Miracle-dz/UniFAR-FTUs huggingface dataset:
Performances of bioinformatics tools for the analysis of sequencing data of Mycobacterium tuberculosis complex strains

Whole genome sequencing of Mycobacterium tuberculosis complex (MTBC) strains is a new and rapidly growing tool to obtain results regarding resistance, virulence factors and phylogeny of the strains. Bioinformatics tools presented as user-friendly and easy to use are available online. The objective of this work was to evaluate the performances of two bioinformatics tools, easily accessible on the internet, for the analysis of sequencing data of MTBC strains. Two hundred and twenty-seven MTBC strains isolated at the laboratory of the Avicenne Hospital between 2015 and 2021 were sequenced using Illumina®(USA) MiSeq technology. An analysis of the sequencing data was performed using the two tools Mykrobe and PhyResSE. Sequencing quality, resistance or susceptibility status and phylogeny were investigated for each strain. Genotypic resistance results were compared to the results obtained by phenotypic drug susceptibility testing performed in the hospital’s routine laboratory. Using the PhyResSE tool we found an average coverage of 98% against the reference strain H37Rv and an average depth of 119X. No information on sequencing quality was obtained with the Mykrobe tool. The concordance of each tool with the phenotypic method for determining susceptibility to first-line anti-tuberculosis drugs was 95%. Mykrobe and PhyResSE tools identified resistance to second-line anti-tuberculosis drugs in 5.3% and 5.7% of cases respectively. The sensitivity and specificity of each tool compared to the phenotypic method was respectively 70% and 98% for Mykrobe and 76% and 97% for PhyResSE. Finally, the two tools showed 99.5% agreement in lineage determination. The Mykrobe and PhyResSE bioinformatics tools were easy to use, fast and efficient. The Mykrobe tool had the advantage of being offline and its interface was more user-friendly. The use of these platforms depends on their accessibility and updating. However, their use is accessible to people not trained in bioinformatics and would allow a complementary approach to phenotypic methods for the study of MTBC strains.
Decision-Making for Managing Climate-Related Risks: Unpacking the Decision Process to Avoid “Trial-and-Error” Responses

We provide an overview of decision support tools and methods that are available for managing climate-related risks and for delivering adaptation and resilience options and solutions. The importance of understanding political, socio-economic and cultural contexts and the decision processes that these tools support is emphasized. No tool or method is universally suited to all circumstances. Some decision processes are structured with formal governance requirements; while others are less so. In all cases, discussions and interactions with stakeholders and other players will have formal and informal aspects. We categorize decision support tools in several broad ways with the aim of helping decision makers and their advisors select tools that are appropriate to their culture, resources and other circumstances. The assessment examines the constraints and methodological assumptions that need be considered.
Young Individuals Are More Stable and Stand More Upright When Using Rollator Assistance During Standing up and Sitting Down

Four-wheeled walkers or rollators are often used to assist older individuals in maintaining an independent life by compensating for muscle weakness and reduced movement stability. However, limited biomechanical studies have been performed to understand how rollator support affects posture and stability, especially when standing up and sitting down. Therefore, this study examined how stability and posture change with varying levels of rollator support and on an unstable floor. The aim was to collect comprehensive baseline data during standing up and sitting down in young participants. In this study, 20 able-bodied, young participants stood up and sat down both 1) unassisted and assisted using a custom-made robot rollator simulator under 2) full support and 3) touch support. Unassisted and assisted performances were analyzed on normal and unstable floors using balance pads with a compliant surface under each foot. Using 3D motion capturing and two ground-embedded force plates, we compared assistive support and floor conditions for movement duration, the relative timing of seat-off, movement stability (center of pressure (COP) path length and sway area), and posture after standing up (lower body sagittal joint angles) using ANOVA analysis. The relative event of seat-off was earliest under full support compared to touch and unassisted conditions under normal but not under unstable floor conditions. The duration of standing up and sitting down did not differ between support conditions on normal or unstable floors. COP path length and sway area during both standing up and sitting down were lowest under full support regardless of both floor conditions. Hip and knee joints were least flexed under full support, with no differences between touch and unassisted in both floor conditions. Hence, full rollator support led to increased movement stability, while not slowing down the movement, during both standing up and sitting down. During standing up, the full support led to an earlier seat-off and a more upright standing posture when reaching a stable stance. These results indicate that rollator support when handles are correctly aligned does not lead to the detrimental movement alterations of increased forward-leaning. Future research aims to verify these findings in older persons with stability and muscle weakness deficiencies.
Impulsivity and Depressive Brooding in Internet Addiction: A Study With a Sample of Italian Adolescents During COVID-19 Lockdown

This contribution presents a study conducted on a sample of Italian adolescents (n = 411) in the period of the first COVID-19 lockdown. The study investigated the role and predictive weight of the impulsivity and depressive brooding variables on Internet addiction, using a hierarchical regression analysis. The participants were administered the Uso-Abuso e Dipendenza da Internet [Internet Use-Abuse and Addiction] (UADI-2), the Barratt Impulsiveness Scale-11 (BIS-11), and the Ruminative Response Scale (RRS). In terms of percentage distribution, 28% of the participants were in the full dependency range, while 34.7% demonstrated Internet abuse behavior. The results highlighted not only the predictive value of impulsiveness (β = 0.323) and ruminative thinking (β = 0.258), but also the role of gender (β = −0.205) on Internet addiction. Thus, male participants showed higher levels of Internet addiction, with higher scores on impulsiveness and brooding way of thinking. The study shows that the issue in question is significantly present among adolescents; in addition, not only targeted awareness programmes but also psycho-educational and clinical interventions to promote greater emotional and cognitive control would be necessary as a preventive and mitigating measure. Psychological interventions can help increase self-awareness, develop emotional regulation and impulse control, and correct maladaptive cognitions which in adolescents are mostly driven by a ruminative cognitive style.
Exposing Atlantic Salmon Post-Smolts to Fluctuating Sublethal Nitrite Concentrations in a Commercial Recirculating Aquaculture System (RAS) May Have Negative Consequences

Salmon farmers are interested in extending the time post-smolts are reared in recirculating aquaculture systems (RAS). However, there is a lack of knowledge regarding optimal water quality for post-smolts in RAS, and regarding potential consequences of long term exposure to different toxic compounds, such as nitrite, in the RAS water. To address this issue, we conducted a case study at a Faroese Atlantic salmon farm, that rears large post-smolts in fresh water RAS for 22 months before sea transfer, with no additional chloride salt, a known treatment for nitrite toxicity. The aim was to document the potential effects of long-term exposure of fluctuating sub-lethal nitrite concentrations in fresh water RAS on blood physiology of large post-smolts. The study was conducted over six weeks, at the end of the RAS production cycle. Our case study shows that after ~22 months in RAS with no additional chloride, the fish had accumulated a plasma nitrite concentration 8 to 16 times higher than the ambient water. Our results indicate that the accumulation may have resulted in extracellular hyperkaliemia, since there was a positive correlation between plasma nitrite and potassium levels (p=0.00095), with potassium levels almost twice as high than previously reported for Atlantic salmon. This could indicate that Atlantic salmon health is challenged due to prolonged sub-lethal nitrite exposure in fresh water RAS. Further research related to long-term nitrite exposure in RAS is needed to asses the potential negative impact, in order to optimize welfare and growth performance during production of Atlantic salmon post-smolts.
Association Between Serum Iron Status and Muscle Mass in Adults: Results From NHANES 2015–2018

Background Iron deficiency or overload may contribute to complications associated with diseases, but the link between iron status and skeletal muscle disorder is poorly understood. This study aimed to investigate the relationship between serum iron status, reflected by serum ferritin concentration, and muscle mass in U.S. adults. Methods We utilized data from National Health and Nutrition Examination Survey (NHANES) 2015-2018 for analysis. Data on serum ferritin, appendicular skeletal muscle mass (ASM), body mass index (BMI) and confounding factors were extracted and analyzed. Multivariate linear regression analyses and smooth curve fittings were employed to investigate the association between serum ferritin and muscle mass. Subgroup analysis based on iron status, age, gender and race were performed. Results A total of 2,078 participants were included, and divided into iron deficiency (n = 225), normal iron status (n = 1,366), and iron overload (n = 487) groups. Participants with iron overload had significantly lower ASM and appendicular skeletal muscle index (ASMI) (ASM: 19.329 ± 4.879, ASMI: 0.709 ± 0.138) compared to those with iron deficiency (ASM: 22.660 ± 6.789, ASMI: 0.803 ± 0.206) and normal iron status (ASM: 22.235 ± 6.167, ASMI: 0.807 ± 0.201). The serum ferritin was negatively linked with muscle mass after adjusting for potential confounders (β = −0.0001, 95% CI: −0.0001, −0.0000). When stratified by iron status, the trend test between them remained significant (P for trend: 0.008). Furthermore, subgroup analysis identified a stronger association in men (β = −0.0001, 95% CI: −0.0002, −0.0001), age ≥ 40 years (β = −0.0001, 95% CI: −0.0002, −0.0000), non-Hispanic black (β = −0.0002, 95% CI: −0.0003, −0.0001) and other races (β = −0.0002, 95% CI: −0.0003, −0.0000). Conclusions Our study revealed an inverse relationship between serum iron status and muscle mass in adults. This finding improves our understanding of the impact of serum iron status on muscle mass, and sheds new light on the prevention and treatment of muscle loss.
Utilizing Social Media Advertisements and Participant Social Networks to Recruit African American Breast Cancer Survivors: Design and Rationale

Purpose Our objective is to pilot an advertisement-driven sampling procedure among African American (AA) breast cancer survivors living in Maryland. These pilot study methods will inform a future population-based study of AA breast cancer survivors at high risk of poor outcomes due to biological differences and social inequities. Methods This cross-sectional study utilizes an innovative, social media-based advertisement campaign with an associated social media study page to recruit 100 AA breast cancer survivors. Participants are biologically female, aged 18 and older, identify as AA/Black, have a diagnosis of breast cancer, and reside in Maryland. A preset “Audience” was created via Meta (formerly Facebook) to automatically target potential interest in the online study via geolocation and public social media interests (estimated range = 101,000 women). Eligible participants complete an online survey including demographic and clinical characteristics, cancer screening, healthcare access, and utilization, COVID-19 impact, quality of doctor-patient communication, and preferences for future study participation. Results Recruitment began on 5 January 2022 and remains ongoing. As of 7 June 2002: 124 completed the screener, 110/124 (88.7%) consented passively, 24/110 (21.8%) started but did not complete survey, 86/110 (78.1%) completed the survey. Conclusions Results from this study will inform a statewide multilevel prospective population-based study to improve health behaviors, disease management, and self-efficacy of chronic disease management among AA breast cancer survivors.
Experimental Study on Shear Strengths of Ice-Roof Interface Aiming the Study of Roof Snow Sliding

Snow sliding of roofs is a threat to the structural safety of roof structures by causing a surcharge of local snow load on the lower roof and may pose a serious threat to pedestrians and vehicles on the ground. Therefore, it is of great significance to study the mechanism of snow sliding on roofs. Under the action of ambient temperature, solar radiation, internal heating of the building, etc., the bottom layer of roof snow is often presented in the form of porous ice after a complicated phase transition of the snow particles. Under this circumstance, the interface between roof snow and the roof can be seen as the contact between porous ice and the roofing material. In order to investigate the initialization of roof snow sliding from the material point of view, the shear performance of the interface between different roofing materials and ice with different porosities was carried out in this study. The effects of different ambient temperatures (−4, −6, and −8°C), different normal stress (0, 50, and 100 kPa), and different ice porosities (represented by the contact area ratio of 1.0, 0.8, and 0.6) on this shear performance were analyzed by direct shear tests. The test results showed that the shear failure between the ice and the roofing material was brittle, and the interface shear strength was affected by the ambient temperature, normal stress, contact area ratio, as well as the material type: the strength increases with the decrease of ambient temperature, the increase of normal stress, the increase of contact area ratio, and the increase of surface roughness of the material. Based on the test results, a quantitative relationship between the interface shear strength and the related factors was given in the article, which provides a useful reference for future experimental or simulation studies on roof snow sliding.
Associations Between Six Core Processes of Psychological Flexibility and Functioning for Chronic Pain Patients: A Three-Level Meta-Analysis

The previous research showed contradictions in the relationships between psychological flexibility processes and functioning. This meta-analysis is the first to provide a comprehensive meta-analysis of the associations between six core processes of psychological flexibility and functioning among chronic pain patients. Four databases were searched (PsycINFO; PubMed; CINAHL; Web of Science) along with reference lists. Thirty-six cross-sectional studies were included (7,812 chronic pain patients). A three-level meta-analytic model was used to examine the associations. The publication bias was assessed with the Egger test, funnel plot, and p-curve analysis. Significant associations were found between functioning and six processes of psychological flexibility (i.e., acceptance, defusion, present moment, committed action, self as context, and values). Except for the relationship between defusion and functioning, the relationships between the other five psychological flexibility processes and functioning were all moderated by domains of functioning. No moderators were found regarding age, percentage of females, country, or type of instrument used to measure functioning. These findings may carry significant implications for chronic pain patients and clinical workers. It might be more effective to focus on functioning-related psychological flexibility processes rather than all therapy packages if the relationships between functioning and specific processes of psychological flexibility were better informed. Limitations were also discussed.
Bioinformatics Analysis Identifies Potential Ferroptosis Key Gene in Type 2 Diabetic Islet Dysfunction

Background Islet β cells dysfunction (IBCD) is a cortical component in pathogenesis of type 2 diabetic mellitus (T2DM). However, the relationship of ferroptosis and IBCD remains unknown. This study was aimed to screen potential ferroptosis key genes to reveal latent physiological and pathological process of IBCD in T2DM. Methods Firstly, T2DM key genes were screened by combining with differentially expressed genes (DEGs) analysis and WGCNA. Then, ferroptosis-related genes (FRGs) in IBCD of T2DM were identified by taking the intersection between T2DM key genes and FRGs. Finally, T2DM-FRGs were validated in another T2DM dataset as well as islet single-cell RNA sequencing dataset and the miRNA regulated T2DM-FRG was predicted by using four miRNA databases. Results 89 T2DM key genes were identified between DEGs and WGCNA. Then, 3 T2DM-FRGs were screened by taking the intersection of T2DM key genes and FRGs, namely ITGA6, MGST1 and ENO2. At last, MGST1 were validated as the T2DM-FRG in another T2DM islet issues dataset and islet single-cell RNA sequencing dataset. Conclusion MGST1 may be the potential ferroptosis key gene of IBCD in T2DM.
Immunogenomic Characteristics of Cell-Death-Associated Genes with Prognostic Implications in Bladder Cancer

Bladder cancer is one of the most common genitourinary malignant cancers worldwide. Cell death processes, including apoptosis, ferroptosis, and necrosis, provide novel clinical and immunological insights promoting the management of precision medicine. Therefore, this study aimed to evaluate the transcriptomic profile of signatures in cell death pathways with significant prognostic implications in patients with bladder cancer from multiple independent cohorts (n = 1999). First, genes involved in apoptosis (n = 19), ferroptosis (n = 31), and necrosis (n = 6) were analyzed to evaluate the prognostic implications in bladder cancer. Significant genes were included to establish the cell-death index (CDI) of 36 genes that distinguished patients according to high and low risks. Survival analysis using the Kaplan-Meier curves clustered patients based on overall survival (18.8 vs. 96.7 months; hazard model [HR] = 3.12, P<00001). Cox proportional hazard model was significantly associated with a higher risk of mortality using 10 external independent cohorts in patients with CDIhigh (HR = 1.31, 95% CI: 1.04–1.62). To explore immune parameters associated with CDI, microenvironment cell-population-counter algorithms indicated increased intratumoral heterogeneity and macrophage/monocyte infiltration and CD8+ T cells in patients with CDIhigh group. Besides, the CDIhigh group showed an increased expression of the following immune checkpoints: CD276, PD-L1, CTLA-4, and T-cell exhaustion signatures. Cytokine expression analysis revealed the highest association of IL-9R, IL-17A, IL-17F, GDF7, and IFNW1 with the high-risk group. In addition, 42 patients with BCa receiving immunotherapies were enrolled from a real-world cohort, and expression patterns of three CDI hub genes (DRD5, SCL2A14, and IGF1) were detected using immunohistochemical staining. Patients with triple-negative staining of tumor tissues had significantly higher tumor-associated macrophage abundance, PD-L1 expression, predicted immunocompromised microenvironment, and prominently progressive progression (HR = 4.316, P = 0.0028). In conclusion, this study highlights the immunoevasive tumor microenvironment characterized by the higher tumor-associated macrophage infiltration with the presence of immune checkpoint and T-cell exhaustion genes in patients with BCa at CDIhigh risk who might suffer progression and be more suitable to benefit from immune checkpoint inhibitors or other immunotherapies.
Integrated Serum Pharmacochemistry, Metabolomics, and Network Pharmacology to Reveal the Material Basis and Mechanism of Danggui Shaoyao San in the Treatment of Primary Dysmenorrhea

Danggui Shaoyao San (DSS), a well-known formula, has been successfully applied in treating primary dysmenorrhea (PD) in China. However, its material basis and mechanism are still unrevealed. This current research aims to reveal the material basis and mechanism of DSS in treating PD by an integrative approach of serum pharmacochemistry, metabolomics, and network pharmacology. The results showed that DSS markedly relieved the physiological and pathological symptoms of PD as confirmed by the improvement of writhing behavior, inhibition of uterine edema, callback of clinical biochemical indexes, and metabolic profiles. Furthermore, a metabolomic analysis demonstrated that the therapeutic effect of DSS was attributed to the modulation of arachidonic acid metabolism, pentose and glucuronate interconversions, and phenylalanine metabolism. Meanwhile, 23 blood ingredients were identified after the oral administration of DSS. By analyzing the correlation coefficient of the identified biomarkers and blood components, active compounds closely associated with core metabolic pathways were extracted. Taking these active compounds as a basis, network pharmacology prediction was executed. It was found that active components of DSS including alisol B,23-acetate, chlorogenic acid, levistilide A, cianidanol, senkyunolide A, atractylenolide II, and sedanolide, were germane to steroid hormone biosynthesis, arachidonic acid metabolism, sphingolipid signaling pathway, etc. Interestingly, PTGS2 and PTGS1 related to the arachidonic acid metabolism may be pivotal targets of DSS. The current study proved that the integration of serum pharmacochemistry, metabolomics, and network pharmacology, was a powerful approach to investigate the material basis and the molecular mechanisms of DSS, and provided a solid basis for DSS application.