bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative analysis of the performance of chatGPT4, Gemini and Claude for the Polish Medical Final Diploma Exam and Medical-Dental Verification Exam
Authors: Wójcik Dorota , Adamiak Ola , Czerepak Gabriela , Tokarczuk Oskar , Szalewski Leszek 
Published: July 2024

AbstractIn the realm of medical education, the utility of chatbots is being explored with growing interest. One pertinent area of investigation is the performance of these models on standardized medical examinations, which are crucial for certifying the knowledge and readiness of healthcare professionals. In Poland, dental and medical students have to pass crucial exams known as LDEK (Medical-Dental Final Examination) and LEK (Medical Final Examination) exams respectively. The primary objective of this study was to conduct a comparative analysis of chatbots: ChatGPT-4, Gemini and Claude to evaluate their accuracy in answering exam questions of the LDEK and the Medical-Dental Verification Examination (LDEW), using queries in both English and Polish. The analysis of Model 2, which compared chatbots within question groups, showed that the chatbot Claude achieved the highest probability of accuracy for all question groups except the area of prosthetic dentistry compared to ChatGPT-4 and Gemini. In addition, the probability of a correct answer to questions in the field of integrated medicine is higher than in the field of dentistry for all chatbots in both prompt languages. Our results demonstrate that Claude achieved the highest accuracy in all areas analysed and outperformed other chatbots. This suggests that Claude has significant potential to support the medical education of dental students. This study showed that the performance of chatbots varied depending on the prompt language and the specific field. This highlights the importance of considering language and specialty when selecting a chatbot for educational purposes.
Causal effect of the gut microbiota on the risk of psychiatric disorders and the mediating role of immunophenotypes
Authors: Hong Zhisheng , He Ao , Huang Guanglong , Chen Xiaofeng , Wang Xiaoyu , Li Xiaoyang , Chen Hailun , Zhao Xinqi , Xu Ying , Xu Yangheng , Ouyang Pei , Wang Hai , Deng Jiapeng , Chen Pengyu , Zhang Xian , Qi Songtao , Li Yaomin 
Published: July 2024

AbstractBackgroundGrowing evidence indicates a significant correlation between the gut microbiota, immune system, and psychiatric disorders. Nevertheless, the impacts and interactions of the gut microbiota and immunophenotypes on psychiatric disorders remain unclear.MethodsWe utilized a bidirectional Mendelian randomization (MR) study to evaluate the causal associations among the gut microbiota, immunophenotypes, and psychiatric disorders, including attention-deficit/hyperactivity disorder (ADHD), major depressive disorder (MDD), posttraumatic stress disorder (PTSD), schizophrenia (SCZ), and Tourette’s syndrome (TS). The primary analysis was conducted using the inverse variance weighted (IVW) method, with several complementary sensitivity analyses being performed to ensure the reliability of the results.ResultsOur study reveals significant causal relationships between 22 immunophenotypes, 15 types of gut microbiota, and various psychiatric disorders. We further sought to ascertain whether immunophenotypes act as intermediaries in the pathway from gut microbiota to psychiatric disorders. In particular, three immunophenotypes were identified that mediate the causal effects of different gut microbiota on ADHD. Additionally, one immunophenotype was detected to mediate the causal effects of gut microbiota on PTSD.ConclusionsOur study indicates that immunophenotypes partially mediate the pathway from the gut microbiota to psychiatric disorders.
Caries incidence in school-based oral health programs
Authors: Ruff Ryan Richard 
Published: July 2024

AbstractBackgroundSchool-based caries prevention can increase access to critical dental services and reduce oral health inequities. However, little is known regarding the incidence of dental caries in children participating in school caries prevention, and caries diagnosis is often interval censored.MethodsIn this paper, we used data from a longitudinal, school-based, randomized clinical trial of minimally invasive treatments for dental caries to estimate the per-visit incidence rate and compare the hazard of dental caries in children receiving either silver diamine fluoride or glass ionomer dental sealants. To account for interval censoring, we used semiparametric transformation models for univariate failure time data and imputed the caries incidence using G-imputation.ResultsThere were 3040 children that met inclusion criteria for analysis, 1516 (49.9%) of which were randomly assigned to receive silver diamine fluoride and 1524 (50.1%) assigned to receive glass ionomer dental sealants. There were no differences in the hazard of caries between treatments (HR = 0.98, 95% CI = 0.73, 1.24), while children with caries at baseline had a significant increase in the hazard of new caries (HR = 2.54, 95% CI = 2.26, 2.83) compared to those that were caries-free. The per-visit caries incidence ranged from 4.8 to 11.1 per 1000 person-years and increased with each successive study observation.ConclusionsSchool-based caries prevention can positively affect caries incidence, and results can be used to inform future program design and implementation.
K-mer Genome-wide Association Study for Anthracnose andBCMVResistance in the Andean Diversity Panel
Authors: Wiersma Andrew T. , Hamilton John P. , Vaillancourt Brieanne , Brose Julia , Awale Halima E. , Wright Evan M. , Kelly James D. , Buell C. Robin 
Published: July 2024

AbstractLimited genomic resources and closely linked marker-trait associations for common beans (Phaseolus vulgarisL.) have limited breeders from fully utilizing molecular genetics technologies to maximize genetic gain. The emergence of virulent races of anthracnose (caused byColletotrichum lindemuthianum) andBean Common Mosaic Virus(BCMV) highlight the need for improved methods to identify and incorporate pan-genomic variation in breeding for disease resistance. We sequenced theP. vulgarisAndean Diversity Panel (ADP) and performed a genome-wide association study (GWAS) to identify associations for resistance to BCMV and eight races of anthracnose. Historical single nucleotide polymorphism (SNP)-chip and phenotypic data enabled a three-way comparison between SNP-chip, reference-based whole genome shotgun sequence (WGS)-SNP, and reference-freek-mer GWAS. Across all traits, there was excellent concordance between SNP-chip, WGS-SNP, andk-mer GWAS results—albeit at a much higher marker resolution for the WGS data sets. Significantk-merhaplotype variation revealed selection of the linkedI-gene andCo-utraits in North American breeding lines and cultivars. Due tok-mer mapping criteria and the absence of target loci in the reference genome due to structural variation, only 9.1 to 47.3% of the significantly associatedk-mers were mapped to the reference genome. To determine the genetic context ofcis-associatedk-mers, we generated whole genome assemblies of four ADP accessions and identified an expanded local repertoire of disease resistance genes associated with resistance to anthracnose and BCMV. With access to variant data in the context of a pan-genome, high resolution mapping of agronomic traits for common bean is now feasible.CORE IDEASK-mer-based GWAS offers new advantages for mapping pan-genomic variationComparison of reference-based SNP to reference-freek-mer GWASNovel discovery ofcis-associatedk-mers for dry bean disease resistancePLAIN LANGUAGE SUMMARYImproving disease resistance in crop species such as bean is critical. We surveyed the genomes of a diverse set of bean lines and identified sequences associated with resistance to a fungal and viral pathogen. Access to the genomes of this diversity panel of beans will permit additional discoveries on the role of structural variation in phenotypes, including disease resistance.
Pervasive neurovascular dysfunction in the ventromedial prefrontal cortex of female depressed suicides with a history of childhood abuse
Authors: Wakid Marina , Almeida Daniel , Denniston Ryan , Chawla Anjali , Aouabed Zahia , Davoli Maria Antonietta , Ellerbeck Kristin , Rahimian Reza , Yerko Volodymyr , Leonova-Erko Elena , Turecki Gustavo , Mechawar Naguib 
Published: July 2024

AbstractExposure to early life adversity (ELA) poses a significant global public health concern, with profound pathophysiological implications for affected individuals. Studies suggest that ELA contributes to endothelial dysfunction, bringing into question the functional integrity of the neurovascular unit in brain regions vulnerable to chronic stress. Despite the importance of the neurovasculature in maintaining normal brain physiology, human neurovascular cells remain poorly characterized, particularly with regard to their contributory role in ELA-associated pathophysiologies. In this study, we present the first comprehensive transcriptomic analysis of intact microvessels isolated from postmortem ventromedial prefrontal cortex samples from adult healthy controls (CTRL) and matched depressed suicides with histories of ELA. Our findings point to substantive differences between men and women, with the latter exhibiting widespread gene expression changes at the neurovascular unit, including the key vascular nodal regulatorsKLF2andKLF4, alongside a broad downregulation of immune-related pathways. These results suggest that the neurovascular unit plays a larger role in the neurobiological consequences of ELA in human females.
Three-Dimensional Quantitative Structure-Activity Relationships and Molecular Dynamic Simulations Studies to Discover Aurora Kinase-B Inhibitors
Authors: Anand Selvam Athavan Alias , Kabilan Senthamaraikannan 
Published: July 2024

AbstractThe serine-threonine kinase gene Aurora–B kinase plays a critical role in spindle assembly, chromosome alignment, mitotic checkpoint activation, and cytokinesis. The overexpression of Aurora-B causes errors in cell division and multinucleation in centrosome numbers leads to cancer. Three–dimensional Quantitative Structure-Activity Relationship studies were conducted on known inhibitors to find valid pharmacophore hypotheses. The five features hypothesis AADRR with better parameters using partial least square analysis has been selected for virtual screening. Molecular docking was applied to find the binding mode interactions of ligands with the Aurora-B binding pocket. Lys 106, Ala 157, Glu 161, and Phe 219 were identified as crucial residues that formed several interactions with the ligands which are essential for Aurora–B inhibition. After the different levels of screening, five compounds from the National Cancer Institute database were acknowledged as novel inhibitors of Aurora–B. The active site interactions of the protein-ligand complex were examined by molecular dynamics simulation studies.Graphical Abstract
Model of a striatal circuit exploring biological mechanisms underlying decision-making during normal and disordered states
Authors: Beck Dirk W. , Heaton Cory N. , Davila Luis D. , Rakocevic Lara I. , Drammis Sabrina M. , Tyulmankov Danil , Vara Paulina , Giri Atanu , Umashankar Beck Shreeya , Zhang Qingyang , Pokojovy Michael , Negishi Kenichiro , Batson Serina A , Salcido Alexis A. , Reyes Neftali F. , Macias Andrea Y. , Ibanez-Alcala Raquel J. , Hossain Safa B. , Waller Graham L. , O’Dell Laura E. , Moschak Travis M. , Goosens Ki A. , Friedman Alexander 
Published: July 2024

SummaryDecision-making requires continuous adaptation to internal and external contexts. Changes in decision-making are reliable transdiagnostic symptoms of neuropsychiatric disorders. We created a computational model demonstrating how the striosome compartment of the striatum constructs a mathematical space for decision-making computations depending on context, and how the matrix compartment defines action value depending on the space. The model explains multiple experimental results and unifies other theories like reward prediction error, roles of the direct versus indirect pathways, and roles of the striosome versus matrix, under one framework. We also found, through new analyses, that striosome and matrix neurons increase their synchrony during difficult tasks, caused by a necessary increase in dimensionality of the space. The model makes testable predictions about individual differences in disorder susceptibility, decision-making symptoms shared among neuropsychiatric disorders, and differences in neuropsychiatric disorder symptom presentation. The model reframes the role of the striosomal circuit in neuroeconomic and disorder-affected decision-making.HighlightsStriosomes prioritize decision-related data used by matrix to set action values.Striosomes and matrix have different roles in the direct and indirect pathways.Abnormal information organization/valuation alters disorder presentation.Variance in data prioritization may explain individual differences in disorders.eTOCBeck et al. developed a computational model of how a striatal circuit functions during decision-making. The model unifies and extends theories about the direct versus indirect pathways. It further suggests how aberrant circuit function underlies decision-making phenomena observed in neuropsychiatric disorders.
Deciphering the transcriptional regulatory network ofYarrowia lipolyticausing machine learning
Authors: Kerssemakers Abraham A.J. , Krishnan Jayanth , Rychel Kevin , Zielinski Daniel C. , Palsson Bernhard O. , Sudarsan Suresh 
Published: July 2024

AbstractThe transcriptional regulatory network (TRN) in Yarrowia lipolytica coordinates its cellular processes, including the response to various stimuli. The TRN has been difficult to study due to its complex nature. In industrial-size fermenters, environments are often not homogenous, resulting in Yarrowia experiencing fluctuating conditions during a fermentation. Compared with homogenous laboratory conditions, these fluctuations result in altered cellular states and behaviors due to the action of the TRN. Here, a machine learning approach was deployed to modularize the transcriptome to enable meaningful description of its changing composition. To provide a sufficiently broad dataset, a wide range of relevant fermentation conditions (nutrient limitations, growth rates, pH values, oxygen availability and CO2 stresses) were run and samples obtained for RNA-Seq generation. We thus significantly increased the number of publicly available transcriptomic dataset on Y. lipolytica W29. In total, 23 independently modulated gene sets (termed iModulons) were identified of which 9 could be linked to corresponding regulons in S. cerevisiae. Strong responses were found in relation to oxygen limitation and elevated CO2 concentrations represented by (i) altered ribosomal protein synthesis, (ii) cell cycle disturbances, (iii) respiratory gene expression, and (iv) redox homeostasis. These results provide a fine-grained systems-level understanding of the Y. lipolytica TRN in response to industrially meaningful stresses, providing engineering targets to design more robust production strains. Moreover, this study provides a guide to perform similar work with poorly characterized single-cellular eukaryotic organisms.Highlights- A large screening setup significantly expands the public RNA-Seq library onY. lipolytica.- This work provides a systems-level understanding of the TRN in response to industrial stresses.- iModulon analysis can help accelerate bioprocess development.- Results can guide similar work on poorly characterized single-cellular eukaryotic organisms.
Carbon monoxide-driven bioethanol production operates via a tungsten-dependent catalyst
Authors: Lemaire Olivier N. , Belhamri Mélissa , Shevchenko Anna , Wagner Tristan 
Published: July 2024

AbstractMicrobial alcohol production from waste gasses is a game changer for sustainable carbon cycling and remediation. While the biotechnological process employingClostridium autoethanogenumto transform syngas (H2/CO2/CO) is blooming, the reactions involved in ethanol biosynthesis remain to be demonstrated. Here, we experimentally showed that ethanol production initiates via a tungsten-dependent aldehyde:ferredoxin oxidoreductase (AFOR), which reduces acetate to acetaldehyde. Such an unfavourable reaction has often been considered unsuitable for a biological process. To answer this riddle, we demonstrated that the thermodynamic pull of CO-oxidation and ethanol synthesis is crucial for triggering acetate reduction. The experimental setup performed with native CO-dehydrogenase and AFOR highlighted the key role of ferredoxin in stimulating the activity of both metalloenzymes and electron shuttling. The crystal structure of holo AFOR refined to 1.59-Å resolution, together with its biochemical characterisation, provides new insights into the reaction mechanism and the specificities of this enzyme fundamental to sustainable biofuel production.
Investigation of Bactericidal effect of Earwax onEscherichia coliandStaphylococcus aureusisolated from skin and stool samples of undergraduate students, Federal University of Agriculture Makurdi, Benue State, Nigeria
Authors: Tsenongu Aondongu Joseph , Ichor Tersagh Smart , Ashar Saaondo James , Mena Ajekwe Stephen , Kwaghve Avalumun 
Published: July 2024

ABSTRACTEarwax is a normal product of the ear, which protects the skin of the ear from water, dirt dust and infection. The aim of this study was to determine the antibacterial activity of earwax onStaphylococcus aureusandEscherichia coliisolated from skin and stool respectively. Bacteriological investigations were carried out using culture and morphological characteristics, conventional biochemical tests and antibiotic susceptibility testing of both earwax and conventional antibiotics against the presumptive isolates. Occurrence ofStaphylococcus aureus(58.3%) andEscherichia coli(45.8%) in skin and stool samples were respectively determined based on cultural and morphological characteristics. Conventional biochemical tests were carried out on the 14 and 10 presumptiveStaphylococcus aureusandEscherichia coliisolates and then 10 and 8 presumptive isolates were detected respectively. The antibacterial activity of the test agent was determined using the agar well diffusion technique; five different concentrations (20% v/v, 40% v/v, 60% v/v, 80% v/v, and 100% v/v) of the test agents were evaluated against the bacterial isolates. The earwax showed antibacterial activity against both isolates (except the 20% v/v forStaphylococcus aureus) at all concentrations used with antibacterial activity directly proportional to earwax concentration and a better antibacterial activity againstStaphylococcus aureus(zone of inhibition 20mm)aureusthanEscherichia coli. Antibiotic susceptibility testing was carried out on the 10(41.7%) and 8(33.3%) presumptive isolates ofStaphylococcus aureusandEscherichia colirespectively based on Kirby Bauer method. Highest rate of susceptibilities of theStaphylococcus aureusisolates to antibiotics were observed in Erythromycin (100%), while forEscherichia coliwere observed in Erythromycin and Levofloxacin (100%). Meanwhile, highest rate of resistant toStaphylococcus aureusisolates were observed in Gentamicin (100%) while forEscherichia coliwas observed in Amoxicillin (100%). This study shows that earwax plays a critical role in the fight against infectious microorganisms as some of the antibiotics.
Contrast gain control is a reparameterization of a population response curve
Authors: Tring Elaine , Moosavi S. Amin , Dipoppa Mario , Ringach Dario L. 
Published: July 2024

AbstractNeurons in primary visual cortex (area V1) adapt in different degrees to the average contrast of the environment, suggesting that the representation of visual stimuli may interact with the state of cortical gain control in complex ways. To investigate this possibility, we measured and analyzed the responses of neural populations to visual stimuli as a function of contrast in different environments, each characterized by a unique distribution of contrast. Our findings reveal that, for a given stimulus, the population response can be described by a vector functionr(gec), where the gaingeis a decreasing function of the mean contrast of the environment. Thus, gain control can be viewed as a reparameterization of a population response curve, which is invariant across environments. Different stimuli are mapped to distinct curves, all originating from a common origin, corresponding to a zero-contrast response. Altogether, our findings provide a straightforward, geometric interpretation of contrast gain control at the population level and show that changes in gain are well coordinated among members of a neural population.
Nonenzymatic, prebiotic aminoacylation couples chirality of RNA and protein
Authors: Davisson Joshua A. , Kalb Evan M. , Knudson Isaac J. , Schepartz Alanna , Engelhart Aaron E. , Adamala Katarzyna P. 
Published: July 2024

AbstractLife as we know it depends on the homochirality of nucleic acids and proteins. However, there is no widely accepted explanation for why life uses only D-sugars for nucleic acids and L-amino acids for proteins. Here we demonstrate a prebiotically plausible method of nonenzymatic aminoacylation in a water ice-eutectic phase. These reactions produce high yields of aminoacyl-tRNAs, which are active in translation. Surprisingly, we discovered these nonenzymatic aminoacylation conditions were stereoselective, favoring coupling of amino acids and RNA of “opposite” L- and D- configurations. D-RNA shows greater aminoacylation yields for L-amino acids. The opposite was true for L-RNA, which had greater yields with D-amino acids. Nucleic acid backbone chirality influencing stereoselectivity of aminoacylation presents the missing link in the origin of modern biochemistry. This phenomenon provides insight into the chirality of the RNA world, and helps to explain the “opposite” stereochemistry of modern biomolecules.