Miracle-dz/UniFAR-FTUs huggingface dataset:
IMPACT OF CROSSING BETWEEN GABALI AND V–LINE RABBITS ON THE PRE-WEANING TRAITS BY USING TRIDIAGONAL AND GENETIC MERIT METHODS.

This study was done inside an assignment that intended to break down options and strategies for the progression of a rabbit line by using two pure breeds (V-line (V), and Gabali (G)). Records of 448 packs delivered by 45 does and 16 bucks were utilized to estimate covariance, Heritability (h), genetic and phenotypic correlations, and breeding values of litter traits were evaluated in composite of crossbreeding arrangement of ten mating groups. The initial five groups comprise of (G♂ X V♀) and reciprocal crosses (V♂ X G♀) for the other five groups. Each buck was represented as a sire to all litters in each group to create F1 (1⁄2G 1⁄2V& 1⁄2 V1⁄2G sire breed is demonstrated first) for four parities. Weaning was performed at 28 days of kits age. Pre-weaning litter traits were measured (for instance, litter size at both birth (LSB), and at weaning (LSW); litter weight either at birth (LWB), and body weight at weaning (BWW)). Data were examined utilizing GLM and VARCOMP procedures of SAS took after by single and multi-trait animal model investigations (AM), which performed utilizing derivate free limited maximum likelihood (MTDFREML). The results revealed that h estimates for LSB and LSW were 0.133±0.01 and 0.15±0.063, respectively. The evaluations of coefficient of inconstancy (CV%) are 34.78% for LSB versus 39% for LSW, and 28.27% for LWB versus 33.53 % for BWW. The impact of mating groups on LSB and LSW, LWB and BWW had exceptionally significant being 7.921, 5.320, 0.402, and 0.450 kg for LSB, LSW, LWB and BWW for (G♂ X V♀), individually, while the proportional (V♂ X G♀) were 6.224, 4.80, 0.360, and 0.490 kg, separately. Parity significantly affected LSB, LWB, and BWW. Meanwhile, the impact of doe within buck as a random impact demonstrated an unacquainted impact altogether influenced all analyzed traits. Negative genetic correlation between litter size at birth and each of litter weight at birth and body weight at weaning. Additionally, environmental correlation between litter size at weaning and litter weight at birth was positive, while the environmental correlation between litter size at waning and body weight at weaning was negative but not significant. Furthermore, the precision of the evaluations of bucks breeding value (0.37 to 0.92) was higher than the exactness of doe (0.27 to 0.88) and progeny (0.36 to 0.85), which might be because of the higher number of descendants per buck. Subsequently, the outcomes demonstrated the significance of utilizing bucks of Gabali in rearing project to build the genetic advance.
Runoff generation in mountain catchments: long-term hydrological monitoring in the Rio Vauz Catchment, Italy

Trying to obtain a more detailed understanding of the hydrological functioning of mountain catchments represents an important challenge in the effort of counteracting possible consequences of climate and land use change on water resources availability. Long-term (> 10 years) hydro-meteorological monitoring in small (typically < 10 km2) experimental catchments constitutes a valuable tool to achieve these goal. One of these sites is the Rio Vauz Catchment (1.9 km2), in the Italian Dolomites, that represents an excellent example of long-term snowmelt-dominated catchment in Dolomitic regions. The strong elevation gradient of the Rio Vauz Catchment and the different physiographic properties of its nested subcatchments make this a unique site for investigating fundamental runoff generation mechanisms in mountain headwaters. In this work, we provide a review of physical processes that have been inferred from 12 years of hydrological monitoring in this catchment. We present the available dataset and summarize the main hydrological mechanisms that explain the internal functioning of the Rio Vauz Catchment, primarily focusing on three characterizing hydrological behaviours, namely thresholds, hysteresis and connectivity. The main control on surface and subsurface runoff threshold response is constituted by a combination of soil moisture antecedent conditions, rainfall amount and topography. Changes in hysteresis patterns (clockwise and anti-clockwise loops) between streamflow and soil moisture, water table depth and electrical conductivity were governed by distinct runoff generation processes and rainfall event characteristics. Hillslope-riparian-stream subsurface connectivity was controlled by antecedent wetness conditions and rainfall amount. The composition in environmental tracers (stable isotopes of water and electrical conductivity) in different water sources and the application of tracer-based mixing models helped to distinguish the geographical sources to runoff and to quantify the role of rainfall and snowmelt in streamflow. Finally, we define a perceptual model of runoff generation processes for dry and wet conditions that can be considered representative for many mountain headwater catchments in the world.
Integrative gene expression profiling reveals that dysregulated triple microRNAs confer paclitaxel resistance in non-small cell lung cancer via co-targeting MAPT

Background Paclitaxel has shown significant anti-tumor activity against non-small cell lung cancer (NSCLC); however, resistance to paclitaxel frequently occurs and represents a significant clinical problem and its underlying molecular mechanism remains elusive. Methods Long-term treatment of culture cell with paclitaxel was carried out to mimic the development of acquired drug resistance in NSCLC. Cell proliferation and clonogenic assay and apoptosis evaluation were carried out to determine the efficacy of paclitaxel on NSCLC cells. Western blot analyses were performed to determine the expression and activation of proteins. Apoptosis enzyme-linked immunosorbent assay was used to quantify cytoplasmic histone-associated DNA fragments. Microarray analyses were applied to explore both mRNA and miRNA expression profiles in NSCLC cells followed by integrative analysis. qRT-PCR was carried out to verify the differentially expressed mRNAs and miRNAs. Results The expression of 652 genes was shown to be changed at least 2-fold in paclitaxel-resistant NSCLC (H460_TaxR) cells with 511 upregulated and 141 downregulated as compared with that in parental H460 cells. The differentially expressed genes were functionally enriched in regulating the cell proliferation, cell death, and response to endogenous stimulus, and clustered in pathways such as cancer and signaling by the G protein-coupled receptor (GPCR). Moreover, 43 miRNAs were shown to be differentially expressed in H460_TaxR cells with 15 upregulated and 28 downregulated as compared with parental H460 cells. A total of 289 pairs of miRNA-potential target gene were revealed in H460_TaxR cells by bioinformatics analysis. Furthermore, integrative analysis of miRNAs and gene expression profiles revealed that dysregulated miR-362-3p, miR-766-3p, and miR-6507-3p might confer paclitaxel resistance in NSCLC via targeting MAPT simultaneously. Conclusion Our findings suggested that specific manipulation of MAPT-targeting miRNAs may be a novel strategy to overcome paclitaxel resistance in patients with NSCLC especially large-cell lung carcinoma.
SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing

Human immunodeficiency virus 1 (HIV-1) genome sequencing is routinely done for drug resistance monitoring in hospitals worldwide. Subtyping these extensive datasets of HIV-1 sequences is a critical first step in molecular epidemiology and surveillance studies. The clinical relevance of HIV-1 subtypes is increasingly recognized. Several studies suggest subtype-related differences in disease progression, transmission route efficiency, immune evasion, and even therapeutic outcomes. HIV-1 subtyping is mainly done using web servers. These tools have limitations in scalability and potential noncompliance with data protection legislation. Thus, the aim of this work was to develop an efficient method for local and high-throughput HIV-1 subtyping. We designed SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. It contains several tasks of phylogenetic inference and BLAST queries, which can be executed sequentially or in parallel, taking advantage of multiple-core processing units. Although it was built for subtyping, SNAPPy is also useful to perform extensive HIV-1 alignments. This tool facilitates large-scale sequence-based HIV-1 research by providing a local, resource efficient and scalable alternative for HIV-1 subtyping. It is capable of analysing full-length genomes or partial HIV-1 genomic regions (GAG, POL, ENV) and recognizes more than 90 circulating recombinant forms. SNAPPy is freely available at: https://github.com/PMMAraujo/snappy.
EFFECT OF ENRICHING MULBERRY LEAVES WITH CERTAIN FOLIAR FERTILIZERS ON SOME PHYSIOLOGICAL ASPECTS OF MULBERRY SILKWORM, Bombyx mori L.

Studies were conducted to evaluate the effect of certain foliar fertilizers (Basfoliar combi ctip, Tecamin max and Stimoful) as a nutritional additives on some physiological aspects in haemolymph of mulberry silkworm, Bombyx mori L. Mulberry leaves were dipped in three concentrations for each tested foliar fertilizer (1, 2 and 3%) and offered to the first group larvae at the beginning of the 4 th larval instar. The second group was treated at the beginning of both 4 th and 5 th instar larvae. Results showed that total protein increased as concentration increased in the two groups. Tecamin max gave the highest mean of total protein in two groups. Stimoful gave the highest mean of total carbohydrate in the two groups. The concentration 3% from stimoful recorded the highest content from total carbohydrate in both groups. Tecamin max gave the highest mean of Glutamic oxaloacetic transaminase (GOT) and glutamic pyruvic transaminase (GPT) enzyme activities in both groups. Larvae fed on leaves treated by Basfoliar combi ctip gave the highest activity of amylase enzyme in both groups and the concentration 3% recorded the highest level of amylase activity. Tecamin max gave the highest level of invertase activity on the first group, while stimoful recorded the highest mean of invertase activity on the second group. The highest level of Trehalase activity was 83.53 mg glucose/ ml for stimoful on the first group, while Basfoliar combi ctip recorded the highest level of trehalase activity on the second group. Conclusively, fortification of mulberry leaves with different nutritional additives as foliar fertilizers increased some physiological aspects of mulberry silkworm B. mori especially as concentration increased.
Altitudinal biodiversity patterns of seed plants along Gongga Mountain in the southeastern Qinghai–Tibetan Plateau

Abstract The mechanisms underlying elevation patterns in species and phylogenetic diversity remain a central issue in ecology and are vital for effective biodiversity conservation in the mountains. Gongga Mountain, located in the southeastern Qinghai–Tibetan Plateau, represents one of the longest elevational gradients (ca. 6,500 m, from ca. 1,000 to 7,556 m) in the world for studying species diversity patterns. However, the elevational gradient and conservation of plant species diversity and phylogenetic diversity in this mountain remain poorly studied. Here, we compiled the elevational distributions of 2,667 native seed plant species occurring in Gongga Mountain, and estimated the species diversity, phylogenetic diversity, species density, and phylogenetic relatedness across ten elevation belts and five vegetation zones. The results indicated that species diversity and phylogenetic diversity of all seed plants showed a hump‐shaped pattern, peaking at 1,800–2,200 m. Species diversity was significantly correlated with phylogenetic diversity and species density. The floras in temperate coniferous broad‐leaved mixed forests, subalpine coniferous forests, and alpine shrublands and meadows were significantly phylogenetically clustered, whereas the floras in evergreen broad‐leaved forests had phylogenetically random structure. Both climate and human pressure had strong correlation with species diversity, phylogenetic diversity, and phylogenetic structure of seed plants. Our results suggest that the evergreen broad‐leaved forests and coniferous broad‐leaved mixed forests at low to mid elevations deserve more conservation efforts. This study improves our understanding on the elevational gradients of species and phylogenetic diversity and their determinants and provides support for improvement of seed plant conservation in Gongga Mountain.
How Top-Down and Bottom-Up Regulation in Fronto-Amygdalar Network Changes over Time during Drug Cue-Exposure: An fMRI Study among Abstinent Heroin User

Top-down regulation is one of the major neural cores in drug-craving management and relapse prevention. The dynamic temporal behavior of top-down regulation between the dorso-lateral and ventro-medial prefrontal cortices (DLPFC and VMPFC) and amygdala during drug cue-exposure has not been studied yet. Fifteen abstinent participants with heroin use disorder were scanned using drug cue-induced craving fMRI task. Using Dynamic Causal Modelling (DCM), the winning model showed a significant reciprocal connection between the VMPFC and DLPFC while there was a one-way effect of the VMPFC on the amygdala. There is also a top-down modulation by DLPFC on the VMPFC-Amygdala connection. Craving contrast input only modulated amygdala directly. Using sliding-window for temporal evaluation, craving input to amygdala increased over time, simultaneously, DLPFC top-down modulatory effect on VMPFC-amygdala connection decreased. Temporal changes in the network connectivity during cue exposure with enhancement in craving input to amygdala and reduction in top-down modulatory effects of DLPFC, could provide us with new insights towards the dynamic nature of the cue-reactivity and failure to control its motivational consequences. Dynamic response of top-down regulatory networks during cue exposure can be considered as a new potential biomarker in the future addiction fMRI studies.
Documenting demise? Sixteen years observing the Swift Parrot Lathamus discolor in suburban Hobart, Tasmania

The Swift Parrot Lathamus discolor is listed as Critically Endangered because modelling suggests that its population is declining by >80% within three generations (12–18 years) as a result of just one of many factors impacting the species: predation by introduced Sugar Gliders Petaurus breviceps. Unfortunately, verification of this prediction through monitoring of the entire population across its breeding range is difficult because of the amount of observer effort required to count all individuals within the often dense canopies of Eucalyptus trees, where it forages predominantly from flowers. This study entails 16 years of opportunistic observations at a single location within this species’ breeding range. Regression models indicated that over 16 breeding seasons the mean size of the largest flock per month declined by ~90%, and grand mean size of all flocks per month by ~70%. This was not the result of decreasing local flowering intensity in the Swift Parrot’s favoured food plants, as adjusting the two measures of abundance for local inter-annual variation in flowering had little effect on the rates of decline. This concordance between observations at the local scale and modelling of the entire population supports the findings of the modelling, suggesting that urgent action is required to prevent extinction of this species.
Metabolite composition of sinking particles differs from surface suspended particles across a latitudinal transect in the South Atlantic

Marine sinking particles transport carbon from the surface and bury it in deep‐sea sediments, where it can be sequestered on geologic time scales. The combination of the surface ocean food web that produces these particles and the particle‐associated microbial community that degrades them creates a complex set of variables that control organic matter cycling. We use targeted metabolomics to characterize a suite of small biomolecules, or metabolites, in sinking particles and compare their metabolite composition to that of the suspended particles in the euphotic zone from which they are likely derived. These samples were collected in the South Atlantic subtropical gyre, as well as in the equatorial Atlantic region and the Amazon River plume. The composition of targeted metabolites in the sinking particles was relatively similar throughout the transect, despite the distinct oceanic regions in which they were generated. Metabolites possibly derived from the degradation of nucleic acids and lipids, such as xanthine and glycine betaine, were an increased mole fraction of the targeted metabolites in the sinking particles relative to surface suspended particles, while algal‐derived metabolites like the osmolyte dimethylsulfoniopropionate were a smaller fraction of the observed metabolites on the sinking particles. These compositional changes are shaped both by the removal of metabolites associated with detritus delivered from the surface ocean and by production of metabolites by the sinking particle‐associated microbial communities. Furthermore, they provide a basis for examining the types and quantities of metabolites that may be delivered to the deep sea by sinking particles.
Data-driven integration of hippocampal CA1 synapse physiology in silico

The anatomy and physiology of synaptic connections in rodent hippocampal CA1 have been exhaustively characterized in recent decades. Yet, the resulting knowledge remains disparate and difficult to reconcile. Here, we present a data-driven approach to integrate the current state-of-the-art knowledge on the synaptic anatomy and physiology of rodent hippocampal CA1, including axo-dendritic innervation patterns, number of synapses per connection, quantal conductances, neurotransmitter release probability, and short-term plasticity into a single coherent resource. First, we undertook an extensive literature review of paired-recordings of hippocampal neurons and compiled experimental data on their synaptic anatomy and physiology. The data collected in this manner is sparse and inhomogeneous due to the diversity of experimental techniques used by different labs, which necessitates the need for an integrative framework to unify these data. To this end, we extended a previously developed workflow for the neocortex to constrain a unifying in silico reconstruction of the synaptic physiology of CA1 connections. Our work identifies gaps in the existing knowledge and provides a complementary resource towards a more complete quantification of synaptic anatomy and physiology in the rodent hippocampal CA1 region.
Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane

Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast responses to changes in temperature. AS is present in around 60% of intron-containing genes in Arabidopsis, 46% in rice and 38% in maize and it is widespread among the circadian clock genes. Little is known about how AS influences the circadian clock of C4 plants, like commercial sugarcane, a C4 crop with a complex hybrid genome. This work aims to test if the daily dynamics of AS forms of circadian clock genes are regulated by environmental factors, such as temperature, in the field. A systematic search for AS in five sugarcane clock genes, ScLHY, ScPRR37, ScPRR73, ScPRR95 and ScTOC1 using different organs of sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 months old plants, revealed temperature- and organ-dependent expression of at least one alternatively spliced isoform in all genes. Expression of AS isoforms varied according to the season. Our results suggest that AS events in circadian clock genes are correlated with temperature.
Hippocampus patagonicus sp. nov., nuevo caballito de mar para la Argentina (Pisces, Syngnathiformes)

Hippocampus patagonicus sp. nov., new seahorse fromArgentina(Pisces, Syngnathiformes). A new seahorse species, Hippocampus patagonicus is described fromSan Antonio OesteBay(Rio NegroProvince), Puerto Piramides (ChubutProvince), and Puerto Madryn (Chubut Province) along the Patagonic Argentine coast. This species is the southernmost occurring species of the genus in theSouth Atlantic Ocean. Morphometrics, meristics and a morphological description are presented. The osteological spine ultrastructure is proposed to define the taxonomic status of the species. Key words: Hyppocampus, new species,South Atlantic Ocean,Argentina.
Neofusicoccum parvumandDiaporthe foeniculinaassociated with twig and shoot blight and branch canker of citrus in Greece

In a survey performed in Chania and Aetoloacarnania, Greece in years 2013–2014, fungal isolates causing twig and shoot blight and branch canker of citrus trees were morphologically characterized and identified by multiple gene sequence analysis. By sequencing the ITS‐5.8S rRNA, the elongation factor 1‐α (EF1‐α), the β‐tubulin and the RNA polymerase II subunit (Rpb2) genes, the isolates examined were associated with Diaporthe foeniculina (six isolates) and Neofusicoccum parvum (one isolate). All six D. foeniculina isolates showed slow colony growth rates (7.4 ± 3.2 mm/day), while the N. parvum isolate exhibited fast growth (41.6 mm/day). Koch's criteria were met after re‐isolation of D. foeniculina isolates from all inoculated Citrus spp. and N. parvum from inoculated C. reticulata “Ortanique” and after having developed symptoms similar to those detected on shoots and branches collected from citrus fields. Based on lesion length on detached C. medica “Lia Kritis” shoots, N. parvum caused long necrotic lesions (58 mm in length) in comparison with a length of 12–21 mm lesions caused by D. foeniculina isolates. Pathogenicity trials on nine Citrus spp. , which had been inoculated with D. foeniculina and N. parvum, revealed different levels of susceptibility, indicating a host‐dependent infection effect, with Poncirus trifoliate × C. paradisi (“Citrumelo Swingle”) being the most resistant citrus genotype. Lack of host specificity suggests that their pathogen–host association could be attributed to ecological rather to co‐evolutionary factors. This work represents the first report, accompanied with pathogenicity tests, on botryosphaeriaceous and diaporthaceous pathogens associated with twig and shoot blight and branch canker of citrus in Greece.