bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of hearing impairment in neonatal encephalopathy due to hypoxia-ischemia: a systematic review and meta-analysis
Authors: Pawale Dinesh , Fursule Anurag , Tan Jason , Wagh Deepika , Patole Sanjay , Rao Shripada 
Published: May 2024

Abstract
Background
This systematic review was undertaken to estimate the overall prevalence of hearing impairment in survivors of neonatal HIE.

Methods
PubMed, EMBASE, CINAHL, EMCARE and Cochrane databases, mednar (gray literature) were searched till January 2023. Randomized controlled trials and observational studies were included. The main outcome was estimation of overall prevalence of hearing impairment in survivors of HIE.

Results
A total of 71studies (5821 infants assessed for hearing impairment) were included of which 56 were from high income countries (HIC) and 15 from low- or middle-income countries (LMIC). Overall prevalence rate of hearing impairment in cooled infants was 5% (95% CI: 3–6%, n = 4868) and 3% (95% CI: 1–6%, n = 953) in non-cooled HIE infants. The prevalence rate in cooled HIE infants in LMICs was 7% (95% CI: 2–15%) and in HICs was 4% (95% CI: 3–5%). The prevalence rate in non-cooled HIE infants in LMICs was 8% (95% CI: 2–17%) and HICs was 2% (95% CI: 0–4%).

Conclusions
These results would be useful for counseling parents, and in acting as benchmark when comparing institutional data, and while monitoring future RCTs testing new interventions in HIE. There is a need for more data from LMICs and standardization of reporting hearing impairment.

Impact

The overall prevalence rate of hearing impairment in cooled infants with HIE was 5% (95% CI: 3–6%) and 3% (95% CI: 1–6%) in the non-cooled infants.

The prevalence rate in cooled HIE infants in LMICs was 7% (95% CI: 2–15%) and in HICs was 4% (95% CI: 3–5%).

The prevalence rate in non-cooled HIE infants in LMICs was 8% (95% CI: 2–17%) and HICs was 2% (95% CI: 0–4%).

These results would be useful for counseling parents, and in acting as benchmark when comparing institutional data, and while monitoring future RCTs testing new interventions in HIE.
DEPDC5 protects CD8+ T cells from ferroptosis by limiting mTORC1-mediated purine catabolism
Authors: Li Song , Ouyang Xinxing , Sun Hongxiang , Jin Jingsi , Chen Yao , Li Liang , Wang Qijun , He Yingzhong , Wang Jiwen , Chen Tongxin , Zhong Qing , Liang Yinming , Pierre Philippe , Zou Qiang , Ye Youqiong , Su Bing 
Published: May 2024

AbstractPeripheral CD8+ T cell number is tightly controlled but the precise molecular mechanism regulating this process is still not fully understood. In this study, we found that epilepsy patients with loss of function mutation of DEPDC5 had reduced peripheral CD8+ T cells, and DEPDC5 expression positively correlated with tumor-infiltrating CD8+ T cells as well as overall cancer patient survival, indicating that DEPDC5 may control peripheral CD8+ T cell homeostasis. Significantly, mice with T cell-specific Depdc5 deletion also had reduced peripheral CD8+ T cells and impaired anti-tumor immunity. Mechanistically, Depdc5-deficient CD8+ T cells produced high levels of xanthine oxidase and lipid ROS due to hyper-mTORC1-induced expression of ATF4, leading to spontaneous ferroptosis. Together, our study links DEPDC5-mediated mTORC1 signaling with CD8+ T cell protection from ferroptosis, thereby revealing a novel strategy for enhancing anti-tumor immunity via suppression of ferroptosis.
Integrating single cell expression quantitative trait loci summary statistics to understand complex trait risk genes
Authors: Wang Lida , Khunsriraksakul Chachrit , Markus Havell , Chen Dieyi , Zhang Fan , Chen Fang , Zhan Xiaowei , Carrel Laura , Liu Dajiang. J. , Jiang Bibo 
Published: May 2024

AbstractTranscriptome-wide association study (TWAS) is a popular approach to dissect the functional consequence of disease associated non-coding variants. Most existing TWAS use bulk tissues and may not have the resolution to reveal cell-type specific target genes. Single-cell expression quantitative trait loci (sc-eQTL) datasets are emerging. The largest bulk- and sc-eQTL datasets are most conveniently available as summary statistics, but have not been broadly utilized in TWAS. Here, we present a new method EXPRESSO (EXpression PREdiction with Summary Statistics Only), to analyze sc-eQTL summary statistics, which also integrates 3D genomic data and epigenomic annotation to prioritize causal variants. EXPRESSO substantially improves existing methods. We apply EXPRESSO to analyze multi-ancestry GWAS datasets for 14 autoimmune diseases. EXPRESSO uniquely identifies 958 novel gene x trait associations, which is 26% more than the second-best method. Among them, 492 are unique to cell type level analysis and missed by TWAS using whole blood. We also develop a cell type aware drug repurposing pipeline, which leverages EXPRESSO results to identify drug compounds that can reverse disease gene expressions in relevant cell types. Our results point to multiple drugs with therapeutic potentials, including metformin for type 1 diabetes, and vitamin K for ulcerative colitis.
Bright and durable scintillation from colloidal quantum shells
Authors: Guzelturk Burak , Diroll Benjamin T. , Cassidy James P. , Harankahage Dulanjan , Hua Muchuan , Lin Xiao-Min , Iyer Vasudevan , Schaller Richard D. , Lawrie Benjamin J. , Zamkov Mikhail 
Published: May 2024

AbstractEfficient, fast, and robust scintillators for ionizing radiation detection are crucial in various fields, including medical diagnostics, defense, and particle physics. However, traditional scintillator technologies face challenges in simultaneously achieving optimal performance and high-speed operation. Herein we introduce colloidal quantum shell heterostructures as X-ray and electron scintillators, combining efficiency, speed, and durability. Quantum shells exhibit light yields up to 70,000 photons MeV−1 at room temperature, enabled by their high multiexciton radiative efficiency thanks to long Auger-Meitner lifetimes (>10 ns). Radioluminescence is fast, with lifetimes of 2.5 ns and sub-100 ps rise times. Additionally, quantum shells do not exhibit afterglow and maintain stable scintillation even under high X-ray doses (>109 Gy). Furthermore, we showcase quantum shells for X-ray imaging achieving a spatial resolution as high as 28 line pairs per millimeter. Overall, efficient, fast, and durable scintillation make quantum shells appealing in applications ranging from ultrafast radiation detection to high-resolution imaging.
Sex-specific developmental gene expression atlas unveils dimorphic gene networks in C. elegans
Authors: Haque Rizwanul , Kurien Sonu Peedikayil , Setty Hagar , Salzberg Yehuda , Stelzer Gil , Litvak Einav , Gingold Hila , Rechavi Oded , Oren-Suissa Meital 
Published: May 2024

AbstractSex-specific traits and behaviors emerge during development by the acquisition of unique properties in the nervous system of each sex. However, the genetic events responsible for introducing these sex-specific features remain poorly understood. In this study, we create a comprehensive gene expression atlas of pure populations of hermaphrodites and males of the nematode Caenorhabditis elegans across development. We discover numerous differentially expressed genes, including neuronal gene families like transcription factors, neuropeptides, and G protein-coupled receptors. We identify INS-39, an insulin-like peptide, as a prominent male-biased gene expressed specifically in ciliated sensory neurons. We show that INS-39 serves as an early-stage male marker, facilitating the effective isolation of males in high-throughput experiments. Through complex and sex-specific regulation, ins-39 plays pleiotropic sexually dimorphic roles in various behaviors, while also playing a shared, dimorphic role in early life stress. This study offers a comparative sexual and developmental gene expression database for C. elegans. Furthermore, it highlights conserved genes that may underlie the sexually dimorphic manifestation of different human diseases.
Absolute dating of the European Neolithic using the 5259 BC rapid 14C excursion
Authors: Maczkowski Andrej , Pearson Charlotte , Francuz John , Giagkoulis Tryfon , Szidat Sönke , Wacker Lukas , Bolliger Matthias , Kotsakis Kostas , Hafner Albert 
Published: May 2024

AbstractAbrupt radiocarbon (14C) excursions, or Miyake events, in sequences of radiocarbon measurements from calendar-dated tree-rings provide opportunities to assign absolute calendar dates to undated wood samples from contexts across history and prehistory. Here, we report a tree-ring and14C-dating study of the Neolithic site of Dispilio, Northern Greece, a waterlogged archaeological site on Lake Kastoria. Findings secure an absolute, calendar-dated time using the 5259 BC Miyake event, with the final ring of the 303-year-long juniper tree-ring chronology dating to 5140 BC. While other sites have been absolutely dated to a calendar year through14C-signature Miyake events, Dispilio is the first European Neolithic site of these and it provides a fixed, calendar-year anchor point for regional chronologies of the Neolithic.
BRCA1/BARD1 ubiquitinates PCNA in unperturbed conditions to promote continuous DNA synthesis
Authors: Salas-Lloret Daniel , García-Rodríguez Néstor , Soto-Hidalgo Emily , González-Vinceiro Lourdes , Espejo-Serrano Carmen , Giebel Lisanne , Mateos-Martín María Luisa , de Ru Arnoud H. , van Veelen Peter A. , Huertas Pablo , Vertegaal Alfred C. O. , González-Prieto Román 
Published: May 2024

AbstractDeficiencies in the BRCA1 tumor suppressor gene are the main cause of hereditary breast and ovarian cancer. BRCA1 is involved in the Homologous Recombination DNA repair pathway and, together with BARD1, forms a heterodimer with ubiquitin E3 activity. The relevance of the BRCA1/BARD1 ubiquitin E3 activity for tumor suppression and DNA repair remains controversial. Here, we observe that the BRCA1/BARD1 ubiquitin E3 activity is not required for Homologous Recombination or resistance to Olaparib. Using TULIP2 methodology, which enables the direct identification of E3-specific ubiquitination substrates, we identify substrates for BRCA1/BARD1. We find that PCNA is ubiquitinated by BRCA1/BARD1 in unperturbed conditions independently of RAD18. PCNA ubiquitination by BRCA1/BARD1 avoids the formation of ssDNA gaps during DNA replication and promotes continuous DNA synthesis. These results provide additional insight about the importance of BRCA1/BARD1 E3 activity in Homologous Recombination.
The sterol C-24 methyltransferase encoding gene, erg6, is essential for viability of Aspergillus species
Authors: Xie Jinhong , Rybak Jeffrey M. , Martin-Vicente Adela , Guruceaga Xabier , Thorn Harrison I. , Nywening Ashley V. , Ge Wenbo , Parker Josie E. , Kelly Steven L. , Rogers P. David , Fortwendel Jarrod R. 
Published: May 2024

AbstractTriazoles, the most widely used class of antifungal drugs, inhibit the biosynthesis of ergosterol, a crucial component of the fungal plasma membrane. Inhibition of a separate ergosterol biosynthetic step, catalyzed by the sterol C-24 methyltransferase Erg6, reduces the virulence of pathogenic yeasts, but its effects on filamentous fungal pathogens like Aspergillus fumigatus remain unexplored. Here, we show that the lipid droplet-associated enzyme Erg6 is essential for the viability of A. fumigatus and other Aspergillus species, including A. lentulus, A. terreus, and A. nidulans. Downregulation of erg6 causes loss of sterol-rich membrane domains required for apical extension of hyphae, as well as altered sterol profiles consistent with the Erg6 enzyme functioning upstream of the triazole drug target, Cyp51A/Cyp51B. Unexpectedly, erg6-repressed strains display wild-type susceptibility against the ergosterol-active triazole and polyene antifungals. Finally, we show that erg6 repression results in significant reduction in mortality in a murine model of invasive aspergillosis. Taken together with recent studies, our work supports Erg6 as a potentially pan-fungal drug target.
Machine learning-aided first-principles calculations of redox potentials
Authors: Jinnouchi Ryosuke , Karsai Ferenc , Kresse Georg 
Published: May 2024

AbstractWe present a method combining first-principles calculations and machine learning to predict the redox potentials of half-cell reactions on the absolute scale. By applying machine learning force fields for thermodynamic integration from the oxidized to the reduced state, we achieve efficient statistical sampling over a broad phase space. Furthermore, through thermodynamic integration from machine learning force fields to potentials of semi-local functionals, and from semi-local functionals to hybrid functionals using Δ-machine learning, we refine the free energy with high precision step-by-step. Utilizing a hybrid functional that includes 25% exact exchange (PBE0), this method predicts the redox potentials of the three redox couples, Fe3+/Fe2+, Cu2+/Cu+, and Ag2+/Ag+, to be 0.92, 0.26, and 1.99 V, respectively. These predictions are in good agreement with the best experimental estimates (0.77, 0.15, 1.98 V). This work demonstrates that machine-learned surrogate models provide a flexible framework for refining the accuracy of free energy from coarse approximation methods to precise electronic structure calculations, while also facilitating sufficient statistical sampling.
A quantum coherent spin in hexagonal boron nitride at ambient conditions
Authors: Stern Hannah L. , M. Gilardoni Carmem , Gu Qiushi , Eizagirre Barker Simone , Powell Oliver F. J. , Deng Xiaoxi , Fraser Stephanie A. , Follet Louis , Li Chi , Ramsay Andrew J. , Tan Hark Hoe , Aharonovich Igor , Atatüre Mete 
Published: May 2024

AbstractSolid-state spin–photon interfaces that combine single-photon generation and long-lived spin coherence with scalable device integration—ideally under ambient conditions—hold great promise for the implementation of quantum networks and sensors. Despite rapid progress reported across several candidate systems, those possessing quantum coherent single spins at room temperature remain extremely rare. Here we report quantum coherent control under ambient conditions of a single-photon-emitting defect spin in a layered van der Waals material, namely, hexagonal boron nitride. We identify that the carbon-related defect has a spin-triplet electronic ground-state manifold. We demonstrate that the spin coherence is predominantly governed by coupling to only a few proximal nuclei and is prolonged by decoupling protocols. Our results serve to introduce a new platform to realize a room-temperature spin qubit coupled to a multiqubit quantum register or quantum sensor with nanoscale sample proximity.
In vitro reconstitution of epigenetic reprogramming in the human germ line
Authors: Murase Yusuke , Yokogawa Ryuta , Yabuta Yukihiro , Nagano Masahiro , Katou Yoshitaka , Mizuyama Manami , Kitamura Ayaka , Puangsricharoen Pimpitcha , Yamashiro Chika , Hu Bo , Mizuta Ken , Tsujimura Taro , Yamamoto Takuya , Ogata Kosuke , Ishihama Yasushi , Saitou Mitinori 
Published: May 2024

AbstractEpigenetic reprogramming resets parental epigenetic memories and differentiates primordial germ cells (PGCs) into mitotic pro-spermatogonia or oogonia. This process ensures sexually dimorphic germ cell development for totipotency1. In vitro reconstitution of epigenetic reprogramming in humans remains a fundamental challenge. Here we establish a strategy for inducing epigenetic reprogramming and differentiation of pluripotent stem-cell-derived human PGC-like cells (hPGCLCs) into mitotic pro-spermatogonia or oogonia, coupled with their extensive amplification (about >1010-fold). Bone morphogenetic protein (BMP) signalling is a key driver of these processes. BMP-driven hPGCLC differentiation involves attenuation of the MAPK (ERK) pathway and both de novo and maintenance DNA methyltransferase activities, which probably promote replication-coupled, passive DNA demethylation. hPGCLCs deficient in TET1, an active DNA demethylase abundant in human germ cells2,3, differentiate into extraembryonic cells, including amnion, with de-repression of key genes that bear bivalent promoters. These cells fail to fully activate genes vital for spermatogenesis and oogenesis, and their promoters remain methylated. Our study provides a framework for epigenetic reprogramming in humans and an important advance in human biology. Through the generation of abundant mitotic pro-spermatogonia and oogonia-like cells, our results also represent a milestone for human in vitro gametogenesis research and its potential translation into reproductive medicine.
Non-invasive spinal cord electrical stimulation for arm and hand function in chronic tetraplegia: a safety and efficacy trial
Authors: Moritz Chet , Field-Fote Edelle C. , Tefertiller Candace , van Nes Ilse , Trumbower Randy , Kalsi-Ryan Sukhvinder , Purcell Mariel , Janssen Thomas W. J. , Krassioukov Andrei , Morse Leslie R. , Zhao Kristin D. , Guest James , Marino Ralph J. , Murray Lynda M. , Wecht Jill M. , Rieger Markus , Pradarelli Jared , Turner Amanda , D’Amico Jessica , Squair Jordan W. , Courtine Gregoire 
Published: May 2024

AbstractCervical spinal cord injury (SCI) leads to permanent impairment of arm and hand functions. Here we conducted a prospective, single-arm, multicenter, open-label, non-significant risk trial that evaluated the safety and efficacy of ARCEX Therapy to improve arm and hand functions in people with chronic SCI. ARCEX Therapy involves the delivery of externally applied electrical stimulation over the cervical spinal cord during structured rehabilitation. The primary endpoints were safety and efficacy as measured by whether the majority of participants exhibited significant improvement in both strength and functional performance in response to ARCEX Therapy compared to the end of an equivalent period of rehabilitation alone. Sixty participants completed the protocol. No serious adverse events related to ARCEX Therapy were reported, and the primary effectiveness endpoint was met. Seventy-two percent of participants demonstrated improvements greater than the minimally important difference criteria for both strength and functional domains. Secondary endpoint analysis revealed significant improvements in fingertip pinch force, hand prehension and strength, upper extremity motor and sensory abilities and self-reported increases in quality of life. These results demonstrate the safety and efficacy of ARCEX Therapy to improve hand and arm functions in people living with cervical SCI. ClinicalTrials.gov identifier: NCT04697472.
The BELSAR dataset: Mono- and bistatic full-pol L-band SAR for agriculture and hydrology
Authors: Bouchat Jean , Tronquo Emma , Orban Anne , de Macedo Karlus A. C. , Davidson Malcolm , Verhoest Niko E. C. , Defourny Pierre 
Published: May 2024

AbstractThe BELSAR dataset consists of high-resolution multitemporal airborne mono- and bistatic fully-polarimetric synthetic aperture radar (SAR) data in L-band, alongside concurrent measurements of vegetation and soil biogeophysical variables measured in maize and winter wheat fields during the summer of 2018 in Belgium. Its collection was funded by the European Space Agency (ESA) to address the lack of publicly-accessible experimental datasets combining multistatic SAR and in situ measurements. As such, it offers an opportunity to advance the development of SAR remote sensing science and applications for agricultural monitoring and hydrology. This paper aims to facilitate its adoption and exploration by offering comprehensive documentation and integrating its multiple data sources into a unified, analysis-ready dataset.
A large and diverse brain organoid dataset of 1,400 cross-laboratory images of 64 trackable brain organoids
Authors: Schröter Julian , Deininger Luca , Lupse Blaz , Richter Petra , Syrbe Steffen , Mikut Ralf , Jung-Klawitter Sabine 
Published: May 2024

AbstractBrain organoids represent a useful tool for modeling of neurodevelopmental disorders and can recapitulate brain volume alterations such as microcephaly. To monitor organoid growth, brightfield microscopy images are frequently used and evaluated manually which is time-consuming and prone to observer-bias. Recent software applications for organoid evaluation address this issue using classical or AI-based methods. These pipelines have distinct strengths and weaknesses that are not evident to external observers. We provide a dataset of more than 1,400 images of 64 trackable brain organoids from four clones differentiated from healthy and diseased patients. This dataset is especially powerful to test and compare organoid analysis pipelines because of (1) trackable organoids (2) frequent imaging during development (3) clone diversity (4) distinct clone development (5) cross sample imaging by two different labs (6) common imaging distractors, and (6) pixel-level ground truth organoid annotations. Therefore, this dataset allows to perform differentiated analyses to delineate strengths, weaknesses, and generalizability of automated organoid analysis pipelines as well as analysis of clone diversity and similarity.
The role of non-uniform magnetization texture for magnon–magnon coupling in an antidot lattice
Authors: Moalic Mathieu , Zelent Mateusz , Szulc Krzysztof , Krawczyk Maciej 
Published: May 2024

AbstractWe numerically study the spin-wave dynamics in an antidot lattice based on a Co/Pd multilayer structure with reduced perpendicular magnetic anisotropy at the edges of the antidots. This structure forms a magnonic crystal with a periodic antidot pattern and a periodic magnetization configuration consisting of out-of-plane magnetized bulk and in-plane magnetized rims. Our results show a different behavior of spin waves in the bulk and in the rims under varying out-of-plane external magnetic field strength, revealing complex spin-wave spectra and hybridizations between the modes of these two subsystems. A particularly strong magnon–magnon coupling, due to exchange interactions, is found between the fundamental bulk spin-wave mode and the second-order radial rim modes. However, the dynamical coupling between the spin-wave modes at low frequencies, involving the first-order radial rim modes, is masked by the changes in the static magnetization at the bulk–rim interface with magnetic field changes. The study expands the horizons of magnonic-crystal research by combining periodic structural patterning and non-collinear magnetization texture to achieve strong magnon–magnon coupling, highlighting the significant role of exchange interactions in the hybridization.