Miracle-dz/UniFAR-FTUs huggingface dataset:
Marker-assisted characterization of frost tolerance in barley (Hordeum vulgare L.).

Five molecular markers associated to two frost tolerance QTLs (Fr-H1 and Fr-H2) were tested both on nine Turkish accessions, classified by breeders as highly frost-tolerant, and on a previously described sample of 26 barleys, winter, facultative and spring. Accessions were characterized in terms of frost tolerance under both field conditions and artificial freezing test at -12°C. The Turkish lines resulted to be equal or superior to the most tolerant European genotypes tested, showing that they can be used to improve the frost tolerance of the EU barley germplasm. The marker HvBM5A (Vrn-H1 and Fr-H1) resulted to be the best predictor for assisted selection within this germplasm, because of its high correlation between allelic variation and phenotypic traits. Only HvCBF4 of the three HvCBF markers tested at Fr-H2 was associated to the trait, but at lower significance than HvBM5A. The PCR-based molecular marker of Vrn-H1 can thus be used in barley breeding not only for selection of facultative and winter types, but also for fast routine selection of frost tolerant genotypes.
DNA-PKcs phosphorylation at the T2609 cluster alters the repair pathway choice during immunoglobulin class switch recombination

Significance DNA-dependent protein kinase (DNA-PK), which is composed of the KU heterodimer and the large catalytic subunit (DNA-PKcs), is a classical nonhomologous end-joining (cNHEJ) factor with important roles in immunoglobulin class switch recombination. Activated DNA-PK phosphorylates many substrates, including DNA-PKcs itself at the T2609 cluster. Using knockin mouse models, we found that while the loss of T2609 phosphorylation of DNA-PKcs does not affect class switch recombination (CSR) efficiency, the CSR junctions recovered from T2609A B cells are generated by the alternative end-joining pathway, providing the evidence for a role of DNA-PKcs T2609 phosphorylation in DNA repair pathway choice. The DNA-dependent protein kinase (DNA-PK), which is composed of the KU heterodimer and the large catalytic subunit (DNA-PKcs), is a classical nonhomologous end-joining (cNHEJ) factor. Naïve B cells undergo class switch recombination (CSR) to generate antibodies with different isotypes by joining two DNA double-strand breaks at different switching regions via the cNHEJ pathway. DNA-PK and the cNHEJ pathway play important roles in the DNA repair phase of CSR. To initiate cNHEJ, KU binds to DNA ends and recruits and activates DNA-PK. Activated DNA-PK phosphorylates DNA-PKcs at the S2056 and T2609 clusters. Loss of T2609 cluster phosphorylation increases radiation sensitivity but whether T2609 phosphorylation has a role in physiological DNA repair remains elusive. Using the DNA-PKcs5A mouse model carrying alanine substitutions at the T2609 cluster, here we show that loss of T2609 phosphorylation of DNA-PKcs does not affect the CSR efficiency. Yet, the CSR junctions recovered from DNA-PKcs5A/5A B cells reveal increased chromosomal translocations, extensive use of distal switch regions (consistent with end resection), and preferential usage of microhomology—all signs of the alternative end-joining pathway. Thus, these results uncover a role of DNA-PKcs T2609 phosphorylation in promoting cNHEJ repair pathway choice during CSR.
Effect of stage and number of lactation on the yield and composition of cow's milk

Summary The effects of stage of lactation and of age on milk and composition yield of cows kept under controlled conditions of feeding and management were investigated. Two groups each of 3 Friesian heifers were used: one group (A) was given a daily diet of 18 lb hay and concentrates at the rate of 3·8 lb/10 lb of milk and kept on experiment throughout the first 3 lactations; a second group (B) was given the same amount of hay and a constant daily amount of concentrates of 10·7 lb and was kept on experiment throughout the 1st lactation only. The total yields of milk and peak yields for the 1st lactation were similar in both groups. In all the cows, fat content was high early and late in lactation and varied little throughout the mid-lactation period. With cows of group A, the content of solids-not-fat declined until about the 5th week of lactation and then remained steady until a marked rise occurred late in lactation. With cows of group B, however, the content of solids-not-fat was at a minimum between the 5th and 10th weeks of lactation and then increased progressively until late lactation when a more marked rise occurred. Lactose content increased rapidly in the first few days of lactation and then remained constant for several months, eventually declining late in lactation. Characteristic changes were also observed in the contents of total protein, and of the various protein fractions, and of the major minerals of milk. The concentrations of all major constituents in milk secreted from the 2nd–5th months of lactation tended to decrease from lactation to lactation. The results are discussed in relation to the development of knowledge of the changes in milk composition throughout lactation.
Comparative Analysis of Flying Capacitor and Diode Clamped Multilevel Inverters Using SPWM

Multilevel inverters are considered as an alternative in the field of high power , medium voltage and power quality applications due to their minimum harmonic distortion, reduced dv/dt stresses, , reduced EMI and EMC issues etc. This paper presents the analysis and comparison of three level Diode Clamped or Neutral Point Clamped (NPC) and Flying Capacitor (FC)or Capacitor Clamped multilevel inverter topologies . For the topologies mentioned above the simulations were carried out for resistive load. The PWM used here is Sinusoidal Pulse Width Modulation (SPWM) and the multicarrier modulation used here is Phase shifted PWM. By comparing the THDs the advantages of Flying Capacitor Multilevel inverter over the Diode Clamped Multilevel inverter is confirmed. The simulations are performed using MATLAB/SIMULINK software and the results are presented.
Partitioning of genotype × environment interactions of winter wheat forage yield

Wheat (Triticum aestivum L. emend. Thell) is used as a dual-purpose crop in the southern Great Plains, with 35 to 55% of the acreage grazed in the fall and winter, followed by grain harvest in late spring. Cultivar selection is primarily based on grain yield. This study was conducted to characterize genotype X environment (GE) interactions for fall and winter forage production in hard red winter wheat and to identify cultivars with favorable levels of stable forage production. Eighteen cultivars were grown in six environments. Forage was clipped until the early joint stage (Feeke's 5-6), when canopy height reached approximately 20 cm. Fall forage produced prior to winter dormancy, and winter regrowth before early joint, were both influenced by GE interactions. The mean correlation of each cultivar with all other cultivars ranged from 0.91 to 0.97 for fall forage and 0.84 to 0.93 for winter forage. Based on Shukla's stability variance (SSV), three cultivars were unstable (SSV > 0) for fall forage, whereas 10 cultivars were unstable for winter forage. Cultivars with low mean correlations were also classified as unstable. Rank stability differences for fall forage resulted primarily from three genotypes (Agripro 'Wrangler', AGSECO '7846', and 'TAM W-101') showing exceptionally high stability rather than lack of stability. Changes in rank order would not be expected to hinder selection of hard red winter wheat genotypes stable for fall forage production. Fall forage yield differences were sufficiently large to be important to wheat-stocker cattle producers.
A proposal for typical eukaryotic meiosis in microsporidians

A review of key publications concerning the biology and life cycles of microsporidians has led us to challenge recent proposals that they exhibit a unique process of meiosis when compared with other eukaryotes. The basic data used to support this challenge are the same as those used by researchers suggesting atypical meiosis, but the data are analyzed from a different viewpoint. Arguments are put forward to support a testable hypothesis that meiosis in microsporidians is identical to that which occurs in other eukaryotes. It is proposed that confusion resulted because two separate cytological developmental sequences for diplokaryotic meronts in mosquito fat body cells were previously interpreted as a single sequence. By rearrangement of the original data into two developmental sequences, one abortive and the other for typical meiosis, a better fit was obtained between cytological stages and microphotometric measurements of nuclear DNA content. This improved data fit and the existence of similar nuclear de.
Applications of transition matrix models in forest dynamics: Araucaria in Papua New Guinea and Nothofagus in New Zealand

This paper describes the application of the Leslie matrix model to single species populations, and a similar transition matrix model to communities of more than one species. Examples are drawn from populations of Araucaria spp. in tropical rainforest in Papua New Guinea, and from Nothofagus fusca stands in temperate montane forest in New Zealand. Both species generally had λ values close to 1.0 (r, the intrinsic rate of natural increase ≃ 0) and in both cases predicted trends were consistent with other ecological information from the stands or elsewhere. Various possible sources of error and empirical tests of the sensitivity of the single species model and the accuracy of its predictions are described. It is concluded that, despite certain limitations, with careful interpretation these models constitute an important tool for the investigation of forest dynamics. The basic model may be modified in various ways, for example, to include vegetative reproduction, or put to use in practical problems such as defining a harvesting strategy for a forest tree species. In studies of succession involving long-lived species these models are particularly valuable, not only for predicting the magnitude and direction of future changes, but also because they suggest a time scale for the trends, and this can then be evaluated in the light of other knowledge about the communities in question. Moreover, the variability of λ values obtained for differen species relates to their life cycle strategies, so that by the use of Leslie matrices it may be possible objectively to rank the species of a community along the continuum of r to k strategies.
Sulphur amino acid requirement of juvenile Asian sea bass Lates calcarifer

The dietary requirement of juvenile Asian sea bass Lates calcarifer Bloch for total sulphur amino acids was studied. Fish (average initial weight of 2.59 ± 0.08 g) were reared in twelve 500 L fibreglass tanks provided with flow-through seawater at 26°C and salinity of 31 p.p.t. for 12 weeks. They were fed semi-purified test diets containing 6.2, 7.2, 8.1, 9.0, 10.8, or 12.6 g methionine kg−1 dry diet and a basal level of 3.1 g cystine kg−1 dry diet. The mean crude protein of the diets (containing defatted Peruvian fishmeal, squid meal, soybean meal, and free amino acid mixture to simulate the pattern of hydrolysed sea bass protein) was 46.02%. The crude fat content of the diets was 10.51% from a 1 : 1 mixture of cod liver oil and soybean oil. Survival was 100% in all treatments. On the basis of the growth response, the total sulphur amino acid requirement of juvenile Asian sea bass was estimated to be 13.4 g kg−1 dry diet (2.9% of protein). Fish fed low levels of l-methionine had significantly lower weight gains and feed efficiency ratios as well as slightly higher hepatosomatic indices. No nutritional deficiency signs were observed other than growth depression in fish fed on diets that were low in methionine. This information is valuable in further refinement of formulations of practical diets for the Asian sea bass.
STRATEGIC NETWORKING: THE CASE STUDY IN DUBROVNIK HOTEL INDUSTRY

Hotel industry is considered one of the most important area in the economy because of its impact on the development of tourism. One of the development strategy is strategic networking. The most common reasons for strategic networking in hotel industry are financial, motivation to acquire and exchange knowledge and technology, competitive position and farmers motives. Forms of strategic networking are clusters, strategic partnerships, strategic alliances, cooperatives and associations. The purpose of this paper is to examine whether the hotel enterprises in Dubrovnik using a strategy of networking either vertically or horizontally. The aim is to examine which forms of networking hotel companies use as a development strategy in the area of Dubrovnik and which form of networks is most represented. Research results have shown that the most commonly used forms of strategic networks in hotel enterprises in Dubrovnik cooperatives and associations.
Genetic removal of p70 S6K1 corrects coding sequence length-dependent alterations in mRNA translation in fragile X syndrome mice

Significance Fragile X syndrome (FXS) is the most prevalent inherited form of intellectual disability. FXS is caused by loss of fragile X mental retardation protein (FMRP), an RNA-binding protein that represses translation. Correspondingly, genetic removal of the translation-stimulating p70 S6 kinase 1 (S6K1) in FXS mice restores translational homeostasis and rescues synaptic and behavioral phenotypes. However, the mechanisms of FMRP function are in dispute, and the molecular basis of the rescue in protein synthesis with reduction of S6K1 is unknown. Here, by carrying out ribosome profiling and molecular assays, we reveal the molecular mechanisms by which reduction of S6K1 corrects altered protein synthesis in FXS. Our study elucidates the molecular foundations of a model for correction of pathophysiological features of FXS. Loss of the fragile X mental retardation protein (FMRP) causes fragile X syndrome (FXS). FMRP is widely thought to repress protein synthesis, but its translational targets and modes of control remain in dispute. We previously showed that genetic removal of p70 S6 kinase 1 (S6K1) corrects altered protein synthesis as well as synaptic and behavioral phenotypes in FXS mice. In this study, we examined the gene specificity of altered messenger RNA (mRNA) translation in FXS and the mechanism of rescue with genetic reduction of S6K1 by carrying out ribosome profiling and RNA sequencing on cortical lysates from wild-type, FXS, S6K1 knockout, and double knockout mice. We observed reduced ribosome footprint (RF) abundance in the majority of differentially translated genes in the cortices of FXS mice. We used molecular assays to discover evidence that the reduction in RF abundance reflects an increased rate of ribosome translocation, which is captured as a decrease in the number of translating ribosomes at steady state and is normalized by inhibition of S6K1. We also found that genetic removal of S6K1 prevented a positive-to-negative gradation of alterations in translation efficiencies (RF/mRNA) with coding sequence length across mRNAs in FXS mouse cortices. Our findings reveal the identities of dysregulated mRNAs and a molecular mechanism by which reduction of S6K1 prevents altered translation in FXS.
Habitat microclimates drive fine‐scale variation in extreme temperatures

Most multicellular terrestrial organisms experience climate at scales of millimetres to metres, yet most species-climate associations are analysed at resolutions of kilometres or more. Because individuals experience heterogeneous microclimates in the landscape, species sometimes survive where the average background climate appears unsuitable, and equally may be eliminated from sites within apparently suitable grid cells where microclimatic extremes are intolerable. Local vegetation structure and topography can be important determinants of fine-resolution microclimate, but a literature search revealed that the vast majority of bioclimate studies do not include fine-scale habitat information, let alone a representation of how habitat affects microclimate. In this paper, we show that habitat type (grassland, heathland, deciduous woodland) is a major modifier of the temperature extremes experienced by organisms. We recorded differences among these habitats of more than 5°C in monthly temperature maxima and minima, and of 10°C in thermal range, on a par with the level of warming expected for extreme future climate change scenarios. Comparable differences were found in relation to variation in local topography (slope and aspect). Hence, we argue that the microclimatic effects of habitat and topography must be included in studies if we are to obtain sufficiently detailed projections of the ecological impacts of climate change to develop detailed adaptation strategies for the conservation of biodiversity.
Selection and local adaptation in capuchin monkeys revealed through fluorescence-activated cell sorting of feces (fecalFACS)

Background: Capuchins have the largest relative brain size of any monkey and a remarkable lifespan of 55 years, despite their small body size. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence, dietary diversity, and ecological flexibility. Despite decades of research into their ecology and life history, little is known about the genomics of this radiation. Results: We assemble a de novo reference genome for Cebus imitator, and provide the first genome annotation of a capuchin monkey. We identified 20,740 and 9,556 for protein-coding and non-coding genes, and recovered 23,402 orthologous groups. Through a comparative genomics approach across a diversity of mammals, we identified genes under positive selection associated with longevity and brain development, which are of particular relevance to capuchin and primate comparative biology. Additionally, we compared populations in distinct habitats, facilitated by our novel method for minimally-biased, whole-genome sequencing from fecal DNA using fluorescence activated cell sorting (FACS). By analyzing 23 capuchin genomes from tropical dry forest and rainforest, we identified population divergence in genes involved in water balance, kidney function, and metabolism, consistent with local adaptation to resource seasonality. Conclusions: Our comparative study of capuchin genomics provides new insights into the molecular basis of brain evolution and longevity. These data also improve our understanding of processes of local adaptation to diverse and physiologically challenging environments. Additionally, we provide a technological advancement in use of non-invasive genomics to study free-ranging mammals through FACS.
Cloning and in silico analysis of a gene encoding a putative β-carbonic anhydrase from cowpea (Vigna unguiculata L. Walp)

A gene encoding putative β-carbonic anhydrase gene (CA) from cowpea (Vigna unguiculata L. Walp.) was characterized and designated as VuCA1 (GenBank ID: JQ429799). While the genomic sequence of CA was found to be 1470 bp long with 4 introns, the open reading frame was 990 bp in length. The deduced amino acid sequence of CA contained two characteristic conserved domains, i.e. CSDSRV and EYAVLHLKVSNIVVIGHSACG, which showed high degree of homology with other β-CA genes of angiosperms. We have reported three-dimensional model of VuCA1 and quality of the predicted model was analysed with PROCHECK. Molecular docking of modeled VuCA1 revealed similar binding pockets for different substrates and products. The expression of VuCA1 transcripts was detected in different parts of the cowpea plant, with highest level observed in leaves, followed by flower buds, weak expression in stems, and the weakest in roots. The expression of VuCA1 transcripts of leaves was downregulated by zinc deficiency but upregulated by salt and dehydration stress.
Plasma Nitrate/Nitrite Concentration in Healthy Population and Patients with Diabetes Mellitus-Relationships with Gender, Aging and Diabetic Complications -

Although there are numerous papers concerning nitrite/nitrate (NOx), most of them are indirect evaluations with acetylcholine or arginine analogue. Measuring the plasma concentration of NOx ([NOx]) may be a useful predictor of the vascular endothelial function. We analyzed [NOx] in healthy mass population and investigated the relationship with gender, aging and some diabetic complications. The subjects were 738 healthy volunteers (512 males and 226 females), who received annual medical check and were considered healthy based on physical and laboratory findings, and 289 patients with type 2 diabetes mellitus attending our hospital, a total of 1,027 subjects. [NOx] was measured by chemiluminescense assay (Sivers Inc. Model 280). The results at the fasting stage were as follows: the mean value of [NOx] in the healthy subjects was 47.5±26 (μM/L), and the ratio of nitrite to nitrate was approximately 1:6. After an intake of celery containing rich nitric compounds, [NOx] markedly increased to 2.5 times, mainly because of an increase in nitrate. In the male subjects, [NOx] gradually increased with aging, whereas in the females, it tended to decrease until the menopausal stage but turned upward after that. [NOx] in the group without any diabetic complication was much lower than that in the control group (P < 0.01), but the group with coronary artery disease showed a higher value (P < 0.001). In conclusion, [NOx] was influenced by exogenous factors, aging, and difference of gender, and showed some correlations with hyperglycemic vascular impairments.
Overcoming bias in gene-set enrichment analyses of brain-wide transcriptomic data

The recent availability of whole-brain atlases of gene expression, which quantify the transcriptional activity of thousands of genes across many different brain regions, has opened new opportunities to understand how gene-expression patterns relate to spatially varying properties of brain structure and function. To aid interpretation of a given neural phenotype, gene-set enrichment analysis (GSEA) has become a standard statistical methodology to identify functionally related groups of genes, annotated using systems such as the Gene Ontology (GO), that are associated with a given phenotype. While GSEA has identified functional groups of genes related to diverse aspects of brain structure and function in mouse and human, here we show that these results are affected by substantial statistical biases. Quantifying the false-positive rates of individual GO categories across an ensemble of completely random phenotypic spatial maps, we found an average 875-fold inflation of significant findings relative to expectation in mouse, and a 582-fold inflation in human, with some categories being judged as significant for over 20% of random phenotypes. Concerningly, the probability of a GO category being reported as significant in the extant literature increases with its estimated false-positive rate, suggesting that published reports are strongly affected by the reporting of false-positive bias. We show that the bias is primarily driven by gene–gene coexpression and spatial autocorrelation in transcriptional data, which are not accounted for in conventional GSEA nulls, and we introduce flexible ensemble-based null models that properly account for these effects. Using case studies of structural connectivity degree in mouse and human, we demonstrate that many GO categories that would conventionally be judged as highly significant are in fact consistent with ensembles of random phenotypes. Our results highlight major pitfalls with applying standard GSEA to brain-wide transcriptomic data and outline a solution to this pervasive problem, which is made available as a toolbox.