Miracle-dz/UniFAR-FTUs huggingface dataset:
A revision of the Genus Scincella (Reptilia: Sauria: Scincidae) of asia, with some notes on its evolution

Of the genus Scincella Mittleman, 1950 (sensu Greer, 1974) 337 specimens from Asia were examined for 74 characters, which were treated in a numerical-taxonomic way. The dendrogram resulting from this analysis was not stringently adhered to. Because of the wide variation in certain numerical scale characters within one taxon or even within one population, these characters (used by many authors as key characters to separate taxa) are not regarded as very important. For sympatric and parapatric species other characters, including relative size of head, body and limbs, are regarded as very important, because these characters are influenced by the way of life (niche separation). For the separation of allopatric species scale-numbers, but many other characters as well, were used. Twelve species, S. ladacensis (Gunther, 1864), S. sikimmensis (Blyth, 1853), S. capitanea spec. nov., S. victoriana (Shreve, 1940), S. travancorica (Beddome, 1870), S. bilineata (Gray, 1846), S. doriae (Boulenger, 1887), S. reevesii (Gray, 1838), S. melanosticta (Boulenger, 1887), S. punctatolineata (Boulenger, 1893), S. barbouri (Stejneger, 1925) and S. modesta (Gunther, 1864), and two subspecies, S. ladacensis himalayana (Gunther, 1864) and S. melanosticta kohtaoensis (Cochran, 1927), are recognized and described. S. capitanea is a newly described species characterized by its large body size and relatively small head. The speciation in the genus is thought to have occurred in wet forest refugia, the size and distribution of which were determined by wet and dry geological periods.
The effect of application of new spawning agents in artificial reproduction of wild common tench, Tinca Tinca (L.)

The aim of this study was compare the results obtained after testing new spawning agents (Ovaprim and PG-600) in artificial reproduction of common tench in comparison to Ovopel, the spawning agent, which worked very well in this species. The tench spawners were collected from open waters. After catching, the selected fish were transported to the hatchery, where the fish were treated with the spawning agents: Ovopel at 1 pellet kg Ovaprim at 0.5 ml kg or PG-600 at 600 IU kg. The fish from the control group received saline (0.9% NaCl). The best parameters recorded during the artificial reproduction, such as the percentage of ovulated females and embryo survival at the eyed-egg-stage were obtained in the group treated with GnRH analogues. In general, the obtained results indicate that all of the tested spawning agents might be used on successful tench artificial reproduction. However, after application of Ovopel better results were recorded. WPŁYW ZASTOSOWANIA NOWYCH ŚRODKÓW HORMONALNYCH NA EFEKTYWNOŚĆ SZTUCZNEGO ROZRODU LINA TINCA TINCA (L.)
22R‐Hydroxycholesterol protects neuronal cells from β‐amyloid‐induced cytotoxicity by binding to β‐amyloid peptide

22R‐hydroxycholesterol, a steroid intermediate in the pathway of pregnenolone formation from cholesterol, was found at lower levels in Alzheimer's disease (AD) hippocampus and frontal cortex tissue specimens compared to age‐matched controls. β‐Amyloid (Aβ) peptide has been shown to be neurotoxic and its presence in brain has been linked to AD pathology. 22R‐hydroxycholesterol was found to protect, in a dose‐dependent manner, against Aβ‐induced rat sympathetic nerve pheochromocytoma (PC12) and differentiated human Ntera2/D1 teratocarcinoma (NT2N) neuron cell death. Other steroids tested were either inactive or acted on rodent neurons only. The effect of 22R‐hydroxycholesterol was found to be stereospecific because its enantiomer 22S‐hydroxycholesterol failed to protect the neurons from Aβ‐induced cell death. Moreover, the effect of 22R‐hydroxycholesterol was specific for Aβ‐induced cell death because it did not protect against glutamate‐induced neurotoxicity. The neuroprotective effect of 22R‐hydroxycholesterol was seen when using Aβ1−42 but not the Aβ25−35 peptide. To investigate the mechanism of action of 22R‐hydroxycholesterol we examined the direct binding of this steroid to Aβ using a novel cholesterol‐protein binding blot assay. Using this method the direct specific binding, under native conditions, of 22R‐hydroxycholesterol to Aβ1−42 and Aβ17−40, but not Aβ25−35, was observed. These data suggest that 22R‐hydroxycholesterol binds to Aβ and the formed 22R‐hydroxycholesterol/Aβ complex is not toxic to rodent and human neurons. We propose that 22R‐hydroxycholesterol offers a new means of neuroprotection against Aβ toxicity by inactivating the peptide.
Microflora of Bulgarian oil contaminated environments

Long term heavy oil polluted soil microrflora from northern Bulgaria was investigated. Microbial community was stable with more than 10 6 CFU/gram dry soils. 80% of heterotrophic microorganisms are able to degrade or co-oxidate crude oil hydrocarbons as a sole carbon source. Each of physiological groups of isolated microorganisms contained over 50% strains (oil-oxidizing and fermenting bacteria, fungi, and streptomycetes) capable to grow on heavy or light crude oil as sole carbon source. Microflora was more abundant in soils with low concentrations of crude oil. Quantity of heterotrophic bacteria was comparable to oligotrophs. The least spore-forming bacteria were found in soil probes containing over 20 g/kg petroleum hydrocarbons. Bacillus, Pseudomonas and Sporosarcina genera representatives were predominated among the obtained bacterial isolates. The presence of family Enterobacteriaceae members was notable, and all investigated bacteria posess lipase. Pure cultures from genera Pseudomonas and Bacillus were chosen for further analyses as the most promising in bioremediation. Classical and molecular approaches were applied to determine the taxonomic status of investigated microbial isolates. PCR and sequence analyses of 16S ribosomal DNA were performed with genus-specific primers. As a result the strains B2-1, B2-2 and 468-1 were determined as members of Pseudomonas libanensis , Klebsiella
General Transcription Factors Play Dual Roles In Initiation And Termination

GENERAL TRANSCRIPTION FACTORS PLAY DUAL ROLES IN INITIATION AND TERMINATION by SCOTT MEDLER August 2014 Advisor: Dr. Athar Ansari Major: Biological Science Degree: Doctor of Philosophy Gene looping, defined as the interaction of the promoter and the terminator regions of a gene during transcription, is emerging as an important gene regulatory mechanism in eukaryotes. The role of promoter bound general transcription factors during initiation is well established. However, recent studies have revealed that some initiation factors also interact with the 3’ end of a gene. The biological role of initiation factors at the 3’ end of a gene is unknown. The general transcription factors TFIIB and TFIIH have been found to interact genetically with Ssu72, a component of CPF 3’ end processing complex. Accordingly, we found that TFIIB and TFIIH localize to the distal ends of genes in a transcription dependent manner. TFIIB localization at the terminator region during transcription requires a functional CF1 complex. TFIIB physically interacts with the all subunits of the CF1 complex in an activator dependent manner. TFIIH also interacts with the CF1 and CPF 3’ end processing complexes in a manner depending on its kinase activity. Employing affinity chromatography and glycerol gradient centrifugation, we show that TFIIB associates with poly(A) polymerase and the CF1 complex in yeast cells to form a holo-TFIIB complex. This complex was resistant to
Disease Gene Prioritization

The identification of genes is an ongoing research issue in the biomedical and bioinformatics community. The Human Genome Project which was completed in 2003, identified approximately 20,000+ genes in the human DNA, but there are still many of these genes for which their function or role is unknown, and this accounts only for healthy DNA. Genetic diseases like Cancer, Alzheimer, Hemophilia and others, have mechanisms that we currently just started to understand. For instance, genes BRCA1 and BRCA2, famous for their role in breast cancer (Friedman et al., 1994), only account for 5% of the incidence of the aforementioned cancer (Oldenburg et al., 2007). Many questions rise: What are the rest of the mechanisms involved in this cancer type? Are there other genes involved? How? This only accounts for one type of cancer, and there are at least 177 different types according to the National Cancer Institute 1. The straightforward method to deal with this problem is to do wet lab experiments with large samples of normal and disease tissue, to test under different conditions the reactions, and check the expression or lack of it in different genes. The complication with this method is the cost, it takes time, it requires specialized equipment, and thus the economic price tag is high. Fortunately the bioinformatics area has acquired maturity during the recent years, biological data is becoming available in different formats throughout different databases and publications are providing new insights. Thanks to these, computational methods can be developed, methods that would save time, effort and money, methods that could help biomedical researchers get clues on which genes to explore on the wet laboratory, so that time is not wasted on genes that are unlikely to contribute in a given disease. Gene Prioritization methods can be used to find genes that were previously unknown to be related to a given disease. The general definition of gene prioritization is: Given a disease D, a candidate gene set C, and the training data T, then input all these data to the method and it will compute a score for each of the candidate genes, higher scoring genes are supposed to be the genes that are most likely related to disease D, see fig. 1. Methods can be classified according to the type of input data that the method uses, as Text and Data MiningMethods and Network Based Methods. Text and Data Mining methods use training data like genetic localisation, gene expression, phenotypic data (van Driel et al., 2003), PubMeb abstracts (Tiffin et al., 2005), spatial gene expression profiles, linkage analysis (Piro et al., 2010), gene ontology and others (Adie et al., 2005; Ashburner et al., 2000; Schlicker et al., 2010); as the name suggests this
A Comparative study for the analysis of outcome in cases of inferior turbinate hypertrophy by various methods of Turbinoplasty

Turbinoplasty is surgery aimed at treating nasal turbinate enlargement. Nasal turbinate hypertrophy (enlargement) is usually caused by nasal allergies and is a major cause of nasal congestion. Usually, this can be treated medically. However, when medical management fails, the turbinates can be surgically reduced in size and repositioned to allow for a larger nasal airway. The term turbinoplasty is used because we try to remove as little tissue as possible in reshaping and repositioning the turbinate. In our study, by using three different methods of turbinate reduction procedures namely Conventional sub mucosal resection of turbinate. Microdebrider assisted submucosal resection, Cryosurgery, 60 patients were operated, and reviewed during first, third, sixth month of post operative period. The outcomes and complication during the post operative period were studied and analyzed. Patients were analyzed by using Diagnostic Nasal Endoscopy and NOSE SCORE methods. In our study Microdebrider assisted sub mucosal resection method of turbinate reduction found to have 100% improvement in relieving the nasal obstruction on six months follow up, when compared with conventional sub mucosal resection and cryosurgery.
An Epidemic of Gnomonia pascoe on Nuts of Castanea sativa in the Cuneo Area

Since 2005, chestnut growers have observed increasing losses in yield in some sweet chestnut orchards lying to the South of Cuneo. In 2007-2008 a health survey was carried out on branches, flowers and developing nuts. A fungus was constantly isolated from the bark, but not from the xylem, of 1 to 3-year old branches, fruit stem, burrs, and with a variable frequency from the stigmas and styles. The fungus could not be isolated from the inner layer of the hylum. It was isolated sporadically from the nuts just after the fruit setting and with frequency increasing 25-80% in 2007 and 4-84% in 2008, in completely ripened nuts. In the diseased nuts, small chalky areas originate at the ripening time from the endosperm outer layers, and develop towards the centre of the kernel; progressively their color turns brown and the endosperm mummifies; the pathogen colonizes the pellicle and the shell on which it produces 122x85 - 251 x 171 μm, globose, black, pycnidium-like acervuli, that split open along the top and release a slimy, globular mass of conidia. Conidia are pale brown, one-celled, ovoid-oblong, biguttulate, 6.1-7.32 x 2.44-2.68 μm. This fungus, being able to colonize asymptomatically the branches and the immature nuts, has an endophytic life style with a true pathological behavior only on the ripened nuts. It is likely that it is unable to colonize the endosperm through the stem. It reproduced the disease in artificially inoculated healthy nuts, and endophytically colonized artificially inoculated chestnut branches. On the basis of such characteristics, the pathogen has been identified as Discula pascoe sp. nov., the anamorphic stage of Gnomonia pascoe sp. nov., a pathogen recently reported in the rainy areas of Australia and New Zealand. The territorial distribution, the epidemiology and the systematic characterization of the pathogen through phylogenetic analyses by unilocus and multilocus markers are under investigation.
EFFECTS OF POST-HATCH HOLDING TIME AND EARLY NUTRITION STRATEGIES ON GROWTH PERFORMANCE, CARCASS AND SKELETAL CHARACTERISTICS OF YOUNG CHICKENS

OF THESIS EFFECTS OF POST-HATCH HOLDING TIME AND EARLY NUTRITION STRATEGIES ON GROWTH PERFORMANCE, CARCASS AND SKELETAL CHARACTERISTICS OF YOUNG CHICKENS The study objectives of this thesis were to evaluate the effects of delayed feeding and specific aspects of the Programmed Nutrition (PN) feeding strategy (Alltech, Inc.) on growth performance, carcass characteristics, and skeletal characteristics of commercial broiler chicks through market age, as well as investigate the effects of breed and the PN feeding strategy on early growth and development. When commercial broiler chicks were fed reduced nutrient diets, delayed feeding decreased early growth performance and carcass yield (P<0.05), whereas post-hatch PN conditioning for 72 hours improved early growth performance and alleviated the negative effects of delayed feeding on carcass yield (P<0.05). Through market age, delayed feeding improved Gain: Feed (P<0.05), while PN had the opposite effect. Interactive effects and main effects of delayed feeding and PN were observed for tissue mineral concentration (P<0.05). PN lowered bone ash % (P<0.05) and increased meat oxidation of broiler chicks during storage (P<0.05). PN also had negative effects on early growth performance and bone breaking strength (P<0.05) of various meat-type breeds, but especially for non-commercial, moderategrowing or fast-growing breeds. In conclusion, PN may be suitable for commercial broiler chicks that experience delayed feeding and are fed reduced nutrient diets.
Wind Resource Mapping in Pakistan : Twelve Month Site Resource Report

The World Bank in collaboration with the Alternative Energy Development Board (AEDB), government of Pakistan is implementing Renewable energy mapping project. In total twelve wind masts were installed at the sites identified in different areas in the province of Khyber Pakhtunkhwa, Punjab, Balochistan, and Sindh between December 2015 and November 2016. They have all completed one full year of measurements and will continue collecting data until end of May 2018. Of the twelve masts installed, eleven have a height of eighty meters. The aim of this report is to have a general idea about the wind regime of different parts of Pakistan by considering the same one-year period for each installed twelve masts.
A novel mutation in the bovine EDA gene causing anhidrotic ectodermal dysplasia

Abstract. X-linked anhidrotic ectodermal dysplasia (EDA), also called hypohidrotic ectodermal dysplasia (HED), represents a group of similar phenotypes described in humans, the tabby mouse mutant, dog, and cattle (KERE et al., 1996; SRIVASTAVA et al., 1997; CASAL et al., 2005; DROGEMULLER et al., 2001, 2002). EDA is characterised by the hypoplasia or absence of hair and eccrine glands in addition to dental abnormalities. Ectodysplasin A1 and A2, the two isoforms encoded by the EDA gene, are transmembrane protein members of the tumor necrosis factor (TNF) family and deleterious mutations in the human, murine, canine, and bovine EDA gene, respectively, result in manifestations of EDA.
The effect of additives on quality, protein degradability, intestinal digestibility and feed intake of wilted grass silages

First-cut wilted herbage (mainly Lolium perenne) was ensiled in barrels (120 l) either untreated (UT), treated with an inoculant, Pioneer 1188 (IN), or with a formic acid-based chemical additive, Foraform (FO). IN silage contained more fermentation products than FO, although applying the inoculant to wilted grass did not result in consistent changes in silage fermentation. Formic acid significantly decreased (P<0.05) the content of lactic and acetic acids and of ammonia-N, but increased the water soluble carbohydrates concentration as compared with UT and IN silages. Ruminal effective protein degradability was slightly but not significantly lower for FO silage (71.6%) than for UT (74.3%) and IN (74.0%) silages. Formic acid treatment significantly increased (P<0.05) intestinal digestibility of rumen-undegraded protein. Dry matter intake measured with sheep was not affected by treatments.
Estimating marten Martes americana population size using hair capture and genetic tagging

We tested non-invasive genetic methods for estimating the abundance of marten Martes americana using baited glue-patch traps to pull hair samples from individual animals. We divided our 800–km2 study area into 3 × 3 km cells and put one hair trap in each cell. We trapped 309 sites for an average of 15 days each between 15 January and 14 March 1997. Based on tracks in snow and hair morphology, we captured hair from marten, red squirrels Tamiasciurus hudsonicus, flying squirrels Glaucomys sabrinus, short or long-tailed weasels Mustela erminea and M.frenata, and several unidentified mouse and vole species. Of 309 sites, 58% collected a marten hair sample while 8% of sites removed weasel hair. When roots were embedded in adhesive, a xylene wash was used to remove them before extracting DNA. All marten samples were genotyped at six microsatellite loci to identify individuals. Xylene-washed samples yielded similar genotyping success to samples that had never been exposed to xylene, and genotyping success increased with the number of hairs in the sample. Genetic data allowed 139 samples to be assigned to 88 individual marten, constituting 124 capture events during the four trapping sessions. The population estimate for our study area was 213 (95% Cl: 148–348) and the average capture probability was 0.15. The density of marten in our study area was 0.33/km2 when inhospitable habitat was removed from the calculation. We believe hair sampling and genetic analysis could be used to measure population distribution, trend and size for marten, and perhaps also for other carnivores.
Growth and maintenance of the mouse adrenal cortex

The adrenal cortex is classically divided into three morphologically and biochemically distinct zones, covered by a thin, cellular capsule. The adult adrenal cortex is a dynamic tissue in which distinct regions of cell proliferation, movement and death have been identified. Several models for stem cell maintenance of the adult adrenal cortex have been proposed, but adrenocortical stem cells have not yet been identified. Adrenal cortices of 21OH/LacZ transgenic mice show similar mosaic patterns of β-galactosidase staining to Xinactivation mosaics and LacZ ↔ wildtype chimeras. 21OH/LacZ mice provide a tool for lineage analysis, which may help to i) identify clones of cells produced by stem cells in the adult, ii) determine when stem cells begin to function and iii) evaluate different models of how stem cells maintain the adrenal cortex. Analysis of 21OH/LacZ transgenic adrenal cortices showed that the randomly orientated clusters of fetal patches change progressively during the perinatal period to adult radial stripes. Correlation of changes in mosaic patterns and the locations of cell proliferation suggests that the stripes arise by edge-biased growth during the perinatal growth period. Although stem cells may not be involved in the initial formation of stripes, it seems likely that stem cells later maintain the stripes by producing clones of cells that move centripetally to displace the earlier fetal patterns and later replace aging cells. Various combinations of BrdU labelling and chase periods demonstrated that most cell division occurred in the outer 40% of the adrenal cortex, confirmed that cells moved towards the medulla and identified a population of label-retaining cells near the capsule, which could include stem cells. (Stem cells have been recognised as BrdU label-retaining cells in other tissues because they divide less frequently than their daughter cells so dilute the incorporated BrdU more slowly.) Stripe patterns in adult 21OH/LacZ transgenic adrenal cortices were examined to try to distinguish between various models proposed for stem cell maintenance of the adrenal cortex. The observed continuous radial stripe pattern favours the general hypothesis that a single population of stem cells in the periphery maintains the entire adrenal cortex,
Contributions to automatic multiple F0 detection in polyphonic music signals

Estimacao de multiplas frequencias fundamentais (MPE, do ingles multipitch estimation) e um problema importante na area de transcricao musical automatica (TMA) e em muitas outras tarefas relacionadas a processamento de audio. Aplicacoes de TMA sao diversas, desde classificacao de generos musicais ao aprendizado automatico de piano, as quais consistem em uma parcela significativa de tarefas de extracao de informacao musical. Metodos atuais de TMA ainda possuem um desempenho consideravelmente ruim quando comparados aos de profissionais da area, e ha um consenso que o desenvolvimento de um sistema automatizado para a transcricao completa de musica polifonica independentemente de sua complexidade ainda e um problema em aberto. O objetivo deste trabalho e propor contribuicoes para a deteccao automatica de multiplas frequencias fundamentais em sinais de musica polifonica. Um metodo de referencia para MPEe primeiramente escolhido para ser estudado e implementado, e uma modificacao e proposta para melhorar o desempenho do sistema. Por fim, tres estrategias de refinamento sao propostas para serem incorporadas ao metodo modificado, com o objetivo de aumentar a qualidade dos resultados. Testes experimentais mostram que tais refinamentos melhoram em media o desempenho do sistema, embora cada um atue de uma maneira diferente de acordo com a natureza dos sinais.