Miracle-dz/UniFAR-FTUs huggingface dataset:
Integration of OMICS Data for Obesity

Introduction: Obesity is a multifactorial condition that results from the interactions among genetic, dietary, environmental, and lifestyle factors. In our study, we have employed a novel integrative approach to identify mechanisms involved in human disease. Method: In contrast to previous methodologies employed for integration of heterogeneous OMIC data, we based the integration on genomic positions of alterations in human disease. A data search for various types of studies on obesity (genome-wide association, meta-analysis, transcriptomic, proteomic studies and epigenetic studies) was conducted in literature sources and OMIC data repositories, using GWAS Central and Medline database with search string (obesity) AND (transcriptome OR proteome OR genome-wide OR microarray OR profiling OR epigenetics). Additionally, Gene Expression Omnibus (GEO) repository, Array Express and Stanford Microarray Database were searched to discover suitable sources of data for inclusion in our initial dataset. Results and Discussion: As a result of the employed high through put technology, 71 high scoring regions were identified. We identified 8 high scoring gene regions (ATP5O, ALK7, CR1, CR2, S100, GAPDH, TLR1 and TLR6) that have not yet been associated to obesity. Interestingly, all of these genes were identified by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes to be implicated in the energy metabolism and the immune response, which are known to be involved in obesity. Conclusion: In our study, we have performed a novel integrative approach to identify candidate regions and genes involved in human disease. The results showed that none of the high scoring genes that were identified were yet associated with obesity per se, but that they were found to be implicated in the immune response or the energy metabolism. Further research will be needed to validate the found gene regions for obesity.
Mapping quantitative trait loci for performance traits on pig chromosome 6 (SSC6)

portuguesO objetivo deste estudo foi obter o mapeamento de QTL no cromossomo 6 suino (SSC6) associado a caracteristicas de desempenho. A populacao F2 foi produzida utilizando o cruzamento divergente de dois reprodutores da raca nativa brasileira Piau e 18 femeas comerciais. Um total de 617 animais F2 foram genotipados para 13 marcadores microssatelites. As caracteristicas avaliadas na populacao F2 foram: numero de tetas (TN), peso ao nascimento (BW), peso aos 21, 42, 63, 77 e 105 dias de idade (W21, W42, W63, W77, W105), peso ao abate (WS), e ganho de peso medio diario (ADG), consumo de racao (FI) e conversao alimentar (FG) dos 77 aos 105 dias de idade. Os dados foram analisados usando a metodologia de regressao multipla desenvolvida para analises de cruzamentos entre linhas divergentes, usando o software QTL Express. Um QTL significativo foi detectado para FI em 99 cM. Um QTL sugestivo foi detectado para W42 localizado em 55 cM. As caracteristicas FI e ADG parecem estar sob a influencia de um loco situado em torno de 100 cM no cromossomo estudado. Nao foram encontrados QTLs para peso em as outras diferentes idades. EnglishThe objective of this study was to perform QTL mapping associated with performance traits on swine chromosome 6 (SSC6). The F2 population was produced by outcrossing using two native Brazilian breed Piau sires and 18 commercial dams. A total of 617 F2 animals were genotyped for 13 microsatellite markers. The traits evaluated in the F2 population were teat number (TN), birth weight (BW), weight at 21, 42, 63, 77 and 105 days of age (W21, W42, W63, W77, W105), weight at slaughter (WS), and average daily gain (ADG), feed intake (FI) and feed/gain ratio (FG) from 77 to 105 days of age. Data were analyzed by multiple regression developed for analysis of crosses between outbred lines, using the QTL Express software. A significant QTL was detected for FI at 99 cM. A suggestive QTL was detected for W42 located at 55 cM. A locus located at 100 cM seems to affect the traits FI and ADG. Evidence for loci affecting weight at the other ages not was not found.
Polychlorinated biphenyls (PCBs): impact on bat activity and foraging behaviour along the upper Hudson River, New York

Sediments of the upper Hudson River, New York, USA, contain polychlorinated biphenyls (PCBs). Consequently, elevated levels of PCBs have been found in the tissues of bats and their insect prey along this region. However, it is not clear whether bat activity and foraging behaviour have been affected. To assess possible effects of PCBs on bat activity and foraging behaviour, we measured the activity of little brown bats (Myotis lucifugus (LeConte, 1831)) and hoary bats (Lasiurus cinereus (Palisot de Beauvois, 1796)) along the upper Hudson River, as well as abundance of insect prey at the same locations. We also measured foraging duration and distances travelled by radio-tagged M. lucifugus. We found that bat activity and insect abundance did not differ with PCB concentration. We did, however, find that foraging behaviour along the Hudson River differed from a control site. Specifically, M. lucifugus foraging along PCB-contaminated areas of the Hudson River travelled shorter distances from their roosts and s.
Latitudinal Variation in Life History Traits and Incubation Patterns of Yellow Warblers (Setophaga petechia)

Latitudinal variation in avian life history strategies is well documented. Clutch size and nest success tend to increase with latitude, while longevity and developmental rates have been argued to decrease with latitude. However, these patterns are largely based on interspecific comparisons of species breeding at tropical and temperate latitudes. We compare the life history of Yellow Warblers breeding in arctic habitat in Inuvik, NT (68oN), at the northern extent of their range with those breeding in Revelstoke, BC (50oN), and use data from 21 populations spanning 0°N to 68°N to evaluate latitudinal trends in life history traits. Yellow Warblers breeding in Inuvik experienced colder and more variable temperatures and shorter breeding seasons relative to those in breeding in Revelstoke. Males arrived later and clutch initiation dates were consistently delayed in Inuvik. Females breeding in Inuvik laid larger clutches and had higher nest success (due to low nest predation rates) which resulted in higher annual productivity compared to their low latitude counterparts. Yellow warblers appeared to trade off higher productivity with lower survival as estimates of male and female apparent annual survival were lower in Inuvik than in Revelstoke. In contrast, incubation and nestling periods of Yellow Warblers were similar for the two sites. Similar patterns were observed when comparing life history traits across the Yellow Warbler breeding range. We observed steep latitudinal increases in clutch sizes, nest success and productivity that were associated with declines in adult survival. We detected weaker latitudinal declines in incubation and nestling periods. We observed latitudinal variation in some life history traits, but not a general transition of traits associated with a shift from a slow to fast life history. Our study suggests that the expectation for a general shift in life history traits may be over-
Effects of age of seedling and nitrogen rates in the nursery bed on growth, yield and yield components of BRII dhan52 under submerged condition

The experiment was conducted at the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh during July to December 2013 in the aman season to investigate the effect of age of seedling and nitrogen rates in the nursery bed on growth, yield and yield components of BRRI dhan52. The experiment comprised of three ages of seedlings viz., 30, 35 and 40 day old and four nitrogen rate N 1 -N@50 kg ha -1 , N 2 -N@75 kg ha -1 , N 3 -N@100 kg ha -1 , N 4 -N@125 kg ha -1 . The experiment was laid out in a split plot design with three replications. Age of seedling showed significant differences for shoot weight, survivor, no. grains panicle -1 , panicle length, grain yield and straw yield. The highest root weight (0.072 gm -2 ), plant height (108 cm), total tillers hill -1 (8.22), effective tillers hill -1 (7.03), non-effective tillers hill -1 (1.19), survivor (95.1%), grains panicle-1 (106.2), grain yield (5.57 t ha -1 ), straw yield (6.26 t ha -1 ) and harvest index (0.47%) were found by transplanting 40 day old seedlings. The highest shoot weight (0.53 gm -2 ), 1000 grain wt. (25.3g) was found by transplanting 35 day old seedlings and 30 day old seedlings produced highest sterile spikelets (28.9) and panicle length (23.8 cm). Nitrogen rate in the nursery showed significant differences for shoot weight, root weight, survivor, plant height, total tillers hill -1 , effective tillers hill -1 , non-effective tillers hill -1 , panicle length, grains panicle -1 , grain yield and straw yield. Application of 50 kg N ha -1 gave higher plant height (108 cm) and harvest index (0.47%). On the other hand, application of 75 kg N ha -1 produced highest noneffective tillers hill -1 (1.0), grains panicle -1 (100.7), 1000 grain weight (25.3 g) and harvest index (0.47%). Application of 100 kg N ha -1 gave highest total tillers hill -1 (7.85), effective tillers hill -1 (6.85), noneffective tillers hill -1 (1.0), survivor (90.5%) and grain yield (5.01 t ha -1 ). Application of 125 kg N ha -1 gave highest panicle length (23.75 cm), grains panicle -1 (100.7), noneffective tillers hill -1 (1.0) and sterile spikelets (30.1). Forty day old seedlings grown with 100 kg N ha -1 at nursery found to be better in respect of grain yield. The result of the experiment also showed that aged seedlings regenerated quickly after desubmerge of water. Res. Agric. , Livest. Fish.2(2): 261-269, August 2015
Utilization of natural green tea and grape seed extracts and nisin to reduce conventional chemical preservatives and to inhibit the the growth of Listeria monocytogenes in ready to eat low and high fat chicken and turkey hotdogs

Effect of potassium lactate (PL) and sodium diacetate (SD) c ombinations at varying levels were evaluated in low (5 %) and high (20 %) fat chicken and turkey hotdog model systems. All samples were surface inoculated with Listeria monocytogenes [approximately 4.62 log colony forming units cfu/g (cfu/g)], vacuum packed, and stored at 4 C for twenty-eight days to determine the effective combination of PL and SD and the effect of fat content on the growth inhibition of L. monocytogenes. In chicken hotdog samples , maximum growth inhibitions (3.42 log cfu/g) were observed in low fat samples formulated with 3.0 % P L and 0.15 % SD. In turkey hotdog samples, maximum growth inhibitions (3.3 log cfu/g) were observe d in low fat samples formulated with 3.0 % PL and 0.2 % SD in turkey. Effective combination l evels determined in low and high fat chicken were 3.0% PL and 0.15% SD, whereas in low and hi gh fat turkey, the effective levels were 3.0% PL and 0.20% SD. Overall, fat content ha d a significant effect ( P < 0.05) on growth inhibition as indicated by higher inhibitions in low fat c hicken and turkey hotdogs than high fat samples. These results demonstrate that commercial usage l evels of PL (2.0 %) and SD (0.15 %) alone are not sufficient to control L. monocytogenes in case of pathogen
Investigation into the relationships between molecular chaperones, mitochondrial antioxidant enzymes, and endothermic vertebrate longevity

The maximum lifespan (MLSP) of endothermic vertebrates can range from as little as a year to over two centuries, yet the underlying phenotype of aging is very similar amongst this group of organisms. One organelle that may be important in the phenotype of aging is the mitochondrion. When damaged, this organelle is thought to contribute to many of the neurodegenerative diseases of aging. For this thesis, mitochondria from brain tissues of 7 mammalian and 2 avian species were isolated to assess whether the antioxidant glutathione system and major molecular chaperone, HSP60, is correlated to species MLSP. Furthermore, HSP60, and the major endoplasmic reticulum chaperone, GRP78, were measured under basal conditions, and following the introduction of an oxidative stress (hydrogen peroxide) in cultured mammalian myoblasts from 10 different species. My results indicate that the enzymes involved in the glutathione defense system are not correlated to species MLSP in brain mitochondria; however HSP60 levels are indeed higher in the longer-lived species. HSP60 levels are also higher at the basal level in cultured mammalian myoblasts and after 1 hour of hydrogen peroxide exposure. GRP78 induction is not correlated to species MLSP at the basal level or following hydrogen peroxide exposure. Therefore, these results suggest that HSP60 is a correlate of longevity in endothermic vertebrate species, but neither the glutathione antioxidant defense system, nor GRP78, correlates to species longevity.
A Simple Penetrometer for Measuring Leaf Toughness in Insect Feeding Studies

The effects of leaf toughness on the feeding activities phytophagous insects have been discussed by many workers, but only a few have undertaken quantitative measurements of this parameter. Rao and Venkatraman (1941), Rao (1947) and Khanna et al. (1947), all studying top-borer infestations in sugar-cane, measured a variety anatomical features such as degree of lignification, and thickness of cell walls in stem sections, and attempted correlate such toughness indices with the incidence of pest attack. Williams (1954) working on the Acrididae, followed by Tanton (1962) on the mustard beetle, Phaedon cochleariae F. , attempted direct measurements of toughness using a simple penetrometer. In this device, an entomological pin with a light card reservoir mounted on top of it was forced through a piece of taut leaf by adding dry sand to the reservoir. The weight of sand required cause penetration of the leaf was then used as an index of toughness.
Effect of seed priming on growth parameters of soybean.

The beneficial effects of seed priming have been demonstrated for many field crops. The objective of this study was to study the effect of seed priming on growth parameters of soybean (Glycine max L.) cv. William-82. For this purpose, experiments were conducted at Khyber Pakhtunkhwa Agricultural University, Peshawar, Pakistan during summer 2003 and 2004. Three seed priming durations (6, 12 and 18 h) and five Polyethylene glycol (PEG 8000) concentrations (0, 100, 200, 300 and 400 g L -1 water) along with dry seed (non primed) as control treatment were included in the experiment. Analysis of the two years average data indicated that AGR, CGR decreased with increase in seed priming duration at I1 during 2003 and AGR, CGR and RGR also showed the same trend at I1 during 2004. Conversely, RGR increased with increase in seed priming duration at I2 during 2003. AGR and CGR enhanced with increase in PEG concentration from 0 to 300 g PEG L -1 water and thereafter decreased at I2 during 2003. Primed seed plots recorded higher AGR and CGR as compared with non-primed seed plots at I1 during 2004 and RGR showed the same trend at I1 and I2 during 2003.
A PRELIMINARY APPRAISAL OF LINE TRANSECTS1

The need for improved methods of measuring abundance of wild animals leads to some sug- gestions for research on line transects. In particular, extensive field data are needed on the frequency of sightings classified by distance from the observer's path. A classification of processes underlying transect observations shows the need for models tailored to fit each kind of application, owing to the importance of distinguishing between those effects which depend on the observer's behavior and those which primarily depend on an animal's reaction to the observer's presence. Some approaches for fur- ther analysis and field study are outlined. There are few, if any, really satisfactory methods of assessing the abundance of wild animals. Difficulties with current methods include both biases and substantial vari- ability in time and space. Line transects suffer badly on both counts, but also offer prospects of convenience and of utility in circumstances where alternate methods may be impracticable or simply not available. The purpose of this paper is to suggest some prospects for evaluating and improv- ing line transects. Unfortunately, we know very little about the physical and psycho- logical processes that lead to the sighting of any animal in the field, so estimates derived from such sightings must often de- pend on uncertain assumptions. A major intent here, then, is to suggest some of these assumptions in forms which may help in devising methods of checking and testing. Radio-tracking and radiotelemetry offer much promise as tools for improving our understanding of the mechanics of animal behavior in the field. Undoubtedly these methods will yield a great deal of informa- tion about census methods in fairly short order. But the rationale, support, and ex- tension of such studies will also depend on the availability of good records of the raw data of field use of line transects. Such data offer much potential for testing assump- tions basic to the estimates, but seem rarely to be published, and perhaps often are not even kept as a permanent record. Usually weather conditions and habitats are re- ported, but individual observations of sight- ing angle and flushing distance are mini- mal requisites for further study of methods.
Characterization of BclA1, a putative C. difficile Exosporium Glycoprotein.

Characterization of BclA1, a Putative C. difficile Exosporium Glycoprotein. (May 2012) James Bregg Reedy Department of Biology Texas A&M University Research Advisor: Dr. Joseph Sorg Department of Biology Clostridium difficile is a spore forming, anaerobic bacterium that can cause diarrhea, pseudomembranous colitis, and toxic mega colon in susceptible hosts. C. difficile spores are highly resistant to extreme chemical and physical environments, and are likely the infectious agent. Spores are formed and matured inside of a mother cell and released into the environment when the mother cell lyses. During spore formation, a loosely attached outer layer, the exosporium, is added before mother cell lysis. The function of the C. difficile exosporium is not known, but has been studied in several Bacillus spp. In Bacillus cereus, the exosporium is the primary barrier that interacts with the host environment, helps the spore adhere to surfaces, and escape phagocytosis by macrophages. In C. difficile 630, bclA1 is an orthologue of B. anthracis bclA and B. cereus bclA, and is a possible exosporium glycoprotein. Mutant C. difficile strains lacking these proteins may have effects on spore adhesion, germination, and spore architecture. Here we attempt to mutate C. difficile bclA1 through TargeTron technology. Though no mutations were observed, we did isolate erythromycin-resistance
Variations in the Total Lipid Content and Biological Characteristics of Diatom Species for Potential Biodiesel Production

The selection of suitable and indigenous species is a fundamental requirement in developing oil-rich microalgae for biodiesel production. So it is necessary to evaluate the growth characteristics and lipid content of the interested microalgae species and obtain a basic knowledge about their potential towards biodiesel production. In this study, the total lipid content and biomass concentration under normal culture conditions of thirty- five diatom species (with twenty-six species being studied for the first time) belonging to nineteen genera obtained from different locations were examined. The results showed that the total lipid content is species-dependent, ranging from 4.86% to 48.61% dry weight. Twenty-four strains (64.9%) had total lipid contents higher than 20% dry weight, and nine strains (24.3%) had total lipid contents greater than 30% dry weight. Achnanthes amoena and Proschkinia sp. had total lipid contents up to 48.61% and 41.42% dry weight, respectively. Compared with the centric diatoms, most species with high lipid content were pennate. In addition, various biological characteristics were documented, including cell size and the ability to survive in various environments. The results revealed that some diatom species here such as Bacillaria paradoxa, Navicula molli, Navicula halophila and Phaeodactylum tricornutum could be regarded as potential sources for biodiesel production.
Using turf transplants to reintroduce native forest understory plants into smelter‐disturbed forests

This study investigated factors affecting transplantation success of native forest understory vegetation on metal‐contaminated soils. One year after transplantation along a gradient of historical Cu–Ni smelter pollution in Sudbury, Canada, community‐level characteristics of the transplanted plots and short‐term indicators expressing the performance of selected species were assessed. Thirty 16‐m2 plots were studied, each established with 45 transplanted 0.56 × 0.64−m turfs 10 cm thick, extracted from mixed‐hardwood forests slated for development. Species richness, diversity, and evenness were not affected by environmental conditions but short‐term responses of root growth and sexual reproduction of selected species to environmental variables indicate a need for long‐term monitoring. Root growth of Clintonia borealis (Aiton) Raf. and Gaultheria procumbens L. was positively related to soil temperature. Root growth of G. procumbens correlated negatively with soil Ni availability, but in all plots, root growth was comparable with the literature values from unaffected forests. Flowering frequency of G. procumbens correlated negatively with soil pH and positively with tree cover, corresponding to ecological requirements of this species. Soil SO4−2 had a negative effect on sexual reproduction of C. borealis. Unexpectedly, fruiting of C. borealis responded positively to Ni, and fruiting of Maianthemum canadense Desf. positively to As, possibly due to interdependencies among soil variables. The results are encouraging with respect to transplant success, as effects of smelter‐related variables were relatively minor, but species‐specific responses of the selected species to environmental factors indicate that species performance is dependent on site‐specific conditions, potentially influencing long‐term success of the transplants.
Crowdsourcing for Educational Assessment in Large Classes

MOOC courses like Coursera and recent Stanford’s Online courses have revolutionized learning by online education. Assessment of the participants in these courses is a big challenge, as these courses have huge strengths of participants. Traditional assessment/evaluation approaches are not suitable, as manual evaluation in such a course, having massive participation, is a highly tedious task. In this report, we present an approach to solve this problem by using crowdsourcing. We also present the problems, that arises when peer evaluation is used in large scale, and discussed the problem of fairness in peer evaluation in more detail, and suggested a methodology to address it. Our approach needs to classify participants on the basis of their knowledge levels, later, the tasks are distributed on the basis of these knowledge classes.