Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of Human Papilloma Virus and Epstein-Barr Virus with Ovarian Cancer in Shiraz, Southwestern Iran

Background & Objective: Ovarian cancer is one of the most common cancers amongst women. The association of Human papillomavirus (HPV) and Epstein-Barr virus (EBV) with ovarian cancer is inconclusive; therefore, the aims of this study were to evaluate the frequency of HPV and EBV in malignant, borderline, benign and normal ovarian tissues. Methods: In this case-control study, 205 Paraffin-embedded ovarian tissue specimens including 68 malignant, 27 borderline, 65 benign, and 45 normal tissues were included from December 2014 to January 2018 and subjected to DNA extraction. The β-globin gene was amplified using PCR to confirm the quality of the extracted DNA. The genomes of HPV (genotypes 16 and 18) and EBV were identified, using specific primers by PCR. Results: The mean age of participants was 43.42 ± 15.4 years. The frequency of HPV was statistically significant between malignant versus benign (P=0.02) and control groups (P=0.002), but not with borderline tumor group (P=0.78). Amongst HPV infected samples, 1 (4.5%) and 14 (63.6%) samples were infected with types 16 and 18, respectively. Also 4 (18.2 %) samples were infected with both genotypes. Eleven samples including 7(10.3%) malignant, 1 (3.7%) borderline, 3 (4.6%) benign and none (0%) of normal control groups were infected with EBV, which was statistically different between malignant and the normal control group (P=0.03). Conclusion: The results of our study showed the possible role of high risk HPVs as well as EBV in pathogenesis of ovarian cancer, and further studies are recommended to confirm these findings.
Proceedings of the 23rd Annual Meeting of the Portuguese Society of Human Genetics

E-cadherin/CDH1 dysfunction is a well-established event in GC initiation and progression in nearly 80% of gastric cancers (GC), independently of histological type. While E-cadherin permanent loss is the trigger for diffuse GC (DGC), transient aberrant expression is common along progression in intestinal GC (IGC). DGC has poorer prognosis than IGC and it spreads to the peritoneum, while IGC metastasizes to distant organs. We hypothesize that the timing (initiation vs progression) and mode of E-cadherin loss of function (permanent vs persistent; complete loss vs aberrant) determine the GC pattern of tumour spreading and prognosis and therefore explored the underlying mechanisms. The pattern of E-cadherin expression was analyzed by immunohistochemistry and correlated with clinicopathological features and overall survival (OS) in 284 patients. Permanent (CRISPR-Cas9) and transient (RNAi) E-cadherin depleted cell models representative of DGC and IGC were established and characterized by RNA-sequencing and label-free quantitative proteomics profiling followed by bioinformatics analysis. GC presenting aberrant E-cadherin expression were more often IGC, more advanced, more often spread to distant organs, and displayed poorer prognosis than GC with complete E-cadherin loss or normal E-cadherin expression. Remarkably, GCs with
Comparison of Analgesic and Adverse Effects of Oxycodone- and Fentanyl-Based Patient-Controlled Analgesia in Patients Undergoing Robot-Assisted Laparoscopic Gastrectomy Using a 55:1 Potency Ratio of Oxycodone to Fentanyl: A Retrospective Study

Purpose Oxycodone has affinities for both kappa- and mu-opioid receptors. Therefore, it has been used for postoperative analgesia of surgeries in which visceral pain is expected to be the main cause of pain. However, there are few studies of the 55:1 potency ratio of oxycodone to fentanyl when using it as intravenous patient-controlled analgesia (IV-PCA). Thus, we compared the analgesic and adverse effects of IV-PCA using the 55:1 potency ratio of oxycodone to fentanyl in patients who underwent robot-assisted laparoscopic gastrectomy. Patients and Methods This retrospective study included 100 patients using an automatic PCA pump with oxycodone or fentanyl who underwent robot-assisted laparoscopic gastrectomy between January and November 2017. All patients were provided with an IV-PCA consisting of 20 μg/kg of fentanyl or 1.1 mg/kg of oxycodone mixed with 0.9% normal saline solution to a total volume of 250 mL, which was infused basally at a rate of 0.1 mL/h with a bolus dose of 1 mL and lockout time of 6 min. The primary and secondary endpoints were to evaluate the efficacies of IV-PCA using the 55:1 potency ratio of oxycodone to fentanyl on analgesic and adverse effects. Results Pain intensity on arrival at the post-anesthesia care unit (PACU; 3.6±1.4 vs 4.4±2.0, P=0.031) and additional analgesic requirement within an hour after surgery (including the PACU period) (12% vs 37%; P=0.005) were significantly lower in the oxycodone group (n=49) than in the fentanyl group (n=51). Regarding adverse effects, the rate of postoperative nausea within 1 h after surgery (2% vs 16%; P=0.031) was also significantly lower in the oxycodone group than that in the fentanyl group. Conclusion Oxycodone-based IV-PCA by dose calculations with a 55:1 potency ratio may achieve better analgesia without any significant adverse effects, when using IV-PCA in patients undergoing robot-assisted laparoscopic gastrectomy.
Effect of irrigation scheduling and nutrient management on yield, water use efficiency and economics in garden pea (Pisum sativum L.)

A field experiment was carried out at Palampur during the rabi season of 2017-18 with 12 treatment combinations of three irrigation levels (I1: Irrigation at 15 days interval at 0.8 CPE Cumulative pan evaporation), I2: Irrigation at 15 days interval at 0.6 CPE and I3: Rainfed) and four nutrient management practices (F1:100% NPK through inorganic sources, F2:10 t FYM + Rhizobium + Jeevamrit at 21 days interval, F3: 5 t FYM +50% NPK through inorganic source and F4:Zero budget farming (seed treatment with Bijamrit + Jeevamrit at 21 days interval) and control (Recommended package of practice + flood irrigation at 10 days interval). Water use efficiency (WUE) was significantly higher under rainfed condition. The higher yield attributes, yield, WUE and net returns were obtained with an irrigation.
Porphyromonas gingivalis adopts intricate and unique molecular mechanisms to survive and persist within the host: a critical update

ABSTRACT Porphyromonas. gingivalis (P. gingivalis) is an obligate, asaccharolytic, gram-negative bacteria commonly associated with increased periodontal and systemic inflammation. P. gingivalis is known to survive and persist within the host tissues as it modulates the entire ecosystem by either engineering its environment or modifying the host’s immune response. It interacts with various host receptors and alters signaling pathways of inflammation, complement system, cell cycle, and apoptosis. P. gingivalis is even known to induce suicidal cell death of the host and other microbes in its vicinity with the emergence of pathobiont species. Recently, new molecular and immunological mechanisms and virulence factors of P. gingivalis that increase its chance of survival and immune evasion within the host have been discovered. Thus, the present paper aims to provide a consolidated update on the new intricate and unique molecular mechanisms and virulence factors of P. gingivalis associated with its survival, persistence, and immune evasion within the host.
An improved pre-culture procedure for the detection of Salmonella in frozen chicken meat by duplex polymerase chain reaction

An improved 18-hour pre-culture procedure coupling with duplex polymerase chain reaction (PCR) method capable of detecting Salmonella in frozen chicken meat is herein reported. Two pairs of primers (TS5/TS11 and S18/S19) were used for the PCR method. Positive PCR results were obtained after the 18-hour preculture (6 h in lactose broth at 37℃ followed by 12 h in Rappaport-Vassiliadis broth at 42℃) for spiked raw and irradiated meats with or without freezing treatment. The applicability of this improved procedure was tested in 50 retail frozen and 50 non-frozen chicken drumstick samples, and the results were compared with those obtained with the BAM standard culture method. No significant difference was found (p≧0.05) between these two methods.
Predictive Factors Associated With Fear Faced by Healthcare Workers During COVID-19 Pandemic: A Questionnaire-Based Study

Background The coronavirus disease 2019 (COVID-19) since the beginning has been a reason of fear among healthcare workers (HCWs) due to the increased mortality, especially in the HCWs themselves. In this survey study, we aimed to explore the predictive factors associated with fear faced by HCWs during the COVID-19 pandemic and to identify the areas which need to be addressed to reduce it. Methods On May 14, 2020, we conducted an observational, cross-sectional survey using a self-administered questionnaire, consisting of the following two parts: (1) focused on factors associated with HCWs’ fear of getting an infection and being a source of carrying the infection to whom they care, and (2) focused on factors associated with HCWs’ fear of uncertainty and lack of support from concerned health authorities. Results The mean age of the participants was 40.04 ± 12.92 years with 79.3% being males. More than half (51.1%) of the participants were consultants. The most important factors associated with fear included getting infected (84.8%), quarantined (69.6%), not getting medical treatment (62%), losing a life (56.8%), and infecting family members (94.2%). Another major factor associated with HCWs' fear was lack of support from concerned health authorities, 80.2% thought of solatium, and 71.7% believed that the job should be given to eligible family members of the deceased. More than 82.2% were concerned about health expenses and around 97.6% felt an additional health risk allowance should be given. Conclusion Our results indicate that the risk of getting infection to themselves and their families, along with a lack of support from concerned health authorities, was strongly associated with fear among HCWs. We hope through these findings that the concerned health authorities will take notice and do something in this regard by developing appropriate policies and measures to make sure that HCWs and their families are cared for if they get infected.
Visceral leishmaniasis lethality in Brazil: an exploratory analysis of associated demographic and socioeconomic factors

Abstract INTRODUCTION: It is believed that delays in diagnosis and treatment of Visceral Leishmaniasis (VL) contribute significantly to the burden of VL lethality in Brazil. METHODS: This study included several parts: a descriptive cross-sectional study of the individual characteristics of deaths from disease; a descriptive ecological study of the spatial distribution of deaths from disease; and an ecological analytical study to evaluate the association between disease lethality rates and the demographic, socioeconomic, and health indicators. The study population comprised all cases diagnosed throughout the country per the National Disease Notification System (SINAN) and the total number of disease deaths recorded in the Mortality Information System (SIM) from 2007 to 2012. RESULTS: Of the 223 deaths from disease captured by pairing the databases, 59.1% were reported as "death from other causes". There were significant associations between VL lethality rate and municipalities with the highest proportion of vulnerable individuals (rate ratio (RR)=1.18, 95% confidence interval (CI): 1.01-1.27), with VL lower incidence rate (RR=0.62, 95% CI: 0.58-0.67) and a higher incidence rate of Acquired Immune Deficiency Syndrome (AIDS) (RR=1.20, 95% CI: 1.17-1.51). CONCLUSIONS: Linking the SINAN and SIM databases allowed the inclusion of 14% of otherwise underreported deaths from VL for the study period, showing that this method is useful for the surveillance of VL-related deaths. The size of the municipal population, proportion of the vulnerable population, incidence of disease, and the incidence of AIDS were associated with municipal lethality rates related to VL in Brazil.
Role of Bicarbonates and Mannitol in Rhabdomyolysis: A Comprehensive Review

Rhabdomyolysis is characterized by rapid muscle breakdown and release of intracellular muscle components into the circulation. Acute renal injury is the most common and fatal complication of rhabdomyolysis. The current literature emphasizes the importance of preventing rhabdomyolysis and finding the benefits of sodium bicarbonates and mannitol in its prevention. A PubMed database search for the keywords "Rhabdomyolysis," "Sodium bicarbonate use in rhabdomyolysis," "Mannitol use in rhabdomyolysis," and a Medical Subject Headings (MeSH) search using the keyword "Rhabdomyolysis; Acute Kidney Injury (Subheading-Prevention and control)" generated 10,005 articles overall. After a thorough application of inclusion/exclusion criteria, 37 relevant studies were selected for this literature study. This analysis demonstrates that aggressive early volume resuscitation with normal saline should continue being the principal focus of therapy, and the use of sodium bicarbonate and mannitol in practical situations is not entirely justified. This article also emphasizes the need for future research on this topic and provides recommendations for future research.
Attitudes of Anesthesiology Residents Toward a Small Group Blended Learning Class

Background Accreditation Council for Graduate Medical Education (ACGME) has been used to evaluate the residents’ competency; however, the thriving of residents needs especial training methods and techniques. Small group learning has been used for this propose. Objectives This study assessed the attitudes of CA-1 to CA-3 anesthesiology residents toward level-specific small-group blended learning. Methods Anesthesiology residents from Department of Anesthesiology, Shahid Beheshti University of Medical Sciences (SBMU), Tehran, Iran participated in this cross-sectional attitude assessment descriptive-analytical study throughout the 2nd academic semester (May-October 2019). They took part in a level-specific small-group blended learning program and filled out an attitude assessment questionnaire. The questionnaire included eight closed questions and was filled out anonymously. Results The residents believed that this program made important contributions to their theory training and clinical skills of anesthesia; while created a greater sense of solidarity. In addition, nearly the majority of the respondents did not believe that participating in the classes made interference in their clinical duties or was a difficult task. Instead, the majority of residents believed that these classes were in favor of reducing their burnout. The reliability of the questionnaire based on Cronbach’s Alpha was 0.885. Conclusions Anesthesiology residents are in favor of small-group learning, especially when considering their clinical setting and the degree of burnout they tolerate.
Patterns of Complementary and Alternative Medicine Use in Saudi Arabian Patients With Inflammatory Bowel Disease: A Cross-Sectional Study

Background Inflammatory bowel disease (IBD) concerns a group of chronic autoimmune diseases that results in uncontrolled inflammation of the gastrointestinal (GI) tract, which can lead to long-term complications. Conventional treatments for IBD usually target inflammation and include biologics and immunosuppressants, which have been associated with significant adverse effects. Also, non-response to biologics has been reported in up to 50% of patients. Hence, patients sometimes turn to unconventional methods of treatment, such as complementary and alternative medicine (CAM). In this study, we examine patterns of CAM use in Saudi patients diagnosed with IBD. Materials and methods We conducted a cross-sectional study of patients with IBD who were seen at the outpatient gastroenterology clinic between January 2018 and December 2019. Adult patients diagnosed with ulcerative colitis (UC) or Crohn’s disease (CD) were identified and surveyed. Clinical, laboratory, endoscopic, radiologic, and histologic data were collected. The patients completed a detailed questionnaire focusing on CAM use. Descriptive statics, quantitative variables, means, standard deviations (SDs), and minimum and maximum values or medians with interquartile ranges were used where appropriate; for qualitative variables, we reported frequencies. The prevalence of CAM use was calculated using standard prevalence formulae. Logistic regression analysis was performed to identify predictors for CAM use. A p-value of <0.05 was set as statistically significant. Results A total of 71 IBD patients were surveyed, of which 75% had CD. Severe symptoms were reported by 54% of patients, and 41% were receiving biological treatment; 90% of this cohort reported using some form of CAM, of which 78% used them within the past year, and 52% reported CAM treatment having a positive effect. Of note, 63% of patients reported using CAM therapy without the knowledge of their treating physician. The most common source of advice regarding the use of CAM medicine was relatives (66%), and the most common forms of CAM used were honey (62%), Zamzam water (54%), and physical activity (32%). Binary logistic regression analysis identified watery diarrhea (OR=5.7, 95% CI=1.0-31, P=0.04) and azathioprine (OR=18.1, 95% CI=1.3-255, P=0.03) as predictors of CAM use. Conclusions CAM use is very common in Saudi patients with IBD. The majority of patients seem to turn to CAM if their symptoms are severe. They generally appear to be influenced by culture, the Internet, local society, and family tradition in their decision to use CAM, rather than expert advice from their treating physician.
Relationships Among Some Quantitative Traits and Heritablities İn Cultivated Oats (Avena sativa L.)

The objectives of this study were to examine the relationships among quantitative traits and to estimate their broad sense heritabilities in cultivated oats (Avena sativa L.). Four oat crosses were used in this experiment. Biological yield had the highest correlation with grain yield in all F2 populations, followed by harvest index. Grains per panicle appeared to be the most useful trait to use in indirect selection for grain yield among yield components in terms of heritability values and correlations with grain yield. Grain yield per plant significantly and positively associated with groat oil content in two oat populations. The broad sense heritability values of groat oil content ranged from 13 to 77%. Grain yield per piânt had heritability estimates between tow and moderate values. •
Spatial and Temporal Aspects of Signalling Synopsis

The function and efficiency of cell signalling pathways are very dependent on their organization both in space and time. With regard to spatial organization, signalling components are highly organized with respect to their cellular location and how they transmit information from one region of the cell to another. This spatial organization of signalling pathways depends on the molecular interactions that occur between signalling components that use signal transduction domains to construct signalling pathways. Very often, the components responsible for information transfer mechanisms are held in place by being attached to scaffolding proteins to form macromolecular signalling complexes. Sometimes these macromolecular complexes can be organized further by being localized to specific regions of the cell, as found in lipid rafts and caveolae or in the T-tubule regions of skeletal and cardiac cells.
Chlorophyll fluorescence, cell death, and transcription profile of long term moderately high temperature heat stressed Arabidopsis thaliana, Boechera arcuata, and Boechera depauperata

OF THE THESIS Chlorophyll Fluorescence, Cell Death, and Transcription Profile of Long Term Moderately High Temperature Heat Stressed Arabidopsis thaliana, Boechera arcuata, and Boechera depauperata by Abdullah Jamali Master of Science in Biology with a Concentration in Molecular Biology San Diego State University, 2014 Most studies of plant responses to heat stress examine basal thermotolerance and short-term acquired thermotolerance to high heat. In nature plants experience moderately high temperatures (30°C-38°C) for long periods of time. The goal of this study is to find the effects of long term moderately high temperature heat stress on the two native California species, Boechera arcuata and Boechera depauperata, and compare it to a model organism Arabidopsis thaliana. We measure chlorophyll fluorescents (CF), cell death, and transcriptional fold change for APX2, HSFA2, HSP101, and HSP18.1 to heat stress at 35°C and 38°C. We asked the following three questions: How is the efficiency of Photosystem II (PSII) affected by moderately high temperature heat stress in A. thaliana, Boechera arcuata, and Boechera depauperata? Is cell death under heat stress different between A. thaliana and the two Boechera species? Is gene expression under heat stress different between A. thaliana and the two Boechera species? B. depauperata is the most thermotolerant of the three species; at both heat stress temperatures, PSII does not lose conformation and continues to absorb light and fixate carbon. Ion leakage is minimized and there is very little cell death. Upregulation of APX2, HSFA2, and HSP18.1 only occur after 72 hours of continuous heat stress at 38°C in B. depauperata. HSP101 is upregulated at 1 hour at 35°C, but decays after that, and at 72 hours at 38°C. A. thaliana can withstand 35°C heat stress, but 38°C results in PSII efficiency loss, and cell death. Transcription of APX2, HSFA2, HSP101, and HSP18.1 is upregulated substantially more than the other two species at both heat stress temperatures. B. arcuata is the least thermotolerant of the three species studied. Both 35°C and 38°C have an effect on PSII efficiency and cell death, but 38°C has a larger affect. Transcription of APX2, HSFA2, and HSP101 are upregulated early at 1 hour, but decay and back to the same levels as the control by hour 12. HSP18.1 is not upregulated at 35°C and upregulated at 38°C after 48 hours of continuous stress. All three species handle moderately high temperature heat stress differently. B. depauperata is the most thermotolerant, A. thaliana is the second most thermotolerant, and B. arcuata is the least thermotolerant. These findings can help us better understand and predict the effects of global rise in temperatures on plant species and it can lead to designing better crops to withstand abiotic stress.
The visualization and measurement of left ventricular deformation using finite element models

Heart diseases cause considerable morbidity and the prognosis after heart failure is poor. An improved understanding of cardiac mechanics is necessary to advance the diagnosis and treatment of heart diseases. This article explains techniques for visualizing and evaluating biomedical finite element models and demonstrates their application to biomedical data sets by using, as an example, two models of a healthy and a diseased human left ventricle. The following contributions are made: we apply techniques traditionally used in solid mechanics and computational fluid dynamics to biomedical data and suggest some improvements and modifications. We obtain new insight into the mechanics of the healthy and diseased left ventricle and we facilitate, the understanding of the complex deformation of the heart muscle by novel visualizations. Finally, we also introduce in this process a toolkit designed for visualizing biomedical data sets. r 2003 Elsevier Ltd. All rights reserved.