Search

Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.

Objective:Orthopaedic surgery is an effective intervention for treating the symptoms of degenerative joint disease or osteoarthritis (OA). Frequent wound dressing changes, unless clinically indicated, can disrupt the healing process and increase the occurrence of incision site contamination. Protection from contamination is critical for surgical incisions and, therefore, undisturbed wound healing (UWH) in surgical wound management is vital. This article describes a retrospective study reporting the clinical performance of a self-adherent, absorbent postoperative dressing, with a focus on dressing wear time.Method:A single-centre, retrospective electronic medical record review of a convenience sample of adult patients treated with a dressing (Mepilex Border Post Op; Mölnlycke, Sweden) following elective hip or knee replacement was undertaken. Data relating to dressing wear time, rationale for dressing changes and patient-reported outcomes were extracted from a mobile health application moveUP Therapy (moveUP NV, Belgium). Health-related quality of life assessment was conducted using the EQ-5D-5L questionnaire and orthopaedic-specific quality of life (QoL) indicator tools.Results:Of the 558 records reviewed, 151 respondents (27.1%) reported outcomes relating to dressing wear time and frequency of dressing change. The average wear time of the first dressing was 13.6 days (second dressing: 5.3 days). The proportion of patients who wore the first dressing for 1–7 days, 8–13 days and for ≥14 days was 17.2%, 13.2% and 69.5%, respectively. Data from the completed questionnaires revealed improvement in QoL over time.Conclusion:The results of this study are a good indicator of the suitability of the postoperative dressing for a 14-day wear time, in line with the principles of UWH.

ABSTRACTBackground and ContextCurrent programming learning research often compares novices and experienced programmers, leaving early learning stages and emotional and cognitive states under-explored.ObjectiveOur study investigates relationships between cognitive and emotional states and learning performance in early stage programming learners with varying expertise (12 novices and 11 beginners; N= 23).MethodMeasures such as electrodermal activity, automated facial emotion recognition, and pupil diameter were collected to study cognitive and emotional states during a programming task. We examined how these states correlated with performance and the influence of expertise on these correlations.FindingsMultiple regression analysis on panel data (n= 690 observations) suggested fear negatively impacts programming performance, irrespective of expertise level. Meanwhile, programming expertise positively moderated cognitive effort applied to the task.ImplicationsOur findings highlight the importance for educators to design early programming experiences that anticipate and reduce fear and cognitive overload, promoting better learning outcomes.

ABSTRACTIntroductionBenznidazole, the drug of choice for treating Chagas Disease (CD), has significant limitations, such as poor cure efficacy, mainly in the chronic phase of CD, association with side effects, and parasite resistance. Understanding parasite resistance to benznidazole is crucial for developing new drugs to treat CD.Areas coveredHere, the authors review the current understanding of the molecular basis of benznidazole resistance. Furthermore, they discuss the state-of-the-art methods and critical outcomes employed to evaluate the efficacy of potential drugs against T.cruzi, aiming to select better compounds likely to succeed in the clinic. Finally, the authors describe the different strategies employed to overcome resistance to benznidazole and find effective new treatments for CD.Expert opinionResistance to benznidazole is a complex phenomenon that occurs naturally among T.cruzistrains. The combination of compounds that inhibit different metabolic pathways of the parasite is an important strategy for developing a new chemotherapeutic protocol.

Recurrent gene fusions are common in salivary gland tumors including benign tumors, such as pleomorphic adenoma (PA) and myoepithelioma (ME). In cases where chromosomal rearrangement is identified in the pleomorphic adenoma gene 1 (PLAG1)gene, different gene partners are found. Oncocytic metaplasia, characterized by oncocytes with abundant eosinophilic granular cytoplasm and hyperchromatic nuclei, is a well-known phenomenon in salivary gland neoplasms. However, the pure oncocytic variant of PA/ME showed PLAG1gene rearrangements involving various gene partners at the molecular level, without any recurrent fusion being found. Our study includes 20 cases of PA/ME, with 11 females and 9 males. The age of patients ranged from 37 to 96 years, with a median age of 62.8 years. Most tumors originate from the parotid gland. The median size of the tumor was 26.5 mm (range: 13 to 60 mm). Among the 20 cases, 14 were a pure oncocytic variant of PA/ME, whereas 6 cases showed focal oncocytic or oncocytic-like aspects. Molecular studies on 20 cases of PA/ME were conducted. A novel recurrent ZBTB47-AS1::PLAG1fusion was identified in 6 of 12 cases with pure oncocytic metaplasia, whereas the other cases had PLAG1gene fusion with different gene partners. The transcriptomic analysis of the cases harboring ZBTB47-AS1::PLAG1fusion demonstrated that these tumors have a distinct molecular profile from conventional PA/ME. This study reveals a unique subset in the oncocytic PA/ME spectrum characterized by pure oncocytic morphology with larger oncocytic cells and recurrent ZBTB47-AS1::PLAG1fusion. It also highlights the transcriptomic distinctness of salivary gland adenomas with pure oncocytic metaplasia in the spectrum of salivary gland neoplasms. Further studies are needed to better understand the oncocytic variant of PA/ME and to determine the true nature of oncocytic cells in PA/ME.

A variety of classification approaches are used to facilitate understanding, prediction, monitoring, and the management of lakes. However, broad‐scale applicability of current approaches is limited by either the need for in situ lake data, incompatibilities among approaches, or a lack of empirical testing of approaches based on ex situ data. We developed a new geographic classification approach for 476,697 lakes ≥ 1 ha in the conterminous U.S. based on lake archetypes representing end members along gradients of multiple geographic features. We identified seven lake archetypes with distinct combinations of climate, hydrologic, geologic, topographic, and morphometric properties. Individual lakes were assigned weights for each of the seven archetypes such that groups of lakes with similar combinations of archetype weights tended to cluster spatially (although not strictly contiguous) and to have similar limnological properties (e.g., concentrations of nutrients, chlorophyll a(Chl a), and dissolved organic carbon). Further, archetype lake classification improved commonly measured limnological relationships (e.g., between nutrients and Chl a) compared to a global model; a discrete archetype classification slightly outperformed an ecoregion classification; and considering lakes as continuous mixtures of archetypes in a more complex model further improved fit. Overall, archetype classification of US lakes as continuous mixtures of geographic features improved understanding and prediction of lake responses to limnological drivers and should help researchers and managers better characterize and forecast lake states and responses to environmental change.

ABSTRACTIntroductionChagas disease (CD) imposes social and economic burdens, yet the available treatments have limited efficacy in the disease’s chronic phase and cause serious adverse effects. To address this challenge, target-based approaches are a possible strategy to develop new, safe, and active treatments for both phases of the disease.Areas coveredThis review delves into target-based approaches applied to CD drug discovery, emphasizing the studies from the last five years. We highlight the proteins cruzain (CZ), trypanothione reductase (TR), sterol 14 α-demethylase (CPY51), iron superoxide dismutase (Fe-SOD), proteasome, cytochrome b(Cytb), and cleavage and polyadenylation specificity factor 3 (CPSF3), chosen based on their biological and chemical validation as drug targets. For each, we discuss its biological relevance and validation as a target, currently related challenges, and the status of the most promising inhibitors.Expert opinionTarget-based approaches toward developing potential CD therapeutics have yielded promising leads in recent years. We expect a significant advance in this field in the next decade, fueled by the new options for Trypanosoma cruzigenetic manipulation that arose in the past decade, combined with recent advances in computational chemistry and chemical biology.

AbstractDuring the pandemic, older adults were perceived as a vulnerable group without considering their various strengths. This study explored the associations between character strengths and resilience, and verified if some of these could predict resilience during the COVID-19 pandemic. A sample of 92 participants (women = 79.1%), ≥ 70 years of age (mean = 75.6 years), completed an online version of the Values in Action Inventory of Strengths – Positively keyed (VIA-IS-P) to assess 24 character strengths (grouped under six virtues) and the Connor and Davidson Resilience Scale. Results showed that 20 of the 24 strengths correlated positively and significantly with resilience. A multiple regression analysis revealed that the virtues of courage and transcendence, as well as attitudes toward aging, uniquely predicted the level of resilience. Interventions should be developed to improve certain strengths (e.g., creativity, zest, hope, humor, and curiosity), while reducing ageism, in order to promote resilience.

Résumé:Au cours de la pandémie, les personnes âgées étaient perçues comme un groupe vulnérable sans que leurs diverses forces soient prises en compte. Cette étude a exploré les liens entre les forces de caractère et la résilience, et vérifié si certaines forces pouvaient prédire la résilience pendant la pandémie de COVID-19. Un échantillon de 92 participants (femmes = 79,1%) âgés de 70 ans et plus (M = 75,6 ans) ont rempli la version en ligne de l’inventaire (VIA-IS-P) des 24 forces de caractère (regroupées sous six vertus), créé par l’Institut VIA. Les participants ont aussi rempli le questionnaire de l’échelle de résilience de Connor et Davidson. Les résultats ont montré que 20 des 24 forces étaient corrélées positivement et significativement avec la résilience. Une analyse de régression multiple a révélé que les vertus de courage et de transcendance, ainsi que les attitudes envers le vieillissement prédisaient tout particulièrement le niveau de résilience. Des interventions devraient être mises au point pour améliorer certaines forces (p. ex., la créativité, la joie de vivre, l’espoir, l’humour et la curiosité), tout en réduisant l’âgisme, afin de promouvoir la résilience.Abstract:During the pandemic, older adults were perceived as a vulnerable group without considering their various strengths. This study explored the associations between character strengths and resilience, and verified if some of these could predict resilience during the COVID-19 pandemic. A sample of 92 participants (women = 79.1%), ≥ 70 years of age (mean = 75.6 years), completed an online version of the Values in Action Inventory of Strengths – Positively keyed (VIA-IS-P) to assess 24 character strengths (grouped under six virtues) and the Connor and Davidson Resilience Scale. Results showed that 20 of the 24 strengths correlated positively and significantly with resilience. A multiple regression analysis revealed that the virtues of courage and transcendence, as well as attitudes toward aging, uniquely predicted the level of resilience. Interventions should be developed to improve certain strengths (e.g., creativity, zest, hope, humor, and curiosity), while reducing ageism, in order to promote resilience.

We report Te-doped GaP nanowires (NWs) with positive tapering and radii measuring as low as 5 nm grown by the self-assisted vapor–liquid–solid mechanism using selective-area molecular beam epitaxy. The occurrence of the ultrathin nanoantenna showed a dependence on pattern pitch (separation between NWs) with a predominance at 600 nm pitch, and exhibited radius oscillations that correlate with polytypic zincblende/wurtzite segments. A growth model explains the positive tapering of the NW leading to an ultrathin tip from the suppression of surface diffusion of Ga adatoms on the NW sidewalls by Te dopant flux. The model also provides a relationship between the radius modulations and the oscillations of the droplet contact angle, predicting the quasi-periodic radius oscillations and corresponding crystal phase transitions. These results establish a link between dopants and the ability to control NW morphology and crystal phase with possible applications in thermoelectrics, quantum emitters, and photodetectors.

L’hexapode est un robot parallèle permettant la mise en position d’objets suivant les six degrés de liberté (trois translations Tx, Ty, Tz et trois rotations Rx, Ry, Rz). Au milieu du xxesiècle, les premiers hexapodes ont servi à tester des pneus ou comme simulateurs de vol. Dans les années 1990, grâce à l’évolution des composants électroniques et à l’augmentation des capacités de calcul, l’arrivée de contrôleurs abordables et performants a permis leur essor. Nous verrons dans cet article comment un hexapode est constitué et étudierons les critères de sélection les plus pertinents avant de décrire quelques exemples d’applications.

We report on the selective area growth (SAG) of GaAs nanowires (NWs) by the catalyst-free vapor-solid mechanism. Well-ordered GaAs NWs were grown on GaAs(111)B substrates patterned with a dielectric mask using hydride vapor phase epitaxy (HVPE). GaAs NWs were grown along the ⟨111⟩B direction with perfect hexagonal shape when the hole’s opening diameter in SiNxor SiOxmask was varied from 80 to 340 nm. The impact of growth conditions and the hole size on the NW lengths and growth rates was investigated. A saturation of the NW lengths was observed at high partial pressures of As4, explained by the presence of As trimers on the (111)B surface at the NW top surface. By decreasing As4partial pressure and decreasing the hole size, high aspect ratio NWs were obtained. The longest and thinnest NWs grew faster than a two-dimensional layer under the same conditions, which strongly suggests that surface diffusion of Ga adatoms from the NW sidewalls to their top contributes to the resulting axial growth rate. These findings were supported by a dedicated model. The study highlights the capability of the HVPE process to grow high aspect ratio GaAs NW arrays with high selectivity.

•Late relapse (>2 years) after allogeneic hematopoietic stem cell transplantation (AHSCT) for acute leukemia occurs at a frequency of 4.2%.•One-third of patients have extramedullary disease with persistent full donor chimerism.•Overall survival (OS) at 2 years after late relapse was 44%.•When feasible, OS is improved by a second AHSCT, without excess toxicity.

In this work, we demonstrate the growth of vertically oriented GaAs nanowires (NWs) and microplatelets directly on a patterned SiO2/Si(111) substrate by hydride vapor-phase epitaxy (HVPE). Direct condensation of GaAs on Si was achieved through a critical surface preparation under an As-controlled atmosphere. GaAs NWs were grown along the ⟨111⟩Bdirection with a hexagonal cross section when the hole opening diameter (D) in the SiO2mask was below 350 nm. Larger apertures (D≥ 500 nm) resulted in uniform microplatelets. This study highlights the capability of HVPE for selective area growth of GaAs directly on Si and thus the potential of HVPE as a generic heterointegration process for III–V semiconductors on silicon.

Background The COVID-19 pandemic led to the prioritization of breast cancer services towards patients who are currently in treatment or diagnosed with advanced stages of breast cancer, and the self-assessment of both tumor growth and treatment side effects. Alongside the stress associated with cancer itself, delays and complications due to COVID-19 may impact patients’ mental health.Purpose To describe the experiences of Canadians living with breast cancer who received a diagnosis and/or treatment during the pandemic, and to identify their recommendations for improving patients well-being during future pandemics.Methods Semi-structured interviews were conducted with eighteen women living with breast cancer who also completed the Distress Thermometer questionnaire. The transcripts were analyzed using a descriptive thematic content methodology.Results Women who started their breast cancer screening or treatment before the pandemic reported fewer delays and less psychological distress than those who started during the pandemic. Participants reported feeling dehumanized while receiving their medical care, being unable to be accompanied during medical visits, and fearing treatment interruption during the pandemic. Patient recommendations for improving care and psychological support included the presence of family caregivers at consultations to receive the diagnosis and for the first treatment session.Conclusion Study findings provide new insights on how healthcare restrictions during the pandemic impacted on patient experiences and their well-being during screening and treatment for breast cancer. The need for cancer nursing practices and care delivery strategies that promote the delivery of compassionate, patient-centred care and the provision of psychological support during future pandemics are identified.

The Arctic region is experiencing notable warming as well as more lightning. Lightning is the dominant source of upper tropospheric nitrogen oxides (NOx), which are precursors for ozone and hydroxyl radicals. In this study, we combine the nitrogen dioxide (NO2) observations from the TROPOspheric Monitoring Instrument (TROPOMI) with Vaisala Global Lightning Dataset 360 to evaluate lightning NO2(LNO2) production in the Arctic. By analyzing consecutive TROPOMI NO2observations, we determine the lifetime and production efficiency of LNO2during the summers of 2019–2021. Our results show that the LNO2production efficiency over the ocean is ∼6 times higher than over continental regions. Additionally, we find that a higher LNO2production efficiency is often correlated with lower lightning rates. The summertime lightning NOxemission in the Arctic (north of 70° N) is estimated to be 219 ± 116 Mg of N, which is equal to 5% of anthropogenic NOxemissions. However, for the span of a few hours, the Arctic LNO2density can even be comparable to anthropogenic NO2emissions in the region. These new findings suggest that LNO2can play an important role in the upper-troposphere/lower-stratosphere atmospheric chemical processes in the Arctic, particularly during the summer.

PurposeTo describe an artificial intelligence platform that detects thyroid eye disease (TED).DesignDevelopment of a deep learning model.Methods1944 photographs from a clinical database were used to train a deep learning model. 344 additional images (‘test set’) were used to calculate performance metrics. Receiver operating characteristic, precision–recall curves and heatmaps were generated. From the test set, 50 images were randomly selected (‘survey set’) and used to compare model performance with ophthalmologist performance. 222 images obtained from a separate clinical database were used to assess model recall and to quantitate model performance with respect to disease stage and grade.ResultsThe model achieved test set accuracy of 89.2%, specificity 86.9%, recall 93.4%, precision 79.7% and an F1 score of 86.0%. Heatmaps demonstrated that the model identified pixels corresponding to clinical features of TED. On the survey set, the ensemble model achieved accuracy, specificity, recall, precision and F1 score of 86%, 84%, 89%, 77% and 82%, respectively. 27 ophthalmologists achieved mean performance of 75%, 82%, 63%, 72% and 66%, respectively. On the second test set, the model achieved recall of 91.9%, with higher recall for moderate to severe (98.2%, n=55) and active disease (98.3%, n=60), as compared with mild (86.8%, n=68) or stable disease (85.7%, n=63).ConclusionsThe deep learning classifier is a novel approach to identify TED and is a first step in the development of tools to improve diagnostic accuracy and lower barriers to specialist evaluation.

The article states that by providing accessible reading materials to people with print disabilities, such as blindness, or physical disabilities, Bookshare is a digital library, which offers a variety of reading formats, including Microsoft Word, and Braille Ready Format. It mentions that in the U.S. complimentary access to Bookshare for K-12 students with qualifying print disabilities is provided by the Department of Education Office of Special Education Programs (OSEP).

AbstractChildren living with domestic violence are exposed to the multiple strategies used by perpetrators to control their mothers, which affects their safety and well-being. However, limited research has investigated children’s relationships with their fathers or their mothers’ partners in this context. This gap in the literature is problematic, as investigating children’s relationships with these men is critical in order to fully understand their experiences and develop policies and practices that respect their rights and adequately respond to their needs. This article reports findings from a study that was conducted with children, and focuses on their relationships with the perpetrators, both before and after separation. The study drew upon a participatory and qualitative methodology, which involved focus groups and individual interviews with 59 participants aged between 6 and 18 years. The research findings revealed that children’s relationships with their fathers and mothers’ partners had been characterized by violence and control, which had resulted in a range of negative feelings. Several participants reported that they had been relieved to have limited or no contact with these men since separation. While some participants expressed ongoing fear, a few participants noted that the relationships with their fathers had improved during this period.

Pigs with similar body weight (BW), same genetic background and sex vary in protein deposition (PD) overgrowth. We aimed to study metabolic factors influencing PD in 65 kg BW gilts. Gilts were fed ad libitum a diet balanced to maximize PD. Dual X-rays were conducted to estimate body protein mass on d 1 and 21, allowing calculation of PD by difference. On d 23, the gilts were categorized into Low (157 g/d) and High (219 ± 9.97 g/d) PD groups. In each group, eight pigs underwent jugular vein cannulation. After a 48-h recovery period, where they were fed at 90% of the measured feed intake, they were fasted for 8 h. All pigs were then given a 300 g meal at time 0, and blood samples were collected at 10, 15, 20, 30, 40, 50, 60, 75, 90, 120, 150, 178, and 178 min, to study insulin and glucose responses. At 180 min post-meal, a solution of L-13C valine was administered i.v. (18 ape – flooding dose), and liver, duodenum, and longissimus dorsi muscle samples were collected within 5 minutes of slaughter. The fractional synthesis rate (FSR, %/d), absolute synthesis rate (ASR, g/d), ribosomal capacity for protein synthesis (Cs), and the efficiency of protein synthesis (KRNA) based on total RNA concentration in skeletal muscle were calculated. The insulin resistance index (HOMA-B) and insulin sensitivity index (QUICKI) were also determined. The difference between Low and High PD gilts was compared using a F-test. The longissimus dorsi muscle exhibited a 31% greater (P= 0.01) FSR in High compared with Low PD group. No significant differences were observed in the FSR of the jejunum and liver. High PD gilts showed a 55% greater ASR in whole-body muscles (P= 0.003) and 42% greater ASR in the liver (P= 0.04) compared with Low PD gilts, with no difference for the ASR in the jejunum. The KRNA in the longissimus dorsi was 48% greater in High PD gilts (P= 0.01), with no differences in KRNA for the jejunum or liver. Cs did not differ between Low and High PD gilts. The QUICKI index tended to be greater in High PD gilts (P= 0.10). Spearman’s correlation revealed that longissimus dorsi FSR was negatively correlated with the HOMA-B index (r = -0.53; P= 0.04). Increases in the HOMA-B index tended to be associated with greater KRNA (r = -0.49; P= 0.06). These correlations highlight the complex interplay of metabolic and hormonal factors involved in the observed differences in protein synthesis and efficiency in growing gilts. Insulin resistance and sensitivity may play a role in influencing skeletal muscle PD variations.

Purpose: Ventricular septal defects (VSD) are congenital heart malformations and, in severe cases, they require complex interventions under echocardiography guidance. Heart phantoms can be helpful to train and to understand the complex hemodynamics of VSD. The goal of this study was to characterize the best blood mimicking fluids in such heart phantoms for modelling the hemodynamics of VSD patients using echocardiography. Methods: Four fluid compositions were considered. Distilled water was used as a baseline, while the other three fluids were developed based on physical properties of human blood, such as the viscosity and the refractive index. Three bi-ventricular heart phantoms of three different pediatric patients with complex VSD were designed from preoperative CT imaging. Custom molds were printed in 3-D and the anatomical structure was casted in polyvinyl alcohol cryogel. The VSD in each heart phantom were observed using echocardiography and color Doppler imaging was used for the hemodynamic study. Results: Heart phantoms with blood mimicking fluids of 30% glycerol and 27% glycerol, 10% sodium iodide were found to be anatomically realistic under echocardiography imaging. Hemodynamic parameters such as the pressure gradient and the volume of the shunt were characterized using color Doppler imaging. Conclusion: Proper composition of blood mimicking fluids are important for improving the realism in echocardiographic heart phantoms and they contribute to better understand the complex hemodynamic of VSD under echocardiography.

Objectif: Les jeunes de 18 à 24 ans constituent la plus grande proportion de consommateurs de cannabis. Dans un contexte de légalisation de cette substance, il importe de promouvoir une consommation à moindre risque. L’échelle Protective Behavioral Strategies for Marijuana Scale (PBSM-17) permet d’identifier les stratégies de protection comportementale utilisées chez les consommateurs. Toutefois, cette échelle n’est pas disponible en français et n’est pas adaptée au contexte canadien. Cet article présente la démarche ayant mené à la traduction, l’adaptation culturelle et l’évaluation des propriétés psychométriques préliminaires du PBSM-17.Méthode: L’étude méthodologique s’est déroulée en six étapes. Les quatre premières étapes ont mené à la traduction et l’adaptation de l’échelle. La validation auprès de 12 jeunes a permis d’établir l’équivalence conceptuelle. L’évaluation des propriétés psychométriques a été réalisée auprès de 211 étudiants universitaires bilingues (61 % femme; âge moyen 22 ans).Résultats: La version traduite et adaptée présente des propriétés psychométriques préliminaires satisfaisantes : la cohérence interne est acceptable (α = 0,88); l’équivalence de critères (validité de construit) est établie entre la version française et la version anglaise (t(210) = 1,04, p= 0,30 ; IC 95 % [-0,20, 0,63]). Les scores obtenus aux deux versions par le même participant s’avèrent fortement corrélées (r = 0,95, p< 0,001).Conclusion: Les résultats soutiennent l’utilisation de la version française du PBSM-17. Les stratégies de protection proposées peuvent être utilisées comme outil de mesure et représentent des comportements à adopter dans un contexte d’usage du cannabis à moindre risque.