Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymorphism of killer cell immunoglobulin-like receptors gene in Sichuan Han population,China

Objective To analyze the polymorphism of killer cell immunoglobulin-like receptors gene in Sichuan Han population.Methods A total of 135 samples were randomly selected from CMDP Sichuan branch,and genotyped by PCR-SSP.Based on those standards established by Hsu,the genotypes and haplotypes of all samples were designated.Results Among the Sichuan Han population,framework genes 3DL3、3DL2 and 2DL4 were found expressed in all samples,genes 2DL3、2DP1、2DL1、3DL1、2DS4*001/002 were with high frequencies and genes 2DS2、2DL2、2DL5、3DS1、2DS3、2DS5、2DS1、2DS4*003 were with low frequencies.A total 31 kinds of KIR genotype were identified,among which the genotype AF(1,2) and AJ(2,2) were most common,with its frequencies of 18.52% and 20.74%,respectively.Meanwhile,a total 12 kinds of KIR haplotypes were identified,among which the haplotype 2 was most common,with frequency of 43.4%. Besides,14 kinds' genotypes were not able to be identified via those standards established by Hsu,7 of which used to be reported in Han populations from other areas,and the other 7 were reported in other populations from all over the world.Furthermore,6 KIR genotypes were not able to designate their haplotype combinations.Conclusion Sichuan Han population share the same feature with other Han populations on KIR gene polymorphism,but also,possess its unique frequencies of KIR gene,genotypes and haplotypes.
Diversity of Plasmid Profile in Multi-drug Resistant Non- E. coli Intestinal Flora Lacking Association with Resistance Phenomenon

Aims: To study the plasmid diversity of intestinal nonEscherichia coli community, describe their potential as a reservoir of antibiotic resistance phenomenon and to find any association of resistance phenomenon with the plasmid content if any. Place and Duration of the Study: Department of Microbiology, Jahangirnagar University, Dhaka between June 2014 to July 2015. Methods: Stool samples were cultured onto MacConkey agar plates for selective isolation of Gram negative bacteria. Identification of intestinal nonE. coli was done through conventional Original Research Article Jahan et al.; BMRJ, 14(6): 1-8, 2016; Article no.BMRJ. 25725 2 biochemical tests according to Bergey’s Manual of Systematic Bacteriology. Plasmid extraction was done according to the modified hot alkaline method. Antibiogram was carried out by disc diffusion method and MIC determination by agar dilution assay. Results: One hundred and forty four representative colonies were selected from stool culture of 60 healthy human subjects. Of 144 colonies, 90 belonged to 21 nonE. coli species shared by 11 genus. Majority of the isolates (81%, 73 of 90) showed resistance to one or more antibiotics while the rest 18.9% (17 of 90) were sensitive to all the antibiotics used (amoxicillin, cefixime, ciprofloxacin, gentamicin, sulfamethoxazole-trimethoprim). Highest resistance frequency was observed against amoxicillin (67%) followed by cefixime (28%), gentamicin (24%), sulphamethoxazole–trimethoprime (16%), tetracycline (14%), and ciprofloxacin (8%). A notable proportion of the bacteria (20%) were found to be multi-drug resistant. Majority of the isolates (57%) were found to contain 1 to 6 plasmids and exhibited 34 different plasmid profiles. Thirty two isolates (of 90) carried plasmids with high molecular weight (> 20 Mdal) including 4 isolates that carried large plasmids of approximately 140 Mdal size. Conclusion: Findings of this study indicate that intestinal nonE. coli population may function as a reservoir of heterogeneous plasmid. Although no direct association was observed between resistance phenomenon and presence of plasmids in general, to study the role(s) of individual plasmid for encoding any particular drug resistance phenomenon and /or pathogenic gene(s) would be an interesting line of inquiry.
Torturing data for the sake of generality: How valid are our regression models?

Abstract Multiple regression analysis continues to be a quantitative tool used extensively in the ecological literature. Consequently, methods for model selection and validation are important considerations, yet ecologists appear to pay little attention to how the choice of method can potentially influence the outcome and interpretation of their results. In this study we review commonly employed model selection and validation methods and use a Monte Carlo simulation approach to evaluate their ability to accurately estimate variable inclusion in the final regression model and model prediction error. We found that all methods of model selection erroneously excluded or included variables in the final model and the error rate depended on sample size and the number of predictor variables. In general, forward selection, backward elimination and stepwise selection showed better performance with small sample sizes, whereas a modified bootstrap approach outperformed other methods with larger sample sizes. Model selection using all-subsets or exhaustive search was highly biased, at times never selecting the correct predictor variables. Methods for model validation were also highly biased, with resubstitution and data-splitting (i.e., dividing the data into training and test samples) techniques producing biased and variable estimates of model prediction error. In contrast, jackknife validation was generally unbiased. Using an empirical example we show that the interpretation of the ecological relationships between fish species richness and lake habitat is highly dependent on the type of model selection and validation method employed. The fact that model selection is frequently unsuited to determine correct ecological relationships, and that traditional approaches for model validation over-estimate the strength and value of our empirical models, is a major concern.
Spawning Characteristics of an Endangered Freshwater Fish Microphysogobio koreensis (Pisces: Gobioninae) in the Semjingang (river) from Korea

Microphysogobio koreensis is an endemic Korean freshwater fish that is protected as an endangered fish by the Ministry of Environment in Korea. In this study, we attempted to investigate the spawning period and spawning characteristics of M. koreensis to obtain basic information for its conservation. Though natural and histological observation, the spawning season occurred between April and May, with peak spawning occurred in early May when the water temperature was 20~23°C. During the spawning season, males had a bright-orange body and a thick red horizontal line from the rear of the operculum to the caudal peduncle, along with a lateral line, while females had a dark brown body. Nuptial organ had not appeared. The number of eggs in the ovaries was 10,705~22,165 (15,573±4,274). The number and appearance ratio of mature eggs were 1,100~5,920 (3,383±2,126) and 10.3~44.8% (22.4±15.6), respectively. And the size of mature eggs was 0.60~1.00 mm (0.74±0.06).
Temporal dynamics and environmental predictors on the structure of planktonic testate amoebae community in four Neotropical floodplains

ABSTRACT Understanding the environmental factors that control community structure has become a major focus of ecological research in recent decades. Here, we aimed to analyze the structure of planktonic testate amoebae community and the impact of environmental variables on the diversity of planktonic species in four floodplains of Brazil (Amazonian, Araguaia, Paraná, and Pantanal) over two hydrological periods (2011 and 2012). We hypothesized that biological diversity (richness, abundance, and diversity) of the testate amoebae community is higher during drought periods. Samples were collected from the subsurface of the limnetic region of 72 lakes in the four floodplains during both drought and flood periods in both years. We identified 109 species, belonging to 11 families. Difflugiidae and Arcellidae exhibited higher species composition and abundance. ANOVA results showed noticeable temporal variation in testate amoebae community structure. We confirmed that the highest richness, abundance, and diversity were primarily recorded during drought periods, with significant differences being documented among floodplains and across the two hydrological periods. Multiple regression analysis also indicated that testate amoebae diversity is related to the productivity of the environments in the Amazonian, Araguaia, and Paraná floodplains. Depth of lakes and phosphorus appeared to be limiting factors in the Paraná and Araguaia floodplains, while dissolved oxygen limited species diversity in the Pantanal floodplain. Our results highlight that testate amoebae community exhibit the greatest biological diversity during drought periods, while species diversity is influenced by the environmental conditions (primarily productivity) of each floodplain.
Seasonal changes in water quality and Sargassum biomass in southwest Australia

Sargassum C. Agardh is one of the most diverse genera of marine macro-algae and commonly inhabits shallow tropical and sub-tropical waters. This study aimed to investigate the effect of seasonality and the associated water quality changes on the distribution, canopy cover, mean thallus length and the biomass of Sargassum beds around Point Peron, Shoalwater Islands Marine Park, Southwest Australia. Samples of Sargassum and seawater were collected every three months from summer 2012 to summer 2014 from four different reef zones. A combination of in situ observations and WorldView-2 satellite remote-sensing images were used to map the spatial distribution of Sargassum beds and other associated benthic habitats. The results demonstrated a strong seasonal variation in the environmental parameters, canopy cover, mean thallus length, and biomass of Sargassum, which were significantly (P < 0.05) influenced by the nutrient concentration (PO43-, NO3-, NH4+) and rainfall. However, no variation in any studied parameter was observed among the four reef zones. The highest Sargassum biomass peaks occurred between late spring and early summer (from September to January). The results provide essential information to guide effective conservation and management, as well as sustainable utilisation of this coastal marine renewable resource.
Depletion of FOXM1 via MET Targeting Underlies Establishment of a DNA Damage–Induced Senescence Program in Gastric Cancer

Purpose: Deregulated signaling via the MET receptor tyrosine kinase is abundant in gastric tumors, with up to 80% of cases displaying aberrant MET expression. A growing body of evidence suggests MET as a potential target for tumor radiosensitization. Experimental Design: Cellular proliferation and DNA damage-induced senescence were studied in a panel of MET-overexpressing human gastric cancer cell lines as well as in xenograft models after MET inhibition and/or ionizing radiation. Pathways activation and protein expression were assessed by immunoblotting and immunohistochemistry. Tumor tissue microarrays (91 gastric cancer patients) were generated and copy number alteration (178 patients) and gene expression (373 patients) data available at The Cancer Genome Atlas were analyzed to assess the coalterations of MET and FOXM1. Results: MET targeting administered before ionizing radiation instigates DNA damage–induced senescence (∼80%, P < 0.001) rather than cell death. MET inhibition–associated senescence is linked to the blockade of MAPK pathway, correlates with downregulation of FOXM1, and can be abrogated (11.8% vs. 95.3%, P < 0.001) by ectopic expression of FOXM1 in the corresponding gastric tumor cells. Cells with ectopic FOXM1 expression demonstrate considerable (∼20%, P < 0.001) growth advantage despite MET targeting, suggesting a novel clinically relevant resistance mechanism to MET inhibition as the copresence of both MET and FOXM1 protein (33%) and mRNA (30%) overexpression as well as gene amplification (24,7%) are common in patients with gastric cancer. Conclusions: FOXM1, a negative regulator of senescence, has been identified as a key downstream effector and potential clinical biomarker that mediates MET signaling following infliction of DNA damage in gastric tumors. Clin Cancer Res; 22(21); 5322–36. ©2016 AACR.
Secondary health education-a site for democratic practice or just another PE theory lesson?

Since the 1980s the health education program at Flinders University has provided a suite of topics which explore the theoretical and ideological constructions of health through a socially –critical lens. The program constructs health education as having its own history and body of knowledge and it is offered independently of Physical Education (PE). With the creation of the Key Learning Area of Health & PE in the 1990s, secondary schools have managed the teaching of health education elements within the curriculum in a variety of ways. This paper focuses on the opportunities graduate health education teachers have to use a socially critical approach to shape curriculum in the secondary school context in South Australia. This paper is framed as practitioner research. Jarvis (1999, p.9) says, ‘Practitioner research is increasingly becoming known as action research, a form of research that began in education, although it has now spread to other professions. ’ A number of questions were examined during the research process. Data was collected initially from a focus group of 8 graduates from Flinders University who had become health education teachers in secondary schools. The resulting transcription was thematically analysed and questions developed. These questions were explored in semi structured in depth interviews with another 11 secondary health education teachers. This paper will highlight through interpretive analysis, the challenges for health education teachers in secondary schools, many of whom are not PE teachers, to develop health education curriculum and pedagogy that promotes social action and works towards a healthier school and community.
Antioxidant Potential Of Lansium Domesticum Corr. Seed Extract In White Male Rat (Rattus Novergicus) Induced By Alcohol

Lansium domesticum Corr. is a typical plant of Indonesia. The seeds have a lot of useful compounds, such as flavonoids. Flavonoids are a natural compound that can act as antioxidants. The aim of this study was to determine the antioxidant potential of Lansium domesticum Corr. seed extract. This study was an experimental research with posttest control group design. The subjects were 32 white male rats. Rats were randomly divided into 4 groups: negative control group was given suspension of Na CMC 1%, dose group I, II and III were given Lansium domesticum Corr. seed extract with each dose of 100mg/kg, 200 mg/kg, and 300 mg/kg. Observation of the subject's response was done by measuring the levels of glutathione (GSH) and malondialdehyde (MDA). Analysis ANOVA test showed that there was a group that had an average difference both GSH levels (p=0.00) and MDA levels (p=0.00). Post hoc test analysis for GSH levels and MDA levels showed that only a dose of 100 mg/kg which have significant differences (p=0.00). Thus, Lansium domesticum Corr. seed extract has antioxidant potential and optimum dose of 100 mg/kg.
RNA transcription and chromatin structure during meiotic and postmeiotic stages of spermatogenesis.

: Autoradiographic procedures for the study of RNA and protein synthesis during spermatogenesis have been complemented with electron microscope techniques for visualization of gene activity. These procedures have enabled us to determine that RNA transcription is highly selective with respect to RNA species, timing of synthesis, types of chromosomes (autosomes and sex chromosomes), segments of chromosomes (i.e., the lampbrush segment), and chromatin structure. In mouse and human spermatocytes, a peak production of ribosomal RNA (rRNA) occurs during leptotene-zygotene, preceding nonnucleolar RNA synthesis, which is at a peak in middle pachytene. Transcription in late spermatids decreases in coincidence with changes in chromatin structure and high incorporation rates of [3H]arginine. In these cells, a particulate repeating pattern of chromatin is replaced by chromatin fibers of uniform diameter as highly arginine-rich proteins replace somatic histones. In spermatogonia, spermatocytes and Sertoli cells, the products of transcription are mainly heterogeneous nuclear RNA (hnRNA) and rRNA, whereas spermatids transcribe predominantly hnRNA during early spermiogenesis. Persistent long-lived [3H]-uridine-labeled RNA species in pachytene spermatocyte nuclei contrast with a fast turnover of [3H]uridine-labeled RNA in Sertoli cells as detected at the same pulse labeling time (8--12 days). From these results one can postulate a still undefined control mechanism of gene expression during spermatogenesis for modulating a cascade of events required for male gamete formation.
Studies on the gastrointestinal properties of Ficus exasperata

The gastrointestinal properties of the aqueous extract of F. exasperata leaves, a popular antiulcer herbal drug, were investigated in animals. On the isolated rabbit jejunum, the extract abolished the pendular movement of the preparation. Intraperitoneal administration in mice significantly reduced small intestinal transit in a dose-related manner The extract significantly and dose-dependently protected rats from induced ulcers. The intraperitoneal LD 50 values in mice was 1124±231mg/kg. These results revealed that F. exasperata has a remarkable potential for the treatment of gastrointestinal diseases.
Identification and evaluation of priority conservation areas for Buprestidae (Coleoptera) in South Africa, Lesotho, Swaziland and Namibia

Representative priority conservation areas of quarter-degree grid size (approximately 25 x 25 km) were identified using an iterative rarity-based algorithm for the beetle family Buprestidae (Coleoptera) in South Africa, Lesotho, Swaziland and Namibia. This algorithm provided similar results (number of grids chosen, grid identity and efficiency) to an algorithm that based selection of areas on the taxonomic distinctiveness of each species. The algorithms were also run after pre-selecting grids containing buprestid records and at least 25, 50, 75 and 100 % protection in the form of established reserves, and the number of additional grids required to adequately represent all species was determined. The existing reserve network was found to be inefficient for the conservation of Buprestidae, although many records fall into grids within or containing protected areas. The Nama Karoo, Northern Cape savanna, and grassland are evident as areas of least known richness owing to undersampling. When the algorithms were run for the entire study area, considerably fewer grids, as well as a different spatial arrangement of grids, was selected within Namibia, but not within the combined regions of South Africa, Lesotho and Swaziland. This illustrates possible asymmetry when sharing conservation responsibilities between nations.
Triplet MaxCut: a new toolkit for rooted supertree

The rapid increase of molecular, as well as other types, of available classification data has created the need to combine this data into a unified hypothesis. Supertree methods are essential when amalgamating phylogenetic information from various, possibly conflicting, sources into a single tree. The goal of a supertree algorithm is to satisfy maximally each such source of information in the output tree. Triplets, rooted trees over three leaves, are the minimal piece of such information when dealing with rooted trees. Due to its fundamental role in phylogenetics, extensive effort has been dedicated to several aspects regarding triplets’ research. We have devised a new tool, Triplet MaxCut (TMC), performing various operations in rooted supertree, principally amalgamating rooted trees based on amalgamating rooted triplets. The utility and efficiency of the algorithm is demonstrated by both simulation study and four real data supertree inputs.
Intraspecific diversity matters in bryophyte conservation – internal transcribed spacer and rpl16 G2 intron variation in some European mosses

Intraspecific diversity and molecular relations among regional populations were studied for 16 moss species in three European regions, Central Europe, Southern Scandinavia, and Northern Scandinavia, based on internal transcribed spacer and rpl16 G2 intron. The range of nuclear diversity values found is mainly similar to that of other organisms, and to that found in bryophytes from other regions, but higher diversity was found in Isothecium alopecuroides (Dubois) Isov. No correlations were found between diversity values or number of haplotypes unique to a region and morphological diversity, geographical distribution range, or regional frequency, possibly since this study did not include sufficiently rare species to reflect the factors affecting such species. Finally, no general differences in diversity levels were found among the three studied regions. When haplotype composition is considered, differences were found among the regions for some species, but again no general inter-regional pattern of intraspecific relationships exists. While it is clear that intraspecific variation is crucial to consider in biodiversity conservation contexts since a high proportion of the total diversity is found below the species level, it is also evident that it is necessary to investigate each individual species rather than to rely on what has been found for other taxa.
Chemical Composition of Xylem Exudate from Bleeding Spurs ofVitis rotundifoliaNoble andVitisHybrid Suwannee in Relation to Pruning Date

Xylem exudate was collected from pruned spurs of Vitis rotundifolia Michx. Noble and Vitis hybrid Suwannee on three dates during late winter and spring in order to determine the influence of pruning date on the chemical profile of xylem fluid. Nineteen amino acids, seven organic acids, three sugars, NH 4 + , NO 3 - , and macro- and microelement concentrations were quantified. Water flux varied greatly with pruning date, but osmolarity remained fairly constant (Noble, 8.6 to 11.2 m M ; Suwannee, 11.2 to 13.7 m M ). Total osmolarity coincided closely to the sum of all organic and inorganic entities quantified, indicating that the major chemical components in the xylem exudate have been identified. The within-vine variance in elemental composition at a given time was often as great as between-vine or between-cultivar. Total inorganic ion concentration varied from 3.1 m M to 4.7 m M , amino acids from 3.3 m M to 5.1 m M , organic acids from 2.0 m M to 6.4 m M , and sugars from 10 µ M to 76 µ M . Glutamine was the predominant N-carrier in xylem exudate of both Vitis species. Amino acid concentration increased, and organic acids concentration decreased in Noble exudate later in the season, but inorganic ion and sugar concentrations varied asynchronously over time. The entire increase in amino acid concentration was a result of an increase in glutamine concentration, whereas the decline in organic acid concentration was mainly a function of reduced malic and succinic acid concentrations. Thus, although xylem fluid osmolarity remained relatively constant over time, substantial differences in chemical profile occurred as a function of pruning date.