Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of moisture stress tolerance indices for the selection of fenugreek (Trigonella foenum-graecum L.) genotypes

Drought and moisture stress is the most limiting factor affecting growth and productivity of crop plants. In order to study the effect of moisture stress, forty eight genotypes of fenugreek were planted in RBD with three replications under two environmental conditions namely, (i) normal irrigation (E1) and (ii) staggered irrigation (E2) during rabi 2016-2017. Eight stress tolerance indices viz., stress tolerance (TOL), stress susceptibility index (SSI), stress tolerance index (STI), mean production (MP), geometric mean production (GMP), yield index (YI), stress susceptibility percentage index (SSPI) and modified stress tolerance index (MSTI) were calculated based on seed yield under moisture stress (Ys) and non-stress condition (Yp). The seed yield under non-stress condition (Yp) had significant positive association with TOL, SSI, STI, MP, GMP, SSPI and K1STI. The seed yield under stress condition (Ys) had significant positive association with STI, MP, GMP, YI and K2STI, while significant negative association with TOL, SSI and SSPI. The results showed that MP, GMP and STI indices were more effective in identifying high yielding genotypes in both stress and non-stress conditions while TOL, SSI, YI and SSPI under moisture stress condition. Based upon the mean seed yield and stress tolerance indices, the genotypes UM-124, UM-60, UM-55, UM-28 and UM-4 were found tolerant to staggered irrigation conditions. Hence, these genotypes may be used further in breeding programmes for moisture stress tolerance.
Refuge size variation and potential for sperm competition in Wellington tree weta

Abstract Ecological variation in resources can influence the distribution and encounter rates of potential mates and competitors and, consequently, the opportunity for sexual selection. Factors that influence the likelihood that females mate multiply could also affect the potential for sperm competition. In Wellington tree weta (Hemideina crassidens, plural “weta”), the size of tree cavities (called galleries) used as refuges affects weta distribution and thus the opportunity for sexual selection and selection on male weaponry size. We examined the predicted effects of gallery size and male weaponry size on the potential for sperm competition. We asked if gallery size influenced the potential for multiple mating by females and potential for sperm competition, if male weaponry size was associated with relative expected sperm competition intensity (SCI), and if estimated male mating success was correlated with potential SCI. To quantify relative competitive environments of males, we created and analyzed networks of potential competitors based on which males could have mated with the same females. We found that small galleries had higher potential for female multiple mating and higher potential for sperm competition. Size of male weaponry was not associated with expected relative SCI. Regardless of gallery size, males with more potential mates were expected to face lower expected relative sperm competition. Thus, in this system, variation in the size of available refuges is likely to influence the potential for sperm competition, in a way that we might expect to increase variation in overall reproductive success.
Reproducible functional connectivity alterations are associated with autism spectrum disorder

Despite the high clinical burden little is known about pathophysiology underlying autism spectrum disorder (ASD). Recent resting state functional magnetic resonance imaging (rs-fMRI) studies have found atypical synchronization of brain activity in ASD. However, no consensus has been reached on the nature and clinical relevance of these alterations. Here we address these questions in the most comprehensive, large-scale effort to date comprising evaluation of four large ASD cohorts. We followed a strict exploration and replication procedure to identify core rs-fMRI functional connectivity (degree centrality) alterations associated with ASD as compared to typically developing (TD) controls (ASD: N=841, TD: N=984). We then tested for associations of these imaging phenotypes with clinical and demographic factors such as age, sex, medication status and clinical symptom severity. We find reproducible patterns of ASD-associated functional hyper- and hypo-connectivity with hypo-connectivity being primarily restricted to sensory-motor regions and hyper-connectivity hubs being predominately located in prefrontal and parietal cortices. We establish shifts in between-network connectivity from outside to within the identified regions as a key driver of these abnormalities. The magnitude of these alterations is linked to core ASD symptoms related to communication and social interaction and is not affected by age, sex or medication status. The identified brain functional alterations provide a reproducible pathophysiological phenotype underlying the diagnosis of ASD reconciling previous divergent findings. The large effect sizes in standardized cohorts and the link to clinical symptoms emphasize the importance of the identified imaging alterations as potential treatment and stratification biomarkers for ASD.
Screening of Aflatoxin B1 in Laboratory Rat Feed

Many hazards can interfere with the safety of the feeding stuffs intended to provide nutrients to experimentalÂ animals. Chemical and biological contaminants of laboratory animal feed can be a problem for toxicologicalÂ and immunological research. Aflatoxin B1 (AFB1) is a secondary toxic metabolite, produced byÂ the ubiquitous fungal genera, Aspergillu s. AFB1 is particularly dangerous for health, inducing cancer of theÂ urinary tract or liver carcinoma. The aim of this preliminary screening was to evaluate the presence of AFB1Â in 31 samples of laboratory rat feed using a method validated in-house, then separated by High PressureÂ Liquid Chromatography (HPLC) coupled to a fluorescence detector. The detection limit (limit of detection:Â LOD) and the quantification limit (LOQ) were 0.2 and 0.4 A¬g/kg respectively. Recoveries ranged from 58. 0Â to 74.5% for spiked samples. The immunoaffinity approach was significantly faster than methods employingÂ conventional chromatography clean-up (Sep-Pak Classic Florisil and Sep-Pak ClassicC18 cartridges). Â Aflatoxins were not detected in any analysed sample. Â
DIMENSÕES DAS FIBRAS E SUA RELAÇÃO COM A IDADE DE TRANSIÇÃO ENTRE LENHO JUVENIL E ADULTO DE Eucalyptus grandis W. Hill ex Maiden

This study was undertaken to evaluate the fiber dimensions and the transition age between juvenile and mature wood of Eucalyptus grandis . It was selected, based on the Assmann’s dominant diameter, four trees of an experimental stand located in the northern coast of Rio Grande do Sul state, with 18 years of age. After cutting down, in the disk corresponding to the region of the DBH (diameter at breast height) were marked and sectioned central baguettes, where crafted fragments were selected at regular intervals in pith-to-bark direction for maceration and, thereafter, determination of the length, the total diameter, the lume diameter and the wall thickness of the fibers with the aid of an optical microscope with a graduated eyepiece. The segregation of both types of wood was determined by the radial variation of the fiber length and using simple and multiple linear regressions; and a transitional age through simple linear regression. The lower values for the dimensions of length, total diameter and wall thickness of the fibers were observed near the pith, with an increasing trend toward the bark, suggesting the existence of differences between wood near the pith and the bark. However, this standard was not observed in the lume diameter of the fibers, which showed an increase to the middle position of the radius followed by a decrease to the outer portion. The transition zone between juvenile and mature wood has been established between the ages of 4.2 and 4.7 up to 8.1 and 9.1 years, range termed juvenile wood that corresponding to 4.2 and 4.7 years; and adult wood exceeding 8.1 and 9.1 years. The transition between adult and juvenile wood occurred at 10 cm from the pith, that is, in the age of about 6.1 years. The definition of the age at which the transition between the juvenile and mature wood occurs facilitates the wood transformation processes once the juvenile portion constitutes an obstacle to the viability of its industrial use.
Biodiversity-ecosystem function relationships change through primary succession

Ecologists traditionally use environmental parameters to predict successional shifts in compositional characteristics of local species assemblages (environmental control). Another important focus in ecology is to understand functional roles of species assemblages in determining local environmental properties (diversity control). Then, the question emerges: which is the cause, and which is the consequence? To clarify the causal relationships between species assemblages and environmental properties, we focused on seral changes in species/functional diversity of vascular plants in tundra ecosystems of the High Arctic. We found that, although species richness was influenced by soil properties in the earlier stages of primary succession, the causalities were reversed in the later stages. We also found functional differentiation among coexisting species in the later stage, suggesting that the 'complementarity effect' of diversity on ecosystem functions likely increased with ecosystem development through time. By contrast, particular species had little disproportional influence on soil properties, suggesting that the 'selection effect' as an alternative mechanism was less important. This result was likely attributed to the importance of facilitation in the marginal High Arctic environment. Plant-microsite associations are shaped by feedback mechanisms and therefore, neither plant nor microsite is a single absolute predictor of the other. Although our observational study has limitations, we demonstrates a possibility that the relative magnitude of the influence of one on the other can change in the process of succession, emphasizing that the causalities underlying biodiversity-ecosystem function relationships change through succession.
Teeth, fossil record and evolutionary history of the cowtail stingray Pastinachus Rüppell, 1829

Abstract Hypolophin ‘dasyatids’ are a common group of large stingrays today frequenting the Indo-Pacific inshores. Being often harvested in their restricted area, few are known about their biology and their evolutionary history despite a very peculiar dental pattern making it easy to track their fossil record. An abundant material consisting of isolated teeth from Late Bartonian (38–40 Ma) lagoonal deposits of Djebel el Kébar, Tunisia, allows to describe a new stingray, Pastinachus kebarensis nov. sp. This taxon represents the oldest occurrence for this genus but also the oldest fossil record for hypolophins. A dental comparison of these fossils with 3D rendered models of fresh specimens testifies that early hypolophin representatives had already a strongly arcuate and bulbous upper jaw, interlocking with a broad and elongated tooth plate on the lower jaw. This new fossil and its fossil relatives (here updated), indicate a pre-Bartonian origination for hypolophins in western Neotethys, and reveal a rapid and widespread colonization of the proto-Mediterranean Sea, western Atlantic and Indo-Pacific coasts during the late Paleogene–early Neogene. Finally, it is worth noting that early hypolophin representatives seemingly entered freshwater habitats occasionally as modern cowtail stingrays do.
EFECTO DE HONGOS MICORRÍCICOS ARBUSCULARES Y EXTRACTO ACUOSO DE VERMICOMPOST SOBRE CALIDAD DE FRESA EFFECT OF ARBUSCULAR MYCORRHIZAL FUNGI AND VERMICOMPOST LIQUID EXTRACT ON QUALITY OF STRABERRY

SUMMARY The application of arbuscular mycorrhizal fungi (AMF) and vermicompost is one of the alternatives to agrochemical protducts, to reach crops yield and quality, reducing costs and environmental damage. In the present study, the effect of applying AMF and vermicompost aquose extract (LV) on strawberry fruit quality, was evaluated. The treatments were: 1) control with water (CTL); 2) fertilized (F); 3) inoculated with AMF (M); 4) with vermicompost aquose extract (LV); 5) inoculated with AMF and fertilized (M+F); 6) fertilized and with vermicompost aquose extract (LV+F); 7) inoculated with AMF, and treated with vermicompost aquose extract (M+LV); 8) inoculated with AMF, fertilized and treated with vermicompost aquose extract (M+F+LV). The evaluated parameters were: color, weight, polar and equatorial diameter, firmness, oBrix, proximal analysis, phenols, flavonoids and anthocyanins contents. LV and M treatments promoted a significant increase of fruit weight (39%) compared to the fertilized treatment. In general, treatments with AMF increased ash except when combined with fertilization. The M treatment caused a significant increase of ash (3.7%) respect to the F treatment. The treatments containing AMF and LV (alone or combined with others) increased fat content in fruits, in comparison with the F treatment. There were no significant effects treatments on fiber content. Fruits from plants treated with LV+F were significantly firmer (20%) than fruits in the F treatment. Fruits in the M+F treatment showed the higher values of °Brix (14% higher than fruits in the F treatment). Interestingly, fruits from the treatments LV and M+F had significantly superior contents of total phenols than fruits from the F treatment (29 and 17% respectively). In general, the treatments containing AMF and LV promoted flavonoides accumulations in fruits. Fruits of the M treatment showed a significantly greater content of this pigments (1.8 times) than fruits of the F treatment. Fruits of the M+VL treatment showed the highest anthocyanins content, being 38% greater than that found in fruits of the F treatment. Results showed that the application of AMF and LV influenced sensorial and nutraceutical fruit quality attributes in strawberry.
Forest Above-Ground Biomass Estimation Using Single-Baseline Polarization Coherence Tomography with P-Band PolInSAR Data

Forest above ground biomass (AGB) extraction using Synthetic Aperture Radar (SAR) images has been widely used in global carbon cycle research. Classical AGB inversion methods using SAR images are mainly based on backscattering coefficients. The polarization coherence tomography (PCT) technology which can generate vertical profiles of forest relative reflectivity, has the potential to improve the accuracy of biomass inversion. The relationship between vertical profiles and forest AGB is modeled by some parameters defined based on geometric characteristics of the relative reflectivity distribution curve. But these parameters are defined without physical characteristics. Among these parameters, tomographic height (TomoH) is considered as the most important one. However, TomoH only corresponds to the highest volume relative reflectivity, which is lower than the actual forest height, affecting the accuracy of forest height and AGB inversion. In this paper, we introduce a new parameter, the canopy height (Hac), for AGB inversion by analyzing the vertical backscatter power loss. Then, we construct an inversion model based on the combination of the new parameter (Hac) and other parameters from the tomographic profile. The P-band polarimetric SAR datasets of the European Space Agency (ESA) BioSAR 2008 campaign acquired over Krycklan Catchment are selected for the verification experiment at two different flight directions. The results show that Hac performs better in estimating forest height and AGB than TomoH does. The inversion root mean square error (RMSE) of the proposed method is 18.325 t ha−1, and the result of using TomoH is 21.126 t ha−1.
Defining subtypes of autism spectrum disorder using static and dynamic functional connectivity

Autism spectrum disorder (ASD) is a highly heterogeneous neurodevelopmental disorder that is characterized by impairments in social communication and restricted and repetitive behaviours. Neuroimaging studies of individuals with ASD have shown complex patterns of functional connectivity (FC), with no clear consensus on defining brain-behaviour attributes of different subtypes of the disorder. In these studies, “static FC”, a metric that considers correlations across the entire time series for a given region, was used. Emerging evidence shows that FC changes over time; this “dynamic FC” can allow for unique detection of the temporal variability of functional connections over time. Here, we used k-means clustering, an unsupervised machine learning algorithm, to characterize two subtypes of ASD based on distinct patterns of static and dynamic FC. A multivariate statistical approach was then implemented to determine optimal relationships between FC patterns and group membership or behaviour. The main objective was to characterize differences in static and dynamic FC between subtypes of ASD defined in a fully data-driven manner, and between subtypes and typically developing individuals. Subtype 2 was defined by increased FC within resting-state networks and decreased FC across networks for static FC, global increases in temporal stability of dynamic FC, and robust relationships between FC and several behaviours, relative to Subtype 1. Further, both ASD subtypes exhibited different patterns of static and dynamic FC compared to controls, particularly within default mode, sensorimotor, and occipital networks. Static and dynamic FC metrics provided both overlapping and unique information about the nature of FC differences between subtypes, and between both subtypes and controls. Our results demonstrate the value of considering FC-based subtypes of ASD to elucidate different relationships between brain and behaviour among individuals with this disorder, and have important clinical implications for catering treatments and behavioural interventions to specific subtypes. Abbreviations ABIDE Autism Brain Image Data Exchange ADI-R Autism Diagnostic Interview Revised ADOS Autism Diagnostic Observation Scale ASD autism spectrum disorder BSR bootstrap ratio CER cerebellar network COMM communication CON cingulo-opercular network Cov covariance DMN default mode network FC functional connectivity FD framewise displacement FPN frontoparietal network LV latent variable OCC occipital network PCP Preprocessed Connectomes Project PLS partial least squares PLS-B behaviour partial least squares PLS-MC mean-centering partial least squares ROI region of interest RRBs restricted and repetitive behaviours rs resting-state RSN resting-state network SA social affect SMN sensorimotor network SRS Social Responsiveness Scale SVD singular value decomposition TD typically developing
Assessing Climate Change Impact on Forest Habitat Suitability and Diversity in the Korean Peninsula

Habitat changes in temperate forests are more vulnerable to climate change than tropical or boreal forests. This study assessed forest habitat suitability and diversity to determine the impact of climate change on the Korean Peninsula. We used the MaxEnt (Maximum Entropy) species distribution model, three key climate indices, and two representative climate change scenarios, using short and long-term data. Two of the three key climate indices related to temperature were more capricious than the precipitation-related index in the future. In the baseline prediction, both statistical and qualitative validation using the actual vegetation map showed excellent results. Regarding forest habitat suitability, northward migration and substantial increase were definitely distinctive in warm temperate evergreen forest. On the other hand, subalpine forest areas decreased significantly due to climate change; the suitable area for Representative Concentration Pathways (RCP) 8.5 2070s decreased by more than half. With regard to forest habitat diversity, regions with high diversity declined due to climate change. In the RCP 8.5 scenario, areas where all three forest types are suitable no longer appeared; however, in the case of RCP 4.5 2050s, suitable areas for two forest types increased, which implies climate change is not only negative in terms of diversity. As this negative prediction of future change is discouraging, active mitigation and adaptation are required to prevent these changes. The sustainability of future ecosystems is still dependent on our efforts.
08. Fluctuating asymmetry and individual variation in the skull shape of the common wall lizard ( Podarcis muralis Laurenti, 1768) estimated by geometric morphometrics

We explored individual variation and asymmetry in the skull shape of the common wall lizard (Podarcis muralis Laurenti, 1768) across four populations representing different habitats, by employing geometric morphometrics. We found directional and fluctuating asymmetry across the analysed populations, without differences in fluctuating asymmetry among populations. Patterns of individual variation and fluctuating asymmetry were highly correlated within and among populations. Asymmetric skull shape variation was similar in all populations, and was mostly related to the jaw adductor muscle chamber. Our results imply that the uniform pattern of skull fluctuating asymmetry results from a high level of canalisation. Directional asymmetry can be related to anatomical and behavioural lateralisation.
Efficient gene tree correction guided by species and synteny evolution

A gene family tree is traditionally inferred from a multiple alignment of homologous sequences according to a model of sequence evolution. Trees for several genes families are thus constructed independently from each other. They often carry unresolved parts or bad resolutions. Information for their full resolution may lie in the poorly exploited dependency between gene families, each bringing information for the resolution of the others. We propose to use several kinds of such dependencies in the construction of gene trees: information from a species tree through a model of gene content evolution by duplication, speciation and loss, information from extant synteny through ortholog predictions, and information from ancestral synteny through a model of gene neighborhood evolution. We develop several " correction " techniques, yielding a software package called " RefineTree ". We report some tests on simulated data and an application on the full set of gene families from the Ensembl database. We perform a genome-wide analysis of duplication and loss patterns on the history of 65 eukaryote species, including ancestral genes and gene orders of all ancestors along this phy-logeny. We show that according to several measures including running time, likelihood, stability of genome content and linearity of ancestral chromosomes, trees corrected by RefineTree are arguably more plausible than the ones stored by Ensembl. We finally discuss the quality criteria in the light of gene definition as a sequence or as a locus and extract some cases where a " true " gene tree should depend on this definition. RefineTree web interface is available at: Gene phylogenies on a whole genome scale are virtually useful to reconstruct ancestral genomes, including genes and gene orders, along with patterns of genome evolution. But the current standard gene trees stored in databases do not yet meet the sufficient quality for this aplicability. We propose a method to correct them, extensively test it, and apply it to the reconstruction of 64 eukaryote ancestral genomes (genes and gene orders when the evolutionary signal allows it).