gebhart/patrepeval huggingface dataset:
Immunosuppression and Chagas Disease: A Management Challenge (2013)

Immunosuppression, which has become an increasingly relevant clinical condition in the last 50 years, modifies the natural history of Trypanosoma cruzi infection in most patients with Chagas disease. The main goal in this setting is to prevent the consequences of reactivation of T. cruzi infection by close monitoring. We analyze the relationship between Chagas disease and three immunosuppressant conditions, including a description of clinical cases seen at our center, a brief review of the literature, and recommendations for the management of these patients based on our experience and on the data in the literature. T. cruzi infection is considered an opportunistic parasitic infection indicative of AIDS, and clinical manifestations of reactivation are more severe than in acute Chagas disease. Parasitemia is the most important defining feature of reactivation. Treatment with benznidazole and/or nifurtimox is strongly recommended in such cases. It seems reasonable to administer trypanocidal treatment only to asymptomatic immunosuppressed patients with detectable parasitemia, and/or patients with clinically defined reactivation. Specific treatment for Chagas disease does not appear to be related to a higher incidence of neoplasms, and a direct role of T. cruzi in the etiology of neoplastic disease has not been confirmed. Systemic immunosuppressive diseases or immunosuppressants can modify the natural course of T. cruzi infection. Immunosuppressive doses of corticosteroids have not been associated with higher rates of reactivation of Chagas disease. Despite a lack of evidence-based data, treatment with benznidazole or nifurtimox should be initiated before immunosuppression where possible to reduce the risk of reactivation. Timely antiparasitic treatment with benznidazole and nifurtimox (or with posaconazole in cases of therapeutic failure) has proven to be highly effective in preventing Chagas disease reactivation, even if such treatment has not been formally incorporated into management protocols for immunosuppressed patients. International consensus guidelines based on expert opinion would greatly contribute to standardizing the management of immunosuppressed patients with Chagas disease.
Continuous control of coherence length in separately pumped (AlGa)As lasers (1986)

Continuous control of coherence length is realized in the output power region of 3–5 mW by changing the current flowing into the loss region of separately pumped (AlGa)As lasers. The controllable saturable absorption makes lasing spectra multimode and broadens the linewidth of an individual laser mode up to 2.5 Å through self-pulsation. The threshold current of the laser is 60–80 mA. The lasing wavelength is around 780 nm.
Transfected human neuropeptide Y cDNA expression in mouse pituitary cells. Inducible high expression, peptide characterization, and secretion. (1987)

An expression vector was constructed that placed the cDNA for human neuropeptide Y (NPY) under the control of the mouse metallothionein promoter and was used to transfect the AtT-20 mouse anterior pituitary corticotrope cell line. AtT-20 cells normally process the pro-ACTH/endorphin precursor but do not produce detectable levels of NPY. The resulting AtT-20/NPY cell line (Mt.NPY1a) was used to study the ability of the corticotrope cells to synthesize, process, and secrete the foreign proNPY-related peptide products. The stable cell line created contains approximately 40 copies of proNPY cDNA per cell. NPY mRNA levels and proNPY synthesis were increased at least 35-fold when maximally induced with cadmium; proNPY synthesis was also induced by glucocorticoids. Upon induction the NPY secretion rate was equimolar to that of the endogenous peptides. ProNPY, NPY, and the COOH-terminal peptide produced by this cell line had molecular weight and amino acid-labeling pattern predicted from cDNA sequence data and from previous isolation of NPY-related molecules from NPY-producing cells. The structures of secreted proNPY, NPY, and COOH-terminal peptide, as well as determination of the site of proteolytic cleavage between NPY and the COOH-terminal peptide, were determined by tryptic mapping and Edman degradation of secreted biosynthetically labeled peptide products. The proNPY molecule appears to be processed in the same pathway responsible for cleavage of the endogenous pro-ACTH/endorphin precursor. Secretion of proNPY-derived peptides paralleled secretion of endogenous pro-ACTH/endorphin-derived products, under both basal and stimulated conditions. With induction proNPY expression there is a dose-dependent inhibition of both proNPY and pro-ACTH/endorphin proteolytic processing.
Pathogenesis of Tuberculosis: Clinical and Epidemiologic Perspective (1989)

Mycobacterium tuberculosis is one of several pathogens that confer resistance to reinfection, but its persistence presents a constant threat to the host. In countries where the incidence of tuberculosis is low, most cases appear to be caused by recrudescence of old infection. The ability of the organism to produce protection against a new infection, at least in theory, affords an opportunity to induce resistance by vaccination. Although exogenous reinfection is documented in a recent paper, data from a recent outbreak of tuberculosis in Arkansas show no evidence of reinfection in the face of documented serious spread of infection to persons who were not reactive to tuberculin. Presently available vaccines have not proven to be reliable in producing resistance. Thus, a search for a means of conferring the ability to mount a quick immune response when the organism is encountered appears to be worthwhile.
Correction: PLGA-Carbon Nanotube Conjugates for Intercellular Delivery of Caspase-3 into Osteosarcoma Cells (2014)

Cancer has arisen to be of the most prominent health care issues across the world in recent years. Doctors have used physiological intervention as well as chemical and radioactive therapeutics to treat cancer thus far. As an alternative to current methods, gene delivery systems with high efficiency, specificity, and safety that can reduce side effects such as necrosis of tissue are under development. Although viral vectors are highly efficient, concerns have arisen from the fact that viral vectors are sourced from lethal diseases. With this in mind, rod shaped nano-materials such as carbon nanotubes (CNTs) have become an attractive option for drug delivery due to the enhanced permeability and retention effect in tumors as well as the ability to penetrate the cell membrane. Here, we successfully engineered poly (lactic-co-glycolic) (PLGA) functionalized CNTs to reduce toxicity concerns, provide attachment sites for pro-apoptotic protein caspase-3 (CP3), and tune the temporal release profile of CP3 within bone cancer cells. Our results showed that CP3 was able to attach to functionalized CNTs, forming CNT-PLGA-CP3 conjugates. We show this conjugate can efficiently transduce cells at dosages as low as 0.05 g/ml and suppress cell proliferation up to a week with no further treatments. These results are essential to showing the capabilities of PLGA functionalized CNTs as a non-viral vector gene delivery technique to tune cell fate.
Monoclonal Antilymphocyte Antibody (OKT3) Treatment of Acute Renal Allograft Rejection (1987)

Recent advances in immunosuppressive therapy have dramatically improved the survival rates for recipients of organ allografts by reducing the frequency of rejection. Cyclosporine, azathioprine, and prednisone for immunoprophylaxis are especially effective. When rejection occurs, the treatment usually includes high doses of oral or intravenous corticosteroids, antilymphocyte globulin, or antithymocyte globulin. A new monoclonal antilymphocyte antibody, OKT3, promises to improve allograft survival rates further.
Crystal structure of full-length KcsA in its closed conformation (2009)

KcsA is a proton-activated, voltage-modulated K(+) channel that has served as the archetype pore domain in the Kv channel superfamily. Here, we have used synthetic antigen-binding fragments (Fabs) as crystallographic chaperones to determine the structure of full-length KcsA at 3.8 A, as well as that of its isolated C-terminal domain at 2.6 A. The structure of the full-length KcsA-Fab complex reveals a well-defined, 4-helix bundle that projects approximately 70 A toward the cytoplasm. This bundle promotes a approximately 15 degree bending in the inner bundle gate, tightening its diameter and shifting the narrowest point 2 turns of helix below. Functional analysis of the full-length KcsA-Fab complex suggests that the C-terminal bundle remains whole during gating. We suggest that this structure likely represents the physiologically relevant closed conformation of KcsA.
Switching Gears for an Influenza Pandemic: Validation of a Duplex Reverse Transcriptase PCR Assay for Simultaneous Detection and Confirmatory Identification of Pandemic (H1N1) 2009 Influenza Virus (2009)

Rapid methods for the detection and confirmatory identification of pandemic influenza A virus (also known as pandemic [H1N1] 2009) are of utmost importance. In this study, a conventional reverse transcriptase PCR (RT-PCR) assay for the detection of influenza A virus and the hemagglutinin of swine lineage H1 (swH1) was designed, optimized, and validated. Nucleic acids were extracted from 198 consecutive nasopharyngeal, nasal, or throat swab specimens collected early in the outbreak (127 negative specimens, 66 specimens with pandemic [H1N1] 2009 influenza virus, 3 specimens with seasonal [H1N1] influenza A virus, and 2 specimens with seasonal [H3N2] influenza A virus). The performance characteristics of the duplex RT-PCR assay were assessed and compared to those of various detection methods: a monoplex RT-PCR assay at the National Microbiology Laboratory, a real-time RT-PCR assay using a Centers for Disease Control and Prevention protocol, an in-house multiplex RT-PCR assay (targeting influenza A virus, influenza B virus, and respiratory syncytial virus), and a rapid antigen test (the Binax Now Influenza A & B assay). The sensitivity of the duplex RT-PCR assay for influenza A virus detection was 97.2%, whereas the sensitivities were 74.6%, 71.8%, 47.8%, and 12.7% for the other four assays, respectively. The duplex RT-PCR assay was also able to identify swH1 in 94% of the cases, thereby reducing the number of specimens forwarded to reference laboratories for confirmatory identification. Only a limited number of specimens that contained influenza A virus had amounts of virus that fell below the limit of detection of the assay with the swH1 primers. Overall, the duplex RT-PCR assay is a reliable method for the simultaneous detection and confirmatory identification of pandemic (H1N1) 2009 influenza virus and would be particularly attractive to laboratories without real-time RT-PCR capabilities.
Tree Scanning (2004)

We use evolutionary trees of haplotypes to study phenotypic associations by exhaustively examining all possible biallelic partitions of the tree, a technique we call tree scanning. If the first scan detects significant associations, additional rounds of tree scanning are used to partition the tree into three or more allelic classes. Two worked examples are presented. The first is a reanalysis of associations between haplotypes at the Alcohol Dehydrogenase locus in Drosophila melanogaster that was previously analyzed using a nested clade analysis, a more complicated technique for using haplotype trees to detect phenotypic associations. Tree scanning and the nested clade analysis yield the same inferences when permutation testing is used with both approaches. The second example is an analysis of associations between variation in various lipid traits and genetic variation at the Apolipoprotein E (APOE) gene in three human populations. Tree scanning successfully identified phenotypic associations expected from previous analyses. Tree scanning for the most part detected more associations and provided a better biological interpretative framework than single SNP analyses. We also show how prior information can be incorporated into the tree scan by starting with the traditional three electrophoretic alleles at APOE. Tree scanning detected genetically determined phenotypic heterogeneity within all three electrophoretic allelic classes. Overall, tree scanning is a simple, powerful, and flexible method for using haplotype trees to detect phenotype/genotype associations at candidate loci.
An inexpensive microslab gel DNA electrophoresis system with real‐time fluorescence detection (2005)

In this paper, we describe the construction of a simple yet powerful gel electrophoresis apparatus that can be used to perform size-selective separations of DNA fragments in virtually any laboratory. This system employs a microslab gel format with a novel gel casting technique that eliminates the need for delicate combs to define sample loading wells. The compact size of the microslab gel format allows rapid separations to be performed at low voltages using submicroliter sample volumes. Real time fluorescence detection of the migrating DNA fragments is accomplished using an inexpensive digital microscope that directly connects to any PC with a USB interface. The microscope is readily adaptable for this application by replacing its white light source with a blue light-emitting diode (LED) and adding an appropriate emission filter. Both polyacrylamide and agarose gels can be used as separation matrices. Separation performance was characterized using standard dsDNA ladders, and correct sizing of a 191 bp PCR product was achieved in 15 min. The low cost and simplicity of this system makes it ideally suited for use in a variety of laboratory and educational settings.
Acute Exacerbations of Idiopathic Pulmonary Fibrosis (2007)

The natural history of idiopathic pulmonary fibrosis (IPF) has been characterized as a steady, predictable decline in lung function over time. Recent evidence suggests that some patients may experience a more precipitous course, with periods of relative stability followed by acute deteriorations in respiratory status. Many of these acute deteriorations are of unknown etiology and have been termed acute exacerbations of IPF. This perspective is the result of an international effort to summarize the current state of knowledge regarding acute exacerbations of IPF. Acute exacerbations of IPF are defined as acute, clinically significant deteriorations of unidentifiable cause in patients with underlying IPF. Proposed diagnostic criteria include subjective worsening over 30 days or less, new bilateral radiographic opacities, and the absence of infection or another identifiable etiology. The potential pathobiological roles of infection, disordered cell biology, coagulation, and genetics are discussed, and future research directions are proposed.
Platinum coil coatings to increase thrombogenicity: a preliminary study in rabbits. (1993)

The authors investigate a modification of the Gugliemi detachable coil. They have developed a rabbit model and coating technique to test differences in thrombogenicity of platinum coils with a variety of polyurethanes.
Systematic comparison of variant calling pipelines using gold standard personal exome variants (2015)

The success of clinical genomics using next generation sequencing (NGS) requires the accurate and consistent identification of personal genome variants. Assorted variant calling methods have been developed, which show low concordance between their calls. Hence, a systematic comparison of the variant callers could give important guidance to NGS-based clinical genomics. Recently, a set of high-confident variant calls for one individual (NA12878) has been published by the Genome in a Bottle (GIAB) consortium, enabling performance benchmarking of different variant calling pipelines. Based on the gold standard reference variant calls from GIAB, we compared the performance of thirteen variant calling pipelines, testing combinations of three read aligners--BWA-MEM, Bowtie2, and Novoalign--and four variant callers--Genome Analysis Tool Kit HaplotypeCaller (GATK-HC), Samtools mpileup, Freebayes and Ion Proton Variant Caller (TVC), for twelve data sets for the NA12878 genome sequenced by different platforms including Illumina2000, Illumina2500, and Ion Proton, with various exome capture systems and exome coverage. We observed different biases toward specific types of SNP genotyping errors by the different variant callers. The results of our study provide useful guidelines for reliable variant identification from deep sequencing of personal genomes.
Integrating Bottom-Up and Top-Down Analysis for Intelligent Hypertext (1994)

The range of hypertext systems continues to expand, from custom-tailored closed systems to dynamic, distributed, and open systems like the World-Wide Web (WWW). The shift from closed to open systems results in a corresponding decrease in the effectiveness of metrics and techniques for providing intelligent hypertext to users. Essentially, the locus of control shifts away from developers towards users. Stated differently, the central question becomes chaotic, loosely constrained environments, like the WorldWide Web, can provide intelligent hypertext. This paper argues that viable answers are derivable from both bottomup and top-down analyses. Furthermore, intelligent hypertext within open, client-server systems may profit by combining these two approaches. Using the WWW as a case study, a method of analysis for each approach is presented, accompanied by a discussion of the implications for implementations in open hypertext systems. INTRODUCTION The proliferation of network and Interne...
Thermotropic Behavior of Structurally-Related Phospholipids and Phosphonolipid Analogs of Lung Surfactant Glycerophospholipids (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermotropic Behavior of Structurally-Related Phospholipids and Phosphonolipid Analogs of Lung Surfactant GlycerophospholipidsHuicai Liu, J. G. Turcotte, and R. H. NotterCite this: Langmuir 1995, 11, 1, 101–107Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/la00001a020https://doi.org/10.1021/la00001a020research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations9LEARN 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 Get e-Alerts
Abstract 4171: Tumor suppressive microRNA-218 mediated focal adhesion pathways in cervical squamous cell carcinoma. (2013)

Abstract Background: MicroRNAs (miRNAs), a class of small non-coding RNAs, regulate protein-coding gene expression by repressing translation or cleaving RNA transcripts in a sequence-specific manner. A growing body of evidence suggests that miRNAs contribute to cervical squamous cell carcinoma (cervical-SCC) progression, development, and metastasis. Recent our miRNA expression signature of SCC (hypopharyngeal-SCC and esophageal-SCC) revealed that microRNA-218 (miR-218) was significantly reduced in cancer tissues. The study of the aim was to investigate the functional significance of miR-218 and its mediated molecular pathways in cervical-SCC. Methods: Gain-of-function studies were performed to investigate cancer cell proliferation, migration and invasion by restoration of mature miRNAs into HPV positive or negative cervical-SCC cell lines (CaSKi, HeLa, ME180 and YUMOTO). To identify the biological processes or pathways potentially regulated by the miRNAs, we applied genome-wide gene expression analysis and in silico study. The GENECODIS software assigned a number of the putative miRNA targets to known pathways in KEGG [http://www.genome.jp/kegg/pathway.html]. Gene expression analyses of all candidate genes involved in each of the pathways using GEO (http://www.ncbi.nlm.nih.gov/geo/) database. Results: Expression levels of miR-218 were significantly reduced in cervical-SCC clinical specimens compared to adjacent non-cancerous tissues (P&amp;lt;0.0001). Restoration of miR-218 significantly inhibited cancer cell migration and invasion in all cervical-SCC cell lines. These data indicated that miR-218 act as a tumor suppressor in cervical-SCC. Our in silico analysis showed that miR-218 appeared to be an important modulator of tumor cell processes through suppression of many targets, particularly those involved in “focal adhesion” signaling pathways (P&amp;lt;0.05). Gene expression data indicated that LAMB3 and LAMC1 were up-regulated in cervical-SCC clinical specimens. The laminins are an important and biologically active part of the basal lamina, the function of that are various such as influencing cell differentiation, migration and adhesion as well as proliferation and cell survival. Conclusions: Aberrant expression of miRNAs has shed light on recent miRNA signatures and identification of tumor suppressive miRNA mediated novel molecular pathways in cervical-SCC. Tumor suppressive miR-218-mediated novel molecular pathways provide a new insight of cervical-SCC oncogenesis and metastasis. Citation Format: Noriko Yamamoto, Takashi Kinosita, Nijiro Nohata, Toshihiko Idesako, Hirofumi Yoshino, Hideki Enokida, Masayuki Nakagawa, Makio Syozu, Naohiko Seki. Tumor suppressive microRNA-218 mediated focal adhesion pathways in cervical squamous cell carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4171. doi:10.1158/1538-7445.AM2013-4171
Planning, Public Art and the Making of Community - the Ponds (2009)

Details of the planning, commissioning and placement of public artworks in 'The Ponds' suburban residential development near Sydney are presented. The salient features of public artworks such as 'Float', 'Waterlines' and 'Creekline' which have been created to represent the social, cultural and environmental history of the place, while also considering its future as a community, are discussed.
Theory of communication. Part 2: The analysis of hearing (1946)

The methods developed in Part 1 are applied to the analysis of hearing sensations, in particular to experiments by Shower and Biddulph, and by Bürck, Kotowski and Lichte on the discrimination of frequency and time by the human ear. It is shown that experiments of widely different character lead to well-defined threshold “areas of discrimination” in the information diagram. At the best, in the interval 60–1 000 c/s the human ear can discriminate very nearly every second datum of information; i.e. the ear is almost as perfect as any instrument can be which is not responsive to phase. Over the whole auditory range the efficiency is much less than 50%, as the discrimination falls off sharply at higher frequencies.The threshold area of discrimination appears to be independent of the duration of the signals between about 20 and 250 millisec. This remarkably wide interval cannot be explained by any mechanism in the inner ear, but may be explained by a new hypothetical effect in nerve conduction, i.e. the mutual influence of adjacent nerve fibres.