bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effective binning of metagenomic contigs using contrastive multi-view representation learning
Authors: Wang Ziye , You Ronghui , Han Haitao , Liu Wei , Sun Fengzhu , Zhu Shanfeng 
Published: January 2024

AbstractContig binning plays a crucial role in metagenomic data analysis by grouping contigs from the same or closely related genomes. However, existing binning methods face challenges in practical applications due to the diversity of data types and the difficulties in efficiently integrating heterogeneous information. Here, we introduce COMEBin, a binning method based on contrastive multi-view representation learning. COMEBin utilizes data augmentation to generate multiple fragments (views) of each contig and obtains high-quality embeddings of heterogeneous features (sequence coverage and k-mer distribution) through contrastive learning. Experimental results on multiple simulated and real datasets demonstrate that COMEBin outperforms state-of-the-art binning methods, particularly in recovering near-complete genomes from real environmental samples. COMEBin outperforms other binning methods remarkably when integrated into metagenomic analysis pipelines, including the recovery of potentially pathogenic antibiotic-resistant bacteria (PARB) and moderate or higher quality bins containing potential biosynthetic gene clusters (BGCs).
VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification
Authors: Yang Yueli , Jia Wenqi , Luo Zhiwei , Li Yunpan , Liu Hao , Fu Lixin , Li Jinxiu , Jiang Yu , Lai Junjian , Li Haiwei , Saeed Babangida Jabir , Zou Yi , Lv Yuan , Wu Liang , Zhou Ting , Shan Yongli , Liu Chuanyu , Lai Yiwei , Liu Longqi , Hutchins Andrew P. , Esteban Miguel A. , Mazid Md. Abdul , Li Wenjuan 
Published: January 2024

AbstractIn contrast to rodents, the mechanisms underlying human trophectoderm and early placenta specification are understudied due to ethical barriers and the scarcity of embryos. Recent reports have shown that human pluripotent stem cells (PSCs) can differentiate into trophectoderm (TE)-like cells (TELCs) and trophoblast stem cells (TSCs), offering a valuable in vitro model to study early placenta specification. Here, we demonstrate that the VGLL1 (vestigial-like family member 1), which is highly expressed during human and non-human primate TE specification in vivo but is negligibly expressed in mouse, is a critical regulator of cell fate determination and self-renewal in human TELCs and TSCs derived from naïve PSCs. Mechanistically, VGLL1 partners with the transcription factor TEAD4 (TEA domain transcription factor 4) to regulate chromatin accessibility at target gene loci through histone acetylation and acts in cooperation with GATA3 and TFAP2C. Our work is relevant to understand primate early embryogenesis and how it differs from other mammalian species.
From chiral laser pulses to femto- and attosecond electronic chirality flips in achiral molecules
Authors: Chen Yunjiao , Haase Dietrich , Manz Jörn , Wang Huihui , Yang Yonggang 
Published: January 2024

AbstractChirality is an important topic in biology, chemistry and physics. Here we show that ultrashort circularly polarized laser pulses, which are chiral, can be fired on achiral oriented molecules to induce chirality in their electronic densities, with chirality flips within femtoseconds or even attoseconds. Our results, obtained by quantum dynamics simulations, use the fact that laser pulses can break electronic symmetry while conserving nuclear symmetry. Here two laser pulses generate a superposition of three electronic eigenstates. This breaks all symmetry elements of the electronic density, making it chiral except at the periodic rare events of the chirality flips. As possible applications, we propose the combination of the electronic chirality flips with Chiral Induced Spin Selectivity.
Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy
Authors: Nguyen Binh An , Singh Virender , Afrin Shumaila , Yakubovska Anna , Wang Lanie , Ahmed Yasmin , Pedretti Rose , Fernandez-Ramirez Maria del Carmen , Singh Preeti , Pękała Maja , Cabrera Hernandez Luis O. , Kumar Siddharth , Lemoff Andrew , Gonzalez-Prieto Roman , Sawaya Michael R. , Eisenberg David S. , Benson Merrill Douglas , Saelices Lorena 
Published: January 2024

AbstractATTR amyloidosis is caused by the deposition of transthyretin in the form of amyloid fibrils in virtually every organ of the body, including the heart. This systemic deposition leads to a phenotypic variability that has not been molecularly explained yet. In brain amyloid conditions, previous studies suggest an association between clinical phenotype and the molecular structures of their amyloid fibrils. Here we investigate whether there is such an association in ATTRv amyloidosis patients carrying the mutation I84S. Using cryo-electron microscopy, we determined the structures of cardiac fibrils extracted from three ATTR amyloidosis patients carrying the ATTRv-I84S mutation, associated with a consistent clinical phenotype. We found that in each ATTRv-I84S patient, the cardiac fibrils exhibited different local conformations, and these variations can co-exist within the same fibril. Our finding suggests that one amyloid disease may associate with multiple fibril structures in systemic amyloidoses, calling for further studies.
Regulating Au coverage for the direct oxidation of methane to methanol
Authors: Xu Yueshan , Wu Daoxiong , Zhang Qinghua , Rao Peng , Deng Peilin , Tang Mangen , Li Jing , Hua Yingjie , Wang Chongtai , Zhong Shengkui , Jia Chunman , Liu Zhongxin , Shen Yijun , Gu Lin , Tian Xinlong , Liu Quanbing 
Published: January 2024

AbstractThe direct oxidation of methane to methanol under mild conditions is challenging owing to its inadequate activity and low selectivity. A key objective is improving the selective oxidation of the first carbon-hydrogen bond of methane, while inhibiting the oxidation of the remaining carbon-hydrogen bonds to ensure high yield and selectivity of methanol. Here we design ultrathin PdxAuy nanosheets and revealed a volcano-type relationship between the binding strength of hydroxyl radical on the catalyst surface and catalytic performance using experimental and density functional theory results. Our investigations indicate a trade-off relationship between the reaction-triggering and reaction-conversion steps in the reaction process. The optimized Pd3Au1 nanosheets exhibits a methanol production rate of 147.8 millimoles per gram of Pd per hour, with a selectivity of 98% at 70 °C, representing one of the most efficient catalysts for the direct oxidation of methane to methanol.
Accelerating the transition to cobalt-free batteries: a hybrid model for LiFePO4/graphite chemistry
Authors: Pozzato Gabriele , Li Xueyan , Lee Donghoon , Ko Johan , Onori Simona 
Published: January 2024

AbstractThe increased adoption of lithium-iron-phosphate batteries, in response to the need to reduce the battery manufacturing process’s dependence on scarce minerals and create a resilient and ethical supply chain, comes with many challenges. The design of an effective and high-performing battery management system (BMS) for such technology is one of those challenges. In this work, a physics-based model describing the two-phase transition operation of an iron-phosphate positive electrode—in a graphite anode battery—is integrated with a machine-learning model to capture the hysteresis and path-dependent behavior during transient operation. The machine-learning component of the proposed “hybrid” model is built upon the knowledge of the electrochemical internal states of the battery during charge and discharge operation over several driving profiles. The hybrid model is experimentally validated over 15 h of driving, and it is shown that the machine-learning component is responsible for a small percentage of the total battery behavior (i.e., it compensates for voltage hysteresis). The proposed modeling strategy can be used for battery performance analysis, synthetic data generation, and the development of reduced-order models for BMS design.
Exfoliation of an extruded Mg-4Li-1Ca alloy in presence of glucose and bovine serum albumin
Authors: Cai Lei , Zeng Mei-Qi , Liu Meng-Jie , Bao Jing-Yu , Ren Yu-Qian , Kannan M. Bobby , Cui Lan-Yue , Liu Cheng-Bao , Zhang Fen , Li Shuo-Qi , Zeng Rong-Chang 
Published: January 2024

AbstractExfoliation corrosion (EFC) on extruded Mg-4Li-1Ca alloys as bone implant materials has not been reported. This study aimed to elucidate the degradation mechanism of a corrosion type-exfoliation occurred on an extruded Mg-4Li-1Ca alloy under the interaction of glucose (Glu) and bovine serum albumin (BSA) in Hank’s solution. The alloy microstructure, chemical composition, texture, stress distribution and Volta potential maps were characterized using metallographic microscopy, scanning electron microscopy and electron backscattered diffraction, and scanning Kelvin Probe. The alloy corrosion behavior was investigated via electrochemical testing and hydrogen evolution rate methods. X-ray diffraction, Fourier transform infrared spectrometry, X-ray photoelectron spectrometer, and fluorescence microscopy were used to analyze the corrosion products and the adsorption of the organic molecules. The experimental results indicated that the anodic second phase (Mg2Ca) were distributed in lamellar and rod-like patterns along the extrusion direction of the alloy, a lower Volta potential for Mg2Ca, texture and residual stresses also promote EFC. An increase in Glu concentration exacerbated the EFC, whereas BSA inhibited the EFC of the alloy. Higher Glu concentrations in BSA in turn inhibited EFC since Glu can complex with amino acids in proteins to form Glu-amino acid amides, which promoted protein adsorption and thereby forming a dense protective film on the alloy surface. The preferential dissolution of the Mg2Ca phase particles led to the complexation and adsorption of Glu and protein. This study enriches the understanding of the corrosion types in biomedical Mg-4Li-1Ca alloy and paving the way for enhancing the EFC resistance of the alloy.
The network characteristics in schizophrenia with prominent negative symptoms: a multimodal fusion study
Authors: Kong Li , Zhang Yao , Wu Xu-ming , Wang Xiao-xiao , Wu Hai-su , Li Shuai-biao , Chu Min-yi , Wang Yi , Lui Simon S. Y. , Lv Qin-yu , Yi Zheng-hui , Chan Raymond C. K. 
Published: January 2024

AbstractPrevious studies on putative neural mechanisms of negative symptoms in schizophrenia mainly used single modal imaging data, and seldom utilized schizophrenia patients with prominent negative symptoms (PNS).This study adopted the multimodal fusion method and recruited a homogeneous sample with PNS. We aimed to identify negative symptoms-related structural and functional neural correlates of schizophrenia. Structural magnetic resonance imaging (sMRI) and resting-state functional MRI (rs-fMRI) were performed in 31 schizophrenia patients with PNS and 33 demographically matched healthy controls.Compared to healthy controls, schizophrenia patients with PNS exhibited significantly altered functional activations in the default mode network (DMN) and had structural gray matter volume (GMV) alterations in the cerebello-thalamo-cortical network. Correlational analyses showed that negative symptoms severity was significantly correlated with the cerebello-thalamo-cortical structural network, but not with the DMN network in schizophrenia patients with PNS.Our findings highlight the important role of the cerebello-thalamo-cortical structural network underpinning the neuropathology of negative symptoms in schizophrenia. Future research should recruit a large sample and schizophrenia patients without PNS, and apply adjustments for multiple comparison, to verify our preliminary findings.
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan
Authors: Urayama Syun-ichi , Fukudome Akihito , Hirai Miho , Okumura Tomoyo , Nishimura Yosuke , Takaki Yoshihiro , Kurosawa Norio , Koonin Eugene V. , Krupovic Mart , Nunoura Takuro 
Published: January 2024

AbstractMetatranscriptome sequencing expanded the known diversity of the bacterial RNA virome, suggesting that additional riboviruses infecting bacterial hosts remain to be discovered. Here we employed double-stranded RNA sequencing to recover complete genome sequences of two ribovirus groups from acidic hot springs in Japan. One group, denoted hot spring riboviruses (HsRV), consists of viruses with distinct RNA-directed RNA polymerases (RdRPs) that seem to be intermediates between typical ribovirus RdRPs and viral reverse transcriptases. This group forms a distinct phylum, Artimaviricota, or even kingdom within the realm Riboviria. We identified viruses encoding HsRV-like RdRPs in marine water, river sediments and salt marshes, indicating that this group is widespread beyond extreme ecosystems. The second group, denoted hot spring partiti-like viruses (HsPV), forms a distinct branch within the family Partitiviridae. The genome architectures of HsRV and HsPV and their identification in bacteria-dominated habitats suggest that these viruses infect thermoacidophilic bacteria.
Solving olympiad geometry without human demonstrations
Authors: Trinh Trieu H. , Wu Yuhuai , Le Quoc V. , He He , Luong Thang 
Published: January 2024

AbstractProving mathematical theorems at the olympiad level represents a notable milestone in human-level automated reasoning1–4, owing to their reputed difficulty among the world’s best talents in pre-university mathematics. Current machine-learning approaches, however, are not applicable to most mathematical domains owing to the high cost of translating human proofs into machine-verifiable format. The problem is even worse for geometry because of its unique translation challenges1,5, resulting in severe scarcity of training data. We propose AlphaGeometry, a theorem prover for Euclidean plane geometry that sidesteps the need for human demonstrations by synthesizing millions of theorems and proofs across different levels of complexity. AlphaGeometry is a neuro-symbolic system that uses a neural language model, trained from scratch on our large-scale synthetic data, to guide a symbolic deduction engine through infinite branching points in challenging problems. On a test set of 30 latest olympiad-level problems, AlphaGeometry solves 25, outperforming the previous best method that only solves ten problems and approaching the performance of an average International Mathematical Olympiad (IMO) gold medallist. Notably, AlphaGeometry produces human-readable proofs, solves all geometry problems in the IMO 2000 and 2015 under human expert evaluation and discovers a generalized version of a translated IMO theorem in 2004.
Inherited polygenic effects on common hematological traits influence clonal selection on JAK2V617F and the development of myeloproliferative neoplasms
Authors: Guo Jing , Walter Klaudia , Quiros Pedro M. , Gu Muxin , Baxter E. Joanna , Danesh John , Di Angelantonio Emanuele , Roberts David , Guglielmelli Paola , Harrison Claire N. , Godfrey Anna L. , Green Anthony R. , Vassiliou George S. , Vuckovic Dragana , Nangalia Jyoti , Soranzo Nicole 
Published: January 2024

AbstractMyeloproliferative neoplasms (MPNs) are chronic cancers characterized by overproduction of mature blood cells. Their causative somatic mutations, for example, JAK2V617F, are common in the population, yet only a minority of carriers develop MPN. Here we show that the inherited polygenic loci that underlie common hematological traits influence JAK2V617F clonal expansion. We identify polygenic risk scores (PGSs) for monocyte count and plateletcrit as new risk factors for JAK2V617F positivity. PGSs for several hematological traits influenced the risk of different MPN subtypes, with low PGSs for two platelet traits also showing protective effects in JAK2V617F carriers, making them two to three times less likely to have essential thrombocythemia than carriers with high PGSs. We observed that extreme hematological PGSs may contribute to an MPN diagnosis in the absence of somatic driver mutations. Our study showcases how polygenic backgrounds underlying common hematological traits influence both clonal selection on somatic mutations and the subsequent phenotype of cancer.
Profiling the interactome of oligonucleotide drugs by proximity biotinylation
Authors: Hanswillemenke Alfred , Hofacker Daniel Tobias , Sorgenfrei Michèle , Fruhner Carolin , Franz-Wachtel Mirita , Schwarzer Dirk , Maček Boris , Stafforst Thorsten 
Published: January 2024

AbstractDrug-ID is a novel method applying proximity biotinylation to identify drug–protein interactions inside living cells. The covalent conjugation of a drug with a biotin ligase enables targeted biotinylation and identification of the drug-bound proteome. We established Drug-ID for two small-molecule drugs, JQ1 and SAHA, and applied it for RNaseH-recruiting antisense oligonucleotides (ASOs). Drug-ID profiles the drug–protein interactome de novo under native conditions, directly inside living cells and at pharmacologically effective drug concentrations. It requires minimal amounts of cell material and might even become applicable in vivo. We studied the dose-dependent aggregation of ASOs and the effect of different wing chemistries (locked nucleic acid, 2′-methoxyethyl and 2′-Fluoro) and ASO lengths on the interactome. Finally, we demonstrate the detection of stress-induced, intracellular interactome changes (actinomycin D treatment) with an in situ variant of the approach, which uses a recombinant biotin ligase and does not require genetic manipulation of the target cell.
The developmental timing of spinal touch processing alterations predicts behavioral changes in genetic mouse models of autism spectrum disorders
Authors: Tasnim Aniqa , Alkislar Ilayda , Hakim Richard , Turecek Josef , Abdelaziz Amira , Orefice Lauren L. , Ginty David D. 
Published: January 2024

AbstractAltered somatosensory reactivity is frequently observed among individuals with autism spectrum disorders (ASDs). Here, we report that although multiple mouse models of ASD exhibit aberrant somatosensory behaviors in adulthood, some models exhibit altered tactile reactivity as early as embryonic development, whereas in others, altered reactivity emerges later in life. Additionally, tactile overreactivity during neonatal development is associated with anxiety-like behaviors and social behavior deficits in adulthood, whereas tactile overreactivity that emerges later in life is not. The locus of circuit disruption dictates the timing of aberrant tactile behaviors, as altered feedback or presynaptic inhibition of peripheral mechanosensory neurons leads to abnormal tactile reactivity during neonatal development, whereas disruptions in feedforward inhibition in the spinal cord lead to touch reactivity alterations that manifest later in life. Thus, the developmental timing of aberrant touch processing can predict the manifestation of ASD-associated behaviors in mouse models, and differential timing of sensory disturbance onset may contribute to phenotypic diversity across individuals with ASD.
A database of thermally activated delayed fluorescent molecules auto-generated from scientific literature with ChemDataExtractor
Authors: Huang Dingyun , Cole Jacqueline M. 
Published: January 2024

AbstractA database of thermally activated delayed fluorescent (TADF) molecules was automatically generated from the scientific literature. It consists of 25,482 data records with an overall precision of 82%. Among these, 5,349 records have chemical names in the form of SMILES strings which are represented with 91% accuracy; these are grouped in a subsidiary database. Each data record contains one of the following four properties: maximum emission wavelength (λEM), photoluminescence quantum yield (PLQY), singlet-triplet energy splitting (ΔEST), and delayed lifetime (τD). The databases were created through text mining using ChemDataExtractor, a chemistry-aware natural-language-processing toolkit, which has been adapted for TADF research. The text-mined corpus consisted of 2,733 papers from the Royal Society of Chemistry and Elsevier. To the best of our knowledge, these databases are the first databases that have been auto-generated for TADF molecules from existing publications. The databases have been publicly released for experimental and computational applications in the TADF research field.
Climate influences scrub typhus occurrence in Vellore, Tamil Nadu, India: analysis of a 15-year dataset
Authors: D’Cruz Solomon , Sreedevi Kotamreddy , Lynette Cheryl , Gunasekaran Karthik , Prakash John Antony Jude 
Published: January 2024

AbstractClimate is one of the major factors determining the prevalence and seasonality of vector borne diseases like scrub typhus (ST). We analyzed, the association of the meteorological factors like temperature, rainfall and humidity with scrub typhus using the 15 years scrub typhus data from a tertiary care hospital in Vellore, South India. Demographic data of permanent residents of Vellore, who had IgM ELISA results for scrub typhus for the time period of May 2005 to April 2020 were included. Meteorological data was correlated with the monthly scrub typhus cases; negative binomial regression model was used to predict the relation between scrub typhus occurrence and climate factors. Maximum number of ST cases were reported between the months August and February with October recording the highest number of cases. Elderly people, farmers, agricultural workers and housewives were at higher risk for scrub typhus. For an increase of 1 °C in mean temperature, the monthly ST cases reduced by 18.8% (95% CI − 24.1, − 13.2%). On the contrary, for 1 percent increase in mean relative humidity (RH), there is an increase of 7.6% (95% CI 5.4, 9.9%) of monthly ST cases. Similarly, an increase of 1 mm of rainfall contributed to 0.5 to 0.7% of monthly ST cases (after 2 months) depending on the variables included in the analysis. This study provides information that meteorological factors influence ST occurrence in Vellore. The rise of scrub typhus cases is maximal 2 months post rainfall. Whereas a rise in relative humidity, causes a rise in scrub typhus cases in same month, while rise in temperature has a negative impact on scrub typhus during the same month. These findings based on a retrospective analysis need validation by prospective studies.
First application of data assimilation-based control to fusion plasma
Authors: Morishita Yuya , Murakami Sadayoshi , Kenmochi Naoki , Funaba Hisamichi , Yamada Ichihiro , Mizuno Yoshinori , Nagahara Kazuki , Nuga Hideo , Seki Ryosuke , Yokoyama Masayuki , Ueno Genta , Osakabe Masaki 
Published: January 2024

AbstractMagnetic fusion plasmas, which are complex systems comprising numerous interacting elements, have large uncertainties. Therefore, future fusion reactors require prediction-based advanced control systems with an adaptive system model and control estimation robust to uncertainties in the model and observations. To address this challenge, we introduced a control approach based on data assimilation (DA), which describes the system model adaptation and control estimation based on the state probability distribution. The first implementation of a DA-based control system was achieved at the Large Helical Device to control the high temperature plasma. The experimental results indicate that the control system enhanced the predictive capability using real-time observations and adjusted the electron cyclotron heating power for a target temperature. The DA-based control system provides a flexible platform for advanced control in future fusion reactors.