Miracle-dz/UniFAR-FTUs huggingface dataset:
Virulence-Related Gene Distribution Among Shigella Isolates in Anhui, China: The Association with Antimicrobial Resistance

Objective The aim of this study was to investigate the antimicrobial resistance profiles and distribution of virulence-related genes (VRGs) among Shigella isolates in Anhui, China, and to identify the correlation between the VRGs and antimicrobial resistance. Materials and Methods A total of 525 non-duplicate Shigella isolates (449 S. flexneri, 68 S. sonnei, 3 S. boydii, and 5 S. dysenteriae) were collected in Anhui Province, China between September 2011 and September 2015. The antimicrobial resistance of the strains was determined by the agar dilution method according to CLSI guidelines. The presence of 16 VRGs, including ipaH, ipaA-D, ial, virB, virF, set, sen, icsA, icsB, sigA, sat, pic, and sepA, was evaluated using PCR amplification and sequencing. Results Shigella flexneri was the most abundant (85.5%), followed by S. sonnei (13.0%). The proportion of males with S. flexneri was higher than that of females (57% vs 43%; P<0.0001). The most common resistance pattern was the combination of ampicillin, nalidixic acid, and tetracycline for S. flexneri (90.2%) and S. sonnei (94.1%). Resistance to ciprofloxacin and levofloxacin was more common among S. flexneri than among S. sonnei (49.7% vs.19.1%, P<0.0001; 30.5% vs 10.3%, P=0.001, respectively). All the isolates were positive for the ipaH gene, while the set, sat, pic, and sepA genes were not detected among the S. sonnei isolates. Except for sigA and sen, resistance to chloramphenicol and ciprofloxacin was more common among VRG-positive S. flexneri than among VRG-negative S. flexneri (P<0.05). Furthermore, resistance to ceftriaxone and ceftazidime was more frequently detected among sat- and set-positive S. flexneri than among sat- and set-negative S. flexneri (P<0.05). However, gentamicin resistance was more prevalent among VRG-negative (ial, virF, set, sat, pic, and sepA) S. flexneri than among VRG-positive S. flexneri (P<0.05). Conclusion Shigella flexneri remains the predominant species in Anhui, China, and the resistance to fluoroquinolones was more widespread among S. flexneri than among S. sonnei. Shigella flexneri strains harboring specific VRGs were associated with antimicrobial resistance. To the best of our knowledge, this is the first report of the correlation between the VRGs and antimicrobial resistance in Anhui, China.
Associated factors for depression, suicidal ideation and suicide attempt among asthmatic adolescents with experience of electronic cigarette use

INTRODUCTION While electronic cigarette (EC) use is rapidly increasing among asthmatic adolescents, little is known about the links between EC use and depression or suicidality. We assessed associated factors for depression and suicidality in asthmatic adolescents with experience of EC use. METHODS We analyzed the data from the 11th to 13th Korea Youth Risk Behavior Web-based Surveys, which were completed from 2015 to 2017. Data were obtained from a stratified, multistage, clustered sample. Students supplied ‘yes or no’ answers to questions about previous asthma diagnosis by a doctor. Associated factors for depression and suicidality were evaluated by logistic regression models after controlling for potential confounding factors. We targeted 203336 adolescents, and 195847 completed the survey. RESULTS The proportion of asthma among the respondents was 8.9%. The rate of experience of EC use was higher among asthmatic respondents than non-asthmatic respondents (10.3% vs 8.6%). Asthmatic respondents with experience of EC use had a much higher proportion of negative mental health states including depression and suicidality than subjects without EC experience. In our adjusted models, perception of stress was most strongly associated with depression (adjusted odds ratio, AOR=4.79; 95% CI: 4.12–5.58), and perception of unhappiness was most strongly associated with suicidal ideation (AOR=5.24; 95% CI: 4.51–6.09) and suicide attempt (AOR=4.37; 95% CI: 3.36–5.69). CONCLUSIONS Many Korean asthmatic adolescents with experience of EC use report relatively high depression and suicidal behaviors. A multidisciplinary approach, including psychological help, may be required to prevent suicide among this population, especially those who report associated factors.
Wogonin Ameliorates Renal Inflammation and Fibrosis by Inhibiting NF-κB and TGF-β1/Smad3 Signaling Pathways in Diabetic Nephropathy

Introduction Diabetic nephropathy (DN) has become an increasing threat to health, and inflammation and fibrosis play important roles in its progression. Wogonin, a flavonoid, has been proven to suppress inflammation and fibrosis in various diseases, including acute kidney injury. This study aimed at investigating the effect of wogonin on diabetes-induced renal inflammation and fibrosis. Materials and Methods Streptozotocin (STZ)-induced diabetic mouse models received gavage doses of wogonin (10, 20, and 40 mg/kg) for 12 weeks. Metabolic indices from blood and urine and pathological damage of glomerulus in the diabetic model were assessed. Glomerular mesangial cells SV40 were cultured in high glucose (HG) medium containing wogonin at concentrations of 1.5825, 3.125, and 6.25 μg/mL for 24 h. Inflammation and fibrosis indices were evaluated by histopathological, Western blotting, and PCR analyses. Results Wogonin treatment ameliorated albuminuria and histopathological lesions in diabetic mice. Inflammatory cytokines, such as monocyte chemotactic protein-1 (MCP-1), tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and related signaling pathway NF-κB were downregulated after the administration of wogonin in vivo and in vitro. Furthermore, wogonin reduced the expression of extracellular matrix (ECM), including fibronectin (FN), collagen IV (Col-IV), α-smooth muscle actin (α-SMA), and transforming growth factor-β1 (TGF-β1) in the kidneys of diabetic mice and HG-induced mesangial cells. Moreover, the inhibition of TGF-β1/Smad3 pathway might be responsible for these changes. Conclusion Wogonin may ameliorate renal inflammation and fibrosis in diabetic nephropathy by inhibiting the NF-κB and TGF-β1/Smad3 signaling pathways.
LPS Enhances the Chemosensitivity of Oxaliplatin in HT29 Cells via GSDMD-Mediated Pyroptosis

Introduction Pyroptosis induced by lipopolysaccharide (LPS) is a dissolved form of cell death. The molecular marker gasdermin D, specifically GSDMD-N, is critically required for the induction of pyroptosis. Recently, there have been studies showing that LPS is closely related to tumor biology. Methods Specimens from 40 patients with colorectal cancer (CRC) were collected. Eight- to twelve-week-old C57BL6 male mice (n=30) were raised. Immunohistochemistry and Western blot were performed to test the expression of GSDMD. Moreover, cytotoxicity assay, IL-18 and IL-1β ELISA, Annexin V and PI stain, and wound healing assay were also made. Gene Expression Profiling Interactive Analysis (GEPIA) was used to verify the expression of GSDMD and overall survival of CRC patients with a high/low expression of GSDMD. Results In the research, we showed that the poor prognosis in CRC patients was significantly related to the GSDMD expression and significantly down-regulated in human colorectal cancer (CRC) tissues. Treatment with LPS, but not TNF-α, induced pyroptosis via promoting the expression of GSDMD and GSDMD-N membrane translocation and enhanced chemosensitivity in response to L-OHP in HT29 cells. Furthermore, the enforced expression of GSDMD in HT29 cells reduced cell survival and induced cell death. Discussion These results of studies suggest that the low expression of GSDMD correlates with a poor CRC prognosis, and that pyroptosis induced by LPS may improve the anti-cancer effect of L-OHP, inhibiting the tumorigenesis of CRC by activating GSDMD. Our findings lay the foundation for further development of GSDMD serving as an important prognostic biomarker and a valid CRC therapeutic target.
Trends in Diagnosis of Alpha-1 Antitrypsin Deficiency Between 2015 and 2019 in a Reference Laboratory

Background Alpha-1 antitrypsin deficiency (AATD) remains largely underdiagnosed despite recommendations of healthcare institutions and programmes designed to increase awareness. The objective was to analyse the trends in AATD diagnosis during the last 5 years in a Spanish AATD reference laboratory. Methods This was a retrospective revision of all alpha-1 antitrypsin (AAT) determinations undertaken in our laboratory from 2015 to 2019. We analysed the number of AAT determinations performed and described the characteristics of the individuals tested, as well as the medical specialties and the reasons for requesting AAT determination. Results A total of 3507 determinations were performed, of which 5.5% corresponded to children. A significant increase in the number of AAT determinations was observed from 349 in 2015 to 872 in 2019. Among the samples, 57.6% carried an intermediate AATD (50–119 mg/dL) and 2.4% severe deficiency (<50 mg/dL). The most frequent phenotype in severe AATD individuals was PI*ZZ (78.5%), and aminotransferase levels were above normal in around 43% of children and 30% of adults. Respiratory specialists requested the highest number of AAT determinations (31.5%) followed by digestive diseases and internal medicine (27.5%) and primary care physicians (19.7%). The main reason for AAT determination in severe AATD adults was chronic obstructive pulmonary disease (41.7%), but reasons for requesting AAT determination were not reported in up to 41.7% of adults and 58.3% of children. Conclusion There is an increase in the frequency of AATD testing despite the rate of AAT determination remaining low. Awareness about AAT is probably increasing, but the reason for testing is not always clear.
Therapeutic Vaccines for HPV-Associated Malignancies

Abstract Human papillomavirus (HPV)-related malignancies are responsible for almost all cases of cervical cancer in women, and over 50% of all cases of head and neck carcinoma. Worldwide, HPV-positive malignancies account for 4.5% of the global cancer burden, or over 600,000 cases per year. HPV infection is a pressing public health issue, as more than 80% of all individuals have been exposed to HPV by age 50, representing an important target for vaccine development to reduce the incidence of cancer and the economic cost of HPV-related health issues. The approval of Gardasil® as a prophylactic vaccine for high-risk HPV 16 and 18 and low-risk HPV6 and 11 for people aged 11–26 in 2006, and of Cervarix® in 2009, revolutionized the field and has since reduced HPV infection in young populations. Unfortunately, prophylactic vaccination does not induce immunity in those with established HPV infections or HPV-induced neoplasms, and there are currently no therapeutic HPV vaccines approved by the US Food and Drug Administration. This comprehensive review will detail the progress made in the development of therapeutic vaccines against high-risk HPV types, and potential combinations with other immunotherapeutic agents for more efficient and rational designs of combination treatments for HPV-associated malignancies.
Medical Student Schwartz Rounds: A Powerful Medium for Medical Student Reflective Practice

Purpose Reflection is a core component of good medical practice and of growing importance given increasing rates of burnout in the field of medicine. Schwartz Rounds (SRs) are a group-based model of reflective practice. This study explored the utility of student-specific Schwartz Rounds as a medium for reflective practice amongst medical students entering their first year of clinical attachments, and how effective these are compared to standard organisation-wide Schwartz Rounds. Methods Three Medical Student Schwartz Rounds (MSSRs) were piloted over the course of a year at a major teaching hospital, focussed on the theme: “Is this what I signed up for? ” Participants were asked to complete a questionnaire following the session, and this data was then analysed. Results Feedback was obtained from 93% (42/45) students who attended. Ninety per cent of students rated the sessions as “excellent or exceptional”, 93% felt the MSSRs added to their “insight and self-awareness”, and 90% plan to attend SRs again in the future. A thematic analysis of the qualitative feedback highlighted three broad themes from the pilot; group reflection is more profound than individual reflection, sharing experiences facilitated a greater sense of belonging, and group reflective practice can be intimidating. There was a statistically significant difference between students’ ratings of MSSRs, rated 8.67/10, versus written reflection, rated 4.64/10 (p<0.01). Conclusion Students were overwhelmingly positive about their experiences in this pilot, with response ratings commensurate with those from organisation-wide Schwartz Rounds. Therefore, MSSRs should be considered as a valid alternative form of reflective practice.
Association of the HDL-c Level with HsCRP, IL-6, U-NAG, RBP and Cys-C in Type 2 Diabetes Mellitus, Hypertension, and Chronic Kidney Disease: An Epidemiological Survey

Purpose To explore the association between the anti-inflammatory and renal protective roles of high-density lipoprotein cholesterol (HDL-c) and its different levels in type 2 diabetes mellitus (T2D), hypertension (HTN), and chronic kidney disease (CKD) and to lay a theoretical basis for precise, maximum-benefit HDL-c-raising therapy for patients with these diseases. Patients and Methods A total of 2127 participants (195 with T2D, 618 with HTN, 162 with CKD, and 1152 controls) were selected and divided into four groups according to their baseline HDL-c level, namely, low HDL-c (L-HDL-c, ≤1.03 mmol/L), medium HDL-c (M-HDL-c, 1.04–1.55 mmol/L), high HDL-c (H-HDL-c, 1.56–2.05 mmol/L) and extremely high HDL-c (E-HDL-c, ≥ 2.06 mmol/L). Serum and morning urine samples were collected to analyze the correlation between high-sensitivity C-reactive protein (HsCRP), interleukin-6 (IL-6), urine n-acetyl-β-d-glucosidase (U-NAG), retinol binding protein (RBP), and cystatin c (Cys-C) levels with the HDL-c levels. Results The HDL-c levels of patients with T2D, HTN and CKD were universally lower than those in the control group in both sexes (p<0.05), while male patients also manifested a lower level of HDL-c than female patients. However, although they had lower values of the renal impairment index, female patients were found to have anomalously higher amounts of proinflammatory cytokines. In addition, the correlations between HsCRP and RBP levels and HDL-c levels were most significant in patients with HTN (p<0.05), whereas in patients with T2D and CKD, such relevance was less significant. Conclusion Existence of substantial differences in HDL-c levels between different types of disease and sex highlighted that a higher HDL level does not always predict a better clinical outcome of patients. Moreover, we found that both HsCRP and RBP correlated negatively with HDL-c in HTN patients, indicating that monitoring HsCRP and RBP may serve as indicators for therapeutic efficacy of HDL-c-raising medications in HTN patients.
Changes in quality of life and dyspnoea after hospitalization in COVID-19 patients discharged at home

Background To date, the effects of COVID-19 pneumonia on health-related quality of life (HRQoL) and dyspnoea are unknown. Methods In a real-life observational study, 20 patients with COVID-19-related pneumonia received usual care plus erdosteine (300 mg twice daily) for 15 days after hospital discharge following local standard operating procedures. At discharge (T0) and on Day 15 (T1), participants completed the St George’s Respiratory Questionnaire (SGRQ), the modified Medical Research Council (mMRC) scale of dyspnoea during daily activity, the BORG scale for dyspnoea during exertion, and Visual Analogue Scale (VAS) for dyspnoea at rest. Paired t-tests compared scores at T0 and T1. Results The mean (SD) SGRQ total score decreased from 25.5 (15.5) at T0 to 16.9 (13.2) at T1 (p<0.01); 65% of patients achieved a clinically important change of ≥4 points. SGRQ domain scores (symptoms, activity, and impact) were also significantly reduced (all p<0.01). The mean (SD) VAS score decreased from 1.6 (1.7) to 1.4 (2.5); p<0.01. The mean mMRC score decreased significantly (p=0.031) and 30% of patients achieved a clinically important change of ≥1 point. The mean (SD) Borg score increased from 12.8 (4.2) to 14.3 (2.4); p<0.01. Conclusion The present proof of concept study is the first to report HRQoL in patients with COVID-19. During 15 days after hospital discharge, patients reported significant improvements in HRQoL and dyspnoea at rest and during daily activities.
Helminth Induced Immunoregulation and Novel Therapeutic Avenue of Allergy

Abstract Allergic diseases are increasing at an alarming rate worldwide, particularly in developed countries. In contrast, there is a decrease in the prevalence of helminthic infections and other neglected diseases. The hygiene hypothesis elaborates parasitic infection, and allergy-associated diseases have an inverse relationship. Acute helminthic infection and allergic reaction stimulate Type 2 helper cells (Th2) immune response with up-regulation of cytokines IL-4-, IL-5-, and IL-13-mediated IgE and mast cell production, as well as eosinophilia. However, people who chronically suffer from helminthic infections are demarcated through polarized Th2 resulting in alternative macrophage activation and T regulatory response. This regulatory system reduces allergy incidence in individuals that are chronically diseased through helminth. As a result, the excretory-secretory (ES) substance derived from parasites and extracellular vesicular components can be used as a novel therapeutic modality of allergy. Therefore, the aim of this review meticulously explored the link between helminth infection and allergy, and utilization of the helminth secretome for therapeutic immunomodulation.
Patient Reported Central Nervous System Adverse Events of Efavirenz-Based Antiretroviral Therapy in People Living with HIV in Northwest Ethiopia

Background Central nervous system (CNS) toxicities from regimens containing efavirenz are the main reasons for non-adherence, switch and discontinuation of antiretroviral therapy (ART). We aimed to assess prevalence of CNS adverse events and associated factors among HIV patients taking efavirenz-based regimens at the University of Gondar Comprehensive and Specialized Hospital (UoGCSH), Northwest Ethiopia. Methods A hospital-based cross-sectional study was conducted from March 15 to May 15, 2018 on 345 patients living with HIV who were taking efavirenz-based regimens. Information on sociodemographic and clinical characteristics was taken from medical records and patient interview. Binary logistic regression analysis was done to determine association. Statistical significance was declared at P value of ≤ 0.05. Results About 52.8% of participants experienced CNS adverse events. Vivid dreams, confusion, insomnia and somnolence were the most frequently reported adverse events. Most of the CNS adverse events occurred in the first year of treatment initiation and resolved within 1–4 weeks. Age, economic status, CD4 count, disease stage, presence of comorbidities and concurrent use of other medication had a significant association with the occurrence of CNS adverse events. Conclusion More than half of HIV patients taking efavirenz-based regimens at UoGCSH experienced CNS adverse events. Health-care providers should give attention to patients on efavirenz therapy to monitor for CNS adverse events, especially for patients who have low CD4 count, advanced disease, comorbidities, low income and are older in age.
Arable weed communities in the south of Western Siberia – impoverished species pools constrain diversity despite low land-use intensity

Despite the high significance of the Western Siberian grain belt for crop production in Russia, its weed communities are largely unknown. In this region spring wheat is grown on fertile Chernozem soils with large field sizes but land-use intensity per area is low compared to Central Europe. By using a randomized sampling design we studied arable weed assemblages in the northern forest-steppe zone of Tyumen region on 99 within-field sampling plots of 100 m2 size. Surprisingly, with average of 9.8 ± 3.8 species 100 m species richness was low when compared with low-input farming in Central Europe and did not differ between areas of different land-use intensity. Against expectations species composition was not predominantly controlled by soil characteristics and climate, most likely due to short natural gradients. Instead, management factors such as fertilization and tillage intensity seemed to be important factors. Except for two species the Tyumen weed flora consisted mainly of species that are widespread throughout the temperate zone. We found only 10 species with an origin or core area in North Asia or Eastern Europe. The species pool was generally small and with 26% the proportion of non-native species (archaeophytes) was low, when compared to Central European weed communities. Given that weed communities with higher species richness are described from neighboring Bashkiria, we conclude that arable land-use intensity in Tyumen region is high enough to reduce community species richness within arable fields estimated by a randomized sampling design. Since measured soil nutrient values did not affect species richness, herbicide use is most likely the crucial management factor. Furthermore, species-richness was vitally restricted by the small species pool. The low proportion of thermophilous arable weed species that originate from the Mediterranean or Middle-Eastern area and contribute significantly to the Central European weed diversity indicate that climatic dispersal limitations may be responsible for the small number of weed species in the Tyumen flora. An additional constraint was the short history of arable farming in Western Siberia, where considerable arable land use was started only by the end of the 17 century.
Intimate Partner Violence, Its Sociocultural Practice, and Its Associated Factors Among Women in Central Ethiopia

Background Intimate partner violence is a serious and widespread problem worldwide. It is a domestic violence by a spouse or partner in an intimate relationship against the other spouse or partner. Even though Ethiopia is also one of the countries where the condition has been seriously happening, there is a dearth of information in the study area. Objective To assess the prevalence of intimate partner violence and its sociocultural practice, and its associated factors among married women in Oromia, Central Ethiopia. Methods A community-based cross-sectional study was conducted on 671 women of Ambo district who were in marriage from March 1 to 30, 2018. Multistage sampling method was employed to select study participants. Data were collected using interviewer-administered WHO Multi-country Study on Women’s Health and Life Experiences Questionnaire. Descriptive, bivariate, and multivariate logistic regression analyses were done using SPSS version 20.0. Results Out of 671 married women expected to participate, 657 of them participated in the study making a response rate of 98%. Overall, 77% (95% CI 73.7–80.1%), and 62.4% (95% CI, 58.6–66.1%) of the respondents reported that they have experienced intimate partner violence in their lifetime and in the last one year, respectively. Lack of formal education by husband (AOR 2.30, 95% CI 1.28–4.15), housewife occupation of respondents (AOR 2.04, 95% CI 1.02–4.06), number of children (AOR 4.37, 95% CI 1.40–13.66), perceived husband dominance (AOR 1.74, 95% CI 1.15–2.63), grow up in domestic violence (AOR 1.53, 95% CI 1.00–2.35) and partner’s alcohol intake (AOR 1.77, 95% CI 1.12–2.79) were independently associated with intimate partner violence. Conclusion Intimate partner violence against women remains an important public health problem. This needs urgent attention at all levels of societal hierarchy including policymakers, stakeholders, and professionals to alleviate the situation.