Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies on triploid oysters in Australia. VII. Assessment of two methods for determining triploidy in oysters: adductor muscle diameter and nuclear size

Two methods for distinguishing triploid Pacific oysters [Crassostrea gigas (Thunberg)] from diploid oysters were assessed. Adductor muscle diameter in relation to valve height was significantly (p < 0.001) greater in samples of triploid oysters than in diploid samples and was influenced by site. However, variation in this measure was too large to allow individual oysters to be distinguished as either triploid or diploid. A second method was assessed that used differences in the nuclear size of hemocytes and the intensity of staining of hemocyte nuclei to distinguish between diploids and triploids. Histological sections, prepared by standard paraffin histology, were stained for nuclear histones with Gill's hematoxylin. Integrated nuclear optical density and nuclear area were recorded with image analysis. This method was effective in distinguishing individual oysters as diploid or triploid. When histological specimens are required, this method is less expensive than other techniques used to determine triploidy.
Horizontal Gene Flow in Managed Ecosystems

Mobilization of DNA by horizontal gene transfer (HGT) is an important process in the evolution of many organisms because it allows the recipient lineage to rapidly acquire metabolic innovations and adapt to new ecological niches. However, the significance of HGT in specific ecosystems remains poorly understood. In this review, we present major findings that illustrate how HGT affects managed ecosystems, such as farmlands, orchards, pastures, and managed grasslands. First, acquisition of functions via HGT can lead to the emergence of novel or more virulent pathogens and parasites of crops by allowing them to circumvent host defenses and currently used pest management approaches. Second, HGT of antibiotic resistance genes from the application of wastewater effluent for irrigation or manure as fertilizer can facilitate the emergence of highly resistant microbial lineages. Lastly, HGT can enhance the functional diversity of microbial communities and potentially influence biogeochemical processes. Characteriza.
Studies on the Effect of Foliar Application of Micronutrients and Ga3 on Yield and Reproductive Parameters of Winter Season Guava

The present investigation entitled “Studies on the effect of foliar application of micronutrient and GA3 on reproductive parameters and fruit yield of winter season guava “ was carried out in the Fruit Research Farm, Horticulture Unit, Banaras Hindu University, Varanasi during the year 2010–2011. The experiment was laid out in Randomized block design with eleven treatments. A perusal of data revealed that maximum fruit set and maximum fruit drop was found in treatment T7 (GA3--50 ppm) and T11 (control) respectively. Maximum fruit retention and minimum fruit drop was found in T4 (Borax-0.4%) while minimum results was recorded in under T11 control (no treatment isgiven) respectively. Maximum yield was recorded in Treatment T4 (Borax-0.4%) while minimum was under control.
Effect of Icosapent Ethyl on Progression of Coronary Atherosclerosis in Patients with Elevated Triglycerides on Statin Therapy: A prospective, placebo-controlled randomized trial (EVAPORATE): Interim Results.

AIMS Though statin therapy is known to slow coronary atherosclerosis progression and reduce cardiovascular(CV) events, significant CV risk still remains. In the REDUCE-IT study, icosapent ethyl (IPE) added to statin therapy reduced initial CV events by 25% and total CV events by 30%, but its effects on coronary atherosclerosis progression have not yet been fully investigated. Therefore, this study is to determine whether IPE 4g/d will result in a greater change from baseline in plaque volume measured by serial multidetector computed tomography (MDCT) than placebo in statin-treated patients. METHODS AND RESULTS EVAPORATE is a randomized, double-blind, placebo-controlled trial. Patients had to have coronary atherosclerosis by coronary computed tomographic angiography CCTA (≥1 angiographic stenoses with ≥20% narrowing), on stable statin therapy with low-density lipoprotein cholesterol levels 40 to 115 mg/dl, and persistently high triglyceride levels (135-499 mg/dL). Patients underwent an interim scan at 9 months and were followed for an additional 9 months with CCTA at 0, 9 and 18 months. Here we present the protocol-specified interim efficacy results.A total of 80 patients were enrolled, with 67 completing the 9-month visit and having interpretable CCTA at baseline and at 9-months (age=57±6 years, male=36, 63%). At the 9-month interim analysis, there was no significant change in low attenuation plaque (LAP) between active and placebo groups (74% vs 94%, p = 0.469). However, there was slowing of total non-calcified plaque (sum of LAP, fibrofatty, and fibrous plaque)(35% v. 43%,p=0.010), total plaque (non-calcified + calcified plaque)(15% v. 26%,p=0.0004), fibrous plaque (17% v. 40%,p=0.011) and calcified plaque (-1% v. 9%,p=0.001), after adjustment by baseline plaque, age, sex, diabetes, baseline triglyceride levels, and statin use. CONCLUSIONS EVAPORATE is the first study using CCTA to evaluate the effects of IPE as an adjunct to statin therapy on atherosclerotic plaque characteristics in a high-risk CV population with persistently high TG levels. It provides important mechanistic data in regards to the reduction in CV events in the REDUCE-IT clinical trial. TRANSLATIONAL POTENTIAL Given the robust cardiovascular event reduction seen in clinical trials of Icosapent ethyl, this study demonstrates that one potential mechanism of benefit of this therapy is to slow atherosclerosis progression. This study shows that most coronary plaque types show slowed rates of progression under the influence of statin plus Icosapent ethyl. A translational use of this information would be to potentially use this therapy in addition to statin therapy in cases with presence of significant atherosclerosis.
Likelihood of hospital readmission in Medicare Advantage and Fee-For-Service within same hospital.

OBJECTIVE To assess the extent to which all-cause 30-day readmission rate varies by Medicare program within the same hospitals. STUDY DESIGN We used conditional logistic regression clustered by hospital and generalized estimating equations to compare the odds of unplanned all-cause 30-day readmission between Medicare Fee-for-Service (FFS) and Medicare Advantage (MA). DATA COLLECTION Wisconsin Health Information Organization collects claims data from various payers including private insurance, Medicare, and Medicaid, twice a year. PRINCIPAL FINDINGS For 62 of 66 hospitals, hospital-level readmission rates for MA were lower than those for Medicare FFS. The odds of 30-day readmission in MA were 0.92 times lower than Medicare FFS within the same hospital (odds ratio, 0.93; 95 percent confidence interval, 0.89-0.98). The adjusted overall readmission rates of Medicare FFS and MA were 14.9 percent and 11.9 percent, respectively. CONCLUSION These findings provide additional evidence of potential variations in readmission risk by payer and support the need for improved monitoring systems in hospitals that incorporate payer-specific data. Further research is needed to delineate specific care delivery factors that contribute to differential readmission risk by payer source.
Retrospective detection of SARS-CoV-2 in hospitalized patients with influenza-like illness

ABSTRACT Since the first report of the coronavirus disease (COVID-19) in late December 2019, the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now widely spread to more than 187 countries and regions. However, it is unclear whether there has been cryptic transmission before these early officially confirmed cases, we therefore retrospectively screened for the SARS-CoV-2 RNA in 1271 nasopharyngeal swab samples, as well as the prevalence of IgM, IgG, and total antibodies against SARS-CoV-2 in 357 matched serum samples collected from hospitalized patients with influenza-like illness between 1 December 2018 and 31 March 2020 in Shanghai Ruijin Hospital. The onset date of the earliest COVID-19 case in this study was 25 January 2020. Before this time point, the presence of SARS-CoV-2 was not observed, which limited the possibility that SARS-CoV-2 has already spread among the population before the large-scale outbreak. Additionally, among 6662 patients with influenza-like illness from 1 December 2017 to 31 March 2020, the overall number of patients positive for influenza and other respiratory viruses during the COVID-19 period decreased significantly when compared with that in the same period of the last two years, reflecting that public health interventions can effectively control the spread of common respiratory viruses.
Reassessment of the conservation status and protected area coverage of Taiwanese birds: How distribution modelling can help species conservation

Summary Taiwan has 145 breeding bird species, but so far no comprehensive attempt has been made to model their distributions. For the first time, we bring together various datasets to model the distributions of the 116 bird species with sufficient sampling coverage. We improved on previous limited modelling efforts by using ensemble modelling, based on five well-performing modelling approaches: multiple discriminant analysis, logistic regression, genetic algorithm for rule-set production, ecological niche factor analysis and maximum-entropy. We then used these ensemble models to improve our knowledge of the status of each bird species by (1) calculating each species’s coverage of Taiwan, (2) calculating each species’s coverage by Taiwan’s protected area network, and (3) comparing these two conservation-relevant measures with already established measures to highlight those species whose status may need to be reassessed. We categorised each species’s coverage of the entire study area as measured by their modelled distributions into four quartiles, thus establishing a new measure of rarity called ‘range quartile’ which we used to highlight the 22 species with a limited distribution on mainland Taiwan. We also calculated that overall, 29.8% of the distribution ranges of the 116 modelled species are covered by Taiwanese protected areas. We then identified those species whose status may need to be reassessed because of possible conflicts between the respective conservation-relevant measures. Thus we identified 10 species which are first-quartile species < 5% of whose distributions are protected, of which only five are considered threatened. We also identified another 12 species with limited distributions, 30 species with limited protection and 19 species whose status may need to be reassessed for various reasons. We recommend that range quartile and protected area coverage be incorporated into future assessments of the conservation status and protected area coverage of Taiwanese birds.
A National Survey of Hearing Loss in the Philippines

This study aimed to estimate the prevalence of hearing loss in the Philippines using a nationally representative sample. A cross-sectional national survey was undertaken utilizing a 3-stage stratified cluster design. Participants in the present study comprised 2275 adults and children with pure tone hearing assessment results. Prevalence of moderate or worse hearing loss, defined as 4FA ≥41 dBHL, was 7.5% in children <18 years, 14.7% in adults between 18 and 65 years, and 49.1% in adults >65 years. Factors associated with greater risk of moderate hearing loss in the better ear were presence of a middle ear condition (adjusted odds ratio = 2.39, 95% confidence interval = 1.49-3.85) and socioeconomic status (household income; adjusted odds ratio = 1.64, 95% confidence interval = 1.23-2.19). Age was also associated with increased risk, with adjusted odds ratios varying with age category. Prevalence of wax occlusion and outer and middle ear disease was 12.2% and 14.2%, respectively. Prevalence of hearing loss, outer, and middle ear disease appear comparatively high in the Philippines when compared with rates reported in high-income countries. Higher proportions of severe to profound hearing loss were also identified, indicating that there is both an increased prevalence and severity of hearing loss in this population.
SeedExtractor: An Open-Source GUI for Seed Image Analysis

Accurate measurement of seed size parameters is essential for both: breeding efforts□aimed at□enhancing yields and basic research□focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that□determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 seconds for analyzing an image, i.e. significantly less compared to the other tools. As this software is open-source, it can be modified by users□to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were subjected to genome-wide association analysis. We identified well-known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrated the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops. HIGHLIGHT SeedExtractor is an open-source application designed to accurately measure seed size and seed color in a time-efficient manner for a wide variety of plant species.
Simple nomogram based on initial laboratory data for predicting the probability of ICU transfer of COVID‐19 patients: Multicenter retrospective study

This retrospective, multicenter study investigated the risk factors associated with intensive care unit (ICU) admission and transfer in 461 adult patients with confirmed coronavirus disease 2019 (COVID‐19) hospitalized from 22 January to 14 March 2020 in Hunan, China. Outcomes of ICU and non‐ICU patients were compared, and a simple nomogram for predicting the probability of ICU transfer after hospital admission was developed based on initial laboratory data using a Cox proportional hazards regression model. Differences in laboratory indices were observed between patients admitted to the ICU and those who were not admitted. Several independent predictors of ICU transfer in COVID‐19 patients were identified including older age (≥65 years) (hazard ratio [HR] = 4.02), hypertension (HR = 2.65), neutrophil count (HR = 1.11), procalcitonin level (HR = 3.67), prothrombin time (HR = 1.28), and D‐dimer level (HR = 1.25). The lymphocyte count and albumin level were negatively associated with mortality (HR = 0.08 and 0.86, respectively). The developed model provides a means for identifying, at hospital admission, the subset of patients with COVID‐19 who are at high risk of progression and would require transfer to the ICU within 3 and 7 days after hospitalization. This method of early patient triage allows a more effective allocation of limited medical resources.
Fluctuations and Oscillatory Instabilities of Intracellular Fiber networks

Biological systems with their complex biochemical networks are known to be intrinsically noisy. The interplay between noise and dynamical behavior is particularly relevant in the case of chemotactic amoeboid cells as their cytoskeleton operates close to an oscillatory instability. Here, we investigate the oscillatory dynamics in the actin system of chemotactic amoeboid cells. We show that the large phenotypic variability in the polymerization dynamics can be accurately captured by a generic nonlinear oscillator model, in the presence of noise. The relative role of the noise is fully determined by a single dimensionless parameter, experimentally measurable, and whose distribution completely characterizes the possible cellular behavior. We find that cells operate either below or above the threshold of self-oscillation, always in a regime where noise plays a very substantial role. To test the limits of this phenomenological description, we perturbed experimentally the cytoskeletal dynamics by a short chemoattractant pulse and measured the spatio-temporal response of filamentous actin reporter, LimE, and depolymerization regulators Coronin1 and Aip1. After pulsing, we observed self oscillating cells to relax back to their oscillatory state after a noisy transient. Particularly long transients were observed for cells initially displaying highly correlated oscillations. The observation of a slow recovery time of the actin polymerizing network provides a link to the long times scales, characteristic of chemotactic cell motility. In the second part of this work, we have characterized the response of LimE, Aip1, and Coronin to cAMP in non oscillating cells. We have used a proposed method that transforms the observed time series into symbolic dynamics, that gives partial information on the interactions between these proteins. We tested the predictions by studying the LimE response in mutant cells that either lacked Aip1 or Coronin. Finally, a model is proposed where Aip1 and Coronin synergizes to control actin polymerization.
Encephalization - An Evolutionary Predisposition to Diabetes: A "Large Brain Hypothesis" explaining the mechanism of Diabetes.

Primates have proportionately three times larger brain as compared to that of other mammals of comparable size and humans, in turn, have three times larger brain as compared to that of all other primates of similar size. So we need to meet higher energy demands because brain is energetically expensive. This has a significant impact on our dietary patterns in addition to shaping of our body composition. Here we propose that our dietary patterns to meet our higher energy demands have been ultimately set by the instinct of higher energy intake and our larger brains have a stress effect on our metabolic organs (organs involved in energy metabolism like gut, liver, pancreas etc.). We discuss these two points from evolutionary (Evolutionary instinct) and physiological (Metabolic stress) point of view and argue that these two points explain the manifestation of diabetes primarily as a human disease and enhance our understanding of its mechanism.
Early Colectomy Saves Lives in Toxic Megacolon Due to Clostridium difficile Infection

Clostridium difficile infection occasionally presents with one of the fulminant toxic colon conditions that results in rapid deterioration of a patient’s condition. Approximately 3% to 4% of patients infected with C. difficile progress to the fulminant course and can result in sepsis and septic shock. In most circumstances, conservative management has failed to improve a patient’s condition and often has led to multiple organ failure and death. Early operative intervention can result in survival benefit. Abstract Objective The purpose of the study was to evaluate whether early colectomy in patients who have toxic megacolon due to Clostridium difficile colitis reduces mortality. Methods The study was performed using the American College of Surgeons National Surgical Quality Improvement Program database from 2012 to 2016. All patients 18 to 89 years of age who underwent colectomy for toxic megacolon resulting from C. difficile colitis were included in the study. Other variables included in the study were patient demography, comorbidities, and outcomes. Patients who underwent colectomy before the presentation of septic shock (early group) were compared with patients who underwent colectomy after the onset of septic shock (late group). The main outcome of the study is 30-day all-cause mortality. Because there were some significant differences found in patient baseline characteristics in the univariate analysis, the propensity score of each patient was calculated and pair-matched analysis was performed. All P values are reported as 2-sided, and P < 0.05 was considered statistically significant. Results One hundred sixty-three patients met the inclusion criteria of the study. Approximately 85% of the patients underwent total abdominal colectomy. The average age of the patients was 65 years old, 51% of the patients were female, and 66% of the patients were white. The overall 30-day mortality was approximately 39%. The mortality rate of patients who underwent colectomy early compared to late was 13 (21%) vs 28 (45%), P = 0.009. The absolute risk difference was 0.24 with 95% CI: 0.07–0.42. Conclusions There was a reduction of 24% in 30-day mortality when colectomies were performed before the development of septic shock.
Genetic diversity, SNP-trait associations and genomic selection accuracy in a west African collection of Kersting’s groundnut [Macrotyloma geocarpum(Harms) Maréchal & Baudet]

Understanding the mechanisms governing complex traits variation is a requirement for efficient crop improvement. In this study, the molecular characterization, marker-trait associations and the possibility for genomic selection in a collection of 281 Kersting’s groundnut accessions were carried out. The diversity panel was phenotyped using an Alpha lattice design with two replicates in two contrasting environments. Accessions were genotyped using genotyping by sequencing technology. Genome-wide association analyses were performed between single nucleotide polymorphism markers and yield-related traits across tested environments. SNP markers were used to calculate the observed (Ho) and expected heterozygosity (He), and the total gene diversity (Ht). Genetic differentiation among accessions across ecological regions of origin was analysed. Our results revealed 493 quality SNPs of which 113 had a minor allele frequency>0.05, a total gene diversity of 0.43 and average Ho and He values of 0.04 and 0.22, respectively. Four clusters, highly differentiated by seed coat colour (Fst = 0.79), were identified. The population structure analysis showed two subpopulations with high differentiation across ecological regions (Fst = 0.37). The GWAS revealed 10 significant marker-trait associations, of which six SNPs were consistent across environments. The genomic selection through cross-validation showed moderate to high prediction accuracies for leaflet length, seed dimension traits, 100 seed weight, days to 50% flowering and days to maturity. This demonstrates the existence of genetic variability within Kersting’s groundnut and shows the potential for the improvement of the species. The findings also provide a first insight into the phenotype-to-genotype relationships in Kersting’s groundnut, using SNP markers.
Haemocytes of larval Malacosoma disstria (Lepidoptera: Lasiocampidae) and factors affecting their adhesion to glass slides

Abstract. Although haemocytes of the forest pest lepidopteran, Malacosoma disstria (L.) have been studied, the physico‐chemical factors and signalling components affecting their non‐self activities have not been examined. Both the ameboid and stellate forms of plasmatocytes and the granular cells from fifth‐instar larvae adhere best to glass slides with phosphate‐buffered saline (PBS), with maximum granular cell binding within a pH range of 6.0–7.0 and plasmatocyte binding at pH 6.0. The divalent cations, calcium and magnesium, do not affect granular cell attachment. However, calcium in Galleria‐anticoagulant and PBS and, to a lesser extent, magnesium in the anticoagulant, increase plasmatocyte‐glass contact. Based upon the use of selective type I protein kinase A inhibitor (Rp‐8‐Br‐cAMPS) and activator (Sp‐8‐Br‐cAMPS), active protein kinase A inhibits the adhesion of both haemocyte types. Similarly, protein kinase C inhibited by Gö 6976 enhances haemocyte adhesion whereas the enzyme activator, phorbol‐myristate‐acetate, impairs attachment.