Miracle-dz/UniFAR-FTUs huggingface dataset:
Motility and recovery of alpaca (Vicugna pacos) spermatozoa after centrifugation in a density gradient solution.

Background One of the factors limiting successful processing of alpaca (Vicugna pacos) semen is the viscosity of seminal plasma. The viscous nature of the collected ejaculate has hindered sperm cryopreservation as well as artificial insemination (AI) under field conditions. Aims The objective of this investigation was to evaluate recovery, motility, and plasma membrane integrity of alpaca spermatozoa after centrifugation in one of two different solutions at one of three different combinations of speed and time. Methods A total of 24 ejaculates was recovered from seven reproductively sound Huacaya males using a modified artificial vagina (AV) after training the animals for semen collection. A 2 × 3 factorial treatment arrangement was utilized for this study. Ejaculates were divided into fractions for centrifugation in one of two solutions (Tris extender or PureSperm®80 density gradient solution) at one of three combinations of speed and time (492 × g for 15 min, 1968 × g for 10 min, or 4448 × g for 7 min). The experiment was replicated eight times. Results Analysis revealed that centrifugation at 4448 × g for 7 min in PureSperm®80 provided a high recovery rate of spermatozoa with the highest sperm motility and functional integrity of plasma membrane post-centrifugation. Conclusion: Results suggest that adoption of this procedure (centrifugation at 4448 × g for 7 min in PureSperm®80) in the initial processing of alpaca ejaculates may enhance subsequent ability to use semen for AI and other assisted reproductive biotechnologies in this species.
Performance and Puberty of Ram Lambs Produced From Ewes Treated with Arginine

Aim of this study was to investigate performance and puberty of ram lambs produced from pregnant ewes treated with different levels of arginine. This study was carried out at Sakha Animal Production Research Station, belonging to the Animal Production Research Institute in a cooperation with Animal Production Department, Faculty of Agriculture, Mansoura University. During November 2016, total of 45 Ossimi ewes (September mating season), 3-4 years of age and 39.59±0.15 kg live body weight (LBW ) were divided into three groups (15 head/each). Ewes in the 1 group (G1) served as a control, ewes in the 2 (G2) and 3 (G3) groups were weekly treated with oral dose of 20 and 30 mg arginine (AR), respectively, for the duration of the treatment from the second month of pregnancy up to lambing. After lambing, total of 8 ram lambs produced from each group were taken and allotted in three groups similar to treatment of their dams. LBW of ram lambs was recorded at birth and monthly up to 12 month of age. In blood plasma of ram lambs, concentration of IgG and IgM at 2 days and 1, 3 and 4 wk of age, while concentration of total proteins, albumin, creatinine and glucose, and activity of aspartate (AST) and alanine (ALT) aminotransferase at 2, 4, 6 and 8 month of age were determined. Age and plasma testosterone concentration (PTC) of each ram lambs were determined at three pubertal stages, while semen of 1 ejaculates (at puberty) was evaluated. Results showed that ram lamb LBW was higher (P<0.05) only in G3 than G1 at birth and at 5 to 12 month of age. Final ram lamb LBW at 12 month of age was higher by 10.2 and 15.9% in G2 and G3 than in G1, respectively. Plasma concentration of Immunoglobulin G (IgG) and Immunoglobulin M (IgM) after 2 days, 1, 3, and 4 wk of lambing was highest (P<0.05) in G3, followed by G2, while, G1 showed the lowest values. Plasma concentration of total proteins at 4 month of age and of albumin at 4 and 6 month of age increased (P<0.05), while glucose decreased (P<0.05) at 2 and 8 month of age in G2 and G3 as compared to those of G1. Creatinine increased (P<0.05) only in G3 as compared to G2 and G1 at 6 and 8 month of age, while activity of AST and ALT was not affected at all ages. At puberty, age of ram lambs was earlier (P<0.05) by 51.4 and 33.0 days and PTC was higher (P<0.05) by 22.5 and 18.8% in G2 and G3 than in G1. Ram lambs in G3 showed the best (P<0.05) semen characteristics of the 1 ejaculation (volume, sperm motility and live sperm output / ejaculate), followed by G2. PTC was higher (P<0.05) in G2 and G3 than in G1 at 6 and 8 month of age, showing significantly (P<0.05) an opposite trend at 7 month of age, while insignificantly different at 5, 9 and 10 month of age. In conclusion, ram lambs of ewes treated with weekly oral dose of L-arginine-HCL (30 mg / ewe) from the second month of pregnancy up to lambing achieved early age and higher weight at puberty.
Supervised learning is an accurate method for network-based gene classification

Background Assigning every human gene to specific functions, diseases, and traits is a grand challenge in modern genetics. Key to addressing this challenge are computational methods such as supervised-learning and label-propagation that can leverage molecular interaction networks to predict gene attributes. In spite of being a popular machine learning technique across fields, supervised-learning has been applied only in a few network-based studies for predicting pathway-, phenotype-, or disease-associated genes. It is unknown how supervised-learning broadly performs across different networks and diverse gene classification tasks, and how it compares to label-propagation, the widely-benchmarked canonical approach for this problem. Results In this study, we present a comprehensive benchmarking of supervised-learning for network-based gene classification, evaluating this approach and a state-of-the-art label-propagation technique on hundreds of diverse prediction tasks and multiple networks using stringent evaluation schemes. We demonstrate that supervised-learning on a gene’s full network connectivity outperforms label-propagation and achieves high prediction accuracy by efficiently capturing local network properties, rivaling label-propagation’s appeal for naturally using network topology. We further show that supervised-learning on the full network is also superior to learning on node-embeddings (derived using node2vec), an increasingly popular approach for concisely representing network connectivity. Conclusion These results show that supervised-learning is an accurate approach for prioritizing genes associated with diverse functions, diseases, and traits and should be considered a staple of network-based gene classification workflows. The datasets and the code used to reproduce the results and add new gene classification methods have been made freely available. Contact arjun@msu.edu
A role for DIS3L2 over human nonsense-mediated mRNA decay targets

The nonsense-mediated decay (NMD) pathway selectively degrades mRNAs carrying a premature translation-termination codon but also regulates the abundance of a large number of physiological mRNAs that encode full-length proteins. In human cells, NMD-targeted mRNAs are degraded by endonucleolytic cleavage and exonucleolytic degradation from both 5’ and 3’ ends. This is done by a process not yet completely understood that recruits decapping and 5’-to-3’ exonuclease activities, as well as deadenylating and 3’-to-5’ exonuclease exosome activities. In yeast, DIS3/Rrp44 protein is the catalytic subunit of the exosome, but in humans, there are three known paralogues of this enzyme: DIS3, DIS3L1, and DIS3L2. DIS3L1 and DIS3L2 exoribonucleases localize in the same compartment where NMD occurs, but little is known about their role in this process. In order to unveil the role of DIS3L2 in NMD, here we show that some NMD-targets accumulate in DIS3L2-depleted cells. mRNA half-life analysis further supports that these NMD-targets are in fact DIS3L2 substrates. Besides, we observed that DIS3L2 acts over full-length transcripts, through a process that also involves UPF1. Moreover, DIS3L2-mediated decay is dependent on the activity of the terminal uridylyl transferases Zcchc6/11 (TUT7/4). Together, our findings establish a role for DIS3L2 and uridylation in NMD.
Level of stress in relation to emotional reactivity of hens

Abstract The aim of the study was to associate behavioural reactions of laying hens with the level of stress and to answer the question whether it is possible to select reactions that will facilitate phenotypic assessment of the level of stress in these birds. The investigations were carried out in 50 Green-legged Partridge, 50 Polbar and 50 Leghorn birds. A modified open-field test (MOFT) and a tonic immobility test were applied. Next, the quality of feathers was evaluated and the level of corticosterone in the feathers was determined. The corticosterone level was assessed in relation to the genetic group and feather quality and in relation to the probability of the presence/absence of specific physiological–behavioural reactions. The analysis of the results revealed no correlations between the corticosterone level in the feathers and the quality of the feathers. In turn, there was a correlation between the hen breed and the corticosterone level in the feathers: a significant difference was found between Zk and Pb hens. It was demonstrated that the corticosterone level was significantly higher in birds that exhibited such behaviours as preening in the open-field test. To sum up the results, it can be concluded that such behaviours as feather preening and latency until tonic immobility occurs can be indicators of stress in laying hens. Highlights There was a correlation between the breed and the corticosterone level in the feathers: there was a significant difference between the Green-legged Partridge (3.97 ± 0.17) and Polbar (4.50 ± 0.19) hens. No significant correlations were found between the corticosterone level and the behavioural reactivity in the analysed hens. It was demonstrated that the corticosterone level was significantly higher in birds that exhibited self-grooming behaviours in the open-field test (4.61) than in hens that did not show such behaviours (3.91).
Cytological Grading of Breast Tumors—The Human and Canine Perspective

Human breast cancers (HBCs) are one of the leading causes of global cancer death among women. Domesticated canines are the most affected domestic species with a prevalence rate of breast cancer more than three times in women. While the human cancer patients receive substantial diagnostic and treatment facilities, inadequacy in canine cancer care, calls for greater attention. Fine Needle Aspiration Cytology (FNAC) is comparatively simple, quick, and easily reproducible technique, which aids in pre-surgical diagnosis. In humans, FNAC has a standard protocol, the Robinson's grading system, which has high correlation with the established histological grading system of Scarff Bloom- Richardson. However, Canine Mammary Tumors (CMTs), which are known to be similar to HBCs in biological behavior and gene expressions, still bank on the histopathological methods for diagnostic purposes. This review sheds light on various factors that could be considered for developing a standard FNAC technique for CMT grading and analyzes its future perspectives.
Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single individual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.
Lateral occipitotemporal cortex encodes perceptual components of social actions rather than abstract representations of sociality

Neuroimaging studies suggest that areas in the lateral occipitotemporal cortex (LOTC) play an important role in the perception of social actions. However, it is unclear what precisely about social actions these areas represent: perceptual features that may be indicative of social actions – such as the presence of persons in a scene, their orientation toward each other, and in particular the directedness of action movements toward persons or other targets – or more abstract representations that capture whether an action is meant to be social. In two fMRI experiments, we used representational similarity analysis (RSA) to test whether LOTC is sensitive to perceptual action components important for social interpretation and/or more general representations of sociality (Experiment 1) and implied person-directedness (Experiment 2). We found that LOTC is sensitive to perceptual action components (person presence, person orientation, and action directedness toward different types of recipients). By contrast, more general levels of sociality and implied person-directedness were not captured by LOTC. Our findings suggest that regions in LOTC provide the perceptual basis for social action interpretation but challenge accounts that posit specialization at more general levels sensitive to social actions and sociality as such. We propose that the interpretation of an action – in terms of sociality or other intentional aspects – arises from the interaction of multiple areas in processing relevant action components in a situation-dependent manner.
Practice Of Therapeutic Exercise, Physical Therapy Modalities And Pet Therapy In Negotiating With Depression In Adolescent, Adults And Elderly Population: A Narrative Review

Depression is a mental stage which affects the quality of life in people around the globe. It’s a phase in one’s life characterized by low mood, reluctance toward performing activities which greatly affect behavior, thought process, short and long term feeling, temporary and permanent well being. A thorough search of the literature was carried out to identify studies investigating therapeutic interventions in treating patients with depression. All the studies were thoroughly searched for the relevant information contained in them. Electronic database, including Embase, Scopus, Pub Med, CINAHL, Web of science were searched for research articles published from the earliest of 2009 to latest of 2016 using keywords of “depression”, “Physical therapy”, “Therapeutic intervention”, “pet therapy”. The present study looked into various therapeutic interventions while writing the article. Earlier reported literatures have employed various interventions in treating adolescent, adults and geriatric populations with depression. Limited study have been performed on Pet therapy, the authors are directed to employ more time and efforts in studying new methods to treat depression.
Histology of the midbrain of the grey breasted helmeted guinea fowl (Numida meleagris galeata) at post-hatch

The study was carried out to investigate the development of the midbrain in the grey breasted helmeted guinea fowl, Numida meleagris galeata, at post-hatch. Domestication of this species of bird is in an increase, but scanty documentation on the development of midbrain (mesencephalon) and how it relates to the neurobiology of this bird is lacking. In our findings, there was a steady increase in the midbrain mean weights found to be 0.0418 ± 0.0081 and 0.2236 ± 0.0224 g on the first day and day 61 post-hatch, respectively. Morphological and cellular development shows the midbrain to develop immediately after hatch at day one. This indicates that auditory-visual activities are fully functional in the wild grey breasted helmeted guinea fowl and capable of independent survival immediately after hatching. Key words: Morpho-histogenesis, midbrain, guinea fowl.
Pelagic methane oxidation in the northern Chukchi Sea

Significant amounts of methane reside in sediments along the continental margins and slope of the Arctic Ocean. Methanotrophic bacteria oxidize methane to bicarbonate and also assimilate some methane‐derived carbon into biomass. Their metabolism transforms methane to other forms of carbon and sequesters it within the system, reducing its emission to the atmosphere. Increases in water temperatures driven by global climate change may accelerate the methane flux from the benthos into the water column, potentially increasing the importance of methanotrophic consumption as a methane sink. We report methane concentrations and oxidation rates in the water column of the Chukchi Sea from August 2017. This area is characterized by seasonally high nutrient concentrations that fuel high rates of pelagic primary productivity and subsequent sedimentation of organic matter, which stimulates benthic methanogenesis. Methane concentrations in the study area ranged from 6 to 72 nmol L−1, consistent with previously published measurements. Methane oxidation rates were as high as 580 pmol L−1 d−1, similar to the rates measured in the East Siberian Arctic Shelf. Depth‐integrated methane oxidation rates were lower than methane efflux rates, suggesting that physiochemical factors prevent the methanotrophic microbial community from efficiently removing methane from the ecosystem. Still, methanotrophic bacteria provide an ecosystem service by removing a fraction of methane prior to its efflux to the atmosphere.
Bioactivity of Alcaligenes faecalis and Lecanicillium sp. isolated from crocker range of Sabah against Erwinia psidii of papaya dieback disease

Aims: Erwinia psidii was first reported in 2017 to be the causal pathogen of papaya dieback disease (PDD) in Sabah, Malaysia. The present study aimed to isolate potential biocontrol agents against this pathogen. Methodology and Results: Out of the 20 samples collected from Crocker Range of Sabah, 154 bacteria and 55 fungi isolates were isolated and screened for their antagonistic activity against E. psidii. The fungi and bacteria which gave the highest inhibition to E. psidii were identified using molecular technique as Alcaligenes faecalis and Lecanicillium sp. , respectively. Both isolates were selected for extraction of their secondary metabolites to determine their bioactivity against E. psidii. Micro-well dilution method was used to determine minimum inhibitory concentration (MIC) for each microbes’ extract. GC-MS analysis was carried out to determine their secondary metabolites. Conclusion, Significance and Impact of study: Lecanicillium sp. (Diethyl ether, chloroform and ethyl acetate) extracts and A. faecalis (Diethyl ether extract) showed positive inhibition against E. psidii. GC-MS analysis revealed that both A. faecalis and Lecanicillium sp. had secreted some secondary metabolites such as N-formylmaleamic acid, Oleamide and D-1-Piperideine-2-carboxylic acid that may relate to the growth inhibition. A. faecalis and Lecanicillium sp. are potential to be further investigated as biocontrol against E. psidii.
Nonideal transport of solute and colloidal tracers through reactive zeolite/iron pellets

Solute and colloidal tracer tests were conducted in laboratory columns to examine the hydraulic properties of a foamed zeolite/iron pellet material that was developed for in situ remediation of contaminated groundwater. The colloidal tracer (1 μm polystyrene microspheres) moved through the columns much faster than the nonreactive solute tracer tritiated water, reflecting the interpellet preferential flow paths in the packed material. Flow interruption experiments with tritium and bromide showed concentration rebound of both tracers after the interruption (during elution), indicating the existence of nonadvective zones inside the pellets. Inverse modeling of microsphere data using a physical nonequilibrium transport model yielded immobile water content (θim) equivalent to the intrapellet porosity (0.40), suggesting that the microspheres were excluded from the small intrapellet pores and could only move through the large interpellet pore spaces. Inverse modeling of tritium data using physical nonequilibrium and dual‐permeability dual‐porosity models yielded θim values of 0.1–0.2, confirming the existence of nonadvective zones inside the pellets as suggested by the flow interruption experiments. The dual‐permeability dual‐porosity model also indicated that 6–11% of the total porosity was preferential flow porosity, consistent with the observation of enhanced microsphere transport with respect to tritiated water. Forward modeling with the dual‐permeability dual‐porosity model suggested that the immobile water in the pellets would not significantly affect the removal efficiency of contaminants subject to sorption and reduction. In contrast, the preferential flow porosity would drastically lower the contaminant removal efficiency.
Reservoir to river: Quantifying fine‐scale fish movements after translocation

Translocation of individuals is a widely used tool in the conservation of threatened species. The movement behaviours of translocated individuals in their new environment are a key factor that can influence translocation success (i.e. survival and reproduction). In this study, eel‐tailed catfish (Tandanus tandanus ) and Murray cod (Maccullochella peelii ) movements were monitored using fine‐scale acoustic telemetry over a 5‐month period in two lowland rivers in eastern Australia. Fine‐scale movement and habitat selection were compared among translocated lacustrine and resident riverine T. tandanus and between species. We found no difference in fine‐scale movement behaviours between translocated and resident T. tandanus ; however, there was some variation in movement response to environmental variation between species. In contrast, habitat selection varied not only between the two species, but also between resident and translocated T. tandanus individuals. Notably, activity was significantly lower in the first day after release compared to the remainder of the study period. Although T. tandanus translocated from a reservoir had never experienced the environmental fluctuations of a riverine system, individuals still responded in the same way as resident riverine fish, suggesting an innate behavioural response. However, this was not the case for habitat selection, where translocated individuals preferred habitats more common in their source population's lacustrine environment. The findings of this study are important in guiding future conservation efforts involving the translocation of wild‐caught fish, primarily the importance of the suitable habitat at the release site to ensure the success and persistence of translocated populations.