Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of the Glycolysis and Lipogenesis in Culture of Hepatocytes

[Abstract] Metabolic flux analyses are needed to provide insights into metabolic regulation that occurs in cells. The current protocol describes fast and reproducible methods for determining glycolysis and de novo lipogenesis of hepatocytes. Primary culture of hepatocytes is an ‘in vitro’ model useful to study liver glucose and lipid metabolism (Denechaud et al., 2016). The protocol is divided in 2 parts. Part I: Glycolysis experiment is assessed using the Seahorse extracellular flux (XF) analyser. Glycolysis is determined via the measurement of the extracellular acidification rate (ECAR) of the media, which come predominately from the cellular excretion of lactic acid after the conversion of glucose in pyruvate. Part II: De novo lipogenesis experiment determines the radioactive C14 incorporation in triglycerides (TG) from acetate C14 precursor. After 2 h acetate supplementation to the media lipids are extracted and separated by TLC (Thin Layer Chromatography) prior quantification of newly synthetized TG labelled.
Biomineralization Abilities of Cupriavidus Strain and Bacillus subtilis Strains In Vitro Isolated from Speleothems, Rani Cave, Chhattisgarh, India

ABSTRACT In vitro culture experiments using three bacterial strains CSJC1, CSJC2, and CSJC3 isolated from speleothems, Rani cave, Chhattisgarh, India, were studied to examine their biomineralization potential. These speleothems showed high microbial cell enumerations on nutrient agar and iron agar (9 × 104 CFU/g) followed by thiosulfate agar (7 × 104 CFU/g), and 60 diverse strains were isolated. The BLASTn sequence search of 16S rRNA sequences with the NCBI database to establish the identity of CSJC1, CSJC2, and CSJC3 strains yielded similarity scores of ≥99% with the respective organisms, and the strains were identified as CSJC1 – Bacillus sp. , CSJC2 – Cupriavidus sp. , CSJC3 – Bacillus sp. The phylogenetic analysis of CSJC2 strain suggests that it formed a separate major cluster with Cupriavidus sp. and Cupriavidus necator. The phylogenetic analysis of CSJC1 and CSJC3 strains revealed that it formed a major cluster with several strains of Bacillus sp. and Bacillus subtilis. The biominerals induced by Cupriavidus sp. CSJC2 strain imaged with an ultra high-resolution field emission scanning electron microscope (FE-SEM) were seen as calcified coccoid shells that transformed into calcified dumbbells. FE-SEM imaging of biominerals induced by B. subtilis CSJC1 and CSJC3 tested both on B4 media and sheep blood agar individually showed that the precipitates formed calcified dumbbells that were almost similar but not identical phenotypically, indicating that strain-specific morphologies and crystal formation is easier when Ca is present in the media. This is the first comprehensive report on the possible evidences about the role of Cupriavidus sp. in calcite precipitation isolated from speleothems in the Indian caves. These results allow us to postulate that the identified strains may have a role in the biogenic influences in mineral formations at Rani cave.
Genetic diversity of Dioscorea japonica germplasm in Taiwan revealed by inter-simple sequence repeat DNA markers

There are three native varieties of edible yams (Dioscorea japonica Thunb.) in Taiwan, but germplasm has been collected from only a few. To assess the genetic diversity of 99 accessions collected from four geographically diverse regions, inter-simple sequence repeat (ISSR) DNA markers were analysed, and 90.2% of the polymorphic markers in these accessions were found. Genetic similarity among accessions ranged from 30.8 to 74.4%, averaging 48.4%. Cluster analyses revealed four main clusters plus one outlier (Dioscorea alata L.). The varieties oldhamii and pseudojaponica were separated into different clusters and var. japonica was grouped with both varieties. Since var. japonica was found to be genetically similar to var. oldhamii and var. pseudojaponica, we suggest that var. japonica is a hybrid or intermediate variety between the two varieties. Molecular analysis of variance results indicated that variation within counties (95.94%) was predominantly greater than variation among counties (3.63%) and among regions (0.43%). Overall, gene flow (N m= 0.970) estimated from genetic differentiation (G st= 0.340) suggests that gene flow among regions is relatively high. The highest genetic diversity (H= 0.191) and Shannon's index (I= 0.312), and a high gene flow (N m= 3.926) of germplasm in the northern region suggest that this region is a possible centre of dispersal and domestication of yams in Taiwan. This study provided valuable information for germplasm collection and genetic improvement.
Autolytinae and Exogoninae (Polychaeta: Syllidae) from northern Cyprus (Eastern Mediterranean Sea) with a checklist of species reported from the Levant Sea

Faunistic analysis of a total of 77 benthic samples collected in different biotopes and depths from northern Cyprus in 1997 and 1998 yielded 36 species and one subspecies of syllid polychaetes belonging to Autolytinae and Exogoninae, of which three species (Exogone (Parexogone) wolfi San Martin, 1991, Sphaerosyllis longipapillata Hartmann-Schroder, 1979 and Sphaerosyllis sp. 2) are new to the Mediterranean, seven species to the eastern Mediterranean, 23 species to the Levantine Sea and 32 species to the Cypriot coast. The morphological, biometrical and distributional features of each species as well as a checklist of species of Autolytinae and Exogoninae reported from the Levant coasts are provided.
Trypanosoma cruzi e outros tripanosomas em primatas não humanos procedentes do Parque Zoológico Municipal de Bauru, São Paulo, Brasil

22 Captive animals, despite the constant care provided by those responsible for the site, are 23 susceptible to infections from different sources. We report herein a natural infection of 11 24 (28.2% positive) of 39 non-human primates, from 13 different species, in a Brazilian 25 zoological park by trypanosomes. Indirect Fluorescent Antibody Technique (IFAT) and 26 conventional Polymerase Chain Reaction (cPCR) ruled out Trypanosoma cruzi, etiological 27 agent of Chagas disease. However, the sequencing performed with positive samples 28 employing hsp70 primers presented similarities from 86% to 88% for diverse trypanosomes, 29 including T. cruzi, Trypanosoma grayi, Trypanosoma lewisi, Trypanosoma rangeli and 30 Trypanosoma vivax. We believe that the low similarity obtained by sequencing reflects the 31 difficulties in molecular identification of trypanosomes, since they share a great portion of 32 genetic material, and points to a possible coinfection by more than one trypanosome specie. 33 Thus, our study demonstrates the presence of diverse trypanosomes in primates, which are 34 susceptible to infection by these parasites. Therefore, actions to combat vector insects must be 35 performed in these environments, besides the quarantining of animals recently introduced into 36 zoos as a preventive measure, to avoid transmitting infection to other animals, staff and the 37 visiting public. 38
AMMI & GGE biplot analysis of multi environment yield trial of soybeanin North Western Himalayan state Uttarakhand of India

The investigation was carried out to study Genotype × Environment (G×E) interaction for seed yield in 36 soybean genotypes including check PS1092 over 3 diverse environments represented by different altitudes in Uttarakhand. Grain yield performances of soybean genotypes were evaluated during Kharif 2013 season using a randomized complete block design. The AMMI analysis indicated that environment, genotypes and genotype by environment interactions had significantly affected seed yield and accounted for 9.76, 28.97 and 47.55% of the total variation, respectively. GGE biplot clearly displayed interrelationships between test locations as well as genotypes and facilitated visual comparisons based on Principal Component Analysis (PCA). The first two principal components PCI and PCII were used to create a two-dimensional GGE biplot that accounted for 45.68 and 38.88% variations respectively and based on discriminating and representative ability, E2 (Majhera) was most suitable location for selecting generally adapted genotypes. Soybean genotype C1 (PS1539) was identified as ideal genotype with high yield and low G×E interaction i.e. high stability.
Taxonomy, larval morphology and cytogenetics of Lihelophorus, the Tibetan endemic subgenus of Helophorus (Coleoptera: Hydrophiloidea)

The taxonomy, larval morphology and cytogenetics of Lihelophorus Zaitzev, 1908, a subgenus of Helophorus Fabricius, 1775 endemic to the Tibetan Plateau, are examined based on recently collected material and the inspection of type and historical specimens. Three species are recognized: Helophorus (Lihelophorus) lamicola Zaitzev, 1908 (type species), H. (L.) ser Zaitzev, 1908 and H. (L.) yangae sp. nov.; all of them are (re)described and their diagnostic characters are discussed and illustrated. First instar larvae of two species, H. lamicola and H. yangae, both obtained from egg cases laid by field-collected adults and confirmed as conspecific with them by means of cox1 DNA sequences, are described and compared in detail with the larva of H. (Helophorus) liguricus Angus, 1970. Larvae of both species differ from all other Helophorus larvae by strongly asymmetrical nasale and extremely long legs, larvae of H. lamicola are unique among Helophorus in the presence of abdominal tracheal gills. Mitotic karyotypes from mid-gut cells and meiotic karyotypes from testes are described for all three species, revealing the karyotype 2n = 20 +Xyp for all of them. All these data (larval morphology, DNA sequences and karyotypes) are in agreement with the presence of three species of Lihelophorus revealed by adult morphology, and also support the monophyly of the subgenus. Known data on biology and distribution of Lihelophorus are summarized, including the highest known altitudinal record for an aquatic beetle (5350 m a.s.l.). The unusual larval morphology of Lihelophorus is discussed in detail and hypothesized as adaptation for high altitude cold changeable environment. The systematic position of Lihelophorus and the composition of the Helophorus fauna of the Tibetan Plateau are briefly discussed.
Crop Diversification Improves pH in Acidic Soils

ABSTRACT Soil acidification has become a major challenge for sustainable crop production in the subsistence farming systems of developing countries. Diversified cropping may reduce soil acidity and improve agricultural sustainability. The main objective of this study was to evaluate the effects of crop diversification on soil acidity in the subsistence farming systems of the mountains and plains of Nepal. We monitored soil pH of 180 sites that included low-diversity farms (LDFs), high-diversity farms (HDFs), and natural forest in mountains of Nuwakot and plains of Chitwan, Nepal. Soils were more acidic in Nuwakot than in Chitwan. The soil pH in HDFs with a value of 5.19 (Chitwan) and 4.03 (Nuwakot) was significantly higher than in LDFs and forests. Soil pH was lowest (4.67) in LDFs in Chitwan and in forest (3.32) in Nuwakot. Crop diversification can potentially improve the sustainability of subsistence farming systems through improvement in pH of the acidic soils.
Substrate Specificity of Human N-Acetyltransferase 8 for Aromatic Cysteine Conjugates

SUBSTRATE SPECIFICITY OF HUMAN N-ACETYLTRANSFERASE 8 FOR AROMATIC CYSTEINE CONJUGATES Reema Deol Advisor: University of Guelph, 2015 Professor P. David Josephy The mercapturic acid pathway is a metabolic route for the detoxication of xenobiotics, processing drugs and toxicants to mercapturic acids (N-acetylcysteine conjugates). An Nacetyltransferase enzyme, NAT8, catalyzes the transfer of an acetyl group from acetyl-CoA to the cysteine amino group, producing a mercapturic acid, which is excreted in the urine. Human NAT8 was recently cloned and expressed but little is known concerning its activity and specificity with regard to substrates of toxicological importance. I expressed human NAT8 in HEK 293T cells and used colorimetric assays with DTNB and HPLC analysis (UV or MS detection) to measure the activity of NAT8 for various cysteine substrates. All of the S-arylsubstituted (benzyl, 4-nitrobenzyl, and menaphthyl) cysteine conjugates tested are substrates for NAT8-catalyzed acetylation, with the exception of S-trityl-cysteine. This information provides insight into the final step in the glutathione-dependent biotransformation of toxicologically significant xenobiotics, such as polycyclic aromatic hydrocarbons.
The type species of the genus Gnomonia, G. gnomon, and the closely related G. setacea

Sogonov, M. V. , L. A. Castlebury, A. Y. Rossman, D. F. Farr & J. F. White (2005): The type species of the genus Gnomonia, G. gnomon, and the closely related G. setacea. Sydowia 57 (1): 102-120. Species of the diaporthalean genus Gnomonia are common yet inconspicuous and poorly known microfungi occurring mostly on overwintered leaves of trees and shrubs in the temperate zone of the northern hemisphere. Confusion exists about the type species of Gnomonia because a type was not designated. Three specific names have been mentioned in the literature as the type species: G. gnomon, G. vulgaris and G. setacea. Gnomonia gnomon was designated as the lectotype species; however, some authors have considered all three taxa to be synonymous with G. setacea having priority. Gnomonia vulgaris is a nomenclatural synonym of G. gnomon. Observations of type specimens and fresh material of G. gnomon and G. setacea reveal that these two species are distinct and can be distinguished by the position of perithecia in the leaf tissue and ascospore morphology. Descriptions and illustrations of G. gnomon and G. setacea are provided. A lectotype specimen and an epitype specimen with ex-type culture for G. gnomon are designated; an epitype for G. setacea is designated. The distinction between G. gnomon and G. setacea is supported by ribosomal DNA sequence analysis.
Predicting landscape connectivity for the Asian elephant in its largest remaining subpopulation

Landscape connectivity between protected areas is crucial for the conservation of megafauna. But often, corridor identification relies on expert knowledge that is subjective and not spatially synoptic. Landscape analysis allows generalization of expert knowledge when satellite tracking or genetic data are not available. The Nilgiri Biosphere Reserve in southern India supports the largest wild populations of the endangered Asian elephant Elephas maximus. Current understanding of connectivity in this region is based on corridors identified by experts, which are not empirically validated and incongruent with each other. To more rigorously assess population connectivity for the Asian elephant, we evaluated a combination of three resistance layers and three dispersal abilities. The resistance models were based on the combined contributions of land cover, topographical slope, elevation, roads and buildings. A spatially explicit connectivity modeling tool predicted optimal movement corridors as a function of factorial least‐cost routes across the resistance maps. A resistant kernel approach produced maps of the expected frequency of elephant movement through each cell to define core areas. We conducted a sensitivity analysis to determine the influence of resistance and dispersal. We selected the resistance surface and dispersal ability that produced the highest correlation with observed elephant densities. We evaluated the optimality of expert corridors by using a path randomization method. Eleven out of 24 expert corridors had connectivity values significantly higher than expected by chance, while only two corridors were spatially congruent between expert teams. Areas with the highest connectivity corresponded well with priority areas identified by conservationists and elephant density predicted by the resistant kernel connectivity model correlated significantly with surveys (Spearman's ρ = 0.85, n = 500, P ≪ 0.001). The results provide the first rigorous, spatially synoptic and empirically validated evaluation of the connectivity of the elephant population across the reserve.
Midbrain Morphogenesis in Beluga Sturgeon (HUSO HUSO) Larvae

The subject of this study was the development of midbrain in beluga sturgeon (Huso huso) larvae. To this end, 36 larvae (6 larvae of each age) were fixed in 10% buffered formalin, dehydrated in an ethanol series, cleared in xylene and embedded in paraffin. The larvae brain were very small in size, total head was fixed and sited in paraffin blocks. Serial sections (6 μm thick) were stained with haematoxylin & eosin, Luxol fast blue, cresyl echt violet and PTAH Mallory for histological studies by light microscope. A stereological study was done by the Cavalieri principle to estimate the different areas of the midbrain, about 10 sections from each specimen were selected and photographed by a camera attached to the light microscope Olympus CX22. From 1 day of age, the two parts of midbrain, optic tectum and tegmentum were obvious. There was an area between these parts called Torus semicircularis. In 6-day-old larvae, the optic tectum cell layers were partially observed and in 54-day-olds, the optic tectum occupied the largest volume of midbrain (12.16±0.07 mm). Tectal ventricle in H. huso larvae was observed from the first day. The tegmentum was located in the ventral part of the midbrain and in its dorsal part joined the hindbrain and contained some nuclei. Stereological results showed significantly distinctive regional differences in midbrain volume (P<0.05). In conclusion, according to the present research, the evolution of midbrain in H. huso was related to ecological activities and in comparison with other ray-finned fishes was not very developed.
Assessing the role of the ATRX chromatin remodeling protein in myelination within the mouse central nervous system

ATRX is a Rad54 translocase homolog implicated in regulating the epigenetic environment of heterochromatin, mitosis, and gene transcription. Myelin is a specialized membrane encompassing axons of neurons, allowing for efficient propagation of action potentials. CNS myelin arises via oligodendrocyte precursor cell (OPC) differentiation into myelinating oligodendrocytes (OLs), which then extend and wrap axons. Myelination is a tightly regulated process, however the mechanisms involved have yet to fully manifest. Here, we report that ATRX loss results in hypomyelination due to a defect in OPC differentiation and OL maturation, as ATRX loss did not affect OPC production, proliferation, or cholesterol biosynthesis. Additionally, myelin sheath formation was unaffected when ATRX was lost specifically from OLs, suggesting a non cell-autonomous role of ATRX in myelination. Clarifying the role of ATRX in myelination presents a novel mechanism that regulates myelin sheath formation, and findings from this study will benefit future treatments of myelin disorders, including ATR-X.
Species‐occupancy distribution removes an excessive parameter from species‐area relationship

Although species‐occupancy distributions (SODs) and species‐area relationships (SARs) arise from the two marginal sums of the same presence/absence matrices, the two biodiversity patterns are usually explored independently. Here, we aim to unify the two patterns for isolate‐based data by constraining the SAR to conserve information from the SOD.
Genetic Diversity between Populations of the Genus Schistura McClelland from the Garhwal and Kumaun Region Using RAPD Marker

Genetic based study provide emphasis on the population study of geographically isolated population, gene flow among them and evolutionary history of the species. In the present study, we aimed to detect the genetic variations in species of genus Schistura from Uttarakhand. Very little is known for the pattern of distribution and genetic diversity of the species of genus Schistura from the Garhwal and Kumaun region. Out of six primer only four primers were used to generate the fragments patterns from the samples collected. Polymorphism within and between the populations were assayed and total 60 bands were amplified ranging from 1-150 kb. Maximum number of bands was observed in Schistura montanus from the Srinagar, Garhwal and Uttarkashi regions. Total 60 bands were amplified in the all four primer with high percentage of polymorphic loci 50% Schistura montanus from Garhwal region and 28.8% in the S. montanus from the Kumaun region were observed. The level of heterozygosity were found 0.006-0.18 in the all three species. The percentage of polymorphism was 50% within the populations and high heterozygosity the sample of S. montanus when compared with other species. Observed pattern of RAPD markers reveals that the samples from the Garhwal region exhibit high diversity and used four primers are sufficient to distinguish the different population in the both region except the samples of the S. gangiticus of Garhwal region.
Handwritten/Machine-printed and Arabic/Latin Mathematical Formula Discrimination and Recognition

In this paper we mainly introduce a method for mathematical formula script and type identification based on handcrafted features. Arabic/Latin scripts are discriminated by detecting specific symbols based on their pixel density and distribution. Once the formula script identified, we proposed to separate between machine-printed and handwritten formulas. For that, we analyzed the spaces between some specific symbols and their neighbors and the pixel density of some other symbols presenting discriminative differences in their form when they are handwritten or machine-printed. The use of such structural characteristics makes the complexity of the method considerably lower than learning based methods. To finally recognize formulas, two main steps are followed: symbol recognition and formula structure analysis. For the first step, we used a combination of statistical features and an instance-based classifier. For the second step, we proceeded by top-down and bottom-up parsing scheme based on operator dominance. A set of replacement rules is defined by a coordinate grammar. Formula parsing consists of applying, from the dominant operator and its context, the appropriate rule to divide the formula into sub-formulas which will be recursively analyzed by the same way. Carried experiments on various mathematical formulas, show the efficiency of both script and type identification and recognition proposed methods.
The Queer Ontology of Digital Method

This article looks at the possibilities of a generative queer engagement with emergent digital and calculative technologies. While most queer writing on methodology has involved discursive and deconstructive interventions into qualitative methods—rejecting the quantitative outright as always already deterministic—I complicate the qualitative/quantitative distinction and advocate for new experimentation with digital networks of everyday practice. In addition, by highlighting uncomfortable resonances between queerly indeterminate epistemologies and the postnormative and nonrepresentational sociocorporal modulations of both “knowing capitalism” and the biodigital sciences, I suggest a reflexive reevaluation of the politics of queer method and a realignment of critical attention.
Methodical approach to analysis of volatility, uncertainty, complexity and ambiguity of the external environment.

The article is devoted to the methodical approach to analysis of volatility, uncertainty, complexity and ambiguity of the external environment. First of all, the external environment is broken down on macro- and microenvironment. In turn, macroenvironment is broken down on classical components: political, economic, social and technological (PEST). Each component is expressed by one or several indicators, which are obtained either from the statistics or from the internationally recognized indexes. Special techniques to evaluate volatility, uncertainty and ambiguity for each indicator are provided. All the obtained indexes are subsequently (level by level) aggregated through the average geometrical to theintegral VUCA index of the external environment.