Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies on the hydroxylation of phenylalanine by 6,7-dimethyl-5,6,7,8-tetrahydropteridine

The hydroxylation of phenylalanine by 6, 7-dimethyl-5, 6, 7, 8-tetrahydropteridine (DMPH4) was investigated. When phenylalanine was treated with DMPH4 in citrate buffer (pH 6.0), p-tyrosine, m-tyrosine and o-tyrosine were identified as hydroxylated products. The hydroxylation was pH-dependent, and the maximum rate was found at around pH 6. Replacement of air with nitrogen gas and the addition of hydroxyl radical scavengers or catalase prevented the hydroxylation. In contrast, ferrous ions significantly accelerated the hydroxylation as compared with other transition metal ions. In an aqueous solution of DMPH4 under aerobic conditions, the electron spin resonance (ESR) spectra of the hydroxyl radical spin adducts with spin traps such as α-phenyl N-tert-butyl nitrone (PBN) and α-4-pyridyl 1-oxide N-tert-butyl nitrone (4-POBN) were observed. The results indicate that the hydroxylating effect of DMPH4 is caused by hydroxyl radicals formed during the autooxidation of DMPH4.
A comparison of the otolith and scale methods of ageing, and the growth of Sarotherodon mossambicus (pisces:Gchlidae) in a Venda impoundment (Southern Africa)

Otoliths and scales were used for age and growth determinations of Sarotherodon mossambicus in the LuphepheNwanedzi impoundment, a subtropical man-made reservoir in Venda, northern South Africa. Two rings are deposited annuallyon the otolith whereas only one ring Is deposited on the scales. Using otoliths the growth of S. mossambicus is described by L t = 27,3 (1 - e -0.425(1+0.299 ) cm and using scales by L t = 26,8 (1 _e -0.389(1+0.045) ) cm. These two curves differ Significantly (P<0.01)_ The adequacy of these curves was tested by means of Ford-Walford plots. It is postulated that otoliths provide a more reliable estimate of age and growth than scales in subtropical and temperate regions. Males grow faster than females. Based on otoliths the growth of male S. mossambicus in the Luphephe-Nwanedzi impoundment is described by L, = 27,0(1- e -0.417(1+0.504) ) cm SL and that of females by L, = 25,8(1-e -0.370(1+0.497) ) cm SL. The growth of S. mossambicus in the Luphephe-Nwanedzi impoundment is compared to other S. mossambicus populations in South Africa.
Intraparenchymal Isolated Bile Ductules in the Needle Biopsy Specimens of the Liver: An Interobserver Variation and Clinicopathological Study

Intraparenchymal isolated bile ductules (IIBDs) are occasionally recognizable in liver specimens, but their characteristics remain poorly understood. Therefore, we (2 pathologists) attempted to identify IIBDs in 81 hematoxylin and eosin-stained needle biopsy specimens of the liver, and examined the interobserver variation and their clinicopathologic features. Aberrant cytokeratin 7 (CK7) expressions of hepatocytes, known to represent hepatic progenitor cell (HPC) activation, were also evaluated. In each specimen, the mean number of IIBDs counted by us was divided by the number of portal areas, which was defined as the IIBD score. Both pathologists detected IIBDs in 53 specimens (65.4%), indicating that they are not rare. Observed agreement was obtained in 81.5%, and the kappa statistic indicated moderate agreement (kappa: 0.515). Higher IIBD score was closely associated with a higher degree of hepatocytic CK7 expression in all areas (P=0.012), periportal areas (P=0.007), and pericentrilobular vein (CV) areas (P=0.032), but not with age, gender, increased serum levels of liver dysfunction tests, or hepatic steatosis. Ductular reaction was also associated with hepatocytic CK7 expression in all areas (P=0.004), periportal areas (P=0.024), and peri-CV areas (P=0.031). However, there was not a relevant relationship between higher IIBD score and a severe degree of ductular reaction. In non-alcoholic steatohepatitis (NASH) cases, significant IIBD score was correlated with grading score (P=0.043), but not with fibrosis staging score. In viral hepatitis cases, it was not associated with grading or staging score. These results suggested that the development of IIBD can highlight HPC activation, but might be independent of periportal HPCs, also known as “periportal niches”. The presence of IIBDs would be due in part to a hepatic necro-inflammatory state in some conditions, such as NASH.
Freshwater Fish Diversity at Greater Noakhali, Bangladesh

ABStRAct This study assessed the spatial-temporal diversity of fish at greater Noakhali, an aquatic ecosystem that supports the most diverse fish communities in Bangladesh. Fish samples were collected from eight locations from July 2010 to June 2011 and diversity analyzed using PAST software. Findings showed that greater Noakhali is the habitat for 128 fish species. For the whole sampling area, the Shannon diversity index, evenness, Margalef richness and dominance index values were 4.501, 0.889, 15.763 and 0.012, respectively. Oreochromis mossambicus, Mastacembelus armatus and Tenualosa toli were the major contributory species in temporal terms and Tenualosa ilisha, Somileptes gongota and Mystus vittatus in spatial terms.
Predicting Amyloid Burden to Accelerate Recruitment of Secondary Prevention Clinical Trials

Screening to identify individuals with elevated brain amyloid (Aβ+) for clinical trials in Preclinical Alzheimer’s Disease (PAD), such as the Anti-Amyloid Treatment in Asymptomatic Alzheimer’s disease (A4) trial, is slow and costly. The Trial-Ready Cohort in Preclinical/Prodromal Alzheimer’s Disease (TRC-PAD) aims to accelerate and reduce costs of AD trial recruitment by maintaining a web-based registry of potential trial participants, and using predictive algorithms to assess their likelihood of suitability for PAD trials. Here we describe how algorithms used to predict amyloid burden within TRC-PAD project were derived using screening data from the A4 trial. We apply machine learning techniques to predict amyloid positivity. Demographic variables, APOE genotype, and measures of cognition and function are considered as predictors. Model data were derived from the A4 trial. TRC-PAD data are collected from web-based and in-person assessments and are used to predict the risk of elevated amyloid and assess eligibility for AD trials. Pre-randomization, cross-sectional data from the ongoing A4 trial are used to develop statistical models. Models use a range of cognitive tests and subjective memory assessments, along with demographic variables. Amyloid positivity in A4 was confirmed using positron emission tomography (PET). The A4 trial screened N=4,486 participants, of which N=1323 (29%) were classified as Aβ+ (SUVR ≥ 1.15). The Area under the Receiver Operating Characteristic curves for these models ranged from 0.60 (95% CI 0.56 to 0.64) for a web-based battery without APOE to 0.74 (95% CI 0.70 to 0.78) for an in-person battery. The number needed to screen to identify an Aβ+ individual is reduced from 3.39 in A4 to 2.62 in the remote setting without APOE, and 1.61 in the remote setting with APOE. Predictive algorithms in a web-based registry can improve the efficiency of screening in future secondary prevention trials. APOE status contributes most to predictive accuracy with cross-sectional data. Blood-based assays of amyloid will likely improve the prediction of amyloid PET positivity.
Genetic Mapping and Properties of Filamentous Mutations in Bacillus, subtilis

Seven filamentous (fil) mutants were isolated from B. subtilis, and the mutations were mapped by means of lysed-protoplast transformation. Five of the mutations were linked to aroD and the others to pyrD. rgn mutations, which lead to a decrease in autolysin(s) and the formation of filaments, were also linked to aroD, and the mapping order was rgn-dnaE-aroD. On comparison with other reported filamentous mutations (lyt-1, lyt-2 and lyt-152), fil-1, fil-3 to -6, rgn and the above lyt mutations were determined to be in the same locus. All of the seven fil strains lacked flagella and showed decreased aμtolysin activity. Among them, only mutants having arod- linked mutations showed low competency. Protease assay results indicated that rgn mutants produce a several times higher amount of the enzyme than the parent strain, and the initiation time for the production in rgn mutants was two hours earlier than in the parent strain.
The Influence of Training on Business Success in Nigeria: Case of Registered Small and Medium Scale Enterprises (SMEs) in Kano State, Nigeria

Training plays a significant role in contributing to SMEs success that resulted in economic growth and sustainable development in Nigeria. The main objective of this study was to examine the influence of training on business success in Nigeria. The sample size of 310 SMEs was drawn through Krejcie and Morgan 1970 table of sample size determination out of the population of 1530 registered SMEs in Kano State, Nigeria. Questionnaire was used as the method of data collection and Structural Equation Modeling (SEM) through AMOS software was employed to test the hypothesis under study. The result of the study shows that training has a significant influence on business success in Nigeria. This study suggest that business entrepreneurs should engage them self and that of their employees in training and also to develop what is called research and development (R&D) department in their enterprises so that it can oversee the training of management and workforce, with that it will lead or add value to their business success.
Energetics, Salinity and Temperature Tolerance in the Mohave Tui Chub, Gila bicolor mohavensis

Metabolic performance at various temperatures and maximal swimming speeds, critical thermal maxima and minima, as well as salinity tolerance were examined in the Mohave tui chub, Gila bicolor mohavensis. Maximal metabolic rates, ca. 0.1 cc O2/g h were attained at 24 and 30 C at swimming speeds of 87 cm/sec. At 18 C fish could attain swimming speeds of only 45 cm/sec and consumed 0.1 cc 02/g h. Factorial metabolic scope dropped from 3.3 at 18 C to 1.57 at 30 C. The mean critical thermal maxima at three acclimation temperatures (18, 24, 30 C) were 33.5, 34.9 and 36.2 C, respectively. Mean critical thermal minima were 2.8, 4.8 and 7.2 C, respectively, for fish acclimated at 18, 24 and 30 C. Mohave chubs osmoregulate well up to salinities of 237 mOsm/1. Higher salinities induce weight loss and antidiuresis. Based on these experimental results it appears that the Mohave chub is not as adaptable to desert conditions as other desert fish, such as the pupfish (Cyprinodon). Therefore, careful consideration must be given to micro-environments when new refugia are sought for this endangered species.
HERMAN DELEECK CENTRE FOR SOCIAL POLICY

This paper assesses the welfare impacts of the 2014 Ebola Virus Disease (EVD) outbreak in Liberia, focusing on changes in age and sex specific mortality rates. The first part of the paper derives a survival function for a counterfactual no-EVD scenario, using mortality data from the Institute for Health Metrics and Evaluation (IHME). This counterfactual survival function is then compared with the actual survival function in 2014 to estimate the change in survival conditions due to EVD. Next, the impact of this change on individual and total welfare is assessed using a marginal willingness to pay approach applied to data from the Liberian Household Income and Expenditure Survey (HIES). The results suggest that the total welfare costs of EVD-related mortality range between $2.5 to $4 billion, depending on the estimate of the survival probabilities adopted. Finally, the robustness of these results is tested using different preference parameter calibrations. The Impact of the Ebola Crisis on Mortality and Welfare in Liberia
Genomic Molecular Markers for the DNA Fingerprinting of Sperm Derived from Epinephelus lanceolatus and E. fuscoguttatus

Groupers belong to the subfamily Epinephelinae of the family Serranidae. They are an economically important marine fisheries resource and are commercially cultivated throughout the tropical and temperate regions of the world. The aquaculture industry relies on artificial breeding of groupers in order to obtain fingerlings which are free of pathogens and demonstrate a uniform growth rate. Rapid validation of sperm and eggs is a major challenge to breeders. Single locus DNA markers are ideal for the authentication of germplasm as they generate single PCR amplicons which do not require further sequencing. This study focused on the development of single locus DNA markers for genotyping of sperm samples derived from two species of grouper, the Giant grouper (Epinephelus lanceolatus) and the Tiger grouper (E. fuscoguttatus). Single locus molecular markers were developed using DNA sequences obtained from shotgun genomic libraries and tested against sperm samples derived from each of the species and the closely related groupers E. coioides and E. corallicola. A total of 54 molecular markers were developed of Research Article Annual Research & Review in Biology, 4(1): 93-104, 2014 94 which six were found to be specific to E. fuscoguttatus and seven to E. lanceolatus. The remaining markers generated PCR products in all of the four species and were rejected as suitable candidates for genotyping. The markers developed as a result of this study are relevant to fish breeders and fish farmers as they species specific, inexpensive and augment traditional methods of identification based on phenotypic characterization.
Tuning retractable, microscale, membrane-breaking protein needles

The refractile (R) bodies found in Caedibacter taeniospiralis, a bacterial endosymbiont of Paramecium tetraurelia, are large, polymeric protein structures that can switch between two conformations. At cytoplasmic pH, they resemble coiled ribbons of protein 500nm in diameter. At low pH, they extend to form hollow needles up to 20 microns long. They can be expressed heterologously from an operon containing four short open reading frames and can function in vitro in diverse buffer conditions. In this study, R bodies purified from Escherichia coli were found to be capable of undergoing many consecutive extension-contraction cycles. Furthermore, the solubility of R bodies, which can easily be interpreted by eye, was found to correlate with their extension state. This macroscopic phenotype was used to develop a quantitative, high-throughput assay for R body state, enabling a visual screen of R body mutants defective in extension. The role of specific amino acids in extension was determined, and this information was used to construct rationally-designed mutants tailored to extend at higher pH. Furthermore, R bodies were able to rupture E. coli spheroplasts to release soluble proteins across lipid bilayers. Taken together, these results show that R bodies act as tunable, pH-actuated pistons suitable for a variety of membrane-breaking applications.
Genetic variability and association of characters in Ethiopian hot pepper (Capsicum annum L.) landraces.

Forty nine hot pepper accessions collected from different agroecologies were compared in a 7x7 simple lattice design to estimate genetic variability and understand the association of characters. Plant characters and yield components were evaluated and analyzed accordingly. The values of genotypic correlation coefficients were higher in magnitude than phenotypic values in most instances in which fruit yield per plant showed high positive significant genotypic correlation value with pericarp thickness (r = 0.91) and number of fruits per plant (r = 0.61). On the other hand, significant negative associations were registered with days to flowering (r = -0.73) and 50% fruiting period (r = -0.75). The phenotypic correlation coefficient of most characters with yield was not significant except for flowering period, fruit length and number of fruits per plant. The path coefficient analysis indicated that pericarp thickness (mm) (5.5), fruit diameter (mm) (1.4), number of fruits per plant (0.8), number of branches (0.33) and flowering period (0.2) had the highest direct positive effect. However, fruit weight (-2.8), number of internodes (-1.66), leaf area index (-1.6) and plant height (-0.4) had a high negative direct effect on yield. The genetic component analysis indicated that phenotypic coefficient of variation (PCV) was higher in magnitude than genotypic coefficient of variation (GCV) for most characters except pericarp thickness and leaf area index. Higher magnitude of GCV was observed in leaf area index (67%) followed by pericarp thickness (34%), number of branches, internode length (23%) and plant height. Close estimates of GCV and PCV were recorded from fruit and internode length, pericarp thickness and fruiting period. Very high PCV and very low GCV estimates were obtained from fruit weight and number of fruits, fruit yield, plant height and canopy width. Broad sense heritability was high for fruiting date, fruit length, plant height, internode length and fruit diameter. However, genetic advance as percent of the mean (GAM) was high to moderate for length and number of internodes, number of branches, fruit diameter and weight, pericarp thickness and leaf area index. Therefore, from this study, fruit diameter, pericarp thickness, leaf area index and internode length exhibited high to moderate genotypic and phenotypic coefficients of variation along with medium to high heritability and genetic advance and can be used as a selection criterion for pepper improvement program.
Dendroecological and Ecophysiological Analysis of Gap Environments in Mixed-Oak Understoreys of Northern Virginia

Ecophysiological, morphological and dendroecological attributes were examined in species growing in understorey and newly formed gap environments in mixed-Quercus forests of northern Virginia. Gap environments were characterized by higher photosynthetic photon flux density (PPFD) but were not different from non-gap control plots in their soil moisture, predawn leaf water potential (Ψ), leaf temperature or leaf to air vapour pressure deficit (VPD). In addition, few significant differences existed between regeneration responses at gap and control sites. Plants in gaps experienced higher rates of net photosynthesis (A) and leaf conductance to water vapour diffusion (g wv ) than control plants, although parameters did not differ between early vs late successional species. Gap plants also produced leaves with smaller leaf area and greater leaf thickness, leaf mass per area (LMA) and stomatal density than control plants. All gap species experienced accelerated height growth compared to non-gap plants, with early successional Sassafras albidum (Sassafras) and Liquidambar styraciflua (Sweetgum) exhibiting the highest rates. In contrast, average radial growth in small, understorey trees was not significantly different between habitat type, although Quercus alba (White Oak) did respond significantly to the most recent gaps. Many small trees (6-12 cm d.b.h.) were surprisingly old - up to 100 years in age. Despite severe suppression periods in these trees, they experienced release events during their lifetime, although not necessarily to the most recent gaps. This may partially explain the lack of correlation between ecophysiological and growth parameters.
Improvement of Biological Assay to Determine Available Phosphorus with Growing Chicks

Experimental condition for biological assay of phosphorus availability by chicks was studied. Breed difference was observed in incidence of ricket of one-day-old chicks fed low phoshorus diet containing 0.3% of phosphorus from soybean meal. Ricket could be prevented by using 7-day-old White Leghorn male chicks reared on the restricted feeding program. Ten days of experimental period was satisfactory to get similar conclusion to those obtained by bioassay of 3 or 4 weeks of period. Toe ash content was superior to tibia ash content. Linear relationship between dietary added phosphorus and toe ash content was observed within the range of added phosphorus from 0 to 0.3%. A simplified bioassay procedure of ten days of feeding period is recommended, which is a slope ratio assay of linear regression lines between added phosphorus and toe ash content.Availability and its 95% fiducial interval of phosphorus in feed grade dibasic calcium phosphate were 99% and 115-84%, respectively. Those of phosphorus in fish meal were 109% and 127-90%, respectively. Those of phosphorus in yellow corn were 0% and 33--31%, respectively.
Downward-facing structures in the Khomas Trough of the Damara Orogen, Namibia

The Khomas Trough (Fig. 1) of the Damara Orogen is characterized by meta-sedimentary sequences, several kilometres thick, which have undergone polyphase deformation (Blaine, 1977; Hälbich, 1977; Miller, 1979; Sawyer, 1981) and upper greenschist to amphibolite facies regional metamorphism (Hoffer, 1977). The succession exhibits extreme lateral persistence of structural and lithological markers over strike lengths of several hundred kilometres (Kukla et al., 1988b). These include major sedimentary cycles, graphitic and scapolitic schists and the Matchless Member amphibolites. While studying the late Proterozoic Kuiseb Formation schists in the Khomas Trough, downward-facing structures were detected for the first time in this part of the orogen (Kukla et al., 1988b). It is the aim of this paper to document these structures in more detail and to discuss their formation and implications for the regional tectonics.
A multi-task convolutional deep learning method for HLA allelic imputation and its application to trans-ethnic MHC fine-mapping of type 1 diabetes

Conventional HLA imputation methods drop their performance for infrequent alleles, which reduces reliability of trans-ethnic MHC fine-mapping due to inter-ethnic heterogeneity in allele frequency spectra. We developed DEEP*HLA, a deep learning method for imputing HLA genotypes. Through validation using the Japanese and European HLA reference panels (n = 1,118 and 5,112), DEEP*HLA achieved the highest accuracies in both datasets (0.987 and 0.976) especially for low-frequency and rare alleles. DEEP*HLA was less dependent of distance-dependent linkage disequilibrium decay of the target alleles and might capture the complicated region-wide information. We applied DEEP*HLA to type 1 diabetes GWAS data of BioBank Japan (n = 62,387) and UK Biobank (n = 356,855), and successfully disentangled independently associated class I and II HLA variants with shared risk between diverse populations (the top signal at HLA-DR{beta}1 amino acid position 71; P = 6.2 x 10-119). Our study illustrates a value of deep learning in genotype imputation and trans-ethnic MHC fine-mapping.
Co-Training for On-Board Deep Object Detection

Providing ground truth supervision to train visual models has been a bottleneck over the years, exacerbated by domain shifts which degenerate the performance of such models. This was the case when visual tasks relied on handcrafted features and shallow machine learning and, despite its unprecedented performance gains, the problem remains open within the deep learning paradigm due to its data-hungry nature. Best performing deep vision-based object detectors are trained in a supervised manner by relying on human-labeled bounding boxes which localize class instances (i.e. objects) within the training images. Thus, object detection is one of such tasks for which human labeling is a major bottleneck. In this article, we assess co-training as a semi-supervised learning method for self-labeling objects in unlabeled images, so reducing the human-labeling effort for developing deep object detectors. Our study pays special attention to a scenario involving domain shift; in particular, when we have automatically generated virtual-world images with object bounding boxes and we have real-world images which are unlabeled. Moreover, we are particularly interested in using co-training for deep object detection in the context of driver assistance systems and/or self-driving vehicles. Thus, using well-established datasets and protocols for object detection in these application contexts, we will show how co-training is a paradigm worth to pursue for alleviating object labeling, working both alone and together with task-agnostic domain adaptation.