bluuebunny/crossref_metadata_2025_split huggingface dataset:
Skin-To-Skin Contact During Cesarean Birth in the United States over the Last Decade
Authors: Junk-Wilson Jessica S. , King Elizabeth K. , Murphy Lindsey M. , Raza Hassan 
Published: September 2023

Abstract

Purpose:
To assess skin-to-skin contact during cesarean birth, including incidence and maternal characteristics.

Study Design and Methods:
A cross-sectional, retrospective study using survey methods was conducted. Women who had a cesarean birth within the last 10 years prior to January 2022 were recruited via social media. Descriptive statistics, chi square, and binary logistic regression analyses were calculated.

Results:
There were 2,327 participants, of which 29.7% experienced skin-to-skin contact during their cesarean birth. This was reported to be less often than desired. Significant associations were found among skin-to-skin contact during cesarean birth and planned cesarean birth, previous cesarean birth, maternal age, level of education, and birth region. Previous vaginal birth and race were not significantly associated with skin-to-skin contact during cesarean birth. Most (93.65%) respondents identified as White. Barriers to skin-to-skin contact during cesarean birth may be birth region, unplanned or emergency cesarean births, younger age, lacking a college degree, and lack of previous cesarean births.

Clinical Implications:
There are differences in incidence and access to skin-to-skin contact during cesarean birth. Our findings emphasize the continued need to address disparities in care, increase maternal health care equity, and make skin-to-skin contact during cesarean birth available for all women who desire it.
Unit costs of needle and syringe program provision: a global systematic review and cost extrapolation
Authors: Killion Jordan A. , Magana Christopher , Cepeda Javier A. , Vo Anh , Hernandez Maricris , Cyr Cassandra L. , Heskett Karen M. , Wilson David P. , Graff Zivin Joshua , Zúñiga María L. , Pines Heather A. , Garfein Richard S. , Vickerman Peter , Terris-Prestholt Fern , Wynn Adriane , Martin Natasha K. 
Published: September 2023

Background:
Needle and syringe programs (NSPs) are effective at preventing HIV and hepatitis C virus (HCV) among people who inject drugs (PWID), yet global coverage is low, partly because governments lack data on the cost and cost-effectiveness of NSP in their countries to plan and fund their responses. We conducted a global systematic review of unit costs of NSP provision to inform estimation of cost drivers and extrapolated costs to other countries.

Methods:
We conducted a systematic review to extract data on the cost per syringe distributed and its cost drivers. We estimated the impact of country-level and program-level variables on the cost per syringe distributed using linear mixed-effects models. These models were used to predict unit costs of NSP provision, with the best performing model used to extrapolate the cost per syringe distributed for 137 countries. The total cost for a comprehensive NSP (200 syringes per PWID/year) was also estimated for 68 countries with PWID population size estimates.

Results:
We identified 55 estimates of the unit cost per syringe distributed from 14 countries. Unit costs were extrapolated for 137 countries, ranging from $0.08 to $20.77 (2020 USD) per syringe distributed. The total estimated spend for a high-coverage, comprehensive NSP across 68 countries with PWID size estimates is $5 035 902 000 for 10 887 500 PWID, 2.1-times higher than current spend.

Conclusion:
Our review identified cost estimates from high-income, upper-middle-income, and lower-middle-income countries. Regression models may be useful for estimating NSP costs in countries without data to inform HIV/HCV prevention programming and policy.
Self-sustained rhythmic behavior ofSynechocystisPCC 6803 under continuous light conditions in the absence of light-dark entrainment
Authors: Berwanger Lutz C. , Thumm Nikolaus , Gholamipoor Rahil , Wiegard Anika , Schlebusch Jeannine , Kollmann Markus , Axmann Ilka M. 
Published: September 2023

AbstractCircadian clocks regulate biological activities, providing organisms a fitness advantage under diurnal changing conditions by allowing them to anticipate and adapt to recurring external changes. In recent years attention was drawn to the entrainment by intracellular cycles. Photosynthetic Cyanobacteria coordinate their gene expression, metabolism, and other activities in a circadian fashion. Solely, three proteins, KaiA, KaiB, and KaiC, constitute the well-studied circadian clock of the cyanobacterial model,Synechococcus elongatusPCC 7942. It remained inconclusive for a long time whetherSynechocystissp. PCC 6803, an important organism for biotechnological applications, can also maintain circadian rhythms under continuous illumination. Using an approach, which does not require genetic modification, we investigated the growth behavior ofSynechocystisvia non-invasive online backscattering measurement and verified all three criteria for true circadian oscillators: temperature compensation, entrainment by external stimuli, and a self-sustained freerunning period of about 24 hours. Since manipulation of the circadian clock (SynechocystisΔkaiA1B1C1) led to a significant reduction in glycogen content, disruption of glycogen synthesis (SynechocystisΔglgC) entirely inhibited glycogen formation and both mutants lost oscillations, we hypothesize that the oscillations reflect glycogen metabolism.Significance StatementMonitoring circadian rhythms in cyanobacteria usually requires genetically modified reporter strains or intensive sampling for downstream analysis. Even for the main cyanobacterial modelSynechocystissp. PCC 6803 it was debated for years to which extent undamped circadian oscillations are really present until a suitable reporter strain was developed. We applied online backscatter measurements as an alternative readout to monitor circadian oscillations in cyanobacteria. InSynechocystisthe temperature-compensatedkaiA1B1C1-driven 24 h metabolic oscillations did not require light-dark entrainment, highlighting the relevance of the clock for the carbon metabolism even under continuous light, an aspect which should be considered for industrial set-ups. Our method opens the possibility to extend circadian analysis to non-GMO and monitor metabolic rhythmicity during high-density cultivation.
Human enteric glia diversity in health and disease: new avenues for the treatment of Hirschsprung disease
Authors: Windster J.D. , Kuil L.E. , Kakiailatu N.J.M. , Antanaviciute A. , Sacchetti A. , MacKenzie K. C. , Peulen-Zink J. , Kan Tsung Wai , Bindels E. , de Pater E. , Doukas M. , Yousefi S. , Barakat T.S. , Meeussen C. , Sloots C.E.J. , Wijnen R.M.H. , Parikh K. , Boesmans W. , Melotte V. , Hofstra R.M.W. , Simmons A. , Alves M.M. 
Published: September 2023

AbstractHirschsprung disease (HSCR) is caused by an absence of the enteric nervous system (ENS), which is crucial for intestinal function. The ENS is composed of enteric neurons and glia, and is mostly derived from migrating vagal neural crest cells. Trunk-derived Schwann cells also play a significant role in postnatal maintenance of the ENS. However, the diversity of the ENS in health and disease remains largely unknown. Here, we performed single cell RNA sequencing on pediatric controls and HSCR individuals, and identified two major classes of enteric glia, being canonical and Schwann-like enteric glia. We show that the latter are the main contributors of enteric glia heterogeneity after birth and importantly, that they are preserved in aganglionic segments of HSCR individuals. In a zebrafish model of HSCR, which also shows preservation of Schwann-like enteric glia, enteric neurogenesis could be stimulated, demonstrating a potential novel therapy for HSCR.
inDrops-2: a flexible, versatile and cost-efficient droplet microfluidics approach for high-throughput scRNA-seq of fresh and preserved clinical samples
Authors: Juzenas Simonas , Kiseliovas Vaidotas , Goda Karolis , Zvirblyte Justina , Quintinal-Villalonga Alvaro , Nainys Juozas , Mazutis Linas 
Published: September 2023

AbstractThe development of a large variety of single-cell analytical techniques has empowered researchers to explore diverse biological questions at the level of individual cells. Among these, droplet-based single-cell RNA sequencing (scRNA-seq) methods have been particularly prevalent owing to their high-throughput capabilities and reduced reaction volumes. While commercial systems have contributed to the widespread adoption of droplet-based scRNA-seq, the relatively high cost impose limitations for profiling large numbers of samples. Moreover, as the scope and scale of single cell sequencing methods keeps expanding, the possibility to accommodate diverse molecular biology workflows and inexpensively profile multiple biospecimens simultaneously becomes highly relevant. Herein, we present inDrops-2: an open-source scRNA-seq platform designed to profile fresh or preserved clinical samples with a sensitivity matching that of state-of-the-art commercial systems, yet at a few folds lower cost. Using inDrops-2, we conducted a comparative analysis of two prominent scRNA-seq protocols – those based on exponential and linear amplification of cDNA – and provide useful insights about the pros and cons inherited to each approach. We showcase the utility of inDrops-2 by simultaneously profiling 18 human lung carcinoma samples, all in one run, following cell preservation, long-term storage and multiplexing, to obtain a multiregional cellular profile of tumor microenvironment. The scalability, experimental flexibility and cost-efficiency offered by inDrops-2 should make it appealing for various single-cell transcriptomic studies.
Phased assembly of neo-sex chromosomes reveals extensive Y degeneration and rapid genome evolution inRumex hastatulus
Authors: Sacchi Bianca , Humphries Zoë , Kružlicová Jana , Bodláková Markéta , Pyne Cassandre , Choudhury Baharul , Gong Yunchen , Bačovský Václav , Hobza Roman , Barrett Spencer C.H. , Wright Stephen I. 
Published: September 2023

AbstractY chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10MYA) and neo (<200,000 years) sex chromosomes in the XYY cytotype of the dioecious plantRumex hastatulusand a hermaphroditic outgroupR. salicifolius. Our assemblies, supported by fluorescence in situ hybridization, confirmed the neo-sex chromosomes were formed by two key events: an X-autosome fusion and a reciprocal translocation between the homologous autosome and the Y chromosome. The enormous sex-linked regions of the X (296 MB) and two Y chromosomes (503 MB) both evolved from large repeat-rich genomic regions with low recombination; however, the complete loss of recombination on the Y still led to over 30% gene loss and major rearrangements. In the older sex-linked region, there has been a significant increase in transposable element abundance, even into and near genes. In the neo sex-linked regions, we observed evidence of extensive rearrangements without gene degeneration and loss. Overall, we inferred significant degeneration during the first 10 million years of Y chromosome evolution but not on very short timescales. Our results indicate that even when sex chromosomes emerge from repetitive regions of already-low recombination, the complete loss of recombination on the Y chromosome still leads to a substantial increase in repetitive element content and gene degeneration.
Threshold public goods game in well mixed populations: Cooperation in density independent and density dependent cases
Authors: Károlyi Adél , Scheuring István 
Published: September 2023

AbstractThe threshold public goods game is one of the best-known models of nonlinear public goods dilemmas. Cooperators and defectors typically coexist in this game when the population is assumed to follow the so-called structured deme model. In this paper we develop a dynamical model of a general N-player game in which there is no deme structure: individuals interact with randomly chosen neighbours and selection occurs between randomly chosen pairs of individuals. We show that in the deterministic limit the dynamics in this model leads to the same replicator dynamics as in the structured deme model, i.e. coexistence of cooperators and defectors is typical in threshold public goods game even when the population is completely well-mixed. We extend the model to study the effect of density dependence and density fluctuation on the dynamics. We show analytically and numerically that decreasing population density increases the equilibrium frequency of cooperators till the fixation of this strategy, but below a critical density cooperators abruptly disappear from the population. Our numerical investigations show that weak density fluctuations enhance cooperation, while strong fluctuations suppress it.HighlightsThe dynamics of threshold dilemma game in a well-mixed population.Fluctuation of density can help or suppress cooperation.Cooperation is more pronounced at lower density.Cooperation abruptly disappears below a critical density level.
Cell and tissue-specific glycosylation pathways informed by single-cell transcriptomics
Authors: Chrysinas Panagiotis , Venkatesan Shriramprasad , Ang Isaac , Ghosh Vishnu , Chen Changyou , Neelamegham Sriram , Gunawan Rudiyanto 
Published: September 2023

ABSTRACTWhile single cell studies have made significant impacts in various subfields of biology, they lag in the Glycosciences. To address this gap, we analyzed single-cell glycogene expressions in the Tabula Sapiens dataset of human tissues and cell types using a recent glycosylation-specific gene ontology (GlycoEnzOnto). At the median sequencing (count) depth, ∼40-50 out of 400 glycogenes were detected in individual cells. Upon increasing the sequencing depth, the number of detectable glycogenes saturates at ∼200 glycogenes, suggesting that the average human cell expresses about half of the glycogene repertoire. Hierarchies in glycogene and glycopathway expressions emerged from our analysis: nucleotide-sugar synthesis and transport exhibited the highest gene expressions, followed by genes for core enzymes, glycan modification and extensions, and finally terminal modifications. Interestingly, the same cell types showed variable glycopathway expressions based on their organ or tissue origin, suggesting nuanced cell- and tissue-specific glycosylation patterns. Probing deeper into the transcription factors (TFs) of glycogenes, we identified distinct groupings of TFs controlling different aspects of glycosylation: core biosynthesis, terminal modifications, etc. We present webtools to explore the interconnections across glycogenes, glycopathways, and TFs regulating glycosylation in human cell/tissue types. Overall, the study presents an overview of glycosylation across multiple human organ systems.
Cardiac Specific Overexpression of Adenylyl Cyclase 8 Reprograms the Mouse Sinoatrial Node Transcriptome
Authors: Qu Jia-Hua , Tarasov Kirill V. , Chakir Khalid , Lakatta Edward G. 
Published: September 2023

AbstractA coupled-clock system intrinsic to sinoatrial node (SAN) pacemaker cells that regulates the rate and rhythm of spontaneous action potential firing, is activated by Ca2+/calmodulin-stimulated Adenylyl Cyclase (AC) types 8 and 1. Our previous work in mice with cardiac specific overexpression of human AC8 gene (TGAC8) discovered that compared to its wild-type (WT) littermates, the heart rate (HR) of TGAC8 is elevated (by about 30%, 24 hours a day, 7days a week), and that the TGAC8 heart rhythm is markedly coherent, i.e., the HR Variability (HRV) lacks complexity, similar to that associated with aging or cardiac pathology. Reprogramming of molecular mechanisms, particularly SAN transcriptomic regulation that underlies the remarkable chronic shift in HR and HRV, however, has not been delineated. We conducted deep RNA sequencing (RNA-seq) in TGAC8 and WT SANs, using Mm10plus with human ADCY8 DNA sequence as the reference genome. Utilizing multiple bioinformatic techniques, we not only profiled the expression of marker genes related to SAN functions and AC-cAMP-PKA signaling, but also discovered negatively enriched hub pathways that differed in TGAC8 vs. WT, the top three being OXPHOS, ribosome, and cardiac muscle contraction. In contrast, signaling pathways related to inositol phosphate and its metabolism were positively enriched in TGAC8. Further, we identified two transcription regulators, KDM5A and PPARGC1A, that mediate effects of TGAC8 on ribosome and mitochondria. In summary, reprogrammed transcriptional regulation increases the HR of TGAC8 at the cost of impairment of other SAN cell functions, i.e., altered ribosome and inositol phosphate signaling and its crosstalk with mitochondria. Because these cell signaling alterations are associated with cardiac aging and age-associated CVDs, the TGAC8 mouse appears to be an ideal model in which to probe for potential therapeutic targets for cardiac aging and age-associated CVDs.
PaGeSearch: A Tool for Identifying Genes within Pathways in Unannotated Genomes
Authors: Won Sohyoung , Yu Jaewoong , Kim Heebal 
Published: September 2023

ABSTRACTIn biological research, the identification and comparison of genes within specific pathways across the genomes of various species are invaluable. However, annotating the entire genome is resource-intensive and sequence similarity searches often yield results that are not actually genes. To address these limitations, we introduce PaGeSearch (Pathway Gene Search), a tool designed to identify genes from predefined lists, especially those in specific pathways, within genomes. The tool employs an initial sequence similarity search to identify relevant genomic regions, followed by targeted gene prediction and neural network-based result filtering. PaGeSearch suggests the regions that are most likely the orthologs of the genes in the query and is designed to be applicable for species within five classes: mammals, fish, birds, eudicotyledons, and liliopsida. When compared with GeMoMa, PaGeSearch consistently outperformed in terms of sensitivity and positive predictive value. Although its performance showed increased variability when applied to actual biological pathways, it nonetheless maintained an acceptable level of accuracy.
Hierarchical VAEs provide a normative account of motion processing in the primate brain
Authors: Vafaii Hadi , Yates Jacob L. , Butts Daniel A. 
Published: September 2023

AbstractThe relationship between perception and inference, as postulated by Helmholtz in the 19th century, is paralleled in modern machine learning by generative models like Variational Autoencoders (VAEs) and their hierarchical variants. Here, we evaluate the role of hierarchical inference and its alignment with brain function in the domain of motion perception. We first introduce a novel synthetic data framework, Retinal Optic Flow Learning (ROFL), which enables control over motion statistics and their causes. We then present a new hierarchical VAE and test it against alternative models on two downstream tasks: (i) predicting ground truth causes of retinal optic flow (e.g., self-motion); and (ii) predicting the responses of neurons in the motion processing pathway of primates. We manipulate the model architectures (hierarchical versus non-hierarchical), loss functions, and the causal structure of the motion stimuli. We find that hierarchical latent structure in the model leads to several improvements. First, it improves the linear decodability of ground truth factors and does so in a sparse and disentangled manner. Second, our hierarchical VAE outperforms previous state-of-the-art models in predicting neuronal responses and exhibits sparse latent-to-neuron relationships. These results depend on the causal structure of the world, indicating that alignment between brains and artificial neural networks depends not only on architecture but also on matching ecologically relevant stimulus statistics. Taken together, our results suggest that hierarchical Bayesian inference underlines the brain’s understanding of the world, and hierarchical VAEs can effectively model this understanding.
Perceptual biases, camouflage patterns, and the origin of sexual signals
Authors: Héjja-Brichard Yseult , Raymond Michel , Cuthill Innes C. , Mendelson Tamra C. , Renoult Julien P. 
Published: September 2023

AbstractNatural and sexual selection can be in conflict in driving the evolution of sexual ornamentation. Sexual selection typically favors detectability to potential mates, whereas natural selection penalizes detectability to avoid predators. Considering signal efficiency in addition to detectability, however, suggests that natural and sexual selection need not be antagonistic. In the visual domain, considerable evidence supports a “processing bias” by which people prefer images that match the spatial statistics of natural scenes, likely because the brain has evolved to process such scenes efficiently. A direct but untested prediction of this bias is that background-matching camouflage can be favored by natural and sexual selection. We conducted an online experiment where we show for the first time human preference for camouflaged patterning and confirm a preference for the average image statistics of natural scenes. Because many of the underlying visual mechanisms are shared across vertebrates, our results suggest that camouflage patterns can serve as evolutionary precursors of sexual signals.
Inhibiting Glutamine Metabolism Blocks Coronavirus Replication in Mammalian Cells
Authors: Greene Kai Su , Choi Annette , Chen Matthew , Yang Nianhui , Li Ruizhi , Qiu Yijian , Lukey Michael J , Rojas Katherine S , Shen Jonathan , Wilson Kristin F , Katt William P , Whittaker Gary R , Cerione Richard A 
Published: September 2023

AbstractDeveloping therapeutic strategies against COVID-19 has gained widespread interest given the likelihood that new viral variants will continue to emerge. Here we describe one potential therapeutic strategy which involves targeting members of the glutaminase family of mitochondrial metabolic enzymes (GLS and GLS2), which catalyze the first step in glutamine metabolism, the hydrolysis of glutamine to glutamate. We show three examples where GLS expression increases during coronavirus infection of host cells, and another in which GLS2 is upregulated. The viruses hijack the metabolic machinery responsible for glutamine metabolism to generate the building blocks for biosynthetic processes and satisfy the bioenergetic requirements demanded by the ‘glutamine addiction’ of virus-infected host cells. We demonstrate how genetic silencing of glutaminase enzymes reduces coronavirus infection and that newer members of two classes of small molecule allosteric inhibitors targeting these enzymes, designated as SU1, a pan-GLS/GLS2 inhibitor, and UP4, which is specific for GLS, block viral replication in mammalian epithelial cells. Overall, these findings highlight the importance of glutamine metabolism for coronavirus replication in human cells and show that glutaminase inhibitors can block coronavirus infection and thereby may represent a novel class of anti-viral drug candidates.TeaserInhibitors targeting glutaminase enzymes block coronavirus replication and may represent a new class of anti-viral drugs.