bluuebunny/crossref_metadata_2025_split huggingface dataset:
A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58
Authors: Reid Cameron J. , Cummins Max L. , Börjesson Stefan , Brouwer Michael S. M. , Hasman Henrik , Hammerum Anette M. , Roer Louise , Hess Stefanie , Berendonk Thomas , Nešporová Kristina , Haenni Marisa , Madec Jean-Yves , Bethe Astrid , Michael Geovana B. , Schink Anne-Kathrin , Schwarz Stefan , Dolejska Monika , Djordjevic Steven P. 
Published: February 2022

AbstractEscherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.
Manipulating the oxygen reduction reaction pathway on Pt-coordinated motifs
Authors: Zhao Jiajun , Fu Cehuang , Ye Ke , Liang Zheng , Jiang Fangling , Shen Shuiyun , Zhao Xiaoran , Ma Lu , Shadike Zulipiya , Wang Xiaoming , Zhang Junliang , Jiang Kun 
Published: February 2022

AbstractElectrochemical oxygen reduction could proceed via either 4e−-pathway toward maximum chemical-to-electric energy conversion or 2e−-pathway toward onsite H2O2 production. Bulk Pt catalysts are known as the best monometallic materials catalyzing O2-to-H2O conversion, however, controversies on the reduction product selectivity are noted for atomic dispersed Pt catalysts. Here, we prepare a series of carbon supported Pt single atom catalyst with varied neighboring dopants and Pt site densities to investigate the local coordination environment effect on branching oxygen reduction pathway. Manipulation of 2e− or 4e− reduction pathways is demonstrated through modification of the Pt coordination environment from Pt-C to Pt-N-C and Pt-S-C, giving rise to a controlled H2O2 selectivity from 23.3% to 81.4% and a turnover frequency ratio of H2O2/H2O from 0.30 to 2.67 at 0.4 V versus reversible hydrogen electrode. Energetic analysis suggests both 2e− and 4e− pathways share a common intermediate of *OOH, Pt-C motif favors its dissociative reduction while Pt-S and Pt-N motifs prefer its direct protonation into H2O2. By taking the Pt-N-C catalyst as a stereotype, we further demonstrate that the maximum H2O2 selectivity can be manipulated from 70 to 20% with increasing Pt site density, providing hints for regulating the stepwise oxygen reduction in different application scenarios.
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber
Authors: Li Hongbo , Wang Shenhao , Chai Sen , Yang Zhiquan , Zhang Qiqi , Xin Hongjia , Xu Yuanchao , Lin Shengnan , Chen Xinxiu , Yao Zhiwang , Yang Qingyong , Fei Zhangjun , Huang Sanwen , Zhang Zhonghua 
Published: February 2022

AbstractStructural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber (Cucumis sativus L.) have been hindered by the lack of a high-quality pan-genome. Here, we report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies. Genotyping of seven large chromosomal rearrangements based on the pan-genome provides useful information for use of wild accessions in breeding and genetic studies. A total of ~4.3 million genetic variants including 56,214 SVs are identified leveraging the chromosome-level assemblies. The pan-genome graph integrating both variant information and reference genome sequences aids the identification of SVs associated with agronomic traits, including warty fruits, flowering times and root growth, and enhances the understanding of cucumber trait evolution. The graph-based cucumber pan-genome and the identified genetic variants provide rich resources for future biological research and genomics-assisted breeding.
Tropical cyclone climatology change greatly exacerbates US extreme rainfall–surge hazard
Authors: Gori Avantika , Lin Ning , Xi Dazhi , Emanuel Kerry 
Published: February 2022

AbstractTropical cyclones (TCs) are drivers of extreme rainfall and surge, but the current and future TC rainfall–surge joint hazard has not been well quantified. Using a physics-based approach to simulate TC rainfall and storm tides, we show drastic increases in the joint hazard from historical to projected future (SSP5–8.5) conditions. The frequency of joint extreme events (exceeding both hazards’ historical 100-year levels) may increase by 7–36-fold in the southern US and 30–195-fold in the Northeast by 2100. This increase in joint hazard is induced by sea-level rise and TC climatology change; the relative contribution of TC climatology change is higher than that of sea-level rise for 96% of the coast, largely due to rainfall increases. Increasing storm intensity and decreasing translation speed are the main TC change factors that cause higher rainfall and storm tides and up to 25% increase in their dependence.
Large-scale deep multi-layer analysis of Alzheimer’s disease brain reveals strong proteomic disease-related changes not observed at the RNA level
Authors: Johnson Erik C. B. , Carter E. Kathleen , Dammer Eric B. , Duong Duc M. , Gerasimov Ekaterina S. , Liu Yue , Liu Jiaqi , Betarbet Ranjita , Ping Lingyan , Yin Luming , Serrano Geidy E. , Beach Thomas G. , Peng Junmin , De Jager Philip L. , Haroutunian Vahram , Zhang Bin , Gaiteri Chris , Bennett David A. , Gearing Marla , Wingo Thomas S. , Wingo Aliza P. , Lah James J. , Levey Allan I. , Seyfried Nicholas T. 
Published: February 2022

AbstractThe biological processes that are disrupted in the Alzheimer’s disease (AD) brain remain incompletely understood. In this study, we analyzed the proteomes of more than 1,000 brain tissues to reveal new AD-related protein co-expression modules that were highly preserved across cohorts and brain regions. Nearly half of the protein co-expression modules, including modules significantly altered in AD, were not observed in RNA networks from the same cohorts and brain regions, highlighting the proteopathic nature of AD. Two such AD-associated modules unique to the proteomic network included a module related to MAPK signaling and metabolism and a module related to the matrisome. The matrisome module was influenced by the APOE ε4 allele but was not related to the rate of cognitive decline after adjustment for neuropathology. By contrast, the MAPK/metabolism module was strongly associated with the rate of cognitive decline. Disease-associated modules unique to the proteome are sources of promising therapeutic targets and biomarkers for AD.
French crop yield, area and production data for ten staple crops from 1900 to 2018 at county resolution
Authors: Schauberger Bernhard , Kato Hiromi , Kato Tomomichi , Watanabe Daiki , Ciais Philippe 
Published: February 2022

AbstractAgricultural performance is influenced by environmental conditions, management decisions and economic circumstances. It is important to quantify their respective contribution to allow for detecting major hazards to production, projecting future yields under climate change and deriving adaptation options. For this purpose, time series of agricultural yields with high spatial and long-term temporal resolution are a primary requisite. Here we present a data set of crop performance in France, one of Europe’s major crop producers. The data set comprises ten crops (barley, maize, oats, potatoes, rapeseed, sugarbeet, sunflower, durum wheat, soft wheat and wine) and covers the years 1900 to 2018. It contains harvested area, production and yield data for all 96 French départements (i.e. counties or NUTS3 level) with a total number of 375,264 data points. Entries until 1988 have been digitized manually from statistical yearbooks. The technical validation indicates a high consistency of the data set within itself and with external resources. The data set may contribute to an enhanced understanding of the manifold influences on agricultural performance.
Agent-based models for detecting the driving forces of biomolecular interactions
Authors: Maestri Stefano , Merelli Emanuela , Pettini Marco 
Published: February 2022

AbstractAgent-based modelling and simulation have been effectively applied to the study of complex biological systems, especially when composed of many interacting entities. Representing biomolecules as autonomous agents allows this approach to bring out the global behaviour of biochemical processes as resulting from local molecular interactions. In this paper, we leverage the capabilities of the agent paradigm to construct an in silico replica of the glycolytic pathway; the aim is to detect the role that long-range electrodynamic forces might have on the rate of glucose oxidation. Experimental evidences have shown that random encounters and short-range potentials might not be sufficient to explain the high efficiency of biochemical reactions in living cells. However, while the latest in vitro studies are limited by present-day technology, agent-based simulations provide an in silico support to the outcomes hitherto obtained and shed light on behaviours not yet well understood. Our results grasp properties hard to uncover through other computational methods, such as the effect of electromagnetic potentials on glycolytic oscillations.
Voltage imaging in the olfactory bulb using transgenic mouse lines expressing the genetically encoded voltage indicator ArcLight
Authors: Platisa Jelena , Zeng Hongkui , Madisen Linda , Cohen Lawrence B. , Pieribone Vincent A. , Storace Douglas A. 
Published: February 2022

AbstractGenetically encoded voltage indicators (GEVIs) allow optical recordings of membrane potential changes in defined cell populations. Transgenic reporter animals that facilitate precise and repeatable targeting with high expression levels would further the use of GEVIs in the in vivo mammalian brain. However, the literature on developing and applying transgenic mouse lines as vehicles for GEVI expression is limited. Here we report the first in vivo experiments using a transgenic reporter mouse for the GEVI ArcLight, which utilizes a Cre/tTA dependent expression system (TIGRE 1.0). We developed two mouse lines with ArcLight expression restricted to either olfactory receptor neurons, or a subpopulation of interneurons located in the granule and glomerular layers in the olfactory bulb. The ArcLight expression in these lines was sufficient for in vivo imaging of odorant responses in single trials using epifluorescence and 2-photon imaging. The voltage responses were odor-specific and concentration-dependent, which supported earlier studies about perceptual transformations carried out by the bulb that used calcium sensors of neural activity. This study demonstrates that the ArcLight transgenic line is a flexible genetic tool that can be used to record the neuronal electrical activity of different cell types with a signal-to-noise ratio that is comparable to previous reports using viral transduction.
Adapting to the pandemic: longitudinal effects of social restrictions on time perception and boredom during the Covid-19 pandemic in Germany
Authors: Wessels Marlene , Utegaliyev Nariman , Bernhard Christoph , Welsch Robin , Oberfeld Daniel , Thönes Sven , von Castell Christoph 
Published: February 2022

AbstractWith the Covid-19 pandemic, many governments introduced nationwide lockdowns that disrupted people’s daily routines and promoted social isolation. We applied a longitudinal online survey to investigate the mid-term effects of the mandated restrictions on the perceived passage of time (PPT) and boredom during and after a strict lockdown in Germany. One week after the beginning of the lockdown in March 2020, respondents reported a slower PPT and increased boredom compared to the pre-pandemic level. However, in the course of the lockdown, PPT accelerated and boredom decreased again until August 2020. Then, in October 2020, when incidence rates sharply rose and new restrictions were introduced, we again observed a slight trend toward a slowing of PPT and an increase of boredom. Our data also show that as the pandemic progressed, respondents adjusted their predictions about the pandemic’s duration substantially upward. In sum, our findings suggest that respondents adapted to the pandemic situation and anticipated it as the new “normal”. Furthermore, we determined perceived boredom and the general emotional state to be predictive of PPT, while depressive symptoms played a minor role.
Energy homeostasis genes modify the association between serum concentrations of IGF-1 and IGFBP-3 and breast cancer risk
Authors: Rodríguez-Valentín Rocío , Torres-Mejía Gabriela , Martínez-Matsushita Louis , Angeles-Llerenas Angélica , Gómez-Flores-Ramos Liliana , Wolff Roger K. , Baumgartner Kathy B. , Hines Lisa M. , Ziv Elad , Flores-Luna Lourdes , Sánchez-Zamorano Luisa Ma. , Ortiz-Panozo Eduardo , Slattery Martha L. 
Published: February 2022

AbstractBreast cancer is a multifactorial disease in which the interplay among multiple risk factors remains unclear. Energy homeostasis genes play an important role in carcinogenesis and their interactions with the serum concentrations of IGF-1 and IGFBP-3 on the risk of breast cancer have not yet been investigated. The aim of this study was to assess the modifying effect of the genetic variation in some energy homeostasis genes on the association of serum concentrations of IGF-1 and IGFBP-3 with breast cancer risk. We analyzed 78 SNPs from 10 energy homeostasis genes in premenopausal women from the 4-Corner’s Breast Cancer Study (61 cases and 155 controls) and the Mexico Breast Cancer Study (204 cases and 282 controls). After data harmonization, 71 SNPs in HWE were included for interaction analysis. Two SNPs in two genes (MBOAT rs13272159 and NPY rs16131) showed an effect modification on the association between IGF-1 serum concentration and breast cancer risk (Pinteraction < 0.05, adjusted Pinteraction < 0.20). In addition, five SNPs in three genes (ADIPOQ rs182052, rs822391 and rs7649121, CARTPT rs3846659, and LEPR rs12059300) had an effect modification on the association between IGFBP-3 serum concentration and breast cancer risk (Pinteraction < 0.05, adjusted Pinteraction < 0.20). Our findings showed that variants of energy homeostasis genes modified the association between the IGF-1 or IGFBP-3 serum concentration and breast cancer risk in premenopausal women. These findings contribute to a better understanding of this multifactorial pathology.
Organic matter removal in a simultaneous nitrification–denitrification process using fixed-film system
Authors: González-Tineo P. , Aguilar A. , Reynoso A. , Durán U. , Garzón-Zúñiga M. , Meza-Escalante E. , Álvarez L. , Serrano D. 
Published: February 2022

AbstractSwine wastewater treatment is a complex challenge, due to the high organic matter (OM) and nitrogen (N) concentrations which require an efficient process. This study focused on evaluating two different support media for OM and N removal from an Upflow Anaerobic Sludge Blanket (UASB) reactor fed with swine wastewater. Maximum specific nitrification (MSNA) and denitrification (MSDA) activity test for both biofilm and suspended biomass were carried out using as supports: polyurethane foam (R1) and polyethylene rings (R2). The results showed that R2 system was more efficiently than R1, reaching OM removal of 77 ± 8% and N of 98 ± 4%, attributed to higher specific denitrifying activity recorded (5.3 ± 0.34 g NO3-N/g TVS∙h). Furthermore, 40 ± 5% of the initial N in the wastewater could have been transformed into molecular nitrogen through SND, of which only 10 ± 1% was volatilized. In this sense, MSDA tests indicated that suspended biomass was responsible for at least 70% of N removal and only 20% can be attributed to biofilm. SND could be confirmed with the analysis of microbial diversity, due to the presence of the genus Pseudomonas dominated the prokaryotic community of the system in 54.4%.
Abnormal corneal nerve morphology and brain volume in patients with schizophrenia
Authors: Ponirakis Georgios , Ghandi Reem , Ahmed Amani , Gad Hoda , Petropoulos Ioannis N. , Khan Adnan , Elsotouhy Ahmed , Vattoth Surjith , Alshawwaf Mahmoud K. M. , Khoodoruth Mohamed Adil Shah , Ramadan Marwan , Bhagat Anjushri , Currie James , Mahfoud Ziyad , Al Hamad Hanadi , Own Ahmed , M. Haddad Peter , Alabdulla Majid , Malik Rayaz A. , Woodruff Peter W. 
Published: February 2022

AbstractNeurodevelopmental and neurodegenerative pathology occur in Schizophrenia. This study compared the utility of corneal confocal microscopy (CCM), an ophthalmic imaging technique with MRI brain volumetry in quantifying neuronal pathology and its relationship to cognitive dysfunction and symptom severity in schizophrenia. Thirty-six subjects with schizophrenia and 26 controls underwent assessment of cognitive function, symptom severity, CCM and MRI brain volumetry. Subjects with schizophrenia had lower cognitive function (P ≤ 0.01), corneal nerve fiber density (CNFD), length (CNFL), branch density (CNBD), CNBD:CNFD ratio (P < 0.0001) and cingulate gyrus volume (P < 0.05) but comparable volume of whole brain (P = 0.61), cortical gray matter (P = 0.99), ventricle (P = 0.47), hippocampus (P = 0.10) and amygdala (P = 0.68). Corneal nerve measures and cingulate gyrus volume showed no association with symptom severity (P = 0.35–0.86 and P = 0.50) or cognitive function (P = 0.35–0.86 and P = 0.49). Corneal nerve measures were not associated with metabolic syndrome (P = 0.61–0.64) or diabetes (P = 0.057–0.54). The area under the ROC curve distinguishing subjects with schizophrenia from controls was 88% for CNFL, 84% for CNBD and CNBD:CNFD ratio, 79% for CNFD and 73% for the cingulate gyrus volume. This study has identified a reduction in corneal nerve fibers and cingulate gyrus volume in schizophrenia, but no association with symptom severity or cognitive dysfunction. Corneal nerve loss identified using CCM may act as a rapid non-invasive surrogate marker of neurodegeneration in patients with schizophrenia.
Suppression of non-selected solutions as a possible brain mechanism for ambiguity resolution in the word fragment task completion task
Authors: Kireev Maxim , Korotkov Alexander , Masharipov Ruslan , Zheltyakova Maya , Cherednichenko Denis , Gershkovich Valeria , Moroshkina Nadezhda , Slioussar Natalia , Allakhverdov Victor , Chernigovskaya Tatiana 
Published: February 2022

AbstractBrain systems dealing with multiple meanings of ambiguous stimuli are relatively well studied, while the processing of non-selected meanings is less investigated in the neurophysiological literature and provokes controversy between existing theories. It is debated whether these meanings are actively suppressed and, if yes, whether suppression characterizes any task that involves alternative solutions or only those tasks that emphasize semantic processing or the existence of alternatives. The current functional MRI event-related study used a modified version of the word fragment completion task to reveal brain mechanisms involved in implicit processing of the non-selected solutions of ambiguous fragments. The stimuli were pairs of fragmented adjectives and nouns. Noun fragments could have one or two solutions (resulting in two words with unrelated meanings). Adjective fragments had one solution and created contexts strongly suggesting one solution for ambiguous noun fragments. All fragmented nouns were presented twice during the experiment (with two different adjectives). We revealed that ambiguity resolution was associated with a reduced BOLD signal within several regions related to language processing, including the anterior hippocampi and amygdala and posterior lateral temporal cortex. Obtained findings were interpreted as resulting from brain activity inhibition, which underlies a hypothesized mechanism of suppression of non-selected solutions.
The gut virome in two indigenous populations from Malaysia
Authors: Lee Chuen Zhang , Zoqratt Muhammad Zarul Hanifah Md , Phipps Maude E. , Barr Jeremy J. , Lal Sunil K. , Ayub Qasim , Rahman Sadequr 
Published: February 2022

AbstractThe human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no standardized protocols. This study established an effective workflow for virome analysis to investigate the virome of stool samples from two understudied ethnic groups from Malaysia: the Jakun and Jehai Orang Asli. By using the virome extraction and analysis workflow with the Oxford Nanopore Technology, long-read sequencing successfully captured close to full-length viral genomes. The virome composition of the two indigenous Malaysian communities were remarkably different from those found in other parts of the world. Additionally, plant viruses found in the viromes of these individuals were attributed to traditional food-seeking methods. This study establishes a human gut virome workflow and extends insights into the healthy human gut virome, laying the groundwork for comparative studies.
A wave finite element approach for modelling wave transmission through laminated plate junctions
Authors: Aimakov Nurkanat , Tanner Gregor , Chronopoulos Dimitrios 
Published: February 2022

AbstractWe present a numerical method for computing reflection and transmission coefficients at joints connecting composite laminated plates. The method is based on modelling joints with finite elements with boundary conditions given by the solutions of the wave finite element method for the plates in the infinite half-spaces connected to the joint. There are no restrictions on the number of plates, inter-plate angles, and material parameters of individual layers forming the composite. An L-shaped laminated plate junction is discussed in more detail. Comparisons of numerically predicted scattering coefficients with semi-analytical solutions for the selected structures are presented. The results obtained are essential for statistical energy analysis and dynamical energy analysis based calculations of the wave energy distribution in full built-up structure.