gebhart/patrepeval huggingface dataset:
Anti-tumor necrosis factor therapy in sepsis: Update on clinical trials and lessons learned (2001)

Anti-TNF strategies are only partially effective in patients with sepsis. Although individual studies show small, nonsignificant benefits, analysis of all trial data as well as data from a recent trial in a large population of septic patients show that anti-TNF strategies may confer a small survival benefit. Better characterization of patients and a more multimodal approach by concomitantly targeting other mediators involved in sepsis may be helpful in enlarging the clinical benefit of anti-TNF therapy.
Characterization of the Signaling Capacities of the Novel gp130-like Cytokine Receptor (2004)

The gp130-like receptor (GPL) is a recently cloned member of the family of type I cytokine receptors. The name reflects its close relationship to gp130, the common receptor subunit of the interleukin (IL)-6-type cytokines. Indeed, the recently proposed ligand for GPL, IL-31, is closely related to the IL-6-type cytokines oncostatin M, leukemia inhibitory factor, and cardiotrophin-1. The second signal transducing receptor for IL-31 seems to be the oncostatin M receptor beta (OSMRbeta). The present study characterizes in depth the molecular mechanisms underlying GPL-mediated signal transduction. GPL is a strong activator of STAT3 and STAT5, whereas STAT1 is only marginally tyrosine-phosphorylated. We identify tyrosine residues 652 and 721 in the cytoplasmic region of the longest isoform of GPL (GPL(745)) as the major STAT5- and STAT3-activating sites, respectively. Additionally, we demonstrate Jak1 binding to GPL and its activation in heteromeric complexes with the OSMRbeta but also in a homomeric receptor complex. Most interesting, unlike OSMRbeta and gp130, GPL is insufficient to mediate ERK1/2 phosphorylation. We propose that this is due to a lack of recruitment of the tyrosine phosphatase SHP-2 or the adaptor protein Shc to the cytoplasmic domain of GPL.
Intercellular Transfer of the Virally Derived Precursor Form of Acid α-Glucosidase Corrects the Enzyme Deficiency in Inherited Cardioskeletal Myopathy Pompe Disease (2001)

Pompe disease is a lethal cardioskeletal myopathy in infants and results from genetic deficiency of the lysosomal enzyme acid alpha-glucosidase (GAA). Genetic replacement of the cDNA for human GAA (hGAA) is one potential therapeutic approach. Three months after a single intramuscular injection of 10(8) plaque-forming units (PFU) of E1-deleted adenovirus encoding human GAA (Ad-hGAA), the activity in whole muscle lysates of immunodeficient mice is increased to 20 times the native level. Direct transduction of a target muscle, however, may not correct all deficient cells. Therefore, the amount of enzyme that can be transferred to deficient cells from virally transduced cells was studied. Fibroblasts from an affected patient were transduced with AdhGAA, washed, and plated on transwell culture dishes to serve as donors of recombinant enzyme. Deficient fibroblasts were plated as acceptor cells, and were separated from the donor monolayer by a 22-microm pore size filter. Enzymatic and Western analyses demonstrate secretion of the 110-kDa precursor form of hGAA from the donor cells into the culture medium. This recombinant, 110-kDa species reaches the acceptor cells, where it can be taken up by mannose 6-phosphate receptor-mediated endocytosis. It then trafficks to lysosomes, where Western analysis shows proteolytic processing to the 76- and 70-kDa lysosomal forms of the enzyme. Patient fibroblasts receiving recombinant hGAA by this transfer mechanism reach levels of enzyme activity that are comparable to normal human fibroblasts. Skeletal muscle cell cultures from an affected patient were also transduced with Ad-hGAA. Recombinant hGAA is identified in a lysosomal location in these muscle cells by immunocytochemistry, and enzyme activity is transferred to deficient skeletal muscle cells grown in coculture. Transfer of the precursor protein between muscle cells again occurs via mannose 6-phosphate receptors, as evidenced by competitive inhibition with 5 mM mannose 6-phosphate. In vivo studies in GAA-knockout mice demonstrate that hepatic transduction with adenovirus encoding either murine or human GAA can provide a depot of recombinant enzyme that is available to heart and skeletal muscle through this mechanism. Taken together, these data show that the mannose 6-phosphate receptor pathway provides a useful strategy for cell-to-cell distribution of virally derived recombinant GAA.
DEBVisDic - First Version of New Client-Server Wordnet Browsing and Editing Tool (2005)

In this paper, we present the new wordnet development tool
called DEBVisDic. It is built on the recently developed
platform for client-server XML databases, called DEB II. This
platform is able to cover many possible applications, from
which we concentrate on the new, complete reimplementation of
one of the most-spread wordnet editor and browser - VisDic. We
argue for the benefits the new DEB II platform brings to
wordnet editing and to XML databases in general. In the paper,
we describe the state of the implementation, the insides and
interfaces of the DEBVisDic tool. We also discuss its
functionality and some distinctions in comparison with other
dictionary writing systems.
Antibody to native human immunodeficiency virus type 1 envelope glycoproteins induced by IIIB and MN recombinant gp120 vaccines. The NIAID AIDS Vaccine Evaluation Group (1996)

The ability of antibody induced by MN and IIIB recombinant gp120 (rgp120) human immunodeficiency virus type 1 (HIV-1) vaccines the bind to oligomeric native and monomeric recombinant HIV-1 envelope glycoproteins (rgp 120) was measured in 25 uninfected, healthy adult volunteers. A major focus was to evaluate the effect of simultaneous and sequential immunization with vaccines representing different strains of HIV-1 on the ability to broaden cross-reactivity of antibodies against these and other HIV-1 strains. A flow cytometric indirect immunofluorescence assay (FIFA) to detect vaccine-induced antibody to envelope glycoprotein expressed by infected and rgp120-coated target cells was used, MN rgp120 HIV-1 vaccine given alone and coadministered with IIIB rgp120 HIV-1 vaccine elicited antibody which bound to cells infected with HIV-1MN, HIV-IIIB, HIV-1RF, and HIV-1-SF2. The presence of envelope glycoprotein-binding antibody detected by FIFA correlated to a moderate degree with functional antibody against HIV-1MN and HIV-IIIB. Priming immunization with IIIB rgp120 HIV-1 vaccine followed by booster injections of MN rgp120 HIV-1 vaccine resulted in increased cross-reactive antibody binding to these and heterologous clade B HIV-1 strains infecting cells. MN rgp120 HIV-1 vaccine given alone was better able to induce cross-reactive antibody to cells infected with heterologous HIV-1 laboratory strains than was IIIB rgp120 HIV-1 vaccine given alone. The vaccines induced binding antibody to rgp120 possessing the amino acid sequence of a clade E HIV-1 strain as measured by enzyme-linked immunosorbent assay. Levels of antibody binding to cells infected with clade B HIV-1 and cells coated with monomeric rgp120 were greater than that induced by HIV-1IIIB-based gp160 vaccines in previous studies.
Study on mechanism of cell damage caused by microbubbles exposed to ultrasound (2003)

To elucidate the mechanisms of cell damage caused by microbubbles exposed to ultrasound, two series of experiments were carried out. In one series of experiments, microbubbles and cells were exposed to 1-MHz pulsed ultrasound and observed using a high-speed camera. In another series of experiments, endothelial cells were exposed to ultrasound with and without microbubbles, and the viabilities of the cells were evaluated by fluorescent staining. In the high-speed images, generation of a small stream of the surrounding liquid caused by nonuniform contraction of a microbubble and deformation of a cell beside the bubble were observed. In the cell viability test, the percentage of damaged cells in the presence of microbubbles that had been exposed to ultrasound was significantly higher than that of cells without microbubbles that had been exposed to ultrasound. These results indicated that bubbles exposed to ultrasound causes mechanical stress to act on cells and that this mechanical stress may cause cell injury.
Ultrafast Pulse Shaping Approaches to Quantum Computing (2003)

Quantum computing exploits the quantum-mechanical nature of matter to exist in multiple possible states simultaneously. This new approach promises to revolutionize the present form of computing. As an approach to quantum computing, we discuss ultrafast laser pulse shaping, in particular, the acousto-optic modulator based Fourier-Transform pulse-shaper, which has the ability to modulate tunable high power ultrafast laser pulses. We show that optical pulse shaping is an attractive route to quantum computing since shaped pulses can be transmitted over optical hardware and the same infrastructure can be used for computation and optical information transfer. We also address the problem of extending coherence-times for optically induced processes.
Resistive-Pulse SensingFrom Microbes to Molecules (2000)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTResistive-Pulse SensingFrom Microbes to MoleculesHagan Bayley and Charles R. MartinView Author Information Department of Medical Biochemistry and Genetics, Texas A&M University System Health Science Center, 440 Reynolds Medical Building, College Station, Texas 77843-1114, Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, and Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32605-1200 Cite this: Chem. Rev. 2000, 100, 7, 2575–2594Publication Date (Web):June 21, 2000Publication History Received19 October 1999Published online21 June 2000Published inissue 1 July 2000https://pubs.acs.org/doi/10.1021/cr980099ghttps://doi.org/10.1021/cr980099gresearch-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views4101Altmetric-Citations452LEARN 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:Ions,Membranes,Molecules,Peptides and proteins,Vesicles Get e-Alerts
Serum biobank certification and the establishment of quality controls for biological fluids: examples of serum biomarker stability after temperature variation (2007)

Biomarkers that have an on-off response to temperature variation could serve as quality indicators for the core processes of biobanking, which are the preparation and storage of biological fluids. The identification of such biomarkers is needed.
An Unlikely Sugar Substrate Site in the 1.65 Å Structure of the Human Aldose Reductase Holoenzyme Implicated in Diabetic Complications (1992)

Aldose reductase, which catalyzes the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of a wide variety of aromatic and aliphatic carbonyl compounds, is implicated in the development of diabetic and galactosemic complications involving the lens, retina, nerves, and kidney. A 1.65 angstrom refined structure of a recombinant human placenta aldose reductase reveals that the enzyme contains a parallel beta 8/alpha 8-barrel motif and establishes a new motif for NADP-binding oxidoreductases. The substrate-binding site is located in a large, deep elliptical pocket at the COOH-terminal end of the beta barrel with a bound NADPH in an extended conformation. The highly hydrophobic nature of the active site pocket greatly favors aromatic and apolar substrates over highly polar monosaccharides. The structure should allow for the rational design of specific inhibitors that might provide molecular understanding of the catalytic mechanism, as well as possible therapeutic agents.
In Vitro Particle Size Distributions in Electronic and Conventional Cigarette Aerosols Suggest Comparable Deposition Patterns (2012)

Nicotine delivery may depend on vaping technique, particle evolution, and cloud effects. Predicted 10% arterial and 15% venous delivery may describe bystander exposure better than vapers exposure.
Fundamentals of tissue engineering: Tissues and applications (2002)

As the average life expectancy has increased with advances in the medical sciences the degenerative diseases have become a critical issue. More organs, joints, and other critical body parts wear out and need to be replaced because people wish to maintain a good quality of life in their old ages. Existing autograft materials involve harvesting a tissue from one location and transplanting it into another part of the same patient (e.g. Coronary bypass and spinal fusion). However, they generally have poor morphologies and limited resource that leads to donor site morbidity. This may impair their population with cells and vascularization. There is also risk of infection and pain. Surgical harvesting is also expensive (Ileac crest graft $1000–$9,000/procedure). Allografting involves harvesting tissue or organs from a donor and then transplanting it to the patient. Transplantation from donors is not always the solution for diseased and dysfunctioned organs because of the high risk of rejection, due to cell-mediated immune responses to transplantation alloantigens and high risk of transmission of disease and tumor development, and scarcity of donor organs. For example, in 1998, there were 22 170 organ transplants in the U.S and this number increased to 74 800 by February 2001 (some patients died while waiting for suitable donor organs) [1]. Man-made materials and devices like artificial hearts and valves, prosthetic hip, and breast implants are also widely used but they are subject to fatigue, fracture, toxicity, inflammation, wear, and do not remodel with time. They are best suited as temporary therapies until a donor organ becomes available. However, they have had limited success due to lack of living cells and slow vascularization. Three general strategies have been adapted for the creation of new tissues [2]. First method is the “cell injection” that can be applied in replacing the function of lost metabolic organs like the liver. However, its applicability to restore the function of structural tissues like cartilage or heart valve is limited. In this method, sufficient cell mass is difficult to achieve to replace lost function. Second method is “closed system” method and that can be implanted or used as an extracorporal device. In this system, cells are isolated from the body by a semipermeable membrane that allows diffusion of nutrients and wastes but prevents large entities such as antibodies, complement factors, or immune cells from destroying the transplant. Major problems of this system are fibrous tissue overgrowth and resultant reduced diffusion of metabolic products, nutrients and wastes. Finally, as opposed to implanting bioinert materials that only mimic the shape of living tissue or provide a support structure, tissue engineering, a new field in biomedical science, has been emerging as an alternative for more than ten years.
Sequence analysis and comparison of ribosomal DNA from bovine Neospora to similar coccidial parasites. (1995)

The nuclear small subunit ribosomal RNA (nss-rRNA) gene sequence of Neospora spp. isolated from cattle was analyzed and compared to the sequences from several closely related cyst-forming coccidial parasites. Double-stranded DNA sequencing of 5 bovine Neospora spp. isolates (BPA1-4), 2 Neospora caninum isolates (NC-1 and NC-3), and 3 Toxoplasma gondii isolates (RH, GT-1, CT-1) were performed and compared to each other, as well as to other sequences available in GenBank for the NC-1 isolate, Sarcocystis muris, and Cryptosporidium parvum. There were no nucleotide differences detected between the Neospora spp. isolates from cattle and dogs. Four nucleotide differences were consistently detected when sequences of Neospora spp. isolates were compared to those of the T. gondii isolates. These results indicate that Neospora spp. and T. gondii are closely related, but distinct, species.
Adaptive Geometry Image (2008)

We present a novel post-processing utility called adaptive geometry image (AGIM) for global parameterization techniques that can embed a 3D surface onto a rectangular1 domain. This utility first converts a single rectangular parameterization into many different tessellations of square geometry images(GIMs) and then efficiently packs these GIMs into an image called AGIM. Therefore, undersampled regions of the input parameterization can be up-sampled accordingly until the local reconstruction error bound is met. The connectivity of AGIM can be quickly computed and dynamically changed at rendering time. AGIM does not have T-vertices, and therefore no crack is generated between two neighboring GIMs at different tessellations. Experimental results show that AGIM can achieve significant PSNR gain over the input parameterization, AGIM retains the advantages of the original GIM and reduces the reconstruction error present in the original GIM technique. The AGIM is also for global parameterization techniques based on quadrilateral complexes. Using the approximate sampling rates, the PolyCube-based quadrilateral complexes with AGIM can outperform state-of-the-art multichart GIM technique in terms of PSNR.
Initial clinical laboratory experience in noninvasive prenatal testing for fetal aneuploidy from maternal plasma DNA samples (2013)

This report suggests that clinical testing of maternal cell-free DNA for fetal aneuploidy operates within performance parameters established in validation studies. Noninvasive prenatal testing is sensitive to biological contributions from placental and maternal sources.
Comparison of the reactivities of baculovirus-expressed recombinant Norwalk virus capsid antigen with those of the native Norwalk virus antigen in serologic assays and some epidemiologic observations (1993)

Since the discovery of the Norwalk virus (NV) by immune electron microscopy (IEM) in 1972, serologic studies with this virus have relied on particle-positive fecal material from infected volunteers as the source of antigen because it has not been possible to propagate this virus in cell culture. However, the recent cloning of the NV (strain 8FIIa) genome and expression of the capsid protein in a baculovirus system to form "virus-like particles" has provided a consistent source of antigen (designated rNV). The purpose of the present study was to compare the antigenicities of these rNV particles with those of native NV antigen derived from human fecal material by using well-characterized sera obtained from earlier studies. In IEM studies, the rNV antigen reacted with NV-specific antibodies in a manner similar to that observed previously when particle-positive fecal material was used as antigen. In addition, a direct enzyme-linked immunosorbent assay, in which the rNV antigen was used as antigen, proved efficient and specific for the detection of serologic responses to NV compared with the previously established techniques of IEM and blocking antibody immunoassays in which particle-positive fecal material was used as the antigen. The availability of an unlimited source of antigen will enable serologic studies that will greatly increase our understanding of the epidemiology of NV and its role in human enteric illness.
The Photochemistry of Steroidal 6-Membered Cyclic α-Nitro Ketones (1988)

Abstract The results of the photolysis of five steroidal 6-membered cyclic α-nitro ketones in ethanol are described. Irradiation with a Pyrex-filtered light of 2-nitro-5α-cholestan-3-one in ethanol, which exists exclusively in the enol form in the solvent, resulted in a new photorearrangement and gave 5α-cholestane-2,3-dione 3-oxime with the accompanying formation of the corresponding α-diketone. We propose a path involving a nitro–nitrite rearrangement for this anomalous formation of 5α-cholestane-2,3-dione 3-oxime. However, similar irradiation of 4,4-dimethyl-2-nitro-5α-choloestan-3-one, which exists exclusively as the enol form in ethanol, and 3-nitro-5α-cholestan-2-one, which is in an 1 : 1 equilibrium mixture of keto and enol forms in ethanol, gave the corresponding α-hydroxyimino ketone and α-diketone respectively. Irradiation of 4β-nitro-5β-cholestan-3-one and 6α-nitro-5α-cholestan-7-one, both of which exist as the keto form in ethanol, gave similarly the corresponding α-hydroxyimino ketone respectively, but without the accompanying formation of α-diketone. The α-hydroxyimino ketones from the above four 6-membered cyclic α-nitro ketones arise through the hydrogen abstraction by the n,π* excited nitro group of the keto forms of the α-nitro ketones followed by the elimination of the element of water, while α-diketones are formed via the nitro–nitrite rearrangement of the excited nitro group of the enol forms.
Phase II study of docetaxel in patients with metastatic pancreatic cancer: a Japanese cooperative study (1999)

Docetaxel has been reported to show promising anti-tumour activity in pancreatic ductal cancer (PC). This study was conducted to evaluate the activity and toxicity of moderate-dose (60 mg m(-2)) docetaxel in Japanese chemo-naive patients with measurable metastatic PC. The patients had a performance status of 0-2. They received docetaxel intravenously over a 1- to 2-h period without any premedication for hypersensitivity reactions. This treatment was repeated every 3-4 weeks with dose adjustments based on the toxic effects observed. Twenty-one patients were eligible and treated with docetaxel. The median number of courses was 2 (range, 1-4). None of the patients achieved an objective response; seven showed no change and 13 showed progressive disease. In one patient, the response was not assessable because of early death. The median survival time for all patients was 118 days. The main grade 3-4 toxicities by patient were leucocytopenia (67%) and neutropenia (86%). Other grade 3-4 toxicities included anaemia (10%), thrombocytopenia (5%), nausea/vomiting (29%), anorexia (29%), GOT/GPT increase (10%), alkaline phosphatase increase (14%), malaise/fatigue (33%) and alopecia (24%). In conclusion, docetaxel, administered on this schedule, did not show significant anti-tumour activity in patients with metastatic PC.