gebhart/patrepeval huggingface dataset:
Structure and regulation of expression of the Bacillus subtilis valyl-tRNA synthetase gene (1997)

We have sequenced the valyl-tRNA synthetase gene (valS) of Bacillus subtilis and found an open reading frame coding for a protein of 880 amino acids with a molar mass of 101,749. The predicted amino acid sequence shares strong similarity with the valyl-tRNA synthetases from Bacillus stearothermophilus, Lactobacillus casei, and Escherichia coli. Extracts of B. subtilis strains overexpressing the valS gene on a plasmid have increased valyl-tRNA aminoacylation activity. Northern analysis shows that valS is cotranscribed with the folC gene (encoding folyl-polyglutamate synthetase) lying downstream. The 300-bp 5' noncoding region of the gene contains the characteristic regulatory elements, T box, "specifier codon" (GUC), and rho-independant transcription terminator of a gene family in gram-positive bacteria that encodes many aminoacyl-tRNA synthetases and some amino acid biosynthetic enzymes and that is regulated by tRNA-mediated antitermination. We have shown that valS expression is induced by valine limitation and that the specificity of induction can be switched to threonine by changing the GUC (Val) specifier triplet to ACC (Thr). Overexpression of valS from a recombinant plasmid leads to autorepression of a valS-lacZ transcriptional fusion. Like induction by valine starvation, autoregulation of valS depends on the presence of the GUC specifier codon. Disruption of the valS gene was not lethal, suggesting the existence of a second gene, as is the case for both the thrS and the tyrS genes.
Adhesion of multiple myeloma peripheral blood B cells to bone marrow fibroblasts: a requirement for CD44 and alpha4beta7. (1997)

We have earlier described the presence of phenotypically unusual monoclonal B cells within the peripheral blood of multiple myeloma (MM) patients. To determine the biological properties of these B cells as compared to B cells from normal donors, we investigated the potential of CD19+ MM blood B cells to adhere to endothelial cell and bone marrow (BM)-fibroblast monolayers. We find that 30-60% of freshly isolated CD19+ MM blood B cells adhere to endothelial cell monolayers, and 50-80% adhere to BM fibroblast monolayers. The adhesion of MM blood B cells to either monolayer was not increased by in vitro activation, suggesting that these cells were activated in vivo. In contrast, fewer than 10% of CD19+ B cells from peripheral blood of normal donors adhered. Function-blocking monoclonal antibodies (mAbs) were used to determine which adhesion receptors were involved in CD19+ MM blood B cell interaction with BM fibroblasts. mAbs against very late antigen 4, the beta7-integrin subunit, and CD44, but not mAbs against very late antigen 5 and beta1, inhibited adhesion 61, 50, and 30%, respectively. The lack of inhibition with mAbs against beta1 implicates alpha4beta7 but not alpha4beta1 in adhesion of CD19+ MM blood B cells. To determine the alpha4beta7 ligand that mediated MM blood B cell adhesion, mAbs against vascular cellular adhesion molecule 1 and fibronectin, as well as CS1 and RGD peptides, were used as inhibitors. These were unable to reduce the adhesion of CD19+ MM blood B cells to BM fibroblasts, suggesting that fibronectin and vascular cellular adhesion molecule 1 are not involved in adhesion. Also, adhesion of MM blood B cells to mucosal addressin cell adhesion molecule 1-transfected Chinese hamster ovary cells was not enhanced compared to control-transfected Chinese hamster ovary cells, suggesting that mucosal addressin cell adhesion molecule 1 was not promoting adhesion of these cells. These data implicate CD44:HA interactions, as well as alpha4beta7 and an as yet unidentified ligand in the adhesion of in vivo activated MM blood B cell adhesion to BM fibroblasts. The adhesion properties of MM CD19+ B cells distinguishes them from normal B cells. Although the malignant status of these cells is as yet undefined, their adhesion properties implicate MM blood B cells in migratory spread of the disease.
In vivo three-dimensional photoacoustic imaging of the renal vasculature in preclinical rodent models (2018)

Noninvasive imaging of the kidney vasculature in preclinical murine models is important for the assessment of renal development, studying diseases and evaluating new therapies but is challenging to achieve using existing imaging modalities. Photoacoustic imaging is a promising new technique that is particularly well suited to visualizing the vasculature and could provide an alternative to existing preclinical imaging methods for studying renal vascular anatomy and function. To investigate this, an all-optical Fabry-Perot-based photoacoustic scanner was used to image the abdominal region of mice. High-resolution three-dimensional, noninvasive, label-free photoacoustic images of the mouse kidney and renal vasculature were acquired in vivo. The scanner was also used to visualize and quantify differences in the vascular architecture of the kidney in vivo due to polycystic kidney disease. This study suggests that photoacoustic imaging could be utilized as a novel preclinical imaging tool for studying the biology of renal disease.
Antibody to selected strains of Saccharomyces cerevisiae (baker's and brewer's yeast) and Candida albicans in Crohn's disease. (1990)

IgG serum antibody was measured by ELISA in patients with Crohn's disease (15), ulcerative colitis (15), and in normal controls (15) to 12 strains of Saccharomyces cerevisiae (baker's and brewer's yeast) and to the two major serotypes of the commensal yeast Candida albicans. Antibody to 11 of the 12 strains of S cerevisiae was raised in patients with Crohn's disease but not in patients with ulcerative colitis when compared with controls (p less than 0.001). The pattern of antibody response to these 11 strains was variable, however, suggesting the likelihood of antigenic heterogeneity within the species. Antibody to C albicans was not significantly different in patient and control groups. The specificity of this unusual antibody response in Crohn's disease for S cerevisiae suggests that it is not simply the result of a generalised increase in intestinal permeability. Furthermore, because brewing and baking strains detected the response, the relevant antigen(s) are presumably common in the diet. Hypersensitivity to dietary antigens may be involved in the pathogenesis of Crohn's disease, and the role of S cerevisiae requires further investigation.
Underwater Image Enhancement by Wavelength Compensation and Dehazing (2011)

Light scattering and color change are two major sources of distortion for underwater photography. Light scattering is caused by light incident on objects reflected and deflected multiple times by particles present in the water before reaching the camera. This in turn lowers the visibility and contrast of the image captured. Color change corresponds to the varying degrees of attenuation encountered by light traveling in the water with different wavelengths, rendering ambient underwater environments dominated by a bluish tone. No existing underwater processing techniques can handle light scattering and color change distortions suffered by underwater images, and the possible presence of artificial lighting simultaneously. This paper proposes a novel systematic approach to enhance underwater images by a dehazing algorithm, to compensate the attenuation discrepancy along the propagation path, and to take the influence of the possible presence of an artifical light source into consideration. Once the depth map, i.e., distances between the objects and the camera, is estimated, the foreground and background within a scene are segmented. The light intensities of foreground and background are compared to determine whether an artificial light source is employed during the image capturing process. After compensating the effect of artifical light, the haze phenomenon and discrepancy in wavelength attenuation along the underwater propagation path to camera are corrected. Next, the water depth in the image scene is estimated according to the residual energy ratios of different color channels existing in the background light. Based on the amount of attenuation corresponding to each light wavelength, color change compensation is conducted to restore color balance. The performance of the proposed algorithm for wavelength compensation and image dehazing (WCID) is evaluated both objectively and subjectively by utilizing ground-truth color patches and video downloaded from the Youtube website. Both results demonstrate that images with significantly enhanced visibility and superior color fidelity are obtained by the WCID proposed.
Psychological health in central hypersomnias: the French Harmony study (2009)

Our data confirmed the high frequency of depressive symptoms and the major impact of central hypersomnias on health related quality of life, especially in patients with cataplexy. We recommend a more thorough assessment of mood impairment in central hypersomnias, especially in narcolepsy-cataplexy.
Contribution of Hepatic Lipase, Lipoprotein Lipase, and Cholesteryl Ester Transfer Protein to LDL and HDL Heterogeneity in Healthy Women (2002)

Hepatic lipase (HL) and cholesteryl ester transfer protein (CETP) have been independently associated with low density lipoprotein (LDL) and high density lipoprotein (HDL) size in different cohorts. These studies have been conducted mainly in men and in subjects with dyslipidemia. Ours is a comprehensive study of the proposed biochemical determinants (lipoprotein lipase, HL, CETP, and triglycerides) and genetic determinants (HL gene [LIPC] and Taq1B) of small dense LDL (sdLDL) and HDL subspecies in a large cohort of 120 normolipidemic, nondiabetic, premenopausal women. HL (P<0.001) and lipoprotein lipase activities (P=0.006) were independently associated with LDL buoyancy, whereas CETP (P=0.76) and triglycerides (P=0.06) were not. The women with more sdLDL had higher HL activity (P=0.007), lower HDL2 cholesterol (P<0.001), and lower frequency of the HL (LIPC) T allele (P=0.034) than did the women with buoyant LDL. The LIPC variant was associated with HL activity (P<0.001), HDL2 cholesterol (P=0.034), and LDL buoyancy (P=0.03), whereas the Taq1B polymorphism in the CETP gene was associated with CETP mass (P=0.002) and HDL3 cholesterol (P=0.039). These results suggest that HL activity and HL gene promoter polymorphism play a significant role in determining LDL and HDL heterogeneity in healthy women without hypertriglyceridemia. Thus, HL is an important determinant of sdLDL and HDL2 cholesterol in normal physiological states as well as in the pathogenesis of various disease processes.
Pvclust: an R package for assessing the uncertainty in hierarchical clustering (2006)

Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap analysis of clustering, which has been popular in phylogenetic analysis. Pvclust calculates probability values (p-values) for each cluster using bootstrap resampling techniques. Two types of p-values are available: approximately unbiased (AU) p-value and bootstrap probability (BP) value. Multiscale bootstrap resampling is used for the calculation of AU p-value, which has superiority in bias over BP value calculated by the ordinary bootstrap resampling. In addition the computation time can be enormously decreased with parallel computing option.
Neuregulin‐1 polymorphism in late onset Alzheimer's disease families with psychoses (2005)

Probands with late onset Alzheimer's disease (LOAD) exhibit positive symptoms of psychosis, 30-60% of the time. Positive symptoms of psychosis have been shown to appear prior to the onset of dementia to be accompanied by greater cognitive deficits, and to predict a more rapid decline. A study of the distribution of AD with psychosis (ADP) in families from the NIMH Alzheimer's Disease Genetic Initiative sample indicates that the trait is heritable, and linkage studies of multiplex ADP families have found suggestive peaks on 2p, 6q, 8p, and 21q. A genome scan of idiopathic psychosis, schizophrenia, in the Icelandic population identified a risk haplotype within the 5' region of neuregulin-1 (NRG1) on 8p12. Associations with NRG1 SNPs have also been found in other schizophrenia populations from Scotland, Ireland, and China. Here, we report results demonstrating a significant linkage peak for ADP on 8p12 in the NIMH AD dataset, encompassing the NRG1 region. We also demonstrate that there is a significant association with a NRG1 SNP (single nucleotide polymorphism), rs392499, with ADP, chi2 = 7.0, P = 0.008. This same SNP is part of a 3-SNP haplotype preferentially transmitted to individuals with this phenotype. Our results suggest that NRG1 plays a role in increasing the genetic risk to positive symptoms of psychosis in a proportion of LOAD families.
CRISPR-Cas9 and CRISPR-Assisted Cytidine Deaminase Enable Precise and Efficient Genome Editing in Klebsiella pneumoniae (2018)

<i>Klebsiella pneumoniae</i> is a promising industrial microorganism as well as a major human pathogen. The recent emergence of carbapenem-resistant <i>K. pneumoniae</i> has posed a serious threat to public health worldwide, emphasizing a dire need for novel therapeutic means against drug-resistant <i>K. pneumoniae</i> Despite the critical importance of genetics in bioengineering, physiology studies, and therapeutic-means development, genome editing, in particular, the highly desirable scarless genetic manipulation in <i>K. pneumoniae</i>, is often time-consuming and laborious. Here, we report a two-plasmid system, pCasKP-pSGKP, used for precise and iterative genome editing in <i>K. pneumoniae</i> By harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 genome cleavage system and the lambda Red recombination system, pCasKP-pSGKP enabled highly efficient genome editing in <i>K. pneumoniae</i> using a short repair template. Moreover, we developed a cytidine base-editing system, pBECKP, for precise C→T conversion in both the chromosomal and plasmid-borne genes by engineering the fusion of the cytidine deaminase APOBEC1 and a Cas9 nickase. By using both the pCasKP-pSGKP and the pBECKP tools, the <i>bla</i><sub>KPC-2</sub> gene was confirmed to be the major factor that contributed to the carbapenem resistance of a hypermucoviscous carbapenem-resistant <i>K. pneumoniae</i> strain. The development of the two editing tools will significantly facilitate the genetic engineering of <i>K. pneumoniae</i><b>IMPORTANCE</b> Genetics is a key means to study bacterial physiology. However, the highly desirable scarless genetic manipulation is often time-consuming and laborious for the major human pathogen <i>K. pneumoniae</i> We developed a CRISPR-Cas9-mediated genome-editing method and a cytidine base-editing system, enabling rapid, highly efficient, and iterative genome editing in both industrial and clinically isolated <i>K. pneumoniae</i> strains. We applied both tools in dissecting the drug resistance mechanism of a hypermucoviscous carbapenem-resistant <i>K. pneumoniae</i> strain, elucidating that the <i>bla</i><sub>KPC-2</sub> gene was the major factor that contributed to the carbapenem resistance of the hypermucoviscous carbapenem-resistant <i>K. pneumoniae</i> strain. Utilization of the two tools will dramatically accelerate a wide variety of investigations in diverse <i>K. pneumoniae</i> strains and relevant <i>Enterobacteriaceae</i> species, such as gene characterization, drug discovery, and metabolic engineering.
The wnt-frizzled cascade in cardiovascular disease (2002)

Time for primary review 31 days. 

Wnt-proteins constitute a family of secreted cystein-rich glycosylated proteins, involved in a variety of modeling and remodeling processes including cell proliferation, differentiation, apoptosis and the control of cell orientation [1–3]. Malfunctioning of the wnt-frizzled pathway has been implied in diseases as divergent as cancer and Alzheimer's disease [1,4]. The wnt-frizzled signal transduction pathway plays an important role during non-vertebrate and vertebrate development [5]. Several studies have shown the importance of wnts in the control of processes such as patterning of the body axis and development of the central nervous system and the limbs [6,7]. Moreover, interventions in wnt signaling have been described to affect cardiac morphogenesis [8,9] and several members of the wnt-frizzled signal transduction pathway were found to be expressed during cardiac development in vertebrates [10–14].

In cardiovascular pathology, re-expression of a fetal gene expression pattern is a generally observed phenomenon [15]. The study of gene expression during development may therefore provide clues about the expression profile during cardiovascular pathology. Recently, considerable progress has been made concerning the role of the wnt-frizzled signal transduction pathway in the development and progression of cardiovascular pathology. This review will focus on the possible role of the wnt-frizzled signal transduction pathway in cardiovascular diseases.

The family of wnt proteins consists of 16 members [5]. These proteins are extremely difficult to purify because they tend to bind to the extracellular matrix [16], which hampers the study of their characteristics. An overview of the wnt proteins and their proposed function during development, derived from the study of null mutants, is provided in Table 1. Based on functional differences, wnt proteins can be divided into two classes, the wnt1 class and the wnt5a class. Members of the wnt1 class are able … 

* Corresponding author. Tel.: +31-43-388-1417; fax: +31-43-388-4149 wm.blankesteijn{at}farmaco.unimaas.nl
Vaccinia Virus Expression Vectors (1986)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Data Warehousing, Data Mining, and OLAP (1997)

Renal sympathetic denervation (RSD) is a new method for the treatment of resistant hypertension (RH). However, few studies have focused on the effects of RSD on blood flow and the interaction between temperature field and flow field. In this paper, firstly, we designed a numerical simulation of electromagnetic field, flow field and temperature field coupling by finite element method. Secondly, numerical simulation results were verified by particle image velocimetry (PIV) and vitro experiment. From the simulation results, when the flow velocity increases to 0.05 m/s, the turbulence near the electrode disappeared and flow state became uniform laminar flow. With the increases of flow velocity (0 m/s to 0.1 m/s), temperature rise of the renal artery, the electrode tip and blood decreased from 13°C, 24°C and 5.4°C to 9.3°C, 9.7°C and 0.2°C, respectively. From PIV experiment and vitro experiment results, when the flow rate increases to 0.5 L/min, it appeared similar phenomenon with the velocity of 0.05 m/s in simulation. With the increases of flow rate (0 L/min to 0.8 L/min), temperature rise of three points decreased from 11.2°C, 20.5°C and 3.6°C to 7.8°C, 8.5°C, and 0.4°C, respectively. When the blood flow rate exceeds 0.5 L/min, there is no large velocity gradient and reflux area in the flow field, so there will be no hemolysis and thrombosis. Therefore, the temperature field has less influence on the flow field. With the increase of flow rate, the temperature at all three points decreases. Therefore, the flow field has an effect on the temperature field. But the central temperature of renal artery can still reach the treatment target in which temperature rises to be more than 6°C. Therefore, this study preliminarily verified the safety and effectiveness of RSD.
Utility-connected power converter for maximizing power transfer from a photovoltaic source while drawing ripple-free current (2003)

This paper presents a power converter for coupling photovoltaic arrays to the utility grid. The converter draws a programmable, ripple-free DC current from the photovoltaic array and injects power into the grid at unity power factor. The programmable input current feature makes this converter ideal for use with maximum power point tracking technology. The proposed converter has an additional unique feature in that the internal dc link carries a large (approximately 25%) ripple voltage. Allowing a large ripple on the DC link reduces the required size of the link capacitor. This paper includes basic system information, analysis of filter requirements, controller design and preliminary hardware results.
Listeria-based vaccines can overcome tolerance by expanding low avidity CD8+ T cells capable of eradicating a solid tumor in a transgenic mouse model of cancer. (2007)

We have created a transgenic mouse with tissue-specific expression of the human papilloma virus (HPV) 16 E6 and E7 oncoproteins in the thyroid as a model of HPV transformed cancer. The expression of the transgenes results in the formation of palpable thyroid tumors. E7 is not expressed in other tissues but is expressed in medullary thymic epithelial cells, which have been implicated in the control of negative selection. We show that Listeria-based vaccines against E7 can induce the regression of solid implanted tumors in the transgenic mice, although at a lower frequency than in wild type (WT) mice. E7-specific CD8+ T cells induced in transgenic mice are of both lower avidity and lower frequency when compared to the WT mice. In this model, Listeria-based vaccines against E7 appear to be overcoming central tolerance by expanding low avidity CD8+ T cells specific for E7 that are not deleted during thymopoesis and can eliminate solid tumors.
Synthesis of deuterium-labelled elliptinium and its use in metabolic studies (1988)

The 9-hydroxy-2-(U-2H3) methylellipticinium acetate (elliptinium) was synthesized with an isotopic purity of at least 96%. The structure was confirmed by proton nuclear magnetic resonance and direct probe fast atom bombardment mass spectrometry. A mixture of elliptinium and its deuterated analogue was administered intravenously to rats. In urine, after analysis by liquid chromatography/mass spectrometry (LC/MS), unchanged drug and N-acetylcysteinylelliptinium were found. In bile, after ion-pair extraction and LC/MS, the glutathionylelliptinium was found in addition to the parent drug and the N-acetylcysteine adduct.