bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity analyses of chickpea (Cicer arietinum L.) through agro-morphological traits
Authors: Dehbaoui Nasser Eddine , Gentzbittel Laurent , Drevon Jean Jacques , Lazali Mohamed 
Published: December 2023

AbstractThe limited genetic resource of chickpea (Cicer arietinum L.) is one of the most critical issue impeding its improvement and production. Collection and characterization of chickpea for agronomic traits is prerequisite to build a successful breeding programme through expanding chickpea's genepool to fulfil the needs of farmers and breeders, such as grain size and yield which supply food to a world rising population. To reach such an objective, numerous collection missions were carried out in Algeria, covering the northern agro-ecological environments, this allows us to gather 56 national and international genotypes that report a phenotypic variability and may provide a valuable diversity of useful features. Characterization experiments of 19 agro-morphological traits were set up at the Technical Institute of Field Crops over two successive seasons 2020 and 2021. All traits were statistically significant and the cluster analysis classified the genotypes into three major group, where local and improved accessions revealed an interesting outcome in terms of seed yield and resistance to Ascochyta blight. In general, the current study's findings clearly demonstrated that plant and seed morphological characteristics could be used to distinguish and identify chickpea genotypes. More often, it might participate as a source of variation in breeding programmes to meet the desirable improvement targets.
Evaluating cognitive and physical work performance: A comparative study of an active and passive industrial back-support exoskeleton
Authors: Govaerts Renée , Turcksin Tom , Vanderborght Bram , Roelands Bart , Meeusen Romain , De Pauw Kevin , De Bock Sander 
Published: December 2023

Abstract
Occupational back-support exoskeletons, categorized as active or passive, hold promise for mitigating work-related musculoskeletal disorders. However, their impact on combined physical and cognitive aspects of industrial work performance remains inadequately understood, especially regarding potential differences between exoskeleton categories. A randomized, counterbalanced cross-over study was conducted, comparing the active CrayX, passive Paexo Back, and a no exoskeleton condition. A 15-min dual task was used to simulate both cognitive and physical aspects of industrial work performance. Cognitive workload parameters included reaction time, accuracy, and subjective measures. Physical workload included movement duration, segmented in three phases: (1) walking to and grabbing the box, (2) picking up, carrying, and putting down the box, and (3) returning to the starting point. Comfort of both devices was also surveyed. The Paexo significantly increased movement duration in the first segment compared to NoExo (Paexo = 1.55 ± 0.19 s; NoExo = 1.32 ± 0.17 s; p < .01). Moreover, both the Paexo and CrayX increased movement duration for the third segment compared to NoExo (CrayX = 1.70 ± 0.27 s; Paexo = 1.74 ± 0.27 s, NoExo = 1.54 ± 0.23 s; p < .01). No significant impact on cognitive outcomes was observed. Movement Time 2 was not significantly affected by both exoskeletons. Results of the first movement segment suggest the Paexo may hinder trunk bending, favoring the active device for dynamic movements. Both devices may have contributed to a higher workload as the movement duration in the third segment increased compared to NoExo.
Audio‐Magnetotelluric Survey for Groundwater Investigation in the Al‐Jaww Plain in Eastern Abu Dhabi, Al‐Ain, United Arab Emirates
Authors: Saibi H. , Ali M. Y. , Cherkose B. A. , Alaran A. , Ullah S. , Tsuji T. 
Published: December 2023

AbstractThe United Arab Emirates (UAE), located in an arid climate zone with low rainfall, relies on shallow aquifers for freshwater. Understanding the depth and extent of such aquifers is crucial for meeting water supply needs. The UAE's hydrogeology is influenced by neighboring mountains in Oman. The Al‐Jaww Plain in southeast of Al‐Ain city is an essential groundwater source, characterized by a large, flat area of gravel and sand deposits from the Oman Mountains. This study aims to map groundwater aquifers in the Al‐Jaww Plain by integrating the audio‐magnetotelluric (AMT) method, seismic reflection profiling, and borehole data. AMT data were collected along an 11‐km ENE–WSW profile and a 2D resistivity model was generated. The resulting model delineates three distinct geo‐electrical zones from the surface to a depth of 5 km. First, a shallow layer with low resistivity (0–15 Ωm) represents the Quaternary and Pliocene aquifers, in addition to the Upper Cretaceous Simsima and Tertiary groundwater aquifer zone, extending to a depth of 1.5 km. Second, a moderately resistive layer (15–250 Ωm) is recorded beneath the first layer, corresponding to the Upper Cretaceous Aruma foreland basin sequence. Finally, a high‐resistivity region (>250 Ωm) at depths exceeding 3 km is attributed to the allochthonous Hawasina thrust sheet, which is associated with Late Cretaceous obduction of the Semail ophiolite. These findings have practical implications for managing groundwater resources in Al‐Ain.
Rediscovering tandem repeat variation in schizophrenia: challenges and opportunities
Authors: Birnbaum Rebecca 
Published: December 2023

AbstractTandem repeats (TRs) are prevalent throughout the genome, constituting at least 3% of the genome, and often highly polymorphic. The high mutation rate of TRs, which can be orders of magnitude higher than single-nucleotide polymorphisms and indels, indicates that they are likely to make significant contributions to phenotypic variation, yet their contribution to schizophrenia has been largely ignored by recent genome-wide association studies (GWAS). Tandem repeat expansions are already known causative factors for over 50 disorders, while common tandem repeat variation is increasingly being identified as significantly associated with complex disease and gene regulation. The current review summarizes key background concepts of tandem repeat variation as pertains to disease risk, elucidating their potential for schizophrenia association. An overview of next-generation sequencing-based methods that may be applied for TR genome-wide identification is provided, and some key methodological challenges in TR analyses are delineated.
Mechanical control of neural plate folding by apical domain alteration
Authors: Matsuda Miho , Rozman Jan , Ostvar Sassan , Kasza Karen E. , Sokol Sergei Y. 
Published: December 2023

AbstractVertebrate neural tube closure is associated with complex changes in cell shape and behavior, however, the relative contribution of these processes to tissue folding is not well understood. At the onset ofXenopusneural tube folding, we observed alternation of apically constricted and apically expanded cells. This apical domain heterogeneity was accompanied by biased cell orientation along the anteroposterior axis, especially at neural plate hinges, and required planar cell polarity signaling. Vertex models suggested that dispersed isotropically constricting cells can cause the elongation of adjacent cells. Consistently, in ectoderm, cell-autonomous apical constriction was accompanied by neighbor expansion. Thus, a subset of isotropically constricting cells may initiate neural plate bending, whereas a ‘tug-of-war’ contest between the force-generating and responding cells reduces its shrinking along the body axis. This mechanism is an alternative to anisotropic shrinking of cell junctions that are perpendicular to the body axis. We propose that apical domain changes reflect planar polarity-dependent mechanical forces operating during neural folding.
Force transmission by retrograde actin flow-induced dynamic molecular stretching of Talin
Authors: Yamashiro Sawako , Rutkowski David M. , Lynch Kelli Ann , Liu Ying , Vavylonis Dimitrios , Watanabe Naoki 
Published: December 2023

AbstractForce transmission at integrin-based adhesions is important for cell migration and mechanosensing. Talin is an essential focal adhesion (FA) protein that links F-actin to integrins. F-actin constantly moves on FAs, yet how Talin simultaneously maintains the connection to F-actin and transmits forces to integrins remains unclear. Here we show a critical role of dynamic Talin unfolding in force transmission. Using single-molecule speckle microscopy, we found that the majority of Talin are bound only to either F-actin or the substrate, whereas 4.1% of Talin is linked to both structures via elastic transient clutch. By reconstituting Talin knockdown cells with Talin chimeric mutants, in which the Talin rod subdomains are replaced with the stretchable β-spectrin repeats, we show that the stretchable property is critical for force transmission. Simulations suggest that unfolding of the Talin rod subdomains increases in the linkage duration and work at FAs. This study elucidates a force transmission mechanism, in which stochastic molecular stretching bridges two cellular structures moving at different speeds.
Building synthetic chromosomes from natural DNA
Authors: Coradini Alessandro L. V. , Ville Christopher Ne , Krieger Zachary A. , Roemer Joshua , Hull Cara , Yang Shawn , Lusk Daniel T. , Ehrenreich Ian M. 
Published: December 2023

AbstractDe novo chromosome synthesis is costly and time-consuming, limiting its use in research and biotechnology. Building synthetic chromosomes from natural components is an unexplored alternative with many potential applications. In this paper, we report CReATiNG (Cloning, Reprogramming, and Assembling Tiled Natural Genomic DNA), a method for constructing synthetic chromosomes from natural components in yeast. CReATiNG entails cloning segments of natural chromosomes and then programmably assembling them into synthetic chromosomes that can replace the native chromosomes in cells. We use CReATiNG to synthetically recombine chromosomes between strains and species, to modify chromosome structure, and to delete many linked, non-adjacent regions totaling 39% of a chromosome. The multiplex deletion experiment reveals that CReATiNG also enables recovery from flaws in synthetic chromosome design via recombination between a synthetic chromosome and its native counterpart. CReATiNG facilitates the application of chromosome synthesis to diverse biological problems.
Monovalent metal ion binding promotes the first transesterification reaction in the spliceosome
Authors: Aupič Jana , Borišek Jure , Fica Sebastian M. , Galej Wojciech P. , Magistrato Alessandra 
Published: December 2023

AbstractCleavage and formation of phosphodiester bonds in nucleic acids is accomplished by large cellular machineries composed of both protein and RNA. Long thought to rely on a two-metal-ion mechanism for catalysis, structure comparisons revealed many contain highly spatially conserved second-shell monovalent cations, whose precise function remains elusive. A recent high-resolution structure of the spliceosome, essential for pre-mRNA splicing in eukaryotes, revealed a potassium ion in the active site. Here, we employ biased quantum mechanics/ molecular mechanics molecular dynamics to elucidate the function of this monovalent ion in splicing. We discover that the K+ ion regulates the kinetics and thermodynamics of the first splicing step by rigidifying the active site and stabilizing the substrate in the pre- and post-catalytic state via formation of key hydrogen bonds. Our work supports a direct role for the K+ ion during catalysis and provides a mechanistic hypothesis likely shared by other nucleic acid processing enzymes.
Amino acid catabolite markers for early prognostication of pneumonia in patients with COVID-19
Authors: Maeda Rae , Seki Natsumi , Uwamino Yoshifumi , Wakui Masatoshi , Nakagama Yu , Kido Yasutoshi , Sasai Miwa , Taira Shu , Toriu Naoya , Yamamoto Masahiro , Matsuura Yoshiharu , Uchiyama Jun , Yamaguchi Genki , Hirakawa Makoto , Kim Yun-Gi , Mishima Masayo , Yanagita Motoko , Suematsu Makoto , Sugiura Yuki 
Published: December 2023

AbstractEffective early-stage markers for predicting which patients are at risk of developing SARS-CoV-2 infection have not been fully investigated. Here, we performed comprehensive serum metabolome analysis of a total of 83 patients from two cohorts to determine that the acceleration of amino acid catabolism within 5 days from disease onset correlated with future disease severity. Increased levels of de-aminated amino acid catabolites involved in the de novo nucleotide synthesis pathway were identified as early prognostic markers that correlated with the initial viral load. We further employed mice models of SARS-CoV2-MA10 and influenza infection to demonstrate that such de-amination of amino acids and de novo synthesis of nucleotides were associated with the abnormal proliferation of airway and vascular tissue cells in the lungs during the early stages of infection. Consequently, it can be concluded that lung parenchymal tissue remodeling in the early stages of respiratory viral infections induces systemic metabolic remodeling and that the associated key amino acid catabolites are valid predictors for excessive inflammatory response in later disease stages.
Single-cell multi-omics analysis of human testicular germ cell tumor reveals its molecular features and microenvironment
Authors: Lu Xiaojian , Luo Yanwei , Nie Xichen , Zhang Bailing , Wang Xiaoyan , Li Ran , Liu Guangmin , Zhou Qianyin , Liu Zhizhong , Fan Liqing , Hotaling James M. , Zhang Zhe , Bo Hao , Guo Jingtao 
Published: December 2023

AbstractSeminoma is the most common malignant solid tumor in 14 to 44 year-old men. However, its molecular features and tumor microenvironment (TME) is largely unexplored. Here, we perform a series of studies via genomics profiling (single cell multi-omics and spatial transcriptomics) and functional examination using seminoma samples and a seminoma cell line. We identify key gene expression programs share between seminoma and primordial germ cells, and further characterize the functions of TFAP2C in promoting tumor invasion and migration. We also identify 15 immune cell subtypes in TME, and find that subtypes with exhaustion features were located closer to the tumor region through combined spatial transcriptome analysis. Furthermore, we identify key pathways and genes that may facilitate seminoma disseminating beyond the seminiferous tubules. These findings advance our knowledge of seminoma tumorigenesis and produce a multi-omics atlas of in situ human seminoma microenvironment, which could help discover potential therapy targets for seminoma.
Synaptic density affects clinical severity via network dysfunction in syndromes associated with frontotemporal lobar degeneration
Authors: Whiteside David J. , Holland Negin , Tsvetanov Kamen A. , Mak Elijah , Malpetti Maura , Savulich George , Jones P. Simon , Naessens Michelle , Rouse Matthew A. , Fryer Tim D. , Hong Young T. , Aigbirhio Franklin I. , Mulroy Eoin , Bhatia Kailash P. , Rittman Timothy , O’Brien John T. , Rowe James B. 
Published: December 2023

AbstractThere is extensive synaptic loss from frontotemporal lobar degeneration, in preclinical models and human in vivo and post mortem studies. Understanding the consequences of synaptic loss for network function is important to support translational models and guide future therapeutic strategies. To examine this relationship, we recruited 55 participants with syndromes associated with frontotemporal lobar degeneration and 24 healthy controls. We measured synaptic density with positron emission tomography using the radioligand [11C]UCB-J, which binds to the presynaptic vesicle glycoprotein SV2A, neurite dispersion with diffusion magnetic resonance imaging, and network function with task-free magnetic resonance imaging functional connectivity. Synaptic density and neurite dispersion in patients was associated with reduced connectivity beyond atrophy. Functional connectivity moderated the relationship between synaptic density and clinical severity. Our findings confirm the importance of synaptic loss in frontotemporal lobar degeneration syndromes, and the resulting effect on behaviour as a function of abnormal connectivity.
Reassessing endothelial-to-mesenchymal transition in mouse bone marrow: insights from lineage tracing models
Authors: Cao Jia , Jin Ling , Yan Zi-Qi , Wang Xiao-Kai , Li You-You , Wang Zun , Liu Yi-Wei , Li Hong-Ming , Guan Zhe , He Ze-Hui , Gong Jiang-Shan , Liu Jiang-Hua , Yin Hao , Tan Yi-Juan , Hong Chun-Gu , Feng Shi-Kai , Zhang Yan , Wang Yi-Yi , Qi Lu-Yue , Chen Chun-Yuan , Liu Zheng-Zhao , Wang Zhen-Xing , Xie Hui 
Published: December 2023

AbstractEndothelial cells (ECs) and bone marrow stromal cells (BMSCs) play crucial roles in supporting hematopoiesis and hematopoietic regeneration. However, whether ECs are a source of BMSCs remains unclear. Here, we evaluate the contribution of endothelial-to-mesenchymal transition to BMSC generation in postnatal mice. Single-cell RNA sequencing identifies ECs expressing BMSC markers Prrx1 and Lepr; however, this could not be validated using Prrx1-Cre and Lepr-Cre transgenic mice. Additionally, only a minority of BMSCs are marked by EC lineage tracing models using Cdh5-rtTA-tetO-Cre or Tek-CreERT2. Moreover, Cdh5+ BMSCs and Tek+ BMSCs show distinct spatial distributions and characteristic mesenchymal markers, suggestive of their origination from different progenitors rather than CDH5+ TEK+ ECs. Furthermore, myeloablation induced by 5-fluorouracil treatment does not increase Cdh5+ BMSCs. Our findings indicate that ECs hardly convert to BMSCs during homeostasis and myeloablation-induced hematopoietic regeneration, highlighting the importance of using appropriate genetic models and conducting careful data interpretation in studies concerning endothelial-to-mesenchymal transition.
Machine learning for automated experimentation in scanning transmission electron microscopy
Authors: Kalinin Sergei V. , Mukherjee Debangshu , Roccapriore Kevin , Blaiszik Benjamin J. , Ghosh Ayana , Ziatdinov Maxim A. , Al-Najjar Anees , Doty Christina , Akers Sarah , Rao Nageswara S. , Agar Joshua C. , Spurgeon Steven R. 
Published: December 2023

AbstractMachine learning (ML) has become critical for post-acquisition data analysis in (scanning) transmission electron microscopy, (S)TEM, imaging and spectroscopy. An emerging trend is the transition to real-time analysis and closed-loop microscope operation. The effective use of ML in electron microscopy now requires the development of strategies for microscopy-centric experiment workflow design and optimization. Here, we discuss the associated challenges with the transition to active ML, including sequential data analysis and out-of-distribution drift effects, the requirements for edge operation, local and cloud data storage, and theory in the loop operations. Specifically, we discuss the relative contributions of human scientists and ML agents in the ideation, orchestration, and execution of experimental workflows, as well as the need to develop universal hyper languages that can apply across multiple platforms. These considerations will collectively inform the operationalization of ML in next-generation experimentation.
Large-scale fully printed “Lego Bricks” type wearable sweat sensor for physical activity monitoring
Authors: Ji Wenhui , Liu Huanzhuan , Liu Yadong , Zhang Wei , Zhou Tong , Liu Xinxin , Tao Chao , Dai Jiangxuan , Zha Baoli , Xie Ruijie , Wu Jiansheng , Wu Qiong , Zhang Weina , Li Lin , Huo Fengwei 
Published: December 2023

AbstractWearable sweat sensors are becoming increasingly popular for their robust capabilities in non-invasive, dynamic, and continuous real-time monitoring of biological information. Real-time monitoring of large-scale samples is crucial for realizing intelligent health. A major bottleneck for enabling large-scale sweat elucidation is the fabrication of wearable sensors equipped with microfluidic devices and flexible electrodes in a cost-effective, homogeneous performance and rapid large-scale way. Herein, a “Screen+Wax”-printing technique was introduced to prepare these components and construct “Lego Bricks” type wearable sweat sensor sensor to monitor sweat Na+ and K+. Flexible electrode arrays and paper-based microfluidic layers (they act as building blocks) were fabricated on polyethylene terephthalate and paper surfaces, respectively, using screen printing and wax printing. Gold nanoparticles and Na+/K+ ion-selective membranes were modified on the electrode surfaces by electrodeposition and drop coating, respectively. In this work, we highlight the excellent performance of the “Lego Bricks” type wearable sweat sensor in testing the Na+ and K+ imbalance of sweat from different body regions during exercise and, more significantly, to track the physical activity during prolonged exercise under different interventions. Furthermore, the prepared “Lego Bricks” wearable sweat ion electrochemical sensor is demonstrated to be capable of large-scale samples elucidation with outstanding performance and cost-effectiveness, which is expected to deeply integrate sweat monitoring into physical activity, providing an important tool for intelligent health.
Association between normal-weight obesity and cardiometabolic risk factors among adults in Addis Ababa, Ethiopia
Authors: Gebremedhin Samson , Mekonene Mulugeta , Hagos Seifu , Baye Kaleab , Shikur Bilal , Berhane Adugnaw , Bekele Tilahun 
Published: December 2023

AbstractThe relationship between normal-weight obesity (NWO)—high percent body fat (%BF) in individuals with normal body mass index (BMI)—and cardiometabolic abnormalities has not been explored in Africa. We determined the prevalence of the NWO and evaluated its association with hypertension, elevated blood sugar and dyslipidaemia among adults in Addis Ababa, Ethiopia. A cross-sectional study was conducted among adults 18–64 years (n = 600). Blood pressure, blood glucose, lipid profile, and anthropometric measurements were completed. As a function of skinfold thickness, body density and %BF were estimated using Durnin & Womersley and Siri Equations, respectively. The relationship between the NWO and the outcomes of interest, assessed using adjusted linear and logit models. The age- and sex-standardised prevalence of NWO was 18.9% (95% confidence interval (CI) 15.8, 22.2%). Comparison between normal-weight lean (normal %BF and BMI) and normal-weight obese individuals suggested no difference in systolic blood pressure (β = 2.55; 95% CI − 0.82, 5.92); however, diastolic blood pressure (β = 3.77: 95% CI 1.37, 6.18) and odds of hypertension (adjusted odds ratio (AOR) = 2.46: 95% CI 1.18, 5.13) were significantly raised in the latter. Similarly, adults with NWO had elevated blood glucose (β = 2.30; 95% CI 1.23, 15.66) and increased odds of high blood sugar level (AOR = 1.68; 95% CI 1.05, 2.67). LDL (β = 8.73: 1.56, 15.90), triglyceride (β = 20.99: 0.78, 41.22), total cholesterol (β = 10.47: 1.44, 19.50), and Cholesterol to HDL ratio (β = 0.65: 0.27, 1.04) were also raised among adults with NWO. NWO is common among adults in Addis Ababa and is associated with cardiometabolic derangements.