Miracle-dz/UniFAR-FTUs huggingface dataset:
Schistosoma mansoni and Schistosoma haematobium infection and morbidity in a co-endemic focus: Integrated study of epidemiological, micro-geographical and immunological patterns

In Africa, polyparasitism is the rule rather than the exception. The aim of this thesis was to get a detailed insight into the micro-geographical distribution and patterns of S. mansoni and S. haematobium co-infections, and how this affects host morbidity. A community-wide study was carried out in a co-endemic focus in the north of Senegal, combining epidemiological, ecological, immunological, and geographical analyses. This multidisciplinary approach led to several new insights. Spatial analyses showed significant clustering of Schistosoma infection and morbidity even on a micro scale; S. mansoni and S. haematobium hotspots were found in different sections of one community. Another major finding was that the presence of S. mansoni in co-infections might protect against S. haematobium-specific urinary tract morbidity. Furthermore, it was observed that S. haematobium antigens induced stronger cytokine responses than those of S. mansoni, indicating that the first species may be more immunogenic. The results of this thesis provide new leads for further research on disease etiology and underlying mechanisms in Schistosoma co-infections. Such knowledge is key to rationalizing and optimizing current schistosomiasis control strategies in co-endemic areas and to developing successful elimination strategies in the future.
Novel metric for hyperbolic phylogenetic tree embeddings

Advances in experimental technologies such as DNA sequencing have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and immunogenomics. Thus, the importance of phylogenetic methods is increasingly being recognized, and the development of a novel phylogenetic approach can contribute to several areas of research. Recently, the use of hyperbolic geometry has attracted attention in artificial intelligence research. Hyperbolic space can better represent a hierarchical structure compared to Euclidean space, and can therefore be useful for describing and analyzing a phylogenetic tree. In this study, we developed a novel metric that considers the characteristics of a phylogenetic tree for representation in hyperbolic space. We compared the performance of the proposed hyperbolic embeddings, general hyperbolic embeddings, and Euclidean embeddings, and confirmed that our method could be used to more precisely reconstruct evolutionary distance. We also demonstrate that our approach is useful for predicting the nearest-neighbor node in a partial phylogenetic tree with missing nodes. This study highlights the utility of adopting a geometric approach for further advancing the applications of phylogenetic methods. The demo code is attached as a supplementary file in a compiled jupyter notebook. The code used for analyses is available on GitHub at https://github.com/hmatsu1226/HyPhyTree.
State-Dependent Decision-Making by Predators and Its Consequences for Mimicry

The mimicry of one species by another provides one of the most celebrated examples of evolution by natural selection. Edible Batesian mimics deceive predators into believing they may be defended, whereas defended Müllerian mimics have evolved a shared warning signal, more rapidly educating predators to avoid them. However, it may benefit hungry predators to attack defended prey, while the benefits of learning about unfamiliar prey depends on the future value of this information. Previous energetic state-dependent models of predator foraging behavior have assumed complete knowledge, while informational state-dependent models have assumed fixed levels of hunger. Here, we identify the optimal decision rules of predators accounting for both energetic and informational states. We show that the nature of mimicry is qualitatively and quantitatively affected by both sources of state dependence. Associative learning weakens the extent of parasitic mimicry by edible prey because naive predators often attack defended models. More importantly, mimicry among equally highly defended prey may be parasitic or mutualistic depending on the ecological context (e.g., the source of mimics and the abundance of alternative prey). Finally, mimicry by prey with intermediate defenses corresponds to Batesian or Müllerian mimicry depending on whether the mimic is profitable to attack by hungry predators, but it is not a special case of mimicry.
Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review

Chickens display a wide spectrum of phenotypic variations in quantitative traits such as egg-related traits. Quantitative trait locus (QTL) analysis is a statistical method used to understand the relationship between phenotypic (trait measurements) and genotypic data (molecular markers). We have performed QTL analyses for egg-related traits using an original resource population based on the Japanese Large Game (Oh-Shamo) and the White Leghorn breeds of chickens. In this article, we summarize the results of our extensive QTL analyses for 11 and 66 traits for egg production and egg quality, respectively. We reveal that at least 30 QTL regions on 17 different chromosomes affect phenotypic variation in egg-related traits. Each locus had an age-specific effect on traits, and a variety in effects was also apparent, such as additive, dominance, and epistatic-interaction effects. Although genome-wide association study (GWAS) is suitable for gene-level resolution mapping of GWAS loci with additive effects, QTL mapping studies enable us to comprehensively understand genetic control, such as chromosomal regions, genetic contribution to phenotypic variance, mode of inheritance, and age-specificity of both common and rare alleles. QTL analyses also describe the relationship between genotypes and phenotypes in experimental populations. Accumulation of QTL information, including GWAS loci, is also useful for studies of population genomics approached without phenotypic data in order to validate the identified genomic signatures of positive selection. The combination of QTL studies and next-generation sequencing techniques with uncharacterized genetic resources will enhance current understanding of the relationship between genotypes and phenotypes in livestock animals.
Roles of Matrix Mechanics in Regulating Aortic Valve Interstitial Cell Pathological Differentiation

Calcific aortic valve disease (CAVD) is associated with increased presence of myofibroblasts, osteoblastic cells and, occasionally, adipocytes and chondrocytes in lesions. The ectopic cell types in diseased valves may be elaborated by an unidentified multipotent progenitor subpopulation within the valve interstitial cells (VICs) that populate the valve interstitium. Notably, lesions form preferentially in the fibrosa layer, the stiffer layer of the valve leaflet. It has been shown that differentiation of VICs to myofibroblasts and osteoblasts is modulated by matrix stiffness. However, the molecular mechanisms involved in mediating stiffnessdependent mechanotransduction remain obscure. The objectives of this thesis were: (1) to determine whether VICs contain a subpopulation of multipotent mesenchymal progenitor cells and to measure the frequencies of the mesenchymal progenitors and osteoprogenitors; (2) to determine the role of β-catenin and matrix stiffness in transforming growth factor-β1 (TGF-β1)induced myofibroblast differentiation of VICs; and (3) to preliminarily investigate the involvement of four and a half LIM domains protein 2 (FHL2) in CAVD and stiffnessdependent mechanotransduction downstream of RhoA in VICs. Firstly, VICs were found to
Fledging Mass Is Color Morph Specific and Affects Local Recruitment in a Wild Bird

Early-life conditions may have long-lasting effects on life history. In color polymorphic species, morph-specific sensitivity to environmental conditions may lead to differential fitness. In tawny owls (Strix aluco), pheomelanin-based color polymorphism is expected to be maintained because the brown morph has higher adult fitness in warmer environments, while selection favors the gray morph under colder conditions. Here we investigate body mass at fledging and its consequences until adulthood in a population at the species’ cold range margin. Using 40 years of data (1979–2017), we show that brown pairs, which mainly produce brown offspring consistent with a one-locus-two-alleles inheritance model, consistently raised heavier offspring than mixed (gray-brown) pairs and gray pairs. Offspring mass declined seasonally, except among offspring raised by brown pairs. Brown offspring could be heavier because of morph-specific parental care and/or offspring growth. Furthermore, mass at fledging is associated with fitness: the probability of local recruitment into the breeding population increased with higher mass at fledging, especially in mild winters and with favorable food conditions, although recruitment is not morph specific. Fledgling mass thus provides a fitness benefit in terms of recruitment probability that is modulated by environmental factors, which appear to level off any direct morph-specific recruitment benefits.
Flower visitation by European birds offers the first evidence of interaction release in continents

All species are imbedded in a network of interactions with other species, which define an important component of their ecological niche. These interactions are dynamic and can change the emergence of vacant niches in the environment. Niche adjustments have been predicted to be particularly common on insular communities as a response to the poor and disharmonic biota of oceanic island – the interaction release hypothesis, however, the phenomena has not yet been reported on continents. Taxonomic groups of specialized nectarivorous birds are present on all continents except in Europe where they became extinct in the Oligocene, likely leaving behind underexplored flower resources. We performed the first community‐level assessment of flower visitation by European birds to evaluate if insectivorous and granivorous birds show an interaction release towards consuming flower resources in Europe.
Localization of Quantitative Trait Loci for Dryland Characters in Barley by Linkage Mapping

The success of breeding for yield stability in stressful environments has been limited due to the high variability, timing, duration and severity of a number of climatic stresses. In the northwest of Syria, these stresses include cold, terminal drought, and heat occurring during the rainfed barley (Hordeum vulgare L.)-growing season. With the advent of DNA-marker techniques, it has become feasible to develop linkage maps for agricultural crops. Together with statistical procedures, these linkage maps can be used to locate and estimate phenotypic effects of quantitative trait loci (QTL). A genetic linkage map has been developed for recombinant inbred lines of the cross ‘Arta’/Hordeum spontaneum 41-1. A total of 194 recombinant inbred lines randomly chosen from a population of 494 RILs were mapped with 189 markers including one morphological trait (brittle rachis locus). The linkage map extended to 890 cM. Agronomic traits such as grain yield, biological yield, days-to-heading, plant height, cold tolerance, and others were evaluated at the ICARDA’s research stations at Tel Hadya and Breda in the years 1996/1997 and 1997/1998 and QTLs for agronomic traits related to drought resistance were localized. For the most important character “plant height under drought stress”, QTLs on 2H, 3H, and 7H were detected. The “plant height” QTLs, especially the one on 3H, showed pleiotropic effects on traits such as days-to heading, grain yield, and biological yield. Cold tolerance on 5H, days to heading on 7H and 2H, kernel weight on 3H were QTLs identified and localized at similar locations as in other QTL studies. However, for a number of traits QTLs and locations have been described for the first time such as for tillering capacity on 3H, growth habit on 6H and 1H, early growth vigor on 6H. This should allow us to exploit the information for marker-assisted selection of lines better adapted to the Mediterranean drylands.
Twentieth century treeline ecotone advance in the Sudetes Mountains (Central Europe) was induced by agricultural land abandonment rather than climate change

Questions What was the main trigger of treeline ecotone advance – rising temperature or agricultural land abandonment? Were the triggering factors of tree expansion homogeneous or did they differ between upper and lower parts of the treeline ecotone? Location Sudetes Mts. , Central Europe (50° N, 15-17° E). Methods Data were gathered from the treeline ecotone formed by Picea abies at elevations ranging from 1250 to 1490 m. The study area experienced a 1 °C temperature increase over the last 100 yr and termination of cattle grazing and grass mowing in the first half of the 20th century. At 38 plots situated at lower (‘timberline’) and middle or upper (‘treeline’ and ‘outpost treeline’) parts of the treeline ecotone, the age structure of all seed origin P. abies was determined. Changes in tree cover and number of trees over the last 60–70 yr were assessed from aerial imagery. The history of agricultural land use for each plot was compiled. Finally, changes in tree establishment were modelled using climatic variables and land-use intensity. Results We found that tree establishment at treeline had occurred with a 30–40-yr lag after the main establishment peak at timberline. Whereas all treeline plots showed gradual increases in tree cover, timberline tree cover first increased, with some plots then undergoing thinning. Enhanced tree establishment was dependent mainly upon agricultural land abandonment. The effect of land-use changes was more important in the lower than in the upper part of the treeline ecotone. Increasing summer temperatures had a negative influence on seedling establishment in the last few decades. Conclusions Treeline ecotone densification was attributable to agricultural land abandonment across the entire treeline ecotone with the most important effect at timberline. More recently, seedling establishment has been limited by the effects of drought and/or absence of suitable microsites. We documented that one or two establishment pulses over 120 yr, together with enhanced growth since the 1980s, were able to trigger treeline ecotone advance.
Spectrophotometric Methods for the Analysis of Polysaccharide Levels in Winemaking Products

The polysaccharide content in 27 white winemaking samples was examined using two colorimetric methods (phenol and o -hydroxydiphenyl reagents, respectively). Total polysaccharide (TPS), acid polysaccharide (APS), and neutral polysaccharide (NPS) fractions were determined. The advantages of these methods were demonstrated: linearity, precision, accuracy, and selectivity were studied. The levels of TPS, APS, and NPS depended on varietal characteristics, harvest, and winemaking process.
Grazing exclusion unleashes competitive plant responses in Iberian Atlantic mountain grasslands

Questions Does the absence of equalizing mechanisms after cessation of grazing unleash strong aboveground competitors to create large patches in the community? Do these competitive intraspecific aggregations displace and exclude other species, thereby reducing species diversity? Location Atlantic grasslands in the Aralar Natural Park, Basque Country, Northern Iberian Peninsula. Methods Large herbivores were experimentally excluded from three sites (50 m × 50 m exclusion fences) during nine years in a productive semi-natural grassland system with long history of grazing, using adjacent grazed plots as experimental controls. Sampling was carried out by placing systematically one hundred quadrats (0.5 m × 0.5 m) in each of the six plots. Floristic composition and abundance, as well as eight hydrological and chemical soil properties, were measured in each quadrat. The spatial structures created by competitive species were analysed using Redundancy analysis in conjunction with Moran's Eigenvector Maps, and soil variables were simultaneously included in the analyses, thus disentangling the structures likely created by niche effects. Competitive exclusion was further determined using linear regressions between species richness and abundance of competitive species. Results Grazing exclusion unleashed competitive species such as Festuca rubra and Agrostis capillaris, which became dominant in the exclusion plots and created large spatial patches. Furthermore, a negative linear relationship, consistent across exclusion plots, was observed between species richness and abundance of competitive species, indicating that strong aboveground competitors outcompeted other species when herbivores were excluded. However, the outcome of grazing exclusion across sites depended to some extent on local environmental conditions (niche effects). Conclusions This work confirms that the powerful equalizing mechanism of disturbance by herbivores is crucial for species co-existence in productive grasslands. However, important differences observed in environmental effects across sites suggest that, even in highly productive grasslands, plant traits and local environmental characteristics (niche effects) do matter for species co-existence. This article is protected by copyright. All rights reserved.
A Survey of Freshwater Annelids in the Peruvian Amazon, South America

A floating meadow habitat within the Pacaya-Samiria National Reserve (Loreto, Peru, South America) was sampled for annelids during September, 2002 as part of a multidisciplinary effort aimed at documenting aquatic animal fauna in the Peruvian Amazon River basin. Among 447 annelid specimens collected, at least seven species were represented, six of which were leeches (Hirudinea). These included predaceous (i.e., Helobdella sp., Helobdella striata) and sanguivorous (i.e., Haementeria depressa, Haementeria maculata) glossiphoniids, a new Ozobranchid (Bogabdella sp.) and one Semiscolecidae (Semiscolex similis). Only one oligochaete species (Allonais inaequalis) was collected. With few exceptions, annelid specimens were found along the periphery of floating vegetation, within one meter below the waterline.
Semi-automated genome annotation using epigenomic data and Segway

Biochemical techniques measure many individual properties of chromatin along the genome. These properties include DNA accessibility (measured by DNase-seq) and the presence of individual transcription factors and histone modifications (measured by ChIP-seq). Segway is software that transforms multiple datasets on chromatin properties into a single annotation of the genome that a biologist can more easily interpret. This protocol describes how to use Segway to annotate the genome, starting with reads from a ChIP-seq experiment. It includes pre-processing of data, training the Segway model, annotating the genome, assigning biological meanings to labels, and visualizing the annotation in a genome browser.
Complete mitochondrial genome of the Korean torrent catfish Liobagrus andersoni (Siluriformes, amblycipitidae)

Abstract The Korean torrent catfish (Liobagrus andersoni), an endemic species in Korea, is a member of the family Amblycipitidae. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of L. andersoni. The complete mitochondrial genome is 16,514 bp long, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 21 species showed that L. andersoni was clustered with L. marginatoides and L. nigricauda. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution.
E2, an Aquatic Hazard Worldwide

Endocrine disruptors are defined as exogenous agents that alter the function of endocrine system, which in turn, causes adverse health effects in an intact organism or its progeny. Of these compounds, 17Beta-estradiol is of primary importance, since it is physiologically present in both men and women, as well as, being produced synthetically as a component in some pharmaceutical products. Once it reaches the aquatic environment through domestic sewage, ground water and streams, it makes a serious threat to the aquatic life. The review tackles the biological significance of these compounds as well as the danger that they present to the surrounding environment, areas at which these compounds have been detected worldwide, the methods used in detection and fundamentally significant solutions to get rid of this hazard using different methods such as; the bioremediation process.
Gene expression in early Drosophila embryos is highly conserved despite extensive divergence of transcription factor binding

To better characterize how variation in regulatory sequences drives divergence in gene expression, we undertook a systematic study of transcription factor binding and gene expression in the blastoderm embryos of four species that sample much of the diversity in the 60 million-­‐year old genus Drosophila: D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. We compared gene expression, as measured by mRNA-­‐seq to the genome-­‐wide binding of four transcription factors involved in early development, as measured by ChIP-­‐seq (Bicoid, Giant, Hunchback and Krüppel). Surprisingly, we found that mRNA levels are much better conserved than individual binding events. We looked at binding characteristics that may explain such evolutionary disparity. As expected, we found that binding divergence increases with phylogenetic distance. Interestingly, binding events in non-­‐coding regions that were bound strongly by single factors, or bound by multiple factors, were more likely to be conserved. As this class of sites are most likely to be involved in gene regulation, the divergence of other bound regions may simply reflect their lack of function. We used a model of quantitative trait evolution to compare the changes of gene expression with nearby regulatory TF binding. We found that changes in gene expression were poorly explained by changes in associated TF binding. These results suggest that some of the differences in sequence and binding have limited effect on gene expression or act in a compensatory manner to maintain the overall expression levels of regulated genes.