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UNLABELLED: There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (functional modules), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida. Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE: This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

Abstract Background Alzheimer’s disease (AD) is the most common human neurodegenerative disorder worldwide. Owing to its chronic nature, our limited understanding of its pathophysiological mechanisms, and because of the lack of effective anti-AD drugs, AD represents a significant socio-economic challenge for all industrialized countries. Neuronal cell death is a key factor in AD pathogenesis and recent studies have suggested that neuronal ferroptosis may play a major patho-physiological role. Since ferroptosis involves free radical-mediated lipid peroxidation, we hypothesized that enteral administration of the radical scavenger butylated hydroxytoluene (BHT) might slow down or even prevent the development of AD-related symptoms in an in vivo animal AD model. Material and methods To test this hypothesis, we employed the rat model of streptozotocin-induced AD and administered butylated hydroxytoluene orally at a dose of 120 mg/kg body weight. Following BHT treatment, neuronal cell death was induced by bilateral stereotactic intraventricular injection of streptozotocin at a dose of 3.0 mg/kg body weight. Three weeks after surgery, we assessed the learning capabilities and the short-term memory of three experimental groups using the conventional y-maze test: (i) streptozotocin-treated rats (BHT pre-treatment), (ii) streptozotocin-treated rats (no BHT pre-treatment), (iii) sham-operated rats (BHT pre-treatment but no streptozotocin administration). After the y-maze test, the animals were sacrificed, hippocampal tissue was prepared and several biochemical (malonyl dialdehyde formation, glutathione homeostasis, gene expression patterns) and histochemical (Congo-red staining, Nissl staining, Perls staining) readout parameters were quantified. Results Intraventricular streptozotocin injection induced the development of AD-related symptoms, elevated the degree of lipid peroxidation and upregulated the expression of ferroptosis-related genes. Histochemical analysis indicated neuronal cell death and neuroinflammation, which were paralleled by aberrant intraneuronal iron deposition. The streptozotocin-induced alterations were significantly reduced and sometimes even abolished by oral BHT treatment. Conclusion Our data indicate that oral BHT treatment attenuated the development of AD-related symptoms in an in vivo rat model, most probably via inhibiting neuronal ferroptosis. These findings suggest that BHT might constitute a promising candidate as anti-AD drug. However, more work is needed to explore the potential applicability of BHT in other models of neurodegeneration and in additional ferroptosis-related disorders.

Comparison of microbial strains for tolerance to and catabolism of lignin stream constituents toward evaluating microbial hosts for lignin bioconversion.

Cervical cancer remains a leading cause of cancer-related deaths in women worldwide, with limited treatment options for advanced stages and therapy-resistant cases. Despite advances in treatment, the variability in the patient response to standard therapies underscores the need for molecular biomarkers to guide personalized treatment strategies. This study aimed to explore the transcriptomic changes associated with the therapeutic response in locally advanced cervical cancer, focusing on 770 immune-related genes. We employed a digital multiplexed gene expression analysis, comparing gene expression profiles between matching pre- and post-treatment samples. The results revealed the significant upregulation of C7 and EGR2 in the post-treatment samples, suggesting that enhanced immune activity is a key factor in therapeutic success. Conversely, IL17RB, S100A7, and SAA1 were upregulated in the pre-treatment samples, potentially indicating resistance mechanisms. Pathway enrichment analysis highlighted that the immune response and apoptosis pathways are crucial to post-treatment changes. These findings suggest that C7, EGR2, and IL17RB may serve as biomarkers for predicting therapeutic outcomes and could inform the development of more effective, individualized treatment strategies for cervical cancer. This study provides new insights into the molecular mechanisms underlying treatment response and resistance.

Abstract Background Wilson disease (WD) is a rare disorder of copper metabolism, causing copper accumulation mainly in the liver and the brain. The prevalence of WD was previously estimated around 20 to 33.3 patients per million for the United States, Europe, and Asia, but data on the prevalence of WD in Germany are limited. Objectives To describe patient characteristics and to assess prevalence of WD in Germany using a representative claims database. Methods WD patients were identified in the WIG2 (Wissenschaftliches Institut für Gesundheitsökonomie und Gesundheitssystemforschung; Scientific Institute for Health Economics and Health Systems Research) benchmark database of 4.5 million insured Germans by combining ICD-10-coding with WD-specific lab tests and treatments. The study period ranged from 2013 to 2016 for assessing patient characteristics, and to 2018 for prevalence, respectively. Results Seventy unique patients were identified. Most patients (86%) were between 18 and 64 years of age and more often male (60%) than female. Two patients (3%) younger than 18 years were included, as well as 8 patients (11%) older than 64 years. Most common WD subtypes were hepatic (57%), psychiatric (49%), and neurologic (44%). Average prevalence was 20.3 patients per million (range: 17.8–24.4), with similar results for two-year prevalence. Generally, prevalence increased steadily over the study period. Observed mortality was low, with only one death during the study period. Conclusions This study adds valuable real-world data on the prevalence and patient characteristics of WD in Germany. Generally, our findings align with other reports and contribute to the global understanding of WD epidemiology. Still, regional and temporal trends remain to be investigated more thoroughly to further the understanding of the natural history and epidemiology of this rare disease.

Myelodysplastic neoplasms (MDS) are a collection of hematopoietic disorders with widely variable prognoses and treatment options. Accurate pathologic diagnoses present challenges because of interobserver variability in interpreting morphology and quantifying dysplasia. We compared local clinical site diagnoses with central, adjudicated review from 918 participants enrolled in the ongoing National Heart, Lung, and Blood Institute National MDS Natural History Study, a prospective observational cohort study of participants with suspected MDS or MDS/myeloproliferative neoplasms (MPNs). Locally, 264 (29%) were diagnosed as having MDS, 15 (2%) MDS/MPN overlap, 62 (7%) idiopathic cytopenia of undetermined significance (ICUS), 0 (0%) acute myeloid leukemia (AML) with

Pulmonary microvascular endothelial cells contribute to the integrity of the lung gas exchange interface, and they are highly glycolytic. Although glucose and fructose represent discrete substrates available for glycolysis, pulmonary microvascular endothelial cells prefer glucose over fructose, and the mechanisms involved in this selection are unknown. 6-Phosphofructo-2-kinase/fructose-2, 6-bisphosphatase 3 (PFKFB3) is an important glycolytic enzyme that drives glycolytic flux against negative feedback and links glycolytic and fructolytic pathways. We hypothesized that PFKFB3 inhibits fructose metabolism in pulmonary microvascular endothelial cells. We found that PFKFB3 knockout cells survive better than wild-type cells in fructose-rich medium under hypoxia. Seahorse assays, lactate and glucose measurements, and stable isotope tracing showed that PFKFB3 inhibits fructose-hexokinase-mediated glycolysis and oxidative phosphorylation. Microarray analysis revealed that fructose upregulates PFKFB3, and PFKFB3 knockout cells increase fructose-specific GLUT5 (glucose transporter 5) expression. Using conditional endothelial-specific PFKFB3 knockout mice, we demonstrated that endothelial PFKFB3 knockout increases lung tissue lactate production after fructose gavage. Last, we showed that pneumonia increases fructose in BAL fluid in mechanically ventilated ICU patients. Thus, PFKFB3 knockout increases GLUT5 expression and the hexokinase-mediated fructose use in pulmonary microvascular endothelial cells that promotes their survival. Our findings indicate that PFKFB3 is a molecular switch that controls glucose versus fructose use in glycolysis and help better understand lung endothelial cell metabolism during respiratory failure.

The World Climate Research Programme (WCRP) envisions a future where actionable climate information is universally accessible, supporting decision makers in preparing for and responding to climate change. In this perspective, we advocate for enhancing links between climate science and decision-making through a better and more decision-relevant understanding of climate impacts. The proposed framework comprises three pillars: climate science, impact science, and decision-making, focusing on generating seamless climate information from sub-seasonal, seasonal, decadal to century timescales informed by observed climate events and their impacts. The link between climate science and decision-making has strengthened in recent years, partly owing to undeniable impacts arising from disastrous weather extremes. Enhancing decision-relevant understanding involves utilizing lessons from past extreme events and implementing impact-based early warning systems to improve resilience. Integrated risk assessment and management require a comprehensive approach that encompasses good knowledge about possible impacts, hazard identification, monitoring, and communication of risks while acknowledging uncertainties inherent in climate predictions and projections, but not letting the uncertainty lead to decision paralysis. The importance of data accessibility, especially in the Global South, underscores the need for better coordination and resource allocation. Strategic frameworks should aim to enhance impact-related and open-access climate services around the world. Continuous improvements in predictive modeling and observational data are critical, as is ensuring that climate science remains relevant to decision makers locally and globally. Ultimately, fostering stronger collaborations and dedicated investments to process and tailor climate data will enhance societal preparedness, enabling communities to navigate the complexities of a changing climate effectively.

Next generation solar cells like tunnel oxide passivated contacts (TOPCon) or perovskite/TOPCon tandem solar cells require efficient interface passivation by ultrathin organic or inorganic layers to uncover their true efficiency potential. Especially the microstructure and the Si suboxide content of the tunnel oxide in poly-Si(Ox)/SiO2/c-Si TOPCon stacks have been shown to have a tremendous influence on macroscopic device properties. Similarly, perovskite/ITO interface modification by a self-assembled monolayer (SAM) molecule is necessary to achieve high power conversion efficiencies of the perovskite sub cell. However, the characterization of such thin film structures and the interfacial composition is challenging. In this contribution, we present characterization results of ultrathin passivation layers using angle-resolved X-ray photoelectron spectroscopy (XPS) and advanced data evaluation routines, including maximum entropy methods and analyses of inelastically-scattered electron background data. In particular, the interfaces in the stacks (1) partially oxidized a-Si/SiO2/c-Si and (2) 2PACz/ITO after different thermal treatment were investigated. It could be shown that already a ~5 nm thin SiNx layer prevents unwanted oxidation from ambient during cooldown of TOPCon-like stacks and that annealing above 100 °C can convert a 2PACz multilayer to a 2PACz monolayer on an ITO substrate.

Purpose: Integrated MRI and linear accelerator systems (MR-Linacs) provide superior soft tissue contrast, and the capability of adapting radiotherapy plans to changes in daily anatomy. In this dataset, serial MRIs of the abdomen of patients undergoing radiotherapy were collected and the luminal gastro-intestinal tract was segmented to support an online segmentation algorithm competition. This dataset may be further utilized by radiation oncologists, medical physicists, and data scientists to further improve auto segmentation algorithms. Acquisition and validation of methods: Serial 0.35T MRIs from patients who were treated on an MR-Linac for tumors located in the abdomen were collected. The stomach, small intestine and large intestine were manually segmented on all MRIs by a team of annotators under the supervision of a board-certified radiation oncologist. Annotator segmentations were validated on 4 representative abdominal MRIs by comparing to the radiation oncologist's contours using 3D Hausdorff distance and 3D Dice coefficient metrics. Data format and usage notes: The dataset includes 467 de-identified scans and their contours from 107 patients. Each patient underwent 1–5 MRI scans of the abdomen. Most of the scans consisted of 144 axial slices with a pixel resolution of 1.5 × 1.5 × 3 mm, leading to 67,248 total slices in the dataset. Images in DICOM format were converted into Portable Graphics Format (PNG) files. Each Portable Graphics Format (PNG) image file stored a slice of the scan, with pixels recorded in 16 bits to cover the full range of intensity values. DICOM-RT segmentations were converted into Comma-Separated Values (CSV) format. Data including images and the annotations is publicly available at https://www.kaggle.com/ds/3577354. Potential applications: While manual segmentations are subject to bias and inter-observer variability, the dataset has been used for the UW-Madison GI Tract Image Segmentation Challenge hosted by Kaggle and may be used for ongoing segmentation algorithm development and potentially for dose accumulation algorithms.

The essential use concept aims to better protect consumers, vulnerable groups, and the environment from the most harmful chemicals by phasing out uses considered non-essential for society. Given the lack of empirical research evaluating this novel approach for chemical management in real-world settings, the aims of the present analysis were to 1) investigate if the information provided in applications for authorisation under REACH allowed for the identification of non-essential uses of substances of very high concern (SVHCs), and 2) identify data gaps, challenges and potential needs for revising the assessment criteria to effectively implement the essential use concept in the REACH authorisation. In total, 100 uses covering 11 SVHCs were analysed. 4-(1,1,3,3-tetramethylbutyl) phenol (OPnEO) and chromium trioxide were among the most frequently used substances, covering 42% and 35% of the analysed uses. Using the current essential use criteria, 55% of all analysed uses were categorised as essential, while 10% were categorised as non-essential. Potentially, authorisations would not have been granted for the identified non-essential uses under REACH if the concept had been implemented at the time. However, for 35% of the uses it was not possible to assess their essentiality and these uses were therefore categorised as “complex.” These challenges were due to the multiple purposes of the technical function, lack of detailed information on the spectrum of end-uses, and difficulties in interpreting the essential use criteria. Consequently, for a successful implementation of the essential use concept, we recommend the European Commission to develop guidance for applicants and refine the essential use criteria to ensure a transparent and resource-efficient authorisation procedure under REACH.

Abstract Background In response to the COVID-19 pandemic, WHO launched a strategic preparedness and response plan, outlining public health measures to support countries worldwide. Healthcare workers have an increased risk of becoming infected and their behaviour regarding infection prevention and control (IPC) influences infection dynamics. IPC strategies are important across the globe, but even more in low-resource settings where capacities for testing and treatment are limited. Our study aimed to assess and implement COVID-19 pandemic preparedness and response measures in Faranah, Guinea, primarily focusing on healthcare workers’ IPC knowledge, attitude and practice (KAP). Methods The study was conducted between April 2020 and April 2021 assessing IPC pandemic preparedness and response measures such as healthcare workers’ KAP, alcohol-based handrub (ABHR) consumption and COVID-19 triaging in the Faranah Regional Hospital and two associated healthcare centres. The assessment was accompanied by IPC training and visual workplace reminders and done in pre- and post- phases to evaluate possible impact of these IPC activities. Results The overall knowledge score in the Faranah Regional Hospital was 32.0 out of 44 at baseline, and did not change in the first, but increased significantly by 3.0 points in the second follow-up. The healthcare workers felt closer proximity to SARS-CoV-2 overtime in addition to higher stress levels in all study sites. There was significant improvement across the observed triaging practices. Hand hygiene compliance showed a significant increase across study sites leading to 80% in Faranah Regional Hospital and 63% in healthcare centers. The average consumption of ABHR per consultation was 3.29 mL with a peak in February 2020 of 23 mL. Conclusion Despite increased stress levels among HCWs, the ongoing IPC partnership well prepared the FRH in terms of triaging processes with a stronger impact on IPC practice than on theoretical knowledge. Throughout the pandemic, global shortages and surges in consumption did not affect the continuous ABHR provision of the FRH. This highlights local ABHR production as a key pandemic preparedness strategy.

Anthelmintic resistance occurs worldwide in strongyles of ruminants but data from low-income countries are sparse and rarely apply most up to date methods, while effects of management practices in these countries are poorly documented. In Mozambique, benzimidazole resistance has been previously reported; the present study followed this up in detail, applying in vivo faecal egg count (FEC) reduction test (FECRT), in vitro egg hatch test (EHT) and molecular deep amplicon sequencing approaches targeting the internal transcribed spacer 2 (ITS-2, nemabiome) and the isotype 1 β-tubulin gene to determine the resistance status on farms and the strongyle species involved. Adult Landim goats (433) from six semi-intensive and ten extensive farms (22–30 animals/farm) from Maputo Province were visited April 2021 to February 2022. Fenbendazole (5 mg/kg bw, Panacur®) was administered orally and FEC determined using Mini-FLOTAC. The eggCounts package was used to calculate FECRs with 90% confidence intervals from paired day 0 and 14 data. In vivo and in vitro tests detected AR on 5/16 (31%) farms. This included 1/10 extensive and 4/6 semi-intensive farms. The odds of finding resistant strongyles on a semi-intensive commercial farm was 40-fold higher than on an extensive farm (p = 0.016, logistic regression). A strong, negative correlation was observed between FECRT and EHT EC50 values (Pearson's R = −0.83, P = 0.001; Cohen's κ coefficient 1.0). Nemabiome data showed that Haemonchus contortus, Trichostrongylus colubriformis and unclassified Oesophagostomum closely related to Oesophagostomum columbianum were most abundant before treatment and in particular H. contortus frequencies increased after treatment. Benzimidazole resistance associated polymorphisms were detected in H. contortus and T. colubriformis. Moreover, there were hints that resistance alleles were present in Trichostrongylus axei and Teladorsagia circumcincta. Farmers should regularly test the efficacy of anthelmintics used and consider more sustainable worm control approaches to reduce selection for resistance.

BackgroundContact tracing was implemented in many countries during the COVID-19 pandemic to prevent disease spread, reduce mortality, and avoid overburdening health care systems. In several countries, including Germany, new systems were needed to trace potentially infected individuals. ObjectiveUsing data collected in the Rhine-Neckar and Heidelberg (RNK/HD) districts in southwest Germany (population: 706,974), this study examines the overall effectiveness and efficiency of contact tracing in different age groups and stages of the pandemic. MethodsFrom January 27, 2020, to April 30, 2022, the RNK/HD Health Authority collected data on COVID-19 infections, quarantines, and deaths. Data on infection, quarantine, and death was grouped by age (young: 0-19 years; adult: 20-65 years; and senior citizens: >65 years) and pandemic phase (infectious wave plus subsequent lull periods) and analyzed for proportion, risk, and relative risk (RR). The overall effectiveness and efficiency of contact tracing were determined by calculating quarantine sensitivity (proportion of the infected population captured in quarantine), positive predictive value (PPV; proportion of the quarantined population that was infected), and the weighted Fβ-score (combined predictive performance). ResultsOf 706,974 persons living in RNK/HD during the study period, 192,175 (27.2%) tested positive for SARS-CoV-2, 74,810 (10.4%) were quarantined, and 932 (0.132%) died following infection. Compared with adults, the RR of infection was lower among senior citizens (0.401, 95% CI 0.395-0.407) and while initially lower for young people, was ultimately higher for young people across all 5 phases (first-phase RR 0.502, 95% CI 0.438-0.575; all phases RR 1.35, 95% CI 1.34-1.36). Of 932 COVID-19–associated deaths during the study period, 852 were senior citizens (91.4%), with no deaths reported among young people. Relative to adults, senior citizens had the lowest risk of quarantine (RR 0.436, 95% CI 0.424-0.448), while young people had the highest RR (2.94, 95% CI 2.90-2.98). The predictive performance of contact tracing was highest during the second and third phases of the pandemic (Fβ-score=0.272 and 0.338, respectively). In the second phase of the pandemic, 5810 of 16,814 COVID-19 infections were captured within a total quarantine population of 39,687 (sensitivity 34.6%; PPV 14.6%). In the third phase of the pandemic, 3492 of 8803 infections were captured within a total quarantine population of 16,462 (sensitivity 39.7%; PPV 21.2%). ConclusionsThe use of quarantine aligned with increasing risks of COVID-19 infection and death. High levels of quarantine sensitivity before the introduction of the vaccine show how contact tracing systems became increasingly effective at capturing and quarantining the infected population. High levels of PPV and Fβ-scores indicate, moreover, that contact tracing became more efficient at identifying infected individuals. Additional analysis of transmission pathways is needed to evaluate the application of quarantine in relation to infection and death risks within specific age groups.

The advent of X-ray free-electron lasers (XFELs) has revolutionized fundamental science, from atomic to condensed matter physics, from chemistry to biology, giving researchers access to X-rays with unprecedented brightness, coherence and pulse duration. All XFEL facilities built until recently provided X-ray pulses at a relatively low repetition rate, with limited data statistics. Here, results from the first megahertz-repetition-rate X-ray scattering experiments at the Spectroscopy and Coherent Scattering (SCS) instrument of the European XFEL are presented. The experimental capabilities that the SCS instrument offers, resulting from the operation at megahertz repetition rates and the availability of the novel DSSC 2D imaging detector, are illustrated. Time-resolved magnetic X-ray scattering and holographic imaging experiments in solid state samples were chosen as representative, providing an ideal test-bed for operation at megahertz rates. Our results are relevant and applicable to any other non-destructive XFEL experiments in the soft X-ray range.

Developing scientific reasoning (SR) is a central goal of science-teacher education worldwide. On a fine-grained level, SR competency can be subdivided into at least six skills: "formulating research questions," "generating hypotheses," "planning experiments," "observing and measuring," "preparing data for analysis," and "drawing conclusions." In a study focusing on preservice chemistry teachers, an organic chemistry lab course was redesigned using problem-solving experiments and SR video lessons to foster SR skills. To evaluate the intervention, a self-assessment questionnaire was developed, and a performance-based instrument involving an experimental problem-solving task was adapted to the target group of undergraduates. The treatment was evaluated in a pre-post design with control group (cook-book experiments, no SR video lessons) and alternative treatment group (problem-solving experiments, unrelated video lessons). Interrater reliability was excellent ([rho] from 0.915 to 1.000; ICC (A1)). Data analysis shows that the adapted instrument is suitable for university students. First insights from the pilot study indicate that the cook-book lab (control group) only fosters students' skill in "observing and measuring," while both treatment groups show an increase in "generating hypotheses" and "planning experiments." No pretest-posttest differences were found in self-assessed SR skills in the treatment groups. Instruments and data are presented and discussed.