Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Endogenous Retrovirus K (HML-2) in Health and Disease

Human endogenous retroviruses (HERVs) are derived from exogenous retrovirus infections in the evolution of primates and account for about 8% of the human genome. They were considered as silent passengers within our genomes for a long time, however, reactivation of HERVs has been associated with tumors and autoimmune diseases, especially the HERV-K (HML-2) family, the most recent integration groups with the least number of mutations and the most biologically active to encode functional retroviral proteins and produce retrovirus-like particles. Increasing studies are committed to determining the potential role of HERV-K (HML-2) in pathogenicity. Although there is still no evidence for HERV-K (HML-2) as a direct cause of diseases, aberrant expression profiles of the HERV-K (HML-2) transcripts and their regulatory function to their proximal host-genes were identified in different diseases. In this review, we summarized the advances between HERV-K (HML-2) and diseases to provide basis for further studies on the causal relationship between HERV-K (HML-2) and diseases. We recommended more attention to polymorphic integrated HERV-K (HML-2) loci which could be genetic causative factors and be associated with inter-individual differences in tumorigenesis and autoimmune diseases.
TNF-α-Induced Growth Suppression of CD34+ Myeloid Leukemic Cell Lines Signals Through TNF Receptor Type I and Is Associated with NF-κB Activation

Conflicting results have been reported regarding the effect of TNF-α on the growth of human primitive hemopoietic cells. In this study, we have examined the effect of TNF-α on the proliferation of several CD34+/CD38+ (KG-1, TF-1) and CD34+/CD38− (KG-1a, TF-1a) myeloid leukemic progenitor cell lines. Our data show that TNF-α markedly inhibits the growth of these cells in both liquid and soft agar cultures. Addition of GM-CSF or IL-3 does not prevent TNF-α-induced growth inhibition. Flow cytometry analyses of propidium iodide-stained cells demonstrated cell death of all four cell lines, as judged by the presence of cells with hypodiploid DNA content after exposure of cells to TNF-α for 4 days. Annexin V assays detected apoptosis in TF-1, but not in TF-1a, KG-1, and KG-1a cells in terms of translocation of phosphatidylserine shortly after TNF-α treatment. Neutralizing anti-TNF receptor type I (TNFR-I; p55) Ab almost completely reversed TNF-α-induced growth inhibition in both liquid and soft agar cultures, whereas anti-TNFR-II (p75) Ab had only a marginal effect. TNF-α rapidly induced marked activation of nuclear transcription factor NF-κB in all 4 cell lines. The majority of this effect was abolished by the type I receptor Ab, whereas the type II receptor neutralizing Ab had no effect. Our data also show that TNF-α is incapable of inducing activation of the mitogen-activated protein kinase pathway in these leukemic cell lines.
Amygdalar and Hippocampal Morphometry Abnormalities in First-Episode Schizophrenia Using Deformation-Based Shape Analysis

In this study, we investigated and quantified the amygdalar and hippocampal morphometry abnormalities exerted by first-episode schizophrenia using a total of 92 patients and 106 healthy control participants. Magnetic resonance imaging (MRI) based automated segmentation was conducted to obtain the amygdalar and hippocampal segmentations. Disease-versus-control volume differences of the bilateral amygdalas and hippocampi were quantified. In addition, deformation-based statistical shape analysis was employed to quantify the region-specific shape abnormalities of each structure of interest. To better identify the key relevant areas in the pathology of first-episode schizophrenia, each structure was divided into four subregions; CA1, CA2, CA3 combined with dentate gyrus for the hippocampus in each hemisphere and basolateral, basomedial, centromedial, and lateral nucleus for the amygdala in each hemisphere. We observed significant global volume reduction and localized shape atrophy in each of the four structures of interest. The amygdalar shape abnormalities mainly occurred at the basolateral and centromedial subregions, whereas the hippocampal shape abnormalities mainly concentrated on the CA1 and CA2 subregions. For the same structure, the one on the right hemisphere was affected more by the disease pathology than that on the left hemisphere. To conclude, we have successfully quantified the global and local morphometric abnormalities of the bilateral amygdalas and hippocampi using a sophisticated statistical analysis pipeline and high-field subregion segmentations, with MRI data of a considerable sample size. This study is one of the very first of such kind in first-episode schizophrenia analyses.
Assessment of Probiotic Properties of Lactobacillus salivarius Isolated From Chickens as Feed Additives

The continued use of sub-therapeutic antibiotics as feed additives in the poultry industry improved health and growth performance. However, the resulting antibiotic resistance increasingly becomes a major threat to public health. Probiotics are promising alternatives for the antibiotics used in poultry industry. The aim of this study was to evaluate the probiotic properties of Lactobacillus salivarius as feed additive in chickens. White leghorn chickens were randomly assigned to experimental groups. Effects of Lactobacillus salivarius supplementation on growth performance, resistance to Escherichia coli O78 challenge and heat-stress, and immune response after vaccinated with attenuated infectious bursal disease virus (IBDV) vaccine were determined. The results showed that Lactobacillus salivarius supplementation improved growth performance, such as weight and longer shank length, increased relative weights of the immune organs and decreased concentrations of odor-causing compounds. In addition, Lactobacillus salivarius supplementation alleviated organ injury caused by Escherichia coli O78 challenge and heat stress. Furthermore, Lactobacillus salivarius results in enhanced immune response after IBDV vaccine immunization, enhanced specific antibody and IFN-γ production, and lymphocyte proliferation. Our results revealed a tremendous potential of Lactobacillus salivarius as antibiotics' substitute in poultry production.
Dormant but Active: Chilling Accumulation Modulates the Epigenome and Transcriptome of Prunus avium During Bud Dormancy

Temperate deciduous fruit tree species like sweet cherry (Prunus avium) require long periods of low temperatures to trigger dormancy release and flowering. In addition to sequence-based genetic diversity, epigenetic variation may contribute to different chilling requirements among varieties. For the low chill variety ‘Royal Dawn’ and high chill variety ‘Kordia’, we studied the methylome of floral buds during chilling accumulation using MethylC-seq to identify differentially methylated regions (DMRs) during chilling hours (CH) accumulation, followed by transcriptome analysis to correlate changes in gene expression with DNA methylation. We found that during chilling accumulation, DNA methylation increased from 173 CH in ‘Royal Dawn’ and 443 CH in ‘Kordia’ and was mostly associated with the CHH context. In addition, transcriptional changes were observed from 443 CH in ‘Kordia’ with 1,210 differentially expressed genes, increasing to 4,292 genes at 1,295 CH. While ‘Royal Dawn’ showed approximately 5,000 genes differentially expressed at 348 CH and 516 CH, showing a reprogramming that was specific for each genotype. From conserved upregulated genes that overlapped with hypomethylated regions and downregulated genes that overlapped with hypermethylated regions in both varieties, we identified genes related to cold-sensing, cold-signaling, oxidation-reduction process, metabolism of phenylpropanoids and lipids, and a MADS-box SVP-like gene. As a complementary analysis, we used conserved and non-conserved DEGs that presented a negative correlation between DNA methylations and mRNA levels across all chilling conditions, obtaining Gene Ontology (GO) categories related to abiotic stress, metabolism, and oxidative stress. Altogether, this data indicates that changes in DNA methylation precedes transcript changes and may occur as an early response to low temperatures to increase the cold tolerance in the endodormancy period, contributing with the first methylome information about the effect of environmental cues over two different genotypes of sweet cherry.
Pollen morphology of Enkianthus (Ericaceae) and its taxonomic significance

Pollen morphology of ten Enkianthus species was examined using light (LM) and scanning electron microscopy (SEM) and previous infrageneric classification of Enkianthus was discussed in the light of the palynological characters obtained in this study. The pollen grains are monads, oblate spheroidal to prolate in shape and 3‐ to 5‐colpor(oid)ate. Exine sculpture varies from granulate to coarsely rugulate‐psilate with faint to distinct minute granules in SEM. Infraspecific geographical differences in palynological characters were found in E. deflexus. The species of Enkianthus are clearly differentiated into two pollen morphological groups that correspond to the sections Enkiantella + Meisteria and Andromedina + Enkianthus, respectively. The members of the sections Enkiantella and Meisteria have pollen grains typically with three apertures, prolate spheroidal to prolate, ratio of colpus length to polar axis (L/P) 0.69–0.84, relatively thinner exine and exine sculpturing tendency to granulate, character states that are probably plesiomorphic in this genus. The members of the sections Andromedina and Enkianthus have more derived pollen grains with four to five apertures, commonly oblate spheroidal, L/P 0.56–0.63, relatively thicker exine and exine sculpturing tendency to coarsely rugulate‐psilate. It seems to be difficult to differentiate between sections of the same group on the basis of palynological characters only. Adding the palynological characters to the infrageneric framework of Anderberg indicates an evolutionary trend in exine sculpture within Enkianthus from finely verrucate‐rugulate through coarsely rugulate to coarsely rugulate‐psilate. A dichotomous key for Enkianthus was prepared based on the palynological characters.
NICHE OVERLAP AND THE POTENTIAL FOR COMPETITION BETWEEN REINTRODUCED BISON AND OTHER UNGULATES IN

The potential for interspecific competition for scarce food resources is a key consideration when newly introduced ungulates occupy a shared range with resident native species. To assess potential competition among ungulates we examined dietary overlap of 7 species during 2009–2010 in southwestern Yukon, Canada. Diet composition at the forage class scale and composite diet indices (diversity, evenness, and niche breadth) were compared among species found at 2 elevation classes (high and low) during 2 broad seasons (summer and winter), using diet data derived from microhistological analyses. Composite diet indices and use of major forage classes differed among species during summer and winter and at both high and low elevations. Dietary overlap for most species pairs was low to moderate (0.10–0.70). However, for reintroduced bison (Bison bison) and thinhorn sheep (Ovis dalli), and bison and semi-feral horses (Equus ferus caballus), it was high (≥0.80) during both summer and winter, indicating a potential of competition for food. Dietary overlap between species appeared to be based primarily on morphophysiological classification (i.e., browser-intermediate-grazer), rather than body size. Bison, horses, and sheep were all grazers. Intermediate species such as introduced elk (Cervus canadensis) had moderate dietary overlap with several species, but did not highly overlap with any other species. We conclude that the potential for competition for food resources between bison and sheep and bison and horses is high, but that for all other species pairs in our study area is low to moderate.
IgG 2 ANTI-GAL&agr;1–3GAL DOES NOT INDUCE PORCINE AORTIC ENDOTHELIAL CELL ACCOMMODATION IN VITRO

Background. Xenografts that have been protected from hyperacute rejection (HAR) are termed accommodated if they are not then rejected despite the presence of xenoantibody.It has been proposed that IgG may confer resistance to complement dependent cytotoxicity (CDC), a conventional in vitro marker of accommodation. We hypothesized that noncytotoxic IgG 2 anti-Gal&agr;1–3Gal was responsible for this effect. Methods and Results. We purified IgG anti-Gal&agr;1–3Gal from pooled human normal immunoglobulin and three sera, by elution from protein G and Gal&agr;1–3Gal-R immunoadsorbents. The eluates were IgM free and ⩾95% IgG 2. They bound to Gal&agr;1–3Gal, porcine aortic endothelial cells (PAEC) and lymphocytes. It was not possible to block IgM binding to PAEC or lymphocytes using IgG anti-Gal&agr;1–3Gal (200 &mgr;g/ml). The eluates were noncytotoxic in micro-CDC assays. To investigate accommodation, PAEC were cultured with subsaturating doses of the four IgG eluates for up to 144 hr. Resistance of nontrypsinized PAEC to CDC by human serum was measured in a cell viability assay. PAEC were not rendered resistant to CDC in any of the experiments. To investigate the possibility that accommodation might be induced by non-Gal&agr;1–3Gal IgG, the experiments were repeated using HNIg, again with no protection demonstrated. Conclusions. Using primary PAEC monolayers, we were unable to induce resistance to CDC with human normal immunoglobulin and its IgG 2 anti-Gal&agr;1–3Gal subset. This contradicts previous experiments using trypsinized, immortalized cells. Although resistance to CDC is not an ideal marker of accommodation, the detrimental effects of IgG make it unlikely that it will become a useful clinical means of inducing accommodation.
Meiotic mutants and DNA repair genes of Coprinus cinereus

We are studying DNA repair and meiosis in the basidiomycete Coprinus cinereus, in which the meiotic cycle is naturally highly synchronous. We have taken two approaches to the study of genes whose products function in these essential and related processes. In the first, we screened mutagenized cultures for y-radiation sensitivity and recovered four complementation groups, rad3, rad9, radll, and radl2, that are required for the survival of y-irradiation and for meiosis. 'These four genes are in the same pathway for survival of y-radiation damage. Surface spreads of meiotic chromosomes of rad3, rod9, and radl2 mutants demonstrated that both axial core development and chromosome synapsis are defective. The rad3-4 mutant exhibits heterogeneity in the appearance of its meiotic cells, which may reflect stochastic effects of the absence of functional rad3 gene product, or cell to cell variation of the abundance of the rad3 protein within the mutant. All four of the rad genes necessary for meiosis have been mapped to the electrophoretic karyotype of C. cinereus, and the rad9 gene has been cloned. In a second approach to the study of DNA repair and meiosis, we have used PCR to isolate the gene Ccrod51, a homolog of the prokaryotic gene recA. Although the precise functions of these genes in DNA repair and meiosis are not known, we hypothesize that their roles in these two fundamental processes are similar, and that this group of genes was recruited during evolution for the application of mitotic DNA repair functions to the metabolism of meiotic chromosomes.
Management recommendations for short‐lived weeds depend on model structure and explicit characterization of density dependence

1. Multiple modelling techniques are currently used to describe population dynamics of established invasions, where intraspecific competition is likely to reduce survival, growth and/or fecundity, suppressing population growth rate. To date, it remains unanswered whether these modelling techniques produce similar management recommendations for density‐dependent weed populations and how to model density dependence to better inform management.
Endocrine and behavioral correlates of drought in wild olive baboons (Papio anubis)

As part of a long‐term study in behavioral endocrinology, wild olive baboons (Papio anubis) living in the Serengeti ecosystem of East Africa have been under study since 1978. The present report documents behavioral and endocrine changes associated with the severe drought of 1984. During this time, the annual rainy season failed and grassland biomass was severely reduced in the Serengeti. Baboons were able to maintain body weight but spent significantly more time foraging for food. In four prior years of study, basal testosterone concentrations were remarkably stable in adult and subadult males. In contrast, during the drought, there was a highly significant 60% decline in basal concentrations of the steroid. This testicular suppression was apparent in males of all ranks (by approach‐avoidance criteria). Prior studies with this population, which examined the role of acute and chronic stressors in similarly suppressing testosterone concentrations, suggested that the present instance was in response to the stress of the drought. The drought was also associated with significant reductions in the rates of escalated aggression among males. However, the distribution of fights between high‐ranking males, between low‐ranking males, and between high‐ and low‐ranking males did not change from prior years, nor was the dominance hierarchy inordinately unstable during this time. These findings agree with previous evidence that indicates that suppressed testosterone concentrations in males can be associated with lower rates of aggressive behaviors but that the steroid plays a predominantly facilitative rather than activational role. Finally, rates of approach‐avoidance interactions and of male sexual behaviors were unchanged during the drought. These findings agree with an endocrine literature that indicates that reproductive behavior or physiology in primates is rarely disrupted by suppression of testosterone concentrations of the magnitude of the present case.
THE OCCURRENCE AND SIGNIFICANCE OF AUXIN IN THE SUBSTRATA OF BRYOPHYTES

Summary Auxin was detected in samples of substrata supporting bryophytes in a variety of locations in both Britain and Malaya. Activity occurred on chromatograms at zones corresponding to the Rf of indole acetic acid. The range of concentrations found, 0.4–10.4 μg/1, probably represents a two- to five-fold underestimate due to losses during extraction and purification. The amounts of auxin in samples of soil on which bryophytes were not growing were within the same range. The importance of this environmental auxin for the induction of rhizoids in liverworts and for roots of higher plants is discussed.
Guidelines for the Early Management of Patients With Acute Ischemic Stroke: A Guideline for Healthcare Professionals From the American Heart Association/American Stroke Association

Background and Purpose— The authors present an overview of the current evidence and management recommendations for evaluation and treatment of adults with acute ischemic stroke. The intended audiences are prehospital care providers, physicians, allied health professionals, and hospital administrators responsible for the care of acute ischemic stroke patients within the first 48 hours from stroke onset. These guidelines supersede the prior 2007 guidelines and 2009 updates. Methods— Members of the writing committee were appointed by the American Stroke Association Stroke Council’s Scientific Statement Oversight Committee, representing various areas of medical expertise. Strict adherence to the American Heart Association conflict of interest policy was maintained throughout the consensus process. Panel members were assigned topics relevant to their areas of expertise, reviewed the stroke literature with emphasis on publications since the prior guidelines, and drafted recommendations in accordance with the American Heart Association Stroke Council’s Level of Evidence grading algorithm. Results— The goal of these guidelines is to limit the morbidity and mortality associated with stroke. The guidelines support the overarching concept of stroke systems of care and detail aspects of stroke care from patient recognition; emergency medical services activation, transport, and triage; through the initial hours in the emergency department and stroke unit. The guideline discusses early stroke evaluation and general medical care, as well as ischemic stroke, specific interventions such as reperfusion strategies, and general physiological optimization for cerebral resuscitation. Conclusions— Because many of the recommendations are based on limited data, additional research on treatment of acute ischemic stroke remains urgently needed.
Rhodococcus coprophilus sp. nov.: An Aerobic Nocardioform Actinomycete Belonging to the ‘rhodochrous’ Complex

SUMMARY: The aerobic nocardioform actinomycete, found to be common in herbivore dung and aquatic habitats and previously given the trivial name Lspi, was studied along with representative strains of taxa within the ‘rhodochrous’ complex. Lspi strains were recovered as a homogeneous cluster which separated from the other reference strains at the 69% similarity level in a numerical taxonomic analysis. The specific name Rhodococcus coprophilus is proposed for this new species. We also consider the generic name Rhodococcus Zopf to be appropriate for most of the species currently accommodated within that rather ill-defined taxon known as the ‘rhodochrous’ complex and variously classified within the genera Nocardia, Mycobacterium, Jensenia, Corynebacterium or Gordona.
Role of Biscuits Enriched with Albumin Protein from Snakehead Fish, Zinc and Iron on Immune Response of under Five Children

This study was aimed to evaluate the effect of administering biscuits enriched with albumin protein from snakehead fish, zinc and iron on immune response of under five children. This was pre-post, single blind, randomized control trial conducted in twenty eight preschool children aged 4-5 year attending Early Childhood Education (PAUD) in Pilar village, sub-district of Semplak, Bogor Regency, West Java. The children were randomly assigned to experimental group which receive biscuit with protein source from snakehead fish flour fortified with zinc and iron and control group which receive biscuit with protein source from milk. Both biscuits had a similar on protein and energy content of 13.34% and 503 kcal, respectively. A 60 g biscu its per day was consumed by the children for 56 days. Results showed that experimental biscuits (biscuits sourced snakehead fish protein) had a higher contribution on energy, protein, Zn and Fe than a control biscuits (biscuits sourced milk protein). Fish biscuit contribution to energy was 14.64% RDA, protein was 14.75% RDA, Zn was 53.52% RDA and Fe was 39.26% RDA. Milk biscuit contribution to energy was 9.40% RDA and protein was 4.29% RDA, Zn was 3.27% RDA and Fe was 5.80% RDA. T-test result showed that milk biscuit group was significantly different (p<0.05) than fish biscuit group on nutrient intakes and contribution to energy, protein, Zn and Fe RDA. Immunoglobulin (IgG) mean increase at the end of the study in fish biscuit group was higher, which was 0.88±0.58 mg/mL compared to milk biscuit group which was decreased by -60.31±81.76 mg/mL. Increase of albumin mean at the end of the study in fish biscuit group was higher, which was 0.48±0.32 g/dL compared to milk biscuit group which was 0.05±0.13 g/dL. T- test result showed that IgG and albumin difference in fish biscuit group was significantly (p<0.05) than milk biscuit group.