gebhart/patrepeval huggingface dataset:
[Anesthetic management of a patient with Sjögren's syndrome and pulmonary fibrosis]. (1990)

We described an anesthetic management of a 63 year old man complicated with Sjögren's syndrome and pulmonary fibrosis. Sjögren's syndrome is characterized by pathological dryness of the mouth, cornea and other exocrine glands. Anesthesia was induced with thiopental and the trachea was intubated smoothly following intravenous succinylcholine. Anesthesia was maintained with enflurane in nitrous oxide and oxygen. Intraoperative muscle relaxation was adequately obtained by pancuronium. Before and during anesthesia, atropine and other drying agents were avoided. Physiological saline solution was instilled on the eyes every ten minutes against dryness. A heat and moisture exchanger (Humi-Vent) was used to maintain high moisture of the respiratory tract. Anesthesia was carried out successfully.
Isolation of Protoplasts and Vacuoles from Storage Tissue of Red Beet (1980)

A fast and efficient method is described for the isolation of protoplasts and vacuoles from storage tissue of Beta vulgaris L. The viability of the isolated protoplasts is indicated by the development within a few hours of plasma strands with active cyclosis as well as by transport activity.The effect of aging of the tissue on the yield and on the properties of the protoplasts is examined. Adding 1 millimolar dithiothreitol to the water during the aging of the tissue prevents a change of the cell wall structure which otherwise reduces the protoplast yield within 2 days to zero. When protoplasts are isolated from tissue after different times of aging, they show an increase in transport activity which parallels that in the intact tissue.
Increased Serum Levels of Advanced Glycation End Products (AGEs) in Children and Adolescents With IDDM (1997)

S-AGEs are increased in young patients with diabetes before puberty. Since AGEs are linked to the pathogenesis of vascular complications, this observation suggests that the pathological processes leading to diabetic late complications start even before puberty.
Phase II Trial of Pertuzumab and Trastuzumab in Patients With Human Epidermal Growth Factor Receptor 2–Positive Metastatic Breast Cancer That Progressed During Prior Trastuzumab Therapy (2010)

The combination of pertuzumab and trastuzumab is active and well tolerated in patients with metastatic HER2-positive breast cancer who had experienced progression during prior trastuzumab therapy.
Lec3 Chinese Hamster Ovary Mutants Lack UDP-N-acetylglucosamine 2-Epimerase Activity Because of Mutations in the Epimerase Domain of the Gne Gene (2003)

Lec3 Chinese hamster ovary (CHO) cell glycosylation mutants have a defect in sialic acid biosynthesis that is shown here to be reflected most sensitively in reduced polysialic acid (PSA) on neural cell adhesion molecules. To identify the genetic origin of the phenotype, genes encoding different factors required for sialic acid biosynthesis were transfected into Lec3 cells. Only a Gne cDNA encoding UDP-GlcNAc 2-epimerase:ManNAc kinase rescued PSA synthesis. In an in vitro UDP-GlcNAc 2-epimerase assay, Lec3 cells had no detectable UDP-GlcNAc 2-epimerase activity, and Lec3 cells grown in serum-free medium were essentially devoid of sialic acid on glycoproteins. The Lec3 phenotype was rescued by exogenously added N-acetylmannosamine or mannosamine but not by the same concentrations of N-acetylglucosamine, glucosamine, glucose, or mannose. Sequencing of CHO Gne cDNAs identified a nonsense (E35stop) and a missense (G135E) mutation, respectively, in two independent Lec3 mutants. The G135E Lec3 mutant transfected with a rat Gne cDNA had restored in vitro UDP-GlcNAc 2-epimerase activity and cell surface PSA expression. Both Lec3 mutants were similarly rescued with a CHO Gne cDNA and with CHO Gne encoding the known kinase-deficient D413K mutation. However, cDNAs encoding the known epimerase-deficient mutation H132A or the new Lec3 G135E Gne mutation did not rescue the Lec3 phenotype. The G135E Gne missense mutation is a novel mechanism for inactivating UDP-GlcNAc 2-epimerase activity. Lec3 mutants with no UDP-GlcNAc 2-epimerase activity represent sensitive hosts for characterizing disease-causing mutations in the human GNE gene that give rise to sialuria, hereditary inclusion body myopathy, and Nonaka myopathy.
Incremental formal design verification (1994)

Language containment is a method for design verification that involves checking if the behavior of the system to be verified is a subset of the behavior of the specifications (properties or requirements), which it has to meet. If this check fails, language containment returns a subset of “fair” states involved in behavior that the system exhibits but the specification does not. Current techniques for language containment do not take advantage of the fact that the process of design is incremental; namely that the designer repeatedly modifies and re-verifies his/her design. This results in unnecessary and cumbersome computation. We present a method, which successively modifies the latest result of verification each time the design is modified. Our incremental algorithm translates changes made by the designer to an addition or subtraction of edges, states or constraints (on acceptable behavior) from the transition behavior or specification of the problem. Next, these changes are used to update the set of “fair” states previously computed. This incremental algorithm is superior to the current techniques for language containment; a conclusion supported by the experimental results presented in this paper.
Some aspects of designing an efficient nitride VCSEL resonator (2001)

The optical model of vertical-cavity surface-emitting lasers (VCSELs) based on the effective frequency method is applied to formulate some guidelines useful for designers of nitride VCSEL resonators. Various materials for resonator distributed Bragg reflectors mirrors are investigated, namely SiO2, TiO2, HfO2, MgO, Y2O3, ZrO2, GaN, AlN, and AlGaN. For pulse-operating nitride VCSELs, both dielectric resonator mirrors (preferably SiO2/TiO2 stacks) are recommended, whereas in the case of continuous-wave operation, the bottom dielectric mirror should be replaced by a semiconducting one (e.g. GaN/Al0.15Ga0.85N stack) to enhance heat extraction. It is shown that the active region radius in the analysed lasers should not be less than 5 µm. The simulation also revealed that the barrier width has a strong influence on the threshold gain. Some thermoelectrical aspects of design have also been addressed.
Double staining immunohistochemistry. (2010)

This article summarized immunohistochemistry methods generally used in research laboratories and clinic including direct immune staining, indirect immune staining, enzyme method, fluorescence method, APC method and PAP method.
OntologyTraverser: an R package for GO analysis (2004)

Abstract Summary: Gene Ontology (GO) annotations have become a major tool for analysis of genome-scale experiments. We have created OntologyTraverser—an R package for GO analysis of gene lists. Our system is a major advance over previous work because (1) the system can be installed as an R package, (2) the system uses Java to instantiate the GO structure and the SJava system to integrate R and Java and (3) the system is also deployed as a publicly available web tool. Availability: Our software is academically available through http://franklin.imgen.bcm.tmc.edu/OntologyTraverser/. Both the R package and the web tool are accessible. Contact: cashaw@bcm.tmc.edu
A multiscale stochastic image model for automated inspection (1995)

We develop a novel multiscale stochastic image model to describe the appearance of a complex three-dimensional object in a two-dimensional monochrome image. This formal image model is used in conjunction with Bayesian estimation techniques to perform automated inspection. The model is based on a stochastic tree structure in which each node is an important subassembly of the three-dimensional object. The data associated with each node or subassembly is modeled in a wavelet domain. We use a fast multiscale search technique to compute the sequential MAP (SMAP) estimate of the unknown position, scale factor, and 2-D rotation for each subassembly. The search is carried out in a manner similar to a sequential likelihood ratio test, where the process advances in scale rather than time. The results of this search determine whether or not the object passes inspection. A similar search is used in conjunction with the EM algorithm to estimate the model parameters for a given object from a set of training images. The performance of the algorithm is demonstrated on two different real assemblies.
Genotypic and Phenotypic Characterization of Human Immunodeficiency Virus Type 1 Variants Isolated from Patients Treated with the Protease Inhibitor Nelfinavir (1998)

Nelfinavir mesylate (formerly AG1343) is a potent and selective inhibitor of human immunodeficiency virus (HIV) protease approved for the treatment of individuals infected with HIV. Nucleotide sequence analysis of protease genes from plasma HIV type 1 (HIV-1) RNA revealed a unique aspartic acid (D)-to-asparagine (N) substitution at residue 30 (D30N) in 25 of 55 patients treated with nelfinavir for a median of 13 weeks. Although the appearance of D30N was occasionally associated with concurrent or sequential emergence of other changes (e.g., at residues 35, 36, 46, 71, 77, and 88), genotypic changes associated with phenotypic resistance to other protease inhibitors were not observed (e.g., at residues 48, 50, 82, and 84) or were only rarely observed (e.g., at residue 90). In phenotypic assays, viral isolates with high-level resistance to nelfinavir remained susceptible to indinavir, saquinavir, ritonavir, and amprenavir (formerly VX-478/141W94). Similar results were observed in phenotypic assays utilizing HIV-1 NL4-3, which contained the D30N substitution alone or in combination with substitutions at other residues (e.g., residues 46, 71, and 88). These data indicate that the initial pathway of resistance to nelfinavir is unique and suggest that individuals failing short courses of nelfinavir-containing regimens may respond to regimens containing other protease inhibitors.
The Interaction between Pyoverdin and Its Outer Membrane Receptor in Pseudomonas aeruginosa Leads to Different Conformers:  A Time-Resolved Fluorescence Study (2002)

In iron limitation conditions, Pseudomonas aeruginosa secretes a major fluorescent siderophore named pyoverdin (PaA). PaA has an extremely high affinity for Fe(3+) but also chelates other ions such as Al(3+) and Ga(3+) with a lower affinity. The transfer of PaA-Fe(3+) across the outer membrane of the bacteria is mediated by the receptor FpvA, a TonB-dependent outer membrane transport protein. FpvA binds the iron-free and iron-loaded forms of pyoverdin with similar affinities, but only PaA-Fe(3+) is taken up by the cell, suggesting that FpvA adopts different conformations depending on its loading status. We used time-resolved fluorescence spectroscopy to characterize the different forms of FpvA-PaA in vitro. We showed that the FpvA-PaA complex adopts two different conformations depending on how it was prepared (formed in vitro or in vivo prior to purification). The dihydroquinoline moiety of both conformers is fully protonated, or coordinated by protein charged groups, but the polarity of its environment, its solvent accessibility, and its rotational dynamics are much slower when the FpvA-PaA complex is formed in vivo than in vitro. In the presence of Ga(3+) or Al(3+) ions, the solvent accessibility and mobility of the dihydroquinoline moiety in the two FpvA-PaA complexes are intermediate between those observed for the metal-free ones. In addition, the Förster resonance energy transfer kinetics from FpvA tryptophan residues to the PaA chromophore differs from one complex to the other, revealing differences in one or more of the donor-acceptor topologies.
An efficient strategy for cell-based antibody library selection using an integrated vector system (2012)

This study demonstrates that scFv-Fc from mammalian transient expression can be chosen as a reliable format for rapid screening and validation in cell-based scFv library selection, and the strategy described here will be applicable to efficient discovery of antibodies to diverse cell-surface targets.
Projecting complete cohort fertility in Singapore (1996)

The discussion concerning fertility in Singapore during the post-Second World War period has been confined to consideration of the reduction in total period fertility. Although a focus on period fertility makes good sense in planning for school and university admissions, for maternal and child health care services, for future national service intakes and so on, it is easy, yet potentially misleading, to go one stage further and deduce that since total period fertility has been below the replacement level for a few years, the population is not replacing itself.
The Exceptionally Large Genome of Hendra Virus: Support for Creation of a New Genus within the Family Paramyxoviridae (2000)

An outbreak of acute respiratory disease in Hendra, a suburb of Brisbane, Australia, in September 1994 resulted in the deaths of 14 racing horses and a horse trainer. The causative agent was a new member of the family Paramyxoviridae. The virus was originally called Equine morbillivirus but was renamed Hendra virus (HeV) when molecular characterization highlighted differences between it and members of the genus Morbillivirus. Less than 5 years later, the closely related Nipah virus (NiV) emerged in Malaysia, spread rapidly through the pig population, and caused the deaths of over 100 people. We report the characterization of the HeV L gene and protein, the genome termini, and gene boundary sequences, thus completing the HeV genome sequence. In the highly conserved region of the L protein, the HeV sequence GDNE differs from the GDNQ found in almost all other nonsegmented negative-strand (NNS) RNA viruses. HeV has an absolutely conserved intergenic trinucleotide sequence, 3'-GAA-5', and highly conserved transcription initiation and termination sequences similar to those of respiroviruses and morbilliviruses. The large genome size (18,234 nucleotides), the unique complementary genome terminal sequences of HeV, and the limited homology with other members of the Paramyxoviridae suggest that HeV, together with NiV, should be classified in a new genus in this family. The large genome of HeV also fills a gap in the spectrum of genome sizes observed with NNS RNA virus genomes. As such, it provides a further piece in the puzzle of NNS RNA virus evolution.
Radiocontrast-induced nephropathy. (1998)

Radiocontrast-induced nephropathy (RCIN) is a common cause of acute renal failure. It results from an ischemic injury to the medullary portion of the kidney secondary to intense renal vasoconstriction. Patients with pre-existing renal insufficiency, diabetes, congestive heart failure, taking certain medications, and exposed to large volumes of high osmolar contrast are at increased risk of developing RCIN. Prophylaxis of high-risk patients by careful hydration and avoidance of exacerbating factors can minimize the incidence of RCIN.
Risk factors for acute GVHD and survival after hematopoietic cell transplantation (2011)

Abstract Risk factors for acute GVHD (AGVHD), overall survival, and transplant-related mortality were evaluated in adults receiving allogeneic hematopoietic cell transplants (1999-2005) from HLA-identical sibling donors (SDs; n = 3191) or unrelated donors (URDs; n = 2370) and reported to the Center for International Blood and Marrow Transplant Research, Minneapolis, MN. To understand the impact of transplant regimen on AGVHD risk, 6 treatment categories were evaluated: (1) myeloablative conditioning (MA) with total body irradiation (TBI) + PBSCs, (2) MA + TBI + BM, (3) MA + nonTBI + PBSCs, (4) MA + nonTBI + BM, (5) reduced intensity conditioning (RIC) + PBSCs, and (6) RIC + BM. The cumulative incidences of grades B-D AGVHD were 39% (95% confidence interval [CI], 37%-41%) in the SD cohort and 59% (95% CI, 57%-61%) in the URD cohort. Patients receiving SD transplants with MA + nonTBI + BM and RIC + PBSCs had significantly lower risks of grades B-D AGVHD than patients in other treatment categories. Those receiving URD transplants with MA + TBI + BM, MA + nonTBI + BM, RIC + BM, or RIC + PBSCs had lower risks of grades B-D AGVHD than those in other treatment categories. The 5-year probabilities of survival were 46% (95% CI, 44%-49%) with SD transplants and 33% (95% CI, 31%-35%) with URD transplants. Conditioning intensity, TBI and graft source have a combined effect on risk of AGVHD that must be considered in deciding on a treatment strategy for individual patients.
Inactivation of Erythropoietin Receptor Function by Point Mutations in a Region Having Homology with other Cytokine Receptors (1993)

The cytoplasmic domain of the erythropoietin receptor (EpoR) contains a region, proximal to the transmembrane domain, that is essential for function and has homology with other members of the cytokine receptor family. To explore the functional significance of this region and to identify critical residues, we introduced several amino acid substitutions and examined their effects on erythropoietin-induced mitogenesis, tyrosine phosphorylation, and expression of immediate-early (c-fos, c-myc, and egr-1) and early (ornithine decarboxylase and T-cell receptor gamma) genes in interleukin-3-dependent cell lines. Amino acid substitution of W-282, which is strictly conserved at the middle portion of the homology region, completely abolished all the functions of the EpoR. Point mutation at L-306 or E-307, both of which are in a conserved LEVL motif, drastically impaired the function of the receptor in all assays. Other point mutations, introduced into less conserved amino acid residues, did not significantly impair the function of the receptor. These results demonstrate that conserved amino acid residues in this domain of the EpoR are required for mitogenesis, stimulation of tyrosine phosphorylation, and induction of immediate-early and early genes.
Geometric pattern matching under Euclidean motion (1997)

Given two planar sets A and B, we examine the problem of determining the smallest ϵ such that there is a Euclidean motion (rotation and translation) of A that brings each member of A within distance ϵ of some member of B. We establish upper bounds on the combinatorial complexity of this subproblem in model-based computer vision, when the sets A and B contain points, line segments, or (filled-in) polygons. We also show how to use our methods to substantially improve on existing algorithms for finding the minimum Hausdorff distance under Euclidean motion.
Protein detection by optical shift of a resonant microcavity (2002)

We present an optical biosensor with unprecedented sensitivity for detection of unlabeled molecules. Our device uses optical resonances in a dielectric microparticle (whispering gallery modes) as the physical transducing mechanism. The resonances are excited by evanescent coupling to an eroded optical fiber and detected as dips in the light intensity transmitted through the fiber at different wavelengths. Binding of proteins on the microparticle surface is measured from a shift in resonance wavelength. We demonstrate the sensitivity of our device by measuring adsorption of bovine serum albumin and we show its use as a biosensor by detecting streptavidin binding to biotin.
Autofluorescence spectroscopy for the diagnosis of cervical intraepithelial neoplasia (2002)

Autofluorescence spectroscopy represents an interesting approach for the detection of cervical neoplasia. Using an excitation wavelength band between 375 and 440 nm, significant differences between normal and precancerous lesions of the cervix can be seen.
A Direct Comparison of the Activities of Two Humanized Respiratory Syncytial Virus Monoclonal Antibodies: MEDI‐493 and RSHZl9 (1999)

Two humanized monoclonal antibodies, MEDI-493 and RSHZ19, were developed independently as potential improvements over RSV-IGIV for prevention of respiratory syncytial virus (RSV) infection. RSV-IGIV is a polyclonal human antibody preparation for intravenous infusion enriched for RSV neutralizing activity. A phase III clinical trial showed that MEDI-493 significantly reduced hospitalizations due to RSV infection. In a separate trial, RSHZ19 failed to show significant efficacy. In new studies, the in vitro and in vivo activities of MEDI-493 and RSHZ19 were compared to determine whether the different clinical results are related to differences in biologic activity. MEDI-493 was consistently 4- to 5-fold more potent than RSHZ19 in antigen binding, RSV neutralization, and fusion inhibition assays. Although both MEDI-493 and RSHZ19 were effective against A and B subtypes of RSV in the cotton rat model of RSV infection, 2- to 4-fold higher doses of RSHZ19 were required for similar protection. The enhanced activity of MEDI-493 compared with RSHZ19 may, in part, explain its better clinical effect.
Cytokines, endotoxin, and glucocorticoids regulate the expression of inducible nitric oxide synthase in hepatocytes. (1993)

Nitric oxide (NO.) is a short-lived mediator which can be induced in a variety of cell types and produces many physiologic and metabolic changes in target cells. The inducible or high-output NO. synthase (NOS) pathway was first characterized in macrophages activated by lipopolysaccharide (LPS) and interferon gamma (IFN-gamma). Hepatocytes also express an inducible NOS following exposure to the combination of endotoxin (LPS) and tumor necrosis factor (TNF), interleukin 1 (IL-1), and IFN-gamma. In this study, to identify which of these cytokines, if any, was acting to induce the gene expression for hepatocyte NOS, we measured the levels of rat hepatocyte NOS mRNA by Northern blot analysis after stimulation by various combinations of endotoxin and cytokines in vitro. We found the mRNA for hepatocyte NOS to be a single band at approximately 4.5 kilobases which was maximally up-regulated (approximately 70-fold) by the combination of TNF, IL-1, IFN-gamma, and LPS. Abundance of NOS mRNA peaked 6-8 hr after stimulation and then declined by 25% at 24 hr. Unstimulated hepatocytes in vitro showed only a trace mRNA band after prolonged autoradiographic exposure. As single agents, TNF and IL-1 were the most effective inducers of hepatocyte NOS mRNA. Combinations of two or three stimuli revealed strong synergy between TNF, IL-1, and IFN-gamma. The increased mRNA levels correlated with elevated nitrogen oxide release and cGMP levels in the culture supernatants. Dexamethasone and cycloheximide inhibited induction of mRNA for hepatocyte NOS in a dose-dependent fashion. The addition of NG-monomethyl-L-arginine had no effect on mRNA levels but effectively blocked NO. formation. The inducible hepatocyte NOS mRNA was also detected in rat hepatocytes following chronic hepatic inflammation triggered by Corynebacterium parvum injection in vivo. These data demonstrate that the inducible NOS is functional in rat hepatocytes both in vitro and in vivo and that this pathway is under complex control. Endotoxin and inflammatory cytokines act synergistically to up-regulate gene expression for hepatocyte NOS, whereas glucocorticoids down-regulate the mRNA.