Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic analysis of multilayer-reinforced concrete frame structures based on NewMark-β method

Abstract The analysis method of the simplified structure formation model provides the basis for the analysis of the reinforced concrete (RC) structure under earthquake and dynamic load, which has important significance for seismic analysis of RC structure. In this paper, the three-layer RC frame structure is simulated and analyzed by MATLAB based on the NewMark-β method, considering the influence of time-varying simple harmonic loads and seismic waves on acceleration, displacement, and velocity of RC structure. The vibration response of the RC structure is analyzed by introducing the stiffness reduction coefficient. The results show that NewMark-β method provides a new idea for the seismic response of RC frame structures, making the seismic analysis of frame structures more practical; the variation range of its elastic modulus is obtained through the analysis of the constitutive model of RC, which provides the basis for the value of the stiffness coefficient; the application of the top load and the bottom load has different structural responses to the RC frame structure, and the impact of the load on the structure is more adverse when the load acts on the bottom; with the change of time, the binding stiffness coefficient will also change, and the stability of the structure will decrease greatly; the function relationship between the acceleration of the third floor and the reduction coefficient of rigidity is obtained by taking different values of the reduction coefficient of rigidity. Graphical abstract
Short‐term running exercise alters DNA methylation patterns in neuronal nitric oxide synthase and brain‐derived neurotrophic factor genes in the mouse hippocampus and reduces anxiety‐like behaviors

Running exercise has beneficial effects on brain health. However, the effects of relatively short‐term running exercise (STEx) on behavior, and its underlying signaling pathways, are poorly understood. In this study, we evaluated the possibility that the regulation by STEx of brain‐derived neurotrophic factor (BDNF) and neuronal nitric oxide synthase (nNOS, encoded by NOS1), which are important molecules for anxiety regulation, might involve mechanisms of epigenetic modification, such as DNA methylation. C57BL/6J male mice were divided into sedentary (SED, n = 12) and STEx (EX, n = 15) groups; STEx was conducted with the mice for a duration of 11 days. STEx reduced anxiety‐like behaviors, and STEx reduced Nos1α and increased Bdnf exon I and IV mRNA levels in the hippocampus. Interestingly, behavioral parameters were associated with Bdnf exon I and IV and Nos1α mRNA levels in the ventral, but not dorsal, hippocampal region. However, STEx had no effect on peroxisome proliferator‐activated receptor‐γ coactivator 1α (Pgc‐1α) or fibronectin type III domain‐containing 5 (Fndc5) mRNA levels, which are relatively long‐term exercise‐induced upstream regulators of BDNF. In parallel with gene expression changes, we found, for the first time, that STEx downregulated Bdnf promoter IV and upregulated Nos1 DNA methylation levels in the hippocampus, and these patterns were partially different between the dorsal and ventral regions. These findings suggest that the beneficial effects of running exercise on mood regulation may be controlled by alterations in epigenetic mechanisms, especially in the ventral hippocampus. These effects occur even after a relatively short‐term period of exercise.
Detection and characterization of replication origins defined by DNA polymerase epsilon

Background Although the process of DNA replication is highly conserved the location of origins of replication (ORI) may vary from one tissue to the next or one round of replication to the next in eukaryotes, suggesting flexibility in the choice of locations to initiate replication. Lists of human ORI therefore vary widely in number and location and there are no methods available to compare them. Results Here we report the genome-wide localization of ORI in POLE-mutated human tumors using whole genome sequencing data. Mutations accumulated after many rounds of replication of unsynchronized dividing cell populations in tumors allow to identify constitutive origins, which we show are shared with high-fidelity between individuals and tumor types. Using a Smith–Waterman-like dynamic programming approach, we compared replication origin positions obtained from multiple different methods. The comparison allowed us to define a consensus set of replication origins, identified consistently by multiple ORI detection methods. Conclusions Many DNA features co-localized with the consensus set of ORI, including chromatin loop anchors, G-quadruplexes, S/MARs and CpGs. Among all features, the H2A.Z histone exhibited the most significant association. Our results show that mutation-based detection of replication origins is a viable approach to determining their location and associated sequence features.
CD8+ T-Cell Metabolic Rewiring Defined by Single-Cell RNA-Sequencing Identifies a Critical Role of ASNS Expression Dynamics in T-Cell Differentiation

Cytotoxic T cells dynamically rewire their metabolism during the course of an immune response. While T-cell metabolism has been extensively studied at phenotypic endpoints of activation and differentiation, the underlying dynamics remain largely elusive. Here, we leverage on single-cell RNA-sequencing (scRNA-seq) measurements of in vitro activated and differentiated CD8+ T cells cultured in physiological media to resolve these metabolic dynamics. We find that our scRNA-seq analysis identifies most metabolic changes previously defined in in vivo experiments, such as a rewiring from an oxidative to an anabolism-promoting metabolic program during activation to an effector state, which is later reverted upon memory polarization. Importantly, our scRNA-seq data further provide a dynamic description of these changes. In this sense, our data predict a differential time-dependent reliance of CD8+ T cells on the synthesis versus uptake of various non-essential amino acids during T-cell activation, which we corroborate with additional functional in vitro experiments. We further exploit our scRNA-seq data to identify metabolic genes that could potentially dictate the outcome of T-cell differentiation, by ranking them based on their expression dynamics. Among the highest-ranked hits, we find asparagine synthetase (Asns), whose expression sharply peaks for effector CD8+ T cells and further decays towards memory polarization. We then confirm that these in vitro Asns expression dynamics are representative of an in vivo situation in a mouse model of viral infection. Moreover, we find that disrupting these expression dynamics in vitro, by depleting asparagine from the culture media, delays central-memory polarization. Accordingly, we find that preventing the decay of ASNS by stable overexpression at the protein level in vivo leads to a significant increase in effector CD8+ T-cell expansion, and a concomitant decrease in central-memory formation, in a mouse model of viral infection. This shows that ASNS expression dynamics dictate the fate of CD8+ T-cell differentiation. In conclusion, we provide a resource of dynamic expression changes during CD8+ T-cell activation and differentiation that is expected to increase our understanding of the dynamic metabolic requirements of T cells progressing along the immune response cascade.
A mutation in the promoter of the pmrD gene of Shigella flexneri abrogates functional PhoPQ-PmrD-PmrAB signaling and polymyxin B resistance

Shigella spp. are the causative agent of bacillary dysentery, a major cause of food-borne morbidity and mortality worldwide. These organisms are recently evolved, polyphyletic pathovar of E. coli, and since their divergence they have undergone multiple cases of gene gain and gene loss and understanding how gene inactivation events alter bacterial behaviour represents an important objective to be better able to understand how virulence and other phenotypes are affected. Here, we identify a frameshift mutation in the pmrD gene of S. flexneri that although it would be predicted to make a functional, full-length protein, no such production occurs, likely due to the non-optimal spacing between the translational initiation site and the Shine-Dalgarno sequence. We show that this loss severs the normal connection between the PhoPQ two-component regulatory system and the PmrAB two-component regulatory system, abrogating low Mg2+ mediated cationic antimicrobial peptide and polymyxin B resistance, while maintaining normal PmrAB-mediated polymyxin B resistance. In contrast, S. sonnei maintains a functional PmrD protein and canonical signaling through this regulatory network. This species specific gene loss suggests that S. flexneri and S. sonnei have evolved different regulatory responses to changing environmental conditions.
Uncoupling of the Diurnal Growth Program by Artificial Genome Relaxation in Synechocystis sp. PCC 6803

In cyanobacteria DNA supercoiling varies over the diurnal light/dark cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knock-down of gyrase subunits and overexpression of topoisomerase I (TopoI), and characterized the phenotypes. Cell division was blocked, most likely due to inhibition of genomic but not plasmid DNA replication. Cell growth continued to 4-5x of the wildtype cell volume, and metabolic flux was redirected towards glycogen in the TopoI overexpression strain. TopoI induction initially lead to down-regulation of GC-rich and up-regulation of AT-rich genes. The response quickly bifurcated and four diurnal co-expression cohorts (dawn, noon, dusk and night) all responded differently, in part with a circadian (≈ 24 h) pattern. A GC-rich region − 50 bp of transcription start sites is differentially enriched in these four cohorts. We suggest a model where energy- and gyrase-gated transcription of growth genes at the dark/light transition (dawn) generates DNA supercoiling which then facilitates DNA replication and initiates the diurnal transcriptome program.
Interactive effects of herbivory and the level and fluctuations of nutrient availability on dominance of alien plants in synthetic native communities

Numerous studies have highlighted the role of nutrient availability and fluctuations therein for invasion success of alien plants. Others also highlighted the role of herbivores in invasion success. However, how herbivory and the level and fluctuations in nutrient availability interact in driving alien plant invasion into resident communities remains largely unexplored. We grew eight invasive alien species as target species in pot□mesocosms with five different synthetic native communities in a three-factorial design with two levels of nutrient availability (low vs high), two levels of nutrient fluctuations (constant vs pulsed) and two levels of herbivory (with vs without). The relative biomass production of the alien target plants decreased in response to an increase in nutrient availability, and increased in response to the presence of herbivores. Furthermore, herbivory could interact with changes in nutrient availability and nutrient fluctuations to affect the dominance of the alien target species (a marginally significant interaction; 90% CIs: [0.125, 2.712]). Our multispecies experiment indicates that herbivory could mediate the interactive effect of nutrient enrichment and variability in nutrient supply on invasion of alien plants into native communities. Therefore, we recommend that studies testing the fluctuating resources hypothesis should also consider interactive effect of other trophic levels.
Extracellular mechanical forces drive endocardial cell volume decrease during cardiac valve morphogenesis

Organ morphogenesis involves dynamic changes of tissue properties at the cellular scale. In addition, cells need to adapt to their mechanical environment through mechanosensitive pathways. How mechanical cues influence cell behaviors during morphogenesis, however, remains poorly understood. Here we studied the influence of mechanical forces during the formation of the atrioventricular canal (AVC) where cardiac valves develop. We show that in zebrafish the AVC forms within a zone of tissue convergence between the atrium and the ventricle which is associated with increased activation of the actomyosin meshwork and endocardial cell orientation changes. We demonstrate that tissue convergence occurs with a major reduction of endocardial cell volume triggered by mechanical forces and the mechanosensitive channels TRPP2/TRPV4. In addition, we show that the extracellular matrix component hyaluronic acid controls cell volume changes. Together, our data suggest that cell volume change is a key cellular feature activated by mechanical forces during cardiovascular morphogenesis. This work further unravels how mechanical forces and extracellular matrix can influence tissue remodeling in developing organs.
The effective family size of immigrant founders predicts their long-term demographic outcome: From Québec settlers to their 20th-century descendants

Human evolution involves population splits, size fluctuations, founder effects, and admixture. Population history reconstruction based on genetic diversity data routinely relies on simple demographic models while projecting the past. No specific demographic assumptions are needed to understand the genetic structure of the founder population of Québec. Because genealogy and genetics are intimately related, we used descending genealogies of this population to pursue the fate of its founder lineages. Maternal and paternal lines reflect the transmission of mtDNA and the Y-chromosome, respectively. We followed their transmission in real-time, from the 17th century down to its 20th-century population. We counted the number of married children of immigrants (i.e., their effective family size, EFS), estimated the proportion of successful immigrants in terms of their survival ratio, and assessed net growth rates and extinction. Likewise, we evaluated the same parameters for their Québec-born descendants. The survival ratio of the first immigrants was the highest and declined over time in association with the decreasing immigrants’ EFS. Parents with high EFS left plentiful married progeny, putting EFS as the most important variable determining the parental demographic success throughout time for generations ahead. The 17th and 18th-century immigrants bear the most remarkable demographic and genetic impact on the 20th-century population of Québec. Lessons learned from Québec genealogies can teach us about the consequences of founder effects and migrations through real people’s history. The effective family size of immigrant founders predicts their long-term demographic outcome.
Quantitation of T-lymphocyte Subsets Using the CELL-DYN Sapphire Automated Haematology Analyser

analyser (CD Sapphire; Abbott Laboratories, Abbott Jimyung Kim, Seung Ryu, Jinsook Lim, Gyechul Kwon, and Sunhoe Koo Departments of Laboratory Medicine and Emergency Medicine, Chungnam National University Hospital, Daejeon, Korea Background: Quantitative analysis of T-lymphocyte subsets is used to assess immune competency. Traditionally, T-lymphocyte subset analysis has been performed using flow cytometry, which requires complex instrumentation and relatively skilled manual operation. We evaluated the performance of an automated haematology analyser, the CELL-DYN Sapphire (CD Sapphire; Abbott Laboratories, USA) for T-lymphocyte subset analysis. Methods: The precision and linearity obtained using the CD Sapphire was evaluated. T-lymphocyte subsets in blood samples from 120 patients were quantified using CD Sapphire and flow cytometry (Cytomics FC 500; Beckman-Coulter, France). The time required for complete T cell subset analysis using both methods was also evaluated. Results: Results of CD Sapphire-based quantitation of CD3, CD3CD4, and CD3CD8 cells showed intra-assay CV of less than 5% for precision and displayed linearity in the ranges of 84 to 5364, 41 to 2615, and 44 to 2800 cells/μL, respectively. There was good correlation among the CD3, CD3CD4, and CD3CD8 cell counts as well as in the CD4/CD8 ratio (r=0.987, 0.982, 0.982, and 0.980, respectively) using CD Sapphire and flow cytometry. The mean turnaround time for the CD Sapphire (10.0±0.5 minutes) was significantly less than that for flow cytometry (111.8±8.4 minutes, P<0.001). Conclusions: T cell subset analysis using the CD Sapphire gives excellent performance and consistent results that correlate well with those obtained by flow cytometry. We conclude that this time-efficient method can replace conventional flow cytometric methods used for measuring T cell subsets. (J Lab Med Qual Assur 2014;36:39-47)
Host-symbiont stress response to lack-of-sulfide in the giant ciliate mutualism

The thiotrophic mutualism between the sulfur-oxidizing, chemoautotrophic (thiotrophic) bacterial ectosymbiont Candidatus Thiobius zoothamnicola and the giant ciliate Zoothamnium niveum thrives in a variety of shallow-water marine environments with highly fluctuating sulfide emission. To persist over time both partners must reproduce and ensure symbiont transmission prior cessation of sulfide, fueling the symbiont’s carbon fixation and host nourishment. We experimentally investigated the response of this mutualism to waning of sulfide. We found that colonies followed the r-strategy and released initially present but also newly produced macrozooids until death. A fraction of middle-sized longer-lived colonies were particularly proficient in producing and releasing swarmers. The symbionts on the colonies proliferated less and became larger and more rod-shaped under oxic conditions compared to symbionts from freshly collected colonies exposed to sulfide and oxygen. The symbiont monolayer was highly disturbed with epigrowth of other microbes and loss of symbionts that were subsequently found in the experimental seawater. We conclude that both partners’ response to cessation of sulfide emission was remarkably fast. The colony experienced death within two days but host reproduction through swarmers carrying the symbiont ensured the continuation of the association.
Anaerobic Biodegradation of Chloroform and Dichloromethane with a Dehalobacter Enrichment Culture

Chloroform (CF) and dichloromethane (DCM) are among the more commonly identified chlorinated aliphatic compounds found in contaminated soil and groundwater. One way to address this problem is to add microbes to the subsurface that can biodegrade these compounds. ABSTRACT Chloroform (CF) and dichloromethane (DCM) are among the more commonly identified chlorinated aliphatic compounds found in contaminated soil and groundwater. Complete dechlorination of CF has been reported under anaerobic conditions by microbes that respire CF to DCM and others that biodegrade DCM. The objectives of this study were to ascertain if a commercially available bioaugmentation enrichment culture (KB-1 Plus CF) uses an oxidative or fermentative pathway for biodegradation of DCM and to determine if the products from DCM biodegradation can support organohalide respiration of CF to DCM in the absence of an exogenous electron donor. In various treatments with the KB-1 Plus CF culture to which 14C-CF was added, the predominant product was 14CO2, indicating that oxidation is the predominant pathway for DCM. Recovery of 14C-DCM when biodegradation was still in progress confirmed that CF first undergoes reductive dechlorination to DCM. 14C-labeled organic acids, including acetate and propionate, were also recovered, suggesting that synthesis of organic acids provides a sink for the electron equivalents from oxidation of DCM. When the biomass was washed to remove organic acids from prior additions of exogenous electron donor and only CF and DCM were added, the culture completely dechlorinated CF. The total amount of DCM added was not sufficient to provide the electron equivalents needed to reduce CF to DCM. Thus, the additional reducing power came via the DCM generated from CF reduction. Nevertheless, the rate of CF consumption was considerably lower compared to that of treatments that received an exogenous electron donor. IMPORTANCE Chloroform (CF) and dichloromethane (DCM) are among the more commonly identified chlorinated aliphatic compounds found in contaminated soil and groundwater. One way to address this problem is to add microbes to the subsurface that can biodegrade these compounds. While microbes are known that can accomplish this task, less is known about the pathways used under anaerobic conditions. Some use an oxidative pathway, resulting mainly in carbon dioxide. Others use a fermentative pathway, resulting in formation of organic acids. In this study, a commercially available bioaugmentation enrichment culture (KB-1 Plus CF) was evaluated using carbon-14 labeled chloroform. The main product formed was carbon dioxide, indicating the use of an oxidative pathway. The reducing power gained from oxidation was shown to support reductive dechlorination of CF to DCM. The results demonstrate the potential to achieve full dechlorination of CF and DCM to nonhazardous products that are difficult to identify in the field.
Heterogeneity and dynamics of ERK and Akt activation by G protein-coupled receptors depend on the activated heterotrimeric G proteins

Kinases are fundamental regulators of cellular functions and play key roles in GPCR-mediated signaling pathways. Kinase activities are generally inferred from cell lysates, hiding the heterogeneity of the individual cellular responses to extracellular stimuli. Here, we study the dynamics and heterogeneity of ERK and Akt in genetically identical cells in response to activation of endogenously expressed GPCRs. We use kinase translocation reporters, high-content imaging, automated segmentation and clustering methods to assess cell-to-cell signaling heterogeneity. We observed ligand-concentration dependent response kinetics to histamine, α2-adrenergic, and S1P receptor stimulation that varied between cells. By using G protein inhibitors, we observed that Gq mediated the ERK and Akt responses to histamine. In contrast, Gi was necessary for ERK and Akt activation in response to α2-adrenergic receptor activation. ERK and Akt were also strongly activated by S1P, showing high heterogeneity at the single cell level, especially for ERK. In all cases, the cellular heterogeneity was not explained by distinct pre-stimulation levels or saturation of the measured response. Cluster analysis of time-series derived from 68,000 cells obtained under the different conditions revealed several distinct populations of cells that display similar response dynamics. The single-cell ERK responses to histamine and UK showed remarkably similar dynamics, despite the activation of different heterotrimeric G proteins. In contrast, the ERK response dynamics to S1P showed high heterogeneity, which was reduced by the inhibition of Gi. To conclude, we have set up an imaging and analysis strategy that reveals substantial cell-to-cell heterogeneity in kinase activity driven by GPCRs.