Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibody Class(es) Predictor for Epitopes (AbCPE): A Multi-Label Classification Algorithm

Development of vaccines and therapeutic antibodies to deal with infectious and other diseases are the most perceptible scientific interventions that have had huge impact on public health including that in the current Covid-19 pandemic. From inactivation methodologies to reverse vaccinology, vaccine development strategies of 21st century have undergone several transformations and are moving towards rational design approaches. These developments are driven by data as the combinatorials involved in antigenic diversity of pathogens and immune repertoire of hosts are enormous. The computational prediction of epitopes is central to these developments and numerous B-cell epitope prediction methods developed over the years in the field of immunoinformatics have contributed enormously. Most of these methods predict epitopes that could potentially bind to an antibody regardless of its type and only a few account for antibody class specific epitope prediction. Recent studies have provided evidence of more than one class of antibodies being associated with a particular disease. Therefore, it is desirable to predict and prioritize ‘peptidome’ representing B-cell epitopes that can potentially bind to multiple classes of antibodies, as an open problem in immunoinformatics. To address this, AbCPE, a novel algorithm based on multi-label classification approach has been developed for prediction of antibody class(es) to which an epitope can potentially bind. The epitopes binding to one or more antibody classes (IgG, IgE, IgA and IgM) have been used as a knowledgebase to derive features for prediction. Multi-label algorithms, Binary Relevance and Label Powerset were applied along with Random Forest and AdaBoost. Classifier performance was assessed using evaluation measures like Hamming Loss, Precision, Recall and F1 score. The Binary Relevance model based on dipeptide composition, Random Forest and AdaBoost achieved the best results with Hamming Loss of 0.1121 and 0.1074 on training and test sets respectively. The results obtained by AbCPE are promising. To the best of our knowledge, this is the first multi-label method developed for prediction of antibody class(es) for sequential B-cell epitopes and is expected to bring a paradigm shift in the field of immunoinformatics and immunotherapeutic developments in synthetic biology. The AbCPE web server is available at http://bioinfo.unipune. ac.in/AbCPE/Home.html.
The Effects of Modest Alcohol Consumption on Non-alcoholic Fatty Liver Disease: A Systematic Review and Meta-Analysis

Background and Objective: There is no consensus regarding modest alcohol consumption in patients with non-alcoholic fatty liver disease (NAFLD) due to conflicting results. The aim of this meta-analysis was to examine the effects of modest alcohol consumption on histological severity, histological course, hepatocellular carcinoma, and long-term clinical outcomes in NAFLD patients. Methods: We searched MEDLINE and EMBASE databases from inception to October 2020 for studies evaluating the effects of modest alcohol consumption among patients with NAFLD. A random-effects meta-analysis using pooled odds ratio (OR) and hazard ratio (HR) was calculated with 95% confidence interval (CI). Study quality was assessed with the Newcastle-Ottawa Scale. Results: Fourteen cross-sectional or cohort studies with aggregate data on 14,435 patients were included in the analysis. Modest alcohol consumption resulted in lower risks for steatohepatitis (OR 0.59; 95% CI 0.45–0.78; I2 = 12%) and advanced fibrosis (OR 0.59, 95% CI 0.36–0.95; I2 = 75%). Histological follow-up data showed that modest alcohol use was associated significantly with less steatohepatitis resolution but not with fibrosis progression. The HR for developing hepatocellular carcinoma was 3.77 (95% CI 1.75–8.15; I2 = 0%). NAFLD patients with modest alcohol intake had a lower mortality risk than lifelong abstainers (HR 0.85; 95% CI 0.75–0.95; I2 = 64%). Conclusion: This meta-analysis suggests that medical advice for modest alcohol drinking should be made cautiously in caring for an individual patient based on the clinical context. Practically, patients with steatohepatitis or advanced fibrosis should avoid alcohol use, whereas patients with low fibrosis risk may be allowed for modest and safe drinking.
HIV Viremia Is Associated With APOL1 Variants and Reduced JC-Viruria

Variants in the Apolipoprotein L1 (APOL1) gene (G1-rs60910145, rs73885319, G2-rs71785313) are common in Africans and in individuals of recent African ancestry and are associated with an increased risk of non-diabetic chronic kidney disease (CKD) and in particular of HIV associated nephropathy (HIVAN). In light of the significantly increased risk of HIVAN in carriers of two APOL1 risk alleles, a role in HIV infectivity has been postulated in the mechanism of APOL1 associated kidney disease. Herein, we aim to explore the association between HIV viremia and APOL1 genotype. In addition, we investigated interaction between BK and JC viruria, CKD and HIV viremia. A total of 199 persons living with HIV/AIDS (comprising 82 CKD cases and 117 controls) from among the participants in the ongoing Human Heredity and Health in Africa (H3Africa) Kidney Disease Research Network case control study have been recruited. The two APOL1 renal risk alleles (RRA) genotypes were associated with a higher risk of CKD (OR 12.6, 95% CI 3.89–40.8, p < 0.0001). Even a single APOL1 RRA was associated with CKD risk (OR 4.42, 95% CI 1.49–13.15, p = 0.007). The 2 APOL1 RRA genotypes were associated with an increased probability of having HIV viremia (OR 2.37 95% CI 1.0–5.63, p = 0.05). HIV viremia was associated with increased CKD risk (OR 7.45, 95% CI 1.66–33.35, P = 0.009) and with a significant reduction of JC virus urine shedding (OR 0.35, 95% CI 0.12–0.98, p = 0.046). In contrast to prior studies, JC viruria was not associated with CKD but was restricted in patients with HIV viremia, regardless of CKD status. These findings suggest a role of APOL1 variants in HIV infectivity and emphasize that JC viruria can serve as biomarker for innate immune system activation.
Immunotherapy for Head and Neck Cancer: A Paradigm Shift From Induction Chemotherapy to Neoadjuvant Immunotherapy

Neoadjuvant immunotherapy has the potential to enhance clinical outcomes by increasing anti-tumor immune responses in the presence of abundant tumor-derived antigen in an immune microenvironment that has not been exposed to previous therapy. The current mainstay of advanced head and neck squamous cell carcinoma (HNSCC) treatment remains surgery and radiotherapy with/without conventional chemotherapy. Despite this multi-modality treatment, advanced human papillomavirus (HPV)-negative HNSCC shows poor prognosis. Treatment intensification with neoadjuvant (induction) chemotherapies with platinum drugs are insufficient to significantly prolong overall survival. Although only 15-20% of patients benefit, immunotherapies have been approved and widely used for recurrent and metastatic HNSCC. These successes have led to checkpoint blockade therapies being testing in earlier treatment settings. Recent clinical trials of neoadjuvant immunotherapy show promising results and this methodology has the potential to change the treatment algorithm of HNSCC. This overview examines the treatment history of neoadjuvant approaches for HNSCC, and especially focuses on the recent topics of neoadjuvant immunotherapy for HNSCC.
Phenotypic and Genetic Heterogeneity in a Thai Glucokinase MODY Family Reveals the Complexity of Young-Onset Diabetes

Glucokinase-Maturity-Onset Diabetes of the Young (GCK-MODY) is characterized by asymptomatic, non-progressive and fasting hyperglycemia, albeit not without phenotypic variability. We used next generation sequencing (NGS) to screen for 34 MODY genes in a non-obese person with familial young-onset diabetes followed by screening in 24 family members within three generations with varying presentations of young-onset diabetes and sensorineural hearing loss. The index patient was found to carry a paternally-inherited heterozygous missense variant (c.716 A>G) of GCK in exon 7 with amino acid change (Q239R). This variant was associated with phenotypic heterogeneity ranging from normal glucose tolerance to diabetes with complications amongst the siblings which might be modified by obesity and chronic hepatitis B infection. Two paternally-inherited variants of SLC29A3 encoding a nucleoside transporter protein and Apo-A1 genes also co-segregated with glucose and lipid traits. Co-occurrence of diabetes and deafness in maternal aunts led to discovery of WFS1 (Wolfram syndrome type 1) as a cause of non-syndromic deafness in multiple members of the maternal pedigree. Our findings highlight the complex causes of familial young-onset diabetes and the need of a multidisciplinary approach to interpret the clinical relevance of discoveries made by NGS in this era of genomic medicine.
A New Subfamily of Glycoside Hydrolase Family 30 with Strict Xylobiohydrolase Function

The Acetivibrio clariflavus (basonym: Clostridium clariflavum) glycoside hydrolase family 30 cellulosomal protein encoded by the Clocl_1795 gene was highly represented during growth on cellulosic substrates. In this report, the recombinantly expressed protein has been characterized and shown to be a non-reducing terminal (NRT)-specific xylobiohydrolase (AcXbh30A). Biochemical function, optimal biophysical parameters, and phylogeny were investigated. The findings indicate that AcXbh30A strictly cleaves xylobiose from the NRT up until an α-1,2-linked glucuronic acid (GA)-decorated xylose if the number of xyloses is even or otherwise a single xylose will remain resulting in a penultimate GA-substituted xylose. Unlike recently reported xylobiohydrolases, AcXbh30A has no other detectable hydrolysis products under our optimized reaction conditions. Sequence analysis indicates that AcXbh30A represents a new GH30 subfamily. This new xylobiohydrolase may be useful for commercial production of industrial quantities of xylobiose.
Temperature Influences on Interactions Among Aflatoxigenic Species of Aspergillus Section Flavi During Maize Colonization

Fungal species within Aspergillus section Flavi contaminate food and feed with aflatoxins. These toxic fungal metabolites compromise human and animal health and disrupt trade. Genotypically and phenotypically diverse species co-infect crops, but temporal and spatial variation in frequencies of different lineages suggests that environmental factors such as temperature may influence structure of aflatoxin-producing fungal communities. Furthermore, though most species within Aspergillus section Flavi produce sclerotia, divergent sclerotial morphologies (small or S-type sclerotia vs. large or L-type sclerotia) and differences in types and quantities of aflatoxins produced suggest lineages are adapted to different life strategies. Temperature is a key parameter influencing pre- and post-harvest aflatoxin contamination of crops. We tested the hypothesis that species of aflatoxin-producing fungi that differ in sclerotial morphology will vary in competitive ability and that outcomes of competition and aflatoxin production will be modulated by temperature. Paired competition experiments between highly aflatoxigenic S-type species (A. aflatoxiformans and Lethal Aflatoxicosis Fungus) and L-type species (A. flavus L morphotype and A. parasiticus) were conducted on maize kernels at 25 and 30°C. Proportions of each isolate growing within and sporulating on kernels were measured using quantitative pyrosequencing. At 30°C, S-type fungi were more effective at host colonization compared to L-type isolates. Total aflatoxins and the proportion of B vs. G aflatoxins were greater at 30°C compared to 25°C. Sporulation by L-type isolates was reduced during competition with S-type fungi at 30°C, while relative quantities of conidia produced by S-type species either increased or did not change during competition. Results indicate that both species interactions and temperature can shape population structure of Aspergillus section Flavi, with warmer temperatures favoring growth and dispersal of highly toxigenic species with S-type sclerotia.
A Three-Dimensional Imaging Method for the Quantification and Localization of Dynamic Cell Tracking Posttransplantation

Cell transplantation has been proposed as a promising therapeutic strategy for curing the diseases requiring tissue repairing and functional restoration. A preclinical method to systematically evaluate the fates of donor cells in recipients, spatially and temporally, is demanded for judging therapeutic potentials for the particularly designed cell transplantation. Yet, the dynamic cell tracking methodology for tracing transplanted cells in vivo is still at its early phase. Here, we created a practical protocol for dynamically tracking cell via a three-dimensional (3D) technique which enabled us to localize, quantify, and overall evaluate the transplanted hepatocytes within a liver failure mouse model. First, the capacity of 3D bioluminescence imaging for quantifying transplanted hepatocytes was defined. Images obtained from the 3D bioluminescence imaging module were then combined with the CT scanner to reconstruct structure images of host mice. With those reconstructed images, precise locations of transplanted hepatocytes in the liver of the recipient were dynamically monitored. Immunohistochemistry staining of transplanted cells, and the serology assay of liver panel of the host mice were applied to verify the successful engraftment of donor cells in the host livers. Our protocol was practical for evaluating the engraftment efficiency of donor cells at their preclinical phases, which is also applicable as a referable standard for studying the fates of other transplanted cells, such as stem cell-derived cell types, during preclinical studies with cell transplantation therapy.
Development and simulation of a highly integrated Solid Oxide Fuel Cell

Die vorliegende Arbeit beschaftigt sich mit der Entwicklung und Untersuchung von oxdikeramischen Brennstoffzellen (engl.: Solid Oxide Fuel Cell (SOFC)) mit direkter interner Reformierung von Methan. Zur Optimierung ihrer Leistungsfahigkeit werden ausgehend von den physikalischen Grundprinzipien, Randbedingungen fur das Design, die Materialauswahl und Herstellungsweise abgeleitet. Aufbauend auf dem aktuellen Stand der Technik im Bereich der SOFC Konstruktion wird aus den gewonnenen Erkenntnissen ein neuartiges Design mit janusformig angeordneten Elektroden entwickelt. Zur Vorbereitung auf eine dreidimensionale Untersuchung des Konzepts mit den Methoden der numerischen Stromungsmechanik (engl.: Computational Fluid Dynamics (CFD)) werden mogliche Einflussparameter auf die Zellleistung und die numerischen Ergebnisse hinterfragt. Dabei handelt es sich einerseits um Abhangigkeiten von der Mikrostruktur und Zusammensetzung der Anode und andererseits um die Bedeutung elementarer Oberflachenreaktionen. Zusatzlich dazu werden fur alle relevanten physikalischen Phanomene separate Submodelle entwickelt und verifiziert. Neben einem alternativen Ansatz, welcher von einer lokalen Beschreibung der potentialabhangigen Gleichungen ausgeht, werden zwei weitere Beschreibungen fur die elektrochemischen Reaktionen in verschieden komplexen Rechengitter formuliert. Die Berechnungsergebnisse zeigen, dass in Folge der geringen ionischen Leitfahigkeit von mit Yttrium stabilisiertem Zirkoniumoxid (engl.: Yttrium Stabilized Zirconium (YSZ)) die optimale isovolumetrische Mischung der Bestandteile des Anodencermets nur innerhalb einer dunnen, elektrochemisch aktiven Reaktionsschicht an der Grenze zum Elektrolyten verwendet werden sollte. Innerhalb der stutzenden Anode sollte die Zusammensetzung zu Gunsten der elektrischen Leitfahigkeit und Gasdurchlassigkeit angepasst werden. Bei den CFD-Simulationen wird eine Reihenschaltung aus drei Zellen einer Parameterstudie bezuglich Einlasstemperatur und Betriebsspannung unterzogen. Es zeigt sich, dass beide Parameter dazu verwendet werden konnen die thermischen Auswirkungen von Elektrochemie und Reformierung gegeneinander auszubalancieren und so die Temperaturgradienten innerhalb der Anodenstruktur zu minimieren. Ferner folgt, dass obwohl der Kohlenmonoxid (CO)-Anteil an der Gesamtstromdichte in Richtung des Gasflusses zunimmt, er nie einen Wert von etwa 10 % uberschreitet. Global betrachtet konvertiert das System daher zunachst den Wasserstoff und nachfolgend das CO. Abschliesend wird gezeigt, dass das entwickelte System fur lange Kaskaden von mehr als zehn Zellen einen hohen Gesamtwirkungsgrad aufweist.
Relationship between Health Literacy and Knowledge, Attitude, and Performance Regarding Cancer Warning Signs

Background: Health literacy (HL) is considered a cancer-preventive strategy. In addition, success in early diagnosis of cancer largely depends on individuals' knowledge, attitude, and performance regarding cancer warning signs. The aim of the present study was to investigate the potential relationship between HL and Knowledge, Attitude, and Performance (KAP) regarding cancer warning signs. Materials and Methods: This descriptive-correlational study was conducted on 280 adults who were referred to 3 health centers in Tehran, Iran, from January to March 2020. Data were collected using the Health Literacy Instrument for Adults (HELIA) and the researcher-made KAP regarding cancer warning signs questionnaire. Data were analyzed using the Pearson correlation test and linear regression in an adjusted model in the statistical package for social sciences software. Results: Total HL score was positively and significantly correlated with knowledge (r = 0.35; p < 0.001), attitude (r = 0.17, p = 0.003), and performance (r = 0.46, p < 0.001). Moreover, after controlling for potential confounders, a significant and positive relationship was found between HL and knowledge (β = 0.48; t275 = 4.45; p < 0.001), attitude (β =0.17; t265 = 4.64; p < 0.001), and performance (β = 0.62; t265 = 8.23; p < 0.001). Conclusions: It seems that adults' KAP regarding cancer warning signs can be promoted by increasing their HL. Therefore, greater attention should be paid to individuals' HL at community health centers when designing and performing programs to improve their KAP regarding cancer warning signs.
Current trends in Extrusion: Development of Functional Foods and Novel Ingredients

Extrusion is a versatile and state-of-art technology and provides enormous opportunity for modifying the functionality of food materials for improved digestibility and high sensory quality. With considerable previous research on cereal based products, the current focus has now shifted towards millets and pulses for enhancing nutritional and functional quality for high-end consumer. The present review highlights the current advances made in development of cereal, millet and pulse based extruded products. In addition, the current trends in use of extruded flours as novel green ingredients as hydrocolloids, fat replacers and for developing gluten-free, phenolic-rich, lowglycemic and functional foods has also been reviewed.
The trends of obstetric anesthesia practice: In a tertiary care center in the Kingdom of Saudi Arabia

Introduction: Obstetric anesthesia provides several methods for the analgesia of labor pain. The neuraxial technique is considered the standard of care for parturient women. The epidural block is widely used in vaginal delivery while the spinal block is the preferred method for cesarean section (C-section). We aim to know the practice of obstetric anesthesia in our center. Methods: A retrospective cross-sectional study was conducted at a tertiary center in Riyadh, Saudi Arabia. The data of all delivery cases from 1/7/2019 to 30/9/2019 were reviewed. Results: We identified a total of 2,140 cases during the 3 months, vaginal delivery was the most common with 72.4% (1550) while the C-section cases were 27.6% (590). Regarding the type of analgesia/anesthesia for vaginal deliveries, intramuscular analgesia was the commonest group with 34.8% (540), followed by the group of ladies who did not receive any analgesia/anesthesia with 31.9% (495), thirdly was epidural cases with 31.8% (493), and the fourth type was spinal 0.6% (10). Regarding C-section, the emergency cases were 65.4% (386). The types of anesthesia for all C-sections were as follows spinal 63.5% (375), GA 23.8% (141), and epidural 12% (74). Regarding anesthesia for elective cases, spinal was 85% (174), GA 14% (28), and epidural 1% (2). Regarding anesthesia for emergency cases, spinal was 52% (201), GA 29% (113), and epidural 19% (72). Conclusions: The use of epidural was low, and the spinal use was relatively on par if we compare with leading western countries. More focused studies and multicenter studies are needed in the country.
Current State of Palliative Care in Iran and Related Issues: A Narrative Review

Background: Palliative research studies seem to be limited and disperse in Iran. The present study was therefore conducted to review and categorize the Palliative Care (PC) studies performed in Iran in terms of the research type, the type/focus of PC, the measured outcomes in interventional palliative studies and their related results, the disease type, and their geographical distribution. Materials and Methods: This narrative review was conducted in 2021 in which both Iranian and international databases including PubMed, Scopus, Web of science, CINAHL, ProQuest, Magiran, SID, Noormags, ISC were searched. The inclusion criteria were original articles conducted in Iran and results published in Persian or English journals ab initio in which PC was assessed as a variable (dependent or independent) or the main concept. Results: A total of 1096 articles were identified from which only 44 articles were reviewed. The research studies were mainly focused on cancer and majority conducted in Tehran. Majority of studies were quantitative-interventional leading to a variety of positive changes in dependent variables, including reduce in pain severity, change in life pattern, a good response to therapy, increase life expectancy, improve in dysphagia, improve quality of life, reduce patients' metastasis, and increase in nurses' self-efficacy. Conclusions: The PC studies distributed across different fields and cities in Iran resulted to a number of positive outcomes for patients. More focused and robust research studies with different patients need to be conducted in this emerging field in Iran.
Early Enteral Nutrition Met Calories Goals Led by Nurse on Improve Clinical Outcome: A Systematic Scoping Review

Background: Critically ill patients face challenges in hypercatabolism due to crisis states, as it may lead to malnutrition. An early Enteral Nutrition (EN) within 24–48 h is recommended to use in order to improve clinical outcomes. This systematic scoping review is examined recently with the evidence of the early EN protocol led by nurses to drive and achieve the daily calorie target and improve clinical outcomes. Materials and Methods: The database of CINAHL, MEDLINE via PubMed and Scopus, Web of Science, and Embase through Ovid from January 2019 to September 2020, comprised of 221 articles which four articles are chosen and entered into the final analysis. Results: The findings show the benefits of the early EN to guide nurses to start the EN as soon as possible after admitted to the Intensive Care Unit or when hemodynamic is stable in order to achieve a daily calorie target regarding the reduced hospitalization, duration of mechanical ventilation, morbidity, and mortality. Conclusions: The synthesized results show the early EN led by a nurse to address the specific needs and the vital role of nutritional support, and also drive the enteral feeding for critically ill patients to reach the calorie target goals in short times to enhance clinical outcomes.