogy and increase motivation and compliance and thus aid in the prevention and treatment of insulin resistance.
- Published
- 2023
- Full Text
- View/download PDF
36. Convex Hull Pricing for Unit Commitment: Survey, Insights, and Discussions
- Author
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Farhan Hyder, Bing Yan, Mikhail Bragin, and Peter Luh
- Subjects
electricity markets ,uplift payments ,convex hull pricing ,survey ,decarbonization ,Technology - Abstract
Energy prices are usually determined by the marginal costs obtained by solving economic dispatch problems without considering commitment costs. Hence, generating units are compensated through uplift payments. However, uplift payments may undermine market transparency as they are not publicly disclosed. Alternatively, energy prices can be obtained from the unit commitment problem which considers commitment costs. But, due to non-convexity, prices may not monotonically increase with demand. To resolve this issue, convex hull pricing has been introduced. It is defined as the slope of the convex envelope of the total cost function over the convex hull of a unit commitment (UC) problem. Although several approaches have been developed, a relevant survey has not been found to aid the understanding of convex hull pricing from the current limited literature. This paper provides a systematic survey of convex hull pricing. It reviews, compares, and links various existing approaches, focusing on the modeling and computation of convex hull prices. Furthermore, this paper explores potential areas of improvement and future challenges due to the ongoing efforts for power system decarbonization.
- Published
- 2024
- Full Text
- View/download PDF
37. Compressive-force induced activation of apo-calmodulin in protein signalling
- Author
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Susovan Roy Chowdhury, H. Peter Lu, and Sunidhi Jaiswal
- Subjects
chemistry.chemical_classification ,0303 health sciences ,Calmodulin ,biology ,Atomic force microscopy ,Protein dynamics ,030302 biochemistry & molecular biology ,General Physics and Astronomy ,Proteins ,Peptide ,Mechanical force ,Biomechanical Phenomena ,Protein Structure, Tertiary ,03 medical and health sciences ,Signalling ,chemistry ,biology.protein ,Biophysics ,Molecule ,Physical and Theoretical Chemistry ,Function (biology) ,030304 developmental biology ,Protein Binding ,Signal Transduction - Abstract
Mechanical force plays a critical role in the relationship between protein structure and function. Force manipulation by Atomic Force Microscope can be significant and trigger chemical and biological activities of proteins. Previously we have reported that Apo-CaM undergoes through a spontaneous tertiary structural rupture under a piconewton compressive force. Here we have observed that the ruptured Apo-CaM molecules can be available to bind with C28W peptide, a typical protein signalling activity that only a Ca2+-activated CaM has. This behaviour is both unexpected and profound, as CaM in its Ca2+-non-activated form has a closed structure which does not presumably allow the molecule to bind to target peptides. In this experiment, we demonstrate that both chemical activation and force activation can play a vital role in biology, such as the cell-signalling protein dynamics and function.
- Published
- 2020
38. Raman Spectroscopic Analysis of Signaling Molecules–Dopamine Receptors Interactions in Living Cells
- Author
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H. Peter Lu and Achut P. Silwal
- Subjects
0301 basic medicine ,Cell signaling ,General Chemical Engineering ,02 engineering and technology ,Article ,Silver nanoparticle ,lcsh:Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,symbols.namesake ,medicine ,Cyclic adenosine monophosphate ,Amphetamine ,General Chemistry ,Methamphetamine ,021001 nanoscience & nanotechnology ,030104 developmental biology ,chemistry ,lcsh:QD1-999 ,Dopamine receptor ,Biophysics ,symbols ,0210 nano-technology ,Raman spectroscopy ,Intracellular ,medicine.drug - Abstract
The selective interaction of signaling compounds including neurotransmitters and drugs with the dopamine receptors (DARs) is extremely important for the treatment of neurodegenerative diseases. Here, we report a method to probe the selective interactions of signaling compounds with D1 and D2 DARs in living cells using the combined approach of theoretical calculation and surface-enhanced Raman spectroscopy (SERS). When signaling compounds such as DA, amphetamine, methamphetamine, and methylenedioxypyrovalerone interact with D1 dopamine receptors (DRD1), the intracellular cyclic adenosine monophosphate (cAMP) level is increased. However, the intracellular level of cAMP is decreased when D2 dopamine receptors (DRD2) interact with the abovementioned signaling compounds. In our experiments, we have internalized the silica-coated silver nanoparticles (AgNP@SiO2) in living cells to adsorb biologically generated cAMP which was probed by using SERS. Besides adsorptions of cAMP, AgNP@SiO2 has a crucial role for the enhancement of Raman cross section of the samples. We observed the characteristic SERS peaks of cAMP when DRD1-overexpressed cells interact with the signaling compounds; these peaks were not observed for other cells including DRD2-overexpressed and DRD1–DRD2-coexpressed cells. Our experimental approach is successful to probe the intracellular cAMP and characterize the selectivity of signaling compounds to different types of DARs. Furthermore, our experimental approach is highly capable for in vivo studies because it can probe intracellular cAMP using a low input power of incident laser without significant cell damage. Our experimental results and density functional theory calculations showed that 780 and 1503 cm–1 are signature Raman peaks of cAMP. The SERS peak at 780 cm–1 is associated with C–O, C–C, and C–N stretching and symmetric and asymmetric bending of two O–H bonds of cAMP, whereas the SERS peak at 1503 cm–1 is contributed by the O9–H3 bending mode.
- Published
- 2018
39. Raman spectroscopy probing of redox states and mechanism of flavin coenzyme
- Author
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H. Peter Lu and Achut P. Silwal
- Subjects
biology ,Chemistry ,02 engineering and technology ,Flavin group ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Photochemistry ,01 natural sciences ,Redox ,Cofactor ,0104 chemical sciences ,symbols.namesake ,biology.protein ,symbols ,General Materials Science ,0210 nano-technology ,Raman spectroscopy ,Spectroscopy ,Mechanism (sociology) - Published
- 2018
40. Ratiometric Near-Infrared Fluorescent Probes Based On Through-Bond Energy Transfer and π-Conjugation Modulation between Tetraphenylethene and Hemicyanine Moieties for Sensitive Detection of pH Changes in Live Cells
- Author
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Wafa Mazi, Nathan Conner, Fen-Tair Luo, Jianheng Bi, Mingxi Fang, Haiying Liu, Jianbo Wang, Yibin Zhang, H. Peter Lu, and Shuai Xia
- Subjects
Cytoplasm ,Fluorescence-lifetime imaging microscopy ,Intracellular pH ,Biomedical Engineering ,Pharmaceutical Science ,Bioengineering ,02 engineering and technology ,010402 general chemistry ,Ring (chemistry) ,Photochemistry ,01 natural sciences ,Article ,chemistry.chemical_compound ,Morpholine ,Humans ,Bond energy ,Fluorescent Dyes ,Pharmacology ,Chemistry ,Optical Imaging ,Organic Chemistry ,Near-infrared spectroscopy ,Carbocyanines ,Hydrogen-Ion Concentration ,021001 nanoscience & nanotechnology ,Fluorescence ,Acceptor ,0104 chemical sciences ,Spectrometry, Fluorescence ,0210 nano-technology ,HeLa Cells ,Biotechnology - Abstract
In this paper, we present three ratiometric near-infrared fluorescent probes (A–C) for accurate, ratiometric detection of intracellular pH changes in live cells. Probe A consists of a tetraphenylethene (TPE) donor and near-infrared hemicyanine acceptor in a through-bond energy transfer (TBET) strategy, while probes B and C are composed of TPE and hemicyanine moieties through single and double sp(2) carbon–carbon bond connections in a π-conjugation modulation strategy. The specific targeting of the probes to lysosomes in live cells was achieved by introducing morpholine residues to the hemicyanine moieties to form closed spirolactam ring structures. Probe A shows aggregation-induced emission (AIE) property at neutral or basic pH, while probes B and C lack AIE properties. At basic or neutral pH, the probes only show fluorescence of TPE moieties with closed spirolactam forms of hemicyanine moieties, and effectively avoid blind fluorescence imaging spots, an issue which typical intensity-based pH fluorescent probes encounter. Three probes show ratiometric fluorescence responses to pH changes from 7.0 to 3.0 with TPE fluorescence decreases and hemicyanine fluorescence increases, because acidic pH makes the spirolactam rings open to enhance π-conjugation of hemicyanine moieties. However, probe A shows much more sensitive ratiometric fluorescence responses to pH changes from 7.0 to 3.0 with remarkable ratio increase of TPE fluorescence to hemicyanine fluorescence up to 238-fold than probes B and C because of its high efficiency of energy transfer from TPE donor to the hemicyanine acceptor in the TBET strategy. The probe offers dual Stokes shifts with a large pseudo-Stokes shift of 361 nm and well-defined dual emissions, and allows for colocalization of the imaging readouts of visible and near-infrared fluorescence channels to achieve more precisely double-checked ratiometric fluorescence imaging. These platforms could be employed to develop a variety of novel ratiometric fluorescent probes for accurate detection of different analytes in applications of chemical and biological sensing, imaging, and diagnostics by introducing appropriate sensing ligands to hemicyanine moieties to form on–off spirolactam switches.
- Published
- 2018
41. Exploration of Multistate Conformational Dynamics upon Ligand Binding of a Monomeric Enzyme Involved in Pyrophosphoryl Transfer
- Author
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H. Peter Lu, Lingci Zhao, and Jin Wang
- Subjects
chemistry.chemical_classification ,Binding Sites ,Protein Conformation ,Molecular Dynamics Simulation ,Ligands ,Pterins ,Surfaces, Coatings and Films ,Enzyme catalysis ,chemistry.chemical_compound ,Molecular dynamics ,Adenosine Triphosphate ,Protein structure ,Monomer ,Enzyme ,chemistry ,Diphosphotransferases ,Materials Chemistry ,Biophysics ,Physical and Theoretical Chemistry ,Binding site ,Flux (metabolism) ,Function (biology) - Abstract
HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) is a monomeric protein with 158 residues, which undergoes large-scale conformational changes between apo, open, and holo states responding to ligand binding for its function. It has been explored widely as an excellent target for potential antibacterial drug development. However, little is known about how conformational dynamics between the native states influences the substrate recognition and the functionality of enzymatic catalysis. Here, we report a coarse-grained triple-basin structure-based model upon ligand binding to describe such multiple-state system by the molecular dynamics simulation. With our model, we have made theoretical predictions that are in good agreement with the experimental measurements. Our results revealed the intrinsic conformational fluctuations between apo and open states without ligand binding. We found that HPPK can switch to the activated holo state upon the ordered binding of the two ligands (ATP and HP). We uncovered the underlying mechanism by which major induced fit and minor population shift pathways coexist upon ligand binding by quantitative flux analysis. Additionally, we pointed out the structural origin for the conformational changes and identified the key residues as well as contact interactions. We further explored the temperature effect on the conformational distributions and pathway weights. It gave strong support that higher temperatures promote population shift, while the induced fit pathway is always the predominant activation route of the HPPK system. These findings will provide significant insights of the mechanisms of the multistate conformational dynamics of HPPK upon ligand binding.
- Published
- 2018
42. Probing Dynamic Heterogeneity in Aggregated Ion Channels in Live Cells
- Author
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Rajeev Yadav and H. Peter Lu
- Subjects
Chemistry ,Depolarization ,Neurotransmission ,Photobleaching ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Cell membrane ,General Energy ,medicine.anatomical_structure ,medicine ,Biophysics ,NMDA receptor ,Physical and Theoretical Chemistry ,Signal transduction ,Receptor ,Ion channel - Abstract
N-Methyl-d-aspartate (NMDA) receptor is a crucial ion channel requiring the concurrent binding of both agonists glycine and glutamate along with the membrane depolarization for its opening and mediates calcium influx, which triggers the signal transduction important for synaptic transmission and plasticity. The efficiency and regulations of such cellular physiological processes are crucially relying on inherent molecular spatial organization and interactions of these channels with ligands as well as trafficking in the confined local environment. To decipher their organization, we have combined two imaging microscopic approaches, photobleaching step counting and single particle tracking analysis, that allow detection of unique organized patterns of NMDA receptor ion channel in the cell membrane. A broad range of photobleaching steps is observed ranging from 1 to 16. Single particle tracking analysis is performed to see the surface mobility of NMDA receptors and measured diffusion coefficient for all the tr...
- Published
- 2018
43. Intermittent single-molecule interfacial electron transfer dynamics
- Author
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Biju, Vasudevanpillai, Micic, Miodrag, Dehong Hu, and H. Peter Lu
- Subjects
Oxygen -- Chemical properties ,Titanium compounds -- Chemical properties ,Electron transport -- Research ,Chemistry - Abstract
Single molecular studies of photosensitized interfacial electron transfer (ET) processes in Coumarin 343 (C343)-TiO(sub 2) nanoparticles (NP) and cresyl violet (CV (super +))-TiO(sub 2) NP systems are reported. The fluorescence fluctuation dynamics were found to be inhomogeneous from molecule to molecule and from time to time, showing significant static and dynamic disorders in the interfacial ET reaction dynamics.
- Published
- 2004
44. Hedgerows for Hedgehogs and Campus Biodiversity
- Author
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Glen Cousquer, Emily Norris, Peter Lurz, Elizabeth Vander Meer, and John Gurnell
- Subjects
hedgehog friendly campus ,vertical literacy ,action learning ,habitat fragmentation ,30x30 biodiversity challenge ,universities ,Social sciences (General) ,H1-99 - Abstract
Across society, organisations find themselves challenged to address the climate and nature emergencies. Universities have a complex set of responsibilities given that they are preparing students for an uncertain future in which the very survival of life is in the balance. A characteristic of this complex challenge is the need to develop the necessary ecological and vertical literacy required to tackle the many aspects of fragmentation we are subject to. The 30x30 biodiversity challenge provides universities with an opportunity to address one particular form of fragmentation, that affecting habitats. The case study presented here explores how a Hedgehog Friendly Campus (HFC) initiative allowed awareness of hedgehog habitat needs and in particular the health of hedgerows to feed into campus environmental management. A surprising finding is that addressing the fragmentation of hedgerows highlights organisational fragmentation, with little communication between landscape managers, research and teaching. A collaborative systems approach to the biodiversity challenge is thus needed and realising this will challenge universities to build their capacity to embrace research and learning for sustainability through living lab projects. This requires a recognition of the responsibility universities have to enable action learning across disciplines in ways that will connect staff and students to, and bring them into relation with, the biodiversity crisis at a local level. The HFC initiative provides a rich opportunity for communities of inquiry and practice to be nurtured and for this process to inform the evolution of our understanding of habitat restoration on university campuses as a corporate responsibility.
- Published
- 2024
- Full Text
- View/download PDF
45. Artistic practice in Waldorf teacher education: a sensory-aesthetic concept for a digital age
- Author
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Peter Lutzker
- Subjects
Waldorf teacher education ,arts-based teacher education ,teaching as an art ,sensory deficits ,aesthetic education ,aesthesis ,Education (General) ,L7-991 - Abstract
One of the general concepts underlying Waldorf education is that teaching is an art. Although this idea is certainly not unique to Waldorf education, what is unique is the way it has been integrated into Waldorf teacher education. While Waldorf teacher education programs are diverse, both in national and international contexts, one of the central elements which they share is the prominent role which different forms of artistic practice play throughout the course of pre-service and in-service programs. This article explores the reasons and aims behind the inclusion of subjects such as music, sculpture, and speech in Waldorf teacher education, at first within the larger context of viewing different perspectives and justifications for the inclusion of the arts in teacher education outside of Waldorf pedagogy. In light of the educational challenges posed by widespread sensory deficits among children and adolescents, viewed here as being connected to the extensive role/s which different forms of digital media play in their lives, the case is made for the potentials of the arts as a way to address those deficits. In examining both the arguments for arts-based courses in teacher education and the pedagogical challenges of our times I propose a concept for the inclusion of the arts in teacher education connected to the concept of aesthesis, from the Ancient Greek concept of aisthésis, understood here as the primary perceptual-sensory basis of aesthetic experience. The integration of scientific courses with arts-based practice in teacher education is seen as providing a fruitful basis for teachers to be able to take on these educational challenges.
- Published
- 2024
- Full Text
- View/download PDF
46. A contemporary training concept in critical care cardiology
- Author
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Leonhard Binzenhöfer, Nils Gade, Daniel Roden, Inas Saleh, Hugo Lanz, Laura Villegas Sierra, Paula Seifert, Clemens Scherer, Benedikt Schrage, Franz Haertel, Peter M. Spieth, Norman Mangner, Christoph Adler, Daniel Hoyer, Tobias Graf, Hannah Billig, Mostafa Salem, Rafael Henrique Rangel, Walter S. Speidl, Christian Hagl, Jörg Hausleiter, Steffen Massberg, Michael Preusch, Benjamin Meder, David M. Leistner, Peter Luedike, Tienush Rassaf, Sebastian Zimmer, Dirk Westermann, Uwe Zeymer, Andreas Schäfer, Holger Thiele, and Enzo Lüsebrink
- Subjects
critical care cardiology ,training concept ,core curriculum ,intensive care unit ,cardiovascular fellows ,fellows in training ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Critical care cardiology (CCC) in the modern era is shaped by a multitude of innovative treatment options and an increasingly complex, ageing patient population. Generating high-quality evidence for novel interventions and devices in an intensive care setting is exceptionally challenging. As a result, formulating the best possible therapeutic approach continues to rely predominantly on expert opinion and local standard operating procedures. Fostering the full potential of CCC and the maturation of the next generation of decision-makers in this field calls for an updated training concept, that encompasses the extensive knowledge and skills required to care for critically ill cardiac patients while remaining adaptable to the trainee’s individual career planning and existing educational programs. In the present manuscript, we suggest a standardized training phase in preparation of the first ICU rotation, propose a modular CCC core curriculum, and outline how training components could be conceptualized within three sub-specialization tracks for aspiring cardiac intensivists.
- Published
- 2024
- Full Text
- View/download PDF
47. The capacity of neurological pupil index to predict the absence of somatosensory evoked potentials after cardiac arrest – An observational study
- Author
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Meena Thuccani, Sara Joelsson, Linus Lilja, Axel Strålin, Josefin Nilsson, Petra Redfors, Araz Rawshani, Johan Herlitz, Peter Lundgren, and Christian Rylander
- Subjects
Cardiac arrest ,Neurological outcome ,Neurological pupil index ,Prognostication ,Pupillometry ,Somatosensory evoked potentials ,Specialties of internal medicine ,RC581-951 - Abstract
Background: In neurologic prognostication of comatose survivors from cardiac arrest, two independent predictors of poor outcome are the loss of the Pupillary light reflex (PLR) and the loss of the N20 response from Somatosensory Evoked potentials (SSEP). The PLR can be quantitatively assessed by pupillometry. Both tests depend on the midbrain, in which a dysfunction reflects a severe hypoxic injury. We reasoned that a certain level of defective PLR would be predictive of a bilaterally absent SSEP N20 response. Method: Neurological Pupil index (NPi) from the pupillometry and the SSEP N20 response were registered >48 h after cardiac arrest in comatose survivors. Clinical data were retrospectively analyzed. A receiver operating characteristic curve was used to evaluate the capacity of NPi to predict bilaterally absent SSEP N20 response. An NPi threshold value resulting in 48 hours after cardiac arrest predicted bilateral loss of the SSEP N20 response with a FPR
- Published
- 2024
- Full Text
- View/download PDF
48. Industrial Scale Gene Editing in Brassica napus
- Author
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Andrew Walker, Javier Narváez-Vásquez, Jerry Mozoruk, Zhixia Niu, Peter Luginbühl, Steve Sanders, Christian Schöpke, Noel Sauer, Jim Radtke, Greg Gocal, and Peter Beetham
- Subjects
canola ,Brassica napus ,gene editing ,multiplex gene editing ,non-transgenic gene editing ,pod shatter ,Science ,Biology (General) ,QH301-705.5 - Abstract
In plants, an increasing number of traits and new characteristics are being developed using gene editing. Simple traits represented by a single gene can be managed through backcross breeding, but this is typically not the case for more complex traits which may result from the function of a large number of genes. Here, we demonstrate two case studies of improving oleic oil content and developing pod shatter reduction in Brassica napus by using gene editing tools on an industrial scale. There are four BnaFAD2 genes involved in oleic oil content and eight BnaSHP genes involved in pod shatter tolerance. In order to develop these two traits, we delivered nuclease ribonucleoproteins with Gene Repair OligoNucleotides (GRONs) into protoplasts, with subsequent regeneration into plants on an industrial scale, which encompassed robust tissue culture protocols, efficient gene editing, robotics sampling, and molecular screening, vigorous plant regeneration, growth, and phenotyping. We can produce precise loss-of-function-edited plants with two improved agronomically important complex traits, high oleic oil or pod shatter reduction, in elite canola varieties within 1–3 years, depending on the trait complexity. In the edited plants carrying loss of function of four BnaFAD2 genes, the seed fatty acid oleic acid content reached 89% compared to 61% in the non-edited wildtype control. The plants carrying eight edited BnaSHP genes achieved 51% pod shatter reduction in multiple year field testing in the target environment compared to the wildtype control.
- Published
- 2023
- Full Text
- View/download PDF
49. Artificial neural network identification of exercise expiratory flow-limitation in adults
- Author
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Hans Christian Haverkamp, Peter Luu, Thomas W. DeCato, and Gregory Petrics
- Subjects
Medicine ,Science - Abstract
Abstract Identification of ventilatory constraint is a key objective of clinical exercise testing. Expiratory flow-limitation (EFL) is a well-known type of ventilatory constraint. However, EFL is difficult to measure, and commercial metabolic carts do not readily identify or quantify EFL. Deep machine learning might provide a new approach for identifying EFL. The objective of this study was to determine if a convolutional neural network (CNN) could accurately identify EFL during exercise in adults in whom baseline airway function varied from normal to mildly obstructed. 2931 spontaneous exercise flow-volume loops (eFVL) were placed within the baseline maximal expiratory flow-volume curves (MEFV) from 22 adults (15 M, 7 F; age, 32 yrs) in whom lung function varied from normal to mildly obstructed. Each eFVL was coded as EFL or non-EFL, where EFL was defined by eFVLs with expired airflow meeting or exceeding the MEFV curve. A CNN with seven hidden layers and a 2-neuron softmax output layer was used to analyze the eFVLs. Three separate analyses were conducted: (1) all subjects (n = 2931 eFVLs, [GRALL]), (2) subjects with normal spirometry (n = 1921 eFVLs [GRNORM]), (3) subjects with mild airway obstruction (n = 1010 eFVLs, [GRLOW]). The final output of the CNN was the probability of EFL or non-EFL in each eFVL, which is considered EFL if the probability exceeds 0.5 or 50%. Baseline forced expiratory volume in 1 s/forced vital capacity was 0.77 (94% predicted) in GRALL, 0.83 (100% predicted) in GRNORM, and 0.69 (83% predicted) in GRLOW. CNN model accuracy was 90.6, 90.5, and 88.0% in GRALL, GRNORM and GRLOW, respectively. Negative predictive value (NPV) was higher than positive predictive value (PPV) in GRNORM (93.5 vs. 78.2% for NPV vs. PPV). In GRLOW, PPV was slightly higher than NPV (89.5 vs. 84.5% for PPV vs. NPV). A CNN performed very well at identifying eFVLs with EFL during exercise. These findings suggest that deep machine learning could become a viable tool for identifying ventilatory constraint during clinical exercise testing.
- Published
- 2023
- Full Text
- View/download PDF
50. Ultra-sensitive lock-in amplifier coupled oscillatory magnetic tweezers for piconewton force manipulation applications
- Author
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H. Peter Lu and Meiling Wu
- Subjects
Physics ,Quantitative Biology::Biomolecules ,Magnetic tweezers ,business.industry ,Amplifier ,Lock-in amplifier ,General Physics and Astronomy ,equipment and supplies ,Signal ,Noise (electronics) ,Synchronization ,Magnetic field ,Optoelectronics ,Detection theory ,business ,human activities - Abstract
We have developed lock-in amplifier coupled oscillatory magnetic tweezers, aiming to synchronize the oscillatory magnetic force application and single-molecule response detection at the applied oscillatory frequency by incorporating an optical lock-in amplifier detection. The designed home-built lock-in amplifier detection instrument enables an exact reference signal input and hence reveals an accurate and sensitive magnetic response synchronization. We have further demonstrated the approach with the rhodamine 6G stained super-paramagnetic beads by monitoring the below-the-noise-background weak fluorescence signal changes due to the magnetic response of the super-paramagnetic beads under the oscillatory force manipulation. The integration of the lock-in amplifier and the oscillating magnetic tweezers can significantly expand the application of the magnetic tweezers for signal detection below the noise background, such as adapting to the important applications in the detailed exploration of mechanical properties of biomolecules and studies of the protein conformational fluctuation dynamics.
- Published
- 2021
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