Miracle-dz/UniFAR-FTUs huggingface dataset:
A deviation from the universal genetic code in Candida maltosa and consequences for heterologous expression of cytochromes P450 52A4 and 52A5 in Saccharomyces cerevisiae

We demonstrate that serine instead of leucine is specified by the CUG codon in the yeast Candida maltosa. Evidence for this deviation from the universal genetic code was obtained by means of in vitro translation experiments. Depending on the cell‐free system used, either serine, in the C. maltosa system, or leucine, in the control with the conventional wheat germ system, was found to be incorporated into the translation products of artificial CUG‐containing mRNAs. Moreover, we were able to transfer the non‐universal decoding of CUG to the wheat germ system by adding a tRNA fraction isolated from C. maltosa. This finding indicates the presence in C. maltosa of an unusual serine tRNA that recognizes CUG. As a consequence of the altered genetic code, expression in Saccharomyces cerevisiae of C. maltosa cytochrome P450 genes required an exchange of their CTG triplets by TCT encoding serine in order to produce the authentic proteins. In contrast, heterologous expression of the original C. maltosa genes resulted in the formation of still active but unstable enzymes probably subject to selective proteolysis in the host cells.
Lipocalin 2 deficient mice develop insulin resistance and cold intolerance 3 Obesity is a major risk for developing insulin resistance , a hallmark of type 2 diabetes and other metabolic complications such as fatty liver , dyslipidemia and atherosclerosis

This is an uncopyedited electronic version of an article accepted for publication in Diabetes. The American Diabetes Association, publisher of Diabetes, is not responsible for any errors or omissions in this version of the manuscript or any version derived from it by third parties. The definitive publisher-authenticated version will be available in a future issue of Diabetes in print and online at http://diabetes.diabetesjournals. org. Diabetes Publish Ahead of Print, published online March 23, 2010
Credit Rationing for Small and Medium Scale Enterprises in the Commercial Bank Loan Market

I TABLE OF CONTENTS . II 1.0 INTRODUCTION. 1 2.0 CREDIT RATIONING RELATED LITERATURE . 7 2.1 INFORMATION ASYMMETRY, TRANSACTION COSTS AND CREDIT RATIONING . 7 2.1 BUSINESS CHARACTERISTICS, ENTREPRENEUR CHARACTERISTICS AND CREDIT RATIONING . 8 2.2 COLLATERAL . 11 2.3 RELATIONSHIP LENDING . 13 2.4 LOAN MATURITY . 15 2.5 CORRUPTION OF BANK OFFICIAL AND BUREAUCRACY . 15 3.0 METHODOLOGY . 16 3.1 IDENTIFICATION OF RATIONED AND NON RATIONED SMES . 17 3.2 METHODOLOGICAL LIMITATIONS . 18 4.0 RESULT AND INTERPRETATION . 20 4.1 RATIONING STATUS . 20 4.2 RATIONING STATUS AND ITS VARIATION ACROSS BORROWER PROFILE . 23 4.3 CONCLUSIONS AND RECOMMENDATIONS . 28 REFERENCES . 30 APPENDICES . 35
Molecular phylogeny and global diversity of the remarkable genus Bondarzewia (Basidiomycota, Russulales)

Bondarzewia is a remarkable polypore genus due to its relatively large poroid basidiocarps and belongs to order Russulales according to recent phylogenetic analyses. Two species, B. berkeleyi and B. mesenterica, are commonly reported in North America and Europe but the genus is poorly known elsewhere. We explored the phylogeny and species diversity of Bondarzewia based on a larger number of samples covering a wider geographic range, including eastern Asia, Europe, North America, Oceania and South America. Sequences were generated from the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) and nuc 28S rDNA D1-D2 domains (28S), and the final dataset included 28 samples of which 21 ITS and 28S sequences were newly generated. As a result of phylogenetic analyses and comparison of morphological features we propose a new classification of the genus recognizing 10 species. Most of the novel taxonomic concepts are geographically restricted in contrast to the past broad species concepts, especially of B. berkeleyi. In addition, a degree of host specificity is observed with B. mesenterica, B. occidentalis, B. podocarpi, B. propria and B. submesenterica apparently restricted to gymnosperms and all others on angiosperm hosts where known. Three new species, B. kirkii, B. occidentalis and B. submesenterica, are described and illustrated. Three new combinations (B. dickinsii, B. propria, B. retipora) are revived from synonymy under B. berkeleyi. A key to known species of Bondarzewia is provided.
Geographic favoritism in liver transplantation--unfortunate or unfair?

Donna Shalala, secretary of the Department of Health and Human Services, recently proposed regulations that would fundamentally change the way in which cadaveric livers for transplantation are allocated in the United States. Currently, livers are distributed first according to geographic region and then according to medical criteria. As a result, patients' chances of living or dying are shaped more by where they live than by how urgently they need a transplant. This system also allows some patients to increase their odds of receiving an organ by listing themselves at more than one transplantation center in different regions, a practice known .
Open Data Commons, a License for Open Data

will remember a wide-ranging discussion of the role that easily accessible data could play in endeavors from scholarly publishing [3] to the creation of canonical product catalogs [4]. The authors argued there and subsequently [5] that an effective and flexible licensing framework is needed in moving forward. Paradoxically, we argue that you need to actively and consciously assert your desire that third parties be able to use data you place online in order for those 'visible' and 'accessible' data sets to be utilized most effectively. Significant progress has been made in the past twelve months, with engagement [6] from Creative Commons [7, 8, 9] and others [10] resulting in a license [11] and notion of 'community norms' [12] upon which all can build.
Molecular Interactions of GBF1 with HY5 and HYH Proteins during Light-mediated Seedling Development in Arabidopsis thaliana*

Background: Light is an important factor for plant growth and development. Results: GBF1 interacts with two other bZIP proteins, HY5 and HYH, in light signaling. Conclusion: This work demonstrates the functional interconnections of GBF1, HY5, and HYH. Significance: The knowledge gained in this study will help to understand light-controlled plant growth and development. Arabidopsis bZIP transcription factor, GBF1, acts as a differential regulator of cryptochrome-mediated blue light signaling. Whereas the bZIP proteins, HY5 (elongated hypocotyl 5) and HYH (HY5 homologue), are degraded by COP1-mediated proteasomal pathways, GBF1 is degraded by a proteasomal pathway independent of COP1. In this study, we have investigated the functional interrelations of GBF1 with HY5 and HYH in Arabidopsis seedling development. The genetic studies using double and triple mutants reveal that GBF1 largely acts antagonistically with HY5 and HYH in Arabidopsis seedling development. Further, GBF1 and HY5 play more important roles than HYH in blue light-mediated photomorphogenic growth. This study reveals that GBF1 is able to form a G-box-binding heterodimer with HY5 but not with HYH. The in vitro and in vivo studies demonstrate that GBF1 co-localizes with HY5 or HYH in the nucleus and physically interacts with both of the proteins. The protein-protein interaction studies further reveal that the bZIP domain of GBF1 is essential and sufficient for the interaction with HY5 or HYH. Taken together, these data demonstrate the functional interrelations of GBF1 with HY5 and HYH in Arabidopsis seedling development.
Study of Challenges in Big Data Analytics and Deep learning Applications

Big Data has become important as many organizations both public and private have been collecting massive amounts of domain-specific information, which can contain useful information about problems such as national intelligence, cyber security, fraud detection, marketing, and medical informatics. Companies such as Google and Microsoft are analyzing large volumes of data for business analysis and decisions, impacting existing and future technology. Big Data Analytics and Deep Learning are two high-focus of data science. Deep Learning algorithms extract highlevel, complex abstractions as data representations through a hierarchical learning process. Complex abstractions are learnt at a given level based on relatively simpler abstractions formulated in the preceding level in the hierarchy. A key benefit of Deep Learning is the analysis and learning of massive amounts of unsupervised data, making it a valuable tool for Big Data Analytics where raw data is largely unlabeled and un-categorized. In the present study, we explore how Deep Learning can be utilized for addressing some important problems in Big Data Analytics, including extracting complex patterns from massive volumes of data, semantic indexing, data tagging, fast information retrieval, and simplifying discriminative tasks. In this paper we study some aspects of Deep Learning research that need further exploration to incorporate specific challenges introduced by Big Data Analytics, including streaming data, high-dimensional data, scalability of models, and distributed computing.
Virtual European School-VES

The Virtual European School (VES) is an ongoing European project-funded by the Educational Multimedia Task Force initiative of the European Union-with the aim to develop a comprehensive online resource of teaching material for secondary school education. The system will be fed by a group of smaller publishing houses from different European countries (Austria, Italy, Greece, Great Britain) specialising in educational material. The offer will contain multimedia material, CBT products, and also additional background materials, such as passages from schoolbooks, or Internet resources. The technical structure of the VES system will be based on Internet technologies, with interconnected VES servers in each participating region. The multimedia material will be stored in a database, with multilingual annotations for each project. There exist three user groups within the VES: publishers, teachers and pupils.
The immediate-early growth response in regenerating liver and insulin-stimulated H-35 cells: comparison with serum-stimulated 3T3 cells and identification of 41 novel immediate-early genes

Liver regeneration provides a unique system for analysis of mitogenesis in intact, fully developed animals. Cellular immediate-early genes likely play an important role in cell cycle regulation and have been extensively studied in mitogen-stimulated fibroblasts lymphocytes but not in liver. We have begun to characterize the immediate-early growth response genes of mitogen-stimulated liver cells, specifically, regenerating liver and insulin-stimulated Reuber H-35 hepatoma cells, and to address differences in growth response between different cell types. Through subtraction and differential screening of cDNA libraries from regenerating liver and insulin-treated H-35 cells, we have extensively characterized 341 differentially expressed clones and identified 52 immediate-early genes. These genes have been partially sequenced and subjected to Northern (RNA) blot analysis, and 41 appear to be novel. Surprisingly, two-thirds of these genes are also expressed in BALB/c 3T3 cells, but only 10 were identified in previous studies of 3T3 cells, and of these, 6 include well-known genes like jun and fos, and only 4 are novel. Approximately one-third of the immediate-early genes identified in mitogen-stimulated liver cells or serum-stimulated NIH 3T3 cells are expressed in a tissue-specific fashion, indicating that cell type-specific regulation of the proliferative response occurs during the immediate-early period. Our findings indicate that the immediate-early response is unusually complex for the first step in a regulatory cascade, suggesting that multiple pathways must be activated. The abundance of immediate-early genes and the highly varied pattern of their expression in different cell types suggest that the tissue specificity of the proliferative response arises from the particular set of these genes expressed in a given tissue.
Personality Traits and Severity of Wife Abuse among Iranian Women

The main purpose of this study was to determine the relationships between personality traits and severity of wife abuse among Iranian women in Tehran city in Iran. The study involved 398 women who sought treatment at 4 selected hospitals by using multistage stratified sampling technique. Conflict Tactic Scale (CTS2) and Five-Factor Personality Inventory (NEO-FFI) were used to measure severity of wife abuse and personality traits respectively.Findings showed that out of 398 women studied, 42.5% received minor abuse and 43.5% received severe abuse. Severity of total wife abuse was positively related to neuroticism personality and negatively related to extraversion, agreeableness and conscientiousness. However, no significant relationship was note for total wife abuse and openness personality. The result of multinomial logistic regression indicated that neuroticism personality trait was a significant predictor of minor and severe total abuse. The results of the current study highlighted the importance of personality traits in explaining the severity of wife abuse in Tehran, Iran. Therefore, strategies to prevent and intervene cases of abuse among wives in Tehran, Iran should take into consideration individual’s personality traits.
The complete mitochondrial genome of the nematophagous fungus Acremonium implicatum

Abstract The complete mitochondrial genome of the nematophagous fungus Acremonium implicatum is reported for the first time. The genome is concatenated with 22,367 bp in length, encoding 13 protein-coding genes, 2 ribosomal RNA genes and a set of 17 transfer RNA genes. The synteny analysis reveals that 50.35% of A. implicatum mitochondrial sequences matched to 48.21% of Acremonium chrysogenum mitochondrial sequences with 85.68% identity. Two proteins of cox3 and nad6, as well as seven tRNAs are lost in A. implicatum mitogenome compared to A. chrysogenum mitogenome. The gene orders in A. implicatum and A. chrysogenum mitogenome is different, which is mainly due to the location of nad4 and cox2. In addition, one transposition event related to tRNAs is identified in these two mitogenomes. This study may provide valuable mitochondrial information for research on A. implicatum and facilitate the study of mitochondrial evolution.
Desorption Electrospray Ionization (DESI) Mass Spectrometric Imaging of Spatially Regulated In Vivo Metabolic Rates

I. ABSTRACT Desorption electrospray ionization (DESI) is an ambient ionization technique used for mass spectrometric imaging of biological samples. When coupled with isotopic ratio measurements of deuterium-labeled tissues, DESI provides a means of measuring metabolic rates on a spatially resolved basis. In vivo metabolic rates are desired to better understand diseases such as Alzheimer’s, Parkinson’s, and Huntington’s and to study the impact of space travel on muscle tissue growth and wasting. Although DESI has been used to image lipids and metabolites of a variety of tissues and other imaging techniques, such as NIMS, have been used to study kinetic turnover rates, DESI has not yet been used to study in vivo metabolic rates using deuterium labeled tissue. This paper describes how we optimized our DESI source for imaging of biological tissue, how we developed a MATLAB graphical user interface (GUI) to process and interpret the large mass spectral data files, and how we conducted our initial mouse brain study for proof-of-concept. Our initial mouse brain study involved labeling mice with deuterium enriched water, preparing tissue slices for DESI analysis, imaging the tissue slices using DESI coupled with a Bruker mass spectrometer, analyzing the mass spectral data using our custom-designed image_inspector program, and creating incorporation curves to measure in vivo metabolic rates.
Towards Effective Representation of Clinical Documents for Search and Retrieval

Recent studies have demonstrated the advantages of structured search of PubMed abstracts when compared with unstructured key word search. We explore whether search on clinical text is similarly enhanced by representing domain specific structures, information, and knowledge. Examples include representations of document structure and sections, local context such as negation, and appropriate modeling of scalar quantities. We examine tasks ranging from recruitment of suitable patients for studies, to chronic disease prevention and management, to longitudinal studies of individual patients or groups, as well as comparative experiments performed on an NLP enhanced clinical search tool that operates on large corpora of clinical text.
Effects of quantum levels on transport through a Coulomb island.

Transport measurements are used to study the quantized energy levels in a small electron gas, referred to as a Coulomb island. First, large-bias measurements reveal the excitation spectrum of the island. Second, small-bias measurements probe the intrinsic line shape of energy levels. Line shapes are generally fit well by thermally broadened Lorentzians. In addition, a decrease in the charging energy of the island is observed as the coupling to its leads is increased. This effect is shown to be consistent with a dramatic increase in one of the island-lead capacitances
Alginate‐coated magnetic nanoparticles for noninvasive MRI of extracellular calcium

Nanoparticles (NPs) have great potential to increase the diagnostic capacity of many imaging modalities. MRI is currently regarded as the method of choice for the imaging of deep tissues, and metal ions, such as calcium ions (Ca2+), are essential ingredients for life. Despite the tremendous importance of Ca2+ for the well‐being of living systems, the noninvasive determination of the changes in Ca2+ levels in general, and extracellular Ca2+ levels in particular, in deep tissues remains a challenge. Here, we describe the preparation and contrast mechanism of a flexible easy to prepare and selective superparamagnetic iron oxide (SPIO) NPs for the noninvasive determination of changes in extracellular Ca2+ levels using conventional MRI. We show that SPIO NPs coated with monodisperse and purified alginate, having a specific molecular weight, provide a tool to selectively determine Ca2+ concentrations in the range of 250 µm to 2.5 mm, even in the presence of competitive ions. The alginate‐coated magnetic NPs (MNPs) aggregate in the presence of Ca2+, which, in turn, affects the T2 relaxation of the water protons in their vicinity. The new alginate‐coated SPIO NP formulations, which have no effect on cell viability for 24 h, allow the detection of Ca2+ levels secreted from ischemic cell cultures and the qualitative examination of the change in extracellular Ca2+ levels in vivo. These results demonstrate that alginate‐coated MNPs can be used, at least qualitatively, as a platform for the noninvasive MRI determination of extracellular Ca2+ levels in myriad in vitro and in vivo biomedical applications. Copyright © 2014 John Wiley & Sons, Ltd.
Glaucomatous Damage Patterns by Short-Wavelength Automated Perimetry (SWAP) in Glaucoma Suspects

Purpose To determine the glaucomatous visual field damage patterns by short-wavelength automated perimetry (SWAP) in glaucoma suspects, and to compare the frequency of diffuse visual field losses and localized defects. Methods 157 eyes of 157 ocular hypertensive subjects who met the selection criteria (intraocular pressure greater than 21 mm Hg and normal standard visual fields) were studied. SWAP was done with a modified Humphrey Field Analyzer. Total (TD) and Pattern Deviation (PD) probability maps were calculated for SWAP. The frequency of abnormlities in the TD and PD were determined, analyzing the visual field loss components. Results The involvement of the test points was more frequent on the TD plots than on the PD plots for all levels of defects (p< 0.001). The glaucomatous defects also showed certain topographical distribution. Conclusions A diffuse sensitivity component of visual field loss was found at all SWAP defect depths in glaucoma suspects.
Self-modeling regression for multivariate curve data

We present self-modeling regression models for flexible nonparametric modeling of multiple outcomes measured longitudinally. Based on penalized regression splines, the models borrow strength across multiple outcomes by specifying a global time profile, thereby yielding a means of dimension reduction and estimates of trend more precise than those based on univariate regressions. The proposed models represent nonparametric regression extensions to existing factor analytic models for a multivariate response recorded at a single timepoint, and are easily generalized to incorporate serial correlation above that captured by nonlinear effects over time. We illustrate the methods by applying them to data on the respiratory effects of residual oil fly ash inhalation in humans.
Sociomics! Using the IssueCrawler to map, monitor and engage with the global proteomics research network

We invite comment upon an experiment to locate proteomics on the WWW using a software tool called the IssueCrawler. We call our research “sociomics” because, like the bioscience omics, it is a semi‐automated, computerised approach to the global analysis of data, whose computerised results can be integrated towards the development of a new “systems sociology” approach to the study of society. Our findings are that proteomics on the web is a scale‐free network whose nodes display considerable “dynamic range”.