Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic network topological properties for classifying primary dysmenorrhoea in the pain‐free phase

Primary dysmenorrhoea (PDM) is known to alter brain static functional activity. This study aimed to explore the dynamic topological properties (DTP) of dynamic brain functional network in women with PDM in the pain‐free phase and their performance in distinguishing PDM in the pain‐free phase from healthy controls.
Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle

Abstract Myofibres (primary and secondary myofibre) are the basic structure of muscle and the determinant of muscle mass. To explore the skeletal muscle developmental processes from primary myofibres to secondary myofibres in pigs, we conducted an integrative three-dimensional structure of genome and transcriptomic characterization of longissimus dorsi muscle of pig from primary myofibre formation stage [embryonic Day 35 (E35)] to secondary myofibre formation stage (E80). In the hierarchical genomic structure, we found that 11.43% of genome switched compartment A/B status, 14.53% of topologically associating domains are changed intradomain interactions (D-scores) and 2,730 genes with differential promoter–enhancer interactions and (or) enhancer activity from E35 to E80. The alterations of genome architecture were found to correlate with expression of genes that play significant roles in neuromuscular junction, embryonic morphogenesis, skeletal muscle development or metabolism, typically, NEFL, MuSK, SLN, Mef2D and GCK. Significantly, Sox6 and MATN2 play important roles in the process of primary to secondary myofibres formation and increase the regulatory potential score and genes expression in it. In brief, we reveal the genomic reorganization from E35 to E80 and construct genome-wide high-resolution interaction maps that provide a resource for studying long-range control of gene expression from E35 to E80.
Cortical excitability threshold can be increased by the AMPA blocker Perampanel in amyotrophic lateral sclerosis

Cortical hyperexcitability is a feature of amyotrophic lateral sclerosis (ALS) and cortical excitability can be measured using transcranial magnetic stimulation (TMS). Resting motor threshold (MT) is a measure of cortical excitability, largely driven by glutamate. Perampanel, a glutamate α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid (AMPA) receptor blocker, is predicted to increase the cortical excitability threshold. This study aimed to evaluate TMS to functionally assess target engagement in a study of perampanel in ALS.
Developmental changes in bone mechanics from Florida manatees (Trichechus manatus latirostris), obligate swimming mammals

ABSTRACT Mammals living in aquatic environments load their axial skeletons differently from their terrestrial counterparts. The structure and mechanical behavior of trabecular bone can be especially indicative of varying habitual forces. Here, we investigated vertebral trabecular bone mechanical properties (yield strength, stiffness and toughness) throughout development in Florida manatees (Trichechus manatus latirostris), obligate undulatory swimmers. Thoracic, lumbar and caudal vertebrae were dissected from manatees (N=20) during necropsies. We extracted 6 mm3 samples from vertebral bodies and tested them in compression in three orientations (rostrocaudal, dorsoventral and mediolateral) at 2 mm min−1. We determined variation in mechanical properties between sexes, and among developmental stages, vertebral regions and testing orientations. We also investigated the relationships between vertebral process lengths and properties of dorsoventrally and mediolaterally tested bone. Rostrocaudally tested bone was the strongest, stiffest and toughest, suggesting that this is the principal direction of stress. Our results showed that bone from female subadults was stronger and stiffer than that of their male counterparts; based on these data, we hypothesize that hormonal shifts at sexual maturity may partially drive these differences. In calves, bone from the posterior region was stronger and tougher than that from the anterior region. We hypothesize that as animals grow rapidly throughout early development, bone in the posterior region would be the most ossified to support the rostrocaudal force propagation associated with undulatory swimming. Summary: Bone mechanical behavior varies among vertebral column regions, between sexes and over development in manatees, which are undulatory swimmers that live in neutrally or near-neutrally buoyant conditions.
The effects of temperature on the defensive strikes of rattlesnakes

ABSTRACT Movements of ectotherms are constrained by their body temperature owing to the effects of temperature on muscle physiology. As physical performance often affects the outcome of predator–prey interactions, environmental temperature can influence the ability of ectotherms to capture prey and/or defend themselves against predators. However, previous research on the kinematics of ectotherms suggests that some species may use elastic storage mechanisms when attacking or defending, thereby mitigating the effects of sub-optimal temperature. Rattlesnakes (Crotalus spp.) are a speciose group of ectothermic viperid snakes that rely on crypsis, rattling and striking to deter predators. We examined the influence of body temperature on the behavior and kinematics of two rattlesnake species (Crotalus oreganus helleri and Crotalus scutulatus) when defensively striking towards a threatening stimulus. We recorded defensive strikes at body temperatures ranging from 15–35°C. We found that strike speed and speed of mouth gaping during the strike were positively correlated with temperature. We also found a marginal effect of temperature on the probability of striking, latency to strike and strike outcome. Overall, warmer snakes are more likely to strike, strike faster, open their mouth faster and reach maximum gape earlier than colder snakes. However, the effects of temperature were less than would be expected for purely muscle-driven movements. Our results suggest that, although rattlesnakes are at a greater risk of predation at colder body temperatures, their decrease in strike performance may be mitigated to some extent by employing mechanisms in addition to skeletal muscle contraction (e.g. elastic energy storage) to power strikes. Highlighted Article: Viper strike kinematics across a range of ecologically relevant temperatures show that defensive strikes of vipers are affected by temperature, but less than would be expected if the movement was purely muscle-driven.
Reliability of pelvic floor muscle surface electromyography (sEMG) recordings during synchronous whole body vibration

The primary aim of the study was to assess intraday and interday reliability of surface electromyography (sEMG) reflex activity of the pelvic floor muscles during synchronous whole-body vibration (S-WBV) of two intensities (30Hz/2mm; 40Hz/4mm) using band-stop filter and high-pass filter signal processing. The secondary aim of the study was to assess intraday and interday (test-retest) reliability of sEMG obtained from maximal voluntary contraction (MVC) test. We evaluated the intraday reliability of sEMG recordings obtained during sessions 1 and 2 performed on the same day. The sessions consisting of maximal voluntary pelvic floor muscle contraction and synchronous vibration sets with 1-hour rest in-between sessions 1 and 2 in healthy nulliparous women. The next intraday reliability was evaluated between the results of sessions 3 and 4 performed on the same day but followed at an interval of 4 weeks. to include the entire menstrual cycle. The interday reliability was determined based on the results of sessions 1 and 3 using the intraclass correlation coefficient (ICC 3,3). The intraday ICCs for band-stop filtered mean and median sEMG frequency and mean normalized sEMGRMS amplitude of the 30Hz/2mm (ICC = 0.89–0.99) and 40Hz/4mm vibration (ICC = 0.95–0.99) indicated substantial reproducibility. The intraday reliability of high-pass filter at 100-450Hz for these parameters was also substantial (30Hz/2mm ICC of 0.92 to 0.98; 40Hz/4mm ICC of 0.88 to 0.98). The interday reliability (session 1 vs. session 3) of the mean normalized sEMGRMS amplitude for band-stop filtered means of 40 Hz/4mm and 30Hz/2mm vibration recordings was substantial (ICC = 0.82 and 0.93). However, ICCs of the mean and median frequency were indicative of fair reliability (ICC of 0.43 to 0.59). The interday reliability of mean normalized sEMGRMS amplitude for high-pass filter at 100-450Hz was substantial (30Hz/2mm ICC of 0.90; 40Hz/4mm ICC of 0.73) for the 30Hz/2mm S-WBV and moderate (ICC = 0.73) for the 40/4mm S-WBV. The ICCs for mean and median sEMG frequency ICCs indicated slight to fair reproducibility (ICC of 0.16 to 0.56). The intraday reliability of the strongest MVC contraction and average MVC turned out substantial (ICC = 0.91–0.98). The interday reliability coefficients of the strongest MVC contraction and average MVCs were 0.91 and 0.82, respectively. Concluded, the intraday reliability proved satisfactory for all variables; however, the interday comparison showed sufficient ICC levels only for the mean amplitude. We therefore recommend this parameter should be used when analyzing PFM sEMG recorded during vibration. ICCs of the mean and median frequency for both signal processing methods were indicative of insufficient reliability and did not reach the threshold for usefulness. Our study showed similar reliability of PFM sEMG during S-WBV in case of the two filtering methods used.
Performance of a Mobile Single-Lead Electrocardiogram Technology for Atrial Fibrillation Screening in a Semirural African Population: Insights From “The Heart of Ethiopia: Focus on Atrial Fibrillation” (TEFF-AF) Study

Background Atrial fibrillation (AF) screening using mobile single-lead electrocardiogram (ECG) devices has demonstrated variable sensitivity and specificity. However, limited data exists on the use of such devices in low-resource countries. Objective The goal of the research was to evaluate the utility of the KardiaMobile device’s (AliveCor Inc) automated algorithm for AF screening in a semirural Ethiopian population. Methods Analysis was performed on 30-second single-lead ECG tracings obtained using the KardiaMobile device from 1500 TEFF-AF (The Heart of Ethiopia: Focus on Atrial Fibrillation) study participants. We evaluated the performance of the KardiaMobile automated algorithm against cardiologists’ interpretations of 30-second single-lead ECG for AF screening. Results A total of 1709 single-lead ECG tracings (including repeat tracing on 209 occasions) were analyzed from 1500 Ethiopians (63.53% [953/1500] male, mean age 35 [SD 13] years) who presented for AF screening. Initial successful rhythm decision (normal or possible AF) with one single-lead ECG tracing was lower with the KardiaMobile automated algorithm versus manual verification by cardiologists (1176/1500, 78.40%, vs 1455/1500, 97.00%; P<.001). Repeat single-lead ECG tracings in 209 individuals improved overall rhythm decision, but the KardiaMobile automated algorithm remained inferior (1301/1500, 86.73%, vs 1479/1500, 98.60%; P<.001). The key reasons underlying unsuccessful KardiaMobile automated rhythm determination include poor quality/noisy tracings (214/408, 52.45%), frequent ectopy (22/408, 5.39%), and tachycardia (>100 bpm; 167/408, 40.93%). The sensitivity and specificity of rhythm decision using KardiaMobile automated algorithm were 80.27% (1168/1455) and 82.22% (37/45), respectively. Conclusions The performance of the KardiaMobile automated algorithm was suboptimal when used for AF screening. However, the KardiaMobile single-lead ECG device remains an excellent AF screening tool with appropriate clinician input and repeat tracing. Trial Registration Australian New Zealand Clinical Trials Registry ACTRN12619001107112; https://www.anzctr. org.au/Trial/Registration/TrialReview.aspx? id=378057&isReview=true
Toxoplasma gondii Matrix Antigen 1 Is a Secreted Immunomodulatory Effector

Toxoplasma gondii is an Apicomplexan that infects a third of humans, causing encephalitis in AIDS patients and intellectual disabilities in congenitally infected patients. We determined that one of the cyst matrix proteins, MAG1, which had been thought to be an innate structural protein, can be secreted into the host cell and suppress the host immune reaction. ABSTRACT Our studies on novel cyst wall proteins serendipitously led us to the discovery that cyst wall and vacuolar matrix protein MAG1, first identified a quarter of a century ago, functions as a secreted immunomodulatory effector. MAG1 is a dense granular protein that is found in the parasitophorous vacuolar matrix in tachyzoite vacuoles and the cyst wall and matrix in bradyzoite vacuoles. In the current study, we demonstrated that MAG1 is secreted beyond the parasitophorous vacuole into the host cytosol in both tachyzoites and bradyzoites. Secretion of MAG1 gradually decreases as the parasitophorous vacuole matures, but prominent MAG1 puncta are present inside host cells even at 4 and 6 days following infection. During acute murine infection, Δmag1 parasites displayed significantly reduced virulence and dissemination. In the chronic stage of infection, Δmag1 parasites generated almost no brain cysts. To identify the mechanism behind the attenuated pathology seen with Δmag1 parasites, various immune responses were screened in vitro using bone marrow-derived macrophages (BMDM). Infection of BMDM with Δmag1 parasites induced a significant increase in interleukin 1β (IL-1β) secretion, which is a hallmark of inflammasome activation. Heterologous complementation of MAG1 in BMDM cells prevented this Δmag1 parasite-induced IL-1β release, indicating that secreted MAG1 in host cytosol dampens inflammasome activation. Furthermore, knocking out GRA15 (an inducer of IL-1β release) in Δmag1 parasites completely inhibited all IL-1β release by host cells following infection. These data suggest that MAG1 has a role as an immunomodulatory molecule and that by suppressing inflammasome activation, it would favor survival of the parasite and the establishment of latent infection. IMPORTANCE Toxoplasma gondii is an Apicomplexan that infects a third of humans, causing encephalitis in AIDS patients and intellectual disabilities in congenitally infected patients. We determined that one of the cyst matrix proteins, MAG1, which had been thought to be an innate structural protein, can be secreted into the host cell and suppress the host immune reaction. This particular immune reaction is initiated by another parasite-secreted protein, GRA15. The intricate balance of inflammasome activation by GRA15 and suppression by MAG1 protects mice from acute death while enabling parasites to disseminate and establish chronic cysts. Our finding contributes to our understanding of how parasites persist in the host and how T. gondii modulates the host immune system.
Integrated transcriptomics and epigenomics reveal chamber-specific and species-specific characteristics of human and mouse hearts

DNA methylation, chromatin accessibility, and gene expression represent different levels information in biological process, but a comprehensive multiomics analysis of the mammalian heart is lacking. Here, we applied nucleosome occupancy and methylome sequencing, which detected DNA methylation and chromatin accessibility simultaneously, as well as RNA-seq, for multiomics analysis of the 4 chambers of adult and fetal human hearts, and adult mouse hearts. Our results showed conserved region-specific patterns in the mammalian heart at transcriptome and DNA methylation level. Adult and fetal human hearts showed distinct features in DNA methylome, chromatin accessibility, and transcriptome. Novel long noncoding RNAs were identified in the human heart, and the gene expression profiles of major cardiovascular diseases associated genes were displayed. Furthermore, cross-species comparisons revealed human-specific and mouse-specific differentially expressed genes between the atria and ventricles. We also reported the relationship among multiomics and found there was a bell-shaped relationship between gene-body methylation and expression in the human heart. In general, our study provided comprehensive spatiotemporal and evolutionary insights into the regulation of gene expression in the heart.
STUDY OF OXYGEN CONTENT ON COMBUSTION CHARACTERISTICS OF PULVERIZED COAL

It must consume vast oil when pulverized coal boilers ignite and low loads operate,so a more economical and applied method is necessary.Study of the combustion characteristics of pulverized coal at oxygen enrichment conditions is very important not only for combustion-supporting but also for ignition.In this paper,the results of a study on the combustion characteristics of Shenmu and Pubai pulverized coals under different oxygen volume content are presented by Netzsch STA 409 PC synchronization thermal analysis instrument.Non-isothermal thermo-gravimetry(TG/DTG)experiments were carried out for five oxygen content(20%,30%,40%,60%,100%)and three different size fractions(88~105μm,63~74μm,45μm respectively.Experi-mental investigation and theoretical analyzing has proved that there are great influences of oxygen content and particle size on ignitability of compositions,and till further influence combustion and burnout characteristics.The results generally show that with the oxygen content increases,TG curves of pulverized coals move to the lower temperature zone,and with higher the oxygen content,the lower the ignition and burnout temperature is,in addition,its combustion characteristics can be improved much more for larger particle sizes at oxygen enrichment conditions.
Red Mud Catalytic Pyrolysis of Pinyon Juniper and Single-Stage Hydrotreatment of Oils

Pinyon juniper biomass feedstocks, which cover a large acreage of rangeland in the western United States, are being eradicated and, therefore, considered as a convenient biomass feedstock for biofuel production. Pinyon juniper whole biomass (wood, bark, and leaves) were pyrolyzed in a pilot-scale bubbling fluidized-bed reactor at 450 °C, and the non-condensable gases were recycled to fluidize the reactor. Red mud was used as the in situ catalyst for the pyrolysis of the pinyon juniper biomass. The pyrolysis products were condensed in three stages, and products were analyzed for physicochemical properties. The condenser oil formed two phases with the aqueous fraction, whereas the electrostatic precipitator oils formed a single phase. The oil pH was 3.3; the higher heating value (HHV) was 28 MJ/kg; and the viscosity was less than 100 cP. There was a direct correlation between the viscosity of the oils and the alcohol/ether content of the oils, and this was also related to the aging rate of the oils. The cat.
Body Size Misperception and Dissatisfaction in Elementary School Children.

Background: To examine the association between body size perception (BSP) and body size dissatisfaction (BSD) in elementary school children and to document the potential contribution of individual factors [age, sex, and actual body size (BMI Z-scores: BMIZ)] that may influence their relationship. Methods: This study included 269 children (124 boys and 145 girls) between 6 and 13 years of age (9.2 ± 1.6 years). The BSP score was calculated as the difference between the perceived actual body size and BMIZ (actual body size). A negative BSP score indicated an underestimation of their body size. To assess the BSD score, the difference between perceived actual body size and desired body size was calculated. A positive BSD score indicated a desire to be thinner. Results: Perceived actual body size was smaller than BMIZ, independent of age group and weight status. Overall, 64% of children underestimated their body size. The young children living with obesity demonstrated the highest misperception. Results also showed that the proportion of children who desired to be thinner was higher in overweight and obese subgroups. No significant relationship was found between BSP and BSD scores in the entire sample, while a positive association was observed among younger children in the normal-weight and obese subgroups (r = 0.40; p < 0.001 and r = 0.78; p < 0.05, respectively). Conclusions: Underestimation and dissatisfaction of body size are more prevalent in children living with overweight/obesity. Moreover, there is an association between BSP and dissatisfaction, yet this association is dependent on age and weight status.
Genome‐wide screening of SARS‐CoV‐2 infection‐related genes based on the blood leukocytes sequencing data set of patients with COVID‐19

Coronavirus disease 2019 (COVID‐19) is a global epidemic disease caused by a novel virus, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), causing serious adverse effects on human health. In this study, we obtained a blood leukocytes sequencing data set of COVID‐19 patients from the GEO database and obtained differentially expressed genes (DEGs). We further analyzed these DEGs by protein–protein interaction analysis and Gene Ontology enrichment analysis and identified the DEGs closely related to SARS‐CoV‐2 infection. Then, we constructed a six‐gene model (comprising IFIT3, OASL, USP18, XAF1, IFI27, and EPSTI1) by logistic regression analysis and calculated the area under the ROC curve (AUC) for the diagnosis of COVID‐19. The AUC values of the training group, testing group, and entire group were 0.930, 0.914, and 0.921, respectively. The six genes were highly expressed in patients with COVID‐19 and positively correlated with the expression of SARS‐CoV‐2 invasion‐related genes (ACE2, TMPRSS2, CTSB, and CTSL). The risk score calculated by this model was also positively correlated with the expression of TMPRSS2, CTSB, and CTSL, indicating that the six genes were closely related to SARS‐CoV‐2 infection. In conclusion, we comprehensively analyzed the functions of DEGs in the blood leukocytes of patients with COVID‐19 and constructed a six‐gene model that may contribute to the development of new diagnostic and therapeutic ideas for COVID‐19. Moreover, these six genes may be therapeutic targets for COVID‐19.
Cell Tracking Profiler – a user-driven analysis framework for evaluating 4D live-cell imaging data

ABSTRACT Accurate measurements of cell morphology and behaviour are fundamentally important for understanding how disease, molecules and drugs affect cell function in vivo. Here, by using muscle stem cell (muSC) responses to injury in zebrafish as our biological paradigm, we established a ‘ground truth’ for muSC behaviour. This revealed that segmentation and tracking algorithms from commonly used programs are error-prone, leading us to develop a fast semi-automated image analysis pipeline that allows user-defined parameters for segmentation and correction of cell tracking. Cell Tracking Profiler (CTP) is a package that runs two existing programs, HK Means and Phagosight within the Icy image analysis suite, to enable user-managed cell tracking from 3D time-lapse datasets to provide measures of cell shape and movement. We demonstrate how CTP can be used to reveal changes to cell behaviour of muSCs in response to manipulation of the cell cytoskeleton by small-molecule inhibitors. CTP and the associated tools we have developed for analysis of outputs thus provide a powerful framework for analysing complex cell behaviour in vivo from 4D datasets that are not amenable to straightforward analysis. Summary: Analysis of cell shape and movement from 3D time-lapses is currently very challenging. Here, we develop Cell Tracking Profiler and use it to examine RhoA and myosin II control of muscle stem cell behaviour during zebrafish regeneration.