Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity of HIV-1 in Krasnoyarsk Krai: Area with High Levels of HIV-1 Recombination in Russia

More than a quarter of HIV-infected individuals registered in Russia live in Siberia. Unlike Central Russia where HIV-1 subtype A6 is predominant, in most Siberian regions since 2012, a new HIV-1 CRF63_02A1 genetic variant has spread, with the share of this variant attaining 75–85% among newly identified HIV cases. Krasnoyarsk Krai is considered to be a high-risk territory according to morbidity rate and HIV infection incidence among the population. The current paper aims to study the molecular epidemiologic characteristics of HIV-1 spreading in Krasnoyarsk Krai. Phylogenetic and recombination analyses of pol (PR-RT, IN) and env regions of the virus were used for genotyping 159 HIV-1 isolated in Krasnoyarsk Krai. 57.2% of the isolates belonged to subtype A (A6) specific to Russia, 12.6% to CRF63_02A1, and 0.6% to CRF02_AGСА, and in 29.6% HIV-1 URFs were detected, including URF63/А (23.9%), URFА/В (4.4%), and URF02/А (1.3%). In 6 of 7, HIV-1 URFА/В identical recombination model was detected; the origin of 38 URF63/А was proven to be the result of individual recombination events. Since 2015, a share of the population with newly diagnosed HIV who were infected with HIV-1 URF reached an exceptionally high rate of 38.6%. As distinct from adjacent Siberian regions, the HIV-1 CRF63_02A1 prevalence rate in Krasnoyarsk Krai is within 16%; however, the increased contribution of new HIV-1 into the regional epidemic development was observed due to the recombination of viruses of subtypes А, В, and CRF63_02A1. The difference between the described molecular epidemiologic picture in Krasnoyarsk Krai and in adjacent areas is likely caused by differences in predominant routes of HIV transmission and by more recent HIV-1 CRF63_02A1 transmission in the PWID group, which had a high prevalence of HIV-1 subtype A by the time of the new virus transmission, resulting in increased possibility of coinfection with various HIV-1 genetic variants.
Efficacy of Lianhua Qingwen Compared with Conventional Drugs in the Treatment of Common Pneumonia and COVID-19 Pneumonia: A Meta-Analysis

Methods Seven English and Chinese databases were used to search for qualified experimental studies as of July 27, 2020. All data were extracted directly from the included studies, and no special conversion formula was used. The weighted mean difference (WMD), 95% confidence interval (CI), and odds ratio (OR) were used for evaluation. Results Forty-two studies involving 3793 subjects met the qualification criteria. For common pneumonia, a short duration of flu-like symptoms (WMD = −1.81, 95% CI = −2.12 to −1.50, P < 0.001), sputum (WMD = −1.10, 95% CI = −1.50 to −0.70, P < 0.001), pulmonary rale (WMD = −2.03, 95% CI = −2.74 to −1.31, P < 0.001), pulmonary imaging improvement (WMD = −1.88, 95% CI = −2.28 to −1.47, P < 0.001), curative effect (OR = 3.65, 95% CI = 2.81 to 4.76, P < 0.001), and healing period (WMD = −1.68, 95% CI = −2.62 to −0.74, P < 0.001) were associated with the Lianhua Qingwen group; subgroup analysis based on flu-like symptoms showed statistically significant improvements in fever and cough. For COVID-19 pneumonia, improvements in flu-like symptoms (OR = 3.18, 95% CI = 2.36 to 4.29, P < 0.001), shortness of breath (OR = 10.62, 95% CI = 3.71 to 30.40, P < 0.001), curative effect (OR = 2.49, 95% CI = 1.76 to 3.53, P < 0.001), healing period (WMD = −2.06, 95% CI = −3.36 to −0.75, P = 0.002), and conversion of severe cases (OR = 0.46, 95% CI = 0.27 to 0.77, P = 0.003) were associated with the Lianhua Qingwen group; subgroup analysis indicated statistically significant improvements of fever, cough, fatigue, and muscle pain in the Lianhua Qingwen group compared to the conventional drug group. Regarding adverse reactions, no significant difference was detected for common pneumonia (OR = 0.75, 95% CI = 0.54 to 1.05, P = 0.097). Conclusions Lianhua Qingwen combined with conventional drugs may be a promising therapy for treating common pneumonia and COVID-19 pneumonia.
Clinical Characteristics and Management of the Hydatid Cyst of the Liver: A Study from a Tertiary Care Center in Nepal

A hydatid cyst of the liver is a significant yet neglected public health problem in Nepal. The present study was carried out to evaluate the demographic characteristics, clinical presentations, and management of the patients of the hydatid cyst of the liver in the setting of a developing country. It was a retrospective, descriptive analysis of 53 patients admitted in the department of surgery with the diagnosis of hydatid cyst of the liver based on clinical manifestations, imaging studies, or serology between 2016 and 2019. The median age of the patients was 36 years, with the age group of 25-45 years being the most commonly affected (23, 43.4%). 58.5% of the patients were female. Abdominal pain (49, 92.5%) and a palpable liver (17, 32.1%) were the most common complaint and physical finding in our study population, respectively. Abdominal ultrasonography and computed tomography scan were the major imaging studies used to establish a diagnosis. A unilocular and anechoic cystic lesion was the most frequent imaging finding. The right lobe of the liver harbored the cysts in the maximum number of patients. Surgery was the preferred modality of treatment (23, 43.4%), with pericystectomy being the most common form of surgical intervention. The hydatid cyst of the liver is a common cause of morbidity in Nepal. Clinical evaluation supplemented by imaging studies is required for diagnosis, and surgery remains the treatment of choice in most cases. To explain the epidemiological pattern of the disease, multicentric studies involving a larger sample of patients should be conducted.
Research protocol for a mixed-methods study to characterise and address the socioeconomic impact of accessing TB diagnosis and care in Nepal

Background: WHO’s 2015 End TB Strategy advocates social and economic (socioeconomic) support for TB-affected households to improve TB control. However, evidence concerning socioeconomic support for TB-affected households remains limited, especially in low-income countries. Protocol: This mixed-methods study in Nepal will: evaluate the socioeconomic impact of accessing TB diagnosis and care (Project 1); and create a shortlist of feasible, locally-appropriate interventions to mitigate this impact (Project 2). The study will be conducted in the Chitwan, Mahottari, Makawanpur, and Dhanusha districts of Nepal, which have frequent TB and poverty. The study population will include: approximately 200 people with TB (Cases) starting TB treatment with Nepal’s National TB Program and 100 randomly-selected people without TB (Controls) in the same sites (Project 1); and approximately 40 key in-country stakeholders from Nepal including people with TB, community leaders, and TB healthcare professionals (Project 2). During Project 1, visits will be made to people with TB’s households during months 3 and 6 of TB treatment, and a single visit made to Control households. During visits, participants will be asked about: TB-related costs (if receiving treatment), food insecurity, stigma; TB-related knowledge; household poverty level; social capital; and quality of life. During Project 2, stakeholders will be invited to participate in: a survey and focus group discussion (FGD) to characterise socioeconomic impact, barriers and facilitators to accessing and engaging with TB care in Nepal; and a one-day workshop to review FGD findings and suggest interventions to mitigate the barriers identified. Ethics and dissemination: The study has received ethical approval. Results will be disseminated through scientific meetings, open access publications, and a national workshop in Nepal. Conclusions: This research will strengthen understanding of the socioeconomic impact of TB in Nepal and generate a shortlist of feasible and locally-appropriate socioeconomic interventions for TB-affected households for trial evaluation.
Stress among Portuguese Medical Students: A National Cross-Sectional Study

Introduction The medical course is extremely stimulating but also demanding, and it can interfere with students' mental health. Stress leads to lower life quality, academic performance, and ultimately to a lower quality of patient care delivered. Objective To analyse stress levels of sixth-year medical students who attend Portuguese colleges. Methodology. This observational cross-sectional study involved Portuguese medical students attending the sixth year of all Portuguese faculties. We applied an online self-response questionnaire, including the 10 items Perceived Stress Scale (PSS) to assess stress levels and sociodemographic variables. Logistic regression was used to estimate the weight of the studied determinants on stress levels. Results A total of 501 participants were included for analysis (69.5% females), with a median age of 24 years old. We found significant levels of stress in 49.9% (95% CI: 45.5–54.3%), with 20.8% of total students presenting extremely high levels, irrespective of age, gender, and faculty. Stress was higher when students presented bad sleeping and eating habits, lack of ability to manage time, dissatisfaction with social life and academic experience, and low family support. Also, these students are more worried about their future and present a higher degree of concern about their graduation test performance. Conclusion This study found high stress levels among Portuguese medical students, associated with social determinants and the intrinsic complexity of the course. This is worrying, and it elucidates the importance of coping strategies to make students deal with stress and be healthier, currently and in the future.
Public perception of COVID-19’s global health crisis on Twitter until 14 weeks after the outbreak

Abstract Because language represents advanced aspects of human cognition, studying linguistic styles and figurative meaning have proven effective in measuring embodied cognition about the external world. This article defines the most worrisome topics people discussed from Weeks 1 to 14 after the outbreak and compares the message delivered by the literal use of words to the figurative use of metaphoric expressions. We bootstrapped representative data from Twitter over 14 weeks since the inception of the outbreak to be analyzed thematically using the Linguistic Inquiry and Word Count (LIWC) 2015 software as well as corpus tools. The MetaNet database, corpus tools, and manual annotation were used to detect expressions that can be linguistically mapped to the formalized list of conceptual metaphors. The most frequently tagged themes included ‘the outbreak of the pandemic, its epidemiology, its prophylaxis measures, national and world economies, media’, as well as the ‘signs and symptoms of COVID-19’. Although LIWC-based analysis showed English-speaking tweeters maintained high levels of analytical thinking, elevated levels of anger, anxiety, and doubtfulness, there were discrepancies and improper conceptualization of the clinical picture of the pandemic.
Preconditioning Effect of High-Intensity Interval Training (HIIT) and Berberine Supplementation on the Gene Expression of Angiogenesis Regulators and Caspase-3 Protein in the Rats with Myocardial Ischemia-Reperfusion (IR) Injury

Objective It has been shown that angiogenesis is a desirable treatment for patients with ischemic heart disease. We set out to investigate the impact of high-intensity interval training (HIIT) and berberine supplementation on the gene expression of angiogenesis-related factors and caspase-3 protein in rats suffering from myocardial ischemic-reperfusion injury. Methods Fifty rats were divided into the following groups: (1) trained, (2) berberine supplemented, (3) combined, and (4) IR. Each cohort underwent five sessions of HIIT per week for a duration of 8 weeks followed by induction of ischemia. Seven days after completion of reperfusion, changes in the gene expression of angiogenesis-related factors and caspase-3 protein were evaluated in the heart tissue. Results We observed a significant difference between four groups in the transcript levels of vascular endothelial cell growth factor (VEGF), fibroblast growth factor-2 (FGF2), and thrombospondin-1(TSP-1) (p ≤ 0.05). However, the difference in endostatin (ENDO) levels was not significant among the groups despite a discernible reduction (p ≥ 0.05). Moreover, caspase-3 protein and infarct size were significantly reduced in the intervention groups (p ≤ 0.05), and cardiac function increased in response to these interventions. Conclusion The treatments exert their effect, likely, by reducing caspase-3 protein and increasing the expression of angiogenesis-promoting factors, concomitant with a reduction in inhibitors of the process.
Home Invasive Mechanical Ventilation Users Quality of Life: Is Response Shift Supported?

Problem: Planning care to support quality of life (QoL) in the adult home invasive mechanical ventilation (HIMV) user is difficult. Limited research with varied results and outcomes makes planning patient centered care very challenging. Goals: This review of literature will serve as an opportunity to shed empirical light on gaps in literature and provide the foundation for further research. Methods: The following literature presents: (a) background information regarding prevalence of HIMV, (b) general characteristics of people who use HIMV and (c) current research on QoL and HIMV. CINAHL, PubMED, Cochrane, EBSCO, and Wiley were searched using the terms ‘home invasive mechanical ventilation’, ‘quality of life’, ‘physical disabilities’, ‘assisted ventilation’ and limited to peer reviewed articles from 2000-2017. The literature search was conducted from August, 2014 to January, 2018. Findings: A total of 30 peer reviewed research articles where located with a focus on HIMV and QoL. Results from each study varied however literature gaps were identified, including: understanding the role of caregivers, the effect of social participation on QoL, the effect of the physical environment on QoL, and the effect of time on QoL in those living on HIMV
Emergency surgery for acute cholecystitis associated with cholecystocolonic fistula caused by gallbladder cancer: a case report

Abstract Preoperative diagnosis of cholecystocolonic fistula (CCF) is difficult and the contribution of gallbladder cancer or colon cancer is unclear when there is associated malignancy. We present a case that was diagnosed with acute cholecystitis associated with CCF by multidetector computed tomography (MDCT) preoperatively and malignant neoplasm during emergency surgery. She was finally diagnosed with gallbladder cancer after the operation and underwent a two-stage surgery for regional lymph node dissection. Gallbladder cancer can be a primary malignant cancer causing CCF, whereas MDCT is useful for preoperative diagnosis of CCF. A treatment plan in consideration of gallbladder cancer is advisable for CCF associated with malignant tumor.
Primary Appendiceal Adenocarcinoma Presenting with Hematochezia due to the Invading Tumor in the Sigmoid Colon

Primary appendiceal tumors are rare malignancies; some cases have been described to invade other organs, and this represents a very rare clinical condition. We report a case of appendiceal adenocarcinoma invading the sigmoid colon and a review of similar cases. A 69-year-old woman with complaints of hematochezia was admitted to the hospital. Colonoscopy revealed a tumor in the sigmoid colon, which was a well-differentiated tubular adenocarcinoma. A computed tomography scan showed an appendiceal mass that involved the sigmoid colon, suggesting an appendiceal cancer invading the sigmoid colon. Ileocecal resection with extended lymphadenectomy and en bloc resection of the sigmoid colon was performed. The appendiceal tumor involved the sigmoid colon and the terminal ileum. The ileocecal part which included the tumor and the involved sigmoid colon was resected in total. Macroscopic findings showed that the appendiceal tumor made a fistula with the sigmoid colon. Pathological examination revealed that the tumor was a well-differentiated tubular adenocarcinoma that invaded the sigmoid colon. The final pathological stage was T4bN0M0, stage IIC. The patient was discharged from the hospital uneventfully. She was alive without relapse after a 20-month follow-up. Although an appendiceal tumor invading the rectosigmoid region is rare, a preoperative diagnosis can be obtained that facilitates the planning of a suitable surgical procedure: en bloc resection of the ileocecal part and the rectosigmoid part.
CDC42EP5/BORG3 modulates SEPT9 to promote actomyosin function, migration, and invasion

Farrugia et al. identify Cdc42EP5 as a regulator of actomyosin activity. Cdc42EP5 potentiates SEPT9-mediated F-actin bundling, which is required for the stabilization of highly contractile actomyosin structures. In melanoma, the Cdc42EP5–SEPT9 axis is required for amoeboid migration, invasion, and metastasis.
Psychological Distress, Drug Use, and Internet Use: The Association with Poor Sleep Quality in a Sample of Secondary School Students

Sleep problems are common among children and adolescents. Sleep quality plays a significant role in their mental health. We aimed to determine the prevalence of poor sleep quality (PSQ) among secondary school students, identify sociodemographic factors associated with PSQ in this group, and examine the independent associations of psychological distress, stimulant use, and internet use with PSQ. Data were collected from 420 secondary school students from four different schools who were selected using a mixture of convenience and random sampling. A set of questionnaires was administered to collect data, and it consisted of 5 sections measuring: the sociodemographic, drug use, psychological distress, internet use, and sleep quality. A total of 378 questionnaires were analyzed. The participants comprised 174 (46.2%) males and 203 (53.8%) females who were between 10 and 21 years. The mean age was 14.78 years. The prevalence of those who had PSQ was 12.2%. A logistic regression model showed that anxiety (AOR = 1.20, 95% CI: 1.10-1.32), depression (AOR = 1.12, 95% CI: 1.00-1.25), and internet use (AOR = 1.02, 95% CI: 1.00-1.03) were significantly associated with PSQ. PSQ commonly exists among students and has a relationship with their psychological state and potentially addictive behavior, such as internet use. We prescribed the optimal treatment of psychological disorders and addictive behavior, of which sleep problems are a typical fallout.
APPLYING FORECAST TRACK AND INTENSITY DIAGNOSTICS TO HIGH-IMPACT NORTHEAST WINTER STORMS

A conventional forecasting notion is that as lead time decreases, numerical weather prediction models exhibit a leftward (i.e., west) trend in the forecast position of low-pressure systems along the East Coast of the U.S. This left trend, which may turn seemingly weak ocean cyclones into high-impact weather events for the Northeast U.S., is attributed to various potential causes, such as variability in upstream shortwave troughs, or the representation of latent heat release in the NWP models downstream of the trough associated with the incipient cyclone. This study seeks to address whether this rule of thumb holds any significant merit, and to examine a long-term climatology of Northeast U.S. cold season cyclones from a forecast skill and error perspective. A climatology of ensemble forecasts of high-impact Northeast winter storms initialized from 0 to 5-day lead times was constructed using the Global Ensemble Forecast System (GEFS) Reforecast version 2, from 1 November 1985 through 31 December 2015. Cases included in this climatology were those identified within 750 km of the 40oN/70oW benchmark from an ERA-I based cyclone track dataset created by Sprenger et al. (2017), but also could be tracked with CFSR data using a 925-hPa area-averaged vorticity maxima and height minima-based tracking algorithm. The verification of the ensemble forecasts at 0 through 5day lead times are computed against the CFSR verification track, and the analysis quantifies the GEFS climatological forecast track and intensity errors and biases. A total of 517 cyclones were identified, with the CFSR verification tracks consistent with prior climatologies of East Coast cyclones. When applying the tracking algorithm to the ensemble forecasts, an underdispersive bias was found in the GEFS for both position and
Cancer Specific CTL Expansion with ZYX Bioreactor

Objective: The use of therapeutic immune cell subsets is becoming an increasingly cost-effective and attractive strategy for the treatment of cancer. Nonetheless, the field of cell therapy is hampered by the inability to consistently generate and expand sufficient numbers of high quality cells from a majority of patients. To address this critical issue, the investigators developed a sophisticated bioreactor technology that maximizes metabolic support and minimizes the damaging shear-stress forces, automatically monitors functional correlates to allow cell harvest at peak functional capacity, and permits cell sorting in situ to minimize cell loss and microbial contamination. In current study, the established cancer-specific CTL expansion system will be tested for its potency of cancer cell killing both in vitro and in vivo. Methods: To test the cell expansion efficiency of ZYX Bioreactor, the CD8+ T cells expanded in different culture systems were enumerated by flow cytometry and the Cancer-specific cytotoxic T lymphocyte (CTL) activity was measured for their cytokine production and against autologous tumor targets by CTL cytotoxicity assay in vitro and in vivo as well as Annexin V staining to detect low-level cytolytic activity. In the in vivo CTL assay, mouse cancer cell line was used as stimulators and targets for the expanded mouse CTL evaluation in BALB/c mice and human lung cancer cells and expanded human CTL were injected into immunodeficient mice for human CTL evaluation. Results: In comparison of other cell culture systems, ZYX Bioreactor has significantly higher efficiency in the cancer specific CD8+ T cell expansion, and these CD8+ T cells expanded in ZYX Bioreactor exhibited higher specific CTL cytotoxicity in both in vivo and in vitro studies. Conclusion: ZYX Bioreactor can provide the adequate metabolic support to the growing cancer-specific CD8+ CTLs and the proper condition for the stimulation of cancer cell-carried antigens to the CTLs.
Microscopy Image Processing for the Human Eye

Vivo confocal microscopy allows scientists to better understand eye health and systemic diseases. Microneuromas could play a role, however, monitoring their growth from a mosaic of images is error prone and time consuming. We used automated image stitching as a solution; focusing on accuracy and computational speed of three different feature detection algorithms: SIFT, SURF and ORB. The results illustrated that SURF was computationally efficient with our data. Future investigation is to create a global solution that can replace the need for manual image stitching in this application.