bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish
Authors: Vernaz Grégoire , Hudson Alan G. , Santos M. Emília , Fischer Bettina , Carruthers Madeleine , Shechonge Asilatu H. , Gabagambi Nestory P. , Tyers Alexandra M. , Ngatunga Benjamin P. , Malinsky Milan , Durbin Richard , Turner George F. , Genner Martin J. , Miska Eric A. 
Published: October 2022

AbstractEpigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges. Here, we assess the epigenetic basis of diversification during the early stages of speciation. Specifically, we focus on the extent and functional relevance of DNA methylome divergence in the very young radiation of Astatotilapia calliptera in crater Lake Masoko, southern Tanzania. Our study focuses on two lake ecomorphs that diverged approximately 1,000 years ago and a population in the nearby river from which they separated approximately 10,000 years ago. The two lake ecomorphs show no fixed genetic differentiation, yet are characterized by different morphologies, depth preferences and diets. We report extensive genome-wide methylome divergence between the two lake ecomorphs, and between the lake and river populations, linked to key biological processes and associated with altered transcriptional activity of ecologically relevant genes. Such genes differing between lake ecomorphs include those involved in steroid metabolism, hemoglobin composition and erythropoiesis, consistent with their divergent habitat occupancy. Using a common-garden experiment, we found that global methylation profiles are often rapidly remodeled across generations but ecomorph-specific differences can be inherited. Collectively, our study suggests an epigenetic contribution to the early stages of vertebrate speciation.
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults
Authors: Kalantar Katrina L. , Neyton Lucile , Abdelghany Mazin , Mick Eran , Jauregui Alejandra , Caldera Saharai , Serpa Paula Hayakawa , Ghale Rajani , Albright Jack , Sarma Aartik , Tsitsiklis Alexandra , Leligdowicz Aleksandra , Christenson Stephanie A. , Liu Kathleen , Kangelaris Kirsten N. , Hendrickson Carolyn , Sinha Pratik , Gomez Antonio , Neff Norma , Pisco Angela , Doernberg Sarah B. , Derisi Joseph L. , Matthay Michael A. , Calfee Carolyn S. , Langelier Charles R. 
Published: October 2022

AbstractWe carried out integrated host and pathogen metagenomic RNA and DNA next generation sequencing (mNGS) of whole blood (n = 221) and plasma (n = 138) from critically ill patients following hospital admission. We assigned patients into sepsis groups on the basis of clinical and microbiological criteria. From whole-blood gene expression data, we distinguished patients with sepsis from patients with non-infectious systemic inflammatory conditions using a trained bagged support vector machine (bSVM) classifier (area under the receiver operating characteristic curve (AUC) = 0.81 in the training set; AUC = 0.82 in a held-out validation set). Plasma RNA also yielded a transcriptional signature of sepsis with several genes previously reported as sepsis biomarkers, and a bSVM sepsis diagnostic classifier (AUC = 0.97 training set; AUC = 0.77 validation set). Pathogen detection performance of plasma mNGS varied on the basis of pathogen and site of infection. To improve detection of virus, we developed a secondary transcriptomic classifier (AUC = 0.94 training set; AUC = 0.96 validation set). We combined host and microbial features to develop an integrated sepsis diagnostic model that identified 99% of microbiologically confirmed sepsis cases, and predicted sepsis in 74% of suspected and 89% of indeterminate sepsis cases. In summary, we suggest that integrating host transcriptional profiling and broad-range metagenomic pathogen detection from nucleic acid is a promising tool for sepsis diagnosis.
Growth temperature and chromatinization in archaea
Authors: Hocher Antoine , Borrel Guillaume , Fadhlaoui Khaled , Brugère Jean-François , Gribaldo Simonetta , Warnecke Tobias 
Published: October 2022

AbstractDNA in cells is associated with proteins that constrain its structure and affect DNA-templated processes including transcription and replication. HU and histones are the main constituents of chromatin in bacteria and eukaryotes, respectively, with few exceptions. Archaea, in contrast, have diverse repertoires of nucleoid-associated proteins (NAPs). To analyse the evolutionary and ecological drivers of this diversity, we combined a phylogenomic survey of known and predicted NAPs with quantitative proteomic data. We identify the Diaforarchaea as a hotbed of NAP gain and loss, and experimentally validate candidate NAPs in two members of this clade, Thermoplasma volcanium and Methanomassiliicoccus luminyensis. Proteomic analysis across a diverse sample of 19 archaea revealed that NAP investment varies from <0.03% to >5% of total protein. This variation is predicted by growth temperature. We propose that high levels of chromatinization have evolved as a mechanism to prevent uncontrolled helix denaturation at higher temperatures, with implications for the origin of chromatin in both archaea and eukaryotes.
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery
Authors: Benns H. J. , Storch M. , Falco J. A. , Fisher F. R. , Tamaki F. , Alves E. , Wincott C. J. , Milne R. , Wiedemar N. , Craven G. , Baragaña B. , Wyllie S. , Baum J. , Baldwin G. S. , Weerapana E. , Tate E. W. , Child M. A. 
Published: October 2022

AbstractNucleophilic amino acids are important in covalent drug development yet underutilized as anti-microbial targets. Chemoproteomic technologies have been developed to mine chemically accessible residues via their intrinsic reactivity towards electrophilic probes but cannot discern which chemically reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based oligo recombineering (CORe) platform to support the rapid identification, functional prioritization and rational targeting of chemically reactive sites in haploid systems. Our approach couples protein sequence and function with biological fitness of live cells. Here we profile the electrophile sensitivity of proteinogenic cysteines in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. Electrophile-sensitive cysteines decorating the ribosome were found to be critical for parasite growth, with target-based screening identifying a parasite-selective anti-malarial lead molecule and validating the apicomplexan translation machinery as a target for ongoing covalent ligand development.
Ultrafast visualization of an electric field under the Lorentz transformation
Authors: Ota Masato , Kan Koichi , Komada Soichiro , Wang Youwei , Agulto Verdad C. , Mag-usara Valynn Katrine , Arikawa Yasunobu , Asakawa Makoto R. , Sakawa Youichi , Matsui Tatsunosuke , Nakajima Makoto 
Published: October 2022

AbstractIn special relativity, four-vectors, such as space–time, energy–momentum and electromagnetic potential vectors, follow the Lorentz transformation. The transformations of space–time and energy–momentum vectors have been tested by time dilation and rest mass energy experiments, respectively. However, the Lorentz transformation of electromagnetic potentials has never been directly demonstrated in experiments due to the limitations of the diagnostics. Here we show the spatiotemporal electric-field profiles around a highly energetic electron beam with a subpicosecond temporal resolution obtained by a terahertz technique based on electro-optic sampling. We observe the Coulomb field contraction in the propagation direction of the beam under the Lorentz transformation. After passing the beam through a metallic plate, we investigate the birth of the Coulomb field around it and follow the spatiotemporal evolution of the spherical wavefront, which is derived by the Liénard–Wiechert potentials. The measured electric-field profile in the far propagation distance is experimentally confirmed to coincide with the calculation of the Liénard–Wiechert potentials and the Lorentz transformation. Our ultrafast measurement of a spatiotemporal relativistic electric field provides both additional experimental evidence of special relativity and a platform for detailed experimental research of energetic charged particle beams and electromagnetic radiation physics.
Modeling gene × environment interactions in PTSD using human neurons reveals diagnosis-specific glucocorticoid-induced gene expression
Authors: Seah Carina , Breen Michael S. , Rusielewicz Tom , Bader Heather N. , Xu Changxin , Hunter Christopher J. , McCarthy Barry , Deans P. J. Michael , Chattopadhyay Mitali , Goldberg Jordan , Dobariya Saunil , Desarnaud Frank , Makotkine Iouri , Flory Janine D. , Bierer Linda M. , Staniskyte Migle ,   NYSCF Global Stem Cell Array® Team, Bauer Lauren , Brenner Katie , Buckley-Herd Geoff , DesMarteau Sean , Fenton Patrick , Ferrarotto Peter , Hall Jenna , Jacob Selwyn , Kroeker Travis , Lallos Gregory , Martinez Hector , McCoy Paul , Monsma Frederick J. , Moroziewicz Dorota , Otto Reid , Reggio Kathryn , Sun Bruce , Tibbets Rebecca , Shin Dong Woo , Zhou Hongyan , Zimmer Matthew , Noggle Scott A. , Huckins Laura M. , Paull Daniel , Brennand Kristen J. , Yehuda Rachel 
Published: October 2022

AbstractPost-traumatic stress disorder (PTSD) can develop following severe trauma, but the extent to which genetic and environmental risk factors contribute to individual clinical outcomes is unknown. Here, we compared transcriptional responses to hydrocortisone exposure in human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons and peripheral blood mononuclear cells (PBMCs) from combat veterans with PTSD (n = 19 hiPSC and n = 20 PBMC donors) and controls (n = 20 hiPSC and n = 20 PBMC donors). In neurons only, we observed diagnosis-specific glucocorticoid-induced changes in gene expression corresponding with PTSD-specific transcriptomic patterns found in human postmortem brains. We observed glucocorticoid hypersensitivity in PTSD neurons, and identified genes that contribute to this PTSD-dependent glucocorticoid response. We find evidence of a coregulated network of transcription factors that mediates glucocorticoid hyper-responsivity in PTSD. These findings suggest that induced neurons represent a platform for examining the molecular mechanisms underlying PTSD, identifying biomarkers of stress response, and conducting drug screening to identify new therapeutics.
In-situ alignment of 3D printed anisotropic hard magnets
Authors: Suppan M. , Huber C. , Mathauer K. , Abert C. , Brucker F. , Gonzalez-Gutierrez J. , Schuschnigg S. , Groenefeld M. , Teliban I. , Kobe S. , Saje B. , Suess D. 
Published: October 2022

AbstractWithin this work, we demonstrate in-situ alignment of the easy axis single-crystal magnetic particles inside a polymer matrix using fused filament fabrication. Two different magnetic materials are investigated: (i) Strontium hexaferrite inside a PA6 matrix, fill grade: 49 vol% and (ii) Samarium iron nitride inside a PA12 matrix, fill grade: 44 vol%. In the presence of the external alignment field, the strontium hexaferrite particles inside the PA6 matrix can be well aligned with a ratio of remnant magnetization to saturation magnetization in an easy axis of 0.7. No significant alignment for samarium iron nitride could be achieved. The results show the feasibility to fabricate magnets with arbitrary and locally defined easy axis using fused filament fabrication since the permanent magnets (or alternatively an electromagnet) can be mounted on a rotatable platform.
Effect study of heat treatment on tensile properties of coarse sandstone
Authors: Yang Yushun , Wei Sijiang , Zhang Jihua , Wu Jingke , Zhang Chunlei 
Published: October 2022

AbstractBrazilian split experiments were carried out on coarse sandstone, obtained from a coal seam roof passed by the Shihuoshan tunnel in Xinjiang, and treated at different temperatures (room temperature 25 °C and high temperature 100 °C ~ 900 °C). The physical and mechanical characteristics of the samples were studied. The results showed that: after heat treatment, the color of the coarse sandstone samples gradually changed from dark gray to brownish red-pink; the higher the treatment temperature was, the darker the sample color. Microcracks and mineral composition changes occured in the coarse sandstone samples after heat treatment, which decreased the longitudinal wave velocity of the samples. The longitudinal wave velocity of the coarse sandstone samples decreased as a quadratic function of the treatment temperature. With the increase in longitudinal wave velocity, the tensile strength of the samples first increased and then decreased, changing as a quadratic function relationship. After heat treatment, the tensile stress–strain curve of the coarse sandstone could be divided into compaction, elasticity, plasticity, and failure stages. The energy was continuously accumulated in the coarse sandstone before its failure, and it was released suddenly after the failure. With increasing treatment temperature, the cumulative energy in the prepeak stages first increased and then decreased, reaching a maximum value at 500 °C. The prepeak energy and tensile strength of the coarse sandstone samples satisfied a linear function fitting relationship, indicating that a higher tensile strength in the coarse sandstone, led to more accumulated energy in the samples.
Centre of pressure during walking after unilateral transfemoral amputation
Authors: Ichimura Daisuke , Hisano Genki , Murata Hiroto , Kobayashi Toshiki , Hobara Hiroaki 
Published: October 2022

AbstractLower-limb amputation imposes a health burden on amputees; thus, gait assessments are required prophylactically and clinically, particularly for individuals with unilateral transfemoral amputation (UTFA). The centre of pressure (COP) during walking is one of the most useful parameters for evaluating gait. Although superimposed COP trajectories reflect the gait characteristics of individuals with neurological disorders, the quantitative characteristics based on the COP trajectories of individuals with UTFA remain unclear. Thus, these COP trajectories were investigated across a range of walking speeds in this study. The COP trajectories were recorded on a split-belt force-instrumented treadmill at eight walking speeds. Asymmetry and variability parameters were compared based on the COP trajectories of 25 individuals with UTFA and 25 able-bodied controls. The COP trajectories of the individuals with UTFA were significantly larger in lateral asymmetry and variability but did not show significant differences in anterior–posterior variability compared with those of the able-bodied controls. Further, the individuals with UTFA demonstrated larger lateral asymmetry at lower speeds. These results suggest that (1) individuals with UTFA adopt orientation-specific balance control strategies during gait and (2) individuals with UTFA could also be exposed to a higher risk of falling at lower walk speeds.
Dynamic econometric analysis on influencing factors of production efficiency in construction industry of Guangxi province in China
Authors: Ouyang Ting , Liu Fengtao , Huang Bingzhang 
Published: October 2022

AbstractChina's construction industry has assumed an important role in China's urbanization process, improving China's urban landscape and the level of national production and living facilities, but the productivity of the construction industry in some regions of China is still at a relatively low level. Taking the construction industry in Guangxi province in southwest China as an example, this paper analyzes the relevant indexes affecting the total factor productivity level of the regional construction industry and composes the statistical relationships among the indexes using dynamic measurement methods, and obtains that: (1) The number of employees, enterprises, labor productivity and construction profit have positive influence on the total factor productivity of Guangxi construction industry, but the improvement of regional construction gross product does not drive the improvement of technical equipment rate; (2) There is a dynamic equilibrium relationship between input and output indicators of total factor productivity of Guangxi construction industry, and the positive driving effect of output indicators on input indicators is not obvious; the influence of input indicators on output indicators is greater, and the positive influence is more. Accordingly, this paper also puts forward corresponding suggestions to promote the technical production level of Guangxi's construction industry.
Novel insights into the geochemical evaluation of polymer drive composition on surfactant retention in carbonates using the surface complexation modeling
Authors: Khurshid Ilyas , Afgan Imran 
Published: October 2022

AbstractSurfactant-polymer (SP) flooding is considered an efficient technique to increase the recovery of oil, especially from carbonates reservoirs, because of their complex nature. The objective of this study is to analyze the effect of polymer drive composition on surfactant retention. We developed a geochemical model that uses various surface complexation reactions at the mineral/brine interface, oil/brine interface, surfactant/brine interface, and oil/surfactant interface. We also incorporated four new surface complexation reactions that honor oil/surfactant geochemical interaction to determine the influence of polymer composition on surface retention for the first time. Then we validated the developed geochemical model against coreflooding experimental data. Additionally, we investigated the influence of various parameters of polymer drive on surface retention under high temperature and salinity using the suggested surface complexation model. The findings showed that our surface complexation model can estimate surfactant retention and its concentration in the effluent with a certain accuracy during polymer drive. The developed geochemical model is validated against single-phase and two-phase coreflooding experimental data. The findings revealed that for a more representative and accurate estimation of surfactant retention in chemical flooding, it is important to consider the oil/surfactant surface complexation reactions. Moreover, the detailed and comprehensive analysis showed that with the increase in temperature of the polymer drive, the retention of surfactant increases, and its concentration in the effluent decreases. The latter shows that surfactant retention is a more chemical process as opposed to physio-retention. It is also shown that the injection of a specific composition of polymer drive after a surfactant slug could decrease the surfactant retention, which is related to the force of repulsion between the ionic species and the rock surface. Moreover, the effect of hard ions (calcium and magnesium) in polymer drive is significant where the increase in the concentration of hard ions increases the retention of surfactant. Furthermore, it is important to mention that the lowest level of surfactant retention was achieved through a certain composition of polymer drive, thus the polymer solution dilution is not an effective approach. This is the first study to test a novel formulation of surface complexation modeling that considers the oil/surfactant effect on surfactant retention corresponding to the composition of polymer drive. The suggested framework to determine surfactant retention is conducted for harsh reservoir conditions of temperature and salinity and suggests that the surface complexation reactions for all rock-forming minerals must be considered.
Physicochemical, structural analysis of coal discards (and sewage sludge) (co)-HTC derived biochar for a sustainable carbon economy and evaluation of the liquid by-product
Authors: Kahilu Gentil Mwengula , Bada Samson , Mulopo Jean 
Published: October 2022

AbstractThis study focused on the hydrothermal treatment (HTC) of coal tailings (CT) and coal slurry (CS) and the co-hydrothermal treatment (Co-HTC) of CT, CS and sewage sludge to assess the potential for increasing the carbon content of the hydrochar produced as an enabler for a sustainable carbon economy. The optimal combination methodology and response surface methodology were used to study the relationship between the important process parameters, namely temperature, pressure, residence time, the coal-to-sewage-sludge ratio, and the carbon yield of the produced hydrochar. The optimized conditions for hydrochar from coal tailing (HCT) and hydrochar from coal slurry (HCS) (150 °C, 27 bar, 95 min) increased fixed carbon from 37.31% and 53.02% to 40.31% and 57.69%, respectively, the total carbon content improved from 42.82 to 49.80% and from 61.85 to 66.90% respectively whereas the ash content of coal discards decreased from 40.32% and 24.17% to 38.3% and 20.0% when compared CT and CS respectively. Optimized Co-HTC conditions (208 °C, 22.5bars, and 360 min) for Hydrochar from the blend of coal discards and sewage sludge (HCB) increased the fixed carbon on a dry basis and the total carbon content from 38.67% and 45.64% to 58.82% and 67.0%, when compared CT and CS respectively. Carbonization yields for HCT, HCS, and HCB were, respectively, 113.58%, 102.42%, and 129.88%. HTC and Co-HTC increase the calorific value of CT and CS, to 19.33 MJ/kg, 25.79 MJ/kg, respectively. The results further show that under Co-HTC conditions, the raw biomass undergoes dehydration and decarboxylation, resulting in a decrease in hydrogen from 3.01%, 3.56%, and 3.05% to 2.87%, 2.98%, and 2.75%, and oxygen from 8.79%, 4.78, and 8.2% to 5.83%, 2.75%, and 6.00% in the resulting HCT, HCS, and HCB, respectively. HTC and Co-HTC optimal conditions increased the specific surface area of the feedstock from 6.066 m2/g and 6.37 m2/g to 11.88 m2/g and 14.35 m2/g, for CT and CS, respectively. Total pore volume rose to 0.071 cm3/g from 0.034 cm3/g, 0.048 cm3/g, and 0.09 cm3/g proving the ability of HTC to produce high-quality hydrochar from coal discards alone or in conjunction with sewage sludge as precursors for decontamination of polluted waters, soil decontamination applications, solid combustibles, energy storage, and environmental protection.