gebhart/patrepeval huggingface dataset:
Separation of Mycobacterium bovis BCG from Mycobacterium tuberculosis and Mycobacterium bovis by using high-performance liquid chromatography of mycolic acids (1992)

Profile analysis of mycolic acid ester patterns of Mycobacterium tuberculosis, Mycobacterium bovis, and Mycobacterium bovis bacillus Calmette-Gúerin (BCG) using high-performance liquid chromatography indicated that separation of BCG from M. tuberculosis and M. bovis by elution and relative retention times is possible. Mycolic acid patterns of BCG eluted from the column 0.5 min before M. tuberculosis or M. bovis, resulting in relative retention times for two peaks not seen in the pattern of M. tuberculosis or M. bovis. Identification was confirmed by phage typing, which has been the standard procedure for confirmation of BCG strains. These results showed that high-performance liquid chromatographic analysis of mycolic acid esters can be used in the mycobacterial reference laboratory for separation of BCG from M. tuberculosis and M. bovis.
The effects of microenvironment and internal programming on plasma cell survival (2007)

Two populations of plasma cells (PCs) are formed after immunization. A short-lived population in the spleen and lymph nodes provides rapid protection. A long-lived population, mainly in the bone marrow, provides lasting immunity. The mechanisms responsible for the differences in PCs life span remain largely unknown. The goal of the current study was to compare the intrinsic survival capacity of isolated short-lived (spleen) versus long-lived (bone marrow) PCs. We approached this question by using a previously established in vitro model that measures PC survival in a supportive stromal environment. Regardless of the tissue source or isolation time point after immunization, the two PC populations showed similar intrinsic ability to survive in vitro. To test differences in the stromal microenvironments, stromal cells from marrow, spleen or lymph nodes were evaluated for ability to support PCs survival. Survival of isolated PC was always greater when co-cultured with marrow stromal cells compared with those from spleen (or lymph node) despite the finding that IL-6, necessary for PC survival in culture, was secreted by all three stromal cell sources. Additionally, low expression of B-cell-activating factor belonging to the tumor necrosis factor-family was detected in all three stromal isolates. In contrast, marrow stromal cells were distinguished by cell-surface phenotype and CXC chemokine ligand (CXCL)12, IL-7 and stem cell factor expression. Although CXCL12 has been suggested as a possible survival factor for PC, addition or neutralization of CXCL12 had minimal effect on PC survival. We conclude the mechanisms regulating PC longevity appear extrinsically driven and marrow favored, but the factors that give marrow stromal cells a unique advantage remain unknown.
<title>Depth-map-based scene analysis for active navigation</title> (1999)

Three dimensional volume data sets provided by CT or MRI allow the user to move virtually around within anatomic structure and to observe them. We propose a new method to guide the path planning based on the local image interpretation during the navigation inside the anatomic structures with cavities, without preprocessing for 3D volume data sets. Thanks to the scene analysis process, the virtual sensor constructs by itself a model of the unknown scene. Qualitative and quantitative characterization of the anatomic structures, derived from this exploration, is of main interest in such a new application of virtual endoscopy that is vascular surgery. In this paper we especially describe the scene analysis process which is based on the processing of the depth map directly produced by the ray casting procedure. Application to vascular surgery, i.e. virtual angioscopy, is then depicted.
Blau Syndrome, the prototypic auto-inflammatory granulomatous disease (2014)

Blau syndrome is a monogenic disease resulting from mutations in the pattern recognition receptor NOD2, and is phenotypically characterized by the triad of granulomatous polyarthritis, dermatitis and uveitis. This paper reviews briefly the classical clinical features of the disease, as well as more recently described extra-triad symptoms. From an ongoing prospective multicenter study, we provide new data on the natural history of Blau syndrome, focusing on functional status and visual outcome. We also present an update of the range of different NOD2 mutations found in Blau syndrome as well as recent data on morphologic and immunohistochemical characteristics of the Blau granuloma. Finally, emerging insights into pathogenic mechanisms including activation of NOD2 signal transduction, and potential biomarkers of disease activity are discussed.
Mitochondria, calcium, and endoplasmic reticulum stress in Parkinson's disease (2011)

Parkinson's disease (PD) is a progressive neurodegenerative disease characterized by a loss of dopaminergic neurons in the substantia nigra pars compacta (SNPC) and the presence of intracytoplasmatic inclusions known as Lewy bodies, largely composed of alpha-synuclein (α-syn). PD is a multifactorial disease and its etiology remains largely elusive. Although more than 90% of the cases are sporadic, mutations in several nuclear encoded genes have been linked to the development of autosomal recessive and dominant familial parkinsonian syndromes (Bogaerts et al. (2008) Genes Brain Behav 7, 129-151), enhancing our understanding of biochemical and cellular mechanisms contributing to the disease. Many cellular mechanisms are thought to be involved in the dopaminergic neuronal death in PD, including oxidative stress, intracellular Ca(2+) homeostasis impairment, and mitochondrial dysfunctions. Furthermore, endoplasmic reticulum (ER) stress together with abnormal protein degradation by the ubiquitin proteasome system is considered to contribute to the PD pathogenesis. This review covers all the aspects related to the molecular mechanisms underlying the interplay between mitochondria, ER, and proteasome system in PD-associated neurodegeneration.
Lineage analysis of the avian dermomyotome sheet reveals the existence of single cells with both dermal and muscle progenitor fates (2005)

The dermomyotome develops into myotome and dermis. We previously showed that overall growth of the dermomyotome and myotome in the mediolateral direction occurs in a uniform pattern. While myofibers arise from all four dermomyotome lips, the dermis derives from both medial and lateral halves of the dermomyotome sheet. Here we mapped the fate of this epithelial sheet by analyzing cell types that arise from its central region. We found that these precursors give rise not only to dermis, as expected, but also to a population of proliferating progenitors in the myotome that maintain expression of PAX7, PAX3 and FREK. Given this dual fate, we asked whether single dermomyotome precursors generate both dermal and mitotic myoblast precursors, or alternatively, whether these cell types derive from distinct epithelial founders. Inovo clonal analysis revealed that single dermomyotome progenitors give rise to both derivatives. This is associated with a sharp change in the plane of cell division from the young epithelium, in which symmetrical divisions occur parallel to the mediolateral plane of the dermomyotome, to the dissociating dermomyotome, in which cell divisions become mostly perpendicular. Taken together with clonal analysis of the dermomyotome sheet, this suggests that a first stage of progenitor self-renewal, accounting for dermomyotomal expansion, is followed by fate segregation, which correlates with the observed shift in mitotic spindle orientation.
Constraint solving for direct manipulation of features (2006)

In current commercial feature modeling systems, support for direct manipulation of features is not commonly available. This is partly due to the strong reliance of such systems on constraints, but also to the lack of speed of current constraint solvers. In this paper, an approach to the optimization of geometric constraint solving for direct manipulation of feature dimensions, orientation, and position is described. Details are provided on how this approach was successfully implemented in the S piff feature modeling system.
Mutations within the Primer Grip Region of HIV-1 Reverse Transcriptase Result in Loss of RNase H Function (1997)

Human immunodeficiency virus (HIV) DNA synthesis is accompanied by degradation of genomic RNA by the RNase H of reverse transcriptase (RT). Two different modes of RNase H activity appear necessary for complete RNA removal. In one, occurring during minus strand synthesis, positioning of the RNase H is determined by binding of the polymerase active site to the DNA 3'-end. In the other, used for removal of remaining RNA fragments, positioning of RT for RNase H-directed cleavage is determined by the RNA 5'-ends. We attempted to identify RT amino acids responsible for these modes of positioning. Twelve RT mutants, each with one alanine replacement in residues 224 to 235, known as the primer grip region, were examined for catalytic abilities. Six of the examined primer grip mutants, although distant from the RNase H active site were altered in their ability to cleave RNA. The mutants P226A, F227A, G231A, Y232A, E233A, and H235A failed to perform RNA 5'-end-directed RNase H cleavage in heparin-challenged reactions. The last four mutants also lacked DNA synthesis and DNA 3'-end-directed RNase H cleavage activities in challenged reactions. Since mutants P226A and F227A carried out these latter reactions normally, these two residues specifically influence 5'-RNA-directed RNase H catalysis.
Compact Modeling of Perpendicular-Anisotropy CoFeB/MgO Magnetic Tunnel Junctions (2012)

Magnetic tunnel junctions (MTJs) composed of ferromagnetic layers with perpendicular magnetic anisotropy (PMA) are of great interest for achieving high-density nonvolatile memory and logic chips owing to its scalability potential together with high thermal stability. Recent progress has demonstrated a capacity for high-speed performance and low power consumption through current-induced magnetization switching. In this paper, we present a compact model of the CoFeB/MgO PMA MTJ, a system exhibiting the best tunnel magnetoresistance ratio and switching performance. It integrates the physical models of static, dynamic, and stochastic behaviors; many experimental parameters are directly included to improve the agreement of simulation with experimental measurements. Mixed simulation based on the 65-nm technology node of a magnetic flip-flop validates its relevance and efficiency for MTJ/CMOS memory and logic chip design.
In Vitro and In Vivo Evaluation of Microparticulate Drug Delivery Systems Composed of Macromolecular Prodrugs (2008)

Macromolecular prodrugs are very useful systems for achieving controlled drug release and drug targeting. In particular, various macromolecule-antitumor drug conjugates enhance the effectiveness and improve the toxic side effects. Also, polymeric micro- and nanoparticles have been actively examined and their in vivo behaviors elucidated, and it has been realized that their particle characteristics are very useful to control drug behavior. Recently, researches based on the combination of the concepts of macromolecular prodrugs and micro- or nanoparticles have been reported, although they are limited. Macromolecular prodrugs enable drugs to be released at a certain controlled release rate based on the features of the macromolecule-drug linkage. Micro- and nanoparticles can control in vivo behavior based on their size, surface charge and surface structure. These merits are expected for systems produced by the combination of each concept. In this review, several micro- or nanoparticles composed of macromolecule-drug conjugates are described for their preparation, in vitro properties and/or in vivo behavior.
Thrice Out of Africa: Ancient and Recent Expansions of the Honey Bee, Apis mellifera (2006)

We characterized Apis mellifera in both native and introduced ranges using 1136 single-nucleotide polymorphisms genotyped in 341 individuals. Our results indicate that A. mellifera originated in Africa and expanded into Eurasia at least twice, resulting in populations in eastern and western Europe that are geographically close but genetically distant. A third expansion in the New World has involved the near-replacement of previously introduced "European" honey bees by descendants of more recently introduced A. m. scutellata ("African" or "killer" bees). Our analyses of spatial transects and temporal series in the New World revealed differential replacement of alleles derived from eastern versus western Europe, with admixture evident in all individuals.
Mesodermal fate decisions of a stem cell: the Wnt switch (2008)

Stem cells are a powerful resource for cell-based transplantation therapies in osteodegenerative disorders, but before some kinds of stem cells can be applied clinically, several aspects of their expansion and differentiation need to be better controlled. Wnt molecules and members of the Wnt signaling cascade have been ascribed a role in both these processes in vitro as well as normal development in vivo. However some results are controversial. In this review we will present the hypothesis that both canonical and non-canonical signaling are involved in mesenchymal cell fate regulation, such as adipogenesis, chondrogenesis and osteogenesis, and that in vitro it is a timely switch between the two that specifies the identity of the differentiating cell. We will specifically focus on the in vitro differentiation of adipocytes, chondrocytes and osteoblasts contrasting embryonic and mesenchymal stem cells as well as the role of Wnts in mesenchymal fate specification during embryogenesis.
Modification of the amino acid specificity of tyrosyl‐tRNA synthetase by protein engineering (1993)

The amino acid specificity of Bacillus stearothermophilus tyrosyl-tRNA synthetase was studied by site-directed mutagenesis of residues close to the active site. X-ray crystallographic studies of the enzyme have suggested that Asp-176 is a major determinant of amino acid specificity, as its carboxylate is observed to make a hydrogen bond with the hydroxyl group of the substrate tyrosine. Previous efforts to test the importance of Asp-176 by site-directed mutagenesis led to inactive enzymes. We have now investigated the catalytic properties of enzymes altered, not at Asp-176 itself, but instead at two amino acids, Asn-123 and Trp-126, that appear in the crystallographic structure to form hydrogen bonds with Asp-176. Mutation of Trp-126 does not affect the kinetics of activation with respect to ATP but leads to modest increases in the Km for tyrosine. Conversely, position Asn-123 mutants are strongly affected: 160-fold lower kcat and 5-fold higher Km for the Ala-123; and 17-fold decrease and 270-fold increase, respectively, of the same parameters for the Asp-123 mutation. The specificity against phenylalanine was determined from the ratios of kcat/Km for the amino acids in the pyrophosphate exchange reaction. The ratio of 1.2 x 10(5) for the wild-type enzyme decreases 4-fold on mutation of Asn-123 but increases 7-fold on the mutation of Trp-126-->Phe and 2-fold on Trp-126-->Leu. The wild-type enzyme has not reached the maximum limit of discrimination between tyrosine and phenylalanine.
Personal telephone services using IC-cards (1989)

An IC-card is a memory card that can be substituted for existing magnetic-striped cards. It is suggested that the IC-card, which can store various information for telephone calls, will become a useful device in multifunction telephone sets because of its portability, security, and large memory capacity. The information that should be stored on an IC-card is discussed, and the practicality of creating personal telephone services by combining telephone services with the stored user information is addressed. An experimental telephone set with an IC-card reader/writer developed to verify feasibility is presented. Service grades of IC-cards, according to their level of functionality versus the functionality of the terminal equipment, are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High-Q Optical Sensors for Chemical and Biological Analysis (2011)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTHigh-Q Optical Sensors for Chemical and Biological AnalysisMatthew S. Luchansky and Ryan C. Bailey*View Author Information Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States*E-mail: [email protected]. Address: 44 Roger Adams Lab 600 South Mathews Avenue, Urbana, IL, 61801. Phone: (217) 333-0676.Cite this: Anal. Chem. 2012, 84, 2, 793–821Publication Date (Web):November 23, 2011Publication History Published online23 November 2011Published inissue 17 January 2012https://pubs.acs.org/doi/10.1021/ac2029024https://doi.org/10.1021/ac2029024review-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views6236Altmetric-Citations223LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Assays,Crystals,Nanoparticles,Quantum mechanics,Sensors Get e-Alerts
Structure and function studies of glucagon‐like peptide‐1 (GLP‐1): the designing of a novel pharmacological agent for the treatment of diabetes (2005)

Glucagon-like peptide-1 (GLP-1) is a proglucagon-derived peptide secreted from gut endocrine cells in response to nutrient ingestion. The multifaceted actions of GLP-1 include the following: (1) the stimulation of insulin secretion and of its gene expression, (2) the inhibition of glucagon secretion, (3) the inhibition of food intake, (4) the proliferation and differentiation of beta cells, and (5) the protection of beta-cells from apoptosis. The therapeutic utility of the native GLP-1 molecule is limited by its rapid enzymatic degradation by a serine protease termed dipeptidyl peptidase-IV (DPP-IV). The present article reviews the research studies aimed at elucidating the biosynthesis, metabolism, and molecular characteristics of GLP-1 since it is from these studies that the development of a GLP-1-like pharmacological agent may be derived.
The Chromogranin–Secretogranin Family (2003)

The members of the chromogranin–secretogranin family of peptide hormones, biogenic amines, and neurotransmitters are enclosed within vesicles in the neuroendocrine system and a variety of neurons. These granins, the chief of which is chromogranin A, participate in sympathoadrenal activity and serve as markers of neuroendocrine tumors, especially pheochromocytoma.
Towards a periodic table of visualization methods of management (2007)

In this paper, we describe the effort of defining and compiling existing visualization methods in order to develop a systematic overview based on the logic, look, and use of the periodic table of elements. We first describe the current fragmented state of the visualization field. Then we outline the rules and criteria we applied in conducting our research in order to present a revised periodic table of 100 visualization methods with a proposition how to use it. KEY WORDS knowledge visualization, knowledge visualization methods, periodic table, problem solving, classification, selection framework, visualisation types 1 The Realm of Visualization Methods The discipline of visualization studies is an emergent one and as such represents a so far still highly unstructured domain of research that includes scholars from such distant domains as human-computer interaction, graphic design, management, or architecture. Thus, there are many parallel, unconnected streams and development activities in this field that may move forward without mutually acknowledging or integrating efforts under way elsewhere. In order to contribute to the consolidation of these efforts and to the emergence of a distinct field that achieves cumulative research progress this article proposes an integrative overview on one aspect of the visualization field, namely the development of easily applicable visualization methods, that is to say systematic graphic formats, that can be used to create, share, or codify knowledge (in the sense of insights, experiences, contacts, or skills). In this paper, we present a simple structure, inspired by the use, look, and logic of the periodic table of elements developed in the domain of chemistry. There are numerous benefits that can be achieved through such a structure: First, it can provide a descriptive overview over the domain [1, p. 12] and can function as an inventory or repository like a structured toolbox. In this
구조물의 손상평가를 위한 인공신경망의 특성평가 (2009)

If you receive a damaged structure that will change the dynamic characteristics of structures. The dynamic nature of these structural changes for the structure damaged by using an artificial neural network to identify the location and size were. In this paper, an artificial neural network training and validation for the same damage as a change of load when using the given input for damage assessment have seen a good looking magazine. Artificial neural networks for learning, and qualified by the same load location and size of the damages it seeks. However, due to load changes regarding the location and size of the damage did not find it.
Second-order distributed feedback lasers with mode selection provided by first-order radiation losses (1985)

We present a theoretical study of the effect of radiation losses on the mode selectivity of DFB lasers with second-order gratings. For a second-order grating, interference of the radiation due to first-order diffraction of oppositely propagating guided waves cancels the radiation loss at one of the edges of the spectrum gap. This provides threshold gain discrimination of order 10 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> against one of the two dominant modes occurring near the edges of the gap. This should allow fabrication of DFB lasers with properties that are nearly independent of the positions of the facets relative to the grating corrugations, which are uncontrolled. By applying antireflection coatings to the two ends, differential quantum efficiencies close to those of conventional Fabry-Perot lasers should be achievable.