bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lower Ordovician synziphosurine reveals early euchelicerate diversity and evolution
Authors: Lustri Lorenzo , Gueriau Pierre , Daley Allison C. 
Published: May 2024

AbstractEuchelicerata is a clade of arthropods comprising horseshoe crabs, scorpions, spiders, mites and ticks, as well as the extinct eurypterids (sea scorpions) and chasmataspidids. The understanding of the ground plans and relationships between these crown-group euchelicerates has benefited from the discovery of numerous fossils. However, little is known regarding the origin and early evolution of the euchelicerate body plan because the relationships between their Cambrian sister taxa and synziphosurines, a group of Silurian to Carboniferous stem euchelicerates with chelicerae and an unfused opisthosoma, remain poorly understood owing to the scarce fossil record of appendages. Here we describe a synziphosurine from the Lower Ordovician (ca. 478 Ma) Fezouata Shale of Morocco. This species possesses five biramous appendages with stenopodous exopods bearing setae in the prosoma and a fully expressed first tergite in the opisthosoma illuminating the ancestral anatomy of the group. Phylogenetic analyses recover this fossil as a member of the stem euchelicerate family Offacolidae, which is characterized by biramous prosomal appendages. Moreover, it also shares anatomical features with the Cambrian euarthropodHabelia optata, filling the anatomical gap between euchelicerates and Cambrian stem taxa, while also contributing to our understanding of the evolution of euchelicerate uniramous prosomal appendages and tagmosis.
Determinants of mosaic chromosomal alteration fitness
Authors: Pershad Yash , Mack Taralynn , Poisner Hannah , Jakubek Yasminka A. , Stilp Adrienne M. , Mitchell Braxton D. , Lewis Joshua P. , Boerwinkle Eric , Loos Ruth J. F. , Chami Nathalie , Wang Zhe , Barnes Kathleen , Pankratz Nathan , Fornage Myriam , Redline Susan , Psaty Bruce M. , Bis Joshua C. , Shojaie Ali , Silverman Edwin K. , Cho Michael H. , Yun Jeong H. , DeMeo Dawn , Levy Daniel , Johnson Andrew D. , Mathias Rasika A. , Taub Margaret A. , Arnett Donna , North Kari E. , Raffield Laura M. , Carson April P. , Doyle Margaret F. , Rich Stephen S. , Rotter Jerome I. , Guo Xiuqing , Cox Nancy J. , Roden Dan M. , Franceschini Nora , Desai Pinkal , Reiner Alex P. , Auer Paul L. , Scheet Paul A. , Jaiswal Siddhartha , Weinstock Joshua S. , Bick Alexander G. 
Published: May 2024

AbstractClonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate as PACER scores for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our mCA fitness estimates, derived by aggregating per-individual PACER scores, were correlated (R2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using population-level distributions of clonal fraction. Among individuals with JAK2 V617F clonal hematopoiesis of indeterminate potential or mCAs affecting the JAK2 gene on chromosome 9, PACER score was strongly correlated with erythrocyte count. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified a TCL1A locus variant associated with mCA clonal expansion rate, with suggestive variants in NRIP1 and TERT.
Replication competent HIV-guided CRISPR screen identifies antiviral factors including targets of the accessory protein Nef
Authors: Prelli Bozzo Caterina , Laliberté Alexandre , De Luna Aurora , Pastorio Chiara , Regensburger Kerstin , Krebs Stefan , Graf Alexander , Blum Helmut , Volcic Meta , Sparrer Konstantin M. J. , Kirchhoff Frank 
Published: May 2024

AbstractInnate antiviral factors are essential for effective defense against viral pathogens. However, the identity of major restriction mechanisms remains elusive. Current approaches to discover antiviral factors usually focus on the initial steps of viral replication and are limited to a single round of infection. Here, we engineered libraries of >1500 replication-competent HIV-1 constructs each expressing a single gRNAs to target >500 cellular genes for virus-driven discovery of antiviral factors. Passaging in CD4+ T cells robustly enriched HIV-1 encoding sgRNAs against GRN, CIITA, EHMT2, CEACAM3, CC2D1B and RHOA by >50-fold. Using an HIV-1 library lacking the accessory nef gene, we identified IFI16 as a Nef target. Functional analyses in cell lines and primary CD4+ T cells support that the HIV-driven CRISPR screen identified restriction factors targeting virus entry, transcription, release and infectivity. Our HIV-guided CRISPR technique enables sensitive discovery of physiologically relevant cellular defense factors throughout the entire viral replication cycle.
Electrochemical C−H deuteration of pyridine derivatives with D2O
Authors: Zhao Zhiwei , Zhang Ranran , Liu Yaowen , Zhu Zile , Wang Qiuyan , Qiu Youai 
Published: May 2024

AbstractHerein, we develop a straightforward, metal-free, and acid-/base-free electrochemical C4-selective C − H deuteration of pyridine derivatives with economic and convenient D2O at room temperature. This strategy features an efficient and environmentally friendly approach with high chemo- and regioselectivity, affording a wide range of D-compounds, such as pyridines, quinolones, N-ligands and biorelevant compounds. Notably, the mechanistic experiments and cyclic voltammetry (CV) studies demonstrate that N-butyl-2-phenylpyridinium iodide is a crucial intermediate during the electrochemical transformation, which provides a general and efficient way for deuteration of pyridine derivatives.
Starch-mediated colloidal chemistry for highly reversible zinc-based polyiodide redox flow batteries
Authors: Wei Zhiquan , Huang Zhaodong , Liang Guojin , Wang Yiqiao , Wang Shixun , Yang Yihan , Hu Tao , Zhi Chunyi 
Published: May 2024

AbstractAqueous Zn-I flow batteries utilizing low-cost porous membranes are promising candidates for high-power-density large-scale energy storage. However, capacity loss and low Coulombic efficiency resulting from polyiodide cross-over hinder the grid-level battery performance. Here, we develop colloidal chemistry for iodine-starch catholytes, endowing enlarged-sized active materials by strong chemisorption-induced colloidal aggregation. The size-sieving effect effectively suppresses polyiodide cross-over, enabling the utilization of porous membranes with high ionic conductivity. The developed flow battery achieves a high-power density of 42 mW cm−2 at 37.5 mA cm−2 with a Coulombic efficiency of over 98% and prolonged cycling for 200 cycles at 32.4 Ah L−1posolyte (50% state of charge), even at 50 °C. Furthermore, the scaled-up flow battery module integrating with photovoltaic packs demonstrates practical renewable energy storage capabilities. Cost analysis reveals a 14.3 times reduction in the installed cost due to the applicability of cheap porous membranes, indicating its potential competitiveness for grid energy storage.
Free-standing ultrathin silicon wafers and solar cells through edges reinforcement
Authors: Wu Taojian , Liu Zhaolang , Lin Hao , Gao Pingqi , Shen Wenzhong 
Published: May 2024

AbstractCrystalline silicon solar cells with regular rigidity characteristics dominate the photovoltaic market, while lightweight and flexible thin crystalline silicon solar cells with significant market potential have not yet been widely developed. This is mainly caused by the brittleness of silicon wafers and the lack of a solution that can well address the high breakage rate during thin solar cells fabrication. Here, we present a thin silicon with reinforced ring (TSRR) structure, which is successfully used to prepare free-standing 4.7-μm 4-inch silicon wafers. Experiments and simulations of mechanical properties for both TSRR and conventional thin silicon structures confirm the supporting role of reinforced ring, which can share stress throughout the solar cell preparation and thus suppressing breakage rate. Furthermore, with the help of TSRR structure, an efficiency of 20.33% (certified 20.05%) is achieved on 28-μm silicon solar cell with a breakage rate of ~0%. Combining the simulations of optoelectrical properties for TSRR solar cell, the results indicate high efficiency can be realized by TSRR structure with a suitable width of the ring. Finally, we prepare 50 ~ 60-μm textured 182 × 182 mm2TSRR wafers and perform key manufacturing processes, confirming the industrial compatibility of the TSRR method.
JARVIS-Leaderboard: a large scale benchmark of materials design methods
Authors: Choudhary Kamal , Wines Daniel , Li Kangming , Garrity Kevin F. , Gupta Vishu , Romero Aldo H. , Krogel Jaron T. , Saritas Kayahan , Fuhr Addis , Ganesh Panchapakesan , Kent Paul R. C. , Yan Keqiang , Lin Yuchao , Ji Shuiwang , Blaiszik Ben , Reiser Patrick , Friederich Pascal , Agrawal Ankit , Tiwary Pratyush , Beyerle Eric , Minch Peter , Rhone Trevor David , Takeuchi Ichiro , Wexler Robert B. , Mannodi-Kanakkithodi Arun , Ertekin Elif , Mishra Avanish , Mathew Nithin , Wood Mitchell , Rohskopf Andrew Dale , Hattrick-Simpers Jason , Wang Shih-Han , Achenie Luke E. K. , Xin Hongliang , Williams Maureen , Biacchi Adam J. , Tavazza Francesca 
Published: May 2024

AbstractLack of rigorous reproducibility and validation are significant hurdles for scientific development across many fields. Materials science, in particular, encompasses a variety of experimental and theoretical approaches that require careful benchmarking. Leaderboard efforts have been developed previously to mitigate these issues. However, a comprehensive comparison and benchmarking on an integrated platform with multiple data modalities with perfect and defect materials data is still lacking. This work introduces JARVIS-Leaderboard, an open-source and community-driven platform that facilitates benchmarking and enhances reproducibility. The platform allows users to set up benchmarks with custom tasks and enables contributions in the form of dataset, code, and meta-data submissions. We cover the following materials design categories: Artificial Intelligence (AI), Electronic Structure (ES), Force-fields (FF), Quantum Computation (QC), and Experiments (EXP). For AI, we cover several types of input data, including atomic structures, atomistic images, spectra, and text. For ES, we consider multiple ES approaches, software packages, pseudopotentials, materials, and properties, comparing results to experiment. For FF, we compare multiple approaches for material property predictions. For QC, we benchmark Hamiltonian simulations using various quantum algorithms and circuits. Finally, for experiments, we use the inter-laboratory approach to establish benchmarks. There are 1281 contributions to 274 benchmarks using 152 methods with more than 8 million data points, and the leaderboard is continuously expanding. The JARVIS-Leaderboard is available at the website: https://pages.nist.gov/jarvis_leaderboard/
Water droplet evaporation in varied gravity and electric fields
Authors: Gibbons M. J. , Garivalis A. I. , O’Shaughnessy S. M. , Robinson A. J. , Di Marco P. 
Published: May 2024

AbstractSessile water droplet evaporation in varied gravity and electric fields has been experimentally studied. Specifically, the influences of gravity and electric fields are investigated in the context of the heat flux distribution beneath the droplets, as well as the droplet mechanics and resulting shapes. Experimental testing was carried out during a European Space Agency (ESA) Parabolic Flight Campaign (PFC 66). The droplets tested evaporated with a pinned contact line, a single wettability condition, and varied droplet volume and substrate heat flux. The peak heat transfer was located at the contact line for all cases. The peak heat flux, average heat flux, and droplet evaporation rate were shown to vary strongly with gravity, with higher values noted for hypergravity conditions and lower values in microgravity conditions. The droplet thermal inertia was shown to play a significant role, with larger droplets taking more time to reach thermal equilibrium during the parabolic testing period. No significant impact of the electric field on the droplet evaporation was noted for these test conditions.
Collective plasticity of binocular interactions in the adult visual system
Authors: Wang Mengxin , McGraw Paul V. , Ledgeway Timothy 
Published: May 2024

AbstractBinocular visual plasticity can be initiated via either bottom-up or top-down mechanisms, but it is unknown if these two forms of adult plasticity can be independently combined. In seven participants with normal binocular vision, sensory eye dominance was assessed using a binocular rivalry task, before and after a period of monocular deprivation and with and without selective attention directed towards one eye. On each trial, participants reported the dominant monocular target and the inter-ocular contrast difference between the stimuli was systematically altered to obtain estimates of ocular dominance. We found that both monocular light- and pattern-deprivation shifted dominance in favour of the deprived eye. However, this shift was completely counteracted if the non-deprived eye’s stimulus was selectively attended. These results reveal that shifts in ocular dominance, driven by bottom-up and top-down selection, appear to act independently to regulate the relative contrast gain between the two eyes.
The transcription factor OCT6 promotes the dissolution of the naïve pluripotent state by repressing Nanog and activating a formative state gene regulatory network
Authors: Waisman Ariel , Sevlever Federico , Saulnier Denisse , Francia Marcos , Blanco Renata , Amín Guadalupe , Lombardi Antonella , Biani Celeste , Palma María Belén , Scarafía Agustina , Smucler Joaquín , La Greca Alejandro , Moro Lucía , Sevlever Gustavo , Guberman Alejandra , Miriuka Santiago 
Published: May 2024

AbstractIn the mouse embryo, the transition from the preimplantation to the postimplantation epiblast is governed by changes in the gene regulatory network (GRN) that lead to transcriptional, epigenetic, and functional changes. This transition can be faithfully recapitulated in vitro by the differentiation of mouse embryonic stem cells (mESCs) to epiblast-like cells (EpiLCs), that reside in naïve and formative states of pluripotency, respectively. However, the GRN that drives this conversion is not fully elucidated. Here we demonstrate that the transcription factor OCT6 is a key driver of this process. Firstly, we show that Oct6 is not expressed in mESCs but is rapidly induced as cells exit the naïve pluripotent state. By deleting Oct6 in mESCs, we find that knockout cells fail to acquire the typical morphological changes associated with the formative state when induced to differentiate. Additionally, the key naïve pluripotency TFs Nanog, Klf2, Nr5a2, Prdm14, and Esrrb were expressed at higher levels than in wild-type cells, indicating an incomplete dismantling of the naïve pluripotency GRN. Conversely, premature expression of Oct6 in naïve cells triggered a rapid morphological transformation mirroring differentiation, that was accompanied by the upregulation of the endogenous Oct6 as well as the formative genes Sox3, Zic2/3, Foxp1, Dnmt3A and FGF5. Strikingly, we found that OCT6 represses Nanog in a bistable manner and that this regulation is at the transcriptional level. Moreover, our findings also reveal that Oct6 is repressed by NANOG. Collectively, our results establish OCT6 as a key TF in the dissolution of the naïve pluripotent state and support a model where Oct6 and Nanog form a double negative feedback loop which could act as an important toggle mediating the transition to the formative state.
Population structure and spatial distribution of Mycobacterium tuberculosis in Ethiopia
Authors: Getahun Muluwork , Beyene Dereje , Mollalign Hilina , Diriba Getu , Tesfaye Ephrem , Yenew Bazezew , Taddess Mengistu , Sinshaw Waganeh , Ameni Gobena 
Published: May 2024

AbstractEthiopia is one of the countries with a high tuberculosis (TB) burden, yet little is known about the spatial distribution of Mycobacterium tuberculosis (Mtb) lineages. This study identifies the spoligotyping of 1735 archived Mtb isolates from the National Drug Resistance Survey, collected between November 2011 and June 2013, to investigate Mtb population structure and spatial distribution. Spoligotype International Types (SITs) and lineages were retrieved from online databases. The distribution of lineages was evaluated using Fisher’s exact test and logistic regression models. The Global Moran’s Index and Getis-Ord Gi statistic were utilized to identify hotspot areas. Our results showed that spoligotypes could be interpreted and led to 4 lineages and 283 spoligotype patterns in 91% of the isolates, including 4% of those with multidrug/rifampicin resistance (MDR/RR) TB. The identified Mtb lineages were lineage 1 (1.8%), lineage 3 (25.9%), lineage 4 (70.6%) and lineage 7 (1.6%). The proportion of lineages 3 and 4 varied by regions, with lineage 3 being significantly greater than lineage 4 in reports from Gambella (AOR = 4.37, P < 0.001) and Tigray (AOR = 3.44, P = 0.001) and lineage 4 being significantly higher in Southern Nations Nationalities and Peoples Region (AOR = 1.97, P = 0.026) than lineage 3. Hotspots for lineage 1 were located in eastern Ethiopia, while a lineage 7 hotspot was identified in northern and western Ethiopia. The five prevalent spoligotypes, which were SIT149, SIT53, SIT25, SIT37 and SIT26 account for 42.8% of all isolates under investigation, while SIT149, SIT53 and SIT21 account for 52–57.8% of drug-resistant TB cases. TB and drug resistant TB are mainly caused by lineages 3 and 4, and significant proportions of the prevalent spoligotypes also influence drug-resistant TB and the total TB burden. Regional variations in lineages may result from both local and cross-border spread.
Determinants of nutritional status of children aged 6–59 months in the case of Itang special woreda, Gambella, Ethiopia
Authors: Alemu Chekol , Wudu Habitamu , Abeje Meseret 
Published: May 2024

AbstractNutritional status is one of the most important causes of improper physical and mental development in children. The study attempts to assess the factors affecting the severity status of children aged 6–59 months’ malnutrition based on the weight-for-age anthropometric index (z-score) and examine between-kebeles-level differences in determinants of the nutritional status of children. A community-based, cross-sectional study design was conducted from October 12 to November 12, 2022. A sample of 397 children aged 6–59 months primary data by applying multi–stage clustered sampling technique was used by considering their heterogeneity. The data were entered by SPSS and analyzed by using R version 3.4.0 and STATA 14.2 statistical software package using a multilevel ordinal logistic regression model and inferences were conducted at a 5% significance level. The results show that birth interval ≥ 24 months (OR = 1.431253, 95% CI 1.221337 1.6763421, P-value = 0.008), economic status of households medium (OR = 16.21466, 95% CI 1.221403 1.423929, P-value = 0.000), economic status of households rich (OR = 223.2856, 95% CI 1.34295 2.582325, P-value = 0.000), employment status of the mother unemployed (OR = 0.2291348, 95% CI 0.0529511 0.9966281, P-value = 0.049), No toilet facility (bush field) (OR = 0.3163329, 95% CI 0.1825356 0.5481975, P-value = 0.000), number of household members (OR = 0.9100682, 95% CI 0.8313481 0.9967315, P-value = 0.042), breastfeeding < 12 months (OR = 0.53803, 95% CI 0.322315 0.898135, P-value = 0.018), educational level of father Primary (OR = 4.601687, 95% CI 1.758009 2.22053, P-value = 0.000), educational level of father Secondary above (OR = 99.65229, 95% CI 2.533502 4.788896, P-value = 0.000) and geographical area (kebeles) were found to be important factors that affect a child's nutritional status between 6 and 59 months. 15% of the overall variation is attributable to the Kebeles level, according to two-level multilevel ordinal logistic regressions with estimates of the variation attributable to the Kebeles level equal to 0.569 and an intraclass correlation coefficient of 0.15. Due to the nature of the response variable random intercept model with random coefficients fitted the data adequately in predicting the severity status of children aged 6–59 months’ malnutrition for the multilevel ordinal logistic regression model analysis. So, the researcher recommended that implementing primary health care and nutrition programs that would fit each kebeles’ features in Itang Special Woreda to safeguard children from nutritional deficiency.
Observing astrocyte polarization in brains from mouse chronically infected with Toxoplasma gondii
Authors: Yao Yong , Yuan Yaping , Sheng Shuyan , Li Yifan , Tang Xiaoniu , Gu Hao 
Published: May 2024

AbstractToxoplasma gondii (T. gondii) is a protozoan parasite that infects approximately one-third of the global human population, often leading to chronic infection. While acute T. gondii infection can cause neural damage in the central nervous system and result in toxoplasmic encephalitis, the consequences of T. gondii chronic infection (TCI) are generally asymptomatic. However, emerging evidence suggests that TCI may be linked to behavioral changes or mental disorders in hosts. Astrocyte polarization, particularly the A1 subtype associated with neuronal apoptosis, has been identified in various neurodegenerative diseases. Nevertheless, the role of astrocyte polarization in TCI still needs to be better understood. This study aimed to establish a mouse model of chronic TCI and examine the transcription and expression levels of glial fibrillary acidic protein (GFAP), C3, C1q, IL-1α, and TNF-α in the brain tissues of the mice. Quantitative real-time PCR (qRT-PCR), enzyme-linked immunosorbent assay, and Western blotting were employed to assess these levels. Additionally, the expression level of the A1 astrocyte-specific marker C3 was evaluated using indirect fluorescent assay (IFA). In mice with TCI, the transcriptional and expression levels of the inflammatory factors C1q, IL-1α, and TNF-α followed an up-down-up pattern, although they remained elevated compared to the control group. These findings suggest a potential association between astrocyte polarization towards the A1 subtype and synchronized changes in these three inflammatory mediators. Furthermore, immunofluorescence assay (IFA) revealed a significant increase in the A1 astrocytes (GFAP+C3+) proportion in TCI mice. This study provides evidence that TCI can induce astrocyte polarization, a biological process that may be influenced by changes in the levels of three inflammatory factors: C1q, IL-1α, and TNF-α. Additionally, the release of neurotoxic substances by A1 astrocytes may be associated with the development of TCI.