Miracle-dz/UniFAR-FTUs huggingface dataset:
Qualitative and Quantitative Detection of Multiple Sexually Transmitted Infection Pathogens Reveals Distinct Associations with Cervicitis and Vaginitis

Scarce information exists with regard to whether STI pathogens can be defined as valid microbiological predictive markers for the diagnosis of cervicitis and vaginitis. We therefore conducted this study to assess the presence and abundance of a wide range of STI pathogens among patients having these two diseases and healthy controls as well. ABSTRACT Many diverse pathogens have been discovered from reproductive-tract infections, but the relationship between the presence and abundance of particular pathogen species and disease manifestations is poorly defined. The present work examined the association of multiple common pathogens causing sexually transmitted infections (STIs) with cervicitis and vaginitis. The presence and abundance of 15 STI pathogens and the genotypes of human papillomavirus were determined in a cohort of 944 women that included 159 cervicitis patients, 207 vaginitis patients, and 578 healthy controls. Logistic regression and random forest models were constructed and validated in a separate cohort of 420 women comprising 52 cervicitis patients, 109 vaginitis patients, and 259 healthy controls. The frequency of individual STI pathogen species varied among the symptomatic patients and healthy controls. Abundance determination was necessary for most pathogens that were associated with the studied diseases. STI pathogens were more commonly associated with cervicitis than with vaginitis. Pathogen identification- and quantification-based diagnosis was observed for cervicitis with high sensitivity and specificity, but for vaginitis, the assay results would need to be combined with results of other diagnostic tests to firmly establish the pathogen-disease correlation. Integrated qualitative and quantitative detection of a selected panel of common STI pathogens can reveal their association with cervicitis and vaginitis. STI pathogen identification and quantification can be used to diagnose cervicitis and also help improve correct diagnosis of vaginitis. IMPORTANCE Scarce information exists with regard to whether STI pathogens can be defined as valid microbiological predictive markers for the diagnosis of cervicitis and vaginitis. We therefore conducted this study to assess the presence and abundance of a wide range of STI pathogens among patients having these two diseases and healthy controls as well. High sensitivity and specificity were observed for cervicitis by pathogen identification- and quantification-based diagnosis. In contrast, the assay results obtained for vaginitis would need to be combined with test results obtained by other diagnostic methods to decisively establish the pathogen-disease correlation. Simultaneous qualitative and quantitative detection of a selected panel of common STI pathogens and further coupling with machine learning models is worthwhile for establishing pathogen-based diagnosis of gynecological inflammations, which could be of great value in guiding the rational use of antimicrobials to control the spread of STIs.
Genotype‐dependent changes of cell wall composition influence physiological traits of a long and a non‐long shelf‐life tomato genotypes under distinct water regimes

SUMMARY Water shortage strongly affects plants' physiological performance. Since tomato (Solanum lycopersicum) non‐long shelf‐life (nLSL) and long shelf‐life (LSL) genotypes differently face water deprivation, we subjected a nLSL and a LSL genotype to four treatments: control (well watering), short‐term water deficit stress at 40% field capacity (FC) (ST 40% FC), short‐term water deficit stress at 30% FC (ST 30% FC), and short‐term water deficit stress at 30% FC followed by recovery (ST 30% FC‐Rec). Treatments promoted genotype‐dependent elastic adjustments accompanied by distinct photosynthetic responses. While the nLSL genotype largely modified mesophyll conductance (g m) across treatments, it was kept within a narrow range in the LSL genotype. However, similar g m values were achieved under ST 30% FC conditions. Particularly, modifications in the relative abundance of cell wall components and in sub‐cellular anatomic parameters such as the chloroplast surface area exposed to intercellular air space per leaf area (S c/S) and the cell wall thickness (T cw) regulated g m in the LSL genotype. Instead, only changes in foliar structure at the supra‐cellular level influenced g m in the nLSL genotype. Even though further experiments testing a larger range of genotypes and treatments would be valuable to support our conclusions, we show that even genotypes of the same species can present different elastic, anatomical, and cell wall composition‐mediated mechanisms to regulate g m when subjected to distinct water regimes.
Functional thresholds alter the relationship of plant resistance and recovery to drought

Abstract The ecological consequences of future droughts are difficult to predict due to a limited understanding of the nonlinear responses of plants to increasing drought intensity, which can change abruptly when critical thresholds of drought intensity are crossed. Drought responses are composed of resistance and postdrought recovery. Although it is well established that higher drought intensity increases the impact and, thus, reduces plant resistance, less is known about how drought intensity affects recovery and how resistance and recovery are related. In this study, we tested the hypothesis that resistance, recovery, and their relationship change abruptly upon crossing critical thresholds of drought intensity. We exposed mesocosms of two monospecific stands of the common grassland species Dactylis glomerata and Plantago lanceolata to a large gradient of drought intensity and quantified the resistance and recovery of multiple measures of plant productivity, including gross‐primary productivity, vegetative height, Normalized Difference Vegetation Index, and aboveground biomass production. Drought intensity had nonlinear and contrasting effects on plant productivity during drought and recovery, which differed between the two species. Increasing drought intensity decreased the resistance of plant productivity and caused rapid compensatory growth during postdrought recovery, the degree of which was highly dependent on drought intensity. Across multiple response parameters two thresholds of drought intensity emerged, upon which we observed abrupt changes in plant resistance and recovery, as well as their relationship. We conclude that across gradients of drought intensity resistance and recovery are tightly coupled and that both the magnitude and the direction of drought effects on resistance and recovery can change abruptly upon specific thresholds of stress intensity. These findings highlight the urgent need to account for nonlinear responses of resistance and recovery to drought intensity as critical drivers of productivity in a changing climate.
Mechano‐regulation of Wnt/β‐Catenin signaling to control paraxial versus lateral mesoderm lineage bifurcation

Mechanical cues are involved in many biological processes, including embryonic development and patterning. For example, external mechanical forces (shear stress), lateral cell–cell interactions, and mechanical properties (stiffness and composition) of the extracellular matrix are thought to modulate Wnt signaling, which is a highly conserved pathway involved in regulating stem cell renewal, proliferation, and differentiation. In this work, we employed a customized higher‐throughput shear stress induction device for the controlled application of mechanical stress to study the effects of shear stress on the differentiation of human induced pluripotent stem cells (hiPSCs) toward the three germ layers. We found that mechanical stress alters lineage commitment during ectoderm and mesoderm differentiation. We show that this effect correlates with reduced Wnt signaling, evaluated in terms of the promoter activity of an established TCF3‐responsive promoter. Whole transcriptome sequencing and pathway enrichment analysis of the differentially expressed genes between hiPSC‐derived mesoderm cells differentiated in the presence or absence of piston‐induced shear stress confirmed that Wnt/β‐catenin signaling is among the most affected developmental pathways. Furthermore, our results suggest that suitably programmed shear stress application could be used to selectively promote differentiation of hiPSCs to either lateral or paraxial mesoderm in commercially available media.
Patients' experience of patient safety information and participation in care during a hospital stay

Having a culture of safety is crucial when providing high‐quality health care, yet preventable adverse events are common in the Swedish healthcare system, especially in the field of surgical care. Research shows that patient participation can improve patient safety. This study aimed to explore patients' experience of the safety leaflet, “Your safety in hospital,” including participation in care and feelings of safe care.
Identification of Motor Unit Firings in H-Reflex of Soleus Muscle Recorded by High-Density Surface Electromyography

We developed and tested the methodology that supports the identification of individual motor unit (MU) firings from the Hoffman (or H) reflex recorded by surface high-density EMG (HD-EMG). Synthetic HD-EMG signals were constructed from simulated 10% to 90% of maximum voluntary contraction (MVC), followed by 100 simulated H-reflexes. In each H-reflex the MU firings were normally distributed with mean latency of 20 ms and standard deviations (SDLAT) ranging from 0.1 to 1.3 ms. Experimental H-reflexes were recorded from the soleus muscle of 12 men (33.6 ± 5.8 years) using HD-EMG array of ${5}\times {13}$ surface electrodes. Participants performed 15 to 20 s long voluntary plantarflexions with contraction levels ranging from 10% to 70% MVC. Afterwards, at least 60 H-reflexes were electrically elicited at three levels of background muscle activity: rest, 10% and 20% MVC. HD-EMGs of voluntary contractions were decomposed using the Convolution Kernel Compensation method to estimate the MU filters. When applied to HD-EMG signals with synthetic H reflexes, MU filters demonstrated high MU identification accuracy, especially for $\text {SD}_{\text {LAT}}>{0.3}$ ms. When applied to experimental H-reflex recordings, the MU filters identified 14.1 ± 12.1, 18.2 ± 12.1 and 20.8 ± 8.7 firings per H-reflex, with individual MU firing latencies of 35.9 ± 3.3, 35.1 ± 3.0 and 34.6 ± 3.3 ms for rest, 10% and 20% MVC background muscle activity, respectively. Standard deviation of MU latencies across experimental H-reflexes were 1.0 ± 0.8, 1.3 ± 1.1 and 1.5 ± 1.2 ms, in agreement with intramuscular EMG studies.
Mental health and well‐being of anaesthetists during the COVID‐19 pandemic: a scoping review

The COVID‐19 pandemic has imposed substantial burdens on clinicians and there is a need to better understand the impact on mental health and well‐being. This scoping review investigates the prevalence of mental health concerns in anaesthetists, risk and protective factors for mental well‐being, and anaesthetists' pandemic‐related concerns and support. We searched online databases for articles published between January 2020 and May 2022, using search terms related to: anaesthesia; burnout, well‐being, mental health or stress; and COVID‐19. We identified 20 articles comprising 19 different populations of anaesthetists (n = 8680) from 14 countries. Studies identified the prevalence of the following condition in anaesthetists: burnout (14–59%); stress (50–71%); anxiety (11–74%); depression (12–67%); post‐traumatic stress (17–25%); psychological distress (52%); and insomnia (17–61%). Significant risk factors for poorer mental health included: direct COVID‐19‐related issues (fear of self and family exposure to infection; requirement for quarantine); practitioner health factors (insomnia; comorbidities); psychosocial factors (loneliness; isolation; perceived lack of support at home and work); demographic factors (female gender; non‐white ethnicity; LGBTQIA+); and workplace factors (redeployment outside area of clinical practice; increased work effort; personal protective equipment shortages). Protective factors identified included: job satisfaction; perceived organisational justice; older age; and male sex. Anaesthetists' self‐reported concerns related to: personal protective equipment; resource allocation; fear of infection; fear of financial loss; increased workload; and effective communication of protocols for patient treatment. Support from family, colleagues and hospital management was identified as an important coping mechanism. Findings from this review may support the design of interventions to enhance anaesthetists' psychological health during pandemic conditions and beyond. Future research should include consistent psychological outcome measures and rigorous experimental design beyond cross‐sectional studies.
Integrated analysis of lncRNA and gene expression in longissimus dorsi muscle at two developmental stages of Hainan black goats

It is deemed that meat quality of kids’ is better than that of adults’ for Hainan black goat. Generally, meat quality is affected by many indicators, such as intramuscular fat (IMF) content, muscle fiber diameter and shear force. It is indicated that long non-coding RNAs (lncRNAs) play essential roles in meat quality of goats. However, it is unclear whether and how lncRNAs and genes play their roles in meat quality of Hainan Black goats. Here, we firstly compared the meat quality between two-month-old kids (kids) and adult goats (adults). Then, the lncRNA-seq and RNA-seq data were integrated and analyzed to explore the potential functions of lncRNAs and genes. The results showed that adults’ IMF content and muscle fiber diameter were extremely significantly higher than that of kids (P<0.01). For the sequenced data, average 84,970,398, and 83,691,250 clean reads were obtained respectively for Kids and adults, among which ~96% were mapped to the reference genome of goats. Through analyzing, 18,242 goat annotated genes, 1,429 goat annotated lncRNAs and 2,967 novel lncRNAs were obtained. Analysis of differential expression genes (DEGs) and lncRNAs (DELs) showed that 328 DEGs and 98 DELs existed between kids and adults. Furthermore, functional enrichment analysis revealed that a number of DEGs and DELs were mainly associated with IMF. Primarily, DGAT2 expressed higher in adults than that in kids and CPT1A expressed higher in kids than that in adults. Both of them were overlapped by DEGs and targets of DELs, suggesting the two DEGs and the DELs targeted by the two DEGs might be the potential regulators of goat IMF deposition. Taken together, our results provide basic support for further understanding the function and mechanism of lncRNAs and genes in meat quality of Hainan black goats.
Mild-to-Moderate Kidney Dysfunction and Cardiovascular Disease: Observational and Mendelian Randomization Analyses

Background: End-stage renal disease is associated with a high risk of cardiovascular events. It is unknown, however, whether mild-to-moderate kidney dysfunction is causally related to coronary heart disease (CHD) and stroke. Methods: Observational analyses were conducted using individual-level data from 4 population data sources (Emerging Risk Factors Collaboration, EPIC-CVD [European Prospective Investigation into Cancer and Nutrition–Cardiovascular Disease Study], Million Veteran Program, and UK Biobank), comprising 648 135 participants with no history of cardiovascular disease or diabetes at baseline, yielding 42 858 and 15 693 incident CHD and stroke events, respectively, during 6.8 million person-years of follow-up. Using a genetic risk score of 218 variants for estimated glomerular filtration rate (eGFR), we conducted Mendelian randomization analyses involving 413 718 participants (25 917 CHD and 8622 strokes) in EPIC-CVD, Million Veteran Program, and UK Biobank. Results: There were U-shaped observational associations of creatinine-based eGFR with CHD and stroke, with higher risk in participants with eGFR values <60 or >105 mL·min–1·1.73 m–2, compared with those with eGFR between 60 and 105 mL·min–1·1.73 m–2. Mendelian randomization analyses for CHD showed an association among participants with eGFR <60 mL·min–1·1.73 m–2, with a 14% (95% CI, 3%–27%) higher CHD risk per 5 mL·min–1·1.73 m–2 lower genetically predicted eGFR, but not for those with eGFR >105 mL·min–1·1.73 m–2. Results were not materially different after adjustment for factors associated with the eGFR genetic risk score, such as lipoprotein(a), triglycerides, hemoglobin A1c, and blood pressure. Mendelian randomization results for stroke were nonsignificant but broadly similar to those for CHD. Conclusions: In people without manifest cardiovascular disease or diabetes, mild-to-moderate kidney dysfunction is causally related to risk of CHD, highlighting the potential value of preventive approaches that preserve and modulate kidney function.
The impact of bariatric surgery procedures on the modulation of cardiometabolic risk factors in patients with severe obesity: a 12-month follow-up

Objective To evaluate the effects of one anastomosis gastric bypass (OAGB), Roux-en-Y gastric bypass (RYGB), and sleeve gastrectomy (SG) on cardiometabolic risk factors (CMRFs) in patients with severe obesity. Methods This retrospective cohort study included patients with severe obesity who had undergone OAGB, RYGB, or SG between 2015 and 2017 and follow-up assessments over 12-months. Results Among 485 included patients, anthropometric measurements, body composition, fasting blood glucose (FBG), lipid profile, and comorbidities were significantly improved for all three procedures throughout the follow-up period. Weight, % total weight loss (%TWL), body mass index, fat mass and fat mass to fat-free mass ratio improvements were higher with RYGB and OAGB than SG. There were no significant differences between procedures in all other variables. A significant trend toward remission rate of dyslipidemia and type 2 diabetes mellitus was observed with all three procedures, with no significant difference between the three groups. %TWL statistically correlated with fat mass, FBG, and triglycerides. Conclusions OAGB, RYGB, and SG had a beneficial impact on CMRFs and comorbidities during 12 months of follow-up. Of note, RYGB and OAGB may result in better outcomes, particularly anthropometric and body composition indices. Further large-sample, long-term follow-up studies are required to expand on the present findings.
Asymmetric information flow in brain networks supporting expressive language in childhood

Low‐beta (13–23 Hz) event‐related desynchrony (ERD), a neural signature of expressive language, lateralizes from bilateral to left hemisphere in development. In contrast, low‐beta event‐related synchrony (ERS), thought to reflect inhibition, lateralizes from bilateral to the right hemisphere across development. Using whole‐brain directed connectivity analyses, we aimed to characterize hemispheric and regional contributions to expressive language, in childhood. We studied 80 children and adolescents, 4 to less than 19 years of age, performing covert auditory verb generation in magnetoencephalography. Outdegree, indegree, and betweenness centrality were used to differentiate regions acting as drivers, receivers, and bridging hubs, respectively. The number of suprathreshold connections significantly increased with age for delta band (p < .01). Delta outflow was mapped to left inferior frontal gyrus (IFG), while regions of right hemisphere, including right IFG, showed significant inflow. The right parietal cortex showed significant ERS, but without corresponding outdegree or indegree. Betweenness mapped to midline cortical and subcortical structures. Results suggest Broca's area develops a driving role in the language network, while Broca's homologue receives information without necessarily propagating it. Subcortical and midline hubs act as intrahemispheric relays. Findings suggest that Broca's homologue is inhibited during expressive language, in development.
On the dynamics of supermassive black holes in gas-rich, star-forming galaxies: the case for nuclear star cluster co-evolution

We introduce a new model for the formation and evolution of supermassive black holes (SMBHs) in the RAMSES code using sink particles, improving over previous work the treatment of gas accretion and dynamical evolution. This new model is tested against a suite of high-resolution simulations of an isolated, gas-rich, cooling halo. We study the effect of various feedback models on the SMBH growth and its dynamics within the galaxy. In runs without any feedback, the SMBH is trapped within a massive bulge and is therefore able to grow quickly, but only if the seed mass is chosen larger than the minimum Jeans mass resolved by the simulation. We demonstrate that, in the absence of supernovae (SN) feedback, the maximum SMBH mass is reached when Active Galactic Nucleus (AGN) heating balances gas cooling in the nuclear region. When our efficient SN feedback is included, it completely prevents bulge formation, so that massive gas clumps can perturb the SMBH orbit, and reduce the accretion rate significantly. To overcome this issue, we propose an observationally motivated model for the joint evolution of the SMBH and a parent nuclear star cluster (NSC), which allows the SMBH to remain in the nuclear region, grow fast and resist external perturbations. In this scenario, however, SN feedback controls the gas supply and the maximum SMBH mass now depends on the balance between AGN heating and gravity. We conclude that SMBH/NSC co-evolution is crucial for the growth of SMBH in high-z galaxies, the progenitors of massive elliptical today.
Medical students’ perceived stress and perceptions regarding clinical clerkship during the COVID-19 pandemic

Background It is important to ensure that both the qualitative and quantitative aspects of clinical education are maintained during the pandemic. Understanding students’ views on clinical rotations and the extent of their perceived pandemic-related stress would thus be useful for designing and implementing effective clerkship programs. Therefore, this study aimed to investigate perceived stress and perceptions regarding clinical clerkship among incoming clinical students (third year) and senior clinical students (fourth year) during the COVID-19 pandemic. Methods After completing orientation programs at the beginning of the academic year, we surveyed students on their perceived stress, their general perspectives regarding the appropriate scope of clinical clerkship, and their preferences regarding level of participation in clerkship. We examined the differences in stress and clerkship-related perceptions based on the students’ study year and sex using independent t-test, chi-squared test, and Fisher’s exact test. In addition, the influences of stress, sex, and study year on clerkship-related perceptions were examined using multinomial logistic regression. Results The independent t-test indicated that third-year students experienced lower stress than did fourth-year students. Clerkship-related perceptions also differed significantly between third- and fourth-year students. Multinomial logistic regression analyses on the scope of and participation levels in clinical clerkship revealed that third-year students had significantly lower odds of preferring a limited range of clinical rotations and lower engagement in clerkships compared to fourth-year students. Conclusion The COVID-19 pandemic has affected clinical education and, consequently, medical students’ inclination toward active participation in clinical rotations. It is thus essential to understand students’ views and provide them with relevant intra-pandemic educational supports.