gebhart/patrepeval huggingface dataset:
Primary Liver Cancers, Part 2 (2018)

Hepatocellular carcinoma (HCC) and primary intrahepatic cholangiocarcinoma (ICC) have been increasing in incidence worldwide and are leading causes of cancer death. Studies of the molecular alterations leading to these carcinomas provide insights into the key mechanisms involved. A literature review was conducted to identify articles with information relevant to current understanding of the etiologies and molecular pathogenesis of HCC and ICC. Chronic inflammatory diseases are the key etiological risk factors for both HCC and ICC, although other diseases play a role, and for many ICCs, an underlying risk factor is not identified. Mutations in catenin beta 1 ( CTNBB1) and tumor protein 53 (P53) are the main genetic alterations in HCC. Isocitrate dehydrogenases 1 and 2 (IDH1/2), KRAS protooncogene GTPase (KRAS), a RAS Viral Oncogene Homolog in neoroblastoma (NRAS) and P53 are primary genetic alterations in ICC. In both diseases, the mutational landscape is dependent on the underlying etiology. The most significant etiologies and genetic processes involved in the carcinogenesis of HCC and ICC are reviewed.
Flow cytometric determination of E-selectin, vascular cell adhesion molecule-1, and intercellular cell adhesion molecule-1 in formaldehyde-fixed endothelial cell monolayers (2000)

The described method permits the reliable determination of surface and intracellular fractions of adhesion molecules in formaldehyde-fixed HUVEC monolayers and may be used for studies on the regulation of adhesion molecule expression.
Polymers Reinforced by Covalently Bonded Inorganic Clusters (2001)

Organically modified transition-metal oxide clusters (OMTOCs) are structurally well-defined nanosized building blocks for the preparation of a new type of inorganic−organic hybrid materials. There are two principal methods to synthesize OMTOCs with polymerizable organic groups attached to their surface: the groups can either be grafted to a preformed cluster (“surface modification” method) or introduced during the cluster synthesis (“in situ” method). The advantages and disadvantages of both methods are discussed. OMTOCs with polymerizable surface groups can be polymerized with or without an organic copolymer to yield polymers which arein most caseshighly cross-linked by the inorganic constituents. The structural integrity and the properties of the clusters are retained upon incorporation into the polymers. Because there are hitherto only a few examples of cluster-reinforced polymers, restricted to tungsten, tin, titanium, and zirconium oxide clusters, the article reviews the early stages of an interesting new approach to inorganic−organic hybrid polymers and highlights possibilities for future materials syntheses.
Emerging Technologies for the Clinical Microbiology Laboratory (2014)

In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.
Development of Novel Cell Surface CD34-Targeted Recombinant Adenoassociated Virus Vectors for Gene Therapy (1998)

Recombinant adenoassociated virus (rAAV) type 2 vectors have been used to transduce a wide variety of cell types, including hematopoietic progenitor cells. For in vivo gene transfer, it is desirable to have an rAAV vector that specifically transduces selected target cells. As a first step toward generating an rAAV vector capable of targeting delivery in vivo, we have engineered a chimeric protein combining the AAV capsid protein and the variable region of a single-chain antibody against human CD34 molecules, a cell surface marker for hematopoietic stem/progenitor cells. Inclusion of the chimeric CD34 single-chain antibody-AAV capsid proteins within an rAAV virion significantly increased the preferential infectivity of rAAV for the CD34+ human myoleukemia cell line KG-1, which is normally refractory to rAAV transduction. Antibodies against the single-chain antibody and the CD34 protein blocked this transduction. This chimeric vector represents a significant improvement in the host range of rAAV and the first step toward specific gene delivery by rAAV vectors to cells of choice, in this case, hematopoietic progenitor cells, for the treatment of human disease.
Impaired Incretin Response After a Mixed Meal Is Associated With Insulin Resistance in Nondiabetic Men (2001)

In insulin resistance, the GIP and GLP-1 responses to a mixed meal are impaired and are related to the degree of insulin resistance. Decreased incretin responsiveness may be of importance for the development of impaired glucose tolerance.
<title>OPTIMASK: an OPC algorithm for chrome and phase-shift mask design</title> (1995)

A mask correction algorithm (OPTIMASK) has been designed and implemented. Its main ingredients are optical proximity correction (OPC) and optical design rule checker (ODRC). The algorithm is based on the lithographic notion that a mask has to print throughout its defocus budget, taking into account multiple defocus planes. In each defocus plane the aerial image is computed using FAIM, and the design failures are reported via ODRC. The mask correction is subjected to physical restrictions that do not allow any feature couplings to occur. The union of the failures at all defocus values determines the first step taken in correcting the mask. Then a (constrained) Newton optimization scheme is applied to optimize line shrinkage, linewidth control, and corner rounding errors. All the tools needed to optimize a specific layer within a particular cell and return the optimized layer to the original mask file have been implemented. Several examples will be shown.
Benefits and risks of intralesional corticosteroid injection in the treatment of dermatological diseases (1995)

Intralesional corticosteroid (CS) injections have been used to treat a variety of dermatological and non-dermatological diseases with variable results. The purpose of the injection is to attain a high concentration of the drug at the diseased site, with minimal systemic absorption. Several CS preparations are available for intralesional injection, although triamcinolone derivatives have gained the widest usage in dermatology. The dose and the interval between injections depend on the type, size and severity of the lesion as well as the response to the previous injections. The most critical issue in the efficacy and also in the development of complications of the injections, is the method of injection. Several local and systemic side-effects have been reported following intralesional injections, but most of them are rare or acceptable. Thus intralesional CS injection is an integral part of the clinical practice of dermatology. Since their introduction in 1951, intralesional CS injections have become an integral part of clinical practice in dermatology. They are used alone or in combination with other therapeutic modalities in the treatment of many skin diseases. The purpose of the injection is to attain a high local concentration of the CS at the diseased site, without significant systemic absorption, thus avoiding the numerous side-effects associated with systemic administration. Intralesional CS injection may be a valuable therapeutic modality in situations where topical CS are not suitable for use, either because of low potency and inefficient epidermal barrier penetration or in clinical conditions associated with epidermal atrophy.
Neutralizing antibodies against hepatitis C virus and the emergence of neutralization escape mutant viruses (1994)

We developed an in vitro assay for antibodies to hepatitis C virus (HCV) that bind to virions and prevent initiation of the replication cycle in susceptible cells in vitro. These antibodies therefore appear to be capable of neutralizing the virus. Using this assay and a standard inoculum of HCV of known infectivity, we have measured the antibody in serial serum samples obtained from the same chronically infected patient over 14 years following onset of his hepatitis. Such antibody was found in sera collected within 5 years of onset of hepatitis but not in later sera. In double immunoprecipitation experiments with anti-human immunoglobulin, the same sera that contained neutralizing antibody were found to contain antibody that bound to HCV to form antigen-antibody complexes immunoprecipitable with anti-human globulin. Similarly, plasma collected from this patient in 1990, 13 years after onset of hepatitis, and which contained HCV that had diverged genetically from the 1977 strain, did not contain antibody capable of neutralizing either the 1977 or the 1990 strain of HCV. However, plasma collected a year later (1991, 14 years after onset of hepatitis) contained neutralizing antibody to the 1990, but not the 1977, strain of HCV. These results suggest that HCV does induce antivirion antibody, as measured by blocking of initiation of the replication cycle of virus in cells and by the formation of immunoprecipitable antigen-antibody complexes but that these antibodies are isolate specific and change over time. Thus, these antivirion antibodies function as neutralizing antibodies and are probably in vitro correlates of the attempt of the host to contain the emergence of neutralization-resistant variants of HCV over time.
Vancomycin MIC plus Heteroresistance and Outcome of Methicillin-Resistant Staphylococcus aureus Bacteremia: Trends over 11 Years (2009)

Vancomycin MICs (V-MIC) and the frequency of heteroresistant vancomycin-intermediate Staphylococcus aureus (hVISA) isolates are increasing among methicillin (meticillin)-resistant Staphylococcus aureus (MRSA) isolates, but their relevance remains uncertain. We compared the V-MIC (Etest) and the frequency of hVISA (Etest macromethod) for all MRSA blood isolates saved over an 11-year span and correlated the results with the clinical outcome. We tested 489 isolates: 61, 55, 187, and 186 isolates recovered in 1996-1997, 2000, 2002-2003, and 2005-2006, respectively. The V-MICs were < or = 1, 1.5, 2, and 3 microg/ml for 74 (15.1%), 355 (72.6%), 50 (10.2%), and 10 (2.1%) isolates, respectively. We detected hVISA in 0/74, 48/355 (13.5%), 15/50 (30.0%), and 8/10 (80.0%) isolates with V-MICs of < or = 1, 1.5, 2, and 3 microg/ml, respectively (P < 0.001). The V-MIC distribution and the hVISA frequency were stable over the 11-year period. Most patients (89.0%) received vancomycin. The mortality rate (evaluated with 285 patients for whose isolates the trough V-MIC was > or = 10 microg/ml) was comparable for patients whose isolates had V-MICs of < or = 1 and 1.5 microg/ml (19.4% and 27.0%, respectively; P = 0.2) but higher for patients whose isolates had V-MICs of > or = 2 microg/ml (47.6%; P = 0.03). However, the impact of V-MIC and hVISA status on mortality or persistent (> or = 7 days) bacteremia was not substantiated by multivariate analysis. Staphylococcal chromosome cassette mec (SCCmec) typing of 261 isolates (including all hVISA isolates) revealed that 93.0% of the hVISA isolates were SCCmec type II. These findings demonstrate that the V-MIC distribution and hVISA frequencies were stable over an 11-year span. A V-MIC of > or = 2 microg/ml was associated with a higher rate of mortality by univariate analysis, but the relevance of the V-MIC and the presence of hVISA remain uncertain. A multicenter prospective randomized study by the use of standardized methods is needed to evaluate the relevance of hVISA and determine the optimal treatment of patients whose isolates have V-MICs of > or = 2.0 microg/ml.
Compact Single-Mode Silicon Hybrid Rib/Strip Waveguide With Adiabatic Bends (2011)

We report a low-loss, hybrid silicon waveguide geometry that consists of straight rib sections with a propagation loss of 0.27 ± 0.012 dB/cm and compact photonic wire bends. The rib and wire waveguides are both single mode and connected through a short double-etched linear taper section. To reduce bend losses, circular bends were combined with variable adiabatic seminatural spline shapes with only a limited footprint penalty.
Selectivity of a replication-competent adenovirus for human breast carcinoma cells expressing the MUC1 antigen (2000)

The DF3/MUC1 gene is aberrantly overexpressed in human breast and other carcinomas. Previous studies have demonstrated that the DF3/MUC1 promoter/enhancer confers selective expression of diverse transgenes in MUC1-positive breast cancer cells. In this study, we show that an adenoviral vector (Ad.DF3-E1) in which the DF3/MUC1 promoter drives expression of E1A selectively replicates in MUC1-positive breast cancer cells. We also show that Ad.DF3-E1 infection of human breast tumor xenografts in nude mice is associated with inhibition of tumor growth. In contrast to a replication-incompetent adenoviral vector that infects along the injection track, Ad.DF3-E1 infection was detectable throughout the tumor xenografts. To generate an Ad.DF3-E1 vector with the capacity for incorporating therapeutic products, we inserted the cytomegalovirus (CMV) promoter upstream of the TNF cDNA. Infection with Ad.DF3-E1/CMV-TNF was associated with selective replication and production of TNF in cells that express MUC1. Moreover, treatment of MUC1-positive, but not MUC1-negative, xenografts with a single injection of Ad.DF3-E1/CMV-TNF was effective in inducing stable tumor regression. These findings demonstrate that the DF3/MUC1 promoter confers competence for selective replication of Ad.DF3-E1 in MUC1-positive breast tumor cells, and that the antitumor activity of this vector is potentiated by integration of the TNF cDNA.
Amyloid precursor protein mRNA stability is controlled by a 29-base element in the 3'-untranslated region. (1994)

In the accompanying paper (Zaidi, S. H. E., Denman, R., and Malter, J. S. (1994) J. Biol. Chem. 269, 24000-24006) we demonstrate that in tumor and normal cells, multiple cytosolic proteins interact with a 29-base sequence in the 3'-untranslated region of amyloid precursor protein (APP) mRNA. These data suggested that APP gene expression may be modulated by regulated APP mRNA decay. We have investigated this prediction by measuring the decay rates of APP mRNA in resting and mitogen-treated peripheral blood mononuclear cells and H4 and K562 tumor cell lines. In resting peripheral blood mononuclear cells, APP mRNA decayed with a half-life of 4 h. Under these conditions, the activity of APP mRNA-binding proteins was not detectable. After activation, binding protein activities were induced, and APP mRNA decay was blocked with a half-life of > 12 h. In log phase neuronal or lymphoid tumor cell lines, binding activity was constitutively present and APP mRNA displayed a half-life of > 12 h. Protein synthesis inhibition by cycloheximide had no effect on APP mRNA decay in normal or tumor cells. Transfected wild type or mutant APP mRNAs that lacked the 29-base region were stable (t1/2 > 10 h) in K562 tumor cells. Therefore, we conclude that the 29-base region functions in cis to destabilize APP mRNA in resting, normal cells. Upon activation APP mRNA-binding proteins are induced, interact with the 29-base region, and likely participate in stabilization of the mRNA.
Unusual Serum Electrophoresis Pattern in a Woman with Pancreatic Carcinoma (2008)

A 51-year-old woman presented with progressive severe icterus associated with advanced inoperable pancreatic carcinoma. Biopsy of the liver revealed metastasis of a moderately differentiated adenocarcinoma, possibly of pancreatic origin. Imaging studies did not show any primary tumor in the pancreas but did reveal a deep vein thrombosis of the left lower extremity and a pulmonary embolism. Bone scans revealed metastases. The patient began treatment with chemotherapy (gemcitabine), radiotherapy to alleviate pain, and placement of a percutaneous transhepatic stent in the right biliary system because of progressive icterus.

Routine biochemical investigation of the patient’s serum revealed increased total bilirubin (275 μmol/L, reference value <22 μmol/L), which consisted mainly of direct bilirubin (215 μmol/L, reference value <4 μmol/L). The cytosolic liver enzymes alanine aminotransferase (115 U/L) and aspartate aminotransferase (143 U/L) were moderately increased. The serum protein concentration was 68 g/L (reference interval 60–85 g/L), but capillary electrophoresis of serum proteins (CAPILLARYS 2, Sebia) demonstrated a low albumin fraction together with a marked additional peak observed between the β and the γ region (Fig. 1⇓ ). Results of immunofixation with antibodies against G, M, and A heavy chains and κ and λ light chains were negative, indicating that this additional electrophoretic fraction did not indicate the presence of a paraprotein. Agarose gel electrophoresis confirmed the abnormal pattern, ruling out analytical interference caused by atypical ultraviolet absorbance.



 Figure 1. 
Capillary electrophoresis of the patient’s serum. 

The arrow points to a marked additional fraction present between the β and γ zone. Absorbance is expressed as ultraviolet absorption …
Characterization of a Mycobacterium tuberculosis H37Rv transposon library reveals insertions in 351 ORFs and mutants with altered virulence b bThe precise locations of all of the insertions examined in this study can be found as supplementary data in Microbiology Online (http://mic.sgmjournals.org). (2002)

A library of Mycobacterium tuberculosis insertional mutants was generated with the transposon Tn5370. The junction sequence between the transposon and the mycobacterial chromosome was determined, revealing the positions of 1329 unique insertions, 1189 of which were located in 351 different ORFs. Transposition was not completely random and examination of the most susceptible genome regions revealed a lower-than-average G+C content ranging from 54 to 62 mol%. Mutants were obtained in all of the recognized M. tuberculosis functional protein-coding gene classes. About 30% of the disrupted ORFs had matches elsewhere in the genome that suggested redundancy of function. The effect of gene disruption on the virulence of a selected set of defined mutants was investigated in a severe combined immune deficiency (SCID) mouse model. A range of phenotypes was observed in these mutants, the most notable being the severe attenuation in virulence of a strain disrupted in the Rv1290c gene, which encodes a protein of unknown function. The library described in this study provides a resource of defined mutant strains for use in functional analyses aimed at investigating the role of particular M. tuberculosis genes in virulence and defining their potential as targets for new anti-mycobacterial drugs or as candidates for deletion in a rationally attenuated live vaccine.
Space-time coding theory and practice (2005)

This book covers the fundamental principles of space-time coding for wireless communications over multiple-input multiple-output (MIMO) channels, and sets out practical coding methods for achieving the performance improvements predicted by the theory. Starting with background material on wireless communications and the capacity of MIMO channels, the book then reviews design criteria for space-time codes. A detailed treatment of the theory behind space-time block codes then leads on to an in-depth discussion of space-time trellis codes. The book continues with discussion of differential space-time modulation, BLAST and some other space-time processing methods and the final chapter addresses additional topics in space-time coding. The theory and practice sections can be used independently of each other. Written by one of the inventors of space-time block coding, this book is ideal for a graduate student familiar with the basics of digital communications, and for engineers implementing the theory in real systems
Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites (1998)

Inspection of the amino acid-base interactions in protein-DNA complexes is essential to the understanding of specific recognition of DNA target sites by regulatory proteins. The accumulation of information on protein-DNA co-crystals challenges the derivation of quantitative parameters for amino acid-base interaction based on these data. Here we use the coordinates of 53 solved protein-DNA complexes to extract all non-homologous pairs of amino acid-base that are in close contact, including hydrogen bonds and hydrophobic interactions. By comparing the frequency distribution of the different pairs to a theoretical distribution and calculating the log odds, a quantitative measure that expresses the likelihood of interaction for each pair of amino acid-base could be extracted. A score that reflects the compatibility between a protein and its DNA target can be calculated by summing up the individual measures of the pairs of amino acid-base involved in the complex, assuming additivity in their contributions to binding. This score enables ranking of different DNA binding sites given a protein binding site and vice versa and can be used in molecular design protocols. We demonstrate its validity by comparing the predictions using this score with experimental binding results of sequence variants of zif268 zinc fingers and their DNA binding sites.
Acyloxy Nitroso Compounds as Nitroxyl (HNO) Donors: Kinetics, Reactions with Thiols, and Vasodilation Properties (2011)

Acyloxy nitroso compounds hydrolyze to nitroxyl (HNO), a nitrogen monoxide with distinct chemistry and biology. Ultraviolet-visible spectroscopy and mass spectrometry show hydrolysis rate depends on pH and ester group structure with the observed rate being trifluoroacetate (3) > acetate (1) > pivalate (2). Under all conditions, 3 rapidly hydrolyzes to HNO. A combination of spectroscopic, kinetic, and product studies show that addition of thiols increases the decomposition rate of 1 and 2, leading to hydrolysis and HNO. Under conditions that favor thiolates, the thiolate directly reacts with the nitroso group, yielding oximes without HNO formation. Biologically, 3 behaves like Angeli's salt, demonstrating thiol-sensitive nitric oxide-mediated soluble guanylate cyclase-dependent vasorelaxation, suggesting HNO-mediated vasorelaxation. The slow HNO-donor 1 demonstrates weak thiol-insensitive vasorelaxation, indicating HNO release kinetics determine HNO bioavailability and activity. These results show that acyloxy nitroso compounds represent new HNO donors capable of vasorelaxation depending on HNO release kinetics.
Mammary Tumorigenesis in Chemical Carcinogen-Treated Mice. I. Incidence in BALB/c and C57BL Mice2 (1974)

Journal Article Mammary Tumorigenesis in Chemical Carcinogen-Treated Mice. I. Incidence in BALB/c and C57BL Mice Get access Daniel Medina Daniel Medina 3Department of Cell Biology, Baylor College of Medicine, Houston, Tex. 77025. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 53, Issue 1, July 1974, Pages 213–221, https://doi.org/10.1093/jnci/53.1.213 Published: 01 July 1974 Article history Received: 11 January 1974 Accepted: 10 April 1974 Published: 01 July 1974