Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle

Simple Summary Structural variants are large changes to the DNA sequences that differ from individual to individual. We discovered and quality-controlled a set of 24,908 structural variants and used a technique called imputation to infer them into 35,588 Holstein and Jersey cattle. We then investigated whether the structural variants affected key dairy cattle traits such as milk production, fertility and overall conformation. Structural variants explained generally less than 10 percent of the phenotypic variation in these traits. Four of the structural variants were significantly associated with dairy cattle production traits. However, the inclusion of the structural variants in the genomic prediction model did not increase genomic prediction accuracy. Abstract Structural variations (SVs) are large DNA segments of deletions, duplications, copy number variations, inversions and translocations in a re-sequenced genome compared to a reference genome. They have been found to be associated with several complex traits in dairy cattle and could potentially help to improve genomic prediction accuracy of dairy traits. Imputation of SVs was performed in individuals genotyped with single-nucleotide polymorphism (SNP) panels without the expense of sequencing them. In this study, we generated 24,908 high-quality SVs in a total of 478 whole-genome sequenced Holstein and Jersey cattle. We imputed 4489 SVs with R2 > 0.5 into 35,568 Holstein and Jersey dairy cattle with 578,999 SNPs with two pipelines, FImpute and Eagle2.3-Minimac3. Genome-wide association studies for production, fertility and overall type with these 4489 SVs revealed four significant SVs, of which two were highly linked to significant SNP. We also estimated the variance components for SNP and SV models for these traits using genomic best linear unbiased prediction (GBLUP). Furthermore, we assessed the effect on genomic prediction accuracy of adding SVs to GBLUP models. The estimated percentage of genetic variance captured by SVs for production traits was up to 4.57% for milk yield in bulls and 3.53% for protein yield in cows. Finally, no consistent increase in genomic prediction accuracy was observed when including SVs in GBLUP.
Microalgae n-3 PUFAs Production and Use in Food and Feed Industries

N-3 polyunsaturated fatty acids (n-3 PUFAs), and especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are essential compounds for human health. They have been proven to act positively on a panel of diseases and have interesting anti-oxidative, anti-inflammatory or anti-cancer properties. For these reasons, they are receiving more and more attention in recent years, especially future food or feed development. EPA and DHA come mainly from marine sources like fish or seaweed. Unfortunately, due to global warming, these compounds are becoming scarce for humans because of overfishing and stock reduction. Although increasing in recent years, aquaculture appears insufficient to meet the increasing requirements of these healthy molecules for humans. One alternative resides in the cultivation of microalgae, the initial producers of EPA and DHA. They are also rich in biochemicals with interesting properties. After defining macro and microalgae, this review synthesizes the current knowledge on n-3 PUFAs regarding health benefits and the challenges surrounding their supply within the environmental context. Microalgae n-3 PUFA production is examined and its synthesis pathways are discussed. Finally, the use of EPA and DHA in food and feed is investigated. This work aims to define better the issues surrounding n-3 PUFA production and supply and the potential of microalgae as a sustainable source of compounds to enhance the food and feed of the future.
Overexpression of the Zygophyllum xanthoxylum Aquaporin, ZxPIP1;3, Promotes Plant Growth and Stress Tolerance

Drought and salinity can result in cell dehydration and water unbalance in plants, which seriously diminish plant growth and development. Cellular water homeostasis maintained by aquaporin is one of the important strategies for plants to cope with these two stresses. In this study, a stress-induced aquaporin, ZxPIP1;3, belonging to the PIP1 subgroup, was identified from the succulent xerophyte Zygophyllum xanthoxylum. The subcellular localization showed that ZxPIP1;3-GFP was located in the plasma membrane. The overexpression of ZxPIP1;3 in Arabidopsis prompted plant growth under favorable condition. In addition, it also conferred salt and drought tolerance with better water status as well as less ion toxicity and membrane injury, which led to more efficient photosynthesis and improved growth vigor via inducing stress-related responsive genes. This study reveals the molecular mechanisms of xerophytes’ stress tolerance and provides a valuable candidate that could be used in genetic engineering to improve crop growth and stress tolerance.
Priority trends and prospects of blackberry breeding in conditions of Central Russia

This overview substantiates the possibility and expediency of blackberry breeding in Central Russia, where it is in demand, but not widespread in horticulture. Significant achievements of world breeding, which gave modern cultivars a large set of economically important qualities and growing interest in it all over the world, including Russian gardeners, make it relevant to work with blackberries as an object of selection, and as a promising garden plant. However, insufficient frost and winter hardiness of the bulk of the cultivars of this culture cause certain difficulties when growing it in the areas with cold winters to which the Central zone of Russia belongs. The expansion of the market of berry products also imposes increasingly high requirements on the complex of economic indicators of new cultivars, primarily the quality of blackberry fruit. In this regard, improving the existing range of varieties of the culture, increasing its adaptive properties and commodity qualities of berries are urgent tasks for breeders when creating new cultivars. The relevance of blackberry breeding is also dictated by the fact that in Russia its domestic range of varieties is represented by only one modern cultivar obtained in the southern region and adapted, first of all, to it. For the Central zone of the country, the cultivars of this plant have not been developed (except for the limited experiments of I.V. Michurin conducted almost 100 years ago). Therefore, the breeding of adapted cultivars of the culture in the climatic conditions of this region may be promising. It is also possible to grow here (with shelter for the winter) the cultivars already created abroad that can give with the right agricultural technology a good industrial harvest, which is confirmed by the practice of amateur and farm gardening, as well as scientific research. The purpose of this work is to designate the leading directions of blackberry breeding, the most important in the conditions of Central Russia and to show prospects of the development of new cultivars of this valuable culture in the specified climatic zone. The analysis of world trends and experience in the blackberry breeding and variety study, as well as the results of our own research of the culture conducted in the Orel region, allow us to consider it promising and relevant to work on improving the range of varieties of this plant in Central Russia. All priority areas of blackberry breeding, indicated in foreign and domestic breeding programs (winter hardiness, high quality of fresh and processed fruit, the correct shape of berries, their large size, the necessary values of biochemical composition, high productivity of plants, thornless shoots and high resistance to diseases and pests), are relevant for this region of our country, while high winter hardiness is currently the most important of them.
Serum Sodium Levels Predict Mortality in Elderly Acute Kidney Injury Patients: A Retrospective Observational Study

Purpose We examined the relationship between different levels of serum sodium and mortality among elderly patients with acute kidney injury (AKI). Methods We retrospectively enrolled elderly patients from Chinese PLA General Hospital from 2007, to 2018. All-cause mortality was examined according to eight predefined sodium levels: <130.0 mmol/L, 130.0–134.9 mmol/L, 135.0–137.9 mmol/L, 138.0–141.9 mmol/L, 142.0–144.9 mmol/L, 145.0–147.9 mmol/L, 148.0–151.9 mmol/L, and ≥152.0 mmol/L. We estimated the risk of all-cause mortality using a multivariable adjusted Cox analysis, with a normal sodium level of 135.0–137.9 mmol/L as a reference. Results In total, 744 patients were suitable for the final evaluation. After 90 days, the mortality rates in the eight strata were 36.1, 27.8, 19.6, 24.4, 30.7, 48.6, 52.8, and 57.7%, respectively. In the multivariable adjusted analysis, patients with sodium levels <130.0 mmol/L (HR: 2.247; 95% CI: 1.117–4.521), from 142.0 to 144.9 mmol/L (HR: 1.964; 95% CI: 1.100–3.508), from 145.0 to 147.9 mmol/L (HR: 2.942; 95% CI: 1.693–5.114), from 148.0 to 151.9 mmol/L (HR: 3.455; 95% CI: 2.009–5.944), and ≥152.0 mmol/L (HR: 3.587; 95% CI: 2.151–5.983) had an increased risk of all-cause mortality. After 1 year, the mortality rates in the eight strata were 58.3, 47.8, 33.7, 38.9, 45.5, 64.3, 69.4, and 78.4%, respectively. Patients with sodium levels <130.0 mmol/L (HR: 1.944; 95% CI: 1.125–3.360), from 142.0 to 144.9 mmol/L (HR: 1.681; 95% CI: 1.062–2.660), from 145.0 to 147.9 mmol/L (HR: 2.631; 95% CI: 1.683–4.112), from 148.0 to 151.9 mmol/L (HR: 2.411; 95% CI: 1.552–3.744), and ≥152.0 mmol/L (HR: 3.037; 95% CI: 2.021–4.563) had an increased risk of all-cause mortality. Conclusion Sodium levels outside the interval of 130.0–141.9 mmol/L were associated with increased risks of 90-day mortality and 1-year mortality in elderly AKI patients.
Environmental Compliance and Enterprise Innovation: Empirical Evidence from Chinese Manufacturing Enterprises

This paper embeds environmental compliance factor and compliance cost factor into the M-O monopolistic competition and multi-product firm model to construct a theoretical model applicable to environmental compliance and enterprise innovation. In addition, we also construct a new environmental compliance index. We use the random-effects Tobit model and the double hurdle model to empirically test the micro-data from the Database of China Industrial Enterprises from 1998 to 2013, then we use the Generalized Propensity Score Matching (GPSM) to conduct a robustness test. The robustness conclusion is that environmental compliance has a significant U-shaped relationship with enterprise innovation, which means, environmental compliance will inhibit enterprise innovation on the left of the inflection point of environmental compliance (0.669), while environmental compliance on the right of the inflection point will promote enterprise innovation. The sub-sample regressions show that, enhanced environmental compliance of state-owned enterprises, mature enterprises, core area enterprises and export enterprises with low level of the environmental compliance, makes the greater inhibition to enterprise innovation, and enhanced environmental compliance of above enterprises with high level of the environmental compliance, makes the greater contribution to enterprise innovation. To this end, the government should adopt the policy, from the shallower to the deeper, to promote the construction of environmental compliance, and identify the inflection point of the environmental compliance on enterprise innovation to stimulate the role of environmental compliance in promoting enterprise innovation.
Amorphous phase formation in irradiated intermetallic compounds

Abstract A variety of intermetallic compounds have been irradiated with high energy ions to determine the criteria for an amorphous transformation. Those compounds with limited compositional range or solubility tend to become amorphous during irradiation, whereas those compounds with wide solubility tend to remain crystalline. This solubility criterion is consistent with the concept that a critical defect density which will result in a greater free energy of the crystal phase than the free energy of the amorphous phase is necessary for the amorphous transformation. This critical defect density is lower in those compounds that become amorphous. The ionicity criterion of Naguib and Kelly does not work for these intermetallic compounds, but the temperature criterion is probably valid and is, in fact, directly related to the proposed solubility criterion.
Outcomes of Lower Extremity Endovascular Revascularization: Potential Predictors and Prevention Strategies

Peripheral artery disease (PAD) is a manifestation of atherosclerosis, which may affect arteries of the lower extremities. The most dangerous PAD complication is chronic limb-threatening ischemia (CLTI). Without revascularization, CLTI often causes limb loss. However, neither open surgical revascularization nor endovascular treatment (EVT) ensure long-term success and freedom from restenosis and revascularization failure. In recent years, EVT has gained growing acceptance among all vascular specialties, becoming the primary approach of revascularization in patients with CLTI. In clinical practice, different clinical outcomes after EVT in patients with similar comorbidities undergoing the same procedure (in terms of revascularization technique and localization of the disease) cause unsolved issues that need to be addressed. Nowadays, risk management of revascularization failure is one of the major challenges in the vascular field. The aim of this literature review is to identify potential predictors for lower extremity endovascular revascularization outcomes and possible prevention strategies.
Integrating Sensor Models in Deep Learning Boosts Performance: Application to Monocular Depth Estimation in Warehouse Automation

Deep learning is the mainstream paradigm in computer vision and machine learning, but performance is usually not as good as expected when used for applications in robot vision. The problem is that robot sensing is inherently active, and often, relevant data is scarce for many application domains. This calls for novel deep learning approaches that can offer a good performance at a lower data consumption cost. We address here monocular depth estimation in warehouse automation with new methods and three different deep architectures. Our results suggest that the incorporation of sensor models and prior knowledge relative to robotic active vision, can consistently improve the results and learning performance from fewer than usual training samples, as compared to standard data-driven deep learning.
Relation of Automated Body Condition Scoring System and Inline Biomarkers (Milk Yield, β-Hydroxybutyrate, Lactate Dehydrogenase and Progesterone in Milk) with Cow’s Pregnancy Success

The aim of the current study was to evaluate the relation of automatically determined body condition score (BCS) and inline biomarkers such as β-hydroxybutyrate (BHB), milk yield (MY), lactate dehydrogenase (LDH), and progesterone (mP4) with the pregnancy success of cows. The cows (n = 281) had 2.1 ± 0.1. lactations on average, were 151.6 ± 0.06 days postpartum, and were once tested with “Easy scan” ultrasound (IMV imaging, Scotland) at 30–35 d post-insemination. According to their reproductive status, cows were grouped into two groups: non-pregnant (n = 194 or 69.0% of cows) and pregnant (n = 87 or 31.0% of cows). Data concerning their BCS, mP4, MY, BHB, and LDH were collected each day from the day of insemination for 7 days. The BCS was collected with body condition score camera (DeLaval Inc., Tumba, Sweden); mP4, MY, BHB, and LDH were collected with the fully automated real-time analyzer Herd Navigator™ (Lattec I/S, Hillerød, Denmark) in combination with a DeLaval milking robot (DeLaval Inc., Tumba, Sweden). Of all the biomarkers, three differences between groups were significant. The body condition score (BCS) of the pregnant cows was higher (+0.49 score), the milk yield (MY) was lower (−4.36 kg), and milk progesterone in pregnant cows was (+6.11 ng/mL) higher compared to the group of non-pregnant cows (p < 0.001). The pregnancy status of the cows was associated with their BCS assessment (p < 0.001). We estimated that cows with BCS > 3.2 were 22 times more likely to have reproductive success than cows with BCS ≤ 3.2.
Dynamic Environmental Physical Cues Activate Mechanosensitive Responses in the Repair Schwann Cell Phenotype

Schwann cells plastically change in response to nerve injury to become a newly reconfigured repair phenotype. This cell is equipped to sense and interact with the evolving and unusual physical conditions characterizing the injured nerve environment and activate intracellular adaptive reprogramming as a consequence of external stimuli. Summarizing the literature contributions on this matter, this review is aimed at highlighting the importance of the environmental cues of the regenerating nerve as key factors to induce morphological and functional changes in the Schwann cell population. We identified four different microenvironments characterized by physical cues the Schwann cells sense via interposition of the extracellular matrix. We discussed how the physical cues of the microenvironment initiate changes in Schwann cell behavior, from wrapping the axon to becoming a multifunctional denervated repair cell and back to reestablishing contact with regenerated axons.
Aphid Assemblages Associated with Urban Park Plant Communities

Simple Summary Some aphid species are important as pests on plants growing in urban areas. The aim of the study was to determine and compare plant communities and the assemblages of aphids associated with them in different urban park habitats. The study was carried out in Bydgoszcz (northern Poland), and four parks were taken into consideration. We have indicated plant communities and plant species most affected by aphids and the least. for example pear, elderberry, maple and jasmine were among those most affected by aphids, and acacia was not. This should be taken into account for aesthetic reasons when arranging parks. The density of buildings turned out to be the factor that differentiated the most from aphids. Abstract Some aphid species are important agricultural pests, sometimes also found on plants growing in urban areas. In this work, we set out to identify the plant species, communities or habitats that are more attractive to aphids in order to limit their spread into new green areas. The aim of the study was to determine and compare plant communities and the assemblages of aphids associated with them in different urban park habitats. The research hypothesis assumed that the differences between aphid assemblages depend on plant diversity and hence reflect urban park habitat environmental conditions, in particular the plant communities and the floral structure. The study was carried out in Bydgoszcz (northern Poland), and four parks were taken into consideration. Herein, floristic lists were used to calculate ecological indicator values for each park. The aphid species richness was determined, as well as the relative abundance and dominance structure similarities of the aphid assemblages. Our results demonstrated that Prunus spp. were strongly infested by Hyalopterus pruni, similarly as Philadelphus inodorus by Aphis fabae, Sambucus nigra by Aphis sambuci, and Acer platanoides and A. pseudoplatanus by Periphyllus testudinaceus. Park plantations of Robinia pseudoacacia were not very attractive to aphids. The most attractive plant communities to aphids were syntaxonomically identifiable as alluvial alder forests in the layer of trees and Cornus sanguinea in the layer of shrubs.
Widely Targeted Metabolomics Analysis of Different Parts of Salsola collina Pall

Salsola collina Pall has a long history of being used as a traditional medicine to treat hypertension, headache, insomnia, constipation and vertigo. However, only a few biologically active substances have been identified from S. collina. Here, the shoots and roots of S. collina, namely L-Sc and R-Sc, were studied. The primary and secondary metabolites were investigated using ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS). A total of 637 putative metabolites were identified and these metabolites were mainly classified into ten different categories. Correlation analysis, hierarchical clustering analysis, principal component analysis and orthogonal partial least squares discriminant analysis of metabolites showed that the L-Sc samples could be clearly separated from the R-Sc samples. Differential accumulated metabolite analysis revealed that most of differential primary metabolites were significantly lower in the L-Sc than in the R-Sc. Conversely, the major differential secondary metabolites had higher levels in the L-Sc than in the R-Sc. Further analysis indicated that the flavonoids were the major putative antioxidant components and most of putative antioxidant components exhibited higher relative concentrations in the L-Sc than the R-Sc. These results improve our understanding of metabolite accumulation and provide a reference for the study of medicinal value in S. collina.
Potential Role of microRNAs in inducing Drug Resistance in Patients with Multiple Myeloma

The prognosis for newly diagnosed subjects with multiple myeloma (MM) has significantly progressed in recent years. However, most MM patients relapse and after several salvage therapies, the onset of multidrug resistance provokes the occurrence of a refractory disease. A continuous and bidirectional exchange of information takes place between the cells of the microenvironment and neoplastic cells to solicit the demands of cancer cells. Among the molecules serving as messengers, there are microRNAs (miRNA), a family of small noncoding RNAs that regulate gene expression. Numerous miRNAs are associated with drug resistance, also in MM, and the modulation of their expression or activity might be explored to reverse it. In this review we report the most recent studies concerning the relationship between miRNAs and chemoresistance to the most frequently used drugs, such as proteasome inhibitors, steroids, alkylating agents and immunomodulators. The experimental use of antagomirs or miRNA mimics have successfully been proven to counteract chemoresistance and display synergistic effects with antimyeloma drugs which could represent a fundamental moment to overcome resistance in MM treatment.
Salinity Changes the Dynamics of Pyrethroid Toxicity in Terms of Behavioral Effects on Newly Hatched Delta Smelt Larvae

Salinity can interact with organic compounds and modulate their toxicity. Studies have shown that the fraction of pyrethroid insecticides in the aqueous phase increases with increasing salinity, potentially increasing the risk of exposure for aquatic organisms at higher salinities. In the San Francisco Bay Delta (SFBD) estuary, pyrethroid concentrations increase during the rainy season, coinciding with the spawning season of Delta Smelt (Hypomesus transpacificus), an endangered, endemic fish. Furthermore, salinity intrusion in the SFBD is exacerbated by global climate change, which may change the dynamics of pyrethroid toxicity on aquatic animals. Therefore, examining the effect of salinity on the sublethal toxicity of pyrethroids is essential for risk assessments, especially during the early life stages of estuarine fishes. To address this, we investigated behavioral effects of permethrin and bifenthrin at three environmentally relevant concentrations across a salinity gradient (0.5, 2 and 6 PSU) on Delta Smelt yolk-sac larvae. Our results suggest that environmentally relevant concentrations of pyrethroids can perturb Delta Smelt larvae behavior even at the lowest concentrations (<1 ng/L) and that salinity can change the dynamic of pyrethroid toxicity in terms of behavioral effects, especially for bifenthrin, where salinity was positively correlated with anti-thigmotaxis at each concentration.