Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Diluents and Storage Time on the Cryopreservation of Collared Peccary (Pecari tajacu) Semen after Cooling Storage in a Transport Container at 5 °C

Simple Summary Given the persistence of certain threats to the survival of several free-living species, the need for efficient strategies for the conservation of genetic resources becomes increasingly urgent. An excellent option to help improve cryopreservation in peccaries would be to combine it with specific protocols and equipment for semen cooling, allowing transport and cooling curves different from those already used in conventional cryopreservation protocols. The ability to transport refrigerated semen from free-living species would allow the exchange of valuable biological material between institutions (zoos, reserves, breeding facilities, etc.), followed by shipment to a specialized laboratory for long-term conservation (cryopreservation), without the need to move the animals. Along with cooling systems, dilution media are fundamental to semen processing protocols. To our knowledge, this is the first study to establish protocols for integrating cooling and cryopreservation techniques for peccary semen using shipping containers. Overall, this study revealed promising new alternative protocols for the cryopreservation of peccary semen, opening new perspectives for this technique. Abstract We verified the possibility of cooling peccary semen for 4, 24, and 48 h before cryopreservation, using different dilution media (TRIS + egg yolk (20%) and PRIMXcell Ultra). Ten ejaculates were divided equally into six aliquots and then diluted. Two aliquots were stored in a biological incubator (4 h), and the remaining aliquots were stored in a commercial container, the Botutainer® (24 and 48 h), both at 5 °C. The samples were cryopreserved and then evaluated for kinetic parameters, functionality, integrity, mitochondrial activity, morphology, and sperm binding capacity. After thawing, samples diluted in TRIS showed total motility of 43.4 ± 6.8%, 48.4 ± 6.2%, and 38.6 ± 5.0% after cooling for 4, 24, and 48 h before cryopreservation, respectively. Such results are significantly greater than those achieved with the use of PRIMXcell diluent for 4 (8.3 ± 2.8%), 24 (4.7 ± 1.4%), and 48 h (4.8 ± 2.9%) storage (p < 0.05). Furthermore, TRIS provided better preservation of sperm membrane integrity when samples were cooled for 24 h (44.5 ± 4.7%) before cryopreservation compared to those samples diluted in PRIMXcell Ultra stored for 24 (25.7 ± 4.0%) and 48 h (25.2 ± 4.0%) before freezing (p < 0.05). In summary, we suggest TRIS diluent + egg yolk (20%) as an effective option to allow semen to cool for 24 or 48 h in a transport container before cryopreservation.
Automatic Active Lesion Tracking in Multiple Sclerosis Using Unsupervised Machine Learning

Background: Identifying active lesions in magnetic resonance imaging (MRI) is crucial for the diagnosis and treatment planning of multiple sclerosis (MS). Active lesions on MRI are identified following the administration of Gadolinium-based contrast agents (GBCAs). However, recent studies have reported that repeated administration of GBCA results in the accumulation of Gd in tissues. In addition, GBCA administration increases health care costs. Thus, reducing or eliminating GBCA administration for active lesion detection is important for improved patient safety and reduced healthcare costs. Current state-of-the-art methods for identifying active lesions in brain MRI without GBCA administration utilize data-intensive deep learning methods. Objective: To implement nonlinear dimensionality reduction (NLDR) methods, locally linear embedding (LLE) and isometric feature mapping (Isomap), which are less data-intensive, for automatically identifying active lesions on brain MRI in MS patients, without the administration of contrast agents. Materials and Methods: Fluid-attenuated inversion recovery (FLAIR), T2-weighted, proton density-weighted, and pre- and post-contrast T1-weighted images were included in the multiparametric MRI dataset used in this study. Subtracted pre- and post-contrast T1-weighted images were labeled by experts as active lesions (ground truth). Unsupervised methods, LLE and Isomap, were used to reconstruct multiparametric brain MR images into a single embedded image. Active lesions were identified on the embedded images and compared with ground truth lesions. The performance of NLDR methods was evaluated by calculating the Dice similarity (DS) index between the observed and identified active lesions in embedded images. Results: LLE and Isomap, were applied to 40 MS patients, achieving median DS scores of 0.74 ± 0.1 and 0.78 ± 0.09, respectively, outperforming current state-of-the-art methods. Conclusions: NLDR methods, Isomap and LLE, are viable options for the identification of active MS lesions on non-contrast images, and potentially could be used as a clinical decision tool.
A relaxation-based approach for the orthogonal Procrustes problem with data uncertainties

The orthogonal Procrustes problem (OPP) deals with matrix approximations. The solution of this problem gives an orthogonal matrix to best transform one data matrix to another, in a Frobenius norm sense. In this work, we use semidefinite relaxation (SDR) to find the solutions of different OPP formulations. For the standard problem formulation, this approach yields an exact solution, i.e. no relaxation gap. We also address uncertainties in the data matrices and formulate a min-max robust problem. The robust problem, being non-convex, turns out to be a difficult optimization problem; however, it is relatively straight forward to approximate it into a convex optimization problem using SDR. Our preliminary results on robust problem show that the solution of the relaxed uncertain problem does not guarantee zero relaxation gap, and as a result, we cannot always find a solution, which satisfies the orthogonality constraint. In such cases we use orthogonalization, which gives the nearest orthogonal matrix from the SDR based solution. All these relaxed formulations, can be easily converted into a semidefinite program (SDP), for which polynomial time efficient algorithms exists. For the nominal problems, the presented approach may not be computationally efficient than other existing methods. In this work, our main contribution is to demonstrate that the SDR approach provides a unified framework to solve not only the standard OPP but can also solve the problems with uncertainties in the data matrices, which other existing approaches cannot handle.
Genome Wide Association Analysis Reveals New Production Trait Genes in a Male Duroc Population

In this study, 796 male Duroc pigs were used to identify genomic regions controlling growth traits. Three production traits were studied: food conversion ratio, days to 100 KG, and average daily gain, using a panel of 39,436 single nucleotide polymorphisms. In total, we detected 11 genome-wide and 162 chromosome-wide single nucleotide polymorphism trait associations. The Gene ontology analysis identified 14 candidate genes close to significant single nucleotide polymorphisms, with growth-related functions: six for days to 100 KG (WT1, FBXO3, DOCK7, PPP3CA, AGPAT9, and NKX6-1), seven for food conversion ratio (MAP2, TBX15, IVL, ARL15, CPS1, VWC2L, and VAV3), and one for average daily gain (COL27A1). Gene ontology analysis indicated that most of the candidate genes are involved in muscle, fat, bone or nervous system development, nutrient absorption, and metabolism, which are all either directly or indirectly related to growth traits in pigs. Additionally, we found four haplotype blocks composed of suggestive single nucleotide polymorphisms located in the growth trait-related quantitative trait loci and further narrowed down the ranges, the largest of which decreased by ~60 Mb. Hence, our results could be used to improve pig production traits by increasing the frequency of favorable alleles via artificial selection.
Protective Effects of Lactobacillus plantarum CCFM8610 against Chronic Cadmium Toxicity in Mice Indicate Routes of Protection besides Intestinal Sequestration

ABSTRACT Our previous study confirmed the ability of Lactobacillus plantarum CCFM8610 to protect against acute cadmium (Cd) toxicity in mice. This study was designed to evaluate the protective effects of CCFM8610 against chronic Cd toxicity in mice and to gain insights into the protection mode of this strain. Experimental mice were divided into two groups and exposed to Cd for 8 weeks via drinking water or intraperitoneal injection. Both groups were further divided into four subgroups, control, Cd only, CCFM8610 only, and Cd plus CCFM8610. Levels of Cd were measured in the feces, liver, and kidneys, and alterations of several biomarkers of Cd toxicity were noted. The results showed that when Cd was introduced orally, cotreatment with Cd and CCFM8610 effectively decreased intestinal Cd absorption, reduced Cd accumulation in tissue, alleviated tissue oxidative stress, reversed hepatic and renal damage, and ameliorated the corresponding histopathological changes. When Cd was introduced intraperitoneally, administration of CCFM8610 did not have an impact on tissue Cd accumulation or reverse the activities of antioxidant enzymes. However, CCFM8610 still offered protection against oxidative stress and reversed the alterations of Cd toxicity biomarkers and tissue histopathology. These results suggest that CCFM8610 is effective against chronic cadmium toxicity in mice. Besides intestinal Cd sequestration, CCFM8610 treatment offers direct protection against Cd-induced oxidative stress. We also provide evidence that the latter is unlikely to be mediated via protection against Cd-induced alteration of antioxidant enzyme activities.
Application of powdered activated carbon (PAC) for membrane fouling control in a pilot-scale MBR system.

Membrane fouling is considered to be the most serious drawback in wastewater treatment when using membrane bioreactors (MBRs), leading to membrane permeability decrease and efficiency deterioration. This work aims to develop an integrated methodology for membrane fouling control, using powdered activated carbon (PAC), which will enhance the adsorption of soluble microbial products (SMP) and improve membrane filterability, by altering the mixed liquor's characteristics. Reversible fouling was assessed in terms of sludge filterability measurements, according to the standard time-to-filter (TTF) method, while irreversible fouling was assessed in terms of SMP removal. Results showed that the addition of PAC at the concentration of 3 g/L in the mixed liquor reduced SMP concentration and enhanced substantially the sludge filterability. Furthermore, the TTFPAC/TTFno PAC ratios were lower, than the corresponding SMPPAC. /SMPno PAC ratios, indicating that the batch-mode, short-term addition of PAC promotes the reversible, rather than the irreversible fouling mitigation.
Angular analysis of two classes of non-polyhedral convex cones: the point of view of optimization theory

There are three related concepts that arise in connection with the angular analysis of a convex cone: antipodality, criticality, and Nash equilibria. These concepts are geometric in nature but they can also be approached from the perspective of optimization theory. A detailed angular analysis of polyhedral convex cones has been carried out in a recent work of ours. This note focus on two important classes of non-polyhedral convex cones: elliptic cones in an Euclidean vector space and spectral cones in a space of symmetric matrices.
Matching People and Jobs: A Bilateral Recommendation Approach

Recommendation systems are widely used on the Internet to assist customers in finding the products or services that best fit with their individual preferences. While current implementations successfully reduce information overload by generating personalized suggestions when searching for objects such as books or movies, recommendation systems so far cannot be found in another potential field of application: the personalized search for subjects such as applicants in a recruitment scenario. Theory shows that a good match between persons and jobs needs to consider both, the preferences of the recruiter and the preferences of the candidate. Based on this requirement for modeling bilateral selection decisions, we present an approach applying two distinct recommendation systems to the field in order to improve the match between people and jobs. Finally, we present first validation test runs from a student experiment showing promising results.
Development of an Asian American parental racial-ethnic socialization scale.

OBJECTIVE To develop a measure of parental racial-ethnic socialization that is appropriate for Asian American families. METHOD To test the reliability and validity of this new measure, we surveyed 575 Asian American emerging adults (49% female, 79% U.S. born). RESULTS Using exploratory and confirmatory factor analyses, the results show 7 reliable subscales: maintenance of heritage culture, becoming American, awareness of discrimination, avoidance of other groups, minimization of race, promotion of equality, and cultural pluralism. Tests of factorial invariance show that overall, the subscales demonstrate, at minimum, partial metric invariance across gender, age, nativity, educational attainment, parent educational attainment, geographic region of residence, and Asian-heritage region. Thus, the relations among the subscales with other variables can be compared across these different subgroups. The subscales also correlated with ethnic identity, ethnic centrality, perceptions of discrimination, and pluralistic orientation, demonstrating construct validity. CONCLUSION In an increasingly complex and diverse social world, our scale will be useful for gaining a better understanding of how Asian American parents socialize their children regarding issues of race, discrimination, culture, and diversity. (PsycINFO Database Record
Brain-derived Neurotrophic Factor Is Associated with Cognitive Impairment in Elderly Korean Individuals

Objective Brain-derived neurotrophic factor (BDNF) is a neurotrophin that is widely expressed in the mammalian brain and acts to regulate neuronal survival and influence cognitive processes. The present study measured serum BDNF levels to investigate the associations of the BDNF Val66Met and 5-hydroxytryptamine transporter linked promoter region (5-HTTLPR) polymorphisms with cognitive function in elderly Korean individuals. Methods Over 60 years, a total of 834 subjects were recruited for the present study. The subjects were classified into groups based on the degree of cognitive impairment (age-associated cognitive decline, mild cognitive impairment, and Alzheimer’s disease) and compared with normal controls in terms of a neuropsychological assessment and a clinical evaluation. Results Of the initial 834 study participants, 165 (59 controls and 106 subjects with cognitive impairments) completed the study. There was a significant increase in serum BDNF levels in subjects with cognitive impairments relative to the control group and the BDNF Val66Met polymorphism was significantly associated with cognitive function but not serum BDNF levels. The 5-HTTLPR polymorphism did not have any associations with cognitive impairment or serum BDNF levels. Conclusion The present findings suggest that BDNF may play a role in the pathophysiology of cognitive impairment and the BDNF Val66Met polymorphism may be an important factor in the susceptibility to these age-related deficits.
Genotypic and Phenotypic Diversity Does Not Affect Productivity and Drought Response in Competitive Stands of Trifolium repens

Clonal plants can form dense canopies in which plants of different genetic origin are competing for the uptake of essential resources. The competitive relationships among these clones are likely to be affected by extreme environmental conditions, such as prolonged drought spells, which are predicted to occur more frequently due to global climate change. This, in turn, may alter characteristics of the ecological system and its associated functioning. We hypothesized that the relative success of individual clones will depend on the size of the ramets as ramets with larger leaves and longer petioles (large ramets) were predicted to have a competitive advantage in terms of increased light interception over smaller-sized ramets. Under drier conditions the relative performances of genotypes were expected to change leading to a change in genotype ranking. We also hypothesized that increased genotypic and phenotypic diversity will increase stand performance and resistance to drought. These hypotheses and the mechanisms responsible for shifts in competitive relationships were investigated by subjecting genotypes of the important pasture legume Trifolium repens to competition with either genetically identical clones, genetically different but similarly sized clones, or genetically as well as morphologically different clones under well-watered and dry conditions. Competitive relationships were affected by ramet size with large genotypes outperforming small genotypes in diverse stands in terms of biomass production. However, large genotypes also produced relatively fewer ramets than small genotypes and could not benefit in terms of clonal reproduction from competing with smaller genotypes, indicating that evolutionary shifts in genotype composition will depend on whether ramet size or ramet number is under selection. In contrast to our hypotheses, diversity did not increase stand performance under different selection regimes and genotype ranking was hardly affected by soil moisture, indicating that increasing fluctuations in water availability result in few short-term effects on genotypic diversity in this stoloniferous grassland species. Communities dominated by stoloniferous herbs such as T. repens may be relatively resilient to environmental change and to low levels of genetic diversity.
High‐resolution urban flood model for risk mitigation validated with records collected by the affected community

The Dupuy catchment (Laferrere, Metropolitan Region of Buenos Aires) has suffered numerous floods in recent years. The frequency and magnitude of these events, coupled with the large number of people affected, has led to some community representatives organising themselves to collect flood records, increase awareness of the problem and push for solutions and mitigating actions. That campaign inspired the study of the flooding dynamics of the catchment, with the aim of developing simple tools for risk mitigation. To analyse the water dynamics in the catchment, a high‐resolution urban numerical model was implemented with the EPA‐SWMM software. Due to the lack of systematic observations of flow variables, the model was validated using data collected by the affected community itself. More than 500 simulations of different synthetic storms were run on a high‐performance computational cluster and analysed. These processed results, coupled with the observation of rainfall intensities during an event, may be used by the community and risk managers to reduce exposure and mitigate flood risk.
Genetic Analysis of Rhizobium leguminosarum bv. Phaseoli Mutants Defective in Nodulation and Nodulation Suppression

Nodulation-defective rhizobia and their nodule-forming derivatives containing cloned DNA from the wild type were used to study nodulation suppression in Phaseolus vulgaris L. Non-nitrogen-fixing derivatives which formed rhizobia-containing white nodules induced partial suppression. Comparison of this with the complete suppression by Fix+ derivatives and a Fix- mutant which formed rhizobia-containing pink nodules suggests that the extent of suppression may be related to successive stages of nodule development.
A novel CSI pre-processing scheme for device-free localization indoors

Device-free localization of people and objects indoors not equipped with radios is playing a critical role in many emerging applications. This paper presents a novel channel state information (CSI) pre-processing scheme that enables accurate device-free localization indoors. The basic idea is simple: CSI is sensitive to a target's location and by modelling the CSI measurements of multiple wireless links as a set of power fading based equations, the target location can be determined. However, due to rich multipaths in indoor environment, the received signal strength (RSS) or even the fine-grained CSI can not be easily modelled. We observe that even in a rich multipath environment, not all subcarriers are equally affected by multipath reflections. Our preprocessing scheme tries to identify the subcarriers not affected by multipath. Thus, CSIs on the "clean" subcarriers can be modelled and utilized for accurate localization. Extensive experiments demonstrate the effectiveness of the proposed pre-processing scheme.
On Coverage and Debug in Random Stimulus Generation

Randomly generated stimulus in functional verification provides significant advantages in validating a wide range of scenarios. However, random generation requires a more sophisticated verification environment, one that is more difficult to build and maintain. To enjoy the benefits that random stimuli has to offer, verification teams need to rely on their tools to fully cover the specified DUT functionality and to provide the right debug technology to cope with the complications arise. In this paper, we explore these requirements. We investigate the distribution aspects required to maximize the functional coverage, and we discuss how to effectively debug a verification environment with random components.
Comparative genomics reveals insights into avian genome evolution and adaptation

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.