Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic Profiling of Plasma in Different Calving Body Condition Score Cows Using an Untargeted Liquid Chromatography-Mass Spectrometry Metabolomics Approach

Simple Summary Over-conditioning around calving predisposes cows to a higher risk of postpartum metabolic disorders and diseases. Using untargeted liquid chromatography-mass spectrometry, seven metabolites were found that were significantly correlated to high body condition, as well as to classic metabolic parameters indicating changes in lipid metabolism and inflammation. These seven metabolites include six distinct lysophosphatidylcholines and a phosphatidylethanolamine. By investigating the depth of metabolic changes in the plasma of over-conditioned fresh cows, this study may provide a metabolic basis for the diseases associated with over-conditioning. Abstract This study was undertaken to identify metabolite differences in plasma of dairy cows with a normal or high calving body condition score (CBCS), using untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics. Sixteen multiparous dairy cows were assigned to one of two groups based on CBCS (0 to 5 scale): Normal group (NBCS, 3.25 ≤ BCS ≤ 3.5, n = 8), and high BCS group (HBCS, BCS ≥ 4, n = 8). Plasma samples were collected for metabolomics analysis and evaluation of biomarkers of lipid metabolism (nonesterified fatty acid (NEFA) and β-hydroxybutyrate (BHB)), and cytokines (leptin, adiponectin, tumor necrosis factor–α (TNF-α) and interleukin 6 (IL-6)). A total of 23 differential metabolites were identified, and functional analyses were performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Among these metabolites, the concentrations of six lysophosphatidylcholines and one phosphatidylethanolamine, were lower in the HBCS group than in the NBCS group (p < 0.01). Furthermore, these metabolites were involved in these four pathways, among others: glycerophospholipid metabolism, retrograde endocannabinoid signaling, autophagy, and glycosylphosphatidylinositol (GPI)-anchor biosynthesis (p < 0.05). In addition, plasma concentrations of leptin (p = 0.06) and TNF-α (p = 0.08) tended to be greater while adiponectin (p = 0.09) lower in HBCS cows than in NBCS cows. The concentrations of NEFA, BHB, or IL-6 did not differ between NBCS and HBCS groups. More importantly, based on the results of the Spearman’s correlation analysis, the seven important metabolites were negatively correlated with indices of lipid metabolisms, proinflammatory cytokines, and leptin, but positively correlated with adiponectin. These results demonstrate that CBCS has a measurable impact on the plasma metabolic profile, even when NEFA and BHB are not different. In addition, the identified differential metabolites were significantly correlated to lipid metabolism and inflammation in the over-conditioned fresh cows, which are expected to render a metabolic basis for the diseases associated with over-conditioned dry cows.
Breast Hematoma Due to an Axillary Pad in an Anticoagulated Patient

To the Editor: Over a period of 4 months, the severe acute respiratory distress syndrome (SARS) infected 1,755 persons, resulting in 298 deaths in Hong Kong. Nursing homes are particularly vulnerable to cross-infection as a result of the crowded living environment, inadequate ventilation, substandard hygiene, and lack of qualified nursing staff. Recognition of clinical features at an earlier stage of the infection and stringent isolation procedures could prevent outbreaks in institutions, but the presentation of SARS may be less florid in older people. Nursing home residents, because of their frailty and comorbidities, are frequent users of hospital services, including emergency rooms (ERs) and acute wards, thus increasing their risk of exposure to infectious agents in hospitals. Demented or extremely frail patients may pose particular risk to other persons, because they may not be able to communicate and are only recognized after those who have come into contact with them fall ill. Also, cognitively impaired older patients may have difficulty keeping their facemasks on and sometimes exhibit high-risk behavior such as spitting. We report a cluster of seven cases (Table 1) illustrating the spread of SARS from a hospital to the community and, in particular, a nursing home. All the cases were diagnosed clinically and had positive viral isolates or serological tests to coronavirus. The nursing home involved was typical of many privately run institutions of its type. Located in an old
Effect of Yeast Culture Based Diet on Growth and Nutrient Utilization in Deoni Bull Calves

Two complete diets (I) without yeast culture (control) and (2) lyophilized yeast culture at 0.1 per cent level were formulated and processed into mash using sorghum straw as sole source of roughage. These two diets were fed to 12 Deoni bull calves of 6 each. (5–6 m old) in a experiment to assess the effect of yeast culture on growth and nutrient utilization. The DMI was 5.3 per cent higher on the diet containing yeast culture. Digestibilities of all the nutrients and DCP and TDN contents were signifincantly (P<0.05) higher on diet containing yeast culture. The ADG was significantly (P<0.05) higher and feed intake/kg gain was significantly (P<0.05) lower on the diet containing yeast culture. These results indicate that incorporation of yeast culture at 0.1 per cent level in the diet of growing Deoni bull calves improved the animal performance in terms of higher ADG (P<0.05) and decreased feed/kg gain.
Regeneration of Pseudocyphellaria aurata transplanted on a tree in Japan

To conserve endangered and/or rare lichens, transplantation methods are considered useful tools to establish new populations (Scheidegger et al. 1995, 1998; Hilmo 1999; Zoller et al. 2000; Lidén et al. 2004; Hilmo et al. 2011; Gustafsson et al. 2013). However, transplantation experiments have been applied to only a limited number of species. Further lichenological knowledge should be accumulated, especially for endangered and rare species. Pseudocyphellaria aurata (Ach.) Vain. (Lobariaceae, Ascomycota) is a cosmopolitan species and widespread in tropical regions of the world. It is also found in drier, warmer, coastal areas in cool temperate regions (Galloway & Arvidsson 1990). The populations in Japan, however, are rather rare and ranked in some local red lists (e.g. The Committee of the Red Data Book Chiba 2009; Saitama Prefecture 2011). We performed transplantation studies on P. aurata using soredia and thallus fragments. This paper describes the growth process into juvenile thalli in each case.
Physical performance and activity among older adults visiting primary healthcare centres in Riyadh

Objective To assess physical performance (PP) and physical activity (PA) among older adults visiting primary healthcare centres (PHCCs) in Riyadh. Methods In this cross-sectional study, men and women (n = 74) aged ≥60 years were recruited from five PHCCs across Riyadh, Saudi Arabia, between 19 February and 6 August 2017. The Timed Up & Go test was used to assess PP. Self-reported PA was assessed using the Physical Activity Scale for the Elderly. Means and standard deviations were used to describe PP and PA scores across genders. A two-tailed independent samples t-test was used to estimate mean differences (MD) and 95% confidence intervals (CI) between genders. Results Men scored significantly lower than women on PP (MD: 2.11, 95% CI: 0.59 to 3.64) and PA (MD: −46.1, 95% CI: −80.96 to −11.25). Significant gender differences were observed for leisure time activities (MD: 17.35, 95% CI: 3.29 to 31.40), light household activities (MD: –10.86, 95% CI: –16.19 to –5.53) and heavy household activities (MD: –6.48, 95% CI: –11.73 to –1.23). Conclusions Men show significantly lower PP and PA than women. There are gender differences in leisure time activities and in light and heavy household activities.
USE OF METHYL JASMONATE TO ENHANCE THE PRODUCTION OF 6-METHOXYPODOPHYLLOTOXIN IN CELL CULTURES OF LINUM THRACICUM SSP. THRACICUM

Secondary metabolites, such as lignans have important ecological role for plants and at the same time are lead structures for drug design in human medicine. The aryltetralin type of lignans are strong cytotoxic agents and are found in members of the genus Linum (Linaceae). Objective: In vitro cultures of Linum thracicum ssp. thracicum were developed to identify a medium type and an elicitation technique that favor enhanced production of the aryltetralin lignan 6-methoxypodophyllotoxin. Method: Methyl jasmonate and salicylic acid were administered to four cell lines of Linum thracicum ssp. thracicum for 24 and 72 hours. The 6-methoxypodophyllotoxin was identified by HPLS-ESI-MS/MS in positive ion mode, and its production was determined via quantitative HPLC analysis. Results: A cell line, called Li-20 , which was developed in reduced sucrose environment proved to be the fastest growing and the highest producing among the tested cell lines. Within 24 hours upon MJ elicitation, the eight-day-old Li-20 increased 2.3-fold in 6-methoxypodophyllotoxin content, reaching 4.3 mg on a dry weight basis. Negative or no effect was registered after salicylic acid application. Conclusion: MJ elicitation is an effective strategy to improve the 6-methoxypodophyllotoxin accumulation within short periods of time, and an optimization of the cultivation medium beforehand is a prerequisite in the pipeline.
Preliminary genome analysis of psychrotolerant marine bacterium Pseudoalteromonas sp.BSw20308 reveals its potential applications

The genus Pseudoalteromonas is ubiquitous in the marine environment and can synthesize a wide range of extracellular compounds.Psychrotolerant Pseudoalteromonas sp.BSw20308 was isolated from the Chukchi Sea,a marginal sea of the Arctic Ocean.It produces a number of extracellular enzymes that can degrade polysaccharides and proteins.The BSw20308 genome was sequenced to 38.1-fold coverage,and the sequences were assembled into 146 contigs(≥500 bp). In total,4 172 open reading frames(ORFs)with an average gene length of 987 bp were detected.At least 86 ORFs were predicted by sequence analysis to encode a variety of catalytic modules involved in the degradation of polysaccharides,proteins,and lipids.In addition,36 ORFs were predicted to encode catalytic modules involved in the degradation of organic pollutants and halogenated compounds,and in the production of bioactive compounds.The draft genome sequence of BSw20308 provides new information about the ecological function and adaptation of the genus Pseudoalteromonas in Arctic marine environments,and also indicates its potential applications in the biotechnology industries(e.g.,enzymology,and pollutant degradation).
A Technique for Physiologically Age-Grading Female Stable Flies, Stomoxys calcitrans (L.)

A method of dissection fo llowed by staining was initiated to allow physiological age-g rading based on ovarian develo pment in orde r to more completely d escribe the phys iological d evelopment of adult fema le stable fli es [S tomoxys calcitrans (L. )]. The gonotrophic d evelopmental co ntinuum fro m a non-differentiated cell in teneral females to mature eggs a t the time o f oviposition was first a rbitrarily divided into six stages by using distinct landma rks within the d evelo ping oocyte . Then , nulliparo us, uniparou s, and biparous+ females were differenti ated o n the basis o f the presence o r absence of stain ed follicula r re lics in th e ovariole shea ths. The combina tio n of the two techniques mad e it possible to ass ign dissec ted adult fe male stable fli es to o ne of 12 age-cl asses. A Technique for Physiologically Age-grading Female Stable Flies, Stomoxys calcitrans (L.)
Genomic study of dilated cardiomyopathy in a group of Mexican patients using site‐directed next generation sequencing

Dilated cardiomyopathy (DCM) is a major cause of nonischemic heart failure and death in young adults. Next generation sequencing (NGS) has become part of the diagnostic workup in idiopathic and familial DCM. More than 50 DCM genes have been identified, revealing great molecular heterogeneity and variable diagnostic yield. Interpretation of variant pathogenicity is challenging particularly in underrepresented populations, as pathogenic variant databases include studies mainly from European/Caucasian populations. To date, no studies on genomic diagnosis of DCM have been conducted in Mexico.
Subspecies divergence and pronounced phylogenetic incongruence in the East-Asia-endemic shrub Magnolia sieboldii.

BACKGROUND AND AIMS The biogeographic patterns of the East-Asia-endemic shrub Magnolia sieboldii, in which the range of the subsp. sieboldii is intervened by the disjunct distribution of subsp. japonica, implies a complex evolutionary history, involving rapid speciation and hybridization. Here, we aim to reveal the evolutionary and phylogeographic histories of the species with a particular focus on the time of subspecies divergence, the hypothesis of secondary hybridization, and the Pleistocene survival of each subspecies, using a combination of genetic analyses and ecological niche modelling. METHODS Genetic variation, genetic structures, and phylogenetic relationships were elucidated based on nuclear low-copy genes, chloroplast DNA, and nuclear SSRs. A scenario selection analysis and divergence time estimation were performed using coalescent simulation in DIYABC and *BEAST . Ecological niche modelling and a test of niche differentiation were performed using Maxent and ENMTools. KEY RESULTS All marker types showed deep, but pronouncedly incongruent, west-east genetic divergences, with the subspecies being delineated only by the nuclear low-copy genes. Phylogenetic tree topologies suggested that ancient hybridization and introgression were likely to have occurred; however, this scenario did not receive significant support in the DIYABC analysis. The subspecies differentiated their niches, but both showed a dependence on high humidity and were predicted to have persisted during the last glacial cycle by maintaining a stable latitudinal distribution via migration to lower altitudes. CONCLUSIONS We found a deep genetic divergence and a pronounced phylogenetic incongruence among the two subspecies of M. sieboldii, which may have been driven by major paleogeographic and paleoclimatic events that occurred since the Neogene in East Asia, including global cooling, climate oscillations and the formation of land bridges. Both subspecies were, however, considered to persist in situ in stable climatic conditions during the late Pleistocene.
Scalable Non-Linear Graph Fusion for Prioritizing Cancer-Causing Genes

In the past few decades, both gene expression data and protein-protein interaction (PPI)networks have been extensively studied, due to their ability to depict important characteristics of disease-associated genes. In this regard, the paper presents a new gene prioritization algorithm to identify and prioritize cancer-causing genes, integrating judiciously the complementary information obtained from two data sources. The proposed algorithm selects disease-causing genes by maximizing the importance of selected genes and functional similarity among them. A new quantitative index is introduced to evaluate the importance of a gene. It considers whether a gene exhibits a differential expression pattern across sick and healthy individuals, and has a strong connectivity in the PPI network, which are the important characteristics of a potential biomarker. As disease-associated genes are expected to have similar expression profiles and topological structures, a scalable non-linear graph fusion technique, termed as ScaNGraF, is proposed to learn a disease-dependent functional similarity network from the co-expression and common neighbor based similarity networks. The proposed ScaNGraF, which is based on message passing algorithm, efficiently combines the shared and complementary information provided by different data sources with significantly lower computational cost. A new measure, termed as DiCoIN, is introduced to evaluate the quality of a learned affinity network. The performance of the proposed graph fusion technique and gene selection algorithm is extensively compared with that of some existing methods, using several cancer data sets.
An exposition on field identification of Clariid catfishes as an important tool in fish breeding and genetics

This paper conducts an exposition on the field identification of Clariid catfishes Heterobranchus, Clarias and their hybrid as an important tool in fish breeding and genetics. The paper explained the classification and aquacultural importance of Clariid catfishes. Parameters necessary for fish identification were highlighted. The identification of Heterobranchus, Clarias, their hybrid and sexual differences were also identified. The paper is of the position that the identification of Heterobranchus, Clarias and their hybrid is important in their genetic conservation and in achieving success in breeding and genetic studies
A revision of the genus Melanoides (Gastropoda : Thiaridae) in Lake Malawi

The genus lIgMelanoidesl/Ig in Lake Malawi is revised based on the morphology of the shell and the radula of collected snails and specimens in museum collections. Extensive morphological variation in the genus led to the conclusion that many of the previously described species are synonymous. M. virgulatal/Ig Ferrusac, 1827, which has erroneously been considered a synonym of M. tuberculatal/Ig in previous studies, is reinstated as a valid species. In Lake Malawi the genus lIgMelanoidesl/Ig comprises five species : M. tuberculata, M. virgulata, M. nodicincta, M. simonsil/Ig and M. polymorpha . The last three are endemic to Lake Malawi.
Short-term CDK4/6 Inhibition Radiosensitizes Estrogen Receptor–Positive Breast Cancers

Purpose: Cyclin-dependent kinase 4/6 (CDK4/6) inhibitors have improved progression-free survival for metastatic, estrogen receptor–positive (ER+) breast cancers, but their role in the nonmetastatic setting remains unclear. We sought to understand the effects of CDK4/6 inhibition (CDK4/6i) and radiotherapy in multiple preclinical breast cancer models. Experimental Design: Transcriptomic and proteomic analyses were used to identify significantly altered pathways after CDK4/6i. Clonogenic assays were used to quantify the radiotherapy enhancement ratio (rER). DNA damage was quantified using γH2AX staining and the neutral comet assay. DNA repair was assessed using RAD51 foci formation and nonhomologous end joining (NHEJ) reporter assays. Orthotopic xenografts were used to assess the efficacy of combination therapy. Results: Palbociclib significantly radiosensitized multiple ER+ cell lines at low nanomolar, sub IC50 concentrations (rER: 1.21–1.52) and led to a decrease in the surviving fraction of cells at 2 Gy (P < 0.001). Similar results were observed in ribociclib-treated (rER: 1.08–1.68) and abemaciclib-treated (rER: 1.19–2.05) cells. Combination treatment decreased RAD51 foci formation (P < 0.001), leading to a suppression of homologous recombination activity, but did not affect NHEJ efficiency (P > 0.05). Immortalized breast epithelial cells and cells with acquired resistance to CDK4/6i did not demonstrate radiosensitization (rER: 0.94–1.11) or changes in RAD51 foci. In xenograft models, concurrent palbociclib and radiotherapy led to a significant decrease in tumor growth. Conclusions: These studies provide preclinical rationale to test CDK4/6i and radiotherapy in women with locally advanced ER+ breast cancer at high risk for locoregional recurrence.
Radiomics for Gleason Score Detection through Deep Learning

Prostate cancer is classified into different stages, each stage is related to a different Gleason score. The labeling of a diagnosed prostate cancer is a task usually performed by radiologists. In this paper we propose a deep architecture, based on several convolutional layers, aimed to automatically assign the Gleason score to Magnetic Resonance Imaging (MRI) under analysis. We exploit a set of 71 radiomic features belonging to five categories: First Order, Shape, Gray Level Co-occurrence Matrix, Gray Level Run Length Matrix and Gray Level Size Zone Matrix. The radiomic features are gathered directly from segmented MRIs using two free-available dataset for research purpose obtained from different institutions. The results, obtained in terms of accuracy, are promising: they are ranging between 0.96 and 0.98 for Gleason score prediction.
Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology

Garcinia kola (Heckel) is a versatile tree indigenous to West and Central Africa. All parts of the tree have value in traditional medicine. Natural populations of the species have declined over the years due to overexploitation. Assessment of genetic diversity and population structure of G. kola is important for its management and conservation. The present study investigates the genetic diversity and population structure of G. kola populations in Benin using ultra-high-throughput diversity array technology (DArT) single nucleotide polymorphism (SNP) markers. From the 102 accessions sampled, two were excluded from the final dataset owing to poor genotyping coverage. A total of 43,736 SNPs were reported, of which 12,585 were used for analyses after screening with quality control parameters including Minor allele frequency (≥ 0.05), call rate (≥ 80%), reproducibility (≥ 95%), and polymorphic information content (≥ 1%). Analysis revealed low genetic diversity with expected heterozygosity per population ranging from 0.196 to 0.228. Pairwise F-statistics (FST) revealed low levels of genetic differentiation between populations while an Analysis of molecular variance (AMOVA) indicated that the majority of variation (97.86%) was within populations. Population structure analysis through clustering and discriminant analysis on principal component revealed two admixed clusters, implying little genetic structure. However, the model-based maximum likelihood in Admixture indicated only one genetic cluster. The present study indicated low genetic diversity of G. kola, and interventions are needed to be tailored towards its conservation.
Biology of Helicoverpa armigera Hub. on rose in laboratory condition

Rose plant is attacked by number of insect pests like bud borer, thrips, scale, aphids, weevils, chafer beetles leaf eating caterpillars and non insect pest like red mite. Amongst them, Helicoverpa armigera is the major coconut pest on rose. Due to the presence of sweet fragrance, absence of bitter principles, Helicoverpa moths are attracted for oviposition on tender rose buds. Infestation of the bud borer is seen on open cultivated roses in severe form from January to March. Female moth lays cream colored eggs singly on young buds. Newly hatched larva bore into buds by making holes and feeds on growing petals. Caterpillars also damage flowers by eating petals and leaving excreta. In south Gujarat, it is considered to be a major limiting factor in production of good quality rose flowers. Its attack coincides with bud and flower stage and in absence of this it also feed on leaves and reduces the market value of flowers.