gebhart/patrepeval huggingface dataset:
Specific binding of cruciform DNA structures by a protein from human extracts (1988)

A gel electrophoresis binding assay has been used to probe extracts from cultured human lymphoblasts for proteins that bind cruciform structures in duplex DNA. Proteins have been detected that form complexes with synthetic X- and Y-junctions. Several lines of evidence suggest that binding is specific for DNA structure rather than sequence: (1) X- and Y-structures were bound whereas linear duplexes containing identical DNA sequences were not, (2) Binding occurred with equal efficiency to two X-junctions that were constructed from DNA strands of different sequence, (3) One X-junction successfully competed with another for binding whereas linear duplex DNA did not; and (4) protein-DNA complexes were observed at probe:non-specific competitor DNA ratios of 1:10,000.
Introduction To A New Geo-Referenced Street Level Content: 3D GEOPANO (2015)

Geospatial mash-up is to produce a new worthy value by combining geo-referenced contents and different kinds of service. Despite of its high popularity in aerial view contents such as Google Earth, it is hardly achieved especially in street level due to the poor georeferencing quality of the underlining street level contents. In this study we propose a new street-level georeferenced panorama image content, ‘3D GeoPano’. While the most existing contents provide only the location and orientation for each entire image not for each pixel, this new content is accurately georeferenced pixel by pixel so that one can derive 3D absolute coordinates for every pixel. Based on the precisely determined 3D ground coordinates per every pixel, GIS database linkage can be more close, flexible and organic. This can improve the quality of geospatial mash-up service in street level. Such ‘3D GeoPano’ will be developed in open source community. By doing so, we expect to activate the geospatial mashup in street-level as well as to spread the geospatial technology.
16S rRNA and 16S to 23S Internal Transcribed Spacer Sequence Analyses Reveal Inter- and Intraspecific Bifidobacterium Phylogeny (1996)

In the last few years many attempts have been made to differentiate more than 20 Bifidobacterium species. It has been recognized that identification of bifidobacterial species is problematic because of phenetic and genetic heterogeneities. In order to contribute to our understanding of Bifidobacterium taxonomy, we studied Bifidobacterium phylogeny by performing both 16S rRNA and 16S to 23S (16S-23S) internally transcribed spacer (ITS) sequence analyses. In this study, we determined 16S rRNA sequences of five Bifidobacterium strains representing four species, and compared them with the sequences available in the GenBank database, and used them to construct a distance tree and for a bootstrap analysis. Moreover, we determined the ITS sequences of 29 bifidobacterial strains representing 18 species and compared these sequences with each other. We constructed a phylogenetic tree based on these sequence data and compared this tree with the tree based on 16S rRNA sequence data. We found that the two trees were similar topologically, suggesting that the two types of molecules provided the same kind of phylogenetic information. However, while 16S rRNA sequences are a good tool to infer interspecific links, the 16S-23S rDNA spacer data allowed us to determine intraspecific relationships. Each of the strains was characterized by its own ITS sequence; hence, 16S-23S rRNA sequences are a good tool for strain identification. Moreover, a comparison of the ITS sequences allowed us to estimate that the maximum level of ITS divergence between strains belonging to the same species was 13%. Our data allowed us to confirm the validity of most of the Bifidobacterium species which we studied and to identify some classification errors. Finally, our results showed that Bifidobacterium strains have no tRNA genes in the 16S-23S spacer region.
Chronic Granulomatous Disease: Report on a National Registry of 368 Patients (2000)

A registry of United States residents with chronic granulomatous disease (CGD) was established in 1993 in order to estimate the minimum incidence of this uncommon primary immunodeficiency disease and characterize its epidemiologic and clinical features. To date, 368 patients have been registered; 259 have the X-linked recessive form of CGD, 81 have 1 of the autosomal recessive forms, and in 28 the mode of inheritance is unknown. The minimum estimate of birth rate is between 1/200,000 and 1/250,000 live births for the period 1980-1989. Pneumonia was the most prevalent infection (79% of patients; Aspergillus most prevalent cause), followed by suppurative adenitis (53% of patients; Staphylococcus most prevalent cause), subcutaneous abscess (42% of patients; Staphylococcus most prevalent cause), liver abscess (27% of patients; Staphylococcus most prevalent cause), osteomyelitis (25% of patients; Serratia most prevalent cause), and sepsis (18% of patients; Salmonella most prevalent cause). Fifteen percent of patients had gastric outlet obstruction, 10% urinary tract obstruction, and 17% colitis/enteritis. Ten percent of X-linked recessive kindreds and 3% of autosomal recessive kindreds had family members with lupus. Eighteen percent of patients either were deceased when registered or died after being registered. The most common causes of death were pneumonia and/or sepsis due to Aspergillus (23 patients) or Burkholderia cepacia (12 patients). Patients with the X-linked recessive form of the disease appear to have a more serious clinical phenotype than patients with the autosomal recessive forms of the disease, based on the fact that they are diagnosed significantly earlier (mean, 3.01 years of age versus 7.81 years of age, respectively), have a significantly higher prevalence of perirectal abscess (17% versus 7%), suppurative adenitis (59% versus 32%), bacteremia/fungemia (21% versus 10%), gastric obstruction (19% versus 5%), and urinary tract obstruction (11% versus 3%), and a higher mortality (21.2% versus 8.6%).
Medical Image Analysis (2010)

Preface. 1. Introduction. 2. Image Formation. 3. Interaction of Electromagnetic Radiation with Matter in Medical Imaging. 4. Medical Imaging Modalities. 5. Image Reconstruction. 6. Image Enhancement. 7. Image Segmentation. 8. Image Representation and Analysis. 9. Image Registration. 10. Image Visualization. 11. Current and Future Trends in Medical Imaging and Image Analysis. Index.
Illnesses Associated with Escherichia coli 0157:H7 Infections (1988)

Infection with E. coli O157:H7 should be considered in all patients with bloody diarrhea, the hemolytic uremic syndrome, or thrombotic thrombocytopenic purpura because the infection can masquerade as gastrointestinal bleeding of noninfectious cause, the antecedent diarrhea may be resolved and forgotten by the time the hemolytic uremic syndrome or thrombotic thrombocytopenic purpura is diagnosed, and the detection of E. coli O157:H7 requires specific stool culture techniques.
Prevalence of suicide attempt and clinical characteristics of suicide attempters with obsessive-compulsive disorder: a report from the International College of Obsessive-Compulsive Spectrum Disorders (ICOCS) (2017)

Our international study found a history of SA prevalence of ~15% in OCD patients, with higher rates of psychiatric and medical comorbidities and previous hospitalizations in patients with a previous SA. Along with potential geographical influences, the presence of the abovementioned features should recommend additional caution in the assessment of suicide risk in OCD patients.
Interleukin-6 is a growth factor for nonmalignant human plasmablasts (2001)

Interleukin-6 (IL-6), although often regarded as a B-cell differentiation factor, was recently described as the essential survival factor for human plasmablasts in vivo in reactive plasmacytosis. The present study reinvestigated the roles of IL-6 and IL-2 in the generation of plasma cells from human memory B cells in vitro. The cells involved in this differentiation process were identified as preplasmablasts (CD20+/-CD38+/-CD138-), plasmablasts (CD20-CD38++CD138-), and early plasma cells (CD20-CD38+++CD138+++). IL-2 or IL-10 induced a strong generation of plasmablasts and early plasma cells (PCs). Compared to IL-2 or IL-10, IL-6 alone was inefficient at PC generation. However, when combined with IL-2 or IL-10, IL-6 enhanced generation of early PCs. Moreover, anti-IL-6 monoclonal antibody markedly reduced IL-2-induced generation of early plasma cells, but not of plasmablasts. These roles of IL-2 and IL-6 were consistent with the difference in the expression of their respective receptors (R). CD25 (IL-2Ralpha) was increased 72 +/- 10-fold on activated B cells, but decreased and then disappeared on plasmablasts. Conversely, CD126 (IL-6Ralpha) was barely expressed on activated B cells, but increased 18 +/- 2-fold on preplasmablasts. Finally, IL-6 enhanced the proliferation (2-fold increase) of IL-2-generated plasmablasts. In conclusion, the data indicate that IL-6 is a growth factor for nonmalignant human plasmablasts.
Novel Method of Converting Metallic-Type Carbon Nanotubes to Semiconducting-Type Carbon Nanotube Field-Effect Transistors (2006)

Depending on the chirality, single-walled carbon nanotubes (SWNTs) can be either metallic or semiconducting. Thus far, the production of SWNTs, irrespective of synthesis methods, still yields a mixture of both types, with the metallic type being prevalent. However, semiconducting-type SWNTs are needed for carbon nanotube field-effect transistors (CNT-FETs) as well as many sensors. This is because only the semiconducting-type SWNTs can be effectively modulated by the gate voltage. In contrast, the lack of field effect in metallic-type SWNTs adversely impacts their applications in high-performance electronic devices. In this study, we demonstrate for the first time a novel plasma treatment method that allows us to convert metallic-type carbon nanotubes to semiconducting-type CNT-FETs. On the basis of our experimental results, we believe that the ion bombardment during Ar plasma treatment attacks both metallic- and semiconducting-type nanotubes; however, the metallic-type carbon nanotubes are more vulnerable to the attack than those of the semiconducting type, and are subsequently transformed into the latter type.
Multicasting to multiple groups over broadcast channels (1994)

Multicasting is a communication mode in which a given source communicates with a subset of the entire network user population. Previous work in this area concentrated on the multicast problem of a single source that always communicates with the same destination group. In this paper we investigate a more natural case of multicast communication where a single source communicates with several different destination groups. Specially, we focus on the design and analysis of multicast data link protocols for this environment. Straightforward implementations of such protocols are inappropriate in the case of a large destination population, as a source will have to store a large amount of state information even if it maintains only a single variable per destination. In most typical applications, though. The total destination population is large, the number of destinations that any given source is in conversation with, is typically small. We propose a framework for adapting protocols so that memory requirement does not grow with the total destination population but depends upon the number of destinations actually in communication with the source. The savings in memory are achieved by slightly increasing the amount of communication. We address the performance of such a protocol in an environment of a broadcast channel. We analyze several strategies and control techniques and demonstrate the tradeoff between throughput and the amount of memory.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Saturation Mutagenesis of Human Interleukin-3 (1995)

A deletion variant of human interleukin-3, hIL-3(15-125), was produced in the periplasmic space of Escherichia coli and had full activity in an AML193.1.3 cell proliferation assay. Libraries of random single-amino acid substitutions were constructed at each of 105 positions in the gene for hIL-3(15-125). Approximately eight single-site substitutions at each position were produced in osmotic shock fractions and screened for activity. 15 mutants were found with bioactivity of 5-26-fold greater than that of native hIL-3. The majority of amino acids in hIL-3(15-125) could be substituted without substantial loss of activity. Substitution of residues predicted to be in the hydrophobic core of the protein often resulted in reduced activity and/or low accumulation levels. Only five residues predicted to be on the surface of the protein were intolerant of substitution and hence are candidates for sites of interaction with the receptor. We therefore propose that the majority of residues in hIL-3 serve a structural role and permit the display of a few key residues in the correct configuration for recognition by the receptor.
Ordered Mesoporous Sb-, Nb-, and Ta-Doped SnO2 Thin Films with Adjustable Doping Levels and High Electrical Conductivity (2009)

This paper describes the synthesis and electrical properties of self-organized Sb-, Nb-, and Ta-doped SnO(2) thin films with adjustable doping levels. These transparent conducting oxides (TCOs) were prepared using a poly(ethylene-co-butylene)-b-poly(ethylene oxide) diblock copolymer as well as a novel polyisobutylene-b-poly(ethylene oxide) as organic templates. All samples are highly crystalline and have ordered cubic pore-solid architectures after removal of the polymer template by calcination; however, the electrical conductivity is not identical. The films are characterized by a combination of small- and wide-angle X-ray diffraction/scattering, SEM/TEM imaging, and X-ray photoelectron spectroscopy. Resistivity measurements conducted on the mesoporous frameworks show that the electrical properties strongly depend on both the degree of crystallinity and the elemental makeup. Considerable enhancements of the electrical properties result when the films are doped with antimony and treated in N(2) at elevated temperatures. Such TCO materials show electrical resistivities which are--despite the mesoporous morphology--only 1 order of magnitude higher than reported values for dense Sb-doped SnO(2) films.
Evidence of relative iron deficiency in platelet‐ and plasma‐pheresis donors correlates with donation frequency (2016)

This pilot study demonstrates that apheresis donors are relatively iron deficient compared to controls and supports the premise that frequent apheresis donation correlates with relatively iron restricted erythropoiesis. An analysis of iron- and erythropoiesis-related parameters in a broader population of frequent apheresis donors (i.e., female and non-white donors) may demonstrate larger deficits and an even greater potential benefit of iron replacement. J. Clin. Apheresis 31:551-558, 2016. © 2015 Wiley Periodicals, Inc.
Immunogenicity of protein therapeutics: The key causes, consequences and challenges (2010)

The immunogenicity of protein therapeutics has so far proven to be difficult to predict in patients, with many biologics inducing undesirable immune responses directed towards the therapeutic resulting in reduced efficacy, anaphylaxis and occasionally life threatening autoimmunity. The most common effect of administrating an immunogenic protein therapeutic is the development of a high affinity anti-therapeutic antibody response. Furthermore, it is clear from clinical studies that protein therapeutics derived from endogenous human proteins are capable of stimulating undesirable immune responses in patients, and as a consequence, the prediction and reduction of immunogenicity has been the focus of intense research. This review will outline the principle causes of the immunogenicity in protein therapeutics, and describe the development of pre-clinical models that can be used to aid in the prediction of the immunogenic potential of novel protein therapeutics prior to administration in man.
Ribonucleases as antiviral agents (2014)

Many ribonucleases (RNases) are able to inhibit the reproduction of viruses in infected cell cultures and laboratory animals, but molecular mechanisms of their antiviral activity remain unclear. The review observes the most known RNases which possess established antiviral effects, actually intracellular RNases (RNase L, MCPIPI protein, eosinophylic RNases) as well as exogenously applied ones (RNase A, BS-RNase, onconase, binase, synthetic RNases). Attention is given on two important but not always obligatory aspects in molecule of RNases, which have antiviral properties: catalytic activity and ability to the dimerization. The hypothetic scheme of virus elimination by exogenous RNases, that reflects possible types of interaction of viruses and RNases with a cell, is proposed. The evidence for RNases as classical components of immune defense which are perspective agents for development of new antiviral therapeutics is produced.
Probing the Origin of Acetyl-CoA and Oxaloacetate Entering the Citric Acid Cycle from the 13C Labeling of Citrate Released by Perfused Rat Hearts (1997)

We present a strategy for simultaneous assessment of the relative contributions of anaplerotic pyruvate carboxylation, pyruvate decarboxylation, and fatty acid oxidation to citrate formation in the perfused rat heart. This requires perfusing with a mix of 13C-substrates and determining the 13C labeling pattern of a single metabolite, citrate, by gas chromatography-mass spectrometry. The mass isotopomer distributions of the oxaloacetate and acetyl moieties of citrate allow calculation of the flux ratios: (pyruvate carboxylation)/(pyruvate decarboxylation), (pyruvate carboxylation)/(citrate synthesis), (pyruvate decarboxylation)/(citrate synthesis) (pyruvate carboxylation)/(fatty acid oxidation), and (pyruvate decarboxylation)/(fatty acid oxidation). Calculations, based on precursor-product relationship, are independent of pool size. The utility of our method was demonstrated for hearts perfused under normoxia with [U-13C3](lactate + pyruvate) and [1-13C]octanoate under steady-state conditions. Under these conditions, effluent and tissue citrate were similarly enriched in all 13C mass isotopomers. The use of effluent citrate instead of tissue citrate allows probing substrate fluxes through the various reactions non-invasively in the intact heart. The methodology should also be applicable to hearts perfused with other 13C-substrates, such as 1-13C-labeled long chain fatty acid, and under various conditions, provided that assumptions on which equations are developed are valid.
Genetic alterations in the peritumoral stromal cells of malignant and borderline epithelial ovarian tumors as indicated by allelic imbalance on chromosome 3p (2003)

Stromal accumulation of hyaluronan in epithelial ovarian cancers is an independent predictor of tumor spreading and unfavorable outcome of the disease. We started to screen for chromosomal causes of this accumulation by studying deletions in 3p21.3, a region harboring 3 hyaluronidase genes (HYAL1-3) among other potentially important tumor suppressors. Using 6 microsatellite markers from this region, allelic imbalance was found in 60-87% of the informative tumor cells microdissected from histologic sections of 58 patients with epithelial ovarian cancer. However, adjacent stromal cells originally intended as controls showed allelic imbalance at a frequency almost as high as the tumor cells (52-80%). A further laser capture microdissection on 10 borderline tumors also showed a high rate of allelic imbalance, both in the epithelial and stromal cells, but with a pattern slightly different from cancers. Allelic imbalance in the tumor epithelium or stroma was not correlated with the accumulation of hyaluronan or clinicopathologic parameters, including tumor stage and grade. The results suggest that factors other than inactivation of the HYAL1-3 genes are responsible for hyaluronan accumulation in epithelial ovarian tumors. Moreover, the results indicate that the stromal cells of the epithelial ovarian cancers not only respond to the signals from malignant epithelium but also have themselves undergone genetic alterations in markers partly identical to those in the cancer epithelial cells and may actively contribute to the development of the tumor from its early stages to the late determinants of patient mortality.
Pain: a review of three commonly used pain rating scales (2005)

In order to use pain-rating scales well clinicians need to appreciate the potential for error within the tools, and the potential they have to provide the required information. Interpretation of the data from a pain-rating scale is not as straightforward as it might first appear.
Interpretation Model for Fracture Calibration Tests in Naturally Fractured Reservoirs (1994)

Abstract Recent work provided a model for the fracture calibration test in a homogeneous reservoir and an interpretation methodology that enables determination of the formation permeability. The previous study used a rate-dependent skin for the filtercake resistance. Pressure drop in the formation was modeled using a closed form solution for linear flow. The need to analyze tests conducted in naturally fractured reservoirs has motivated the work in this paper. To model dual-porosity reservoir heterogeneity, the linear flow closed form solution was replaced by an analytical solution. The heterogeneous model uses a standard pressure transient model formulation while incorporating the filtercake resistance from the previous work. Analysis of data from fracture calibration tests in naturally fractured reservoirs shows that the homogeneous model fails to capture transient behavior attributed to natural fractures. Sensitivity studies using the new model illustrate the pressure falloff response behavior and show what can be determined from the failoff analysis.
A role for survivin in chemoresistance of endothelial cells mediated by VEGF (2002)

Although standard anticancer chemotherapeutic drugs have been designed to inhibit the survival or growth of rapidly dividing tumor cells, it is possible to enhance the efficacy of such drugs by targeting the proliferating host endothelial cells (ECs) of the tumor vasculature. A theoretical advantage of this strategy lies in the possibility of circumventing, or significantly delaying, acquired drug resistance driven by the genetic instability of tumor cells. Here, we show that both vascular endothelial growth factor (VEGF) and basic fibroblast growth factor significantly reduce the pro-apoptotic potency of chemotherapy on both micro- and macrovascular ECs. This cytoprotection to drug toxicity was found to be phosphatidylinositol 3-kinase-dependent and could be recapitulated in the absence of VEGF by overexpressing the dominant-active form of the serine/threonine kinase protein kinase B/Akt. Downstream of phosphatidylinositol 3-kinase, we also show that survivin plays a pivotal role in VEGF-mediated EC protection by preserving the microtubule network. In this respect, its induction effectively protects ECs against chemotherapeutic damage, whereas overexpression of its dominant-interfering mutant (C84A) abrogates the protective effects of VEGF. Accordingly, the potency of VEGF as a chemoprotectant was more pronounced with drugs that interfere with microtubule dynamics than those that damage DNA. These studies implicate a role for survivin up-regulation as a novel mechanism of EC drug "resistance" and support the notion that angiogenic factors that induce the expression of survivin may act to shield tumor ECs from the apoptotic effects of chemotherapy. Thus, exploiting chemotherapeutic drugs as antiangiogenics is likely to be compromised by the high concentrations of proangiogenic survival/growth factors present in the tumor microenvironment; targeting EC survival pathways should improve the antiangiogenic efficacy of antineoplastic agents, particularly microtubule-inhibitor drugs.