Miracle-dz/UniFAR-FTUs huggingface dataset:
Virulence Studies of Clostridium difficile

[Abstract] Clostridium difficile (a Gram-positive, spore-forming, strict anaerobe) can colonize antibiotic-treated hosts (McFarland, 2008). Antibiotics alter the composition of the normal, benign microbial flora which leads to loss of colonization resistance (Wilson and Perini, 1988; Antonopoulos et al ., 2009). C. difficile spores germinate to actively growing bacteria which secrete toxins that damage the colonic epithelium (Voth and Ballard, 2005). The use of animal models of C. difficile disease have allowed the identification of mechanisms of colonization and virulence factors (Lyras et al ., 2009; Kuehne et al ., 2010; Francis et al ., 2013; Aubry et al ., 2012; Carter et al ., 2011). This protocol describes virulence studies of C. difficile in the hamster model of C. difficile infection (Bartlett et al ., 1978; Sambol et al ., 2001).
THE CORRELATIONS BETWEEN TOTAL ANTIOXIDANT CAPACITY AND TOTAL POLYPHENOLS CONTENT ESTABLISHED FOR TOMATOES

Tomatoes (Lycopersicum esculentum) are the most popular garden vegetable crop in world [6]. Tomatoes have been reported to be an important source of antioxidants such as lycopene, phenolics, and vitamin C in human diet [1], and have been linked with reduced risk of prostate and various other forms of cancer, as well as heart diseases [2]. The aim of the study was to determine the total antioxidant capacity and total polyphenol content and to establish some correlations between this parameters in two summer-autumn tomatoes varieties (Campbell 1327 and Ace Royal), cultivated in field condition, in west area country. The analyses were performed on control soil samples (without extra fertilization substances) and soil sampled after differentiated NPK fertilization in variable dozes: N30P30K30, N45P45K45, N60P60K60, N120P60K60. The total antioxidant capacity was studied using FRAP method and the total polyphenol content by Folin-Ciolcalteu method.
Cold Storage of Kiwifruit Shoot Tips in Vitro

Kiwifruit (Actinidia chinensis Planch, cv. Hayward) shoot tip cultures were stored in the dark successfully at 8°C. After a year, their fresh weight had increased 8-fold and they produced more shoot tips than at the start of storage. Storage was less successful at 4°. Chemical names used: 1H-indole-3-butanoic acid (IBA), N6-benzyla-minopurine (BAP).
A STUDY OF OXYGEN METABOLISM IN DROSOPHILA MELANOGASTER

Several results emerge from this study which, it is believed, should assist in defining the problem and, at the same time, should suggest types of investigation which are most likely to contribute to an understanding of metabolism in Drosophila melanogaster.It has been shown that a close approach to a knowledge of metabolism in Drosophila pupae cannot be made if sole dependence is placed on weight of respiring tissues as a guide. In a very rough way, pupal weights show a correspondence with the trends of metabolic rates, but, for particular matings, especially when the larvae are maintained at lower temperatures, the correspondence is largely lost. It has also been shown that rates of oxygen consumption are very irregular and vary in a manner highly suggestive of the influence of environmental agencies. The not infrequently pronounced elevations above the general level of metabolism lend support to the conclusion that the metabolic rates for comparable samples of respiring tissue are not necessarily fixed .
Market Basket Analysis using Apriori and Correlation Measures

: Association Rule Mining is a branch of Data mining which aims at identifying associations between different items stored in large databases. Market Basket Analysis is one of the applications of Association Rule Mining which emphasizes on analysis of shopping baskets of customers to analyse their buying habits and mine such patterns from the massive amount of transactional records which can help retailers and shopping websites in developing their marketing strategies to increase their sales and hence maximize the profit. In this paper, Apriori algorithm is used to find the strong association rules which are then judged for their interestingness on the basis of correlation measures.
Detection of Hepatitis B Virus X Gene Mutation from Local Clinical Samples

Hepatitis B virus (HBV) belongs to the Hepadnaviridae family and it infects hepatocytes, which is the most common cell in liver. HBV infection is distinguished into acute and chronic infection based on the duration of infection. Chronic infection of HBV exists more than six months and it can develop into liver cirrhosis and hepatocellular carcinoma (HCC). The development of chronic HBV infection is affected by viral particle load, genotype and subgenotype, as well as its association with HBV X gene mutation. The aim of this study is to determine the genotype and subgenotype based on X gene, and to detect its mutation. The X gene in DNA samples was amplified with nested PCR, which produced two fragments with size of 469bp and 395bp. The DNA sequencing results of the amplified product were analyzed by BLAST program to determine their HBV genotype and subgenotype based on the X gene sequences. The analysis showed that patients were infected mainly by HBV subgenotype B3, which are common in Indonesia. The obtained HBx gene sequences were aligned with HBx gene sequences from database to determine the genotype, subgenotype and amino acid substitution. In this study, we described the presence of known HCC-related HBx mutant, i.e. V5L, A47T, I127T and K130M/V131I, as well as new HBx mutant, i.e. G22S and A85T. The presence of HBx T118N mutant was detected at the highest percentage and occurred from samples with high HBV DNA titer.
Effects of UVC Radiation on the Thickness of Glomerular Basement Membrane in Mole Rats

In general, the Glomerular Basement Membrane (GBM) is the main part of the Glomerular Filtration Barrier (GBF) in living organisms which border the urinary space and capillary lumen. It is thought that, the GBF comprises the endothelium, the basement membrane and the foot processes of podocytes. In this study, the effects of ultraviolet (UV) C radiation on the thickness of GBM in mole rats (Spalax leucodon) kidneys were examined by transmission electron microscope. Thirteen adult mole rats of both sexes, weighing 180-200 g were used in this study. The mole rats were divided into four groups. Group I was separated as the control and did not take any radiation. The other groups were irradiated by artificially produced UVC radiation for 14, 28 and 60 days. After the euthanasia, the kidney samples were taken, dissected out and fixed. Then the specimens were examined on transmission electron microscope. The results showed that the thickening of the GBM was evident at 14 days after UVC radiation exposure and the thickness of GBM increased more than twice of control value at 28 days. But after 60 days of radiation exposure, the thickening decreased slightly. The results showed that UVC radiation caused the thickness of GBM in mole rats according to radiation dose and exposure times.
Influence in vitro de divers facteurs abiotiques (température, pH, salinité) sur la croissance mycélienne de trois souches locales de Trichoderma sp.

Les Trichoderma sont des champignons imparfaits saprophytes que l’on retrouve dans divers milieux comme le sol, le bois mort, les debris des vegetaux et les organes aeriens des plantes. Ils ont un role phytoprotecteur et stimulateur du developpement des plantes associees. L’effet de differents facteurs abiotiques (temperature, pH, salinite) sur la croissance mycelienne de trois souches locales de Trichoderma a ete evalue. Ces souches ont ete isolees a partir de la rhizosphere de la tomate. Une etude preliminaire a ete effectuee sur quatre milieux de culture (PDA, MEA, SB et DOX) pour la selection du milieu d’etude. Les resultats obtenus montrent que le milieu PDA permet une meilleure croissance des souches de Trichoderma . La temperature optimale de croissance des differentes souches est de 29 °C et le pH 5 se revele etre le plus adequat pour la culture des Trichoderma . Cette etude montre egalement que les souches de Trichoderma resistent a des concentrations de sel (NaCl) allant jusqu’a 3%. © 2016 International Formulae Group. All rights reserved. Mots cles: Trichoderma , facteurs limitant, temperature, pH, salinite, milieu de culture English Title: In vitro influence of various abiotic factors (temperature, pH, salinity) on mycelium growth of three local strains of Trichoderma sp. English Abstract Trichoderma are saprophytic imperfect fungi that are found in various environments such as soil, dead wood, vegetable fragments and plant aerial organs. They protect and stimulate development of related plants. Effects of various abiotic factors (temperature, pH, salinity) on mycelium growth of three local Trichoderma strains were investigated. These strains were isolated from tomato rhizosphere. A preliminary study was performed on four culture media (PDA, MEA, SB and DOX) for the selection of the best media. The results showed that PDA medium was highly growth of Trichoderma strains. The optimum temperature for growth of different strains is 29 °C and pH 5 was found to be most suitable for Trichoderma culture. Indeed, Trichoderma strains resistant to salt concentrations (NaCl) up to 3%. © 2016 International Formulae Group. All rights reserved. Keywords: Trichoderma , limiting factors, temperature, pH, salinity, culture media
Socio-demographic study of hypertension and its risk factors

The aim of this study was to assess the socio-demographic factors in prevalence of hypertension and its risk factors, among patients attended in OPD at Regional Research Institute of Unani Medicine, New Delhi, India. In this context study subjects were either having the disease hypertension or having symptoms related to the same. Habit of smoking, tobacco chewing, alcohol intake, high BMI and laziness is a social problem increasing day by day and has a clear association with the problem of hypertension. More over people having hypertension generally suffer from the problem of anxiety, vertigo, palpitation, headache, laziness, breathlessness and vise versa. Hence this is an understood fact that if some people suffer from these above mentioned symptoms may have a chance to reach to the problem of hypertension or people having hypertension may suffer from these symptoms. More over age, gender and family history may be a contributing factor in developing a disease like hypertension. Hence in this study it is tried to show the risk of hypertension in view of socio-demographic factors. The overall mean±sem age of study hypertension patients was 57.38 ± 1.32 years (59.88 ± 2.47 years in men and 52.18 ± 2.47 years in women) and non- hypertension was patients was 40.49 ± 1.38 years (42.65 ± 1.88 years in men and 37.83 ± 2.02 years in women). Median-unbiased estimation was used to assess the odds ratio to identify association of hypertension with socio-demographic factors and its risk factors. In this study, Age, Gender, habit of chewing tobacco, alcohol intake, BMI, anxiety, vertigo, palpitation, headache, laziness, breathlessness and family history of hypertension was found to be significantly associated with hypertension. Significant association was not found with Income Group, Dietary Habits, Residence and Smoking Status. Hence it is clear that socio-demographic factors related to hypertension and its risk are subject to having a cause and effect relationship. This underscores the need for preventive efforts to changes in lifestyle modifications which may lower the chance of a person to developed hypertension.
Diffuse axonal injury

This chapter discusses the factors involved in the genesis of diffuse axonal injury and the factors involved in its attendant morbidity. Topics covered include the pathobiology of brain injury, evidence for injury of axons in human traumatic brain injury, evidence for the occurrence of diffuse axonal injury in experimental animals, pathogenesis of diffuse axonal injury in experimental animal models, and consequences of diffuse axonal injury.
Interactive effects of grazing and drought on desert rangelands of Tunisia

Arid rangelands worldwide regularly confront drought and overgrazing. Land degradation is mostly apparent in desert rangelands, where drought events are important and grazing influences and intrinsic vegetation change act intermittently. The objectives of this study were to determine the effects of grazing and drought stress on diversity, species richness and primary production in desert rangeland of southern Tunisia. This assessment was conducted in March 2008 (wet year) and March 2009 (dry year) both on grazed and ungrazed sites. Diversity, species richness and biomass production exhibited bigger variation between years than among sites within two years. Although protection from grazing could slightly increase rangeland production in favorable years, the additive effects of heavy grazing and drought could result in restoration failure. This study suggests that climatic variations, particularly droughts, control major trends in plant species composition, diversity and biomass. Under grazing, plants of desert regions are able to respond very rapidly to small drought. The latter is the most debilitating risk in desert areas.
Novel Sources of Partial Resistance against Phytophthora sojae in Soybean PI 399036

With the rapid emergence of novel pathogen pathotypes, durable sources of resistance against Phytophthora sojae in soybean [Glycine max (L.) Merrill] are needed to manage Phytopthora stem and root rot (PRR). This study used an inoculum source composed of multiple isolates of the pathogen to characterize partial resistance (PR) to P. sojae in plant introduction (PI) 399036. Two recombinant inbred line (RIL) F5:7 populations developed by crossing PI 399036 (high PR), with two germplasm lines (low PR), AR2 (AX20925) and AR3 (AX20931), were screened. Corrected dry weights (CDW—root and shoot) and percentage root rot data were collected. Inclusive composite interval mapping identified one putative quantitative trait locus (QTL) on chromosome 2 by all disease assessment parameters in the AX20925 population that explained 6 to 14% of the total phenotypic variation and five putative minor QTL on 5 chromosomes (3, 6, 12, 15, and 19) that individually explained 5 to 9% of the phenotypic variation. In the AX20931 population, two QTL, mapped to chromosome 9 and 17, were commonly identified by CDW while the QTL identified on chromosome 9 accounted for 21 to 30% of the total phenotypic variation. Additional QTL identified by CDW on chromosomes 9, 13, 14, and 15 individually accounted for 5 to 8% of the phenotypic variation. PI 399036 contributed the favorable alleles for the majority of the identified QTL. This study demonstrates the usefulness of PI 399036 as a novel source for breeding for resistance to PRR and that an inoculum mixture of P. sojae isolates with varying pathotypes can be used to identify putative QTL for PR to P. sojae using the rice (Oryza sativa) method. N.S. Abeysekara, R.L. Matthiesen, and A.E. Robertson, Dep. of Plant Pathology and Microbiology, Iowa State Univ., Ames, IA 50011; S.R. Cianzio and M.K. Bhattacharyya, Dep. of Agronomy, Iowa State Univ., Ames, IA 50011. Received 26 Sept. 2015. Accepted 11 May 2016. *Corre sponding author (alisonr@iastate.edu). Abbreviations: CDRW, corrected dry root weight; CDSW, corrected dry shoot weight; CDW, corrected dry weight; CIM, composite interval mapping; %DRL, percentage of diseased root length; %DSA, percentage of diseased root surface area; ICIM, inclusive composite interval mapping; LOD, logarithm of odds; PI, plant introduction; PR, partial resistance; PRR, Phytophthora root rot; QTL, quantitative trait loci; RIL, recombinant inbred line; %RR, percentage of root rot; SNP, single nucleotide polymorphism. Published in Crop Sci. 56:1–14 (2016). doi: 10.2135/cropsci2015.09. 0578 © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA All rights reserved. Published July 28, 2016
miRNA based signature for predicting epithelial ovarian cancer relapse-progression: a step forward to prime time clinical adoption?

Epithelial ovarian cancer (EOC) is an extremely genomically heterogeneous disease (1) with a unique clinical phenotype: high rate of chemosensitivity but also high risk of relapse, also after adequate primary treatment (2). Even so, the development of predictive tools to stratify relapse risk can be helpful in identifying high risk populations, which represent 70% of advanced stage disease patients, and in tailoring following treatment. The Cancer Genome Atlas (TCGA) project aimed to unravel this genomic complexity, providing gene expression profiles to discriminate prognosis among patients (3,4). More recently, a meta-analytic approach merging all the gene expression signatures for EOC increased the prognostic accuracy of the model, but no clinically relevant prognostic differences among groups were identified (5).
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9 Science Highlights Climate Change in Southern Patagonia Modeling the Atmospheric Circulation Solar Variability and Holocene Climate 18O/16O Ratio during Heinrich Event 1 Climate Change around 117 ka BP Climate Transitions: Forcings Feedbacks Tree Rings, Isotopes and Climate Modeling the Last Glacial Cycle Global Holocene Climate Variability Late Glacial Changes in Central Europe The Global Carbon Cycle around 20 ka BP North Atlantic Coral Climate History
Evolutionary stable migration in salmon : a simulation study of homing and staying

The evolutionary stable homing and straying of migratory salmon populations are studied in this paper. Homing behaviour is a well-known character in the life history of many migratory fish. After emerging as fry Pacific salmon spend one to three years in fresh water and then migrate out to sea. After spending several years migrating in the sea the adults return to spawn in their natal rivers. The few available estimates e.g. in sockeye salmon populations show that straying, i.e., spawning in non-natal rivers, also occurs. It has been proposed that the fraction of straying increases as the river-lake systems where the fish reproduce and where the young fish spend their first years become more uncertain. In this paper I develop a simulation model to study the evolutionary stable homing and straying strategies of migratory salmon populations. Special reference is made to the problem of how uncertainties in reproduction affect homing and straying in salmon. I also discuss the relationship between evolutionary risk spreading and evolu tionary stable strategies.
ORDINATION OF CHIRONOMID (DIPTERA : CHIRONOMIDAE) COMMUNITIES CHARACTERIZING HABITATS IN A MINNESOTA PEATLAND

Chironomidae were sampled with emergence traps in fen, swamp forest, and sedge mat plant communities during two summers in order to characterize these habitats on the basis of their insect fauna. Canonical correspondence analysis was used to ordinate chi ronomid taxa, traps, and environmental parameters, including plants, to see whether habitats could be distinguished by their midge fauna as they had already been characterized by their flora. Clusters of traps, plant, and chironomid species produced by the ordination closely re sembled the results of optimal agglomeration and recurrent group analysis which had been performed on plant quadrat data alone. Chironomids are the most abundant insects in wetlands (Judd, 1953, 1958; Wrubleski, 1987) and play an important role in wetland food webs (Batzer et al., 1993; Batzer and Wissinger, 1996). They are a significant food source for waterfowl (Sjoberg and Danell, 1982), particularly as a protein source for hens during egg for mation (Krapu, 1974), and they have been shown to influence the development of mal lard ducks (Street, 1977). The presence of chironomids may even influence whether ducks use particular wetlands (Danell and Sjoberg, 1982; Talent et al., 1982). Despite their reported importance, wetland chironomids are not as well-studied as stream (Boerger, 1981), reservoir (Mundie, 1957; Rosenberg et al., 1984), and lake (Oliver, 1964; Iwakuma, 1992) chironomids. Furthermore, in the semi-terrestrial habitats of peatlands, chironomids have been virtually ignored (Rosenberg et al., 1988). There is a lack of studies at the species level, and often all chironomids are lumped together (Wrubleski, 1987). Knowledge of wetland chironomid communities will increase in importance as restoration ecologists attempt to use them as evaluative criteria. Zedler (1993) has suggested that evaluation of wetland restoration should be based on more than veg etation. Streever et al. (1996) used thirty-four chironomid taxa in their comparison of natural and created wetlands and argued that dipteran larvae are good evaluative criteria because they quickly and efficiently invade new areas. A broader database of the natural wetland fauna would be useful for such evaluations. Distinct chironomid communities have been associated with particular vegetation by Griffiths (1973) and Macan (1965) in moorland ponds, Rosine (1955) on sub merged aquatic plant surfaces, and Streever et al. (1995) in freshwater herbaceous wetlands in central Florida. This study attempts to describe the habitat-specific spa tial patterns of midge and plant communities in a small Minnesota peatland, and to compare that description with previous multivariate analyses of the vegetation. E-mail: rlammer@luc.edu Accepted for publication 2 December 1997. This content downloaded from 207.46. 13.184 on Sun, 10 Apr 2016 04:17:40 UTC All use subject to http://about.jstor. org/terms VOLUME 71, ISSUE 4 415
AFFINITAS PENEMPELAN LARVA KARANG (SCLERACTINIA) PADA SUBSTRAT KERAS

Penelitian ini dilaksanakan di ekosistem terumbu karang Kepulauan Seribu DKI Jakarta dengan tujuan untuk mengkaji kemampuan (affinitas) rekrutmen karang (Ordo Scleractinia) pada tiga jenis substrat keras berbeda, yaitu semen, genteng dan batu kapur. Substrat penempelan berukuran 20 x 20 x 3 cm3 diletakkan secara vertikal pada rak yang ditanam di dasar perairan dengan kedalaman 5 m. Substrat ditempatkan di dalam perairan selama tiga bulan, kemudian diambil dan dibawa kelaboratorium untuk diidentifikasi serta dihitung jumlah rekruit karang yang menempel. Hasil penelitian menunjukkan bahwa terdapat perbedaan affinitas rekrutmen karang pada tiga substrat yang dicobakan. Affinitas terbaik adalah substrat batu kapur yang ditandai kelimpahan rekruit paling tinggi dibandingkan substrat lain. Selama penelitian ditemukan enam spesies rekruit karang pada ketiga jenis substrat, yaitu: Pocillopora damicornis, Seriatopora hystrix dan Stylophora pistillata dari Famili Pocilloporidae; Acropora millepora dan A. tenuis dari Famili Acroporidae, dan; Porites sp. dari Famili Poritidae. Kelimphan spesies P. damicornis dominan pada ketiga jenis substrat. Kondisi terumbu karang di lokasi penelitian (Pulau Payung) tergolong baik dengan tutupan karang keras 67%, sedangkan dilokasi sekitarnya yaitu Pulau Pari tergolong sedang (36%) dan Pulau Lancang tergolong buruk (15%). Kata kunci: rekrutmen, karang, substrat penempelan.