bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thrombocytopenia as a prognostic marker in COVID-19 patients: diagnostic test accuracy meta-analysis
Authors: Pranata Raymond , Lim Michael Anthonius , Yonas Emir , Huang Ian , Nasution Sally Aman , Setiati Siti , Alwi Idrus , Kuswardhani Raden Ayu Tuty 
Published: January 2021

Abstract
This systematic review and meta-analysis aimed to evaluate thrombocytopenia as a prognostic biomarker in patients with coronavirus disease 2019 (COVID-19). We performed a systematic literature search using PubMed, Embase and EuropePMC. The main outcome was composite poor outcome, a composite of mortality, severity, need for intensive care unit care and invasive mechanical ventilation. There were 8963 patients from 23 studies. Thrombocytopenia occurred in 18% of the patients. Male gender (P = 0.037) significantly reduce the incidence. Thrombocytopenia was associated with composite poor outcome (RR 1.90 (1.43–2.52), P < 0.001; I2: 92.3%). Subgroup analysis showed that thrombocytopenia was associated with mortality (RR 2.34 (1.23–4.45), P < 0.001; I2: 96.8%) and severity (RR 1.61 (1.33–1.96), P < 0.001; I2: 62.4%). Subgroup analysis for cut-off <100 × 109/l showed RR of 1.93 (1.37–2.72), P < 0.001; I2: 83.2%). Thrombocytopenia had a sensitivity of 0.26 (0.18–0.36), specificity of 0.89 (0.84–0.92), positive likelihood ratio of 2.3 (1.6–3.2), negative likelihood ratio of 0.83 (0.75–0.93), diagnostic odds ratio of 3 (2, 4) and area under curve of 0.70 (0.66–0.74) for composite poor outcome. Meta-regression analysis showed that the association between thrombocytopenia and poor outcome did not vary significantly with age, male, lymphocyte, d-dimer, hypertension, diabetes and CKD. Fagan's nomogram showed that the posterior probability of poor outcome was 50% in patients with thrombocytopenia, and 26% in those without thrombocytopenia. The Deek's funnel plot was relatively symmetrical and the quantitative asymmetry test was non-significant (P = 0.14). This study indicates that thrombocytopenia was associated with poor outcome in patients with COVID-19.
PROSPERO ID: CRD42020213974
Star formation efficiency of magnetized, turbulent and rotating molecular cloud
Authors: Kumssa Gemechu M. , Tessema Solomon Belay 
Published: January 2021

AbstractThe formation of stars constitutes one of the basic problems in astrophysics. Understanding star formation efficiency of molecular clouds (MCs) of a galaxy is necessary for studying the galactic evolution. Present data and theoretical formulations show that the structure and dynamics of the interstellar medium (ISM) are extremely complex. Therefore, there is no simple model that can explain adequately the star formation efficiency of MCs because of its complex nature. The initial mass of the cloud needed for collapse varies based on the environment in which the cloud resides and the strength of its magnetic field, turbulence, as well as the speed of rotation. In this paper, we estimate the star formation efficiency by combining pre-determined models and the critical mass formulated by Kumssa & Tessema (2018).
HORACE'S MONUMENT
Authors: Woodman A. J. 
Published: January 2021

Exegi monumentum aere perenniusregalique situ pyramidum altius,quod non imber edax, non Aquilo impotenspossit diruere aut innumerabilisannorum series et fuga temporum.Horace,Odes3.30.1–5I have finished a monument more durable than bronze and higher than the royalsitusof the pyramids, the kind which neither biting rain nor the uncontrolled North Wind can destroy, or the procession of unnumbered years or flying time.The paper argues thataltiusin line 2 is variously inappropriate; a clue to the true reading is to be found in the passage of Pindar to which Horace is alluding.
Lateral Variations of Moho Depth and Average Crustal Properties Across the Taiwan Orogen From H‐V Stacking of P and S Receiver Functions
Authors: Goyal Ayush , Hung Shu‐Huei 
Published: January 2021

AbstractThe complexity of the young Taiwan orogen mainly resulting from arc‐continent collision is manifold. As the Moho and crustal properties are crucial to unravel the still‐debated orogenic models, we adopt a H‐V stacking method jointly utilizing P and S receiver functions for simultaneously reliable determination of crustal thickness and average P‐ and S‐wave velocity, their ratio (Vp/Vs), and bulk sound speed (Vb) beneath 50 stations in Taiwan and offshore islands. Results indicate the Moho is inclined from ∼20 km in the north and west coastal areas to ∼47 km in the midwest of the Central Range (CR), and abruptly elevated >25 km at the eastern edge of the CR and adjacent collision suture zone. The uplifted Moho along with exclusively high Vp/Vs (2.1) suggest the subducted Eurasian crust may have been exhumed and compositionally modified by the accreted ophiolite complex of oceanic affinity during forearc basin closure. Our Moho mostly lies in the depths of the sharpest positive velocity gradient, a few to a dozen kilometers shallower than the Vp = 7.5 km/s isosurface assumed in the tomographic models. The unusually thin crust (∼20 km) with high Vp/Vs (1.9–2.0) is observed in the northern Taiwan volcanic zone, plausibly attributed to the post‐orogenic extensional thinning and induced melting in the sublithospheric mantle producing magmatic fluids trapped in the crust. Moreover, Vb apparently decreases from the coasts to the middle CR coinciding with the thickest crust, implying the crust under the central mountain range is more compressible and easily deformed/thickened by ongoing collisional compression.
Bayesian Model for HOPE Mass Spectrometers on Van Allen Probes
Authors: Vira A. D. , Larsen B. A. , Skoug R. M. , Fernandes P. A. 
Published: January 2021

AbstractSpace instruments rely heavily on modeling to predict and understand the instrument response, enabling a determination of the capabilities and resolution. The Bayesian approach provides a framework to incorporate prior knowledge and propagate uncertainty to predict the instrument response. We present an empirical Bayes model for the end‐to‐end performance of the Helium, Oxygen, Proton, and Electron mass spectrometers aboard the Van Allen Probes mission. In this model, we use a combination of external modeling, laboratory calibration, and expert opinion to construct the time‐of‐flight spectra and demonstrate good agreement with on‐orbit data. The empirical Bayes model is applied to explore doubly charged ions and carbon, nitrogen, oxygen discrimination during the Van Allen Probes mission.
Strong Amplification of ELF/VLF Signals in Space Using Neutral Gas Injections From a Satellite Rocket Engine
Authors: Bernhardt Paul A. , Bougas William C. , Griffin Michael K. , Watson Chris , Langley Richard B. , Howarth Andrew D. , James H. Gordon , Siefring Carl L. , Perry Gareth W. , Huba Joseph. D. , Moore Robert C. , Cohen Morris. B. , Gołkowski Mark. 
Published: January 2021

AbstractThe first demonstration of rocket exhaust driven amplification (REDA) of whistler mode waves occurred on May 26, 2020 by transferring energy from pickup ions in a rocket exhaust plume to EM waves. The source of coherent VLF waves was the Navy NML Transmitter at 25.2 kHz located in LaMoure, North Dakota. The topside ionosphere at 480 km altitude became an amplifying medium with a 60 s firing of the Cygnus BT‐4 engine. The rocket engine injected exhaust as a neutral cloud moving perpendicular to field lines that connected the NML transmitter to the VLF Radio Receiver Instrument (RRI) on e‐POP/SWARM‐E. Charge exchange between the ambient O+ ions and the hypersonic water molecules in the exhaust produced H2O+ ions in a ring‐beam velocity distribution. The 25.2 kHz VLF signal from NML was amplified by 30 dB for a period 77 s as observed by the RRI. Simultaneously, preexisting coherent ELF waves at 300 Hz were amplified by 50 dB during and after the Cygnus burn. Extremely strong coherent emissions and quasiperiodic bursts in the 300–310 Hz frequency range lasted for 200 s after the release. The excitation of an ELF whistler cavity may have lasted even longer, but the orbit of the SWARM‐E/e‐POP moved the RRI sensor away from the wave emission region. The amplified 300 Hz ELF waves may have gained even more energy by cyclotron resonance with radiation belt electrons as they were ducted between geomagnetic‐conjugate hemispheres.
Definitions of neonatal abstinence syndrome in clinical studies of mothers and infants: an expert literature review
Authors: Jilani Shahla M. , Jordan Chloe J. , Jansson Lauren M. , Davis Jonathan M. 
Published: January 2021

AbstractNeonatal abstinence syndrome (NAS) results from discontinuation of in utero exposures to opioids/substances. The rising incidence of NAS has prompted an increased need for accurate research and public health data. To examine how NAS has been defined in clinical studies of opioid-exposed mothers and infants, a review process was developed based on the RAND/UCLA Appropriateness Method, yielding 888 abstracts. Per inclusion criteria, 57 abstracts underwent full-text review. To define NAS, studies cited using modified versions of the Finnegan NAS scoring tool (n = 21; 37%), ICD-9/10 coding (n = 17; 30%), original Finnegan tool (n = 16; 28%), Eat Sleep Console (n = 3; 5%), and Lipsitz (n = 3; 5%) tools, (3 cited 2+ tools). Most studies utilized subjective NAS scoring/assessment algorithms and neonatal coding as key elements defining NAS. While most cited opioid exposure as integral to their inclusion criteria, 26% did not. These approaches highlight the need for a more refined and standardized definition of NAS.
Habitat heterogeneity induced by pyrogenic organic matter in wildfire-perturbed soils mediates bacterial community assembly processes
Authors: Zhang Lujun , Ma Bin , Tang Caixian , Yu Haodan , Lv Xiaofei , Mazza Rodrigues Jorge L , Dahlgren Randy A , Xu Jianming 
Published: January 2021

Abstract
Although pyrogenic organic matter (PyOM) generated during wildfires plays a critical role in post-fire ecosystem recovery, the specific mechanisms by which PyOM controls soil microbial community assembly after wildfire perturbation remain largely uncharacterized. Herein we characterized the effect of PyOM on soil bacterial communities at two independent wildfire-perturbed forest sites. We observed that α-diversity of bacterial communities was the highest in wildfire-perturbed soils and that bacterial communities gradually changed along a sequence of unburnt soil → burnt soil → PyOM. The microbial communities reconstructed from unburnt soil and PyOM resembled the real bacterial communities in wildfire-perturbed soils in their α-diversity and community structure. Bacterial specialists in PyOM and soils clustered in phylogenetic coherent lineages with intra-lineage pH-niche conservatism and inter-lineage pH-niche divergence. Our results suggest that PyOM mediates bacterial community assembly in wildfire-perturbed soils by a combination of environmental selection and dispersal of phylogenetic coherent specialists with habitat preference in the heterogeneous microhabitats of burnt soils with distinct PyOM patches.
Painful intervertebral disc degeneration and inflammation: from laboratory evidence to clinical interventions
Authors: Lyu Feng-Juan , Cui Haowen , Pan Hehai , MC Cheung Kenneth , Cao Xu , Iatridis James C. , Zheng Zhaomin 
Published: January 2021

AbstractLow back pain (LBP), as a leading cause of disability, is a common musculoskeletal disorder that results in major social and economic burdens. Recent research has identified inflammation and related signaling pathways as important factors in the onset and progression of disc degeneration, a significant contributor to LBP. Inflammatory mediators also play an indispensable role in discogenic LBP. The suppression of LBP is a primary goal of clinical practice but has not received enough attention in disc research studies. Here, an overview of the advances in inflammation-related pain in disc degeneration is provided, with a discussion on the role of inflammation in IVD degeneration and pain induction. Puncture models, mechanical models, and spontaneous models as the main animal models to study painful disc degeneration are discussed, and the underlying signaling pathways are summarized. Furthermore, potential drug candidates, either under laboratory investigation or undergoing clinical trials, to suppress discogenic LBP by eliminating inflammation are explored. We hope to attract more research interest to address inflammation and pain in IDD and contribute to promoting more translational research.
A novel CD4+ CTL subtype characterized by chemotaxis and inflammation is involved in the pathogenesis of Graves’ orbitopathy
Authors: Wang Yue , Chen Ziyi , Wang Tingjie , Guo Hui , Liu Yufeng , Dang Ningxin , Hu Shiqian , Wu Liping , Zhang Chengsheng , Ye Kai , Shi Bingyin 
Published: January 2021

AbstractGraves’ orbitopathy (GO), the most severe manifestation of Graves’ hyperthyroidism (GH), is an autoimmune-mediated inflammatory disorder, and treatments often exhibit a low efficacy. CD4+ T cells have been reported to play vital roles in GO progression. To explore the pathogenic CD4+ T cell types that drive GO progression, we applied single-cell RNA sequencing (scRNA-Seq), T cell receptor sequencing (TCR-Seq), flow cytometry, immunofluorescence and mixed lymphocyte reaction (MLR) assays to evaluate CD4+ T cells from GO and GH patients. scRNA-Seq revealed the novel GO-specific cell type CD4+ cytotoxic T lymphocytes (CTLs), which are characterized by chemotactic and inflammatory features. The clonal expansion of this CD4+ CTL population, as demonstrated by TCR-Seq, along with their strong cytotoxic response to autoantigens, localization in orbital sites, and potential relationship with disease relapse provide strong evidence for the pathogenic roles of GZMB and IFN-γ-secreting CD4+ CTLs in GO. Therefore, cytotoxic pathways may become potential therapeutic targets for GO.
Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization
Authors: Uzan-Yulzari Atara , Turta Olli , Belogolovski Anna , Ziv Oren , Kunz Christina , Perschbacher Sarah , Neuman Hadar , Pasolli Edoardo , Oz Aia , Ben-Amram Hila , Kumar Himanshu , Ollila Helena , Kaljonen Anne , Isolauri Erika , Salminen Seppo , Lagström Hanna , Segata Nicola , Sharon Itai , Louzoun Yoram , Ensenauer Regina , Rautava Samuli , Koren Omry 
Published: January 2021

AbstractExposure to antibiotics in the first days of life is thought to affect various physiological aspects of neonatal development. Here, we investigate the long-term impact of antibiotic treatment in the neonatal period and early childhood on child growth in an unselected birth cohort of 12,422 children born at full term. We find significant attenuation of weight and height gain during the first 6 years of life after neonatal antibiotic exposure in boys, but not in girls, after adjusting for potential confounders. In contrast, antibiotic use after the neonatal period but during the first 6 years of life is associated with significantly higher body mass index throughout the study period in both boys and girls. Neonatal antibiotic exposure is associated with significant differences in the gut microbiome, particularly in decreased abundance and diversity of fecal Bifidobacteria until 2 years of age. Finally, we demonstrate that fecal microbiota transplant from antibiotic-exposed children to germ-free male, but not female, mice results in significant growth impairment. Thus, we conclude that neonatal antibiotic exposure is associated with a long-term gut microbiome perturbation and may result in reduced growth in boys during the first six years of life while antibiotic use later in childhood is associated with increased body mass index.
Perspectives on skeletal muscle stem cells
Authors: Relaix F. , Bencze M. , Borok M. J. , Der Vartanian A. , Gattazzo F. , Mademtzoglou D. , Perez-Diaz S. , Prola A. , Reyes-Fernandez P. C. , Rotini A. , Taglietti  
Published: January 2021

AbstractSkeletal muscle has remarkable regeneration capabilities, mainly due to its resident muscle stem cells (MuSCs). In this review, we introduce recently developed technologies and the mechanistic insights they provide to the understanding of MuSC biology, including the re-definition of quiescence and Galert states. Additionally, we present recent studies that link MuSC function with cellular heterogeneity, highlighting the complex regulation of self-renewal in regeneration, muscle disorders and aging. Finally, we discuss MuSC metabolism and its role, as well as the multifaceted regulation of MuSCs by their niche. The presented conceptual advances in the MuSC field impact on our general understanding of stem cells and their therapeutic use in regenerative medicine.
Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction
Authors: Grau Daniel , Zhang Yixiao , Lee Chul-Hwan , Valencia-Sánchez Marco , Zhang Jenny , Wang Miao , Holder Marlene , Svetlov Vladimir , Tan Dongyan , Nudler Evgeny , Reinberg Danny , Walz Thomas , Armache Karim-Jean 
Published: January 2021

AbstractPolycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the selective incorporation of one of two paralogs of the catalytic subunit, EZH1 or EZH2. Each of these enzymes has specialized biological functions that may be partially explained by differences in the multivalent interactions they mediate with chromatin. Here, we present two cryo-EM structures of PRC2:EZH1, one as a monomer and a second one as a dimer bound to a nucleosome. When bound to nucleosome substrate, the PRC2:EZH1 dimer undergoes a dramatic conformational change. We demonstrate that mutation of a divergent EZH1/2 loop abrogates the nucleosome-binding and methyltransferase activities of PRC2:EZH1. Finally, we show that PRC2:EZH1 dimers are more effective than monomers at promoting chromatin compaction, and the divergent EZH1/2 loop is essential for this function, thereby tying together the methyltransferase, nucleosome-binding, and chromatin-compaction activities of PRC2:EZH1. We speculate that the conformational flexibility and the ability to dimerize enable PRC2 to act on the varied chromatin substrates it encounters in the cell.
Nontrivial band geometry in an optically active system
Authors: Ren Jiahuan , Liao Qing , Li Feng , Li Yiming , Bleu Olivier , Malpuech Guillaume , Yao Jiannian , Fu Hongbing , Solnyshkov Dmitry 
Published: January 2021

AbstractOptical activity, also called circular birefringence, is known for two hundred years, but its applications for topological photonics remain unexplored. Unlike the Faraday effect, the optical activity provokes rotation of the linear polarization of light without magnetic effects, thus preserving the time-reversal symmetry. In this work, we report a direct measurement of the Berry curvature and quantum metric of the photonic modes of a planar cavity, containing a birefringent organic microcrystal (perylene) and exhibiting emergent optical activity. This experiment, performed at room temperature and at visible wavelength, establishes the potential of organic materials for implementing non-magnetic and low-cost topological photonic devices.
Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean
Authors: Garcia Tatiana , Duitama Jorge , Zullo Stephanie Smolenski , Gil Juanita , Ariani Andrea , Dohle Sarah , Palkovic Antonia , Skeen Paola , Bermudez-Santana Clara Isabel , Debouck Daniel G. , Martínez-Castillo Jaime , Gepts Paul , Chacón-Sánchez Maria Isabel 
Published: January 2021

AbstractLima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.
One-step synthesis of single-site vanadium substitution in 1T-WS2 monolayers for enhanced hydrogen evolution catalysis
Authors: Han Ali , Zhou Xiaofeng , Wang Xijun , Liu Sheng , Xiong Qihua , Zhang Qinghua , Gu Lin , Zhuang Zechao , Zhang Wenjing , Li Fanxing , Wang Dingsheng , Li Lain-Jong , Li Yadong 
Published: January 2021

AbstractMetallic tungsten disulfide (WS2) monolayers have been demonstrated as promising electrocatalysts for hydrogen evolution reaction (HER) induced by the high intrinsic conductivity, however, the key challenges to maximize the catalytic activity are achieving the metallic WS2 with high concentration and increasing the density of the active sites. In this work, single-atom-V catalysts (V SACs) substitutions in 1T-WS2 monolayers (91% phase purity) are fabricated to significantly enhance the HER performance via a one-step chemical vapor deposition strategy. Atomic-resolution scanning transmission electron microscopy (STEM) imaging together with Raman spectroscopy confirm the atomic dispersion of V species on the 1T-WS2 monolayers instead of energetically favorable 2H-WS2 monolayers. The growth mechanism of V SACs@1T-WS2 monolayers is experimentally and theoretically demonstrated. Density functional theory (DFT) calculations demonstrate that the activated V-atom sites play vital important role in enhancing the HER activity. In this work, it opens a novel path to directly synthesize atomically dispersed single-metal catalysts on metastable materials as efficient and robust electrocatalysts.
Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza
Authors: Ma Ying , Cui Guanghong , Chen Tong , Ma Xiaohui , Wang Ruishan , Jin Baolong , Yang Jian , Kang Liping , Tang Jinfu , Lai Changjiangsheng , Wang Yanan , Zhao Yujun , Shen Ye , Zeng Wen , Peters Reuben J. , Qi Xiaoquan , Guo Juan , Huang Luqi 
Published: January 2021

AbstractTanshinones are the bioactivenor-diterpenoid constituents of the Chinese medicinal herb Danshen (Salvia miltiorrhiza). These groups of chemicals have the characteristic furan D-ring, which differentiates them from the phenolic abietane-type diterpenoids frequently found in the Lamiaceae family. However, how the 14,16-epoxy is formed has not been elucidated. Here, we report an improved genome assembly of Danshen using a highly homozygous genotype. We identify a cytochrome P450 (CYP71D) tandem gene array through gene expansion analysis. We show that CYP71D373 and CYP71D375 catalyze hydroxylation at carbon-16 (C16) and 14,16-ether (hetero)cyclization to form the D-ring, whereas CYP71D411 catalyzes upstream hydroxylation at C20. In addition, we discover a large biosynthetic gene cluster associated with tanshinone production. Collinearity analysis indicates a more specific origin of tanshinones inSalviagenus. It illustrates the evolutionary origin of abietane-type diterpenoids and those with a furan D-ring in Lamiaceae.