bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monocytes use protrusive forces to generate migration paths in viscoelastic collagen-based extracellular matrices
Authors: Adebowale Kolade , Allan Cole , Ha Byunghang , Saraswathibhatla Aashrith , Zhu Junqin , Indana Dhiraj , Popescu Medeea C. , Demirdjian Sally , Martinez Hunter A. , Esclamado Alex , Yang Jin , Bassik Michael C. , Franck Christian , Bollyky Paul L. , Chaudhuri Ovijit 
Published: June 2023

AbstractCirculating monocytes are recruited to the tumor microenvironment, where they can differentiate into macrophages that mediate tumor progression. To reach the tumor microenvironment, monocytes must first extravasate and migrate through the type-1 collagen rich stromal matrix. The viscoelastic stromal matrix around tumors not only stiffens relative to normal stromal matrix, but often exhibits enhanced viscous characteristics, as indicated by a higher loss tangent or faster stress relaxation rate. Here, we studied how changes in matrix stiffness and viscoelasticity, impact the three-dimensional migration of monocytes through stromal-like matrices. Interpenetrating networks of type-1 collagen and alginate, which enable independent tunability of stiffness and stress relaxation over physiologically relevant ranges, were used as confining matrices for three-dimensional culture of monocytes. Increased stiffness and faster stress relaxation independently enhanced the 3D migration of monocytes. Migrating monocytes have an ellipsoidal or rounded wedge-like morphology, reminiscent of amoeboid migration, with accumulation of actin at the trailing edge. Matrix adhesions were dispensable for monocyte migration in 3D, but migration did require actin polymerization and myosin contractility. Mechanistic studies indicate that actin polymerization at the leading edge generates protrusive forces that open a path for the monocytes to migrate through in the confining viscoelastic matrices. Taken together, our findings implicate matrix stiffness and stress relaxation as key mediators of monocyte migration and reveal how monocytes use pushing forces at the leading edge mediated by actin polymerization to generate migration paths in confining viscoelastic matrices.Significance StatementCell migration is essential for numerous biological processes in health and disease, including for immune cell trafficking. Monocyte immune cells migrate through extracellular matrix to the tumor microenvironment where they can play a role in regulating cancer progression. Increased extracellular matrix (ECM) stiffness and viscoelasticity have been implicated in cancer progression, but the impact of these changes in the ECM on monocyte migration remains unknown. Here, we find that increased ECM stiffness and viscoelasticity promote monocyte migration. Interestingly, we reveal a previously undescribed adhesion-independent mode of migration whereby monocytes generate a path to migrate through pushing forces at the leading edge. These findings help elucidate how changes in the tumor microenvironment impact monocyte trafficking and thereby disease progression.
BIFROST: a method for registering diverse imaging datasets of theDrosophilabrain
Authors: Brezovec Bella E. , Berger Andrew B. , Hao Yukun A. , Lin Albert , Ahmed Osama M. , Pacheco Diego A. , Thiberge Stephan Y. , Murthy Mala , Clandinin Thomas R. 
Published: June 2023

AbstractThe heterogeneity of brain imaging methods in neuroscience provides rich data that cannot be captured by a single technique, and our interpretations benefit from approaches that enable easy comparison both within and across different data types. For example, comparing brain-wide neural dynamics across experiments and aligning such data to anatomical resources, such as gene expression patterns or connectomes, requires precise alignment to a common set of anatomical coordinates. However, this is challenging because registeringin vivofunctional imaging data toex vivoreference atlases requires accommodating differences in imaging modality, microscope specification, and sample preparation. We overcome these challenges inDrosophilaby building anin vivoreference atlas from multiphoton-imaged brains, called the Functional Drosophila Atlas (FDA). We then develop a two-step pipeline, BrIdge For Registering Over Statistical Templates (BIFROST), for transforming neural imaging data into this common space and for importingex vivoresources such as connectomes. Using genetically labeled cell types as ground truth, we demonstrate registration with a precision of less than 10 microns. Overall, BIFROST provides a pipeline for registering functional imaging datasets in the fly, both within and across experiments.SignificanceLarge-scale functional imaging experiments inDrosophilahave given us new insights into neural activity in various sensory and behavioral contexts. However, precisely registering volumetric images from different studies has proven challenging, limiting quantitative comparisons of data across experiments. Here, we address this limitation by developing BIFROST, a registration pipeline robust to differences across experimental setups and datasets. We benchmark this pipeline by genetically labeling cell types in the fly brain and demonstrate sub-10 micron registration precision, both across specimens and across laboratories. We further demonstrate accurate registration betweenin-vivobrain volumes and ultrastructural connectomes, enabling direct structure-function comparisons in future experiments.
HIV self-testing positivity rate and linkage to confirmatory testing and care: a telephone survey in Côte d’Ivoire, Mali, and Senegal
Authors: Kra Arsène Kouassi , Fotso Arlette Simo , Rouveau Nicolas , Maheu-Giroux Mathieu , Boily Marie-Claude , Silhol Romain , d’Elbée Marc , Vautier Anthony , Larmarange Joseph 
Published: June 2023

AbstractHIV self-testing (HIVST) empowers individuals to decide when and where to test and with whom to share their results. From 2019 to 2022, the ATLAS program distributed ∼ 400 000 HIVST kits in Côte d’Ivoire, Mali, and Senegal. It prioritised key populations, including female sex workers and men who have sex with men, and encouraged secondary distribution of HIVST to their partners, peers and clients.To preserve the confidential nature of HIVST, use of kits and their results were not systematically tracked. Instead, an anonymous phone survey was carried out in two phases during 2021 to estimate HIVST positivity rates (phase 1) and linkage to confirmatory testing (phase 2). Initially, participants were recruited via leaflets from March to June and completed a sociobehavioural questionnaire. In the second phase (September-October), participants who had reported two lines or who reported a reactive result were recontacted to complete another questionnaire. Of the 2 615 initial participants, 89.7% reported a consistent response between the number of lines on the HIVST and their interpretation of the result (i.e., ‘non-reactive’ for 1 line, ‘reactive’ for 2 lines).Overall positivity rate based on self-interpreted HIVST results was 2.5% considering complete responses, and could have ranged from 2.4% to 9.1% depending on the interpretation of incomplete responses. Using the reported number of lines, this rate was estimated at 4.5% (ranging from 4.4% to 7.2%). Positivity rates were significantly lower only among respondents with higher education. No significant difference was observed by age, key population profile, country or history of HIV testing.The second phase saw 78 out of 126 eligible participants complete the questionnaire. Of the 27 who reported a consistent reactive response in the first phase, 15 (56%, 95%CI: 36 to 74%) underwent confirmatory HIV testing, with 12 (80%) confirmed as HIV-positive, all of whom began antiretroviral treatment.The confirmation rate of HIVST results was fast, with 53% doing so within a week and 91% within three months of self-testing. Two-thirds (65%) went to a general public facility, and one-third to a facility dedicated to key populations.The ATLAS HIVST distribution strategy reached people living with HIV in West Africa. Linkage to confirmatory testing following a reactive HIVST remained relatively low in these first years of HIVST implementation. However, if confirmed HIV-positive, almost all initiated treatment. HIVST constitutes a relevant complementary tool to existing screening services.
Computational prediction of gamma-oryzanol as potential agonist of human peroxisome proliferator-activated receptor gamma (ppar-γ)
Authors: Biswal Prasanta Kumar , Behera Swagatika , Mohapatra Snehamayee , Kar Durga Madhab , Samanta Luna , Behera Pabitra Mohan , Kar Rajat Kumar 
Published: June 2023

AbstractDiabetes mellitus is one of the complex metabolic disorders associated with individuals leading sedentary lifestyles. It leads to several complications rendering the normal function of vital organs like heart, liver, kidney, eye and brain. Scientists and doctors across the globe are involved in research for understanding the complex genetics of this disorder and formulating newer therapeutics accordingly. The finding of potential chemical entities and their underlying agonists or antagonist activities significantly controls the disorder but with some consequences. Thus there is demand for natural compounds and indigenous treatment methods for controlling the disorder with least or no adverse consequences. In the current work we present computational prediction of gamma-oryzanol as potential agonist of human peroxisome proliferator-activated receptor gamma (PPAR-γ). A group of four gamma-oryzanol compound structures reported in PubChem database were downloaded and docked in the ligand binding site of five different human PPAR-γ structures reported in PDB database. It was observed that most of the gamma-oryzanol compounds occupied themselves in the ligand binding P1, P2, P3, P4 sites with similar orientations as that of co-crystal agonists. Their binding conformations were assisted by some reasonable docking scores (−7 to -11 kcal/mol) and hydrogen bond interactions with some important conserved amino acid residues lining the ligand binding site. Additionally we have done a comparative molecular dynamics studies to reveal the flexibility of gamma-oryzanol in the ligand binding site in comparison to the co-crystal agonist and a scaffold analysis using the structure of six agonists and gamma-oryzanol for fetching potential scaffolds which may helpful in designing of new chemical entities.
AraENCODE: a comprehensive epigenomic database ofArabidopsis Thaliana
Authors: Wang Zhenji , Liu Minghao , Lai Fuming , Fu Qiangqiang , Xie Liang , Fang Yaping , Zhou Qiangwei , Li Guoliang 
Published: June 2023

AbstractArabidopsis (Arabidopsis thaliana) is a vital model organism in plant biology and genetics. In the last two decades, researchers have made significant progresses in characterizing the chromatin conformation and epigenomic information within the Arabidopsis genome. This information includes but is not limited to the higher structure of chromosomes, histone modification, DNA methylation, and chromatin accessibility. The results of these studies have provided an additional layer of information that complements the DNA sequence data. However, utilizing such knowledge poses a challenge for certain groups that lack bioinformatics analysts or adequate computing resources. A user-friendly and reproducible platform for accessing this information is urgently needed. In this study, we have developed a comprehensive epigenomic database for Arabidopsis (AraENCODEhttp://glab.hzau.edu.cn/AraENCODE), which comprises a total of 4,511 data libraries, including published chromatin conformation capture datasets (Hi-C, HiChIP), epigenomic datasets (ChIP-Seq, ATAC-Seq, FAIRE-Seq, MNase-Seq, DNase-Seq, BS-seq), and transcriptome data (RNA-Seq, miRNA-Seq). Furthermore, we have incorporated various existing resources, such as single nucleotide polymorphisms (SNPs), cis-regulatory modules, and multi-omics associations. We aim to provide a novel platform for investigating the regulation of epigenetic and chromatin interactions in Arabidopsis in relation to biological processes.
Deep learning-based survival prediction using DNA methylation-derived 3D genomic information
Authors: Yang Jeewon , Lee Dohoon , Koo Bonil , Kim Sun 
Published: June 2023

ABSTRACTThree-dimensional (3D) genome states are closely related to cancer development. Nonetheless, the 3D genome information has not been clinically utilized to the best of our knowledge, due to the costly production of Hi-C data which is a manifest source of 3D genome information. Therefore, there is a need for a novel metric computable from a 3D genome-related data which is more easily accessible for the clinical utilization of 3D genome information. We here propose a method to extract 3D genome-aware epigenetic features from DNA methylation data and use these features for a deep learning-based survival prediction. These features are derived from the 3D genome structures which are rebuilt from the DNA methylation data in an individual level. The results showed that usage of 3D genome-aware features contributed to more accurate risk prediction across seven cancer types, suggesting the effectiveness of the knowledge about 3D genome structure embedded in these features. The deeper biological investigation revealed that altered DNA methylation level in risk-high group could be related to the anomalously activated genes involved in cancer-related pathways. Altogether, the risks predicted from 3D genome-aware epigenetic features showed its significance as a survival predictor in seven cancer types, along with its biological importance.
In Vitro Reduction of Device Thrombosis Using a Combined Nitrite and Red Light Treatment
Authors: Alipour Elmira , Jordan James E. , Poudel Laxman , Files D. Clark , Kim-Shapiro Daniel B. 
Published: June 2023

AbstractDevice thrombosis occurs in otherwise life-saving procedures involving blood-contacting medical devices. Despite the use of systemic blood thinners, anticoagulants, and antiplatelet agents, device thrombosis can lead to substantial neurological damage, limb loss, death, and prolonged illness. Systemic treatments can also lead to bleeding. New methods to locally reduce thrombosis are urgently needed. Earlier work has shown that nitrite is a unique nitric oxide (NO) donor that is well-suited to use in blood and that its ability to inhibit platelet activation is potentiated by far-red light. In this study, we have applied our combined nitrite/light treatment in a prototypical technique used to prevent device thrombosis in extracorporeal circulation. We show that circuit pressure and survival are improved by an average of 213 percent with our treatment compared to the control. In addition, the dual therapy preserved platelet numbers at the end of the circulation time (%17 difference in platelet loss), and it reduced circuit hemolysis 2.3 fold. Thus, the combination of nitrite and red-light illumination has potential to prevent device thrombosis and to lead new clinical applications and practices.
Genomics resolves historical uncertainties on phylogenetics and accommodates the systematics of marmosets and Goeldi’s monkey (Primates: Platyrrhini)
Authors: Costa-Araújo Rodrigo , Roos Christian , Röhe Fabio , de Sousa e Silva José , de Freitas Patricia Domingues , Pissinatti Alcides , Boubli Jean P. , Farias Izeni P. , Hrbek Tomas 
Published: June 2023

AbstractMarmosets, with a total of 24 species classified into four genera (Callithrix,Cebuella,MicoandCallibella), are the smallest of the anthropoids and one of the most diverse and widespread groups of primates in South America. In contrast, the Goeldi’s monkey (Callimico goeldii) is represented by a single species of black, small, fungi-eating primates, endemic to west Amazonia. The phylogenetic relationships of marmoset genera and the phylogenetic position of Goeldi’s monkey, and consequently their systematics, remain uncertain and subject to debate because earlier studies revealed incongruent conclusions. Here we tackle this issue by first reviewing the systematics and the history of phylogenetic studies of marmosets and Goeldi’s monkey. We then explore their phylogenetic relationships by reconstructing a time-calibrated phylogeny using a genome-wide sampling of all lineages of marmosets, tamarins, Goeldi’s monkey, lion tamarins, capuchins, and squirrel monkeys. Our results clearly demonstrate that historical disagreements on phylogenetics and systematics of marmosets are due to incomplete lineage sorting, low phylogenetic signal of morphological and ecological characters, and low sampling at the DNA level. We show that Goeldi’s monkey is a sister lineage to marmosets and suggest that past incongruencies between studies on its phylogenetics and systematics are due to homoplasy of morphological characters traditionally used to infer primate relationships. Accordingly, we accommodate a genus-level classification for marmosets based on a fully-resolved phylogeny and multiple biological traits, redefine the genusMico, update the definitions ofCallibella,Callithrix, andCebuella, and sediment the family-level classification of Goeldi’s monkey.
Plant-mycorrhizal associations may explain the latitudinal gradient of plant community assembly
Authors: Shinohara Naoto , Kobayashi Yuta , Nishizawa Keita , Kadowaki Kohmei , Yamawo Akira 
Published: June 2023

AbstractBiogeographical variation in community assembly patterns forms the basis of large-scale biodiversity gradients. Previous studies on community assembly have suggested the dominant role of environmental filtering at higher latitudes. However, recent evidence indicates that plant community distributions at higher latitudes exhibit more spatial clustering, suggesting the importance of spatial assembly processes. In this study, we propose a hypothesis that resolves this paradox by incorporating biogeographic variations in dominant mycorrhizal types: the increasing prevalence of ectomycorrhizal (EcM) trees with latitude contributes to the spatially clustered distribution of plants, as EcM trees tend to exhibit positive plant-soil feedback. We analyzed a large-scale standardized dataset of Japanese forests covering a latitudinal gradient of >10° and found that (i) the proportion of EcM trees was higher at higher latitudes, and (ii) EcM tree-rich communities exhibited more spatially clustered distributions. Consequently, (iii) the tree species composition at higher latitudes was better explained by spatial variables. Moreover, consistent with predictions derived from the plant-soil feedback theory, these findings were particularly evident in the understory rather than the canopy communities. This study demonstrates that plant-soil feedback influences plant community distributions at metacommunity scales, thereby giving rise to a paradox within the latitudinal gradient of plant community assembly.
WITHDRAWN: Estimates of Undernutrition among migrant/refugee children in lower-middle-income countries: A meta-analysis of published evidence from 2010-2022
Authors: Talukdar Rounik , Kumar Vivek , Barman Diplina 
Published: June 2023

Withdrawal statementThis manuscript is hereby withdrawn owing to the methodological flaws in inclusion criteria used, high heterogeneity and less generalizability of the results.
Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales
Authors: Yang Ying-Ying , Stull Gregory W. , Qu Xiao-Jian , Zhao Lei , Hu Yi , Wang Zhi-Heng , Ma Hong , Li De-Zhu , Smith Stephen A. , Yi Ting-Shuang 
Published: June 2023

SummaryFlowering plant lineages display remarkable diversity in life history and morphological form. However our understanding of how this phenotypic diversity or disparity, arises and what, if any, relation there is to processes such as gene and genome duplication remains unlcear.Here we investigate the relationship between phenotypic and genomic evolution in the angiosperm order Fagales, a lineage of woody plants that has been a dominant component of temperate and subtropical forests since the Late Cretaceous. To this end, we examine newly generated trait and transcriptomic datasets spanning the phylogenetic breadth of the order, including most extant genera as well as a rich diversity of Cretaceous fossil representatives.Our phylogenomic analyses resolved the location of an ancient polyploidization event in Juglandaceae and identified hotspots of gene-duplication and genomic conflict across the order. Examinations of phenotypic evolution (including morphospace occupancy and rate shifts) show that the morphospace occupied by Fagales was filled by the early Cenozoic and rates of evolution were highest during the early radiation of the Fagales crown and its major families. Many instances of phenotypic rates also correspond to hotspots of gene duplication.Our results show that Fagales conform to an “early burst” model of phenotypic diversification, with morphospace being filled early in the group’s evolutionary history. Our study is consistent with others showing a decoupling of species diversification with other biological processes (e.g., phenotypic and genomic evolution), underscoring the complexity of understanding the major drivers of plant evolution over broad timescales.
Hippocampal memory reactivation during sleep is correlated with specific cortical states of the Retrosplenial and Prefrontal Cortices
Authors: Feliciano-Ramos PA , Galazo MJ , Penagos H. , Wilson MA 
Published: June 2023

AbstractEpisodic memories are thought to be stabilized through the coordination of cortico-hippocampal activity during sleep. However, the timing and mechanism of this coordination remain unknown. To investigate this, we studied the relationship between hippocampal reactivation and slow-wave sleep UP and Down states of the retrosplenial cortex (RTC) and prefrontal cortex (PFC). We found that hippocampal reactivation are strongly correlated with specific cortical states. Reactivation occurred during sustained cortical UP states or during the transition from UP to Down state. Interestingly, sustained UP states from the PFC were more coordinated with memory reactivation in the hippocampus, whereas hippocampal reactivation was biased to occur during the cortical UP to Down state transition of the RTC. Reactivation usually occurred within 150-200 ms of a cortical UP-state onset, indicating that a build-up of excitation during cortical UP state activity influences the probability of memory reactivation in CA1. Conversely, CA1 reactivation occurred 30-50 ms before the onset of a cortical Down state, suggesting that memory reactivation affects Down state initiation in RTC and PFC, but the effect in RTC was more robust. Our findings provide evidence that supports and highlights the complexity of bidirectional communication between cortical regions and the hippocampus during sleep.