gebhart/patrepeval huggingface dataset:
Construction and Characterization of Vaccine Strains of Salmonella Harboring Mutations in Two Different aro Genes (1988)

Derivatives of the mouse-virulent Salmonella typhimurium strain SL1344 were constructed harboring stable mutations in aroC alone or in aroC and aroA together. Fifty percent lethal doses after intravenous inoculation of the mutants into BALB/c mice were determined, and the mutants were as highly attenuated as were SL1344 aroA derivatives. All aro-dependent derivatives persisted in vivo at similar levels and for similar intervals in the livers and spleens of BALB/c mice infected intravenously. Mice vaccinated orally with 10(10) live organisms of the different derivatives survived and were well protected against oral challenge with virulent S. typhimurium. A Salmonella typhi Ty2 derivative, designated WBL2000, was constructed that harbors well-defined, stable mutations in both aroA and aroC.
Critical proinflammatory role of thymic stromal lymphopoietin and its receptor in experimental autoimmune arthritis (2011)

TSLP and its receptor enhance Th17-driven arthritis and tissue destruction in experimental arthritis. The increased expression of TSLP as well as the increased number of TSLPR-expressing cells in the joints of patients with RA suggest that TSLP and its receptor constitute novel therapeutic targets in RA.
Corinthian White-Ground Lekythoi (2007)

Prenatal suspicion of DSD can occur through discordant prenatal testing and has been observed at our clinic in recent years, in line with other recent studies. Contributing factors to these prenatal presentations could be increased referrals to the clinic, and increased use of non-invasive prenatal testing, which can lead to inaccurate or discordant sex identification. The prenatal suspicion of a potential DSD can be associated with parental distress, underscoring the need for adequate counseling for tests that determine fetal sex, including cell-free DNA.
A genomic screen identifies TYRO3 as a MITF regulator in melanoma (2009)

Malignant melanoma is the most aggressive form of cutaneous carcinoma, accounting for 75% of all deaths caused by skin cancers. Microphthalmia-associated transcription factor (MITF) is a master gene regulating melanocyte development and functions as a "lineage addiction" oncogene in malignant melanoma. We have identified the receptor protein tyrosine kinase TYRO3 as an upstream regulator of MITF expression by a genome-wide gain-of-function cDNA screen and show that TYRO3 induces MITF-M expression in a SOX10-dependent manner in melanoma cells. Expression of TYRO3 is significantly elevated in human primary melanoma tissue samples and melanoma cell lines and correlates with MITF-M mRNA levels. TYRO3 overexpression bypasses BRAF(V600E)-induced senescence in primary melanocytes, inducing transformation of non-tumorigenic cell lines. Furthermore, TYRO3 knockdown represses cellular proliferation and colony formation in melanoma cells, and sensitizes them to chemotherapeutic agent-induced apoptosis; TYRO3 knockdown in melanoma cells also inhibits tumorigenesis in vivo. Taken together, these data indicate that TYRO3 may serve as a target for the development of therapeutic agents for melanoma.
Immunological responses to a multi-peptide vaccine targeting cancer-testis antigens and VEGFRs in advanced pancreatic cancer patients (2013)

The prognosis of patients with advanced pancreatic cancer is extremely poor and there are only a few standard treatments. Here, we report the results of a Phase I clinical trial to investigate the safety, immunostimulatory effects, and antineoplastic activity of a multi-target vaccine composed of four distinct peptides derived from cancer-testis (CT) antigens and vascular endothelial growth factor receptors (VEGFRs). Nine patients with unresectable, advanced pancreatic cancer who were refractory to standard chemotherapy were enrolled. Each patient was vaccinated with HLA-A*2402-restricted peptides derived from the CT antigens kinesin family member 20A (KIF20A) and cell division cycle-associated 1 (CDCA1) as well as from VEGFR1 and VEGFR2 subcutaneously once a week, and disease progression was evaluated up to 6 mo later. Adverse events were assessed using the Common Terminology Criteria for Adverse Events v. 3.0. Immunological responses were monitored by ELISPOT assays and flow cytometry based on peptide-specific dextramers. The clinical outcomes that were measured were tumor response, progression-free survival (PFS) and overall survival (OS). In general, the multi-peptide vaccine was well-tolerated, and no grade 3 or 4 adverse events were observed upon vaccination. Peptide-specific T-cell responses were detected in all 9 patients, and clinical benefits were observed in four of them. Median PFS and OS were 90 and 207 d, respectively. The elicitation of multiple and robust peptide-specific T-cell responses as well as the status of host lymphocytes may be useful prognostic factors among patients with advanced pancreatic cancer treated with peptide-based anticancer vaccines.
Parallel patterning with nanochannel glass replica membranes (1996)

Nanochannel glass replica membranes , a recent invention, can be used for parallel patterning of substrates, for example as a shadow mask in reactive ion etching. The preparation of the membranes—formed by physical vapor deposition on wafers that have been cut from bundles of two types of glass fibers that are repeatedly drawn down to the correct dimensions—their uses and their advantages are described. How the size, position, geometric pattern, and packing density of the voids in the membranes can be controlled to a high degree is outlined.
COPING WITH COMPETITION. (1993)

8 ASUBTITLE: KOREAN AIR IS ALREADY THE THIRD-LARGEST AIRLINE IN ASIA AND IS EYEING NEW OPPORTUNITIES FOR EXPANSION: JOHN BAILEY DISCOVERS HOW KOREAN IS FACING UP TO COMPETITION AND RECESSION AT HOME AND ABROAD.
Regulation of cytokines, cytokine inhibitors, and acute-phase proteins following anti-TNF-alpha therapy in rheumatoid arthritis. (1999)

Treatment with a chimeric mAb to TNF-alpha has been shown to suppress inflammation and improve patient well-being in rheumatoid arthritis (RA), but the mechanisms of action of such treatment have not been fully explored. Here we show that in vivo administration of anti-TNF-alpha Ab, using a longitudinal analysis, results in the rapid down-regulation of a spectrum of cytokines, cytokine inhibitors, and acute-phase proteins. Marked diurnal variation in the serum levels of some of these were detected. These results were consistent with the concept of a cytokine-dependent cytokine cascade, and the degree of clinical benefit noted after anti-TNF-alpha therapy is probably due to the reduction in many proinflammatory mediators apart from TNF-alpha, such as IL-6, which reached normal levels within 24 h. Serum levels of cytokine inhibitors such as soluble p75 and p55 TNFR were reduced as was IL-1 receptor antagonist. Reductions in acute-phase proteins occurred after serum IL-6 fell and included serum amyloid A, haptoglobin, and fibrinogen. The latter reduction could be of importance, as it is a risk factor for atherosclerosis, which is augmented in RA patients.
SYNTHESIS AND PROPERTIES OF OLIGOADENYLIC ACIDS CONTAINING 2′-5′ PHOSPHORAMIDE LINKAGE (1984)

Abstract Oligoadenylic acids containing 2′-5′ phosphoramide linkage were prepared by poly (U) template-directed condensation. Some of their properties are described.
Development of Spectral Disease Indices for ‘Flavescence Dorée’ Grapevine Disease Identification (2017)

Spectral measurements are employed in many precision agriculture applications, due to their ability to monitor the vegetation's health state. Spectral vegetation indices are one of the main techniques currently used in remote sensing activities, since they are related to biophysical and biochemical crop variables. Moreover, they have been evaluated in some studies as potentially beneficial for detecting or differentiating crop diseases. Flavescence Dorée (FD) is an infectious, incurable disease of the grapevine that can produce severe yield losses and, hence, compromise the stability of the vineyards. The aim of this study was to develop specific spectral disease indices (SDIs) for the detection of FD disease in grapevines. Spectral signatures of healthy and diseased grapevine leaves were measured with a non-imaging spectro-radiometer at two infection severity levels. The most discriminating wavelengths were selected by a genetic algorithm (GA) feature selection tool, the Spectral Disease Indices (SDIs) are designed by exhaustively testing all possible combinations of wavelengths chosen. The best weighted combination of a single wavelength and a normalized difference is chosen to create the index. The SDIs are tested for their ability to differentiate healthy from diseased vine leaves and they are compared to some common set of Spectral Vegetation Indices (SVIs). It was demonstrated that using vegetation indices was, in general, better than using complete spectral data and that SDIs specifically designed for FD performed better than traditional SVIs in most of cases. The precision of the classification is higher than 90%. This study demonstrates that SDIs have the potential to improve disease detection, identification and monitoring in precision agriculture applications.
Efficient planar fiber-to-chip coupler based on two-stage adiabatic evolution (2010)

A new, efficient adiabatic in-plane fiber-to-chip coupler design is proposed. In this design, the light from the fiber is coupled into a low-index waveguide with matching mode size. The mode is first adiabatically reduced in size with a rib taper, and then transferred into a high-index (e.g. silicon) waveguide with an inverse taper. The two-stage design allows to reduce the coupler length multiple times in comparison with pure inverse taper-based couplers of similar efficiency. The magnitude of length reduction increases with the refractive index of the low-index waveguide and the fiber mode size.
Rate of Loss of Tritiated Thymidine Label In Basal Cells In Mouse epithelial tissues (1986)

A subpopulation of epithelial cells which retains a tritiated thymidine label (termed label-retaining cells, LRCs) has been previously demonstrated in skin and oral mucosae of mice and hamsters. To examine the rate of decrease in the number of LRCs and the changes in degree of labelling, young mice were labelled with tritiated thymidine and the rate at which label was diluted from basal keratinocytes assessed for up to 90 days. The number of LRCs in each tissue examined decreased from 15 to 90 days after labelling with the epidermal tissues maintaining a higher percentage of LRCs than the oral mucosae. Grain counts for LRCs in each tissue at each time period indicated that the number of silver grains overlying LRCs also decreased with time. The observed decrease in numbers of LRCs and the change in their degree of labelling with time suggest that such cells divide slowly, a property associated with stem cells.
Production of combinatorial libraries of fused genes by sequential transposition reactions (2002)

The use of in vivo and in vitro transposition reactions to perform non-combinatorial manipulation of DNAs in molecular biology is widespread. In this work we describe a technique that utilizes two sequential, directed transposition reactions in order to carry out combinatorial DNA manipulations. The methodology relies on the use of two different mutant Tn5 transposase proteins that have different transposon end recognition specificities. We demonstrate that the technique can be used to create large libraries of random fusions between two genes. These transpositional fusions are defined by insertion of a 32 bp linker sequence. We applied the technique to a model system, chloramphenicol acetyl transferase, to create functional fusions from N- and C-terminally truncated, non-functional genes. Comparative structural analysis suggests that both sides of the linker are inserted into disordered regions in functional proteins.
Macroscopic, Hierarchical, Two-Dimensional Self-Assembly (1999)

By tailoring capillary interactions at a fluid-fluid interface, a hierarchical two-dimensional self-assembly of hexagonal millimeter-sized poly(dimethylsiloxane) plates has been demonstrated (see picture). The strength and direction of capillary forces between plates was controlled by patterning of the surfaces of the plates to be hydophobic or hydrophilic. The thick lines indicate hydrophobic faces whose mutual attraction forms the basis of capillarity.
Lethal photosensitization of bacteria in subgingival plaque from patients with chronic periodontitis (1993)

Subgingival plaque samples from patients with chronic periodontitis were exposed to light from a 7.3 mW Helium/Neon laser for 30 s in the presence and absence of 50 micrograms/ml toluidine blue O as a photosensitizer. Viable counts of various groups and species of bacteria were carried out before and after irradiation. The median numbers of viable bacteria initially present in the 30-microliters aliquots irradiated were 1.13 x 10(5) cfu (aerobes), 4.08 x 10(5) cfu (anaerobes), 4.92 x 10(3) cfu (black-pigmented anaerobes), 4.75 x 10(2) cfu (Porphyromonas gingivalis), 6.15 x 10(3) cfu (Fusobacterium nucleatum) and 1.7 x 10(4) cfu (streptococci). The dye/laser combination achieved significant reductions in the viability of these organisms, the median reductions in the viable counts being 91.1% for aerobes, 96.6% for anaerobes, 100% for black-pigmented anaerobes, P. gingivalis and F. nucleatum and 94.2% for streptococci. Overall, the viability of bacteria in the 20 plaque samples was not significantly decreased by the dye alone. However, in a small minority of samples there were indications of light-independent, dye-induced toxicity. Low-power lasers, in conjunction with appropriate photosensitizers, may be a useful adjunct to mechanical debridement in the treatment of inflammatory periodontal diseases if a similar effectiveness against subgingival plaque bacteria can be achieved in vivo.
The Prosegments of Furin and PC7 as Potent Inhibitors of Proprotein Convertases (1999)

All proprotein convertases (PCs) of the subtilisin/kexin family contain an N-terminal prosegment that is presumed to act both as an intramolecular chaperone and an inhibitor of its parent enzyme. In this work, we examined inhibition by purified, recombinant bacterial prosegments of furin and PC7 on the in vitro processing of either the fluorogenic peptide pERTKR-MCA or the human immunodeficiency virus envelope glycoprotein gp160. These propeptides are potent inhibitors that display measurable selectivity toward specific proprotein convertases. Small, synthetic decapeptides derived from the C termini of the prosegments are also potent inhibitors, albeit less so than the full-length proteins, and the C-terminal P1 arginine is essential for inhibition. The bacterial, recombinant prosegments were also used to generate specific antisera, allowing us to study the intracellular metabolic fate of the prosegments of furin and PC7 expressed via vaccinia virus constructs. These vaccinia virus recombinants, along with transient transfectants of the preprosegments of furin and PC7, efficiently inhibited the ex vivo processing of the neurotrophins nerve growth factor and brain-derived neurotrophic factor. Thus, we have demonstrated for the first time that PC prosegments, expressed ex vivo as independent domains, can act in trans to inhibit precursor maturation by intracellular PCs.
Comparison of Eight Diagnostic Algorithms for Liver Fibrosis in Hepatitis C (2011)

SAFE and BA for significant fibrosis or cirrhosis are very accurate. However, their successive use induces a significant decrease in diagnostic accuracy and a significant increase in required liver biopsy. A new fibrosis classification that synchronously combines two fibrosis tests was as accurate as successive SAFE or BA, while providing an entirely noninvasive (0% liver biopsy) and more precise (six versus two or three fibrosis classes) fibrosis diagnosis.
Development of a Mathematical Model for the Simulation of the Biodegradation of Organic Substrates in a High-Solids Anaerobic Digestion Process (1996)

A kinetic model is developed to simulate the biodegradation of the organic fraction of municipal solid waste in a high-solids complete-mix continuous-flow anaerobic digestion process. A mass balance correction factor (f) is used to account for (i) the water that is incorporated into the production of biogas, and (ii) the water vapor present in the biogas. With the inclusion of the factor f, expressions are developed to determine the substrate removal efficiency based on first-order and Monod kinetic models. Simulations using first-order and Monod kinetic models are carried out to illustrate the importance of the f factor on the substrate mass removal and microorganism concentration in the high-solids anaerobic digestion process. The effect of the value of f on kinetic constants, and the error involved in considering the high-solids process as a low-solids process are discussed. Finally, experimental results from a pilot-scale high-solids complete-mix batch-fed anaerobic digestion process are used to estimate the first-order rate constant for the biodegradable fraction of municipal solid waste.
Extending the graphics pipeline with adaptive, multi-rate shading (2014)

Due to complex shaders and high-resolution displays (particularly on mobile graphics platforms), fragment shading often dominates the cost of rendering in games. To improve the efficiency of shading on GPUs, we extend the graphics pipeline to natively support techniques that adaptively sample components of the shading function more sparsely than per-pixel rates. We perform an extensive study of the challenges of integrating adaptive, multi-rate shading into the graphics pipeline, and evaluate two- and three-rate implementations that we believe are practical evolutions of modern GPU designs. We design new shading language abstractions that simplify development of shaders for this system, and design adaptive techniques that use these mechanisms to reduce the number of instructions performed during shading by more than a factor of three while maintaining high image quality.
Recommendations for the best possible use of botulinum neurotoxin type a (Speywood units) for aesthetic applications. (2013)

The botulinum neurotoxin (BoNT) product Azzalure (manufactured by Ipsen Biopharm Limited, Wrexham, UK; distributed by Galderma), measured in Speywood units (s.U) has been available since 2009 for temporary improvement in the appearance of moderate to severe glabellar lines. Although we know much about the use of Azzalure for aesthetic indications, some aspects of product use in the clinic still require an update based on continuing and prevailing misconceptions and new clinical data. Therefore, a group of experts experienced with the use of Azzalure convened to formulate the following recommendations: (1) The key to an optimal effect is adequate dosing per injection point. Ten s.U are indicated for strong muscular activity, 5 s.U for medium activity, and approximately 2 s.U for minor activity. (2) The main factor that influences the area of effectiveness is the dosage per injection point. (3) In contrast to former beliefs, we know now that Azzalure works very fast, with some patients reporting initial drug activity after hours. (4) Various volumes can be used for dilution. However, the first choice is the recommended volume, 0.63 mL per vial of 125 s.U. Nevertheless, for clinicians changing products, keeping the volume they are used to might be an option. (5) Clinicians changing products have to be very careful not to confuse the units between different products. (6) In aesthetic BoNT-A usage, the development of antibodies is very rare and is not the common reason for insufficient results. (7) Probably the most common reason when BoNT-A is not working is the absolute or relative underdosage. The present adjunctive recommendations elaborated in an informal expert meeting should help physicians to optimize their treatment with Speywood unit products.
Automatic phrase indexing for document retrieval (1987)

An automatic phrase indexing method based on the term discrimination model is described, and the results of retrieval experiments on five document collections are presented. Problems related to this non-syntactic phrase construction method are discussed, and some possible solutions are proposed that make use of information about the syntactic structure of document and query texts.
Evaluation of Serum Procollagen Aminoterminal Propeptide III, Laminin, and Hydroxyproline as Predictors of Severe Fibrosis in Patients with Chronic Hepatitis C (2007)

In an attempt to identify biochemical analytes that could enhance the discrimination between the patients with severe liver fibrosis (F3-F4) and mild fibrosis (F1-F2) based on absolute values of biochemical markers, we measured 12 analytes, including procollagen III aminoterminal propeptide (PIIINP), laminin, proline, hydroxylproline, glycine, AST, ALT, alkaline phosphatase, albumin, total bilirubin, total protein, and prothrombin time in 252 individuals with chronic hepatitis C infection (CHC). PIIINP and laminin were determined by radio-immunoassay; the degraded amino acids were determined using high performance liquid chromatography. Statistical analyses were performed by logistic regression, and receiver operating characteristic (ROC) curves. The best linear combination of blood markers was selected by multivariate discriminant analysis (MDA) for construction of the fibrosis discriminant score (FDS). FDS, an index of five markers (PIIINP, laminin, hydroxyproline, prothrombin activity, and AST/ALT) correctly classified 82% of the patients with severe liver fibrosis at a discriminant cut-off score=-0.5 (i.e., less than -0.5 indicated severe liver fibrosis and greater than -0.5 indicated mild liver fibrosis with sensitivity (76%) and specificity (89%). This result was reproduced in a validation study with no significant difference. In conclusion, FDS is useful for identifying severe liver fibrosis in patients with CHC.
Wild-type PCSK9 inhibits LDL clearance but does not affect apoB-containing lipoprotein production in mouse and cultured cells (2005)

Mutations in Proprotein Convertase Subtilisin Kexin 9 (PCSK9) have been associated with autosomal dominant hypercholesterolemia. In vivo kinetic studies indicate that LDL catabolism was impaired and apolipoprotein B (apoB)-containing lipoprotein synthesis was enhanced in two patients presenting with the S127R mutation on PCSK9. To understand the physiological role of PCSK9, we overexpressed human PCSK9 in mouse and cellular models as well as attenuated the endogenous expression of PCSK9 in HuH7 hepatoma cells using RNA interference. Here, we show that PCSK9 dramatically impairs the expression of the low density lipoprotein receptor (LDLr) and, in turn, LDL cellular binding as well as LDL clearance from the plasma compartment in C57BL6/J mice but not in LDLr-deficient mice, establishing a definitive role for PCSK9 in the modulation of the LDLr metabolic pathway. In contrast to data obtained in S127R-PCSK9 patients presenting with increased apoB production, our study indicates that wild-type PCSK9 does not significantly alter the production and/or secretion of VLDL apoB in either cultured cells or mice. Finally, we show that unlike PCSK9 overexpression in mice, the S127R mutation in patients led to increased VLDL apoB levels, suggesting a potential gain of function for S127R-PCSK9 in humans.