bluuebunny/crossref_metadata_2025_split huggingface dataset:
A general exposome factor explains individual differences in functional brain network topography and cognition in youth
Authors: Keller Arielle S. , Moore Tyler M. , Luo Audrey , Visoki Elina , Gataviņš Mārtiņš M. , Shetty Alisha , Cui Zaixu , Fan Yong , Feczko Eric , Houghton Audrey , Li Hongming , Mackey Allyson P. , Miranda-Dominguez Oscar , Pines Adam , Shinohara Russell T. , Sun Kevin Y. , Fair Damien A. , Satterthwaite Theodore D. , Barzilay Ran 
Published: August 2023

ABSTRACTOur minds and brains are highly unique. Despite the long-recognized importance of the environment in shaping individual differences in cognitive neurodevelopment, only with the combination of deep phenotyping approaches and the availability of large-scale datasets have we been able to more comprehensively characterize the many inter-connected features of an individual’s environment and experience (“exposome”). Moreover, despite clear evidence that brain organization is highly individualized, most neuroimaging studies still rely on group atlases to define functional networks, smearing away inter-individual variation in the spatial layout of functional networks across the cortex (“functional topography”). Here, we leverage the largest longitudinal study of brain and behavior development in the United States to investigate how an individual’s exposome may contribute to functional brain network organization leading to differences in cognitive functioning. To do so, we apply three previously-validated data driven computational models to characterize an individual’s multidimensional exposome, define individual-specific maps of functional brain networks, and measure cognitive functioning across broad domains. In pre-registered analyses replicated across matched discovery (n=5,139, 48.5% female) and replication (n=5,137, 47.1% female) samples, we find that a child’s exposome is associated with multiple domains of cognitive functioning both at baseline assessment and two years later – over and above associations with baseline cognition. Cross-validated ridge regression models reveal that the exposome is reflected in children’s unique patterns of functional topography. Finally, we uncover both shared and unique contributions of the exposome and functional topography to cognitive abilities, finding that models trained on a single variable capturing a child’s exposome can more accurately and parsimoniously predict future cognitive performance than models trained on a wealth of personalized neuroimaging data. This study advances our understanding of how childhood environments contribute to unique patterns of functional brain organization and variability in cognitive abilities.
Comparative Phylogeography of Tree Species in the Hyrcanian Forests, Iran by Genome-wide SNPs
Authors: Vatanparast Mohammad , Madsen Palle , Sagheb-Talebi Khosro , Larsen Jørgen Bo , Ayan Sezgin , Hansen Ole K. 
Published: August 2023

AbstractThe Hyrcanian forests in Iran are one of the last remaining natural deciduous forests in the world and a UNESCO World Heritage site. We investigated the population genetics of representative indigenous tree species,Acer velutinumBoiss.,Fagus orientalisLipsky, andQuercus castaneifoliaC.A. Mey. in northern Iran and alsoF. orientalispopulations in the Euro-Siberian and Colchic sub-regions in northern Türkiye. We used the double-digest RAD-seq method and genotyped 90 populations and 1,589 individuals across the distribution range of the species. Our analyses yielded 1,347, 2,091, and 8,881 genome-wide SNPs from 28 populations ofA. velutinum, 32 populations ofF. orientalis, and 30Q. castaneifolia, respectively. Our results revealed higher genetic differentiations amongA. velutinumpopulations than those ofF. orientalisandQ. castaneifoliawithin the Hyrcanian forests. The globalFSTvalue was lowest forF. orientalispopulations (0.019) and highest forA. velutinumpopulations (0.12), while theFISvalue was negative forA. velutinum(–0.095). Demographic history analysis indicated a bottleneck during the last glacial maximum for theA. velutinumpopulations with reduced effective population size. The three species showed evidence of population bottlenecks during the Pliocene. Our findings highlight the pronounced genetic divergence amongA. velutinumpopulations in the Hyrcanian forests compared to the other two species, suggesting cryptic speciation. Conversely,F. orientalisandQ. castaneifoliapopulations demonstrated a reduced level of genetic structure, indicating that species-specific factors, such as pollen production and pollination efficiency, may have influenced the genetic patterns within these species in similar environments. We did not observe significant elevational genetic differentiation within populations of the studied species. Furthermore, theF. orientalispopulations from Türkiye exhibited a distinct west-east genetic structure and were highly diverged from the IranianF. orientalispopulations.
SSDraw: software for generating comparative protein secondary structure diagrams
Authors: Chen Ethan A. , Porter Lauren L. 
Published: August 2023

AbstractThe program SSDraw generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring. Diagrams of homologous proteins can be registered according to an input multiple sequence alignment. Linear visualization allows the user to stack registered diagrams, facilitating comparison of secondary structure and other properties among homologous proteins. SSDraw can be used to compare secondary structures of homologous proteins with both conserved and divergent folds. It can also generate one secondary structure diagram from an input protein structure of interest. The source code can be downloaded (https://github.com/ethanchen1301/SSDraw) and run locally for rapid structure generation, while a Google Colab notebook allows easy use.
Genomic insights into post-domestication expansion and selection of body size in ponies
Authors: Li Xingzheng , Wang Zihao , Zhu Min , Wang Binhu , Teng Shaohua , Yan Jing , Yuan Pengxiang , Cao Shuwei , Qu Xiaolu , Wang Zhen , Choudhury Panir , Yang Xintong , Bao Qi , He Sang , Liu Lei , Zhao Pengju , Jiang Jicai , Xiang Hai , Fang Lingzhao , Tang Zhonglin , Liao Yuying , Yi Guoqiang 
Published: August 2023

AbstractHorses domestication revolutionized human civilization by changing transportation, farming, and warfare patterns. Despite extensive studies on modern domestic horse origins, the intricate demographic history and genetic signatures of pony size demand further exploration. Here, we present a high-quality genome of the Chinese Debao pony and extensively analyzed 385 individuals from 49 horse breeds. We reveal the conservation of ancient components in East Asian horses and close relationships between Asian horses and specific European pony lineages. Genetic analysis uncovers Asian paternal origin for European pony breeds, and these pony-sized horses share a close genetic affinity due to the presence of a potential ancestral ghost pony population. Additionally, we identify promising cis-regulatory elements influencing horse withers height by regulating genes likeRFLNAandFOXO1. Overall, our study provides insightful perspectives into the development history and genetic determinants underlying body size in ponies and offers broader implications for horse population management and improvement.TeaserDecoding pony genetics: exploring origins and size determinants sheds light on their historical and biological impacts.
Characterization of thyroid function in euthyroid and children with subclinical hypothyroidism using a multivariate homeostatic model
Authors: Giannakopoulos Aristeidis , Efthymiadou Alexandra , Kritikou Dimitra , Chrysis Dionisios 
Published: August 2023

AbstractBackgroundSubclinical hypothyroidism (SH) is biochemically defined by increased TSH, and normal thyroid hormones and its management is a matter of debate. Herein, we investigated thyroid function in euthyroid and children with SH using published data from population-based curves and a structure parameter inference approach (SPINA) model.MethodsThe study included 179 children and adolescents with SH and 311 healthy controls. The predicted and calculated secretory capacity of thyroid gland (SPINA-GT) was calculated in all euthyroid children divided into quartiles according to TSH values, and in children with SH, further subcategorized into those with mild SH (TSH: 4.5 – 10 mIU/L) and severe SH (TSH > 10 mIU/L).ResultsCalculated SPINA-GT values decreased significantly (P < 0.001) from the 1stto the 2ndquartile of normal TSH values in euthyroid children. It was also significantly decreased in mild SH compared to euthyroid children with TSH values within the upper 2 quartiles of TSH range and in severe SH compared to mild SH.ConclusionsThe implementation of SPINA model for thyroid function gives a wider perspective of thyroid gland’s performance within the euthyroid range of TSH, as well as in SH and add to the discussion for the long-term effects of SH and its management.
Genetic Insights into the Microevolutionary Dynamics and Early Introductions of Human Monkeypox Virus in Mexico
Authors: Gómez-Sánchez Israel , Castelán-Sánchez Hugo G. , Martínez-Castilla León P. , Hurtado-Ramírez Juan Manuel , López-Leal Gamaliel 
Published: August 2023

ABSTRACTThe recent global outbreak of Monkeypox, caused by the Monkeypox virus (MPVX) emerged in Europe in 2022 and rapidly spread to over 40 countries. The Americas are currently facing the highest impact, reporting over 50,000 cases by early 2023. Here, we analyze 880 MPXV isolates worldwide to gain insights into the evolutionary patterns and initial introduction events of the virus in Mexico. We found that MPXV entered Mexico on multiple occasions, from the United Kingdom, Portugal, and Canada, and subsequently spread locally in different regions of Mexico. Additionally, we show that MPXV has an open pangenome, highlighting the role of gene turnover in shaping its genomic diversity, rather than SNPs variations, which do not contribute significantly to genome diversity. Although the genome presents multiple SNP sites in coding regions, these remain under purifying selection, suggesting their evolutionary conservation. One notable exception is the amino acid site 63 of the protein encoded by the Cop-A4L gene, intricately related to viral maturity, for which we picked up a strong signal of positive selection. Ancestral state reconstruction deduced that the ancestral state at site 63 corresponds to the amino acid valine, present only in isolates of clade I. However, the isolates of the current outbreak evolved for threonine at site 63. Finally, our findings contribute to the knowledge of the evolutionary processes of the Monkeypox virus.
Skipping without and with hurdles in bipedal macaque: Global mechanics
Authors: Blickhan Reinhard , Andrada Emanuel , Hirasaki Eishi , Ogihara Naomichi 
Published: August 2023

AbstractMacaques trained to perform bipedally used running gaits across a wide range of speed. At higher speeds they preferred unilateral skipping (galloping). The same asymmetric stepping pattern was used while hurdling across two low obstacles placed at the distance of a stride within our experimental track. In bipedal macaques during skipping, we expected a differential use of the trailing and leading legs. The present study investigated global properties of the effective and virtual leg, the location of the virtual pivot point (VPP), and the energetics of the center of mass (CoM), with the aim of clarifying the differential leg operation during skipping in bipedal macaques. Macaques skipping displayed minor double support and aerial phases during one stride. Asymmetric leg use indicated by differences in leg kinematics. Axial damping and tangential leg work did not influence the indifferent peak ground reaction forces and impulses, but resulted in a lift of the CoM during contact of the leading leg. The aerial phase was largely due to the use of the double support. Hurdling amplified the differences. Here, higher ground reaction forces combined with increased double support provided the vertical impulse to overcome the hurdles. Following CoM dynamics during a stride skipping and hurdling represented bouncing gaits. The elevation of the VPP of bipedal macaques resembled that of human walking and running in the trailing and leading phases, respectively. Due to anatomical restrictions, macaque unilateral skipping differs from that of humans, and may represent an intermediate gait between grounded and aerial running.
Is It There? - Estimating The Invasion of Armoured Sailfin Catfish (Pterygoplichthys Sp.) in the Water Bodies of Eastern Ghats, India Using eDNA Approach
Authors: Ganguly Neeldeep , Umapathy Govindhaswamy 
Published: August 2023

1.ABSTRACTEarly detection of invasive species is crucial for effective control of the potential damage they can inflict on the ecosystems. In contrast to the many limitations that traditional detection methods like visual surveys and netting hold, the use of environmental DNA assay provides a powerful alternative. This non-invasive, highly sensitive, and user-friendly technique offers the advantage of detecting invasive species even in areas where direct observation is challenging, thus addressing the shortcomings of traditional techniques and enhancing overall accuracy in estimating distribution. The spread of invasivePterygoplichthys sp. has become a cause for concern in biodiversity-rich countries like India. Despite this, comprehensive studies on the prevalence of this invasive species are limited. The Eastern Ghats of India remain underexplored with a high potential for supporting diverse lifeforms. Studying the extent of biological invasions in the Eastern Ghats is very essential for effective conservation management to mitigate the ecological and socioeconomic impacts of invasive species. In this study, we have designed and optimised an eDNA-based quantitative PCR assay to map the presence and spread of invasivePterygoplichthys sp. in selected freshwater ecosystems of the Eastern Ghats. With this assay, we detected invasivePterygoplichthys spin almost 65% of the total locations sampled. This study can be further extended to larger geographical areas, which in turn can contribute in formulating necessary measures by the authorities to manage invasion and conserve the diversity of the freshwater ecosystem.
Deep metric learning for few-shot X-ray image classification
Authors: Prokop Jakub , Tordera Javier Montalt , Jaworek-Korjakowska Joanna , Mohammadi Sadegh 
Published: August 2023

AbstractDeep learning models have proven the potential to aid professionals with medical image analysis, including many image classification tasks. However, the scarcity of data in medical imaging poses a significant challenge, as the limited availability of diverse and comprehensive datasets hinders the development and evaluation of accurate and robust imaging algorithms and models. Few-shot learning approaches have emerged as a potential solution to address this issue. In this research, we propose to deploy the Generalized Metric Learning Model for Few-Shot X-ray Image Classification. The model comprises a feature extractor to embed images into a lower-dimensional space and a distance-based classifier for label assignment based on the relative distance of these embeddings. We extensively evaluate the model using various pre-trained convolutional neural networks (CNNs) and vision transformers (ViTs) as feature extractors. We also assess the performance of the commonly used distance-based classifiers in several few-shot settings. Finally, we analyze the potential to adapt the feature encoders to the medical domain with both supervised and self-supervised frameworks. Our model achieves 0.689 AUROC in 2-way 5-shot COVID-19 recognition task when combined with REMEDIS (Robust and Efficient Medical Imaging with Self-supervision) domain-adapted model as feature extractor, and 0.802 AUROC in 2-way 5-shot tuberculosis recognition task with domain-adapted DenseNet-121 model. Moreover, the simplicity and flexibility of our approach allows for easy improvement in the feature, either by incorporating other few-shot methods or new, powerful architectures into the pipeline.
Relative cost of counselling compared to supplementary foods for acute malnutrition: a time and motion study in Nairobi Kenya
Authors: Mutoro Antonina N. , Grieve Eleanor , Garcia Ada L. , Wright Charlotte 
Published: August 2023

AbstractAimsWe aimed to describe the relative cost of supplying supplementary food, compared to counselling, in children with acute malnutrition managed in one urban area.MethodA cross-sectional costing study was undertaken. Interviews with staff and time-and-motion observations of children with acute malnutrition and their carers attending 6 ambulatory nutrition treatment centres in Nairobi were conducted to assess the time nutritionists spent treating acute malnutrition and managing ready to use food supplies. Kenyan standard pay rates ($) were used to calculate the monthly staff cost of reviewing each child and speaking to their parent. These were compared to the published cost of purchasing daily ready to use food sachets.ResultsConsultations with 32 children were observed, 3-8 per clinic. Staff spent mean (SD) 9.84 (4.9) minutes seeing each child, of which at most only 3.5 (2.0) minutes were spent counselling the family. With an hourly pay rate of $4.87, the median (IQR) contact and dispensing cost per child visit was $0.77 (0.49-1.16). The cost of RUF was estimated to be $7.84 for a month’s treatment, giving a total treatment cost of $8.61 per child per month. If ready to use food was not prescribed and more staff time purchased instead, this would pay for 1.6 hours staff time per child per month.ConclusionsVery little time was spent speaking to mothers of malnourished children and supplies of ready to use food represented 91% of total treatment costs.
Excellent recanalization and small core volumes are associated with favorable AMPAC score in patients with acute ischemic stroke secondary to large vessel occlusion
Authors: Yedavalli Vivek , Koneru Manisha , Hoseinyazdi Meisam , Copeland Karen , Xu Risheng , Luna Licia , Caplan Justin , Dmytriw Adam , Guenego Adrien , Heit Jeremy , Albers Gregory , Wintermark Max , Gonzalez Fernando , Urrutia Victor , Huang Judy , Leigh Richard , Marsh Elisabeth , Llinas Rafael , Gonzalez Hernandez Marlis , Hillis Argye 
Published: August 2023

AbstractBackground and aimAcute ischemic stroke due to large vessel occlusion (AIS-LVO) is a major cause of functional dependence, an important determinant of discharge disposition. The aim of this study is to assess the utility of pretreatment and interventional parameters as predictors of favorable Activity Measure for Post Acute Care (AMPAC) scores for optimal discharge planning.MethodsIn this retrospective multicenter analysis, inclusion criteria were as follows: a) CT angiography (CTA) confirmed LVO from 9/1/2017 to 9/22/2022; b) diagnostic CT perfusion; and c) available AMPAC scores. Patients were then dichotomized into favorable and unfavorable AMPAC for analysis. A multivariate logistic regression was performed using specific variables that were clinically relevant and significant on univariate regression analyses. A receiver operator characteristics (ROC) analysis was then performed to assess the diagnostic performance of the logistic regression model. A p value of <= 0.05 was considered significant.ResultsIn total, 229 patients (mean +-SD 70.65 +-15.2 [55.9% female]) met our inclusion criteria. Favorable AMPAC patients were younger (61.3 versus 70.7, p < 0.0001), had lower admission glucose (mean, 124.19 versus 136.83, p = 0.042), lower blood urea nitrogen (mean, 15.59 versus 19.11, p = 0.0009), and lower admission National Institutes of Health Stroke Scale (NIHSS) (mean, 10.58 versus 16.15, p < 0.0001). Multivariate regression analyses revealed age, admission NIHSS, relative cerebral blood flow (rCBF) < 30% volume, and modified thrombolysis in cerebral infarction (mTICI) score to be independent predictors of favorable AMPAC (p<0.047 for all predictors). ROC analysis of the combined model revealed an area under the curve (AUC) of 0.83 (IQR 0.75 - 0.86).ConclusionExcellent recanalization, smaller core volumes, younger age and lower stroke severity independently predict favorable outcomes as measured by AMPAC. Our study further emphasizes the significance of minimizing core volume and aiming for excellent recanalization in order to optimize discharge disposition in AIS-LVO patients.
Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport
Authors: Watanabe Satoshi , Kise Yoshiaki , Yonezawa Kento , Inoue Mariko , Shimizu Nobutaka , Nureki Osamu , Inaba Kenji 
Published: August 2023

AbstractERGIC-53 is a cargo receptor that promotes the transport of certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum (ER) to the Golgi apparatus (GA)1,2. Despite numerous structural and functional studies since its identification, the overall architecture and mechanism of action of this cargo receptor in its full-length form remain unclear. Here we present cryo-electron microscopy (cryo-EM) structures of full-length ERGIC-53 in complex with its functional partner MCFD2. These structures, in combination with SEC-MALS/SAXS analysis, reveal that ERGIC-53 exists as a homotetramer, not a homohexamer as previously suggested, and comprises a four-leaf clover-like head structure and a long stalk composed of three sets of four-helix coiled-coil followed by a transmembrane (TM) domain. The tetrameric head of ERGIC-53 consists of the vertically assembled carbohydrate recognition domains and the central four-helix coiled-coil. 3D variability analysis visualizes the globally flexible motion of the long stalk and local plasticity of the head region. Notably, MCFD2 has been found to possess a Zn2+binding site in its N-terminal lid, which appears to modulate cargo binding. Altogether, unique mechanisms of regulated cargo capture and release by ERGIC-53 via the stalk bending and metal binding are proposed.