bluuebunny/crossref_metadata_2025_split huggingface dataset:
An anti-CRISPR that represses its own transcription while blocking Cas9-target DNA binding
Authors: Deng Xieshuting , Sun Wei , Li Xueyan , Wang Jiuyu , Cheng Zhi , Sheng Gang , Wang Yanli 
Published: February 2024

AbstractAcrIIA15 is an anti-CRISPR (Acr) protein that inhibits Staphylococcus aureus Cas9 (SaCas9). Although previous studies suggested it has dual functions, the structural and biochemical basis for its two activities remains unclear. Here, we determined the cryo-EM structure of AcrIIA15 in complex with SaCas9-sgRNA to reveal the inhibitory mechanism of the Acr’s C-terminal domain (CTD) in mimicking dsDNA to block protospacer adjacent motif (PAM) recognition. For the N-terminal domain (NTD), our crystal structures of the AcrIIA15-promoter DNA show that AcrIIA15 dimerizes through its NTD to recognize double-stranded (ds) DNA. Further, AcrIIA15 can simultaneously bind to both SaCas9-sgRNA and promoter DNA, creating a supercomplex of two Cas9s bound to two CTDs converging on a dimer of the NTD bound to a dsDNA. These findings shed light on AcrIIA15’s inhibitory mechanisms and its autoregulation of transcription, enhancing our understanding of phage-host interactions and CRISPR defense.
Tuning light-driven oxidation of styrene inside water-soluble nanocages
Authors: Ghosal Souvik , Das Ankita , Roy Debojyoti , Dasgupta Jyotishman 
Published: February 2024

AbstractSelective functionalization of innate sp2 C-H bonds under ambient conditions is a grand synthetic challenge in organic chemistry. Here we combine host-guest charge transfer-based photoredox chemistry with supramolecular nano-confinement to achieve selective carbonylation of styrene by tuning the dioxygen concentration. We observe exclusive photocatalytic formation of benzaldehyde under excess O2 (>1 atm) while Markovnikov addition of water produced acetophenone in deoxygenated condition upon photoexcitation of confined styrene molecules inside a water-soluble cationic nanocage. Further by careful tuning of the nanocage size, electronics, and guest preorganization, we demonstrate rate enhancement of benzaldehyde formation and a complete switchover to the anti-Markovnikov product, 2-phenylethan-1-ol, in the absence of O2. Raman spectroscopy, 2D 1H-1H NMR correlation experiments, and transient absorption spectroscopy establish that the site-selective control on the confined photoredox chemistry originates from an optimal preorganization of styrene molecules inside the cavity. We envision that the demonstrated host-guest charge transfer photoredox paradigm in combination with green atom-transfer reagents will enable a broad range of sp2 carbon-site functionalization.
Geographic range of plants drives long-term climate change
Authors: Gurung Khushboo , Field Katie J. , Batterman Sarah A. , Poulton Simon W. , Mills Benjamin J. W. 
Published: February 2024

AbstractLong computation times in vegetation and climate models hamper our ability to evaluate the potentially powerful role of plants on weathering and carbon sequestration over the Phanerozoic Eon. Simulated vegetation over deep time is often homogenous, and disregards the spatial distribution of plants and the impact of local climatic variables on plant function. Here we couple a fast vegetation model (FLORA) to a spatially-resolved long-term climate-biogeochemical model (SCION), to assess links between plant geographical range, the long-term carbon cycle and climate. Model results show lower rates of carbon fixation and up to double the previously predicted atmospheric CO2 concentration due to a limited plant geographical range over the arid Pangea supercontinent. The Mesozoic dispersion of the continents increases modelled plant geographical range from 65% to > 90%, amplifying global CO2 removal, consistent with geological data. We demonstrate that plant geographical range likely exerted a major, under-explored control on long-term climate change.
Field-free spin–orbit torque switching in ferromagnetic trilayers at sub-ns timescales
Authors: Yang Qu , Han Donghyeon , Zhao Shishun , Kang Jaimin , Wang Fei , Lee Sung-Chul , Lei Jiayu , Lee Kyung-Jin , Park Byong-Guk , Yang Hyunsoo 
Published: February 2024

AbstractCurrent-induced spin torques enable the electrical control of the magnetization with low energy consumption. Conventional magnetic random access memory (MRAM) devices rely on spin-transfer torque (STT), this however limits MRAM applications because of the nanoseconds incubation delay and associated endurance issues. A potential alternative to STT is spin-orbit torque (SOT). However, for practical, high-speed SOT devices, it must satisfy three conditions simultaneously, i.e., field-free switching at short current pulses, short incubation delay, and low switching current. Here, we demonstrate field-free SOT switching at sub-ns timescales in a CoFeB/Ti/CoFeB ferromagnetic trilayer, which satisfies all three conditions. In this trilayer, the bottom magnetic layer or its interface generates spin currents with polarizations in both in-plane and out-of-plane components. The in-plane component reduces the incubation time, while the out-of-plane component realizes field-free switching at a low current. Our results offer a field-free SOT solution for energy-efficient scalable MRAM applications.
Synthesis and superconductivity in yttrium-cerium hydrides at high pressures
Authors: Chen Liu-Cheng , Luo Tao , Cao Zi-Yu , Dalladay-Simpson Philip , Huang Ge , Peng Di , Zhang Li-Li , Gorelli Federico Aiace , Zhong Guo-Hua , Lin Hai-Qing , Chen Xiao-Jia 
Published: February 2024

AbstractFurther increasing the critical temperature and/or decreasing the stabilized pressure are the general hopes for the hydride superconductors. Inspired by the low stabilized pressure associated with Ce 4f electrons in superconducting cerium superhydride and the high critical temperature in yttrium superhydride, we carry out seven independent runs to synthesize yttrium-cerium alloy hydrides. The synthetic process is examined by the Raman scattering and X-ray diffraction measurements. The superconductivity is obtained from the observed zero-resistance state with the detected onset critical temperatures in the range of 97-141 K. The upper critical field towards 0 K at pressure of 124 GPa is determined to be between 56 and 78 T by extrapolation of the results of the electrical transport measurements at applied magnetic fields. The analysis of the structural data and theoretical calculations suggest that the phase of Y0.5Ce0.5H9 in hexagonal structure with the space group of P63/mmc is stable in the studied pressure range. These results indicate that alloying superhydrides indeed can maintain relatively high critical temperature at relatively modest pressures accessible by laboratory conditions.
Data leakage inflates prediction performance in connectome-based machine learning models
Authors: Rosenblatt Matthew , Tejavibulya Link , Jiang Rongtao , Noble Stephanie , Scheinost Dustin 
Published: February 2024

AbstractPredictive modeling is a central technique in neuroimaging to identify brain-behavior relationships and test their generalizability to unseen data. However, data leakage undermines the validity of predictive models by breaching the separation between training and test data. Leakage is always an incorrect practice but still pervasive in machine learning. Understanding its effects on neuroimaging predictive models can inform how leakage affects existing literature. Here, we investigate the effects of five forms of leakage–involving feature selection, covariate correction, and dependence between subjects–on functional and structural connectome-based machine learning models across four datasets and three phenotypes. Leakage via feature selection and repeated subjects drastically inflates prediction performance, whereas other forms of leakage have minor effects. Furthermore, small datasets exacerbate the effects of leakage. Overall, our results illustrate the variable effects of leakage and underscore the importance of avoiding data leakage to improve the validity and reproducibility of predictive modeling.
Prediction of ambient pressure conventional superconductivity above 80 K in hydride compounds
Authors: Sanna Antonio , Cerqueira Tiago F. T. , Fang Yue-Wen , Errea Ion , Ludwig Alfred , Marques Miguel A. L. 
Published: February 2024

AbstractThe primary challenge in the field of high-temperature superconductivity in hydrides is to achieve a superconducting state at ambient pressure rather than the extreme pressures that have been required in experiments so far. Here, we propose a family of compounds, of composition Mg2XH6 with X = Rh, Ir, Pd, or Pt, that achieves this goal. These materials were identified by scrutinizing more than a million compounds using a machine-learning accelerated high-throughput workflow. We predict that their superconducting transition temperatures are in the range of 45–80 K, or even above 100 K with appropriate electron doping of the Pt compound. These results indicate that, although very rare, high-temperature superconductivity in hydrides is achievable at room pressure.
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation
Authors: Weerakoon Harshi , Mohamed Ahmed , Wong Yide , Chen Jinjin , Senadheera Bhagya , Haigh Oscar , Watkins Thomas S. , Kazakoff Stephen , Mukhopadhyay Pamela , Mulvenna Jason , Miles John J. , Hill Michelle M. , Lepletier Ailin 
Published: February 2024

AbstractEngagement of the T cell receptor (TCR) triggers molecular reprogramming leading to the acquisition of specialized effector functions by CD4 helper and CD8 cytotoxic T cells. While transcription factors, chemokines, and cytokines are known drivers in this process, the temporal proteomic and transcriptomic changes that regulate different stages of human primary T cell activation remain to be elucidated. Here, we report an integrative temporal proteomic and transcriptomic analysis of primary human CD4 and CD8 T cells following ex vivo stimulation with anti-CD3/CD28 beads, which revealed major transcriptome-proteome uncoupling. The early activation phase in both CD4 and CD8 T cells was associated with transient downregulation of the mRNA transcripts and protein of the central glucose transport GLUT1. In the proliferation phase, CD4 and CD8 T cells became transcriptionally more divergent while their proteome became more similar. In addition to the kinetics of proteome-transcriptome correlation, this study unveils selective transcriptional and translational metabolic reprogramming governing CD4 and CD8 T cell responses to TCR stimulation. This temporal transcriptome/proteome map of human T cell activation provides a reference map exploitable for future discovery of biomarkers and candidates targeting T cell responses.
Changes in vaccine attitudes and recommendations among US Healthcare Personnel during the COVID-19 pandemic
Authors: Dudley Matthew Z. , Schuh Holly B. , Forr Amanda , Shaw Jana , Salmon Daniel A. 
Published: February 2024

AbstractA recommendation from healthcare personnel (HCP) is a strong predictor of vaccination. This study aimed to measure how HCP vaccine attitudes and recommendations changed during the COVID-19 pandemic. HCP were surveyed in January 2023 using a double opt-in network panel. Survey responses were summarized and stratified by HCP type and COVID-19 booster status. Multivariable logistic regression models were fitted. Comparisons were made to a September 2021 survey, with differences tested for significance (p < 0.05) using Pearson’s χ2 Test. Nearly 82% of the 1207 HCP surveyed had received a COVID-19 booster, most commonly pediatricians (94%), followed by family medicine doctors (87%), pharmacists (74%), and nurses (73%) (p < 0.01). HCP with high trust in the Centers for Disease Control and Prevention (CDC) had nearly 6 times the odds (OR: 5.5; 95%CI: 3.9–7.7) of being boosted compared to HCP with low trust. From September 2021 to January 2023, the proportion of HCP recommending vaccines (COVID-19 and routine) to their patients decreased substantially for nearly all vaccines and patient populations specified. Trust in CDC also decreased (from 79 to 73%, p < 0.01), as did support for HCP COVID-19 vaccine mandates (from 65 to 46%, p < 0.01). HCP interest in additional online resources to improve their vaccine discussions with patients increased from 46 to 66% (p < 0.01). Additional regularly updated online resources from trusted medical sources that clarify progressing science and address dynamic public concerns are needed to improve vaccine confidence among HCP and help them support their patients’ decision-making.
GEOWEALTH-US: Spatial wealth inequality data for the United States, 1960–2020
Authors: Suss Joel , Kemeny Tom , Connor Dylan S. 
Published: February 2024

AbstractWealth inequality has been sharply rising in the United States and across many other high-income countries. Due to a lack of data, we know little about how this trend has unfolded across locations within countries. Examining the subnational geography of wealth is crucial because, from one generation to the next, it shapes the distribution of opportunity, disadvantage, and power across individuals and communities. By employing machine-learning-based imputation to link national historical surveys conducted by the U.S. Federal Reserve to population survey microdata, the data presented in this article addresses this gap. The Geographic Wealth Inequality Database (“GEOWEALTH-US”) provides the first estimates of the level and distribution of wealth at various geographical scales within the United States from 1960 to 2020. The GEOWEALTH-US database enables new lines of investigation into the contribution of spatial wealth disparities to major societal challenges including wealth concentration, income inequality, social mobility, housing unaffordability, and political polarization.
City-level livestock methane emissions in China from 2010 to 2020
Authors: Du Mingxi , Kang Xiang , Liu Qiuyu , Du Haifeng , Zhang Jianjun , Yin Yulong , Cui Zhenling 
Published: February 2024

AbstractLivestock constitute the world’s largest anthropogenic source of methane (CH4), providing high-protein food to humans but also causing notable climate risks. With rapid urbanization and increasing income levels in China, the livestock sector will face even higher emission pressures, which could jeopardize China’s carbon neutrality target. To formulate targeted methane reduction measures, it is crucial to estimate historical and current emissions on fine geographical scales, considering the high spatial heterogeneity and temporal variability of livestock emissions. However, there is currently a lack of time-series data on city-level livestock methane emissions in China, despite the flourishing livestock industry and large amount of meat consumed. In this study, we constructed a city-level livestock methane emission inventory with dynamic spatial-temporal emission factors considering biological, management, and environmental factors from 2010 to 2020 in China. This inventory could serve as a basic database for related research and future methane mitigation policy formulation, given the population boom and dietary changes.
A multiomics dataset for the study of RNA modifications in human macrophage differentiation and polarisation
Authors: Pinello Natalia , Song Renhua , Lee Quintin , Calonne Emilie , Larance Mark , Fuks François , Wong Justin J. -L. 
Published: February 2024

AbstractRNA modifications have emerged as central regulators of gene expression programs. Amongst RNA modifications are N6-methyladenosine (m6A) and RNA 5-hydroxymethylcytosine (5hmC). While m6A is established as a versatile regulator of RNA metabolism, the functions of RNA 5hmC are unclear. Despite some evidence linking RNA modifications to immunity, their implications in gene expression control in macrophage development and functions remain unclear. Here we present a multi-omics dataset capturing different layers of the gene expression programs driving macrophage differentiation and polarisation. We obtained mRNA-Seq, m6A-IP-Seq, 5hmC-IP-Seq, Polyribo-Seq and LC-MS/MS data from monocytes and resting-, pro- and anti-inflammatory-like macrophages. We present technical validation showing high quality and correlation between samples for all datasets, and evidence of biological consistency of modelled macrophages at the transcriptomic, epitranscriptomic, translational and proteomic levels. This multi-omics dataset provides a resource for the study of RNA m6A and 5hmC in the context of macrophage biology and spans the gene expression process from transcripts to proteins.
Phenotypic characterisation of regulatory T cells in patients with gestational diabetes mellitus
Authors: Zhang Ya-nan , Wu Qin , Deng Yi-hui 
Published: February 2024

AbstractGestational diabetes mellitus (GDM) is a common complication that occurs during pregnancy. Emerging evidence suggests that immune abnormalities play a pivotal role in the development of GDM. Specifically, regulatory T cells (Tregs) are considered a critical factor in controlling maternal–fetal immune tolerance. However, the specific characteristics and alterations of Tregs during the pathogenesis of GDM remain poorly elucidated. Therefore, this study aimed to investigate the changes in Tregs among pregnant women diagnosed with GDM compared to healthy pregnant women. A prospective study was conducted, enrolling 23 healthy pregnant women in the third trimester and 21 third-trimester women diagnosed with GDM. Participants were followed up until the postpartum period. The proportions of various Treg, including Tregs, mTregs, and nTregs, were detected in the peripheral blood of pregnant women from both groups. Additionally, the expression levels of PD-1, HLA-G, and HLA-DR on these Tregs were examined. The results revealed no significant differences in the proportions of Tregs, mTregs, and nTregs between the two groups during the third trimester and postpartum period. However, GDM patients exhibited significantly reduced levels of PD-1+ Tregs (P < 0.01) and HLA-G+ Tregs (P < 0.05) in the third trimester compared to healthy pregnant women in the third trimester. Furthermore, GDM patients demonstrated significantly lower levels of PD-1+ mTregs (P < 0.01) and HLA-G+ (P < 0.05) mTregs compared to healthy pregnant women in the third trimester. Overall, the proportion of Tregs did not exhibit significant changes during the third trimester in GDM patients compared to healthy pregnant women. Nevertheless, the observed dysregulation of immune regulation function in Tregs and mTregs may be associated with the development of GDM in pregnant women.
Electrically-driven modulation of flow patterns in liquid crystal microfludics
Authors: Fedorowicz Kamil , Prosser Robert 
Published: February 2024

AbstractThe flow of liquid crystals in the presence of electric fields is investigated as a possible means of flow control. The Beris-Edwards model is coupled to a free energy incorporating electric field effects. Simulations are conducted in straight channels and in junctions. Our findings reveal that local flow mediation can be achieved by the application of spatially varying electric fields. In rectangular straight channels, we report a two-stream velocity profile arising in response to the imposed electric field. Furthermore, we observe that the flow rate in each stream scales inversely with the Miesowicz viscosities, leading to the confinement of 70% of the throughput to one half of the channel. Similar flow partitioning is also demonstrated in channel junction geometries, where we show that using external fields provides a novel avenue for flow modulation in microfluidic circuits.
Comprehensive characterization of the structure of Zr-based metallic glasses
Authors: Lahiri Debdutta , Krishna K. V. Mani , Verma Ashok K. , Modak P. , Vishwanadh B. , Chattopadhyay Soma , Shibata Tomohiro , Sharma S. K. , Sarkar Sudip Kumar , Clifton Peter H. , Biswas A. , Garg Nandini , K.Dey G. 
Published: February 2024

AbstractStructure of metallic glasses fascinates as the generic amorphous structural template for ubiquitous systems. Its specification necessitates determination of the complete hierarchical structure, starting from short-range-order (SRO) → medium-range-order (MRO) → bulk structure and free volume (FV) distribution. This link has largely remained elusive since previous investigations adopted one-technique-at-a-time approach, focusing on limited aspects of any one domain. Reconstruction of structure from experimental data inversion is non-unique for many of these techniques. As a result, complete and precise structural understanding of glass has not emerged yet. In this work, we demonstrate the first experimental pathway for reconstruction of the integrated structure, for $${\text{Zr}}_{{{67}}} {\text{Ni}}_{{{33}}}$$

Zr
67

Ni
33

and $${\text{Zr}}_{{{52}}} {\text{Ti}}_{{6}} {\text{Al}}_{{{10}}} {\text{Cu}}_{{{18}}} {\text{Ni}}_{{{14}}}$$

Zr
52

Ti
6

Al
10

Cu
18

Ni
14

glasses. Our strategy engages diverse (× 7) multi-scale techniques [XAFS, 3D-APT, ABED/NBED, FEM, XRD, PAS, FHREM] on the same glass. This strategy complemented mutual limitations of techniques and corroborated common parameters to generate complete, self-consistent and precise parameters. Further, MRO domain size and inter-void separation were correlated to identify the presence of FV at MRO boundaries. This enabled the first experimental reconstruction of hierarchical subset: SRO → MRO → FV → bulk structure. The first ever image of intermediate region between MRO domains emerged from this link. We clarify that determination of all subsets is not our objective; the essence and novelty of this work lies in directing the pathway towards finite solution, in the most logical and unambiguous way.
Low-dose GBCA administration for brain tumour dynamic contrast enhanced MRI: a feasibility study
Authors: Lewis Daniel , Li Ka-Loh , Waqar Mueez , Coope David J. , Pathmanaban Omar N. , King Andrew T. , Djoukhadar Ibrahim , Zhao Sha , Cootes Timothy F. , Jackson Alan , Zhu Xiaoping 
Published: February 2024

AbstractA key limitation of current dynamic contrast enhanced (DCE) MRI techniques is the requirement for full-dose gadolinium-based contrast agent (GBCA) administration. The purpose of this feasibility study was to develop and assess a new low GBCA dose protocol for deriving high-spatial resolution kinetic parameters from brain DCE-MRI. Nineteen patients with intracranial skull base tumours were prospectively imaged at 1.5 T using a single-injection, fixed-volume low GBCA dose, dual temporal resolution interleaved DCE-MRI acquisition. The accuracy of kinetic parameters (ve, Ktrans, vp) derived using this new low GBCA dose technique was evaluated through both Monte-Carlo simulations (mean percent deviation, PD, of measured from true values) and an in vivo study incorporating comparison with a conventional full-dose GBCA protocol and correlation with histopathological data. The mean PD of data from the interleaved high-temporal-high-spatial resolution approach outperformed use of high-spatial, low temporal resolution datasets alone (p < 0.0001, t-test). Kinetic parameters derived using the low-dose interleaved protocol correlated significantly with parameters derived from a full-dose acquisition (p < 0.001) and demonstrated a significant association with tissue markers of microvessel density (p < 0.05). Our results suggest accurate high-spatial resolution kinetic parameter mapping is feasible with significantly reduced GBCA dose.