Miracle-dz/UniFAR-FTUs huggingface dataset:
Top-dressing of chelated phytogenic feed additives in the diet of lactating Friesian cows to enhance feed utilization and lactational performance

Abstract The present experiment evaluated the inclusion of chelated phytogenic feed additives mixture in the diet of lactating cows for the first 3 months of lactation. A week before calving, thirty multiparous Friesian cows were divided into three treatments in a complete randomized design and fed a basal diet without supplementation (Control treatment), or the control diet supplemented with chelated phytogenic additives at 3 g (PHY3 treatment), or at 6 g/cow/d (PHY6 treatment). Menthol, levomenthol, β-linaloolm, anethole, hexadecanoic acid and pmenthane were the principal compounds identified in the additives mixture. Milk production, total solid, protein, fat, and lactose were increased with PHY3, but decreased by PHY6 (P<0.01). Whereas the PHY3 treatment increased (P<0.05) milk contents of Ca and Zn, PHY3 and PHY6 treatments increased (P<0.05) milk Fe and Mn concentrations. Though the PHY3 treatment increased (P<0.05) nutrient digestibility, the PHY6 treatment decreased (P<0.05) the digestibility of organic matter, crude protein and neutral detergent fiber. The PHY3 treatment increased (P<0.05) ruminal volatile fatty acids (VFA) concentration and proportional acetate and propionate and decreased butyrate, while the PHY6 treatment decreased ruminal VFA concentration and proportional acetate. The PHY3 treatment increased (P<0.05) serum total protein, glucose, total antioxidant capacity, and the concentrations of Ca and Zn. Both PHY3 and PHY6 treatment decreased (P<0.05) the concentrations of serum triglycerides, and cholesterol. Daily inclusion of 3 g/cow of chelated feed additives mixture in diet of lactating cows improved milk production and ruminal fermentation, but additives dose of 6 g/cow/d had negative impact on cows’ performance.
Evidence for a multicellular symplasmic water pumping mechanism across vascular plant roots

With global warming, climate zones are projected to shift poleward, and the frequency and intensity of droughts to increase, driving threats to crop production and ecosystems. Plant hydraulic traits play major roles in coping with such droughts, and process-based plant hydraulics (water flowing along decreasing pressure Ψp or total water potential Ψtot gradients) has newly been implemented in land surface models. An enigma reported for the past 35 years is the observation of water flowing along increasing water potential gradients across roots. By combining the most advanced modelling tool from the emerging field of plant micro-hydrology with pioneering cell solute mapping data, we found that the current paradigm of water flow across roots of all vascular plants is incomplete: it lacks the impact of solute concentration (and thus negative osmotic potential Ψo) gradients across living cells. This gradient acts as a water pump as it reduces water tension without loading solutes in plant vasculature (xylem). Importantly, water tension adjustments in roots may have large impacts in leaves due to the tension-cavitation feedback along stems. Here, we mathematically demonstrate the water pumping mechanism by solving water flow equations analytically on a triple-cell system. Then we show that the simplistic upscaled equations hold in 2- and 3-D maize, grapevine and Arabidopsis complex hydraulic anatomies, and that water may flow “uphill” of water potential gradients toward xylem as observed experimentally. Besides its contribution to the fundamental understanding of plant water relations, this study lays new foundations for future multidisciplinary research encompassing plant physiology and ecohydrology, and has the ambition to mathematically capture a keystone process for the accurate forecasting of plant water status in crop models and LSMs. Graphical Abstract Highlights - We provide a scale-consistent solution of water flow equations across root tissues - Symplasmic osmotic potential gradients are missing in the current theory of root water uptake - The model solves the empirical enigma of root water uptake uphill of water potential gradients
The Psychometrics of Automatic Speech Recognition

Deep neural networks have had considerable success in neuroscience as models of the visual system, and recent work has suggested this may also extend to the auditory system. We tested the behaviour of a range of state of the art deep learning-based automatic speech recognition systems on a wide collection of manipulated sounds used in standard human psychometric experiments. While some systems showed qualitative agreement with humans in certain tests, in others all tested systems diverged markedly from humans. In particular, all systems used spectral invariance, temporal fine structure and speech periodicity differently from humans. We conclude that despite some promising results, none of the tested automatic speech recognition systems can yet act as a strong proxy for human speech recognition. However, we note that the more recent systems with better performance also tend to better match human results, suggesting that continued cross-fertilisation of ideas between human and automatic speech recognition may be fruitful. Our open source toolbox allows researchers to assess future automatic speech recognition systems or add additional psychoacoustic measures.
Deep Mutagenesis of a Transporter for Uptake of a Non-Native Substrate Identifies Conformationally Dynamic Regions

The serotonin transporter, SERT, catalyzes serotonin reuptake at the synapse to terminate neurotransmission via an alternating access mechanism, and SERT inhibitors are the most widely prescribed antidepressants. Here, deep mutagenesis is used to determine the effects of nearly all amino acid substitutions on human SERT surface expression and transport of the fluorescent substrate analogue APP+, identifying many mutations that enhance APP+ import. Comprehensive simulations of the entire ion-coupled import process reveal that while binding of the native substrate, serotonin, reduces free energy barriers between conformational states to promote SERT dynamics, the conformational free energy landscape in the presence of APP+ instead resembles Na+ bound-SERT, with a higher free energy barrier for transitioning to an inward-facing state. The deep mutational scan for SERT-catalyzed import of APP+ finds mutations that promote the necessary conformational changes that would otherwise be facilitated by the native substrate. Indeed, hundreds of gain-of-function mutations for APP+ import are found along the permeation pathway, most notably mutations that favor opening of a solvent-exposed intracellular vestibule. The mutagenesis data support the simulated mechanism in which the neurotransmitter and a symported sodium share a common cytosolic exit pathway to achieve coupling. Furthermore, the mutational landscape for SERT surface trafficking, which likely filters out misfolded sequences, reveals that residues along the permeation pathway are mutationally tolerant, providing plausible evolutionary pathways for changes in transporter properties while maintaining folded structure.
Wood ants express uncertainty when engaging with magnetic cues for directional guidance

Wood ants were trained indoors to follow a route in a chosen magnetic direction from the centre of a small, circular arena to find a drop of sucrose at the edge. The arena, surrounded by a white cylindrical wall, was in the centre of a 3D coil system that generated an inclined Earth strength magnetic field in any horizontal direction. Between trials, the chosen magnetic training direction was rotated to a new orientation. Tests were given without food and with fresh or reversed paper on the floor of the arena. In a significant number of tests, ants left the centre facing the goal, or in the opposite direction, but they mostly failed to reach the goal. Tests given early in the day, before any training, show that ants remember the magnetic route direction overnight. On some training trials, the position of the sucrose was also indicated by a black stripe. Not uncommonly, ants first moved in the opposite direction to the stripe before switching to the correct direction. Travel away from the reward seems to express the ant’s uncertainty about the correct path to take. Tests show that this uncertainty may stem from competing directional cues linked to the room, suggesting that ants are reluctant to rely on magnetic information alone. We conclude that ants can remember a route direction defined by an Earth-strength magnetic field and that they express any uncertainty about the correct direction by moving for a stretch in the opposite direction. In a second experiment, an upright and an inverted triangle were fixed 90° from each other to the inside of the cylinder. Sucrose was placed beneath one of the triangles, dependent on the direction of the magnetic field. Ants failed to master this task and to approach the magnetically cued triangle. Instead, they preferred to approach the upright triangle. The ants were again uncertain of the correct direction and expressed this uncertainty through paths that had segments directed towards both the inverted and the upright triangles.
Bio-based elastomer nanoparticles with controllable biodegradability

Recently, biodegradable polymers and nanoscale polymers have become hot topics in advanced polymer research. In this manuscript, we report novel electron beam irradiation vulcanized soft polyester nanoparticles through a three-step method. Some dicarboxylic acids (e.g., succinic acid, sebacic acid, itaconic acid) and diols (e.g., 1,3-propanediol and 1,4-butanediol), which can also be derived from biomass resources, were firstly synthesized into the aliphatic unsaturated polyester by using melt polycondensation, which was followed with polyester emulsification and radiation crosslinking to obtain the elastic polyester nanoparticles. Interestingly, the crosslinked soft polyester nanoparticles with controllable gel content, controllable biodegradability (exhibiting a weight loss ratio of 52.3% within 5 days in the presence of lipase) and low glass transition temperature of about −55 °C are potential candidates to meet the requirements not only for drug delivery carriers but also for modifying some biodegradable brittle polymers which are widely used in pharmaceutical sciences, biotechnology, and biomedicine.
The Great Deceiver: miR-2392’s Hidden Role in Driving SARS-CoV-2 Infection

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic data, we have discovered a circulating miRNA, miR-2392, that is directly involved with SARS-CoV-2 machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia as well as promoting many symptoms associated with COVID-19 infection. We demonstrate miR-2392 is present in the blood and urine of COVID-19 positive patients, but not detected in COVID-19 negative patients. These findings indicate the potential for developing a novel, minimally invasive, COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we have developed a novel miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters and may potentially inhibit a COVID-19 disease state in humans.
RAP80 suppresses the vulnerability of R-loops during DNA double-strand break repair

R-loops, consisting of ssDNA and DNA-RNA hybrids, are potentially vulnerable unless they are appropriately processed. Recent evidence suggests that R-loops can form in the proximity of DNA double-strand breaks (DSBs) within transcriptionally active regions. Yet, how the vulnerability of R-loops is overcome during DSB repair remains unclear. Here, we identify RAP80 as a factor suppressing the vulnerability of ssDNA in R-loops and chromosome translocations and deletions during DSB repair. Mechanistically, RAP80 prevents unscheduled nucleolytic processing of ssDNA in R-loops by CtIP. This mechanism promotes efficient DSB repair via transcription-associated end-joining dependent on BRCA1, Polθ, and LIG1/3. Thus, RAP80 suppresses the vulnerability of R-loops during DSB repair, thereby precluding genomic abnormalities in a critical component of the genome caused by deleterious R-loop processing.
Pooling in a predictive model of V1 explains functional and structural diversity across species

Neurons in the primary visual cortex are selective to orientation with various degrees of selectivity to the spatial phase, from high selectivity in simple cells to low selectivity in complex cells. Various computational models have suggested a possible link between the presence of phase invariant cells and the existence of cortical orientation maps in higher mammals’ V1. These models, however, do not explain the emergence of complex cells in animals that do not show orientation maps. In this study, we build a model of V1 based on a convolutional network called Sparse Deep Predictive Coding (SDPC) and show that a single computational mechanism, pooling, allows the SDPC model to account for the emergence of complex cells as well as cortical orientation maps in V1, as observed in distinct species of mammals. By using different pooling functions, our model developed complex cells in networks that exhibit orientation maps (e.g., like in carnivores and primates) or not (e.g., rodents and lagomorphs). The SDPC can therefore be viewed as a unifying framework that explains the diversity of structural and functional phenomena observed in V1. In particular, we show that orientation maps emerge naturally as the most cost-efficient structure to generate complex cells under the predictive coding principle. Significance Cortical orientation maps are among the most fascinating structures observed in higher mammals brains: In such maps, similar orientations in the input image activate neighboring cells in the cortical surface. However, the computational advantage brought by these structures remains unclear, as some species (rodents and lagomorphs) completely lack orientation maps. In this study, we introduce a computational model that links the presence of orientation maps to a class of nonlinear neurons called complex cells. In particular, we propose that the presence or absence orientation maps correspond to different strategies employed by different species to generate invariance to complex stimuli.
Augmenting Quality and Microbial Safety of Broiler Meat at Refrigeration Storage by Applying Chemical Interventions

The spoilage of meat may arise from several intrinsic and extrinsic factors including physical damage or chemical changes. It is well established fact that microbial activity is by far the most significant cause of meat deterioration. This study was conducted with the aim to investigate the role of chlorine (0.5, 1 and 1.5%), trisodium phosphate (TSP, 5, 10 and 15%) and ascorbic acid (1, 2 and 3%) solutions in meat preservation. Quality parameters including color, texture, pH, TVB-N values and sensory attributes of meat were also analyzed during the storage period of 8 days at refrigeration temperature. Results showed that 15% TSP solution showed the minimum value of total plate count (2.09 log CFU/cm2) which indicated its greater potential for surface decontamination of raw chicken as compared to the other treatments. Practical Applications The key objective of this study was to explore the potential of different antimicrobial agents such as chlorinated water, trisodium phosphate and ascorbic acid for surface decontamination, quality attributes and sensory characteristics of raw poultry meat. Currently, poultry industry is looking for different antimicrobial solutions for online applications to curb microbial load of meat and meat products during processing and preservation. This research work is important for developing countries because most of the meat is being sold in butcher's shop under unhygienic conditions. Accordingly, the current project will help the meat professionals to improve the meat quality and to mitigate the microbial load through deploying different antimicrobial regimens.
Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by the production of autoantibodies predominantly to nuclear material. Many aspects of disease pathology are mediated by the deposition of nucleic acid containing immune complexes, which also induce the type 1interferon response, a characteristic feature of SLE. Notably, SLE is remarkably heterogeneous, with a variety of organs involved in different individuals, who also show variation in disease severity related to their ancestries. Here, we probed one potential contribution to disease heterogeneity as well as a possible source of immunoreactive nucleic acids by exploring the expression of human endogenous retroviruses (HERVs). We investigated the expression of HERVs in SLE and their potential relationship to SLE features and the expression of biochemical pathways, including the interferon gene signature (IGS). Towards this goal, we analyzed available and new RNA-Seq data from two independent whole blood studies using Telescope. We identified 481 locus specific HERV encoding regions that are differentially expressed between case and control individuals with only 14% overlap of differentially expressed HERVs between these two datasets. We identified significant differences between differentially expressed HERVs and non-differentially expressed HERVs between the two datasets. We also characterized the host differentially expressed genes and tested their association with the differentially expressed HERVs. We found that differentially expressed HERVs were significantly more physically proximal to host differentially expressed genes than non-differentially expressed HERVs. Finally, we capitalized on locus specific resolution of HERV mapping to identify key molecular pathways impacted by differential HERV expression in people with SLE.
Psychological Predictors of Precautionary Behaviors in Response to COVID-19: A Structural Model

The first lines of defense during an epidemic are behavioral interventions, including stay-at-home measures or precautionary health training, aimed at reducing contact and disease transmission. Examining the psychosocial variables that may lead to greater adoption of such precautionary behaviors is critical. The present study examines predictors of precautionary practices against coronavirus disease 2019 (COVID-19) in 709 Mexican participants from 24 states. The study was conducted via online questionnaire between the end of March and the beginning of April 2020, when the pandemic response was in its initial stages in Mexico. The instrument included demographic items, as well as scales assessing COVID-19-resembling symptoms, empathy, impulsivity, anhedonic depression, general health practices, alcohol consumption, and COVID-19-associated precautionary behaviors. Most participants reported adopting limited social distancing or other precautionary behaviors against COVID-19. The results of a structural equation model demonstrated that the presence of COVID-19 symptoms was related to impulsivity and general health behaviors. However, no direct association between precautionary behaviors and the presence of COVID-19 symptoms was found. In turn, precautionary behaviors were more prevalent among participants who reported higher empathy and general health behaviors and were inhibited indirectly by impulsivity via alcohol consumption. Furthermore, the model suggests that anhedonic depression symptoms have a negative indirect effect on precautionary behaviors via general health behaviors. Finally, impulsivity showed a negative direct effect on general health behavior. These results highlight the role that general physical health and mental health play on precautionary behavior and the critical importance of addressing issues such as depression, general health behaviors, and impulsivity in promoting safe actions and the protection of self and others.
Geopolitical Inhomogeneities in the Registered Voters’ Distribution and Their Influence in the Voters’ Participation Ratio Distribution: The Mexican Case

Stylized facts appear in electoral processes worldwide, from Brazil to India. Here, we update a statistics carried on in Mexican elections but considering the inhomogeneities in electoral districts through the Nominal List (NL) (the list of valid electors in a given decision process) for the last three presidential elections. We find that the NL distribution at polling station detail is composed of, at least, three windows with a step function structure. Next, we study the consequences of the windows structure for the statistical properties of the processes. We obtain that the asymmetric vote distribution by polling station recovers a Gaussian shape for two of the windows; meanwhile, the standardized distribution of votes follows a distorted Gaussian, near to a skew normal. The distribution of the turnout at each polling station or voters’ participation ratio is close to a skew normal one in the bulk and failing at the wings. The average of voters increases in a linear way with the Nominal List and depends on the window considered. The results do not depend on the municipality, political district or urban versus nonurban distinction, and the electoral process considered.
Controllable Synthesis of 2D and 1D MoS2 Nanostructures on Au Surface

A bottom‐up growth approach based on the assembly of binary atomic constituents delivers precise control over the edge termination and dimensions of nanostructures. Here, the dimensional crossover of MoS2 from 1D nanoribbons to 2D islands synthesized by the assembly of Mo and S atoms on Au(100) surface is studied. Low‐temperature scanning tunneling microscopy and in situ Q‐plus non‐contact atomic force microscopy are employed to elucidate the edge structure of MoS2 nanoribbons at the atomic scale, where three types of zigzag Mo‐edges with different sulfur terminations are observed. It is found that the thermodynamic instability of the armchair edges causes the 1D system to develop faceted zigzag edges which manifests in the morphological evolution from 1D ribbons to 2D triangles as the system size increases.
Evaluation of the compatibility of ketorolac tromethamine with selected polymers and common tablet excipients by thermal and isothermal stress testing

The assessment of potential incompatibilities between an active drug substance and excipients is an important exercise in the early stages of formulation development to ensure essential product stability Differential scanning calorimetry (DSC) and high performance liquid chromatography (HPLC) were successfully employed to evaluate the compatibility of ketorolac tromethamine (KTM) with various polymers and common tablet excipients in the process of developing a controlled release delivery system. The results of DSC and HPLC were combined in order to assess the incompatibility. Among the excipients tested, sodium carboxymethylcellulose and chitosan exhibited potential signs of chemical interaction with the drug. A physical type of drug-excipient interaction was found with magnesium stearate. Overall, a good correlation was observed between DSC and HPLC results in the assessment of compatibility.