Miracle-dz/UniFAR-FTUs huggingface dataset:
The evolution of protein domain repertoires: shedding light on the origins of herpesviruses

Herpesviruses (HVs) have large genomes that can encode thousands of proteins. Apart from amino acid mutations, protein domain acquisitions, duplications and losses are also common modes of evolution. HV domain repertoires differ across species, and only a core set is shared among all viruses, aspect that raises a question: How have HV domain repertoires diverged while keeping some similarities? To answer such question, we used profile HMMs to search for domains in all possible translated ORFs of fully sequenced HV genomes. With at least 274 domains being identified, we built a matrix of domain counts per species, and applied a parsimony method to reconstruct the ancestral states of these domains along the HV phylogeny. It revealed events of domain gain, duplication and loss over more than 400 millions of years, where Alpha-, Beta- and Gammaherpesviruses expanded and condensed their domain repertoires at distinct rates. Most of the acquired domains perform ‘Modulation and Control’, ‘Envelope’ or ‘Auxiliary’ functions, categories that showed high flexibility (number of domains) and redundancy (number of copies). Conversely, few gains and duplications were observed for domains involved in ‘Capsid assembly and structure’, and ‘DNA Replication, recombination and metabolism’. Among the 41 primordial domains encoded by herpesvirus ancestors, 28 are still found in all present-day HVs. Because of their distinct evolutionary strategies, herpesvirus domain repertoires are very specific at the subfamily, genus and species levels. Differences in domain composition may not just explain HV host range and tissue tropism, but also provide hints to the origins of herpesviruses.
Sigma metrics - A guide to quality control strategy in clinical Biochemistry laboratory

Introduction and Aims: Clinical laboratories are backbone of health care system & the responsibility lies in the laboratory to produce reliable, reproducible & timely interpreted test results. Presently Westgard quality control(QC) rules are the basis for quality control validation of laboratories. A new quality assessment system known as Six sigma is considered as world class quality & is a uniquely defined scale with which one can assess the performance of a laboratory. An analytical procedure should achieve a good sigma levels for high reliability for the results. Many laboratories are not aware about the usefulness of six sigma. Hence this study was aimed to assess and to plan the quality control strategy. Materials and Methods: In this study, the internal quality control data of urea, creatinine, sodium, potassium & chloride analysed for a period of 6 months & used to calculate bias, coefficient of variation (CV)%, mean & standard deviation(SD) for each levels(L1,L2). Results: Sigma value calculated shown Highest for Urea & Potassium (Level1 & Level 2) COBAS 6000 an integrated modular analyser. Sigma of 3 is the minimum acceptable level of quality. The frequency of internal QC should be increased and corrective action should be taken for those parameters with sigma <3. Sigma metrics of each parameter helped us to identify the right QC strategy for that analyte using Westgard sigma rule. Conclusion: Hence six sigma is a more efficient way to control quality & is a self-assessment tool for quality improvement. © 2020 Published by Innovative Publication. This is an open access article under the CC BY-NC license (https://creativecommons.org/licenses/by-nc/4.0/)
Neuromodulation leads to a burst-tonic switch in a subset of VIP neurons in mouse primary somatosensory (barrel) cortex

Neocortical GABAergic interneurons expressing vasoactive intestinal polypeptide (VIP) contribute to sensory processing, sensorimotor integration and behavioral control. In contrast to other major subpopulations of GABAergic interneurons, VIP neurons show a remarkable diversity. Studying morphological and electrophysiological properties of VIP cells, we found a peculiar group of neurons in layer II/III of mouse primary somatosensory (barrel) cortex, which showed a highly dynamic burst firing behavior at resting membrane potential that switched to tonic mode at depolarized membrane potentials. Furthermore, we demonstrate that burst firing depends on T-type calcium channels. The burst-tonic switch could be induced by acetylcholine and serotonin. Acetylcholine mediated a depolarization via nicotinic receptors whereas serotonin evoked a biphasic depolarization via ionotropic and metabotropic receptors in 48% of the population and a purely monophasic depolarization via metabotropic receptors in the remaining cells. These data disclose an electrophysiologically-defined subpopulation of VIP neurons that via neuromodulator-induced changes in firing behavior is likely to regulate the state of cortical circuits in a profound manner.
β‐diversity scaling patterns are consistent across metrics and taxa

β‐diversity (variation in community composition) is a fundamental component of biodiversity, with implications for macroecology, community ecology and conservation. However, its scaling properties are poorly understood. Here, we systematically assessed the spatial scaling of β‐diversity using 12 empirical large‐scale datasets including different taxonomic groups, by examining two conceptual types of β‐diversity and explicitly considering the turnover and nestedness components. We found highly consistent patterns across datasets. Multiple‐site β‐diversity (i.e. variation across multiple sites) scaling curves were remarkably consistent, with β‐diversity decreasing with sampled area according to a power law. For pairwise dissimilarities, the rates of increase of dissimilarity with geographic distance remained largely constant across scales, while grain size (or scale level) had a stronger effect on overall dissimilarity. In both analyses, turnover was the main contributor to β‐diversity, following total β‐diversity patterns closely, while the nestedness component was largely insensitive to scale changes. Our results highlight the importance of integrating both inter‐ and intraspecific aggregation patterns across spatial scales, which underpin substantial differences in community structure from local to regional scales.
Asupan kafein dari kopi dan teh serta hubungannya dengan kepadatan tulang pada perempuan pascamenopause

LATAR BELAKANGOsteoporosis merupakan kondisi patologis tulang dengan karakteristik bone mineral density (BMD) yang rendah disertai perubahan mikro-arsitektur jaringan tulang, sehingga meningkatkan risiko fraktur. Faktor risiko osteoporosis yaitu perempuan pascamenopause, genetik, indeks massa tubuh, aktivitas fisik, asupan gizi dan mineral, merokok, serta asupan alkohol, dan kafein. Penelitian ini bertujuan untuk menilai efek kafein dari kopi dan teh terhadap kepadatan tulang pada perempuan pascamenoapuse. METODEPenelitian ini merupakan penelitian analitik observasional dengan desain cross-sectional. Subjek penelitian adalah perempuan pascamenopause yang berusia >40 tahun berjumlah 92 orang. Asupan kafein dinilai dari total asupan yang berasal dari kopi dan teh dengan menggunakan kuesioner dan wawancara. Perhitungan asupan total kafein diperhitungkan dengan penyetaraan asupan kopi dan teh per minggu. Kepadatan tulang dinilai menggunakan alat calcaneal quantitative ultrasound untuk menetukan nilai-T sebagai parameter osteoporosis. Subjek dikelompokkan sebagai kepadatan tulang normal (nilai-T≥-1), osteopenia (nilai-T antara -1 sampai -2.5) dan osteoporosis (nilai-T<-2.5) Analisis statistik dilakukan untuk menilai hubungan kedua variabel dilakukan dengan uji Chi-square. HASILRerata (simpang baku) usia subjek adalah 57.84 ± 7.57. Sebanyak 26 (28.3%) subjek dengan kategori osteoporosis, 50 (54.3%) osteopenia, dan 16 (17.4%) normal. Asupan kafein didapatkan 69 subjek (75%) dengan kategori rendah dan 23 (25%) tinggi. Hasil analisis didapatkan tidak terdapat hubungan yang bermakna antara asupan kafein dan kepadatan tulang (p=0.419; p>0.05). KESIMPULANTidak terdapat hubungan antara asupan kafein dari kopi dan teh dengan kepadatan tulang pada perempuan pascamenopause.
Role of selective progesterone receptor modulators in the treatment of symptomatic uterine fibroids

Uterine leiomyomas are benign tumours of smooth muscle cells and fibrous tissue that develop within the wall of the uterus. They may grow as a single tumor or in clusters and one such single fibroid can measure up to 20 cm or more and may range in size from seedlings to large uterine tumors. Uterine fibroids (UFs) are the most frequent tumor of the female genital tract with an increasing frequency during the women’s fertile years with a prevalence of 20-77% depending on the population and method of assessment. Its incidence increases with increasing age and the life time risk for women to develop uterine fibroids is 70%. Uterine fibroids (65%) are attributed to inadequate endometrial receptivity to embryo implantation secondary to deleterious effects of uterine fibroids on endometrium. Many women, if given the option, would prefer medical treatment for their uterine fibroids over a surgical solution to avoid the possible risks associated with surgery, and preserve their uterus for future fertility and also for psychological/feminine reasons. ABSTRACT
The Whole Antarctic Ocean Model (WAOM v1.0): Development and Evaluation

Abstract. The Regional Ocean Modeling System (ROMS), including an ice shelf component, has been applied on a circum-Antarctic domain to derive estimates of ice shelf basal melting. Significant improvements made compared to previous models of this scale are the inclusion of tides and a horizontal spatial resolution of 2 km, which is sufficient to resolve onshelf heat transport by bathymetric troughs and eddy scale circulation. We run the model with ocean-atmosphere-sea ice conditions from the year 2007, to represent nominal present day climate. We force the ocean surface with buoyancy fluxes derived from sea ice concentration observations and wind stress from ERA-Interim atmospheric reanalysis. At the northern boundaries ocean conditions are derived from the ECCO2 reanalysis and tides are incorporated as sea surface height and barotropic currents. The accuracy of tidal height signals close to the coast is comparable to those simulated from widely-used barotropic tide models, while off-shelf hydrography agrees well with the Southern Ocean State Estimate (SOSE) model. On the shelf, most details of ice shelf-ocean interaction are consistent with results from regional modelling and observational studies, although a paucity of observational data (particularly taken during 2007) prohibits a full verification. We conclude that our improved model is well suited to derive a new estimate of present day Antarctic ice shelf melting at high resolution and is able to quantify its sensitivity to tides.
Duration of Antibiotic Therapy for General Medicine and General Surgery Patients Throughout Transitions of Care: An Antibiotic Stewardship Opportunity for Noninfectious Disease Pharmacists

Background Overuse of antibiotics from the inpatient to outpatient setting is an antibiotic stewardship initiative where noninfectious disease (ID) pharmacists can have a large impact. Our purpose was to evaluate antibiotic durations across transitions of care from the inpatient to outpatient setting. Methods This is a single-center, retrospective cohort analysis evaluating antibiotic durations from the inpatient and outpatient setting in adult patients admitted to general surgery and medicine services at an academic medical center between January 1, 2017 and September 20, 2017. The primary outcome was to assess total antibiotic duration for patients with uncomplicated and complicated urinary tract infections (UTI, cUTI), community-acquired pneumonia (CAP), and hospital-acquired pneumonia (HAP). Outpatient electronic discharge prescriptions were used to calculate intended antibiotic duration upon transitions of care. Excessive duration of therapy was defined as >3 days—UTI, >5 days—CAP, and >7 days—cUTI or HAP. Results One hundred and one patients met inclusion criteria. Overall, most of the patients (81%) had antibiotics longer than recommended with only 3% receiving less than the recommended duration. Median total duration of therapy compared with recommended duration specified in national guidelines was UTI: 10 days [7 –10], cUTI: 12 days [7.5-12.5], CAP: 7 days [7 –9], HAP: 10 days [8 –12]. The median antibiotic duration was shorter in patients with no cultures or culture negative results compared with patients with positive cultures for all indications (UTI: 10.3 vs 10.8 days, cUTI: 9 vs 12 days, CAP: 8 vs 9.1 days, HAP: 10.5 vs 19.8 days). Overall, the recommended duration of antibiotics was completed while inpatient in 34.7%, but varied by infection. More patients with UTI or cUTI completed recommended duration of therapy while inpatient vs for CAP or HAP (53.8% vs 28%, P = .03). Eighty percent of those with UTI, 18.2% with cUTI, 25.6% with CAP, and 31.2% with HAP had already received the recommended duration of treatment, or more, on day of hospital discharge. Conclusions The median duration of antibiotic therapy for all indications evaluated was longer than recommended in national guidelines. Opportunities for stewardship by non-ID pharmacists to impact postdischarge antimicrobial use at transitions of care have been identified.
Dietary Modifications in Fissure-in-ano: A Qualitative Study Based on Persian Medicine

Anal fissure (AF) is a common disease associated with severe pain and reduced quality of life. Factors related to lifestyle, including diet and bowel habits, play a pivotal role in its pathogenesis. Most of the chronic fissures are not responsive to drugs and more likely to recur. Given the significance of diet in Persian medicine (PM), investigation on physiopathology and appropriate foods can be useful for decreases in AF symptoms and consequences. This study was intended to evaluate the role of diet in the formation and progression of AF from the perspective of PM. In this study, the most important resources of PM dating back to thousands of years were reviewed. All these textbooks contained a section on AF, its causes, and treatment. Further analysis was performed on these resources in comparison with databank and resources of modern medicine to develop a food-based strategy for AF management. From the view of PM, the warmth and dryness of anus temperament accounted for AF. Both Persian and modern medicine identified constipation as another cause for AF. Therefore, avoidance from some foods and commercial baked goods was recommended. Both Persian and modern medicine forbad the following foods: potato, cabbage, cauliflower, pasta, beef, fish, and so forth. High fiber and oligo-antigen diets with some limitations have garnered more attention. An integrative approach is recommended employing both Persian and modern medicine for AF. There have been some evidence in this regard, however standardized clinical trials are required for future research.
Development of SSR markers based on the head transcriptome of Pantala flavescens (Fabricius, 1798) (Odonata: Libellulidae)

Pantala flavescens (Fabricius, 1798) is one of the most common species of dragonflies and has been found throughout from tropic to temperate zones worldwide. In this study, RNA-seq of P. flavescens was carried out through Illumina high-throughput sequencing technology. Approximately 37,868 unigenes and 47,188 transcripts were obtained. The average length of the assembled unigenes was 908.59 bp. We identified 1442 cDNA simple sequence repeats (SSRs) among the 37,868 unigenes, with 864 (59.91%) di-nucleotide repeats, 537 (37.32%) tri-nucleotide repeats, 32 (2.22%) complex-nucleotide repeats, and 9 (0.62%) with tetra-nucleotide repeats. Sixty microsatellite molecular markers were randomly selected to test amplification. Of the 60 markers, 32 (53.33%) produced clear amplicons of the expected size, 10 (16.67%) amplified nonspecific products, and 18 (30%) failed to amplify the DNA products. In order to assess their applicability, genetic diversity of the 32 SSR loci was tested in 32 individuals from Nanchang in China. Of these loci, 14 markers were highly polymorphic, with the observed (Ho) and expected (He) heterozygosities ranged 0.69 to 0.88 and from 0.96 to 0.98 respectively. PIC ranged from 0.52 to 0.83. These highly polymorphic loci will be valuable for the genetic analysis of distinct populations of P. flavescens.
Development and reproductive performance of Chrysoperla externa (Neuroptera: Chrysopidae) using preys from wheat crop

Biological parameters of Chrysoperla externa were assessed in laboratory. The effect of the preys on biological parameters and reproductive performance were assessed when the following food treatments were provided: Sitobion avenae in all larval instars; Rhopasosiphum padi in all larval instars; Anagasta kuehniella eggs in the first and second instars and Dichelops melacanthus eggs in the third; R. padi in the first and second instars and D. melacanthus in the third instar. All foods provided satisfactory development and reproductive performance. Changing larvae food from A. kuehniella to D. melacanthus did not affect its survival. However, changing larvae food from R. padi to D. melacanthus reduced survival. When larvae were fed with R. padi (1st and 2nd instars) and D. melacanthus (3rd instar), C. externa laid more eggs than when larvae were fed only with aphids. Other parameters either were not affected, or were little affected by the diet change. Results showed that aphis are important food sources for C. externa, and this predator may also predate and develop on D. melacanthus eggs.
Satellite Based Interpretation of Stability Parameters on Convective Systems over India and Srilanka

India is frequently exposed to convective systems (CS) during the hot period of pre-monsoon season. Huge thunderstorms are more often over India in the recent years. To analyze these systems, the stability parameters considered as good precursors for understanding the physics of the convective systems in prior to their occurrence. The present study is concerned about the analysis of stability parameters such as K Index (KI), Lifted Index (LI), Total Totals Index (TTI), Humidity Index (HI), Convective available potential energy (CAPE), Convective Inhibition (CIN), Lifting Condensation Level (LCL) and Level of free Convection (LFC) associated with severe convective systems over India and Srilanka during April, 2015. First, INSAT-3D satellite based brightness temperature (BT) product was used for analyzing the initial, mature and dissipation stages of the convective system at every 30 min interval. The data products from MODIS Terra satellite, MODIS Aqua satellite, Era-Interim ECMWF reanalysis satellite data and IASI satellite were used for understanding the thermodynamics related to the occurrence of these convective systems. The results of stability parameters that were derived from MODIS Terra and Aqua satellite’s data products indicated the favorable threshold values for the occurrence of convective systems. Results from Era-Interim ECMWF reanalysis satellite data also helps us to understand the dynamics involved behind the convective system. The results from IASI satellite also helped us to understand the severity of convective systems during cloudy situations. The results of this study impulse the need of satellites for analyzing the convective systems prior to their occurrence.
Assessemnet of haemato - biochemical and stress parameters during the transition period in buffaloes

The present study was designed to record the haematological, serum biochemical changes and stress parameters during the transition period in buffaloes. Ten apparently healthy buffaloes which were in mid-lactation were selected for the study and treated as Group I; twenty apparently healthy buffaloes which were in advance pregnancy were selected for the study and treated as Group II and blood was collected at the time of transition period (i.e. 0 to 6 days of after parturition). Blood samples were collected from the buffaloes for analysis. Buffaloes in the transition period showed the significant changes in haematology by increased levels of packed cell volume, elevation of total leukocyte and lymphocyte count. Serum biochemical changes noticed are reduced levels of total protein, albumin, calcium, phosphorous, glucose levels and increased serum cortisol levels. AST, BUN levels were within the normal range. In conclusion, the study suggests the provision of protein-rich fodder, mineral mixture at the time of parturition along with the supplementation of anti stressor products up to 3 weeks of after parturition.
Characteristics of shrub morphology on nest site selection of Greater Sage-Grouse (Centrocercus urophasianus) in high-elevation sagebrush habitat

ABSTRACT Selection of nest sites directly influences reproductive success for Greater Sage-Grouse (Centrocercus urophasianus); thus, regional evaluation of how this species selects nest sites is necessary for effective habitat management. We evaluated fine-scale nest site selection of Greater Sage-Grouse in the Centennial Valley of southwest Montana. We conducted vegetation surveys at nest sites (n = 90) of radio-tagged Greater Sage-Grouse and paired random locations across 2 breeding seasons (2014–2015). The majority of nests were located under mountain big sagebrush (Artemisia tridentata ssp. vaseyana), three-tip sagebrush (A. tripartita), and basin big sagebrush (A. tridentata ssp. tridentata) shrubs. We used generalized linear models and information theory to evaluate competing hypotheses about nest site selection. Our top model indicated that nest site selection was primarily associated with nest shrub morphological characteristics and cover provided by the nest shrub. Mountain big sagebrush and three-tip sagebrush provided twice the amount of lateral cover that basin big sagebrush shrubs provided. Our results suggest that herbaceous cover was unimportant at fine scale nest site selection of Greater Sage-Grouse in our study area. Managers should focus on conserving large intact stands of mountain big sagebrush and three-tip sagebrush habitats because they provided the most lateral cover and supported the majority of nest sites.
Vitamin C does not improve the efficacy of Helicobacter pylori eradication in
smokers

__________________________________________________________________________________________ Purpose: To evaluate the hypothesis that vitamin C improves the efficacy of Helicobacter pylori eradication in smokers when combined with pantoprazole, amoxicillin, and clarithromycin. Materials and methods: The study completed 90 subjects of 98 enrolled, 58 smokers 32 nonsmokers. Helicobacter pylori status was determined by two methods, CLO test, and histology. Vitamin C (500 mg) was administered three times daily. The patients were considered as cured of H. pylori if the CLO test result and histology were negative 4 weeks after completion of eradication therapy. Results: Smokers had lower effectiveness of eradication therapy than non-smokers and the administration of vitamin C had not affected the outcome of eradication therapy. Conclusions: Vitamin C (500 mg tid) does not improve the eradication therapy when pantoprazole, amoxicillin, and clarithromycin were used.
Genetic Diversity and Geographic Relationship Studies in Chickpea (Cicer arietinum L.) Germplasm

The genus Cicer comprises 34 wild perennial, eight annual wild and one annual cultivated species. Chickpea (Cicer arietinum) is the third most important food legumes in the world in terms of area (11.55 million hectares) and production (10.46 million tons) (FAOSTAT 2014). India is the largest producer of chickpea in the world sharing about 70% of area and production (FAOSTAT 2014). In India, chickpea is cultivated in an area of 9.39 million ha with the production of 9.53 million tons (Dixit 2015) with productivity of 960 kg/ha.