Miracle-dz/UniFAR-FTUs huggingface dataset:
A paradigm shift in Enterococcal infections: A cause of concern

Introduction: Infections due to Gram-positive bacteria are on a rise, of which those due to Enterococcus spp. form a major part. The shifting pattern of infections caused by Enterococci from novel urinary tract infections to soft tissue and wound infections are increasingly reported. Objective: The aim of the present study is to isolate, speciate Enterococci, determine the antibiotic resistance pattern and to detect vancomycin resistance by Etest. Materials and Methods: All wound swabs, pus samples sent for bacterial culture, irrespective of the diagnosis of the patients which were received to the department of microbiology for a period of one year were included in the study. The samples were processed for isolation, identification and speciation of Enterococci. Antimicrobial susceptibility testing was done by KirbyBauer disk diffusion method. Vancomycin resistance was determined by E-test. Results: A total of 3000 pus samples were received over a period of one year. Out of which 43 isolates were detected as Enterococcus species. Among 43 isolates, 26 were E.faecalis, 17 were E.faecium. In present study, ampicillin resistance was seen in 88% followed by resistance to erythromycin (86%) and clindamycin (72%). High level gentamycin resistance was seen in 28% cases. Vancomycin resistance was not detected in any of the samples. Conclusion: The shifting spectrum of infections due to Enterococcus is gaining inquisitiveness among health care workers especially in the trauma care units. Thus there is a prerequisite to isolate speciate and determine the resistance that helps in holistic health care.
Receptor Revision in Peripheral T Cells Creates a Diverse Vβ Repertoire1

In Vβ5 transgenic mice, the age-dependent accumulation of Vβ5−CD4+ T cells expressing endogenous Vβ elements represents an exception to the rule of strict allelic exclusion at the TCRβ locus. The appearance of these cells is limited to the lymphoid periphery and is driven by a peripherally expressed tolerogen. Expression of the lymphoid-specific components of the recombinase machinery and the presence of recombination intermediates strongly suggest that TCR revision rescues tolerogen-reactive peripheral T cells from deletion. Here, we report that the appearance of Vβ5−CD4+ T cells is CD28-dependent. In addition, we find that the TCR repertoire of this unusual population of T cells in individual Vβ5 transgenic mice is surprisingly diverse, both at the level of surface protein and at the nucleotide level within a given family of V(D)Jβ rearrangements. This faithful recreation of the nontransgenic repertoire suggests that endogenous Vβ-expressing populations do not arise from expansion of an initially rare subset. Furthermore, the undersized N regions in revised TCR genes distinguish these sequences from those generated in the adult thymus. The diversity of the revised TCRs, the minimal mouse-to-mouse variation in the expressed endogenous Vβ repertoire, the atypical length of junctional sequences, and the CD28 dependence of the accumulation of Vβ5−CD4+ T cells all point to their extrathymic origin. Thus, tolerogen-driven receptor revision in peripheral T cells can expand the TCR repertoire extrathymically, thereby contributing to the flexibility of the immune repertoire.
Robust Inference and Model Criticism Using Bagged Posteriors

Standard Bayesian inference is known to be sensitive to model misspecification, leading to unreliable uncertainty quantification and poor predictive performance. However, finding generally applicable and computationally feasible methods for robust Bayesian inference under misspecification has proven to be a difficult challenge. An intriguing, easy-to-use, and widely applicable approach is to use bagging on the Bayesian posterior ("BayesBag"); that is, to use the average of posterior distributions conditioned on bootstrapped datasets. In this paper, we develop the asymptotic theory of BayesBag, propose a model-data mismatch index for model criticism using BayesBag, and empirically validate our theory and methodology on synthetic and real-world data in linear regression, sparse logistic regression, and a hierarchical mixed effects model. We find that in the presence of significant misspecification, BayesBag yields more reproducible inferences and has better predictive accuracy than the standard Bayesian posterior; on the other hand, when the model is correctly specified, BayesBag produces superior or equally good results. Overall, our results demonstrate that BayesBag combines the attractive modeling features of standard Bayesian inference with the distributional robustness properties of frequentist methods, providing benefits over both Bayes alone and the bootstrap alone.
The Sejong Suite: Cosmological Hydrodynamical Simulations with Massive Neutrinos, Dark Radiation, and Warm Dark Matter

We present the Sejong Suite, an extensive collection of state-of-the-art high-resolution cosmological hydrodynamical simulations spanning a variety of cosmological and astrophysical parameters, primarily developed for modeling the Lyα forest. The suite is organized into three main categories (Grid Suite, Supporting Suite, and Systematics Suite), addressing different science targets. Adopting a particle-based implementation, we follow the evolution of gas, dark matter (cold and warm), massive neutrinos, and dark radiation, and consider several combinations of box sizes and number of particles. With additional enhancing techniques, we are able to reach an equivalent resolution up to 3 × 33283 = 110 billion particles in a (100h−1 Mpc)3 box size, ideal for current and future surveys (e.g., Extended Baryon Oscillation Spectroscopic Survey and Dark Energy Spectroscopic Instrument). Noticeably, for the first time, we simulate extended mixed scenarios describing the combined effects of warm dark matter, neutrinos, and dark radiation, modeled consistently by taking into account the neutrino mass splitting. In addition to providing multicomponent snapshots from z = 5.0 to z = 2.0 in intervals of Δz = 0.2 for all of the models considered, we produced over 288 million Lyα skewers in the same z-range and extended parameter space. The skewers are well suited for Lyα forest science studies, for mapping the high-z cosmic web and the matter-to-flux relation and bias, and for quantifying the critical role of baryons at small scales. We also present a first analysis of the suite focused on the matter and flux statistics, and show that we are able to accurately reproduce the 1D flux power spectrum down to scales as mapped by recent high-resolution quasar data, as well as the thermal history of the intergalactic medium. The simulations and products described here will be progressively made available.
Effect of common waterhemp (Amaranthus rudis) emergence date on growth and fecundity in soybean

Abstract Field experiments were conducted in central Iowa to determine the growth of common waterhemp emerging after postemergence herbicide applications in soybean. Common waterhemp survival declined as emergence was delayed in relation to soybean. Ninety percent of plants emerging at approximately the same time as soybean survived, whereas only 13% of plants emerging approximately 50 d after planting (DAP) survived to maturity. Biomass accumulation declined rapidly as emergence was delayed in relation to soybean. Delaying emergence from 14 to 28 DAP resulted in a 50 to 80% reduction in shoot biomass. Common waterhemp emerging 50 DAP produced only 1 to 10% of the biomass of plants emerging at the same time as soybean. Plants emerging with soybean produced approximately 300,000 to 2.3 million seeds plant−1 depending on the location. Fecundity of common waterhemp plants was closely related to biomass accumulation and declined rapidly with delayed emergence. Although common waterhemp emerging after the V4 stage of soybean (40 DAP) are unlikely to affect crop yield because of high mortality levels and reduced growth, these plants may contribute significant seeds to the soil seed bank. Nomenclature: Common waterhemp, Amaranthus rudis Sauer AMATA; soybean, Glycine max (L.) Merr.
Visual impairment and depression: Age-specific prevalence, associations with vision loss, and relation to life satisfaction

BACKGROUND To our knowledge, no study has obtained specific estimates of depression for young and middle-aged adults with visual impairment (VI). As estimates of depression varies across age groups in the general population, it is of interest to examine whether the same applies to adults with low vision or blindness. AIM To estimate depression prevalence and its association with VI-related characteristics and life satisfaction in adults with VI. METHODS A telephone-based cross-sectional survey was conducted between January and May 2017 in an age-stratified sample of adults who were members of the Norwegian Association of the Blind and Partially Sighted. Participants were asked questions about their sociodemographic characteristics, VI characteristics, and life satisfaction. Depression was measured with the Patient Health Questionnaire. The diagnostic scoring algorithm was used to calculate the point prevalence of depression (i.e., major depression and other depressive disorders) across categories of gender and age (years: 18-35, 36-50, 51-65, ≥ 66). The associations were estimated using regression models. RESULTS Overall, 736 adults participated in the study (response rate: 61%). The prevalence estimates of depression varied across different age groups, ranging from 11.1%-22.8% in women and 9.4%-16.5% in men, with the highest rates for the two youngest age groups. Results from the multivariable models including sociodemographic and VI-related variables showed that losing vision late in life [Prevalence ratio (PR), 1.76, 95%CI: 1.11, 2.79] and having other impairments (PR: 1.88, 95%CI: 1.32, 2.67) were associated with higher rates of depression, whereas older age was associated with lower rates (PR: 0.83, 95%CI: 0.74, 0.93). Additionally, participants who were depressed had lower life satisfaction than those who were not depressed (adjusted β: -2.36, 95%CI: -2.75, -1.98). CONCLUSION Our findings suggest that depression in adults with VI, and especially among young and middle-aged adults, warrants greater attention by user organisations, clinicians, and healthcare authorities.
Deriving Differential Target Propagation from Iterating Approximate Inverses

We show that a particular form of target propagation, i.e., relying on learned inverses of each layer, which is differential, i.e., where the target is a small perturbation of the forward propagation, gives rise to an update rule which corresponds to an approximate Gauss-Newton gradient-based optimization, without requiring the manipulation or inversion of large matrices. What is interesting is that this is more biologically plausible than back-propagation yet may turn out to implicitly provide a stronger optimization procedure. Extending difference target propagation, we consider several iterative calculations based on local auto-encoders at each layer in order to achieve more precise inversions for more accurate target propagation and we show that these iterative procedures converge exponentially fast if the auto-encoding function minus the identity function has a Lipschitz constant smaller than one, i.e., the auto-encoder is coarsely succeeding at performing an inversion. We also propose a way to normalize the changes at each layer to take into account the relative influence of each layer on the output, so that larger weight changes are done on more influential layers, like would happen in ordinary back-propagation with gradient descent.
Anxiety and Depression Among Women Living with HIV: Prevalence and Correlations

Introduction: It has been found that HIV positive women are becoming increasingly affected by various illnesses, including Common Mental Disorders (CMDs) such as depression. Such comorbidity escalates the disease progression to the severe stage and commonly hinders treatment adherence. This study determined the prevalence of anxiety and depression amidst women living with HIV. Methods: Based on a cross-sectional and facility-based study, 357 HIV positive women were recruited using the systematic sampling technique from two public hospitals in Jijiga town, Ethiopia. The Hospital Anxiety and Depression Scale (HADS) was administered for screening, and followed by a pre-tested questionnaire that comprised of Perceived Social Support and HIV stigma. Results: The results revealed that the prevalence of both anxiety and depression amidst HIV positive women was 28.9% and 32.5%, respectively. In the multivariate analysis, it was discovered that lack of formal education, being divorced, unemployed, and earning a monthly income less than 1400 ETB (37.5 USD) were significantly associated with depression. Women with symptomatic HIV clinical stage III (AOR =2.06, 95% C.I (0.75-5.61), with CD4 cell count below 250 (AOR = 1.14, 95% C.I (0.57-2.28), and with co-infections (AOR= 1.04, 95% C.I (0.40-2.71) also suffered from depression. Conclusion: The study outcomes show that the prevalence of depression in women with HIV was 32.5%, but they were more likely to be depressed if they were illiterate, divorced, unemployed or had a financial burden. In addition, HIV positive women with less CD4 cell count and in the final clinical stage or suffered from a co-infection were also associated with depressive symptoms. This signifies the public health implications of psychological and cognitive morbidities of the illness among these women with chronic illnesses. Hence, future mental health interventions and HIV care should be integrated with substantial emphasis given to vulnerable groups, including HIV positive women.
Effect of Donepezil on Cognitive Impairment, Quality of Life, and Depression in Multiple Sclerosis Patients: A Randomized Clinical Trial

Background: Cognitive impairment is one of the debilitating consequences of multiple sclerosis (MS) with negative effects on daily life, individual and social activities, quality of life (QOL), and depression. No approved medication is introduced so far for affected individuals. We aimed to evaluate the efficacy of donepezil on cognitive performance, QOL, and depression in MS. Methods: This is a double-blinded randomized clinical trial conducted on 100 patients with MS during 2018. Patients were assessed prior to intervention abbreviated mental test (AMT), prospective and retrospective mental questionnaire (PRMQ), everyday memory questionnaire (EMQ), digit span test, Beck depression inventory (BDI), and MSQOL questionnaire. Then patients were randomly divided into two groups of treatment (daily regimen of 10 mg donepezil) and placebo for 3 months. Subjects were reassessed using the same instruments at the end of intervention. Results: Fifty patients remained in each group at the end of study. The mean age in donepezil and placebo groups was 31.9 ± 5.89 and 30.65 ± 5.43 years, respectively. EMQ, PRMQ, digit span test, MSQOL, and depression scores improved following donepezil therapy (P < 0.001) while no statistically significant difference was found in the placebo group (P > 0.05). Comparison of two groups also showed more favorable scores in donepezil group with respect to all assessment tools (P < 0.001). Conclusions: Donepezil could effectively improve cognitive impairment in MS patients. Also, its positive effect on QOL and depression could result in a smaller number of interventions in this group of patients.
Internode elongation pattern, internode diameter and hormone changes in soybean (Glycine max) under different shading conditions

Abstract. Internode length and diameter in soybean (Glycine max (L.) Merr. ) are closely associated with lodging. The pattern of internode elongation and increase in internode diameter and factors involved were studied in two soybean cultivars, HN48 (tall-stem cultivar) and HN60 (dwarf cultivar), in the growing seasons of 2017 and 2018. Four treatments included natural lighting, shading of the apical meristem, covering of all internodes with aluminium foil, and whole-plant shading with plastic shading nets. When the number of internodes (N) on the main stem was >3, internode N began to elongate. Internode N – 1 exhibited the most rapid elongation, and internode N – 2 elongated slowly. Internode N – 3 stopped elongating, but the increase in internode diameter did not cease as internode elongation stopped. Shading the soybean apical meristem, the stem, and the whole plant all led to internode elongation. Different shading conditions did not alter the pattern of internode elongation. Soybean stem and apical meristem were both light-sensitive tissues. With an increase in shading, internode length increased, whereas internode diameter decreased. Contents of gibberellic acid (GA3) and salicylic acid in the stem also increased, but abscisic acid content decreased. Shading reduced the size of starch grains but increased the number of osmiophilic granules in the chloroplast. Elevated GA3 level was the main cause of the changes in internode length and diameter induced by shading. These results suggest that reduction in GA3 synthesis and enhancement in carbohydrates formation could a strategy for soybean plants to avoid lodging.
The crustacean lacinia mobilis: a reconsideration of its origin, function and phylogenetic implications

The lacinia mobilis of the Crustacea Malacostraca is a more or less spine-like movable appendage of the medial mandibular edge, inserted near the base of the incisor process. It occurs in two or possibly three eumalacostracan superorders but is retained in the adult stage only in the Peracarida. The lacinia has been interpreted as the distal member of the spine-row found in many adult Malacostraca and/or their larvae, or alternatively as a derivative of a certain cusp (‘cusp b’) of the biting edge of the primitive lophogastrids. The distribution, ontogeny and function of the lacinia were studied in a variety of Eumalacostraca. There is great variability in the guiding and locking mechanisms involved in biting, within the subclass and even within single orders. A lacinia-based guiding and locking system is likely to function only in weak mandibles. New evidence is produced in favour of derivation of the lacinia from the spine-row, and the ‘cusp b’ derivation hypothesis is rejected, ‘cusp b’ being only a highly specialized lacinia. Doubt is cast upon the unity of the superorder Peracarida mainly because the place of the order Amphipoda within it is regarded as insecure.
An integrated study of individualism in Lentinula edodes in nature and its implication for cultivation strategy

A field study was carried out in a remote broadleaved Fagus longipetiolata forest in Shaanxi province, China to study the natural local distribution of Lentinula edodes. Following spatial mapping, 24 fruit bodies were collected for tissue isolation into axenic culture. 24 genets distributed on fallen tree trunks within a distance of 120 m were identified and clustered into 7 groups using the unweighted pair-group method algorithm using data based on colony morphologies, abilities to degrade aromatic poly-R478 dye, somatic incompatibility reaction patterns and DNA fingerprints. Among the parameters used, the somatic incompatibility reaction, a polygenic phenotype, was the most differentiating, identifying 22 incompatible classes. Two sets of fruit bodies of different genets were so close together that they would otherwise have been described as aggregate fruits of presumed identical origin. Eighteen genets found on the same 5.6 m long tree trunk divided roughly into two clusters, matching their spatial distribution, and a nearby branch bore another distinct cluster. More heterogeneity was encountered between isolates the greater the distance separating them on the original site. Genets on the same tree trunk showed more compatible somatic reactions among themselves, and their DNA fingerprints showed higher similarity. Nevertheless, considering the totality of phenotypic characters, each fruit body is a genet in L. edodes. Such features are concluded to result from a reproductive strategy which depends on basidiospore dispersal. Within each cluster of isolates from the collection site genets seemed to have arisen from multiple sib-mating events. Thus, a cluster may represent a lineage of L. edodes. Individualism in L. edodes is based on a strong somatic incompatibility system. Strong competition from contaminating individuals arriving as air-borne basidiospores could explain decreased and fluctuating crop yields which are now frequently observed in later flushes from the outdoor wood log cultivation system. Further, it would also explain why multispore spawn is not favoured in artificial cultivation of this economically important edible mushroom.
Disparities in PM2.5 air pollution in the United States

Cleaner skies Particulate air pollution in the contiguous United States has decreased considerably over recent decades, but where exactly has that progress been made? Colmer et al. analyzed 36 years of data and found that the spatial distribution of fine particulate matter concentrations has remained largely unchanged over that interval (see the Perspective by Ma). Although, fine particulate pollution levels have dropped overall, those areas that were most and least polluted in 1981 remain so today. We may have made important strides in pollution control, but we have been less successful in addressing disparities of exposure between communities. Science, this issue p. 575; see also p. 503 Particulate air pollution in the United States has fallen substantially over the past four decades, but the relative pattern persists. Air pollution at any given time is unequally distributed across locations. Average concentrations of fine particulate matter smaller than 2.5 micrometers in diameter (PM2.5) have fallen over time. However, we do not know how the spatial distribution of PM2.5 has evolved. Here, we provide early evidence. We combine 36 years of PM2.5 concentrations measured over ~8.6 million grid cells with geographic, economic, and demographic data from ~65,000 U.S. census tracts. We show that differences in PM2.5 between more and less polluted areas declined substantially between 1981 and 2016. However, the most polluted census tracts in 1981 remained the most polluted in 2016. The least polluted census tracts in 1981 remained the least polluted in 2016. The most exposed subpopulations in 1981 remained the most exposed in 2016. Overall, absolute disparities have fallen, but relative disparities persist.
Simuliidae (Diptera) of Rendalen, Norway

Eusimulium rendalense n.sp. et E. fallisi n.sp. ont decrit. Les femelles ont ete trouveer se nourrissant sur canards domestiques, Anas boschas L. , exposes sur le fleuve Rena a Rendalen, Norvege, et ils ont ete attrait aux trapp avec CO2 principalement aux habitat aquatique. Ces deux especes sont placee dans un groupe primitif de Eusimulium Roubaud que l'on considere intermediaire entre ce genus et Cnephia Enderlein s.str. Ces deux especes sont les vecteurs naturel du Leucocytozoon simondi Mathis & Leger aux canards en Norvege.