bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning the electric field response of condensed phase systems using perturbed neural network potentials
Authors: Joll Kit , Schienbein Philipp , Rosso Kevin M. , Blumberger Jochen 
Published: September 2024

AbstractThe interaction of condensed phase systems with external electric fields is of major importance in a myriad of processes in nature and technology, ranging from the field-directed motion of cells (galvanotaxis), to geochemistry and the formation of ice phases on planets, to field-directed chemical catalysis and energy storage and conversion systems including supercapacitors, batteries and solar cells. Molecular simulation in the presence of electric fields would give important atomistic insight into these processes but applications of the most accurate methods such as ab-initio molecular dynamics (AIMD) are limited in scope by their computational expense. Here we introduce Perturbed Neural Network Potential Molecular Dynamics (PNNP MD) to push back the accessible time and length scales of such simulations. We demonstrate that important dielectric properties of liquid water including the field-induced relaxation dynamics, the dielectric constant and the field-dependent IR spectrum can be machine learned up to surprisingly high field strengths of about 0.2 V Å−1 without loss in accuracy when compared to ab-initio molecular dynamics. This is remarkable because, in contrast to most previous approaches, the two neural networks on which PNNP MD is based are exclusively trained on molecular configurations sampled from zero-field MD simulations, demonstrating that the networks not only interpolate but also reliably extrapolate the field response. PNNP MD is based on rigorous theory yet it is simple, general, modular, and systematically improvable allowing us to obtain atomistic insight into the interaction of a wide range of condensed phase systems with external electric fields.
Temperature overshoot responses to ambitious forestation in an Earth System Model
Authors: Moustakis Yiannis , Nützel Tobias , Wey Hao-Wei , Bao Wenkai , Pongratz Julia 
Published: September 2024

AbstractDespite the increasing relevance of temperature overshoot and the rather ambitious country pledges on Afforestation/Reforestation globally, the mitigation potential and the Earth system responses to large-scale non-idealized Afforestation/Reforestation patterns under a high overshoot scenario remain elusive. Here, we develop an ambitious Afforestation/Reforestation scenario by harnessing 1259 Integrated Assessment Model scenarios, restoration potential maps, and biodiversity constraints, reaching 595 Mha by 2060 and 935 Mha by 2100. We then force the Max Planck Institute’s Earth System Model with this scenario which yields a reduction of peak temperature by 0.08 oC, end-of-century temperature by 0.2 oC, and overshoot duration by 13 years. Afforestation/Reforestation in the range of country pledges globally could thus constitute a useful mitigation tool in overshoot scenarios in addition to fossil fuel emission reductions, but socio-ecological implications need to be scrutinized to avoid severe side effects.
Fasting shapes chromatin architecture through an mTOR/RNA Pol I axis
Authors: Al-Refaie Nada , Padovani Francesco , Hornung Johanna , Pudelko Lorenz , Binando Francesca , del Carmen Fabregat Andrea , Zhao Qiuxia , Towbin Benjamin D. , Cenik Elif Sarinay , Stroustrup Nicholas , Padeken Jan , Schmoller Kurt M. , Cabianca Daphne S. 
Published: September 2024

AbstractChromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom, yet how it impacts three-dimensional (3D) genome organization is unknown. Here we show that fasting induces an intestine-specific, reversible and large-scale spatial reorganization of chromatin in Caenorhabditis elegans. This fasting-induced 3D genome reorganization requires inhibition of the nutrient-sensing mTOR pathway, acting through the regulation of RNA Pol I, but not Pol II nor Pol III, and is accompanied by remodelling of the nucleolus. By uncoupling the 3D genome configuration from the animal’s nutritional status, we find that the expression of metabolic and stress-related genes increases when the spatial reorganization of chromatin occurs, showing that the 3D genome might support the transcriptional response in fasted animals. Our work documents a large-scale chromatin reorganization triggered by fasting and reveals that mTOR and RNA Pol I shape genome architecture in response to nutrients.
Benchmarking the reproducibility of all-solid-state battery cell performance
Authors: Puls Sebastian , Nazmutdinova Elina , Kalyk Fariza , Woolley Henry M. , Thomsen Jesper Frost , Cheng Zhu , Fauchier-Magnan Adrien , Gautam Ajay , Gockeln Michael , Ham So-Yeon , Hasan Md Toukir , Jeong Min-Gi , Hiraoka Daiki , Kim Jong Seok , Kutsch Tobias , Lelotte Barthélémy , Minnmann Philip , Miß Vanessa , Motohashi Kota , Nelson Douglas Lars , Ooms Frans , Piccolo Francesco , Plank Christian , Rosner Maria , Sandoval Stephanie E. , Schlautmann Eva , Schuster Robin , Spencer-Jolly Dominic , Sun Yipeng , Vishnugopi Bairav S. , Zhang Ruizhuo , Zheng Huang , Adelhelm Philipp , Brezesinski Torsten , Bruce Peter G. , Danzer Michael , El Kazzi Mario , Gasteiger Hubert , Hatzell Kelsey B. , Hayashi Akitoshi , Hippauf Felix , Janek Jürgen , Jung Yoon Seok , McDowell Matthew T. , Meng Ying Shirley , Mukherjee Partha P. , Ohno Saneyuki , Roling Bernhard , Sakuda Atsushi , Schwenzel Julian , Sun Xueliang , Villevieille Claire , Wagemaker Marnix , Zeier Wolfgang G. , Vargas-Barbosa Nella M. 
Published: September 2024

AbstractThe interlaboratory comparability and reproducibility of all-solid-state battery cell cycling performance are poorly understood due to the lack of standardized set-ups and assembly parameters. This study quantifies the extent of this variability by providing commercially sourced battery materials—LiNi0.6Mn0.2Co0.2O2 for the positive electrode, Li6PS5Cl as the solid electrolyte and indium for the negative electrode—to 21 research groups. Each group was asked to use their own cell assembly protocol but follow a specific electrochemical protocol. The results show large variability in assembly and electrochemical performance, including differences in processing pressures, pressing durations and In-to-Li ratios. Despite this, an initial open circuit voltage of 2.5 and 2.7 V vs Li+/Li is a good predictor of successful cycling for cells using these electroactive materials. We suggest a set of parameters for reporting all-solid-state battery cycling results and advocate for reporting data in triplicate.
Improving rigor and reproducibility in western blot experiments with the blotRig analysis
Authors: Omondi Cleopa , Chou Austin , Fond Kenneth A. , Morioka Kazuhito , Joseph Nadine R. , Sacramento Jeffrey A. , Iorio Emma , Torres-Espin Abel , Radabaugh Hannah L. , Davis Jacob A. , Gumbel Jason H. , Huie J. Russell , Ferguson Adam R. 
Published: September 2024

AbstractWestern blot is a popular biomolecular analysis method for measuring the relative quantities of independent proteins in complex biological samples. However, variability in quantitative western blot data analysis poses a challenge in designing reproducible experiments. The lack of rigorous quantitative approaches in current western blot statistical methodology may result in irreproducible inferences. Here we describe best practices for the design and analysis of western blot experiments, with examples and demonstrations of how different analytical approaches can lead to widely varying outcomes. To facilitate best practices, we have developed the blotRig tool for designing and analyzing western blot experiments to improve their rigor and reproducibility. The blotRig application includes functions for counterbalancing experimental design by lane position, batch management across gels, and analytics with covariates and random effects.
Cryptic population structure and insecticide resistance in Anopheles gambiae from the southern Democratic Republic of Congo
Authors: Dennis Tristan P. W. , Pescod Poppy , Barasa Sonia , Cerdeira Louise T. , Lucas Eric R. , Clarkson Chris S. , Miles Alistair , Asidi Alex , Manzambi Emile Z. , Metelo Emery , Zanga Josue , Nsalambi Steve , Irish Seth R. , Donnelly Martin James , Agossa Fiacre , Weetman David , Tezzo Francis Wat’senga 
Published: September 2024

AbstractThe Democratic Republic of Congo (DRC) suffers from one of the highest malaria burdens worldwide, but information on its Anopheles vector populations is relatively limited. Preventative malaria control in DRC is reliant on pyrethroid-treated nets, raising concerns over the potential impacts of insecticide resistance. We sampled Anopheles gambiae from three geographically distinct populations (Kimpese, Kapolowe and Mikalayi) in southern DRC, collecting from three sub-sites per population and characterising mosquito collections from each for resistance to pyrethroids using WHO tube bioassays. Resistance to each of three different pyrethroids was generally high in An. gambiae with < 92% mortality in all tests, but varied between collections, with mosquitoes from Kimpese being the most resistant. Whole genome sequencing of 165 An. gambiae revealed evidence for genetic differentiation between Kimpese and Kapolowe/Mikalayi, but not between the latter two sample sites despite separation of approximately 800 km. Surprisingly, there was evidence of population structure at a small spatial scale between collection subsites in Kimpese, despite separation of just tens of kilometres. Intra-population (H12) and inter-population (FST) genome scans identified multiple peaks corresponding to genes associated with insecticide resistance such as the voltage gated sodium channel (Vgsc) target site on chromosome 2L, a Cyp6 cytochrome P450 cluster on chromosome arm 2R, and the Cyp9k1 P450 gene on chromosome X. In addition, in the Kimpese subsites, the P450 redox partner gene Cpr showed evidence for contemporary selection (H12) and population differentiation (FST) meriting further exploration as a potential resistance associated marker.
Prevalence of onychomycosis among psoriasis patients: a clinico-mycological and dermoscopic comparative cross sectional study
Authors: Abdo Hamed M. , Hassab-El-Naby Hussein M. , Bashtar Mohamed R. , Hasan Mohamed S. , Elsaie Mohamed L. 
Published: September 2024

AbstractOnychomycosis, a nail infection caused by dermatophytes, yeast, and molds makes up roughly half of all onychopathies and is the most prevalent nail condition in the world. Clinically, nail psoriasis and onychomycosis can frequently be difficult to distinguish from one another. To assess the prevalence of onychomycosis in patients with psoriasis. Fifty patients with psoriasis associated with nail disease were included in this study. After taking clinical history, nail samples were gathered for dermoscopic inspection, culture, direct microscopy with 20% KOH solution, and nail clipping with PAS stain. Of the 50 patients recruited, 43 were males and 7 were females, with mean age 6–71 years (mean ± SD 44.06 ± 16.2). Eleven patients (22%) tested positive for onychomycosis. Dermatophytes were isolated from 2% of patients, yeast from 14% of patients, and non-dermatophytic mold from 38% of patients. Histopathological results revealed fungal hyphae and spores in 18% of patients. The most prevalent dermoscopic sign in psoriatic patients with onychomycosis was spikes (81.8%) with statistical significance (P-value < 0.001), while nail pitting was the most prevalent dermoscopic feature in nail psoriasis. This study lays the way for an accurate diagnosis of nail lesions by highlighting the significance of cooperation between mycology, histology, and dermoscopy in the diagnosis of onychomycosis in patients with nail psoriasis.
Follicular mediated etodolac phosalosomal gel for contact dermatitis alleviation, insights from optimization to in-vivo appraisal
Authors: Abo Aasy Noha Khalifa , Ragab Doaa , Sallam Marwa Ahmed , Elkhodairy Kadria A. 
Published: September 2024

AbstractDespite its long history as a preferential cyclooxygenase-2 inhibitor, the topical application of etodolac in inflammatory disorders does not achieve the desired clinical efficiency because of its poor water solubility and poor skin permeation. In the ongoing study, phosalosomes were designed to mitigate the etodolac drawbacks and to enhance its skin localization. Hyaluronic acid was utilized to prepare a dermal gel for the alleviation of skin inflammation. Etodolac loaded hyaluronic acid phosalosomal gel had a sustainable release profile and 10.59-fold enhanced skin retention compared to free etodolac, with boosted skin tolerability on histopathological examination after acute and chronic applications. Confocal laser microscopy imaging indicated that the etodolac amounts accumulated in the liver and kidney following dermal application were 29 and 5.7-fold lower than those following the systemic dose, respectively. For in vivo studies, etodolac loaded hyaluronic acid phosalosomal gel presented superior anti-oedemic and significant anti-nociception potential. The promising homogenous localization highlighted its potential for the delivery of lipophilic drugs for the targeted treatment of other localized skin disorders.
Phenotypic and genotypic characterization of Enterococcus faecalis and Enterococcus faecium isolated from fish, vegetables, and humans
Authors: Mubarak Asmaa Gaber , El-Zamkan Mona Ahmed , Younis Waleed , Saleh Sahar Osman , Abd-Elhafeez Hanan H. , Yoseef Asmaa Gahlan 
Published: September 2024

AbstractEnterococci, common hospital-acquired infections in immunocompromised patients, have garnered attention in clinical microbiology. To determine the clinical relevance of enterococci as food-borne pathogens, 116 fish, 90 vegetables, and 120 human diarrheal samples were tested for E. faecalis and E. faecium pathogenicity. Conventionally, 69 of 326 (21.17%) samples were positive for Enterococcus species, 52 (15.95%) of which were molecularly classified as E. faecalis and 13 (3.99%) as E. faecium. The E. faecalis contamination percentage of fresh fish (19.70%) was higher than frozen fish (4%). Cauliflower had the highest E. faecalis percentage (16.67%) when fish and vegetable samples didn’t harbor the E. faecium atpA gene. 23.33% and 10.83% of participants’ samples were molecularly confirmed as E. faecalis and E. faecium positive, respectively. E. faecalis isolates had all virulence genes, with gels being the most common (65.38%), while cylA and asa1 genes couldn’t be detected in E. faecium isolates. E. faecalis showed the highest resistance against vancomycin and tetracycline (69.23%), whereas E. faecium extremely resisted tetracycline (76.92%) and erythromycin (69.23%) with the recognition of MDR among 44.2% of E. faecalis and 38.5% of E. faecium isolates. The great similarity of our isolates showed the clinical importance of food-borne antibiotic-resistant enterococci.
Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping
Authors: Foran Gregory , Hallam Ryan Douglas , Megaly Marvel , Turgambayeva Anel , Antfolk Daniel , Li Yifeng , Luca Vincent C. , Necakov Aleksandar 
Published: September 2024

AbstractThe Notch receptor is a pleiotropic signaling protein that translates intercellular ligand interactions into changes in gene expression via the nuclear localization of the Notch intracellular Domain (NICD). Using a combination of immunohistochemistry, RNA in situ, Optogenetics and super-resolution live imaging of transcription in human cells, we show that the N1ICD can form condensates that positively facilitate Notch target gene expression. We determined that N1ICD undergoes Phase Separation Coupled Percolation (PSCP) into transcriptional condensates, which recruit, enrich, and encapsulate a broad set of core transcriptional proteins. We show that the capacity for condensation is due to the intrinsically disordered transcriptional activation domain of the N1ICD. In addition, the formation of such transcriptional condensates acts to promote Notch-mediated super enhancer-looping and concomitant activation of the MYC protooncogene expression. Overall, we introduce a novel mechanism of Notch1 activity in which discrete changes in nuclear N1ICD abundance are translated into the assembly of transcriptional condensates that facilitate gene expression by enriching essential transcriptional machineries at target genomic loci.
A feasibility study on predicting cow calving time over 40 h in advance using heart rate and financial technical indicators
Authors: Kishi Shigeki , Kojima Tomoki , Huang Chen-Yu , Yayou Ken-ichi , Fujioka Kouki 
Published: September 2024

AbstractIn dairy farming, the uncertainty of cow calving date often imposes waiting costs for days on farmers. Improving the accuracy of calving date prediction would mitigate these costs, specifically before a few days of the event. We monitored and analyzed the heart rate patterns of eight pregnant cows in the days leading up to calving using a dedicated monitoring device. We decomposed the heart rate data into three distinct components: trend, daily cycle, and the remainder, and discovered that the heart rate trend exhibited a sharp decline more than 40 h before the calving event via the trend turning point. To detect the turning point, we applied common financial technical indicators traditionally used to identify turning points of asset prices in trading markets for the extracted heart rate trend. This study remains a feasibility study because of the limited observations, but it indicates that these indicators can effectively capture the trend’s turning point in real time, offering a promising approach for enhanced calving prediction. In addition to discussing the practical implications for cow management, we also contemplate the broader utility of these technical indicators in the context of various dynamic scientific data analyses.
Collaborative weighting in federated graph neural networks for disease classification with the human-in-the-loop
Authors: Hausleitner Christian , Mueller Heimo , Holzinger Andreas , Pfeifer Bastian 
Published: September 2024

AbstractThe authors introduce a novel framework that integrates federated learning with Graph Neural Networks (GNNs) to classify diseases, incorporating Human-in-the-Loop methodologies. This advanced framework innovatively employs collaborative voting mechanisms on subgraphs within a Protein-Protein Interaction (PPI) network, situated in a federated ensemble-based deep learning context. This methodological approach marks a significant stride in the development of explainable and privacy-aware Artificial Intelligence, significantly contributing to the progression of personalized digital medicine in a responsible and transparent manner.
FGFR2-fusions define a clinically actionable molecular subset of pancreatic cancer
Authors: Stein Leah , Murugesan Karthikeyan , Reeser Julie W. , Risch Zachary , Wing Michele R. , Paruchuri Anoosha , Samorodnitsky Eric , Hoskins Emily L. , Dao Thuy , Smith Amy , Le Dat , Babcook Melissa A. , Chang Yi Seok , Avenarius Matthew R. , Imam Muhammad , Freud Aharon G. , Roychowdhury Sameek 
Published: September 2024

AbstractGenomic alterations in fibroblast growth factor receptor (FGFR) genes are present in a small number of metastatic pancreatic ductal adenocarcinomas (PDAC) and may represent an emerging subgroup of patients likely to benefit from FGFR targeted therapies. Here we present four FGFR2 fusion-positive metastatic PDAC patients who exhibited durable responses or disease control to FGFR kinase inhibitors. Utilizing our custom FGFR focused cell-free DNA assay, FGFR-Dx, we serially monitored variant allele fractions of FGFR2 fusions during FGFR inhibitor treatment and observed dynamic changes correlating with clinical responses. Genomic analysis of 30,229 comprehensively profiled pancreatic cancers revealed FGFR1-3 fusions in 245 cases, an incidence of 0.81%. FGFR fusions were generally mutually exclusive from other known oncogenes. Our findings provide clinical evidence for identifying and treating FGFR2 fusion-positive PDAC patients with FGFR targeted therapy.
Microreserves are an important tool for amphibian conservation
Authors: Steigerwald Emma , Chen Julia , Oshiro Julianne , Vredenburg Vance T. , Catenazzi Alessandro , Koo Michelle S. 
Published: September 2024

AbstractInitiatives to protect 30% of Earth by 2030 prompt evaluation of how to efficiently target shortcomings in the global protected area (PA) network. Focusing on amphibians, the most vulnerable vertebrate class, we illustrate the conservation value of microreserves, a term we employ here to refer to reserves of <10 km2. We report that the network continues to under-represent threatened amphibians and that, despite this clear shortcoming in land-based conservation, the creation of PAs protecting amphibians slowed after 2010. By proving something previously assumed–that amphibians generally have smaller ranges than other terrestrial vertebrates–we demonstrate that microreserves could protect a substantial portion of many amphibian ranges, particularly threatened species. We find existing microreserves are capable of hosting an amphibian species richness similar to PAs 1000–10,00X larger, and we show that amphibians’ high beta diversity means that microreserves added to a growing PA network cover amphibian species 1.5—6x faster than larger size categories. We propose that stemming global biodiversity loss requires that we seriously consider the conservation potential of microreserves, using them to capture small-range endemics that may otherwise be omitted from the PA network entirely.
Trade-offs between grassland plant biodiversity and yields are heterogenous across Germany
Authors: Schulz Dario , Stetter Christian , Muro Javier , Spekker Jonas , Börner Jan , Cord Anna F. , Finger Robert 
Published: September 2024

AbstractGrasslands are key for food security and provide important ecosystem services. Intensive management, such as frequent mowing, increases productivity but decreases other ecosystem services as well as plant biodiversity. We here estimate large scale effects of mowing frequency on plant species richness and provide spatial assessments of yield-species richness trade-offs. We use a unique, multisource remote sensing-based dataset covering all permanent agricultural grassland fields across Germany (N = 1,313,073) over four years to estimate the causal impact of mowing frequency, as a proxy of grassland management intensity, on plant species richness. We identify spatially explicit and heterogeneous treatment effects using generalized random forests. We find that more frequent mowing significantly reduces plant species richness, but these effects vary by environmental and socioeconomic context. We quantify the trade-offs between species richness and yield due to changes in mowing frequency, finding an average cost of 126 euros per additional plant species, and demonstrate how spatial targeting can improve the cost-effectiveness of a hypothetical conservation policy, reducing this cost to 51 euros per species. Motivated by the 30 by 30 goal to protect 30% of terrestrial ecosystems by 2030, we further estimate opportunity cost of marginally extensifying 30% of German grasslands to be 131–181 million euros annually, depending on targeting priorities.
gem-Difluoroallene (DFA): an emerging versatile synthetic precursor to enable diverse fluorinated molecules
Authors: Sathish Kota , Jain Swati , Sihag Naveen , Yadav M. Ramu 
Published: September 2024

This review article presents a comprehensive overview of the latest progress in utilizing gem-difluoroallenes for selective additions, defluorination, as well as cycloaddition and cyclization reactions.