Miracle-dz/UniFAR-FTUs huggingface dataset:
Blood parasitaemia in a high latitude flexible breeder, the white-winged crossbill, Loxia leucoptera: contribution of seasonal relapse versus new inoculations

SUMMARY We measured seasonal changes in the prevalence of haematozoa (Leucocytozoon fringillinarum, Haemoproteus fringillae, and Trypanosoma avium) in free-ranging White-winged Crossbills, Loxia leucoptera, over 1·5 year in Fairbanks, Alaska, USA. This prevalence was low during early winter. L. fringillinarum prevalence increased in late winter/early spring, in the absence of vectors, suggesting relapse of latent infection. By contrast, the prevalence of T. avium and H. fringillae did not increase until mid-spring, coincident with the emergence of putative vectors and suggestive of new inoculations. The winter breeding period was not associated with lower body condition or elevated blood heterophil/lymphocyte ratios than the summer post-breeding period. Thus, birds unlikely perceived their breeding effort as particularly stressful. Adult males in May and June had low plasma testosterone and their blood prevalence of L. fringillinarum, but not other haemoparasites, was higher than in adult females. This difference may have resulted from sex differences in behaviour and/or plumage colouration – bright red in males, dull green/yellow in females. Species in which reproduction and vector abundance are seasonally dissociated may constitute important models for investigating the respective contribution of reproductive hormones, breeding effort, and vector abundance to patent and latent hemoparasitic infections and to new inoculations.
ournal of Statistical Mechanics : J Theory and Experiment

Neural network configurations with random weights play an important role in the analysis of deep learning. They define the initial loss landscape and are closely related to kernel and random feature methods. Despite the fact that these networks are built out of random matrices, the vast and powerful machinery of random matrix theory has so far found limited success in studying them. A main obstacle in this direction is that neural networks are nonlinear, which prevents the straightforward utilization of many of the existing mathematical results. In this work, we open the door for direct applications of random matrix theory to deep learning by demonstrating that the pointwise nonlinearities typically applied in neural networks can be incorporated into a standard method of proof in random matrix theory known as the moments method. The test case for our study is the Gram matrix FF, F = f(WX), where W is a random weight matrix, X is a random data matrix, and f is a pointwise nonlinear activation function. We derive an explicit representation for the trace of the resolvent of this matrix, which defines its limiting spectral distribution. We apply these results to the computation of the asymptotic performance of single-layer random feature networks on a memorization task and to the analysis of the eigenvalues of the data covariance matrix as it propagates through a neural network. As a byproduct of our analysis, we identify an intriguing new class of activation functions with favorable properties.
Tremella fuciformis polysaccharide suppresses hydrogen peroxide-triggered injury of human skin fibroblasts via upregulation of SIRT1

Tremella fuciformis polysaccharide (TFPS), which is the extract of Tremella fuciformis Berk, has previously been demonstrated to exhibit potent anti-oxidative, anti-inflammatory and anti-aging effects. However, the mechanisms underlying these protective and therapeutic effects remain to be elucidated. The aim of the present study was to investigate the protective effects of TFPS on hydrogen peroxide-induced injury of human skin fibroblasts and to elucidate the aforementioned underlying mechanisms. A hydrogen peroxide-induced human skin fibroblast injury model was firstly established. MTT and reactive oxygen species (ROS) production assays, in addition to terminal deoxynucleotidyl transferase dUTP nick end labeling, reverse transcription-quantitative polymerase chain reaction and western blotting, were performed to investigate the protective effects of TFPS. Hydrogen peroxide decreased human skin fibroblast viability with a concurrent increase in ROS generation and cell apoptosis. Treatment with 0–400 µg/ml TFPS alone for up to 48 h did not result in alteration in cell viability. Notably, TFPS pre-treatment reduced oxidative stress and cell apoptosis in hydrogen peroxide-treated skin fibroblasts. In addition, there was profound inhibition of p16, p21, p53 and caspase-3 expression, and activation of extracellular-signal regulated kinase and Akt serine/threonine kinase 1, following TFPS pre-treatment. Furthermore, it was revealed that TFPS additionally protected fibroblasts via the upregulation of SIRT1 expression, and this was abrogated by the SIRT1 inhibitor niacinamide. These results indicated that TFPS alleviated hydrogen peroxide-induced oxidative stress and apoptosis in skin fibroblasts via upregulation of SIRT1 expression, indicating that TFPS may act as a potential therapeutic agent for oxidative-stress-associated skin diseases and aging.
Predictive Score for 30-Day Readmission or Death in Heart Failure.

Readmissions shortly after heart failure (HF) are common, expensive, and usually considered preventable.1 However, despite the use of several interventions, rates of readmission after HF remain stable.2 An effective risk score might permit the targeting of resource-intensive interventions (such as disease-management programs) specifically on high-risk patients. We sought to determine the combination of clinical and nonclinical factors that would have the best discriminatory power in predicting 30-day readmission or death in HF.
The Relationship between Stroop and Stop-Signal Measures of Inhibition in Adolescents: Influences from Variations in Context and Measure Estimation

The Stroop and stop-signal tasks are commonly used to index prepotent response inhibition in studies of cognitive development and individual differences. Inhibitory measures from the two tasks have been derived using a variety of methods. Findings of low inter-correlations amongst these measures have been interpreted as evidence for different kinds of inhibitory functions. Our previous study found Stroop and stop-signal accuracy measures to be uncorrelated and they loaded on different inhibitory components in a principal component analysis. The present study examined whether this finding is replicated across different task contexts, derived measures, and methods of derivation. Adolescents (N = 247) were administered a number-quantity Stroop and word and number stop-signal tasks. For each stop-signal task, inhibitory efficiency was estimated using a stop-signal reaction time measure estimated with the central versus the integration methods. For the Stroop interference task, inhibitory efficiency was indexed by reaction time measures (including inverse efficiency scores) generated from difference scores and regression residuals, and delta-plot slopes. The reaction time measures from the two tasks were generally not correlated. The only exception was that Stroop inhibitory ability, indexed by Stroop errors, was related to stop-signal inhibitory efficiency, indexed by stop-signal reaction time. These findings are consistent with previous findings suggesting that measures from the Stroop and stop-signal tasks are influenced by different underlying processes. The impact of variations in dependent measure derivation on the resulting reliabilities of Stroop and stop-signal measures and on observed correlations between them were examined. Variables that may have contributed to the null findings are discussed.
Functional Traits Help Predict Post-Disturbance Demography of Tropical Trees

How tropical tree species respond to disturbance is a central issue of forest ecology, conservation and resource management. We define a hierarchical model to investigate how functional traits measured in control plots relate to the population change rate and to demographic rates for recruitment and mortality after disturbance by logging operations. Population change and demographic rates were quantified on a 12-year period after disturbance and related to seven functional traits measured in control plots. The model was calibrated using a Bayesian Network approach on 53 species surveyed in permanent forest plots (37.5 ha) at Paracou in French Guiana. The network analysis allowed us to highlight both direct and indirect relationships among predictive variables. Overall, 89% of interspecific variability in the population change rate after disturbance were explained by the two demographic rates, the recruitment rate being the most explicative variable. Three direct drivers explained 45% of the variability in recruitment rates, including leaf phosphorus concentration, with a positive effect, and seed size and wood density with negative effects. Mortality rates were explained by interspecific variability in maximum diameter only (25%). Wood density, leaf nitrogen concentration, maximum diameter and seed size were not explained by variables in the analysis and thus appear as independent drivers of post-disturbance demography. Relationships between functional traits and demographic parameters were consistent with results found in undisturbed forests. Functional traits measured in control conditions can thus help predict the fate of tropical tree species after disturbance. Indirect relationships also suggest how different processes interact to mediate species demographic response.
Ambient Air Quality Status in Uttarakhand (India): A Case Study of Haridwar And Dehradun Using Air Quality Index

This paper examines the significant differences in seasonal variations of air pollutants concentrations at urban, industrial, commercial and agricultural areas of Uttarakhand. PM10 (RSPM), suspended particulate matter (SPM), sulphur dioxide (SO2) and oxides of nitrogen (NOx) were collected over four sites in Haridwar and Dehradun Valley, Uttarakhand. The first one, Shivalik Nagar, Haridwar is an urban area. The second site SIDCUL, which is one of the most industrial areas of Haridwar. The third site is famous Clock Tower of Dehradun Valley, one of the busiest commercial centres. The fourth site was an agricultural area where pollution level was very low, considered as a control site. The present study deals with the effect of industrialization, urbanization and automobile emission on ambient air quality in Haridwar and Dehradun City. Meteorological parameters like temperature, relative humidity, wind speed and rainfall were also recorded simultaneously during the sampling period. Monthly and seasonal variation of these pollutants have been observed and recorded. The annual average and range values have also been calculated. It has been observed that the concentrations of the pollutants are high in winter in comparison to the summer or the monsoon seasons. In the present study, it was noticed that the SPM and PM10 levels at all selected sites (excluding Roshnabad) exceeds the prescribed limits as stipulated by Central Pollution Control Board (CPCB) New Delhi, India. Apart from this the SO2 and NOx levels in residential, industrial and commercial areas remain under prescribed limits of CPCB. (Journal of American Science 2010; 6(9):565-574). (ISSN: 1545-1003).
Cross-Scale Interactions and the Distribution-Abundance Relationship

Positive interspecific relationships between local abundance and extent of regional distribution are among the most ubiquitous patterns in ecology. Although multiple hypotheses have been proposed, the mechanisms underlying distribution-abundance (d-a) relationships remain poorly understood. We examined the intra- and interspecific distribution-abundance relationships for a metacommunity of 13 amphibian species sampled for 15 consecutive years. Mean density of larvae in occupied ponds was positively related to number of ponds occupied by species; employing the fraction of ponds uniquely available to each species this same relationship sharply decelerates. The latter relationship suggested that more abundant species inhabited most available habitats annually, whereas rarer species were dispersal limited. We inferred the mechanisms responsible for this pattern based on the dynamics of one species, Pseudacris triseriata, which transitioned between a rare, narrowly distributed species to a common, widely distributed species and then back again. Both transitions were presaged by marked changes in mean local densities driven by climatic effects on habitat quality. We identified threshold densities separating these population regime shifts that differed with landscape configuration. Our data suggest that these transitions were caused by strong cross-scale interactions between local resource/niche processes and larger scale metapopulation processes. The patterns we observed have relevance for understanding the mechanisms of interspecific d-a relationships and critical thresholds associated with habitat fragmentation.
Effects of Sublethal Doses of Imidacloprid on Young Adult Honeybee Behaviour

Imidacloprid (IMI), a neonicotinoid used for its high selective toxicity to insects, is one of the most commonly used pesticides. However, its effect on beneficial insects such as the honeybee Apis mellifera L is still controversial. As young adult workers perform in-hive duties that are crucial for colony maintenance and survival, we aimed to assess the effect of sublethal IMI doses on honeybee behaviour during this period. Also, because this insecticide acts as a cholinergic-nicotinic agonist and these pathways take part in insect learning and memory processes; we used IMI to assess their role and the changes they suffer along early adulthood. We focused on appetitive behaviours based on the proboscis extension response. Laboratory reared adults of 2 to 10 days of age were exposed to sublethal IMI doses (0.25 or 0.50ng) administered orally or topically prior to behavioural assessment. Modification of gustatory responsiveness and impairment of learning and memory were found as a result of IMI exposure. These outcomes differed depending on age of evaluation, type of exposure and IMI dose, being the youngest bees more sensitive and the highest oral dose more toxic. Altogether, these results imply that IMI administered at levels found in agroecosystems can reduce sensitivity to reward and impair associative learning in young honeybees. Therefore, once a nectar inflow with IMI traces is distributed within the hive, it could impair in-door duties with negative consequences on colony performance.
Fractography Observing Measuring And Interpreting Fracture Surface Topography

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Identifying Differences in Early Literacy Skills Across Subgroups of Language-Minority Children: A Latent Profile Analysis

Despite acknowledgment that language-minority children come from a wide variety of home language backgrounds and have a wide range of proficiency in their first (L1) and second (L2) languages, it is unknown whether differences across language-minority children in relative and absolute levels of proficiency in L1 and L2 predict subsequent development of literacy-related skills. The purpose of this study was to identify subgroups of language-minority children and evaluate whether differences in level and rate of growth of early literacy skills differed across subgroups. Five-hundred and twenty-six children completed measures of Spanish and English language and early literacy skills at the beginning, middle, and end of the preschool year. Latent growth models indicated that children’s early literacy skills were increasing over the course of the preschool year. Latent profile analysis indicated that language-minority children could be classified into nine distinct groups, each with unique patterns of absolute and relative levels of proficiency in L1 and L2. Results of three-step mixture models indicated that profiles were closely associated with level of early literacy skills at the beginning of the preschool year. Initial level of early literacy skills was positively associated with growth in code-related skills (i.e., print knowledge, phonological awareness) and inversely associated with growth in language skills. These findings suggest that language-minority children are a diverse group with regard to their L1 and L2 proficiencies and that growth in early literacy skills is most associated with level of proficiency in the same language.
Douglas-Fir Seedlings Exhibit Metabolic Responses to Increased Temperature and Atmospheric Drought

In the future, periods of strongly increased temperature in concert with drought (heat waves) will have potentially detrimental effects on trees and forests in Central Europe. Norway spruce might be at risk in the future climate of Central Europe. However, Douglas-fir is often discussed as an alternative for the drought and heat sensitive Norway spruce, because some provenances are considered to be well adapted to drier and warmer conditions. In this study, we identified the physiological and growth responses of seedlings from two different Douglas-fir provenances to increased temperature and atmospheric drought during a period of 92 days. We analysed (i) plant biomass, (ii) carbon stable isotope composition as an indicator for time integrated intrinsic water use efficiency, (iii) apparent respiratory carbon isotope fractionation as well as (iv) the profile of polar low molecular metabolites. Plant biomass was only slightly affected by increased temperatures and atmospheric drought but the more negative apparent respiratory fractionation indicated a temperature-dependent decrease in the commitment of substrate to the tricarboxylic acid cycle. The metabolite profile revealed that the simulated heat wave induced a switch in stress protecting compounds from proline to polyols. We conclude that metabolic acclimation successfully contributes to maintain functioning and physiological activity in seedlings of both Douglas-fir provenances under conditions that are expected during heat waves (i.e. elevated temperatures and atmospheric drought). Douglas-fir might be a potentially important tree species for forestry in Central Europe under changing climatic conditions.
Mixotrophy in the Phototrophic Harmful Alga Cochlodinium polykrikoides (Dinophycean): Prey Species, the Effects of Prey Concentration, and Grazing Impact

Abstract We first reported here that the harmful alga Cochlodinium polykrikoides, which had been previously known as an autotrophic dinoflagellate, was a mixotrophic species. We investigated the kinds of prey species and the effects of the prey concentration on the growth and ingestion rates of C. polykrikoides when feeding on an unidentified cryptophyte species (Equivalent Spherical Diameter, ESD = 5.6 μm). We also calculated grazing coefficients by combining field data on abundances of C. polykrikoides and co-occurring cryptophytes with laboratory data on ingestion rates obtained in the present study. Cocholdinium polykrikoides fed on prey cells by engulfing the prey through the sulcus. Among the phytoplankton prey offered, C. polykrikoides ingested small phytoplankton species that had ESD's ≤ 11 μm (e.g. the prymnesiophyte Isochrysis galbana, an unidentified cryptophyte, the cryptophyte Rhodomonas salina, the raphidophyte Heterosigma akashiwo, and the dinoflagellate Amphidinium carterae). It did not feed on larger phytoplankton species that had ESD's ≥ 12 μm (e.g. the dinoflagellates Heterocapsa triquetra, Prorocentrum minimum, Scrippsiella sp., Alexandrium tamarense, Prorocentrum micans, Gymnodinium catenatum, Akashiwo sanguinea, and Lingulodinium polyedrum). Specific growth rates of C. polykrikoides on a cryptophyte increased with increasing mean prey concentration, with saturation at a mean prey concentration of approximately 270 ng C ml−1 (i.e. 15,900 cells ml−1). The maximum specific growth rate (mixotrophic growth) of C. polykrikoides on a cryptophyte was 0.324 d−1, under a 14:10 h light-dark cycle of 50 μE m−2 s−1, while its growth rate (phototrophic growth) under the same light conditions without added prey was 0.166 d−1. Maximum ingestion and clearance rates of C. polykrikoides on a cryptophyte were 0.16 ng C grazer−1d−1 (9.4 cells grazer−1d−1) and 0.33 μl grazer−1h−1, respectively. Calculated grazing coefficients by C. polykrikoides on cryptophytes were 0.001–0.745 h−1 (i.e. 0.1–53% of cryptophyte populations were removed by a C. polykrikoides population in 1 h). The results of the present study suggest that C. polykrikoides sometimes has a considerable grazing impact on populations of cryptophytes.
The Time-Scale of Recombination Rate Evolution in Great Apes

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequencing data of 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez et al. 2013). Using species-specific PRDM9 sequences to predict potential binding sites, we identified an important role for PRDM9 in predicting recombination rate variation broadly across great apes. Our results are contrary to previous research that PRDM9 is not associated with recombination in western chimpanzees (Auton et al. 2012). Additionally, we show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time-scale of complete hotspot turnover. We quantified the variation in the biased distribution of recombination rates towards recombination hotspots across great apes. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, based on multiple linear regression analysis, we found that various correlates of recombination rate persist throughout primates including repeats, diversity, divergence and local effective population size (Ne). Our study is the first to analyze within-and between-species genome-wide recombination rate variation in several close relatives.