Miracle-dz/UniFAR-FTUs huggingface dataset:
The Wood Index: An Innovative Index for Determining Vine Vigour

Precision farming is a farming management technique already known in the agricultural sector [1,2]. It makes possible to perform agronomic intervention taking into account actual cultivation needs. This is possible by calibrating input on the basis of images that show the shape, size and vigour of various crops. The remote sensing technique allows to obtain these images using different technology, such as multispectral images acquired from satellites and airborne or unmanned aerial vehicles (UAV) [3-10]. Proximal sensing represents another instrument for obtaining this kind of information, but in this case the technology is based on various types of sensors suitable for continuous measurements of soil or canopy parameters [11-14]. Viticulture is one of the most extensively investigated sectors, due to its economic significance at European level. The possibility of collecting information about vineyard vegetation development allows farmers to better direct management strategies and calibrate decision-making in relation to the different vigour of the vines in the vineyard. This represents the VRT (Variable Rate Technology) concept as a way of calibrating input according to actual vine requirements [15-17].
Diversitree: comparative phylogenetic analyses of diversification in R

1. The R package ‘diversitree’ contains a number of classical and contemporary comparative phylogenetic methods. Key included methods are BiSSE (binary state speciation and extinction), MuSSE (a multistate extension of BiSSE), and QuaSSE (quantitative state speciation and extinction). Diversitree also includes methods for analysing trait evolution and estimating speciation/extinction rates independently.
Analysis of SNPs in Bovine CSRP3, APOBEC2 and Caveolin Gene Family

The cysteine and glycine rich protein 3 (CSRP3), apolipoprotein B mRNA editing enzyme catalytic polypeptide‐like 2(APOBEC2) and caveolin (CAV) gene family(CAV1, CAV2, CAV3) have been reported to play important roles for carcass and meat quality traits in pig, mouse, human and cattle. As an initial step, we investigated SNPs in these 5 genes among eight different cattle breeds. Eighteen primer pairs were designed from bovine sequence data of NCBI database to amplify the partial gene fragments. Sequencing results revealed 9 SNPs in the coding regions of three caveolin genes, 1 SNP in CSRP3 and 3 SNPs in APOBEC2 gene. All the identified SNPs were confirmed by PCR-RFLP. Also, 9 more intronic SNPs were detected in these genes. However, all identified mutations in the coding region do not change amino acid sequence. Allelic distributions were significantly different for 5 SNPs in CAV2, CAV3, CSRP3 and APOBEC2 genes among the eight different breeds. These results gave some clues about the polymorphisms of these genes among the cattle breeds and will be useful for further searches for identifying association between these SNPs and meat quality traits in cattle.
Six Newly Discovered Eclipsing Binary Systems in the TESS field

We present the first detailed investigation of six eclipsing binary systems in the TESS field. The TESS light curves of the targets are analyzed by determining the initial effective temperatures via SED fits. The absolute parameters are derived and the systems are compared to well-known binaries of the same type. Results show that CD-58791, CD-621257 and TYC 9356-355-1 are detached binary systems. CD-54942 and UCAC4 136-007295 are contact binaries while TYC 8508-1413-1 is a semidetached system.
Induced Spawning in the Sea Cucumber Apostichopus japonicus by Neuropeptide, Cubifrin (The 41st Scientific Symposium of the UJNR Aquaculture Panel : Advanced Aquaculture Technologies)

In hatcheries the induction of spawning in sea cucumbers has been typically carried out by regulation of rearing conditions such as temperature and light intensity. However, this method is relatively ineffective and the rate of spawning is unpredictable. In this study we established an efficient method for inducing spawning in the Japanese sea cucumber Apostichopus japonicus by injecting a neuropeptide, cubifrin. We purified peptides that can induce oocyte maturation from the buccal tissues containing the nerve ring, using liquid chromatography and in vitro assay with ovarian fragments in combination. The effective dose of each peptide was evaluated with chemically synthesized peptides. Consequently, the most potent peptide was identified as NGIWY-amide. We also found that synthetic derivatives replaced the third amino acid, isoleucine, with a different basic amino acid could be 10-100 times more potent than the natural hormone. When injected into the body cavity of sexually matured individuals, NGIWY-amide, or its derivative, induced spawning in both males and females. NGIWY-amide was then named cubifrin after the Japanese word “kubifuri” meaning waving head, which is a reproductive behavior of sea cucumbers. Gamete shedding started about 60 min and 80 min after the injection in males and females, respectively, and was completed almost simultaneously in the two sexes about 2 hours after the administration. The in vitro responsiveness of biopsied ovarian fragments was well correlated with the spawning success induced by an injection. Therefore, cubifrin can be used as an excellent detector of maturity as well as an inducer of spawning in A. japonicus in a hatchery
Regulation of Pancreatic α and β Cell Function by the Bile Acid Receptor TGR5

REGULATION OF PANCREATIC α AND β CELL FUNCTION BY THE BILE ACID RECEPTOR TGR5 Divya P. Kumar A dissertation submitted in partial fulfillment of the requirement for the degree of Doctor of Philosophy at Virginia Commonwealth University Virginia Commonwealth University, 2014 Directors: Dr. Arun Sanyal and Dr. S. Murthy Karnam Departments of Internal Medicine and Physiology and Biophysics The discovery that bile acids act as endogenous ligands of the membrane receptor TGR5 and the nuclear receptor FXR increased their significance as regulators of cholesterol, glucose and energy metabolism. Activation of TGR5, expressed on enteroendocrine L cells, by bile acids caused secretion of GLP-1, which stimulates insulin secretion from pancreatic β cells. Expression of TGR5 on pancreatic islet cells and the direct effect of bile acids on the endocrine functions of pancreas, however, are not fully understood. The aim of this study was to identify the expression of TGR5 in pancreatic islet cells and determine the effect of bile acids on insulin secretion. Expression of TGR5 was identified by quantitative PCR and western blot in islets from human and mouse, and in α (αTC1-6) and β (MIN6) cells. Release of insulin, glucagon and GLP-1 were measured by ELISA. The signaling pathways coupled to TGR5 activation were identified by direct measurements such as stimulation of G proteins, adenylyl cyclase activity, PI hydrolysis and intracellular Ca in response to bile acids; and confirmed by the use of selective inhibitors that block specific steps in the signaling pathway. Our studies identified the expression of TGR5 receptors in β cells and demonstrated that activation of these receptors by both pharmacological ligands (oleanolic acid (OA) and INT-777) and physiological ligands (lithocholic acid, LCA) induced insulin secretion. TGR5 receptors are also expressed in α cells and, activation of TGR5 by OA, INT-777 and LCA at 5 mM glucose induced release of glucagon, which is processed from proglucagon by the selective expression of prohormone convertase 2 (PC2). However, under hyperglycemia, activation of TGR5 in α cells augmented the glucose-induced increase in GLP-1 secretion, which in turn, stimulated insulin secretion. Secretion of GLP-1 from α cells reflected TGR5-mediated increase in PC1 promoter activity and PC1 expression, which selectively converts proglucagon to GLP-1. The signaling pathway activated by TGR5 to mediate insulin and GLP-1 secretion involved Gs/cAMP/Epac/PLC-ε/Ca. These results provide insight into the mechanisms involved in the regulation of pancreatic α and β cell function by bile acids and may lead to new therapeutic avenues for the treatment of diabetes.
Homo- and Hetero-oligomerization of β-Arrestins in Living Cells*

Arrestins are important proteins, which regulate the function of serpentine heptahelical receptors and contribute to multiple signaling pathways downstream of receptors. The ubiquitous β-arrestins are believed to function exclusively as monomers, although self-association is assumed to control the activity of visual arrestin in the retina, where this isoform is particularly abundant. Here the oligomerization status of β-arrestins was investigated using different approaches, including co-immunoprecipitation of epitope-tagged β-arrestins and resonance energy transfer (BRET and FRET) in living cells. At steady state and at physiological concentrations, β-arrestins constitutively form both homo- and hetero-oligomers. Co-expression of β-arrestin2 and β-arrestin1 prevented β-arrestin1 accumulation into the nucleus, suggesting that hetero-oligomerization may have functional consequences. Our data clearly indicate that β-arrestins can exist as homo- and hetero-oligomers in living cells and raise the hypothesis that the oligomeric state may regulate their subcellular distribution and functions.
The structural analysis of histone H3 lysine 56 acetylation and related histone chaperone complexes

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The IWSLT 2019 KIT Speech Translation System

This paper describes KIT’s submission to the IWSLT 2019 Speech Translation task on two sub-tasks corresponding to two different datasets. We investigate different end-to-end architectures for the speech recognition module, including our new transformer-based architectures. Overall, our modules in the pipe-line are based on the transformer architecture which has recently achieved great results in various fields. In our systems, using transformer is also advantageous compared to traditional hybrid systems in term of simplicity while still having competent results.
Histopathological features of subcutaneous mycosis: a retrospective study

Background: Subcutaneous fungal infection is commonly seen in tropical and subtropical countries particularly in India. The lesions are usually presented as swelling, in the localized form. Subcutaneous mycosis is caused by penetration of causative fungi into the subcutaneous tissue. Histopathology is one of the main tools of diagnosis in mycology as it has the advantages of early diagnosis compared to culture, low cost and it provides a presumptive identification of the infecting fungus. It also gives information about tissue reaction and supplement culture report. It gives the idea about the fungus isolated in culture is contaminant or pathogenic. Many a times tissue might be sent in formalin as fungal infection is not suspected clinically. Role of histopathologist is very important in diagnosing these subcutaneous fungal lesions. Material & Methods: A retrospective study was conducted on subcutaneous fungal infections seen between January 2014 to December 2018 in the Department of pathology, IGMC&RI, Puducherry. Twenty-two patients with biopsy proven subcutaneous fungal infections were included in the study. In the present study, the varied histopathological features like type of inflammatory response, presence of granulomas, necrosis, eosinophils and abscess formation were seen in the tissue sections. Results: The most common histopathology feature was giant cell reaction seen in 21 (95.5%) cases, followed by epithelioid cell granuloma in 13(59%) cases and areas of necrosis in 13 (59%) cases. Eight (36%) cases showed numerous eosinophilic infiltration 10(46%) cases of scant eosinophils and 4 (18%) cases showed absent eosinophils. These fungal structures were identified in H&E stain itself in 13 (59%) cases. Conclusion: Histopathological study is most important in subcutaneous mycosis as most of the time diagnosis is unsuspected and delayed because of its rarity and varied presentation. Fungal infection should be suspected in cases with localized cystic swelling. High index of suspicion, careful microscopic examination and special stains are important for accurate diagnosis.
Cattle yield prediction for the transamazon highway of Brazil

The Brazilian government is presently encouraging the rapid development of cattle pasture in large parts of the Amazon Basin through a massive program of financial and tax incentives. This has been encouraged by recent claims in Brasil that pasture improves soil quality, and there/ore presumably could supply an indefinite yield of cattle to the ranchers that are responding to the incentives program. Calculation of beef productivity to be expected in areas such as Brazil's Transamazon Highway by a variety of means all lead to the conclusion that government expectations are overoptimistic. The present paper develops equations for prediction of cattle yields for a study area on the Transainazon Highway including the effects of both soil nutrients and competition from weeds. Low levels of soil phosphorus and invasion of inedible weeds soon reduce grass and cattle yields to very low levels. Results of a computer simulation of cattle yields based on the relatiomhips developed linking yield to soil nutrients and weeds. and 011 the soil information gathered in the Transamazon Highway study area, are presented. The pasture simulation forms a part of a larger . 1·imularion of the agroecosystcm of :he Tramamazon Hig/m·ay colonists which is aimed at assessing the importance of \'arious factors 011 the carrying capacity of the area for human populations. Although the carrying capacity study shall'S that agriculture based largely on annual crops is a risky business, it also casts doubt on the presumption of secure and sustainable · yields from the pasture de\'elopment schemes currently being promoted in the Brazilian A mazon.
Bactericidal Mechanisms of Escapin, A Protein in the Ink of a Sea Hare

A 60 kDa monomeric protein isolated from the defensive purple ink secretion of the sea hare Aplysia californica has broad antimicrobial activity in tryptone peptone rich medium. This protein, which we call ‘escapin’, belongs to an L-amino acid oxidase family. The goals of my project were 1) to determine the products of escapin’s oxidation of its main substrate L-lysine, 2) to characterize the antimicrobial effects of escapin’s products, and 3) determine bactericidal mechanisms of action of these products. Escapin is a powerful bactericidal agent against several bacteria species including Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Vibrio harveyi. Escapin operates through a two-step process: 1) deamination of L-amino acids (especially L-lysine) by enzymatic activity to produce escapin intermediate products of Llysine (EIP-K), hydrogen peroxide, and ammonia; and 2) EIP-K simultaneously reacts with hydrogen peroxide to generate escapin end products (EEP-K). EIP exists as an equilibrium mixture of the linear α-keto analogue of lysine and its cyclic forms, and the relative amount of the linear form increases with pH decreases. The powerful bactericidal effect of escapin requires the simultaneous presence of hydrogen peroxide and EIP-K in weak acidic conditions, which suggests that linear form of EIP-K with hydrogen peroxide is responsible for the bactericidal effect of escapin. Using E. coli MC4100 as a model, the mechanism of action of escapin was examined. Brief treatment with EIP-K + H2O2, but not EIP-K or H2O2 alone, causes irreversible DNA condensation with a time course similar to the bactericidal effect. A mutant strain resistant to EIP-K + H2O2 was isolated, and a single point mutation was found in the oxidative stress regulator gene (oxyR). Through a complementary assay, it was shown that wild type E. coli is conferred resistance to EIP-K + H2O2 by carrying mutated oxyR plasmid. Furthermore, in this bactericidal effect, heat or cold shock does not substitute for hydrogen peroxide induced oxidative stress. Thus, escapin’s powerful bactericidal effect may be through irreversible DNA condensation mediated through hydrogen peroxide generating an oxidative stress response, but the pathway mediating EIP-K’s synergistic effect is still unclear. INDEX WORDS: Toxin, Chemical defense, Flavin, Gastropod, Inking, Opisthobranchia, L-Amino acid oxidase (LAAO), Amino acids, Enols, Imino compounds, Oxidation, DNA condensation. BACTERICIDAL MECHANISMS OF ESCAPIN, A PROTEIN IN THE INK OF A SEA HARE
Mutational-kinetic Analysis Reveals the Roles of Arginines and Aromatics in the Core of the GABAA Receptor Ligand-binding Pocket

MUTATIONAL-KINETIC ANALYSIS REVEALS THE ROLES OF ARGININES AND AROMATICS IN THE CORE OF THE GABAA RECEPTOR LIGAND-BINDING POCKET Phu N. Tran, B.S. Marquette University, 2011 The γ-aminobutyric acid type A (GABA) receptor is a member of the cys-loop family of ligandgated ion channels that plays a crucial role in normal brain function by transducing the majority of inhibitory neurotransmission in the central nervous system. The studies documented in this dissertation were aimed at validating and refining the current best model for the interaction of GABA with the GABAA receptor via structure-function perturbation analysis. Mutationalkinetic data was used in conjunction with homology modeling knowledge to draw up architectural and functional roles of the arginines and aromatics in GABA-binding pocket. The results provide interesting new insights. Two positively charged arginine residues, which have been implicated in ligand binding, were profiled through serial mutagenesis, to get at the specific side chain properties required for the roles they serve. The structural and functional contribution of four aromatic residues were examined through measuring the influence of their side chain on GABA binding rate with respect to changes caused by point mutations. An interaction between two aromatic residues critical for proper ligand binding was discovered through a screen for functional coupling between them and four neighboring arginines. These results were subsequently employed in an attempt to refine the current ligand-receptor interaction model, proposing specific roles for the amino acid residues studied. In the current best model of the GABAA receptor’s ligand-binding pocket, the amino moiety of GABA is coordinated by a cation-π interaction with β2Y97 and the carboxyl moiety coordinated by an interaction with either β2R207 or α1R67 (or possibly both). Here, we incorporate the results of this dissertation to modify and add significant detail to this model. The model proposed here includes the following features: a hydrophobic interaction between β2Y97 and β2F200, an inter-subunit cation-π interaction between β2Y97 and α1R132, a cation-π interaction between the amino group of GABA and β2F200, hydrogen bond(s) between the carboxyl end of GABA and the guanidinium group of α1R67, and an interaction between the side chain of β2R207 and the backbone carbonyl of β2Y97.
The Relationship between Positive Emotional Styles with Life Expectancy and Mediation of Quality of Life in Older Men

Purpose : The aim of the present study was to investigate the relationship between positive transsexual styles and life expectancy and mediation of quality of life in male seniors. Methodology : This study was a descriptive-correlational study that was conducted to investigate the mediating role of quality of life in relation to positive metaphysical styles with life expectancy in male seniors. The statistical population of this study included all elderly men over 60 years of age in the Neishabour Welfare Department. The sample of the present study included 132 of these elderly people who were selected as available samples. Beck, Hoe per (2009), Snyder, et al (1991) Life Hope Questionnaire and the World Health Organization's Quality of Life Questionnaire (1998) were used to collect information. Data were analyzed and analyzed based on structural equations and correlation coefficients. Findings : The direct effect of positive transcendental styles on life expectancy was 0.425 with a significance level of 0.008 and the indirect effect of positive transcendental styles on life expectancy was 0.404 and the corresponding significance level was lower considering the quality of life of the elderly. It is from 0.05, so the mediating role of quality of life is confirmed. The results of regression analysis and structural equations showed that there was a relationship between positive metaphysical styles with life expectancy and median quality of life in male seniors. (P<0.001). The results also showed that the role of quality of life in the relationship between positive metaphysical positive meta-sympathy and meta-interest with life expectancy was partial. (P<0.001). Conclusion : Findings from this study show that extra-emotional styles such as being pleasant, sociable, restraining, and accepting a change in quality of life in older men increase their chances of experiencing a higher life expectancy.
Molecular genetics of the 1q23.3 schizophrenia susceptibility locus

Family based linkage studies have confirmed that part of chromosome lq23.3 contains a susceptibility gene for schizophrenia. This region was investigated by tests of allelic and haplotypic association in order to fine map a specific gene in the lq23.3 region. Previously published studies claimed that the genes RGS4 and CAPON on lq23.3 were associated with schizophrenia. For this research thesis multiple markers were genotyped at the RGS4 and CAPON loci in a London based case control sample, no evidence for association was found. Therefore further fine mapping was carried out in the region between the RGS4 and CAPON genes. Allelic and haplotypic associations with schizophrenia were found with three microsatellite and four SNP markers within the serine threonine kinase (UHMK1) gene. A replication study using an Aberdeen based case control sample also found statistically significant evidence of allelic and haplotypic association between TJHMK1 and schizophrenia. Re-sequencing of the UHMK1 gene was carried out in those individuals who had inherited alleles and haplotypes associated with schizophrenia. Three genetic variants were found. Genotyping of the whole case control sample showed that these changes were not associated with schizophrenia. The previously reported associations between schizophrenia and RGS4 as well as CAPON could possibly be explained by linkage disequilibrium between UHMK1 and both CAPON and RGS4. Alternatively there could be two or even three susceptibility genes within the 700 Kb region. At present no potential aetiological base pair changes have been detected in any of the three genes. UHMK1 is known to be highly expressed in regions of the brain implicated in schizophrenia and was found to be significantly down regulated in mice treated with the antipsychotic drug Clozapine. Further confirmation of the involvement of this gene in schizophrenia is needed followed by further efforts to detect genetic variation in or next to the gene which has an effect on expression and function of UHMK1.