Miracle-dz/UniFAR-FTUs huggingface dataset:
Abnormal retinal development in Cloche mutant zebrafish

Background: Functions for the early embryonic vasculature in regulating development of central nervous system tissues, such as the retina, have been suggested by in vitro studies and by in vivo manipulations that caused additional ocular vessels to develop. Here, we use an avascular zebrafish embryo, cloche−/− (clo−/−), to begin to identify necessary developmental functions of the ocular vasculature in regulating development and patterning of the neural retina, in vivo. These studies are possible in zebrafish embryos, which do not yet rely upon the vasculature for tissue oxygenation. Results: clo−/− embryos lacked early ocular vasculature and were microphthalmic, with reduced retinal cell proliferation and cell survival. Retinas of clo mutants were disorganized, with irregular synaptic layers, mispatterned expression domains of retinal transcription factors, morphologically abnormal Müller glia, reduced differentiation of specific retinal cell types, and sporadically distributed cone photoreceptors. Blockade of p53‐mediated cell death did not completely rescue this phenotype and revealed ectopic cones in the inner nuclear layer. clo−/− embryos did not upregulate a molecular marker for hypoxia. Conclusions: The disorganized retinal phenotype of clo−/− embryos is consistent with a neural and glial developmental patterning role for the early ocular vasculature that is independent of its eventual function in gas exchange. Developmental Dynamics 244:1439–1455, 2015. © 2015 Wiley Periodicals, Inc.
Chi sites in combination with RecA protein increase the survival of linear DNA in Escherichia coli by inactivating exoV activity of RecBCD nuclease.

In Escherichia coli, unprotected linear DNA is degraded by exoV activity of the RecBCD nuclease, a protein that plays a central role in the repair of double‐strand breaks. Specific short asymmetric sequences, called chi sites, are hotspots for RecBCD‐promoted recombination and are shown in vitro to attenuate exoV activity. To study RecBCD‐chi site interactions in vivo we used phage lambda's terminase to introduce a site‐specific double‐strand break at lambda's cos site inserted into a plasmid. We show that after terminase has cut cos in vivo, nucleases degrade linearized DNA only from the end that does not have a strong terminase binding site. Linearized cosmid DNA containing chi sites in the proper orientation to the unprotected end is degraded more slowly in rec+ E. coli than is chi‐less DNA. Increased survival of chi‐containing DNA is a result of partial inactivation of exoV activity and is dependent on RecA and SSB proteins. The linearization of chi‐containing DNA molecules leads to RecA‐dependent formation of branched structures which have been proposed as intermediates in the RecBCD pathway of double‐strand break repair.
Regulation of Vibrio parahaemolyticus T3SS2 gene expression and function of T3SS2 effectors that modulate actin cytoskeleton

Vibrio parahaemolyticus is a leading causative agent of seafood‐borne gastroenteritis worldwide. Most clinical isolates from patients with diarrhoea possess two sets of genes for the type III secretion system (T3SS) on each chromosome (T3SS1 and T3SS2). T3SS is a protein secretion system that delivers effector proteins directly into eukaryotic cells. The injected effectors modify the normal cell functions by altering or disrupting the normal cell signalling pathways. Of the two sets of T3SS genes present in V. parahaemolyticus, T3SS2 is essential for enterotoxicity in several animal models. Recent studies have elucidated the biological activities of several T3SS2 effectors and their roles in virulence. This review focuses on the regulation of T3SS2 gene expression and T3SS2 effectors that specifically target the actin cytoskeleton.
Methylomics in psychiatry: Modulation of gene–environment interactions may be through DNA methylation

Fine‐tuning of neuronal connections during development is regulated through environmental interactions. Some fine‐tuning occurs through changes in gene expression and/or epigenetic gene‐specific DNA methylation states. DNA methylation occurs by transfer of a methyl group from S‐adenosyl methionine to cytosine residues in the dinucleotide sequence CpG. Although CpG sequences spread throughout the genome are usually heavily methylated, those occurring in CpG islands in the promoter regions of genes are less methylated. In most cases, the extent of DNA methylation correlates with the extent of gene inactivation. Other known epigenetic mechanisms include histone deacetylation and chromatin remodeling, RNA inhibition, RNA modification, and DNA rearrangement. Exposure memory expressed as epigenetic DNA modifications allows genomic plasticity and short‐term adaptation of each generation to their environment. Environmental factors that affect DNA methylation include diet, proteins, drugs, and hormones. Induced methylation changes may produce altered gene response upon subsequent hormonal stimulation. The gene‐specific DNA methylation state may be preserved upon transmission through mitosis and meiosis. An increasing amount of data implicates a role for DNA methylation in multi‐factorial psychiatric disorders. For example, l‐methionine treatment can exacerbate psychosis; while valproate, a drug producing hypomethylated DNA, reduces such symptoms. Hypermethylation of the promoter region of the RELN gene correlates with reduced gene expression. This gene's protein Reelin, which is necessary for neuronal migration and synaptogenesis, is reduced in schizophrenia and bipolar disorder, suggesting hypermethylation of the promoter region in these disorders. Some evidence implicates methylation of the promoter regions of the DRD2 and HTR2A genes in schizophrenia and mood disorders as well. DNA methylation usually increases with age, although hypomethylation of the promoter region of the amyloid A4 precursor gene during aging may play a role in Alzheimer's disease. More studies are needed to define the role of methylomics and other epigenetic phenomena in the nervous system. © 2003 Wiley‐Liss, Inc.
Targeting calcineurin and associated pathways in cardiac hypertrophy and failure

Cardiac hypertrophy occurs in response to long-term increases in haemodynamic load related to a variety of physiological and pathological conditions. Cardiac hypertrophy developing in pathological conditions with increased load often progresses to a decompensated stage with cardiac contractile dysfunction, clinical signs of heart failure and premature death. Cardiac hypertrophy associated with adverse outcomes is said to be maladaptive. Conversely, there are settings where cardiac hypertrophy appears to be purely adaptive (e.g., hypertrophy in response to regular physical exercise). In these circumstances, hypertrophy is associated with preserved contractile performance and a favourable prognosis. Cardiac myocyte hypertrophy is controlled by growth factor receptors and mechanical stress sensors which activate a complex network of signalling pathways. These pathways promote a multitude of qualitative and quantitative changes in gene expression levels in cardiomyocytes. Reprogramming of gene expression, much more than cardiac (myocyte) hypertrophy per se, ultimately determines if cardiac hypertrophy will be adaptive or maladaptive. Pharmacological modification of gene expression in the hypertrophied heart may, therefore, be an attractive approach to prevent or even treat maladaptive hypertrophy and heart failure. Calcineurin is a serine-threonine phosphatase that is activated by sustained increases in [Ca2+]i in cardiomyocytes. Although it has been firmly established that calcineurin plays a critical role in the development of cardiac hypertrophy, the question of whether calcineurin activation serves an adaptive or maladaptive role is still unresolved. An answer to this question is crucial if calcineurin is to be developed as a drug target. The authors propose that calcineurin acts as a double-edged sword; excessive activation of calcineurin is maladaptive, its activation at endogenous levels and at specific subcellular microdomains, however, promotes adaptation. Calcineurin itself may, therefore, not be a convenient target for drug development. However, because maladaptive hypertrophy is ultimately a transcriptional disorder, definition of the transcriptional programme activated by distinct calcineurin activation levels may permit identification of novel, attractive drug targets.
Voluntary Disclosures When Seller's Level of Information Is Unknown

In this paper we report the results of experimental markets designed to test a disclosure model based on the models of Dye [1985] and Jung and Kwon [1988]. These authors show that when receivers of information do not know whether senders possess private information, the senders will not fully disclose their private information. Their models were motivated by the discrepancy between the theoretical predictions for voluntary disclosures and empirical results. In the theoretical area, Grossman [1981] and Milgrom [1981] predicted that private information will be fully disclosed when disclosures are credible and receivers know the holder has private information; agents disclose to identify themselves as not possessing the worst possible information. Watts [1977] argued that voluntary disclosure will occur because of market pressures and the threat of regulatory intervention. Beaver [1977; 1988] described how auditing and legal liability may induce full disclosure. Nevertheless, empirical research indicates full disclosure is not always observed (e.g., Penman [1980] and Seligman [1986]).
Child growth as a measure of livelihood security: The case of the Gwembe Tonga

This article outlines an approach to the study of child growth and development in adverse environments that utilizes growth to measure the success of the human/environment interaction. This type of biocultural, human adaptability perspective focuses on within group variation to gain an understanding of the differential ability of households to negotiate opportunities and constraints in the ecological/social/cultural environment. As an example, we report preliminary findings of on‐going research in a migrant Gwembe Tonga community in Zambia. Our analysis indicates that average height‐for‐age and weight‐for‐height z‐scores of school children are below international references, representing compromised community well‐being in context of new and shifting environments. We report variation in average household child height‐for‐age z‐scores that is linked to differential livelihood strategies in the community. We conclude that in the context of shared circumstances that focus risk for poor health on this community as a whole, the ability of households to adapt to their circumstances varies as evidenced by differential growth outcomes. Am. J. Hum. Biol., 2007. © 2007 Wiley‐Liss, Inc.
Structural determinants of species‐selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies

To identify potential determinants of substrate selectivity in serotonin (5‐HT) transporters (SERT), models of human and Drosophila serotonin transporters (hSERT, dSERT) were built based on the leucine transporter (LeuTAa) structure reported by Yamashita et al. (Nature 2005;437:215–223), PBDID 2A65. Although the overall amino acid identity between SERTs and the LeuTAa is only 17%, it increases to above 50% in the first shell of the putative 5‐HT binding site, allowing de novo computational docking of tryptamine derivatives in atomic detail. Comparison of hSERT and dSERT complexed with substrates pinpoints likely structural determinants for substrate binding. Forgoing the use of experimental transport and binding data of tryptamine derivatives for construction of these models enables us to critically assess and validate their predictive power: A single 5‐HT binding mode was identified that retains the amine placement observed in the LeuTAa structure, matches site‐directed mutagenesis and substituted cysteine accessibility method (SCAM) data, complies with support vector machine derived relations activity relations, and predicts computational binding energies for 5‐HT analogs with a significant correlation coefficient (R = 0.72). This binding mode places 5‐HT deep in the binding pocket of the SERT with the 5‐position near residue hSERT A169/dSERT D164 in transmembrane helix 3, the indole nitrogen next to residue Y176/Y171, and the ethylamine tail under residues F335/F327 and S336/S328 within 4 Å of residue D98. Our studies identify a number of potential contacts whose contribution to substrate binding and transport was previously unsuspected. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Depth and breadth away from the desktop: the optimal information hierarchy for mobile use

The optimal way to structure information in hierarchies has occupied researchers for at least two decades. In the last few years, mobile devices added new challenges to this research: the limited screen size, navigation methods and data transfer rates make the search for the optimal information structure even more complex. In this paper an experiment is presented that investigates the usability of 4 different information hierarchies (46, 84, 163 and 642) on three mobile devices. It turns out that the narrow hierarchies (46 and 84) perform better than the broader hierarchies on the three devices. The experiment was repeated on two more occasions with the same participants to test expertise effects; the preference for narrow hierarchies did not change over the three occasions.
The effect of betaine on in vitro fermentation of carbohydrate and protein combinations under osmotic stress in pigs.

BACKGROUND There is evidence that dietary betaine might improve nutrient digestibilities in pigs due to its osmoprotective properties. This in vitro study was performed to assess the potential of supplemented betaine sources to affect fermentation characteristics of different carbohydrate and protein combinations, under conditions of osmotic stress. In vitro fermentation was performed by use of the modified Hohenheim gas test with pig faeces as microbial inoculum. RESULTS At the end of in vitro fermentation under osmotic stress conditions, differences (P < 0.05) in gas production, ammonia concentration, and concentration of short-chain fatty acids were observed for the different carbohydrates, while for the two proteins only differences (P < 0.05) in ammonia and short-chain fatty acid concentration were obtained. Supplementation of a native betaine source rather than addition of pure betaine increased propionic acid (P < 0.05) and butyric acid (P < 0.05) production. CONCLUSION These results suggest that only supplementation of a native betaine source but not of pure betaine products affects microbial fermentation under osmotic stress. Furthermore, both the carbohydrate and protein source play an important role in modifying microbial activity under osmotic stress conditions. It can also be concluded that the modified Hohenheim gas test is suitable to scrutinise fermentation activity of different assay substrates under osmotic stress.
Study of discretization methods in classification

Classification is one of the important tasks in Data Mining or Knowledge Discovery with prolific applications. Satisfactory classification depends on characteristics of the dataset too. Numerical and nominal attributes are commonly occurred in the dataset. However, classification performance may be aided by discretization of numerical attributes. At present, several discretization methods and numerous techniques for implementing classifiers exist. This study has three main objectives. First is to study the effectiveness of discretization of attributes, and second is to compare the efficiency of eight discretization methods. These are ChiMerge, Chi2, Modified Chi2, Extended Chi2, Class-Attribute Interdependence Maximization (CAIM), Class-Attribute Contingency Coefficient (CACC), Autonomous Discretization Algorithm (Ameva), and Minimum Description Length Principle (MDLP). Finally, the study investigates suitability of the eight discretization methods when applied to the five commonly known classifiers, Neural Network, K Nearest Neighbour (K-NN), Naive Bayes, C4.5, and Support Vector machine (SVM).
A Unified Closed-Form Formula for the SPERs of Full-Diversity Rate-1 Single-Complex-Symbol Decodable STBCs in Rayleigh Fading Channels

In this letter, a generic unified closed-form formula is derived, which can be applied for the derivation of average symbol pairwise error rates (SPERs) of quasi-orthogonal space-time block codes with minimum decoding complexity (MDC-QSTBCs) and space-time block codes obtained from coordinate interleaved orthogonal designs (STBCs-CIODs) over quasi-static frequency-nonselective i.i. d. Rayleigh fading channels. Based on the derived closed-form formula, we also provide its asymptotic approximate expression that can be effectively utilized to explicitly obtain the coding gain and verify the full-diversity achievability for both the STBCs.
Religion, spirituality, and health outcomes in cancer: A case for a meta‐analytic investigation

A growing body of research shows that a majority of patients with cancer report having religious and spiritual (R/S) beliefs, engaging in R/S behaviors, or deriving comfort from R/S experiences. These studies have been reviewed but not subjected to rigorous critical analysis. A meta‐analytic approach is needed to provide a more definitive understanding of the relationships between R/S (affective, behavioral, and cognitive dimensions) and physical, mental, and social health in all phases of cancer including diagnosis, treatment, survivorship, and palliative care. A meta‐analysis can quantify the degree of association between R/S dimensions and patient‐reported health outcomes and the conditions under which these associations are strengthened or attenuated. Results can, in turn, help focus future work in this area by highlighting key variables for inclusion in studies of R/S and cancer and identifying particular subgroups for whom dimensions of R/S are particularly important to their health. Cancer 2015;121:3754–3759. © 2015 American Cancer Society.
Enhancement-Mode GaN MIS-HEMTs With LaHfOx Gate Insulator for Power Application

This letter reports an E-mode GaN MIS-HEMT using a composite La<sub>2</sub>O<sub>3</sub>/HfO<sub>2</sub> gate insulator for power device applications. The composite dielectric formed an amorphous LaHfOx layer after post-deposition annealing. The GaN MIS-HEMT with amorphous LaHfOx gate dielectric showed good oxide film quality and excellent HfLaOx/GaN interface properties, as demonstrated by the measured C–V characteristics. Consequently, the E-mode MIS-HEMT was determined to show good <inline-formula> <tex-math notation="LaTeX">${V} _{\mathrm {th}}$ </tex-math></inline-formula> stability with only a slight increase in the dynamic <inline-formula> <tex-math notation="LaTeX">${R} _{\mathrm {on}}$ </tex-math></inline-formula> after high drain bias stress.
Preparation, Physicochemical Characterization and Pharmacological Study of Novel Ruthenium (III) Complexes with Imidazole and Benzimidazole Derivatives

Summary Complex compounds of ruthenium(III) with 1,2-dimethylimidazole (CAS 1739-84-0), 2-phenylimidazole (CAS 670-96-2) and 2-aminobenzimidazole (CAS 934-32-7) were prepared and were characterised by physicochemical methods. Coordination sites were determined. The complexes were tested for cytotoxic activity using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) dye-reduction assay and the values LD50 were evaluated.
Impact of uncertainty propagation on the design of state estimation for hybrid ac-dc grids

In order to ensure safe and reliable operation of the grids of the future, hybrid ac-dc grids are being considered as a promising solution. Traditionally state estimation (SE) of hybrid ac-dc grids has been performed with sequential SE algorithms. In this paper the authors show the inherent problems of the sequential SE algorithms, especially due to the incorrect propagation of the uncertainty of the boundary bus quantities. Instead, a two-step SE accounting for the converter losses is proposed, which updates the boundary results of the ac and dc grids respectively, to improve the accuracy. Tests of a simple hybrid ac-dc grid are presented to show the flaws in the sequential SE algorithms and the benefits of the proposed two-step method. Furthermore the accuracy improvements achievable through the inclusion of the converter losses in the SE algorithm are presented.
Polymorphisms and haplotypes of the NBS1 gene are associated with risk of sporadic breast cancer in non-Hispanic white women ≤55 years

Biomarker: three Nijmegen breakage syndrome 1 (NBS1) protein haplotype-tagging polymorphisms (i.e. 924T>C, 8360G>C and 30537G>C) of Effect studied: breast cancer risk; DNA damage. Tissue/biological material/sample size: 30 ml of blood. Method of analysis: PCR-RFLP assay. Study design: case-control study. Study size: 421 cases and 423 controls Impact on outcome (including dose-response): compared with 924TT homozygotes the variant homozygote 924CC carriers had a 4.55-fold increased risk of breast cancer [95% confidence interval (CI) = 1.51-13.7] and that compared with the 8360GG genotype the variant genotypes were also associated with a significantly increased risk [adjusted odds ratio (OR) = 1.33, 95% CI = 1.00-1.78 for 8360CG; adjusted OR = 1.83, 95% CI = 1.14-2.94 for 8360CC]. However, these effects were not observed for the 30537G>C polymorphism. Furthermore, the derived haplotypes were associated with risk in a dose-response manner as the number of variant (risk) alleles (i.e. 8360C, 924C or 30537C) increased (adjusted OR = 1.07, 95% CI = 0.78-1.46 for 1-2 variant alleles; adjusted OR = 2.47, 95% CI = 1.48-4.14 for 3-6 variant alleles; P(trend) = 0.006). KEYWORDS - CLASIFFICATION: Aged;analysis;biomarkers of individual susceptibility: field studies;blood;Breast;Breast Neoplasms;cancer epidemiology;Cell Cycle;Cell Cycle Proteins;Environmental Health;Epidemiology;etiology;European Continental Ancestry Group;Female;field studies;genetic;Genetic Predisposition to Disease;genetics;Genotype;Haplotypes;Homozygote;Humans;Middle Aged;Models,Genetic;Nuclear Proteins;Odds Ratio;Polymorphism,Genetic;Proteins;Research;Risk;