bluuebunny/crossref_metadata_2025_split huggingface dataset:
A likelihood-based framework for demographic inference from genealogical trees
Authors: Fan Caoqi , Cahoon Jordan L. , Dinh Bryan L. , Ortega-Del Vecchyo Diego , Huber Christian , Edge Michael D. , Mancuso Nicholas , Chiang Charleston W.K. 
Published: October 2023

AbstractThe demographic history of a population drives the pattern of genetic variation and is encoded in the gene-genealogical trees of the sampled alleles. However, existing methods to infer demographic history from genetic data tend to use relatively low-dimensional summaries of the genealogy, such as allele frequency spectra. As a step toward capturing more of the information encoded in the genome-wide sequence of genealogical trees, here we propose a novel framework called the genealogical likelihood (gLike), which derives the full likelihood of a genealogical tree under any hypothesized demographic history. Employing a graph-based structure, gLike summarizes across independent trees the relationships among all lineages in a tree with all possible trajectories of population memberships through time and efficiently computes the exact marginal probability under a parameterized demographic model. Through extensive simulations and empirical applications on populations that have experienced multiple admixtures, we showed that gLike can accurately estimate dozens of demographic parameters when the true genealogy is known, including ancestral population sizes, admixture timing, and admixture proportions. Moreover, when using genealogical trees inferred from genetic data, we showed that gLike outperformed conventional demographic inference methods that leverage only the allele-frequency spectrum and yielded parameter estimates that align with established historical knowledge of the past demographic histories for populations like Latino Americans and Native Hawaiians. Furthermore, our framework can trace ancestral histories by analyzing a sample from the admixed population without proxies for its source populations, removing the need to sample ancestral populations that may no longer exist. Taken together, our proposed gLike framework harnesses underutilized genealogical information to offer exceptional sensitivity and accuracy in inferring complex demographies for humans and other species, particularly as estimation of genome-wide genealogies improves.
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM
Authors: Schaeffer R. Dustin , Zhang Jing , Medvedev Kirill E. , Cong Qian , Grishin Nick V. 
Published: October 2023

AbstractProtein structure prediction has now been deployed widely across several different large protein sets. Large-scale domain annotation of these predictions can aid in the development of biological insights. Using our Evolutionary Classification of Protein Domains (ECOD) from experimental structures as a basis for classification, we describe the detection and cataloging of domains from 48 whole proteomes deposited in the AlphaFold Database. On average, we can provide positive classification (either of domains or other identifiable non-domain regions) for 90% of residues in all proteomes. We classified 746,349 domains from 536,808 proteins comprised of over 226,424,000 amino acid residues. We examine the varying populations of homologous groups in both eukaryotes and bacteria. In addition to containing a higher fraction of disordered regions and unassigned domains, eukaryotes show a higher proportion of repeated proteins, both globular and small repeats. We enumerate those highly populated domains that are shared in both eukaryotes and bacteria, such as the Rossmann domains, TIM barrels, and P-loop domains. Additionally, we compare the sampling of homologous groups from this whole proteome set against our stable ECOD reference and discuss groups that have been enriched by structure predictions. Finally, we discuss the implication of these results for protein target selection for future classification strategies for very large protein sets.Author SummaryProteins can contain one or more domains, regions that are evolutionary independent and convey fiction and function. Here we present our classification of proteins within 48 proteomes provided by the AlphaFold Structural Database. These proteomes span multiple model organisms used in research as a common ground for studying biological principles as well as organisms involved in prevalent human infectious diseases. We classify these domains by our AlphaFold-specific Domain Parser for AlphaFold Models (DPAM), which was previously tested on the human proteome. We find that eukaryotic and bacterial proteomes can be classified to different degrees, with significantly more disordered and low-confident regions in eukaryotic proteins.
Effects of hippocampal noninvasive theta-burst stimulation on consolidation of associative memory in healthy older adults
Authors: Popa Traian , Beanato Elena , Wessel Maximilian J. , Menoud Pauline , Windel Fabienne , Vassiliadis Pierre , Violante Ines R. , Alania Ketevan , Dzialecka Patrycja , Grossman Nir , Neufeld Esra , Hummel Friedhelm C. 
Published: October 2023

AbstractStimulation of deep brain areas can offer benefits against cognitive impairments associated with aging. So far, this was only possible via invasive methods accompanied by risks. Grossmanet al.proposed a new noninvasive stimulation technique, transcranial temporal interference electric stimulation (tTIS), which can be steered to target and modulate activity of deep brain structures. Memory capacity depends on subcortical structures such as the hippocampus, hence, modulation of hippocampal activity could benefit declining cognitive functions. The current study investigates whether theta-burst patterned tTIS targeting the hippocampus influences performance of associative memory in older adults. We found that theta-burst patterned tTIS, but not the control stimulation, improved recollection time in a follow-up 24h after the stimulation, suggesting that theta-burst patterned tTIS can influence the efficiency of longer-term encoding. This outcome indicates that tTIS may provide a new noninvasive deep brain stimulation method to modulate senescent memory processes.
Panera: A novel framework for surmounting uncertainty in microbial community modelling using Pan-genera metabolic models
Authors: Palanikumar Indumathi , Sinha Himanshu , Raman Karthik 
Published: October 2023

AbstractOver the last decade, microbiome research has witnessed exponential growth, largely driven by the widespread availability of metagenomic data. Despite this influx of data, 16S ‘targeted amplicon’ sequencing, which offers relatively lower resolution, still dominates the landscape over whole-genome shotgun sequencing. Existing algorithms for constructing metabolic models of microbial communities primarily rely on whole-genome sequences and do not fully harness the potential of 16S datasets.In this study, we report ‘Panera’, a novel framework designed to model microbial communities under uncertainty and yet perform inferences by building pan-genus metabolic models. We tested the performance of the models from our approach by analysing their ability to capture the functionality of the entire genus and individual species within a genus. We further exercise the model to explore the comprehensive metabolic abilities of a genus, shedding light on metabolic commonalities between microbial groups. Furthermore, we showcase its application in characterising microbial community models using 16S data. Our hybrid community models, which combine both GSMM and pan-genus metabolic models, exhibit a 10% reduction in prediction error, with error rates diminishing as community size increases.Overall, the Panera framework represents a potent and effective approach for metabolic modelling, enabling robust predictions of the metabolic phenotypes of microbial communities, even when working with limited 16S data. This advancement has the potential to greatly impact the field of microbiome research, offering new insights into the metabolic dynamics of diverse microbial ecosystems.
Exploring the genetic architecture of ecophysiological traits in microbial ecology using statistical analysis of the properties of protein sequences: application to the glycogen accumulating organism (GAO) phenotype
Authors: Williams Rohan B. H. , Bessarab Irina , Wise Michael J. , Arumugam Krithika 
Published: October 2023

AbstractNearly 50 years ago, King and Wilson introduced a key distinction between two types of genetic variation–named structural and regulatory variation–for exploring the molecular basis for phenotypic traits. Structural variation is genetic variation that will influence gene product structure via changes in coding sequence, whereas regulatory variation will influence the control of gene product expression. Here we repurpose these concepts to study the molecular basis of eco-physiological traits observed in microbial ecology, focusing on a specialized glycogen accumulating phenotype, known to be exhibited by a phylogenetically diverse group of microbes. We analyse the statistical properties of the protein sequence of the 1,4–α–glucan branching enzyme (glgB), a key enzyme responsible for formation of glycogen from linear glucans. We show that theglgBproteins in a subgroup of these organisms show unusual statistical properties of protein sequence length, sequence similarity and patterning of functional domains, compared to organisms that do not exhibit this phenotype. These findings suggest a role for structural genetic variation in determining this phenotype in some species. Our analysis holds implications for dissecting the genetic/genomic architecture of complex traits exhibited by microbial communities and also provides a complementary framework to presence–absence level analyses that are ubiquitous in microbial ecology.
Exclusive D-lactate-isomer production during a reactor-microbiome conversion of lactose-rich waste by controlling pH and temperature
Authors: Schütterle Dorothea M. , Hegner Richard , Temovska Monika , Ortiz-Ardila Andrés E. , Angenent Largus T. 
Published: October 2023

AbstractLactate is among the top-ten-biobased products. It occurs naturally as D– or L-isomer and as a racemic mixture (DL-lactate). Generally, lactate with a high optical purity is more valuable. In searching for suitable renewable feedstocks for lactate production, unutilized organic waste streams are increasingly coming into focus. Here, we investigated acid whey, which is a lactose-rich byproduct of yogurt production, that represents a considerable environmental footprint for the dairy industry. We investigated the steering of the lactate-isomer composition in a continuous and open culture system (HRT = 0.6 d) at different pH values (pH 5.0vs.pH 6.5) and process temperatures (38°C to 50°C). The process startup was achieved by autoinoculation. At a pH of 5.0 and a temperature of 47°C-50°C, exclusive D-lactate production occurred because of the dominance ofLactobacillusspp. (> 95% of relative abundance). The highest volumetric D-lactate production rate of 722 ± 94.6 mmol C L-1d-1(0.90 ± 0.12 g L-1h-1), yielding 0.93 ± 0.15 mmol C mmol C-1, was achieved at a pH of 5.0 and a temperature of 44°C (n= 18). At a pH of 6.5 and a temperature of 44°C, we found a mixture of DL-lactate (average D-to-L-lactate production rate ratio of 1.69 ± 0.90), which correlated with a high abundance ofStreptococcusspp. andEnterococcusspp. However, exclusive L-lactate production could not be achieved. Our results show that for the continuous conversion of lactose-rich dairy waste streams, the pH was a critical process parameter to control the yield of lactate isomers by influencing the composition of the microbiota. In contrast, temperature adjustments allowed the improvement of bioprocess kinetics.
Decrypting corals: Does regulatory evolution underlie environmental specialization of coral cryptic lineages?
Authors: Gallery Dominique N , Rippe John P , Matz Mikhail V 
Published: October 2023

AbstractA recent study has shown that two common Caribbean corals,Montastrea cavernosaandSiderastrea siderea, in the Florida Keys each consist of four genetically distinct lineages. These lineages are strongly specialized to a certain depth and, to a lesser extent, to nearshore or offshore habitat. We hypothesized that the lineages’ environmental specialization is at least in part due to regulatory evolution, which would be manifested as the emergence of groups of coregulated genes (“modules”) demonstrating lineage-specific responses to different reef environments. Our hypothesis also predicted that genes belonging to such modules would show greater genetic divergence between lineages than other genes. Contrary to these expectations, responses of cryptic lineages to natural environmental variation were essentially the same at the genome-wide gene coexpression network level. Moreover, none of the identified coregulated gene modules exhibit elevated between-lineage divergence. The environmental specialization of cryptic lineages must, therefore, come from relatively subtle adjustments to gene function or regulation that are not detectable at the gene network level and/or involve other constituents of the coral holobiont rather than the coral host.
Investigating the Impact of Microplastics on Fish Muscle Cell Proliferation and Differentiation: Enhancing Food Safety in Cultivated Meat Production
Authors: Sun Taozhu , Timoneda Alfonso , Banavar Amiti , Ovissipour Reza 
Published: October 2023

AbstractCultivated meat, a sustainable alternative to traditional livestock farming, has gained attention for its potential environmental and health benefits. However, concerns about microplastic contamination pose challenges, especially when sourcing cells from marine organisms prone to microplastic bioaccumulation. Additionally, the pervasive presence of microplastics in laboratory settings, ingredients, and during the production, increases the risk of unintentional contamination. This study focused on Atlantic mackerel (Scomber scombrus) skeletal muscle cell lines to examine the effects of microplastic exposure, represented by fluorescent polyethylene microspheres (10-45 µm) on cell performance including cell proliferation, cell viability, gene expression, and differentiation processes critical for cultivated meat production. The results revealed significant impacts on cell attachment and proliferation at microplastic concentrations of 1 µg/mL, 10 µg/mL, and 50 µg/mL. Notably, the 10 µg/mL concentration exerted the most pronounced effects on cell viability during both attachment and proliferation phases. While the results indicated that both microplastic concentration and size influence cell viability, cell differentiation remained unaffected, and additional contributing factors require further investigation. These findings underscore the necessity of thoroughly exploring microplastic-cell interactions to ensure food safety and safeguard health within the burgeoning cultivated meat industry.
Non-contact respiratory measurements of outdoor-housed rhesus macaques (Macaca mulatta) using millimeter-wave radar systems
Authors: Minami Toshiki , Sanematsu Daisuke , Iwata Itsuki , Sakamoto Takuya , Myowa Masako 
Published: October 2023

ABSTRACTRespiration is an invaluable signal that facilitates the real-time observation of physiological dynamics. In recent years, the advancement of non-contact measurement technology has gained momentum in capturing physiological dynamics in natural settings. This technology is anticipated to find utility in healthcare, not only in humans but also in captive animals, to enhance animal welfare. Currently, the predominant non-contact approach for captive animals involves measuring vital signs through subtle variations in skin color. However, this approach is limited when dealing with body regions covered with hair or outdoor environments under fluctuating sunlight. In contrast, millimeter-wave radar systems, which employ millimeter waves that can penetrate animal fur, exhibit minimal susceptibility to sunlight interference. Thus, this method holds promise for non-contact vital measurements in natural and outdoor settings. In this study, we validated a millimeter-wave radar methodology for capturing respiration in outdoor-housed rhesus macaques (Macaca mulatta). The radar was positioned beyond the captive enclosure and maintained at a distance of > 5 m from the target. Millimeter waves were transmitted to the target, and the reflected waves were used to estimate skin surface displacement associated with respiration. The results revealed periodic skin surface displacement, and the estimated respiratory rate was within the reported range of respiratory rates for rhesus macaques. This result suggests the potential applicability of millimeter-wave radar for non-contact respiration monitoring in outdoor-housed macaques. The continued advancement of non-contact vital measurement technology will contribute to the mental and physical monitoring of captive animals to establish comfortable captive environments.Research HighlightsMillimeter-wave radar systems succeeded in the non-contact measurement of respiration in outdoor-housed rhesus macaques from > 5 m. Our results demonstrate the feasibility of radar-based remote monitoring to assess the welfare of zoo-housed animals.
Human Motor Endplate Survival after Chronic Peripheral Nerve Injury
Authors: Gupta Ranjan , Johnston Tyler R. , Chen Vivian Y. , Gonzales Luigi P. , Steward Oswald 
Published: October 2023

AbstractObjectiveDegeneration of motor endplates (MEPs) in denervated muscle is thought to be a key factor limiting functional regeneration after peripheral nerve injury (PNI) in humans. However, there is currently no paradigm to determine MEP status in denervated human muscle to estimate likelihood of reinnervation success. Here, we present a quantitative analysis of MEP status in biopsies of denervated muscles taken during nerve repair surgery and ensuing functional recovery.MethodsThis is a retrospective single-surgeon cohort study of patients (n=22) with upper extremity PNI confirmed with electromyography (EMG), treated with nerve transfers. Muscle biopsies were obtained intra-operatively from 10 patients for MEP morphometric analysis. Age at time of surgery ranged from 22-77 years and time from injury to surgery ranged from 2.5 -163 months. Shoulder range of motion (ROM) and Medical Research Council (MRC) scores were recorded pre-op and at final follow-up.ResultsSurviving MEPs were observed in biopsies of denervated muscles from all patients, even those greater than six months from injury. Average postoperative ROM improvement (assessed between 6-9 months post-surgery) was: forward flexion 84.3 ± 51.8°, abduction 62.5 ± 47.9°, and external rotation 25.3 ± 28.0°.InterpretationWhile it is believed that MEP degeneration 6 months post-injury prevents reinnervation, this data details MEP persistence beyond this timepoint along with significant functional recovery after nerve surgery. Accordingly, persistence of MEPs in denervated muscles may predict the extent of functional recovery from nerve repair surgery.
Nurse-led point-of-care ultrasonography with telemedicine review to improve the impact of antenatal care: a formative qualitative study in Kenya
Authors: Kumar Meghan Bruce , Mulongo Caleb Mike , Pincerato Lucia , DeVita MariaVittoria , Saidi Salima , Gakii Yvonne , Morino GianFranco , Kumar Pratap 
Published: October 2023

AbstractThe informal settlements of Nairobi have higher neonatal and infant mortality rates than the average for Nairobi. Universal access to important diagnostics like ultrasonography is poor and inequitable due to the high cost of devices and limited availability of skilled sonographers. Recent advances of mobile ultrasound probes connected to smartphones, with or without artificial intelligence support, have improved access to devices; but skills to perform and interpret scans continue to be limited. The SonoMobile intervention involved training nurse-midwives to conduct point-of-care obstetric ultrasound scans in antenatal care clinics in urban informal settlements. Scan data and images were shared, using telemedicine technology, with remote sonographers, who reviewed scan images and data, and provided reports. This qualitative study of 61 respondents from diverse stakeholder groups describes the acceptability, utility and potential sustainability of nurse-led, point-of-care obstetric ultrasonography with telemedicine review. Perceived value of nurse-led obstetric ultrasonography include improving access and affordability of obstetric ultrasonography services, timely identification and referral of high-risk pregnancies, and improving awareness of appropriate antenatal care among underserved populations. The relative affordability of SonoMobile was described as a critical enabler for a business model targeting low- and middle-income segments of the population, and for increasing quality and equity of antenatal care coverage. Areas highlighted for improvement include strengthening supervision of nurse trainees, broadening the scope of nurse training, and development of clear regulatory guidelines for nurse-led obstetric ultrasonography. The study highlights the complex task shifting required to provide universal access to a life-saving technology in an LMIC health system.
An annual gene expression profile of markers for programmed cell death and polyphenols biosynthesis across heartwood forming stems inRobinia pseudoacacia
Authors: Lau Sylas , Lange Henrik , Magel Elisabeth 
Published: October 2023

AbstractHeartwood formation is a developmental defense strategy in trees that transforms the inner stem core through the deposition of natural antimicrobial preservatives. The defining cellular events in this process are the accumulation of specialized metabolites conjoined with the death of living cells in the transition zone. While previous studies have characterized heartwood compounds and deposition, the cell death aspects are often neglected. Thus, the correlation of these defining cellular events remained unclear, while the exact timing of occurrence and regional involvement within the stem became topics for debate. In this study, members of metacaspases and vacuolar processing enzymes were isolated as programmed cell death (PCD) markers to explore their correlation with those of polyphenol biosynthesis. We collected heartwood-forming stems fromR. pseudoacaciamonthly for a year and monitored their expression through real-time PCR. Our results revealed novel markers of PCD in xylem parenchyma cells and demonstrated their corresponding fluctuation in expression with markers of polyphenols across the stem regions. The annual expression profile demonstrated regional stem development along with weather data on a monthly scale. This work provides a framework to compare the xylem-specific PCD in stages of stem development and a preliminary overview of how they correspond to external conditions over an annual cycle.