Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media

Objetivo. Determinar la precisión y el sesgo de predicción de valores genómicos directos (VGD) usando genotipos imputados a densidad media, en características productivas y reproductivas en ganado Holstein de Antioquia, Colombia. Materiales y métodos. Fueron genotipificados 31 animales con el chip Illumina BovineLD, 64 con el chip Illumina BovineSNP50v2 y 48 con el chip Illumina BovineHD. La imputación se realizó usando dos paneles de SNPs (6K y 40K) a una densidad 44K, usando el programa FINDHAP.f90 v4. Los efectos de los SNPs fueron estimados mediante el método bayes_C, usando genotipos de baja densidad (6K) y genotipos imputados a una densidad media (44_imputado). La precisión y el sesgo de los VGDs fueron determinados mediante validación cruzada. Las características evaluadas fueron: producción de leche (PL), porcentaje de proteína (PRO), porcentaje de grasa (GRA), puntaje de células somáticas (SCS), intervalo entre partos (IEP) y días abiertos (DA). Resultados. Las precisiones de VGD (rpVGD;EBV) en todas las características evaluadas oscilaron entre 0.19 y 0.24 y el sesgo (bVGD;EBV) entre 0.03 y 0.16 cuando se usó el panel 6K y usando el panel 44K_imputado las precisiones fueron mayores, oscilado entre 0.24 y 0.33 y sesgo entre 0.03 y 0.26. Conclusiones. La precisión de predicción de los VGDs fue mayor cuando se usaron genotipos imputados a densidad media, en comparación con la precisión de predicción obtenida empleando genotipos de baja densidad. Por lo cual, en este estudio se concluye que la imputación de genotipos es muy útil dado que aumenta la confiabilidad de la evaluación genómica.
Mathematical modeling with single-cell sequencing data

Single-cell sequencing technologies have revolutionized molecular and cellular biology and stimulated the development of computational tools to analyze the data generated from these technology platforms. However, despite the recent explosion of computational analysis tools, relatively few mathematical models have been developed to utilize these data. Here we compare and contrast two approaches for building mathematical models of cell state-transitions with single-cell RNA-sequencing data with hematopoeisis as a model system; by solving partial differential equations on a graph representing discrete cell state relationships, and by solving the equations on a continuous cell state-space. We demonstrate how to calibrate model parameters from single or multiple time-point single-cell sequencing data, and examine the effects of data processing algorithms on the model calibration and predictions. As an application of our approach, we demonstrate how the calibrated models may be used to mathematically perturb normal hematopoeisis to simulate, predict, and study the emergence of novel cell types during the pathogenesis of acute myeloid leukemia. The mathematical modeling framework we present is general and can be applied to study cell state-transitions in any single-cell genome sequencing dataset. Author summary Here we compare and contrast graph- and continuum-based approaches for constructing mathematical models of cell state-transitions using single-cell RNA-sequencing data. Using two publicly available datasets, we demonstrate how to calibrate mathematical models of hematopoeisis and how to use the models to predict dynamics of acute myeloid leukemia pathogenesis by mathematically perturbing the process of cellular proliferation and differentiation. We apply these modeling approaches to study the effects of perturbing individual or sets of genes in subsets of cells, or by modeling the dynamics of cell state-transitions directly in a reduced dimensional space. We examine the effects of different graph abstraction and trajectory inference algorithms on calibrating the models and the subsequent model predictions. We conclude that both the graph- and continuum-based modeling approaches can be equally well calibrated to data and discuss situations in which one method may be preferable over the other. This work presents a general mathematical modeling framework, applicable to any single-cell sequencing dataset where cell state-transitions are of interest.
ER membranes exhibit phase behavior at sites of organelle contact

Significance Membrane phase behavior in cells permits transient concentration of specific proteins and lipids into dynamic nanoscopic domains. Here, we tested the existence and role of such phase behavior in endoplasmic reticulum (ER) membranes. Employing hypotonic cell swelling, we created large intracellular vesicles (LICVs) from internal organelles. ER LICVs maintained stable interorganelle contacts, with known protein tethers concentrated at the contact sites. Cooled ER LICVs underwent reversible phase separation into microscopically visible domains with different lipid order and membrane fluidity. The phase-separated domains specified sites of contact between the ER and different organelles. The endoplasmic reticulum (ER) is the site of synthesis of secretory and membrane proteins and contacts every organelle of the cell, exchanging lipids and metabolites in a highly regulated manner. How the ER spatially segregates its numerous and diverse functions, including positioning nanoscopic contact sites with other organelles, is unclear. We demonstrate that hypotonic swelling of cells converts the ER and other membrane-bound organelles into micrometer-scale large intracellular vesicles (LICVs) that retain luminal protein content and maintain contact sites with each other through localized organelle tethers. Upon cooling, ER-derived LICVs phase-partition into microscopic domains having different lipid-ordering characteristics, which is reversible upon warming. Ordered ER lipid domains mark contact sites with ER and mitochondria, lipid droplets, endosomes, or plasma membrane, whereas disordered ER lipid domains mark contact sites with lysosomes or peroxisomes. Tethering proteins concentrate at ER–organelle contact sites, allowing time-dependent behavior of lipids and proteins to be studied at these sites. These findings demonstrate that LICVs provide a useful model system for studying the phase behavior and interactive properties of organelles in intact cells.
Contributions of spatial and temporal control of step length symmetry in the transfer of locomotor adaptation from a motorized to a non-motorized split-belt treadmill

Background Locomotor adaptation during motorized split-belt walking depends on independent processes for spatial and temporal control of step length symmetry. The unique mechanics of motorized split-belt walking that constrains two limbs to move at different speeds during double support may limit transfer of step length adaptations to new walking contexts. Research question How do spatial and temporal locomotor outputs contribute to transfer of step length adaptation from constrained motorized split-belt walking to unconstrained non-motorized split-belt walking? Methods We built a non-motorized split-belt treadmill that allows the user to walk at their own pace while simultaneously allowing the two belts to be self-propelled at different speeds. 10 healthy young participants walked on the non-motorized split-belt treadmill after an initial 10-minute adaptation on the motorized split-belt with a 2:1 speed ratio. Foot placement relative to the body and timing between heel strikes were calculated to determine spatial and temporal motor outputs, respectively. Separate repeated measures ANOVAs were used for step length difference and its spatial and temporal components to assess for transfer to the non-motorized treadmill. Results We found robust after-effects in step length difference during transfer to non-motorized split-belt treadmill walking that were primarily driven by changes in temporal motor outputs. Conversely, residual after-effects observed during motorized tied-belt treadmill walking (post-transfer) were driven by changes in spatial motor outputs. Significance Our data showed decoupling of adapted spatial and temporal locomotor outputs during the transfer to non-motorized split-belt walking, raising the new possibility of using a non-motorized split-belt treadmill to target specific spatial or temporal gait deficits.
Retos en el diagnóstico y control del virus de la enfermedad de Marek en Colombia

Aunque la industria avícola colombiana ha crecido casi el doble en producción durante la última década, el diagnóstico de agentes infecciosos y caracterización de estos aún es escasa, y es poca la información acerca de las cepas virales circulantes en el país. Dentro de estos agentes se encuentra el Virus de la Enfermedad de Marek (VEM), el cual es un patógeno inmunosupresor que puede causar mortalidad elevada y graves pérdidas en la producción. Aunque es poco probable que ocurran casos clínicos de la enfermedad causada por el VEM, debido a los programas de vacunación generalizada con GaHV-2 (serotipo I) y HVT (serotipo III), la inmunosupresión que causan las infecciones subclínicas puede estar causando pérdidas considerables en la producción avícola nacional. El objetivo de esta revisión es describir brevemente la enfermedad de Marek y el estado actual del estudio de la infección en Colombia.
Neglected and Underutilized Legume Crops: Improvement and Future Prospects

Sustainable agricultural productivity is hampered by over-dependency on major staple crops, neglect and underutilization of others, climate change, as well as land deterioration. Challenges posed by these limiting factors are undoubtedly contribut-ing to global food insecurity, increased rural poverty, and malnutrition in the less developed countries. Miscellaneous neglected and underutilized grain legumes (MNUGLs) are crops primarily characterized by inherent features and capabilities to withstand the effects of abiotic stress and climate change, significantly replenish the soil, as well as boost food and protein security. This chapter provides insight into the benefits of MNUGLs as food and nutritional security climate smart crops, capable of growing on marginal lands. Exploring and improving MNUGLs depend on a number of factors among which are concerted research efforts, cultivation and production, as well as utilization awareness across global populace geared toward reawakening the interest on the abandoned legumes. The emergence of the clustered regularly interspaced short palindromic repeat (CRISPR/cas9) technology combined with marker-assisted selection (MAS) offers great opportunities to improve MNUGLs for sustainable utilization. Advances in improvement of MNUGLs using omic technologies and the prospects for their genetic modification were highlighted and discussed.
Target localization accuracy improvement via sensor mobility

ABSTRACT Sensor deployment positions play an important factor in determining target location estimation error performance in sensor networks employing received signal strength indicator measurements. The problem we investigate is as follows: Given a deployment area that has possibly non-uniform estimation error requirements and some initial sensor positions, then how can these sensors be deployed such that requirements are met as best as possible? We propose three variants of a low-complexity distributed strategy that require little information exchange between neighboring sensors. Each sensor locally calculates both the direction and magnitude of movement necessary to reduce the difference between achieved and required estimation errors at points within it sensing radius. The direction of movement is calculated as a weighted combination of these points. The weights can incorporate the error difference, number of sensors covering a point, the distance to a sensor and sensor density. Depending on the parameters chosen, three different weighing methods (namely, the density weighted centroid, error weighted centroid (EWC) and modified EWC) are proposed in this paper. We also provide an analytic derivation of the necessary distance a sensor should move. The proposed strategy is compared against a the RELOCATE algorithm and centralized generic genetic algorithm (GA) relocation method. Simulation results demonstrate that using the distributed strategy can achieve a comparable performance (within 10%) of the GA’s performance and significantly outperform that of the RELOCATE. Sensor movement for different k. GRAPHICAL ABSTRACT
Effect of Ground and Pelleted Sericea Lespedeza Whole Plant and Leaf Only on Gastrointestinal Nematode and Coccidial Infection in Goats

Two 42-day feeding trials in pens were completed with young goats (Spanish, intact male, six months old, n = 29 Trial 1; n = 20 Trial 2) to determine the anti-parasitic bioactivity of whole plant and leaf only sericea lespedeza (SL; Lespedeza cuneata) fed as a ground meal or in pelleted form. In Trial 1, goats were fed SL leaf only pellets, SL whole plant pellets, or a commercial goat pellet as 50% of a complete ration, while in Trial 2, kids were fed either ground SL leaf meal or ground whole plant SL meal as 25% of a complete ration. Fecal samples were collected weekly for determination of gastrointestinal nematode (GIN) fecal egg counts (FEC) and coccidia fecal oocyst counts (FOC). In Trial 1, both of the pelleted SL rations reduced FEC (p < 0.06) relative to the kids fed the control ration, and for FOC, there were lower values on Days 7 to 42 relative to Day 0 for goats on either pelleted SL diet, while FOC for control animals did not change over time (interaction, p < 0.01). In Trial 2, both ground whole plant and leaf only SL diets reduced (p < 0.05) FEC of the goats over time, but the effect was faster in the kids on the SL leaf meal ration. At 50% of the diet, SL leaf and whole plant meal pellets were equally effective against GIN egg and coccidial oocyst production in young kids, but SL leaf meal was more effective in reducing GIN egg production than whole plant SL meal when fed at 25% of the diet.
Antifungal Potentiality and Physiological Characterization of Trichoderma Isolates from Port Said Governorate

A TOTAL of twenty Trichoderma isolates belonging to seven species were isolated from several locations at Port Said Governorate. Physiological characteristics of these isolates and their antagonistic effect against Sclerotinia sclerotiorum, the causative agent of white mold of Phaseolus vulgaris were evaluated. Trichoderma polysporum 2 showed the highest activity of total cellulase reached up to 2.95 filter paper unit ml-1. T. harzianum 2 had the highest endoglucanase activity (5.47 IU ml-1), whereas T. polysporum 1 had the highest chitinase activity (1.01 IU ml-1). Siderophores production was assayed using FeCl3, tetrazolium, Arnow’s and spectrophotometric tests. Most of the isolates were able to produce hydroxamate and carboxylate types of siderophores. The ability of Trichoderma to produce indole acetic acid (IAA) and gibberellic acid (GA3) were also investigated. Trichoderma harzianum 2 showed the highest concentration of IAA in broth medium reached up to 13. 19μg/ml, whereas T. polysporum 1 showed the highest concentration of GA3 by 586. 51μg/ml. The antagonistic potentialities of Trichoderma isolates against Sclerotinia sclerotiorum were tested in vitro by using dual culture, base to base assay and the crude liquid extract effect of the isolates. Percentages of inhibition of radial growth of the pathogen by T. polysporum 1 in dual culture and crude extract methods were 45.97% and 87.78%, respectively. Also, the volatiles of T. piluliferum 2 showed a reduction of the radial growth by 66.85%. So, some Trichoderma isolates collected from Port Said soil showed high biocontrol activity against S. sclerotiorum.
Holocene Indian Summer Monsoon variability from the core monsoon zone of India, a pollen-based review

Abstract Palaeoclimatic reconstructions from sediment cores of the Arabian Sea, Bay of Bengal, and other terrestrial ecosystems including lakes, peatlands and proglacial areas from the Indian subcontinent have been used to understand the past Indian Summer Monsoon (ISM) variability. The core monsoon zone (CMZ) of India is one of the most important regions to understand past ISM dynamics. Pollen based palaeoclimatic reconstructions in the CMZ of India suggest a progressive increase in the ISM during the Holocene. However, the results suggesting a weak ISM after the Younger Dryas (YD) cooling event are contrary to the observations made in other parts of the country. Besides this, the minor climatic fluctuations are difficult to find in most of the reconstructions. This may be attributed to poor sample resolution and chronological control. These limitations make it difficult to ascertain whether the response of vegetation to climatic change has been insignificant or whether this change is not reflected in the proxy (proxy response). As a consequence, we argue that pollen based palaeoclimatic reconstructions are one of the most widely used proxies and will be meaningful as backbone for climate models only if the reconstructions become more quantitative.
Sensory Modality-Independent Activation of the Brain Network for Language

The meaning of a sentence can be understood, whether presented in written or spoken form. Therefore, it is highly probable that brain processes supporting language comprehension are at least partly independent of sensory modality. To identify where and when in the brain language processing is independent of sensory modality, we directly compared neuromagnetic brain signals of 200 human subjects (102 males) either reading or listening to sentences. The meaning of a sentence can be understood, whether presented in written or spoken form. Therefore, it is highly probable that brain processes supporting language comprehension are at least partly independent of sensory modality. To identify where and when in the brain language processing is independent of sensory modality, we directly compared neuromagnetic brain signals of 200 human subjects (102 males) either reading or listening to sentences. We used multiset canonical correlation analysis to align individual subject data in a way that boosts those aspects of the signal that are common to all, allowing us to capture word-by-word signal variations, consistent across subjects and at a fine temporal scale. Quantifying this consistency in activation across both reading and listening tasks revealed a mostly left-hemispheric cortical network. Areas showing consistent activity patterns included not only areas previously implicated in higher-level language processing, such as left prefrontal, superior and middle temporal areas, and anterior temporal lobe, but also parts of the control network as well as subcentral and more posterior temporal-parietal areas. Activity in this supramodal sentence-processing network starts in temporal areas and rapidly spreads to the other regions involved. The findings indicate not only the involvement of a large network of brain areas in supramodal language processing but also that the linguistic information contained in the unfolding sentences modulates brain activity in a word-specific manner across subjects. SIGNIFICANCE STATEMENT The brain can extract meaning from written and spoken messages alike. This requires activity of both brain circuits capable of processing sensory modality-specific aspects of the input signals as well as coordinated brain activity to extract modality-independent meaning from the input. Using traditional methods, it is difficult to disentangle modality-specific activation from modality-independent activation. In this work, we developed and applied a multivariate methodology that allows for a direct quantification of sensory modality-independent brain activity, revealing fast activation of a wide network of brain areas, both including and extending beyond the core network for language.
Temperature‐mediated responses of carbon fluxes to precipitation variabilities in an alpine meadow ecosystem on the Tibetan Plateau

Abstract Effects of climate warming and changing precipitation on ecosystem carbon fluxes have been intensively studied. However, how they co‐regulate carbon fluxes is still elusive for some understudied ecosystems. To fill the gap, we examined net ecosystem productivity (NEP), gross ecosystem productivity (GEP,) and ecosystem respiration (ER) responses to multilevel of temperature increments (control, warming 1, warming 2, warming 3, warming 4) in three contrasting hydrological growing seasons in a typical semiarid alpine meadow. We found that carbon fluxes responded to precipitation variations more strongly in low‐level warming treatments than in high‐level ones. The distinct responses were attributable to different soil water conditions and community composition under low‐level and high‐level warming during the three growing seasons. In addition, carbon fluxes were much more sensitive to decreased than to increased precipitation in low‐level warming treatments, but not in high‐level ones. At a regional scale, this negative asymmetry was further corroborated. This study reveals that future precipitation changes, particularly decreased precipitation would induce significant change in carbon fluxes, and the effect magnitude is regulated by climate warming size.
Seroprevalence of viral and vector-borne bacterial pathogens in domestic dogs (Canis familiaris) in northern Botswana

Background Domestic dogs (Canis familiaris) have the potential to act as disease reservoirs for wildlife and are important sentinels for common circulating pathogens. Therefore, the infectious disease seroprevalence among domestic dogs in northern Botswana may be indicative of pathogen exposure of various wildlife species. The objective of this study was to assess the seroprevalence of Ehrlichia spp. , Borrelia burgdorferi, Anaplasma spp. , Dirofilaria immitis, canine adenovirus, canine parvovirus, and canine distemper virus in domestic dogs as proxies of disease prevalence in the local wildlife in the Okavango Delta region of Botswana. Statistical analysis assessed crude and factor-specific seroprevalence proportions and assessed the factors age, sex, and geographical location as predictors of seropositivity. Logistic regression was used to identify adjusted predictors of seropositivity for each of the pathogens of interest. Results Samples from 233 dogs in a total of 7 locations in Maun, Botswana, and surrounding villages were collected and serologically analyzed. No dogs were seropositive for B. burgdorferi, while low seroprevalence proportions were observed for Anaplasma spp. (2.2%) and D. immitis (0.9%). Higher seroprevalence proportions were observed for the tick-borne pathogen, Ehrlichia spp. (21.0%), and 19.7% were seropositive for canine adenovirus (hepatitis). The highest seroprevalence proportions were for canine parvovirus (70.0%) and canine distemper virus (44.8%). The predictors of seropositivity revealed that adults were more likely to be seropositive for canine adenovirus, canine distemper virus, and canine parvovirus than juveniles, and location was a risk factor for canine adenovirus, canine distemper virus, canine parvovirus, and Ehrlichia spp. Conclusions Results indicate that increasing tick control and vaccination campaigns for domestic dogs may improve the health of domestic animals, and potentially wildlife and humans in the Okavango Delta since viral and vector-borne bacterial pathogens can be transmitted between them.