Miracle-dz/UniFAR-FTUs huggingface dataset:
ROX Index Predicts Intubation in Patients with COVID-19 Pneumonia and Moderate to Severe Hypoxemic Respiratory Failure Receiving High Flow Nasal Therapy.

Introduction Use of high flow nasal therapy (HFNT) to treat COVID-19 pneumonia has been greatly debated around the world due to concern for increased healthcare worker transmission and delays in invasive mechanical Ventilation (IMV). Methods A retrospective analysis of consecutive patients admitted to Temple University Hospital in Philadelphia, Pennsylvania, from March 10, 2020, to May 17, 2020 with moderate to severe respiratory failure treated with High Flow nasal therapy (HFNT). HFNT patients were divided into two groups: HFNT only and HFNT progressed to IMV. The primary outcome was the ability of the ROX index to predict the need of IMV. Results Of the 837 patients with COVID-19, 129 met inclusion criteria. The mean age was 60.8 ({+/-}13.6) years, BMI 32.6 ({+/-}8), 58 (45 %) were female, 72 (55.8%) were African American, 40 (31%) Hispanic. 48 (37.2%) were smokers. Mean time to intubation was 2.5 days ({+/-} 3.3). ROX index of less than 5 at HFNT initiation was predictive of progression to IMV (OR = 2.137, p = 0,052). Any decrease in ROX index after HFNT initiation was predictive of intubation (OR= 14.67, p <0.0001). {Delta}ROX (<=0 versus >0), peak D-dimer >4000 and admission GFR < 60 ml/min were very strongly predictive of need for IMV (ROC = 0.86, p=). Mortality was 11.2% in HFNT only group versus 47.5% in the HFNT progressed to IMV group (p,0.0001). Mortality and need for pulmonary vasodilators were higher in the HNFT progressed to IMV group. Conclusion ROX index is a valuable, noninvasive tool to evaluate patients with moderate to severe hypoxemic respiratory failure in COVID-19 treated with HFNT. ROX helps predicts need for IMV and thus limiting morbidity and mortality associated with IMV.
Performance of Bt cotton against sucking pests

Studies were taken up to monitor the population of sucking pests as well as boll damage in commercially released Bt cotton entries. In the present study it was found that the jassid population was almost negligible (< one per three leaves) both in Bt as well as non Bt cotton hybrids. In five Bt cotton hybrids (JKCH 1947, RCH 317, NCEH 6, Ankur 2534 and MRC 6301) it was less than that of non Bt cotton hybrid. However, whitefly incidence was more in all Bt cotton hybrids than that of the non Bt cotton hybrid, which may be due to reduction in the spray of chemical insecticides or the negligible infestation of bollworms. The bollworm damage in the current experiments revealed almost nil damage to the bolls in Bt cotton compared to non Bt cotton hybrid. The seed cotton yield in 12 out of 13 Bt cotton hybrids were more than that of non Bt cotton hybrid. This reveals the superiority of Bt cotton hybrids in terms of yield.
Redescription of the Geikiid Pelanomodon (Therapsida, Dicynodontia), with a Reconsideration of ‘Propelanomodon’

ABSTRACT Cryptodont dicynodonts are some of the most abundant therapsid taxa in the upper Permian fossil record. Despite extensive taxonomic study of these families, the species diversity of geikiid cryptodonts remains problematic, particularly for the set of edentulous taxa in the genera Pelanomodon, Propelanomodon, and Geikia. Here, all known specimens of tuskless geikiid dicynodonts from the upper Permian Karoo Basin of South Africa are reevaluated. The genus Pelanomodon is redescribed based on a series of skulls representing a range of sizes. All tuskless geikiids from the Karoo Basin are considered to represent a single species (Pelanomodon moschops) that exhibited cranial dimorphism as adults. The nominal species Pe. moschops and Pe. rubidgei differ only in degree of facial boss development and are most parsimoniously interpreted as sexual dimorphs. Propelanomodon is considered to represent the juvenile morphotype of Pelanomodon moschops, as indicated by the geographic and stratigraphic overlap of the two taxa, the lack of any small skulls of the Pelanomodon morphotype in well-sampled localities, and the presence of specimens of intermediate size and morphology. ‘Propelanomodon’ specimens are distinctive among juvenile dicynodonts in having a significantly narrower intertemporal region than adults. Analysis of intertemporal width relative to total skull size in Pelanomodon and the abundant cryptodont taxa Aulacephalodon, Oudenodon, and Tropidostoma suggests that Pelanomodon had a unique growth trajectory. Based on available stratigraphic data, Pelanomodon was restricted to the uppermost Permian Daptocephalus Assemblage Zone of the South African Beaufort Group and was a victim of the end-Permian mass extinction. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline. com/UJVP
River macrophyte indices: not the Holy Grail!

Summary 1. Recent studies have demonstrated that there is generally no unambiguous relationship between plant species composition and specific environmental conditions in rivers. Nevertheless, indices of environmental pressures based on macrophytes are flourishing, because of the requirements of the Water Framework Directive (WFD). 2. We first reviewed nine such indices against 13 criteria for bioindicators. Then, using data from France and England, we tested whether the IBMR (Macrophyte Biological Index for Rivers) and LEAFPACS (predictions and classification system for macrophytes) methods could reliably indicate nutrient and hydromorphological pressures. Finally, we used an improved bootstrapping method to estimate accuracy. 3. Currently, most indices lack ecological meaning for a variety of reasons, including partial sampling (backwaters are excluded); reliance on list of taxa (there are identification difficulties) rather than structure and functions; correlation rather than causation; application within a limited biogeographical area; reliance on ‘expert’ judgement; high precision but poor accuracy; poorly defined reference conditions; lack of independent tests; and an inability to discriminate reliably between the target pressures of interest from confounding background variables. 4. IBMR was a far better indicator of pH (or HCO3-pCO2) than it was of soluble reactive phosphorus, SRP (or SRP-NH4). While there was a highly significant correlation between IBMR and SRP after removing the effect of pH, the relationship was weak (r2 = 0.08, n = 215, P < 0.001). 5. LEAFPACS is a multi-metric method summing up five individual indices, each compliant with the WFD. Its individual metrics were not better correlated with nutrient and hydromorphological pressures (with r2 < 0.1, n = 62, P < 0.05) than was the IBMR. The meaning of the overall metric is questionable. 6. There are problems in determining the precision of the indices, owing to uncertainties in recording, but they are less than the uncertainties in determining accuracy (because species optima and tolerances are sometimes poorly known). 7. Reliable information is needed to improve the state of our rivers. Macrophyte indices are able to detect statistically significant pressures from a large population of sites but cannot be applied at specific sites, as required by the WFD, owing to large uncertainties and low explanatory power. Typically, more than 90% of the variability in macrophyte indices is attributed to factors other than human pressure. The WFD would be better served by a simpler, holistic approach based on our current mechanistic understanding of river processes. These findings are likely to apply also to other taxonomic groups (macroinvertebrates, diatoms, fish) used in the assessment of purported ecological quality and to palaeolimnological measures of reference status.
Diagnostic accuracy of serological tests for covid-19: systematic review and meta-analysis

Abstract Objective To determine the diagnostic accuracy of serological tests for coronavirus disease-2019 (covid-19). Design Systematic review and meta-analysis. Data sources Medline, bioRxiv, and medRxiv from 1 January to 30 April 2020, using subject headings or subheadings combined with text words for the concepts of covid-19 and serological tests for covid-19. Eligibility criteria and data analysis Eligible studies measured sensitivity or specificity, or both of a covid-19 serological test compared with a reference standard of viral culture or reverse transcriptase polymerase chain reaction. Studies were excluded with fewer than five participants or samples. Risk of bias was assessed using quality assessment of diagnostic accuracy studies 2 (QUADAS-2). Pooled sensitivity and specificity were estimated using random effects bivariate meta-analyses. Main outcome measures The primary outcome was overall sensitivity and specificity, stratified by method of serological testing (enzyme linked immunosorbent assays (ELISAs), lateral flow immunoassays (LFIAs), or chemiluminescent immunoassays (CLIAs)) and immunoglobulin class (IgG, IgM, or both). Secondary outcomes were stratum specific sensitivity and specificity within subgroups defined by study or participant characteristics, including time since symptom onset. Results 5016 references were identified and 40 studies included. 49 risk of bias assessments were carried out (one for each population and method evaluated). High risk of patient selection bias was found in 98% (48/49) of assessments and high or unclear risk of bias from performance or interpretation of the serological test in 73% (36/49). Only 10% (4/40) of studies included outpatients. Only two studies evaluated tests at the point of care. For each method of testing, pooled sensitivity and specificity were not associated with the immunoglobulin class measured. The pooled sensitivity of ELISAs measuring IgG or IgM was 84.3% (95% confidence interval 75.6% to 90.9%), of LFIAs was 66.0% (49.3% to 79.3%), and of CLIAs was 97.8% (46.2% to 100%). In all analyses, pooled sensitivity was lower for LFIAs, the potential point-of-care method. Pooled specificities ranged from 96.6% to 99.7%. Of the samples used for estimating specificity, 83% (10 465/12 547) were from populations tested before the epidemic or not suspected of having covid-19. Among LFIAs, pooled sensitivity of commercial kits (65.0%, 49.0% to 78.2%) was lower than that of non-commercial tests (88.2%, 83.6% to 91.3%). Heterogeneity was seen in all analyses. Sensitivity was higher at least three weeks after symptom onset (ranging from 69.9% to 98.9%) compared with within the first week (from 13.4% to 50.3%). Conclusion Higher quality clinical studies assessing the diagnostic accuracy of serological tests for covid-19 are urgently needed. Currently, available evidence does not support the continued use of existing point-of-care serological tests. Study registration PROSPERO CRD42020179452.
Evidence of recent increased pathogenicity within the Australian Ascochyta rabiei population

Ascochyta Blight (AB), caused by Ascochyta rabiei (syn Phoma rabiei), is the major endemic foliar fungal disease affecting the Australian chickpea industry, resulting with potential crop loss and management costs. This study was conducted to better understand the risk posed by the Australian A. rabiei population to current resistance sources and to provide informed decision support for chemical control strategies. Recent changes in the pathogenicity of the population were proposed based on disease severity and histopathological observations on a host set. Controlled environment disease screening of 201 isolates on the host set revealed distinct pathogenicity groups, with 41% of all isolates assessed as highly aggressive and a significant increase in the proportion of isolates able to cause severe damage on resistant and moderately resistant cultivars since 2013. In particular, the frequency of highly aggressive isolates on the widely adopted PBA HatTrick cultivar rose from 18% in 2013 to 68% in 2017. In addition, isolates collected since 2016 caused severe disease on Genesis 090, another widely adopted moderately resistant cultivar and on ICC3996, a commonly used resistance source. Of immediate concern was the 10% of highly aggressive isolates able to severely damage the recently released resistant cultivar PBA Seamer (2016). Histopathology studies revealed that the most aggressive isolates were able to germinate, develop appressoria and invade directly through the epidermis faster than lower aggressive isolates on all hosts assessed, including ICC3996. The fungal invasion triggered a common reactive oxygen species (ROS) and hypersensitive response (HR) on all assessed resistant genotypes with initial biochemical and subsequent structural defence responses initiated within 24 hours of inoculation by the most highly aggressive isolates. These responses were much faster on the less resistant and fastest on the susceptible check host, indicating that speed of recognition was correlated with resistance rating. This will inform fungicide application timing so that infected crops are sprayed with prophylactic chemistries prior to invasion and with systemic chemistries after the pathogen has invaded.
Genomic stability and adaptation of beer brewing yeasts during serial repitching in the brewery

Ale brewing yeast are the result of admixture between diverse strains of Saccharomyces cerevisiae, resulting in a heterozygous tetraploid that has since undergone numerous genomic rearrangements. As a result, comparisons between the genomes of modern related ale brewing strains show both extensive aneuploidy and mitotic recombination that has resulted in a loss of intragenomic diversity. Similar patterns of intraspecific admixture and subsequent selection for one haplotype have been seen in many domesticated crops, potentially reflecting a general pattern of domestication syndrome between these systems. We set out to explore the evolution of the ale brewing yeast, to understand both polyploid evolution and the process of domestication in the ecologically relevant environment of the brewery. Utilizing a common brewery practice known as ‘repitching’, in which yeasts are reused over multiple beer fermentations, we generated population time courses from multiple breweries utilizing similar strains of ale yeast. Applying whole-genome sequencing to the time courses, we have found that the same structural variations in the form of aneuploidy and mitotic recombination of particular chromosomes reproducibly rise to detectable frequency during adaptation to brewing conditions across multiple related strains in different breweries. Our results demonstrate that domestication of ale strains is an ongoing process and will likely continue to occur as modern brewing practices develop.
Positive Welfare and the Like: Distinct Views and a Proposed Framework

Positive welfare and related terms such as good welfare, happiness, and a good life are increasingly used in the animal welfare science literature. Overall, they highlight the welfare benefits of providing animals opportunities for positive experiences, beyond the alleviation of suffering. However, the various terms remain loosely defined and are sometimes used interchangeably, resulting in discrepancy. In this perspective article, we lay out the terms and concepts used in the literature. We identify two distinct views: “hedonic positive welfare,” arising from likes and wants and their positive outcomes on welfare; and “positive welfare balance,” as an overall positive welfare state based on positive experiences outweighing negative ones. Eudaimonia, satisfaction with one's life, may emerge as a third view. We propose a framework that is applicable across the different views. The “Vienna Framework” outlines different facets: frequency, duration, arousal, context, previous experience, individual differences, sense of agency, and long-term benefit. The framework aims to encourage researchers to consider the relevance of these facets for their own research, to indicate how the facets are affected by different interventions (e.g., greater sense of agency in enriched compared to non-enriched animals), or to compare different topics with respect to the different facets (e.g., high arousal of play behavior and low arousal of social affiliation). We encourage researchers to carefully consider and clearly state how their work falls along these views and facets, conceptually, and operationally. This should prevent dilution of the meaning of positive welfare and thereby preserve its potential to improve the welfare of animals.
Factors influencing the phycobilisome rod composition of the cyanobacterium Synechococcus sp. PCC 7942: Effects of reduced phycocyanin content, lack of rod-linkers, and over-expression of the rod-terminating linker

Four novel mutants with altered phycobilisomes were constructed in the cyanobacterium Synechococcus 7942 to study factors influencing the rod length and composition. These mutants show (1) reduced phycocyanin content, (2) reduced phycocyanin content combined with loss of the 33 kDa linker, (3) loss of the 30 kDa rod-linker and (4) overexpression of the 9 kDa rod terminating linker. For these mutants we determined the 33 to 27 kDa and 30 to 27 kDa linker ratios in the isolated phycobilisomes and compared these ratios with those in the wild type. The 30 kDa linker can be incorporated into the rods in absence of the 33 kDa linker. The incorporation of the 30 kDa linker is lower in absence of the 33 kDa linker. When the 30 kDa linker is missing, an increase in the level of the 33 kDa linker is seen, indicating that there could be an excess of the 33 kDa linker in the cells. Our results also show that a reduction in the phycocyanin content causes a decrease in the rod length simultaneously with a reduction of the 30/27 linker ratio, without altering the 33/27 ratio. Reduced phycocyanin content and absence of the 33 kDa linker cause a dramatic reduction in the incorporation of the 30 kDa linker into the rods in the mutant B2SMIKM. Over-expression of the 9 kDa linker results in a decreased incorporation of both the 33 and 30 kDa linkers into the rods, the effect being more pronounced for the 30 kDa linker. This result indicates that the level of the 9 kDa linker relative to those of the 33 and the 30 kDa linkers may be an important determinant of the phycobilisome rod length.
Metagenomics Study Reveals Changes in Gut Microbiota in Centenarians: A Cohort Study of Hainan Centenarians

Several studies based on 16SrDNA analysis have revealed certain unique characteristics of gut microbiome in centenarians. We established a prospective cohort of fecal microbiota and conducted the first metagenomics-based study among centenarians. The objective was to explore the dynamic changes of gut microbiota in healthy centenarians and centenarians approaching end of life and to unravel the characteristics of aging-associated microbiome. Seventy-five healthy centenarians residing in three regions of Hainan participated in follow-up surveys and collection of fecal samples at intervals of 3 months. Data pertaining to dietary status, health status scores, cause of disease and death, and fecal specimens were collected for 15 months. Twenty participants died within 20 months during the follow-up period. The median survival time was 8–9 months (range, 1–17) and the mortality rate was 14.7% per year. The health status scores before death were significantly lower than those at 3 months before the end of the follow-up period [median score: 3 (range, 1–5), P < 0.05]. At this time, the participants mainly exhibited symptoms of anorexia and reduced dietary intake and physical activity. Metagenomics sequencing and analysis were carried out to characterize the gut microbiota changes in the centenarians during their transition from healthy status to death. Anosim analysis showed a significant change in gut microbiota from 7 months prior to death (R = 0.10, P = 0.02). All participants were grouped with 7 months before death as cut-off; no significant difference in α diversity was found between the two groups (P = 0.45). Semi-supervised monitoring and log rank sum analysis revealed significant changes in the abundance of ten bacterial species before death; of these, eight species were significantly reduced (Akkermansia muciniphila, Alistipes finegoldii, Alistipes shahii, Bacteroides faecis, Bacteroides intestinalis, Butyrivibrio crossotus, Bacteroides stercoris, and Prevotella stercorea) while two were significantly increased before death (Bifidobacterium longum and Ruminococcus bromii). Compared to centenarians in northern Italy, Hainan centenarians exhibited unique characteristics of gut microbiome. The abundance of ten bacterial species showed significant changes starting from 7 months before death. We speculate that these changes might occur before the clinical symptoms of deterioration in health status.
Development of a Lived Experience-Based Digital Resource for a Digitally-Assisted Peer Support Program for Young People Experiencing Psychosis

This paper describes the creation of a web-based digital resource designed for tablet computer use during peer work sessions to structure discussion about recovery in early psychosis. The resource consisted of a series of videos featuring young people who have used early psychosis services discussing how they navigated issues in their own recovery. A participatory process was used to create the resource. Researchers held a series of collaborative development workshops with early psychosis service users, peer workers, other mental health practitioners, and academics. These were used to derive a framework of recovery processes relevant to young people experiencing psychosis, which was considered as useful areas of discussion within a peer work relationship. A semi-structured interview guide based on this framework was then used in video-recorded interviews with young people in recovery from psychosis. Footage was edited into 14 videos and organized into six final themes: My Journey, Self-Care, Connections, My Identity, Life, and Mental Health. The combined expertise of young mental health service users, peer support workers, mental health practitioners, and digital mental health researchers throughout the development process enabled the creation of tailored digital resource for peer work in an early psychosis service.
Line-Up Image Position in Simultaneous and Sequential Line-Ups: The Effects of Age and Viewing Distance on Selection Patterns

It is known that children and older adults produce more false alarms in target absent line-ups and that weaker facial encoding increases choosing bias. However, there has been no investigation of how age or facial encoding strength impacts line-up position selections in either sequential or simultaneous line-ups. In the present study, we presented participants with four live targets (one by one) while manipulating sequential and simultaneous line-ups between participants and target present and target absent line-ups within participants. In order to investigate facial encoding strength, we presented the targets at distances between 5 and 110 m. Our main hypotheses were that children due to deficits with inhibition would be more biased toward indiscriminate selections in the first position of sequential line-ups compared with subsequent line-up positions and that first position selections would increase for all age groups as facial encoding became weaker. In simultaneous line-ups, we expected to find a top row bias. In our sample (N = 1,588 participants; 6–77 years), we found that younger children (6–11 years) and the oldest adults (60–77 years) showed a first position bias in sequential line-ups, and as facial encoding became weaker, all age groups (6–11, 12–17, 18–44, 45–59, and 60–77 years) showed an increased tendency to make first position selections. We also found a weak top row preference in simultaneous line-ups, which was moderated by age and increased distance. The main finding is that the results suggest that younger children and the oldest adults had a tendency toward a first position selection bias in sequential line-ups. Based on the combined results, we recommend caution when using sequential line-ups with younger children or older adults.