bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated analysis of surface facets: the example of cesium telluride
Authors: Saßnick Holger-Dietrich , Cocchi Caterina 
Published: February 2024

AbstractHigh-throughput screening combined with ab initio calculations is a powerful tool to explore technologically relevant materials characterized by complex configurational spaces. Despite the impressive developments achieved in this field in the last few years, most studies still focus on bulk materials, although the relevant processes for energy conversion, production, and storage occur on surfaces. Herein, we present an automatized computational scheme that is capable of calculating surface properties in inorganic crystals from first principles in a high-throughput fashion. After introducing the method and its implementation, we showcase its applicability, focusing on four polymorphs of Cs2Te, an established photocathode material for particle accelerators, considering slabs with low Miller indices and different terminations. This analysis gives insight into how the surface composition, accessible through the proposed high-throughput screening method, impacts the electronic properties and, ultimately, the photoemission performance. The developed scheme offers new opportunities for automated computational studies beyond bulk materials.
Skeletal muscle regeneration after extensive cryoinjury of caudal myomeres in adult zebrafish
Authors: Oudhoff Hendrik , Hisler Vincent , Baumgartner Florian , Rees Lana , Grepper Dogan , Jaźwińska Anna 
Published: February 2024

AbstractSkeletal muscles can regenerate after minor injuries, but severe structural damage often leads to fibrosis in mammals. Whether adult zebrafish possess the capacity to reproduce profoundly destroyed musculature remains unknown. Here, a new cryoinjury model revealed that several myomeres efficiently regenerated within one month after wounding the zebrafish caudal peduncle. Wound clearance involved accumulation of the selective autophagy receptor p62, an immune response and Collagen XII deposition. New muscle formation was associated with proliferation of Pax7 expressing muscle stem cells, which gave rise to MyoD1 positive myogenic precursors, followed by myofiber differentiation. Monitoring of slow and fast muscles revealed their coordinated replacement in the superficial and profound compartments of the myomere. However, the final boundary between the muscular components was imperfectly recapitulated, allowing myofibers of different identities to intermingle. The replacement of connective with sarcomeric tissues required TOR signaling, as rapamycin treatment impaired new muscle formation, leading to persistent fibrosis. The model of zebrafish myomere restoration may provide new medical perspectives for treatment of traumatic injuries.
The Gaze of Schizophrenia Patients Captured by Bottom-up Saliency
Authors: Adámek Petr , Grygarová Dominika , Jajcay Lucia , Bakštein Eduard , Fürstová Petra , Juríčková Veronika , Jonáš Juraj , Langová Veronika , Neskoroďana Iryna , Kesner Ladislav , Horáček Jiří 
Published: February 2024

AbstractSchizophrenia (SCHZ) notably impacts various human perceptual modalities, including vision. Prior research has identified marked abnormalities in perceptual organization in SCHZ, predominantly attributed to deficits in bottom-up processing. Our study introduces a novel paradigm to differentiate the roles of top-down and bottom-up processes in visual perception in SCHZ. We analysed eye-tracking fixation ground truth maps from 28 SCHZ patients and 25 healthy controls (HC), comparing these with two mathematical models of visual saliency: one bottom-up, based on the physical attributes of images, and the other top-down, incorporating machine learning. While the bottom-up (GBVS) model revealed no significant overall differences between groups (beta = 0.01,p = 0.281, with a marginal increase in SCHZ patients), it did show enhanced performance by SCHZ patients with highly salient images. Conversely, the top-down (EML-Net) model indicated no general group difference (beta = −0.03,p= 0.206, lower in SCHZ patients) but highlighted significantly reduced performance in SCHZ patients for images depicting social interactions (beta = −0.06,p< 0.001). Over time, the disparity between the groups diminished for both models. The previously reported bottom-up bias in SCHZ patients was apparent only during the initial stages of visual exploration and corresponded with progressively shorter fixation durations in this group. Our research proposes an innovative approach to understanding early visual information processing in SCHZ patients, shedding light on the interplay between bottom-up perception and top-down cognition.
Multivalent cytomegalovirus glycoprotein B nucleoside modified mRNA vaccines did not demonstrate a greater antibody breadth
Authors: Wang Hsuan-Yuan , Li Leike , Nelson Cody S. , Barfield Richard , Valencia Sarah , Chan Cliburn , Muramatsu Hiromi , Lin Paulo J. C. , Pardi Norbert , An Zhiqiang , Weissman Drew , Permar Sallie R. 
Published: February 2024

AbstractHuman cytomegalovirus (HCMV) remains the most common congenital infection and infectious complication in immunocompromised patients. The most successful HCMV vaccine to date, an HCMV glycoprotein B (gB) subunit vaccine adjuvanted with MF59, achieved 50% efficacy against primary HCMV infection. A previous study demonstrated that gB/MF59 vaccinees were less frequently infected with HCMV gB genotype strains most similar to the vaccine strain than strains encoding genetically distinct gB genotypes, suggesting strain-specific immunity accounted for the limited efficacy. To determine whether vaccination with multiple HCMV gB genotypes could increase the breadth of anti-HCMV gB humoral and cellular responses, we immunized 18 female rabbits with monovalent (gB-1), bivalent (gB-1+gB-3), or pentavalent (gB-1+gB-2+gB-3+gB-4+gB-5) gB lipid nanoparticle-encapsulated nucleoside-modified RNA (mRNA–LNP) vaccines. The multivalent vaccine groups did not demonstrate a higher magnitude or breadth of the IgG response to the gB ectodomain or cell-associated gB compared to that of the monovalent vaccine. Also, the multivalent vaccines did not show an increase in the breadth of neutralization activity and antibody-dependent cellular phagocytosis against HCMV strains encoding distinct gB genotypes. Interestingly, peripheral blood mononuclear cell-derived gB-2-specific T-cell responses elicited by multivalent vaccines were of a higher magnitude compared to that of monovalent vaccinated animals against a vaccine-mismatched gB genotype at peak immunogenicity. Yet, no statistical differences were observed in T cell response against gB-3 and gB-5 variable regions among the three vaccine groups. Our data suggests that the inclusion of multivalent gB antigens is not an effective strategy to increase the breadth of anti-HCMV gB antibody and T cell responses. Understanding how to increase the HCMV vaccine protection breadth will be essential to improve the vaccine efficacy.
Mechanical stimulation and electrophysiological monitoring at subcellular resolution reveals differential mechanosensation of neurons within networks
Authors: Kasuba Krishna Chaitanya , Buccino Alessio Paolo , Bartram Julian , Gaub Benjamin M. , Fauser Felix J. , Ronchi Silvia , Kumar Sreedhar Saseendran , Geissler Sydney , Nava Michele M. , Hierlemann Andreas , Müller Daniel J. 
Published: February 2024

AbstractA growing consensus that the brain is a mechanosensitive organ is driving the need for tools that mechanically stimulate and simultaneously record the electrophysiological response of neurons within neuronal networks. Here we introduce a synchronized combination of atomic force microscopy, high-density microelectrode array and fluorescence microscopy to monitor neuronal networks and to mechanically characterize and stimulate individual neurons at piconewton force sensitivity and nanometre precision while monitoring their electrophysiological activity at subcellular spatial and millisecond temporal resolution. No correlation is found between mechanical stiffness and electrophysiological activity of neuronal compartments. Furthermore, spontaneously active neurons show exceptional functional resilience to static mechanical compression of their soma. However, application of fast transient (∼500 ms) mechanical stimuli to the neuronal soma can evoke action potentials, which depend on the anchoring of neuronal membrane and actin cytoskeleton. Neurons show higher responsivity, including bursts of action potentials, to slower transient mechanical stimuli (∼60 s). Moreover, transient and repetitive application of the same compression modulates the neuronal firing rate. Seemingly, neuronal networks can differentiate and respond to specific characteristics of mechanical stimulation. Ultimately, the developed multiparametric tool opens the door to explore manifold nanomechanobiological responses of neuronal systems and new ways of mechanical control.
Beyond MD17: the reactive xxMD dataset
Authors: Pengmei Zihan , Liu Junyu , Shu Yinan 
Published: February 2024

AbstractSystem specific neural force fields (NFFs) have gained popularity in computational chemistry. One of the most popular datasets as a bencharmk to develop NFF models is the MD17 dataset and its subsequent extension. These datasets comprise geometries from the equilibrium region of the ground electronic state potential energy surface, sampled from direct adiabatic dynamics. However, many chemical reactions involve significant molecular geometrical deformations, for example, bond breaking. Therefore, MD17 is inadequate to represent a chemical reaction. To address this limitation in MD17, we introduce a new dataset, called Extended Excited-state Molecular Dynamics (xxMD) dataset. The xxMD dataset involves geometries sampled from direct nonadiabatic dynamics, and the energies are computed at both multireference wavefunction theory and density functional theory. We show that the xxMD dataset involves diverse geometries which represent chemical reactions. Assessment of NFF models on xxMD dataset reveals significantly higher predictive errors than those reported for MD17 and its variants. This work underscores the challenges faced in crafting a generalizable NFF model with extrapolation capability.
Bayesian spatio-temporal analysis of the COVID-19 pandemic in Catalonia
Authors: Satorra Pau , Tebé Cristian 
Published: February 2024

AbstractIn this study, we modelled the incidence of COVID-19 cases and hospitalisations by basic health areas (ABS) in Catalonia. Spatial, temporal and spatio-temporal incidence trends were described using estimation methods that allow to borrow strength from neighbouring areas and time points. Specifically, we used Bayesian hierarchical spatio-temporal models estimated with Integrated Nested Laplace Approximation (INLA). An exploratory analysis was conducted to identify potential ABS factors associated with the incidence of cases and hospitalisations. High heterogeneity in cases and hospitalisation incidence was found between ABS and along the waves of the pandemic. Urban areas were found to have a higher incidence of COVID-19 cases and hospitalisations than rural areas, while socio-economic deprivation of the area was associated with a higher incidence of hospitalisations. In addition, full vaccination coverage in each ABS showed a protective effect on the risk of COVID-19 cases and hospitalisations.
High spatiotemporal-resolution mapping for a seasonal erosion flooding inundation using time-series Landsat and MODIS images
Authors: Zhu Jingrong , Jin Yihua , Zhu Weihong , Lee Dong-Kun 
Published: February 2024

AbstractSeasonal erosion flooding events present a significant challenge for effective disaster monitoring and land degradation studies. This research addresses this challenge by harnessing the combined capabilities of time-series Landsat and MODIS images to achieve high spatiotemporal-resolution mapping of flooding during such events. The study underscores the critical importance of precise flood monitoring for disaster mitigation and informed land management. To overcome the limitations posed by the trade-off between spatial and temporal resolution in current satellite sensors, we emplyedand theflexible spatiotemporal data fusion (FSDAF) methods to produce synthetic flood images with enhanced spatiotemporal resolutions for mapping by using MODIS and Landsat data from August 29 to September 3, 2016. A comparison was made between flood maps from several post-disaster forecasts based on ground-obtained time-series images of the Tumen River flood in China. According to the FSDAF approach, the input Landsat image of March 25, 2016, and the fused results had a root mean square error (RMSE) of 0.0301, average difference of 0.001, r of 0.941, and structure similarity indexof 0.939, indicating that temporal variation data had been effectively incorporated into a forecast on August 16, 2016. Results also indicated that the FSDAF forecast values are lower than those from the actual Landsat image. The results of the study also showed that the generated images could be effectively used for flood mapping. By using our newly developed simulation model, we were able to produce a comprehensive map of the inundated areas during the event from August 29 to September 3, 2016. This shows that FSDAF holds great potential for flood prediction and study and has the potential to benefit further disaster-related land degradation by combining multi-source images to provide high temporal and spatial resolution remote sensing information.
Controlled release herbicide formulation for effective weed control efficacy
Authors: Paul Santosh Kumar , Xi Yunfei , Sanderson Peter , Naidu Ravi 
Published: February 2024

AbstractControlled release formulation (CRF) of herbicide is an effective weed management technique with less eco-toxicity than other available commercial formulations. To maximise the effectiveness of CRFs however, it is crucial to understand the herbicide-releasing behaviour at play, which predominately depends on the interaction mechanisms between active ingredients and carrier materials during adsorption. In this study, we investigated and modelled the adsorption characteristics of model herbicide 2,4-D onto two organo-montmorillonites (octadecylamine- and aminopropyltriethoxysilane-modified) to synthesise polymer-based CRFs. Herbicide-releasing behaviour of the synthesised CRF microbeads was then analysed under various experimental conditions, and weed control efficacy determined under glasshouse conditions. Results revealed that adsorption of 2,4-D onto both organo-montmorillonites follows the pseudo-second-order kinetics model and is predominately controlled by the chemisorption process. However, multi-step mechanisms were detected in the adsorption on both organoclays, hence intra-particle diffusion is not the sole rate-limiting step for the adsorption process. Both organoclays followed the Elovich model, suggesting they have energetically heterogeneous surfaces. Herbicide-releasing behaviours of synthesised beads were investigated at various pH temperatures and ionic strengths under laboratory and glasshouse conditions. Furthermore, weed control efficacy of synthesised beads were investigated using pot studies under glasshouse condition. Desorption studies revealed that both synthesised microbeads have slow releasing behaviour at a wide range of pHs (5–9), temperatures (25–45 °C), and ionic strengths. The results also revealed that synthesised microbeads have excellent weed control efficacy on different broad-leaf weed species under glasshouse conditions.
Survival of a microbial inoculant in soil after recurrent inoculations
Authors: Papin M. , Philippot L. , Breuil M. C. , Bru D. , Dreux-Zigha A. , Mounier A. , Le Roux X. , Rouard N. , Spor A. 
Published: February 2024

AbstractMicrobial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (106 and 108 cfu.g soil−1). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.
ALDH2 is a novel biomarker and exerts an inhibitory effect on melanoma
Authors: Lei Hua , Liao Jinfeng , Wang Xinyu , Huang Rong , Ying Chuanpeng , Yang Jianing 
Published: February 2024

AbstractMelanoma is a malignant skin tumor. This study aimed to explore and assess the effect of novel biomarkers on the progression of melanoma. Differently expressed genes (DEGs) were screened from GSE3189 and GSE46517 datasets of Gene Expression Omnibus database using GEO2R. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted based on the identified DEGs. Hub genes were identified and assessed using protein–protein interaction networks, principal component analysis, and receiver operating characteristic curves. Quantitative real-time polymerase chain reaction was employed to measure the mRNA expression levels. TIMER revealed the association between aldehyde dehydrogenase 2 (ALDH2) and tumor immune microenvironment. The viability, proliferation, migration, and invasion were detected by cell counting kit-8, 5-ethynyl-2′-deoxyuridine, wound healing, and transwell assays. Total 241 common DEGs were screened out from GSE3189 and GSE46517 datasets. We determined 6 hub genes with high prediction values for melanoma, which could distinguish tumor samples from normal samples. ALDH2, ADH1B, ALDH3A2, DPT, EPHX2, and GATM were down-regulated in A375 and SK-MEL-2 cells, compared with the human normal melanin cell line (PIG1 cells). ALDH2 was selected as the candidate gene in this research, presenting a high diagnostic and predictive value for melanoma. ALDH2 had a positive correlation with the infiltrating levels of immune cells in melanoma microenvironment. Overexpression of ALDH2 inhibited cell viability, proliferation, migration, and invasion of A375/SK-MEL-2 cells. ALDH2 is a new gene biomarker of melanoma, which exerts an inhibitory effect on melanoma.
Genome-wide identification of fitness-genes in aminoglycoside-resistant Escherichia coli during antibiotic stress
Authors: Wellner Sandra Marina , Alobaidallah Mosaed Saleh A. , Fei Xiao , Herrero-Fresno Ana , Olsen John Elmerdahl 
Published: February 2024

AbstractResistance against aminoglycosides is widespread in bacteria. This study aimed to identify genes that are important for growth of E. coli during aminoglycoside exposure, since such genes may be targeted to re-sensitize resistant E. coli to treatment. We constructed three transposon mutant libraries each containing > 230.000 mutants in E. coli MG1655 strains harboring streptomycin (aph(3″)-Ib/aph(6)-Id), gentamicin (aac(3)-IV), or neomycin (aph(3″)-Ia) resistance gene(s). Transposon Directed Insertion-site Sequencing (TraDIS), a combination of transposon mutagenesis and high-throughput sequencing, identified 56 genes which were deemed important for growth during streptomycin, 39 during gentamicin and 32 during neomycin exposure. Most of these fitness-genes were membrane-located (n = 55) and involved in either cell division, ATP-synthesis or stress response in the streptomycin and gentamicin exposed libraries, and enterobacterial common antigen biosynthesis or magnesium sensing/transport in the neomycin exposed library. For validation, eight selected fitness-genes/gene-clusters were deleted (minCDE, hflCK, clsA and cpxR associated with streptomycin and gentamicin resistance, and phoPQ, wecA, lpp and pal associated with neomycin resistance), and all mutants were shown to be growth attenuated upon exposure to the corresponding antibiotics. In summary, we identified genes that are advantageous in aminoglycoside-resistant E. coli during antibiotic stress. In addition, we increased the understanding of how aminoglycoside-resistant E. coli respond to antibiotic exposure.
Association between triglyceride glucose index and total bone mineral density: a cross-sectional study from NHANES 2011–2018
Authors: Tian Ningsheng , Chen Shuai , Han Huawei , Jin Jie , Li Zhiwei 
Published: February 2024

AbstractThe Homeostatic Model Assessment for Triglyceride Glucose Index (TyG) and its related indices, including triglyceride glucose-waist circumference (TyG-WC), triglyceride glucose-waist-to-height ratio (TyG-WHtR) and triglyceride glucose-body mass index (TyG-BMI), has emerged as a practical tool for assessing insulin resistance in metabolic disorders. However, limited studies have explored the connection between TyG, TyG-related indices and osteoporosis. This population-based study, utilizing data from the National Health and Nutrition Examination Survey 2011–2018, involved 5456 participants. Through weighted multivariate linear regression and smoothed curve fitting, a significant positive correlation was found between TyG, TyG-related indices and total bone mineral density (BMD) after adjusting for covariates [β = 0.0124, 95% CI (0.0006, 0.0242), P = 0.0390; β = 0.0004, 95% CI (0.0003, 0.0004), P < 0.0001; β = 0.0116, 95% CI (0.0076, 0.0156), P < 0.0001; β = 0.0001, 95% CI (0.0001, 0.0001), P < 0.0001]. In subgroup analysis, race stratification significantly affected the relationship between TyG and total BMD. Additionally, gender and race were both significant for TyG-related indices. Non-linear relationships and threshold effects with inflection points at 9.106, 193.9265, 4.065, and 667.5304 (TyG, TyG-BMI, TyG-WHtR, TyG-WC) were identified. Saturation phenomena were observed between TyG-BMI, TyG-WC and total BMD with saturation thresholds at 314.177 and 1022.0428. These findings contributed to understanding the association between TyG, TyG-related indices and total BMD, offering insights for osteoporosis prevention and treatment.