Miracle-dz/UniFAR-FTUs huggingface dataset:
IgM Antibody Repertoire Fingerprints in Mice Are Personalized but Robust to Viral Infection Status

Antibody repertoire sequencing provides a molecular fingerprint of current and past pathogens encountered by the immune system. Most repertoire studies in humans require measuring the B cell response in the blood, resulting in a large bias to the IgM isotype. The extent to which the circulating IgM antibody repertoire correlates to lymphoid tissue-resident B cells in the setting of viral infection remains largely uncharacterized. Therefore, we compared the IgM repertoires from both blood and bone marrow (BM) plasma cells (PCs) following acute or chronic lymphocytic choriomeningitis virus (LCMV) infection in mice. Despite previously reported serum alterations between acute and chronic infection, IgM repertoire signatures based on clonal diversity metrics, public clones, network, and phylogenetic analysis were largely unable to distinguish infection cohorts. Our findings, however, revealed mouse-specific repertoire fingerprints between the blood and PC repertoires irrespective of infection status.
A Cost Reduced Variant of Epi-Genotyping by Sequencing for Studying DNA Methylation in Non-model Organisms

Reference-free reduced representation bisulfite sequencing uses enzymatic digestion for reducing genome complexity and allows detection of markers to study DNA methylation of a high number of individuals in natural populations of non-model organisms. Current methods like epiGBS enquire the use of a higher number of methylated DNA oligos with a significant cost (especially for small labs and first pilot studies). In this paper, we present a modification of this epiGBS protocol that requires the use of only one hemimethylated P2 (common) adapter, which is combined with unmethylated barcoded adapters. The unmethylated cytosines of one chain of the barcoded adapter are replaced by methylated cytosines using nick translation with methylated cytosines in dNTP solution. The basic version of our technique uses only one restriction enzyme, and as a result, genomic fragments are integrated into two orientations with respect to the adapter sequences. Comparing the sequences of two chain orientations makes it possible to reconstruct the original sequence before bisulfite treatment with the help of standard software and newly developed software written in C and described here. We provide a proof of concept via data obtained from almond (Prunus dulcis). Example data and a detailed description of the complete software pipeline starting from the raw reads up until the final differentially methylated cytosines are given in Supplementary Material making this technique accessible to non-expert computer users. The adapter design showed in this paper should allow the use of a two restriction enzyme approach with minor changes in software parameters.
Region-Wide Annual Glacier Surface Mass Balance for the European Alps From 2000 to 2016

Studying glacier mass changes at regional scale provides critical insights into the impact of climate change on glacierized regions, but is impractical using in situ estimates alone due to logistical and human constraints. We present annual mass-balance time series for 239 glaciers in the European Alps, using optical satellite images for the period of 2000 to 2016. Our approach, called the SLA-method, is based on the estimation of the glacier snowline altitude (SLA) for each year combined with the geodetic mass balance over the study period to derive the annual mass balance. In situ annual mass-balances from 23 glaciers were used to validate our approach and underline its robustness to generate annual mass-balance time series. Such temporally-resolved observations provide a unique potential to investigate the behavior of glaciers in regions where few or no data are available. At the European Alps scale, our geodetic estimate was performed for 361 glaciers (75% of the glacierized area) and indicates a mean annual mass loss of −0.74 ± 0.20 m w.e. yr–1 from 2000 to 2016. The spatial variability in the average glacier mass loss is significantly correlated to three morpho-topographic variables (mean glacier slope, median, and maximum altitudes), altogether explaining 36% of the observed variance. Comparing the mass losses from in situ and SLA-method estimates and taking into account the glacier slope and maximum elevation, we show that steeper glaciers and glaciers with higher maximum elevation experienced less mass loss. Because steeper glaciers (>20°) are poorly represented by in situ estimates, we suggest that region-wide extrapolation of field measurements could be improved by including a morpho-topographic dependency. The analysis of the annual mass changes with regard to a global atmospheric dataset (ERA5) showed that: (i) extreme climate events are registered by all glaciers across the European Alps, and we identified opposite weather regimes favorable or detrimental to the mass change; (ii) the interannual variability of glacier mass balances in the “central European Alps” is lower; and (iii) current strong imbalance of glaciers in the European Alps is likely mainly the consequence of the multi-decadal increasing trend in atmospheric temperature, clearly documented from ERA5 data.
Should I Stay or Should I Go? The Role of Motivational Climate and Work–Home Spillover for Turnover Intentions

Emerging trends in the workforce point to the necessity of facilitating work lives that foster constructive and balanced relationships between professional and private spheres in order to retain employees. Drawing on the conservation of resources theory, we propose that motivational climate influences turnover intention through the facilitation of work–home spillover. Specifically, we argue that employees working in a perceived mastery climate are less likely to consider voluntarily leaving their employer because of increased positive–and reduced negative—work–home spillover experiences. We further argue that employees working in a perceived performance climate are more likely to consider voluntarily leaving their employer because of reduced positive—and increased negative—work–home spillover experiences. In a cross—lagged survey of 1074 employees in a Norwegian financial-sector organization, we found that work–home spillover partly mediates the relationship between a perceived motivational climate and turnover intention. Specifically, mastery climates seem to facilitate positive—and reduce negative—spillover between the professional and private spheres, which in turn decreases employees’ turnover intention. Contrary to our expectations, a perceived performance climate slightly increased both positive and negative work-home spillover, however increasing employees’ turnover intention. We discuss implications for practice and future research.
Free Amino Acids in Human Milk: A Potential Role for Glutamine and Glutamate in the Protection Against Neonatal Allergies and Infections

Breastfeeding is indicated to support neonatal immune development and to protect against neonatal infections and allergies. Human milk composition is widely studied in relation to these unique abilities, which has led to the identification of various immunomodulating components in human milk, including various bioactive proteins. In addition to proteins, human milk contains free amino acids (FAAs), which have not been well-studied. Of those, the FAAs glutamate and glutamine are by far the most abundant. Levels of these FAAs in human milk sharply increase during the first months of lactation, in contrast to most other FAAs. These unique dynamics are globally consistent, suggesting that their levels in human milk are tightly regulated throughout lactation and, consequently, that they might have specific roles in the developing neonate. Interestingly, free glutamine and glutamate are reported to exhibit immunomodulating capacities, indicating that these FAAs could contribute to neonatal immune development and to the unique protective effects of breastfeeding. This review describes the current understanding of the FAA composition in human milk. Moreover, it provides an overview of the effects of free glutamine and glutamate on immune parameters relevant for allergic sensitization and infections in early life. The data reviewed provide rationale to study the role of free glutamine and glutamate in human milk in the protection against neonatal allergies and infections.
Effect of Within-Herd Variance and Herd Mean Production on Response to Selection Within Herd

Abstract Lactation records of 1,032,438 Jersey and 1,490,909 Holstein cows on official DHI test from 20,380 and 33,858 herd-years, respectively, were used to compute herd-year means and within-herd-year standard deviations for mature equivalent fat percent, fat, and milk. Within-herd-year means and standard deviations were used to stratify records into five classes for each trait. Regressions of individual daughter's modified contemporary deviation on sire's PD were calculated for each of the 25 subclass combinations of within-herd-year mean and standard deviation. For milk and fat yield, low-low and high-high mean-variance subclasses contained more herd-years than low-high and high-low mean-variance subclasses. This was less evident for fat percent. Regression coefficients ranged from . 66 to 1.41, . 69 to 1.41, and . 78 to 1.34 for fat percent, fat, and milk, respectively, for both breeds. Estimates of regressions indicated that coefficients increased with increases in within-herd-year variance but were nearly constant across herd-year means.
Highly Efficient Regioselective Decanoylation of Hyperoside Using Nanobiocatalyst of Fe3O4@PDA-Thermomyces lanuginosus Lipase: Insights of Kinetics and Stability Evaluation

The immobilization of Thermomyces lanuginosus lipase on polydopamine-functionalized Fe3O4 magnetic nanoparticles (Fe3O4@PDA-TLL) as a nanobiocatalyst was successfully performed for the first time, and the Fe3O4@PDA-TLL was used for regioselective acylation of natural hyperoside with vinyl decanoate. The effects of several crucial factors, such as the reaction solvent, substrate molar ratio, temperature, and immobilized enzyme dosage, were investigated. Under optimum conditions, the reaction rate, 6″-regioselectivity, and maximum substrate conversion were as high as 12.6 mM/h, 100%, and 100%, respectively. An operational stability study demonstrated that the immobilized enzyme could maintain 90.1% of its initial maximum conversion even after reusing it five times. In addition, further investigations on the kinetic parameters, like Vmax, Km, Vmax/Km, and Ea, also revealed that the biocompatible Fe3O4@PDA could act as an alternative carrier for the immobilization of different enzymes.
Methods of age determination in Grey squirrels (Sciurus carolinensis) in Britain

Using X-ray and lens weight techniques on wild and known age captive animals age criteria have been established for Grey squirrels in Britain. Adults have fused epiphyses of the radius and ulna and a paired dried lens weight above 76.0 mg. The longevity of Grey squirrels in Britain is considered. Comparisons with similar data from the USA are made.
Estimativa indireta de teores de licopeno em frutos de genótipos de tomateiro via análise colorimétrica

Indirect estimation of lycopene concentration in fruits of tomato genotypes via chromaticity values Lycopene (C 40 H 56 ) is a red carotenoid pigment, which naturally accumulates in flowers, fruits and roots of some vegetable and fruit crops. The unique properties of the lycopene molecule make this pigment one of the most powerful antioxidants available. Tomato (Lycopersicon esculentum Mill.) fruits and processed tomato products are the main sources of lycopene in the human diet. There is a growing amount of experimental data indicating that lycopene intake is associated with decreased risk of many types of degenerative and cardiovascular diseases as well as cancers in humans. In addition, lycopene concentration is associated with improved visual perception of tomato products. Therefore, there is a strong demand to increase the total amount of lycopene in tomato cultivars for either fresh market or processing. The development of cultivars for improved lycopene content is dependent upon the availability of simple yet accurate methodologies to quantify this carotene in tomato fruits and processed tomato products. The main objective of this work was to estimate the degree of correlation between the total lycopene content in tomato fruits measured spectrophotometrically and the chromaticity values (L*, a* and b*) obtained using a tristimulus colorimeter. Colorimetric readings were taken using three sampling strategies: (1) external fruit wall; (2) internal fruit wall and (3) the whole homogenized fruit pulp. For the achromatic component L* (relative darkness or lightness), the obtained R 2 range from 0.86 to 0.91), with these correlation values being consistently higher when the chromaticity readings were taken in whole homogenized fruit pulp. These results confirmed the feasibility of obtaining precise indirect estimation of lycopene content from chromaticity readings. The methodology described here could be useful for large scale selection of tomato lines with improved levels of lycopene without of high costs and of residue disposal problems associated with the employment of organic solvents in the standard spectrophotometric methods.
Cannibals and parasites: conflicting regulators of bimodality in high latitude Arctic char, Salvelinus alpinus

Unexploited populations of Arctic char (Salvelinus alpinus) sampled in autonomous lake ecosystems in northern Svalbard demonstrate extraordinary catch curves with age and size frequency distributions characterized by discrete bimodality. Analyses of size-age relationship, summer diet and food-related intestinal parasite intensities of modal char groups revealed a pattern of discrete ontogenetic niche shifts. Life-history changes at age 10-15 and size 200-300 mm/50-300 g involved shifting from an initial mode of small-sized, slow-growing and sexually mature individuals feeding on micro-crustaceans and aquatic insects (Chironomidae, Trichoptera), to a terminal mode of large-sized and fast-growing cannibals. Cannibalism, however, was found to result in accumulation of cestodan parasites, of which Diphyllobothrium ditremum increases age-related mortality rates and may be lethal at 1500-2000 plerocercoids. Genetically allopatric populations with cannibalism demonstrated a female-biased sex ratio, primarily in the initial mode, suggesting sexual asynchrony in their ontogeny. By contrast, a small population of large-sized, non-cannibalistic Arctic char feeding exclusively on the large amphipod Gammaracanthus lacustris, demonstrated unimodal size and age frequency distribution, faster growth, an excess of males and lower parasite burden. Seasonal prey shortage and slow juvenile growth in association with fitness components favoring large body size is a suggested mechanism for inducing cannibalism. Although not the basic cause of bimodality as such, it is concluded that ontogenetic niche shift by cannibalism reinforces discrete age modal divergence resulting in the numerical preponderance of large-sized individuals in these marginal char populations. Cannibalism is thus considered an important strategy for survival of landlocked Arctic char in the High Arctic. As a conflicting cost to the more efficient use of available energy by larger individuals, the accumulation of cestodan parasites in cannibals, however, will reduce the survival rate of old individuals and accelerate their termination within this modal group.
Comparison of Decision Modeling Approaches for Health Technology and Policy Evaluation

We discuss tradeoffs and errors associated with approaches to modeling health economic decisions. Through an application in pharmacogenomic (PGx) testing to guide drug selection for individuals with a genetic variant, we assessed model accuracy, optimal decisions, and computation time for an identical decision scenario modeled 4 ways: using 1) coupled-time differential equations (DEQ), 2) a cohort-based discrete-time state transition model (MARKOV), 3) an individual discrete-time state transition microsimulation model (MICROSIM), and 4) discrete event simulation (DES). Relative to DEQ, the net monetary benefit for PGx testing (v. a reference strategy of no testing) based on MARKOV with rate-to-probability conversions using commonly used formulas resulted in different optimal decisions. MARKOV was nearly identical to DEQ when transition probabilities were embedded using a transition intensity matrix. Among stochastic models, DES model outputs converged to DEQ with substantially fewer simulated patients (1 million) v. MICROSIM (1 billion). Overall, properly embedded Markov models provided the most favorable mix of accuracy and runtime but introduced additional complexity for calculating cost and quality-adjusted life year outcomes due to the inclusion of “jumpover” states after proper embedding of transition probabilities. Among stochastic models, DES offered the most favorable mix of accuracy, reliability, and speed.
A unified evaluation framework for head motion prediction methods in 360° videos

The streaming transmissions of 360° videos is a major challenge for the development of Virtual Reality, and require a reliable head motion predictor to identify which region of the sphere to send in high quality and save data rate. Different head motion predictors have been proposed recently. Some of these works have similar evaluation metrics or even share the same dataset, however, none of them compare with each other. In this article we introduce an open software that enables to evaluate heterogeneous head motion prediction methods on various common grounds. The goal is to ease the development of new head/eye motion prediction methods. We first propose an algorithm to create a uniform data structure from each of the datasets. We also provide the description of the algorithms used to compute the saliency maps either estimated from the raw video content or from the users' statistics. We exemplify how to run existing approaches on customizable settings, and finally present the targeted usage of our open framework: how to train and evaluate a new prediction method, and compare it with existing approaches and baselines in common settings. The entire material (code, datasets, neural network weights and documentation) is publicly available.
UVG dataset: 50/120fps 4K sequences for video codec analysis and development

This paper provides an overview of our open Ultra Video Group (UVG) dataset that is composed of 16 versatile 4K (3840×2160) test video sequences. These natural sequences were captured either at 50 or 120 frames per second (fps) and stored online in raw 8-bit and 10-bit 4:2:0 YUV formats. The dataset is published on our website (ultravideo.cs.tut.fi) under a non-commercial Creative Commons BY-NC license. In this paper, all UVG sequences are described in detail and characterized by their spatial and temporal perceptual information, rate-distortion behavior, and coding complexity with the latest HEVC/H.265 and VVC/H.266 reference video codecs. The proposed dataset is the first to provide complementary 4K sequences up to 120 fps and is therefore particularly valuable for cutting-edge multimedia applications. Our evaluations also show that it comprehensively complements the existing 4K test set in VVC standardization, so we recommend including it in subjective and objective quality assessments of next-generation VVC codecs.
Prolyl Oligopeptidase From Leishmania infantum: Biochemical Characterization and Involvement in Macrophage Infection

Leishmania infantum is a flagellated protozoan and one of the main causative agents of visceral leishmaniasis. This disease usually affects the human reticuloendothelial system, can cause death and available therapies may lead to serious side effects. Since it is a neglected tropical disease, the incentives for the development of new drugs are insufficient. It is important to know Leishmania virulence factors that contribute most to the disease in order to develop drugs. In the present work, we have produced L. infantum prolyl oligopeptidase (rPOPLi) in Escherichia coli, and investigated its biochemical properties as well as the effect of POP inhibitors on its enzymatic activity and on the inhibition of the macrophage infection by L. infantum. The optimal activity occurred at pH 7.5 and 37°C in the presence of DTT, the latter increased rPOPLi catalytic efficiency 5-fold on the substrate N-Suc-Gly-Pro-Leu-Gly-Pro-AMC. The enzyme was inhibited by TPCK, TLCK and by two POP specific inhibitors, Z-Pro-prolinal (ZPP, IC50 4.2 nM) and S17092 (IC50 3.5 nM). Besides being a cytoplasmic enzyme, POPLi is also found in punctuate structures within the parasite cytoplasm or associated with the parasite plasma membrane in amastigotes and promastigotes, respectively. Interestingly, S17092 and ZPP prevented parasite invasion in murine macrophages, supporting the involvement of POPLi in the invasive process of L. infantum. These data suggest POPLi as a virulence factor that offers potential as a target for designing new antileishmanial drugs.
Preparation and Characterization of Chitin and Chitosan—A Review

Various procedures for preparation of the biopolymers chitin and chitosan have been developed over the years. Preparation methodology and analysis of physicochemical properties of these biopolymers are reviewed in terms of crustacean species and diverse characterization methodology. Such properties influence biopolymer functionality differing with crustacean species and preparation methods. Monitoring of the relationship between process conditions and chitin/chitosan products is needed to insure uniformity and proper product quality control. Research with chitosan derived from crawfish processing operations indicates the need for a more integrated approach for total resource utilization. Examples of value-added processing by-products, coupled with chitosan recovery, are noted.
Automated and partially-automated contact tracing: a rapid systematic review to inform the control of COVID-19

Background Automated or partially-automated contact tracing tools are being deployed by many countries to contain SARS-CoV-2; however, the evidence base for their use is not well-established. Methods We undertook a rapid systematic review of automated or partially-automated contact tracing, registered with PROSPERO (CRD42020179822). We searched PubMed, EMBASE, OVID Global Health, EBSCO COVID Portal, Cochrane Library, medRxiv, bioRxiv, arXiv and Google Advanced for articles relevant to COVID-19, SARS, MERS, influenza or Ebola from 1/1/2000-14/4/2020. Two authors reviewed all full-text manuscripts. One reviewer extracted data using a pre-piloted form; a second independently verified extracted data. Primary outcomes were the number or proportion of contacts (and/or subsequent cases) identified; secondary outcomes were indicators of outbreak control, app/tool uptake, resource use, cost-effectiveness and lessons learnt. The Effective Public Health Practice Project tool or CHEERS checklist were used in quality assessment. Findings 4,033 citations were identified and 15 were included. No empirical evidence of automated contact tracing's effectiveness (regarding contacts identified or transmission reduction) was identified. Four of seven included modelling studies suggested that controlling COVID-19 requires high population uptake of automated contact-tracing apps (estimates from 56% to 95%), typically alongside other control measures. Studies of partially-automated contact tracing generally reported more complete contact identification and follow-up, and greater intervention timeliness (0.5-5 hours faster), than previous systems. No meta-analyses were possible. Interpretation Automated contact tracing has potential to reduce transmission with sufficient population uptake and usage. However, there is an urgent need for well-designed prospective evaluations as no studies provided empirical evidence of its effectiveness.