gebhart/patrepeval huggingface dataset:
Humanized Antibodies: Enhancing Therapeutic Utility Through Antibody Engineering (1993)

The promise of antibody therapeutics has been greatly expanded by the development of monoclonal antibody technology and more recently antibody humanization. By transferring the mouse antibody binding site into a human antibody gene, we can engineer a "human antibody" which retains the specificity and biological effects of the original mouse antibody but has the potential to be nonimmunogenic in humans. Additionally, antibody effector functions can be improved through manipulation of the antibody constant region genes. We have produced a humanized version of OKT3 with human IgG4 and kappa constant regions. This antibody retains all of the in vitro characteristics of murine OKT3 including induction of cytokine release and T cell activation markers. Humanized OKT3 has an affinity of 1.4 x 10(9) M-1 relative to a 1.2 x 10(9) M-1 affinity of murine OKT3. Substitution of a glutamic acid for leucine at residue 235 in the antibody constant region abrogates FcR I binding and causes a marked reduction of T cell activation. The humanized FcR mutant of OKT3 has potential to be an improved therapeutic for transplantation and may have applications in autoimmune disease treatment.
Does Vasopressin Infusion Improve the Outcome of Severe Septic-Shock without any Adverse Effects? (2003)

To the Editor:—We read with great interest the report by Patel et al. on beneficial effects of short-term infusion of vasopressin for severe septic shock. 1The authors reported that for 24 patients with severe septic shock, 4 h infusion of vasopressin spared norepinephrine to maintain mean arterial pressure and improved urine output and creatinine clearance compared with the control group (norepinephrine infusion) in a double-blinded, randomized, controlled fashion. We were impressed with the results showing that low-dose vasopressin therapy may increase survival of septic shock. However, there was no information about the outcome of their patients. To survive from severe septic shock, there may be a need for long-term vasopressin infusion to maintain stable cardiovascular status. Dunser et al. demonstrates 72-h vasopressin infusion brings about a significant increase in liver enzymes and total bilirubin concentration and a significant decrease in platelet count. 2
Role of androgens and fibroblast growth factors in prostatic development (2001)

This review focuses on the role of androgens and fibroblast growth factors (FGFs) in regulating the growth and development of the prostate. It is known that androgens and mesenchymal-epithelial interactions are required for the formation and growth of the prostate, but little is known of the molecular mediators regulating prostatic organogenesis. Paracrine signalling from the mesenchyme to the epithelium is a key element of prostatic development and the action of androgens in mesenchymal cells is essential for prostatic development. This finding has led to the hypothesis that androgens regulate the expression of paracrine-acting growth factors. Although several families of growth factors play a role in regulating prostatic growth, the FGF family contains members that have been studied most comprehensively in regard to prostatic growth and branching morphogenesis. The role of FGFs in prostatic development is described in detail, since two members of the FGF family function as mesenchymal paracrine-acting factors in the prostate. It has been shown that FGF7 and FGF10 play important roles during prostatic development yet they do not appear to be regulated directly by androgens. Current models propose that growth factor expression (including FGF7 and 10) is regulated directly by androgens. However, it is possible that androgen regulation is indirect and a model outlining indirect androgen regulation of growth factors is proposed.
An empirical study of context in object detection (2009)

This paper presents an empirical evaluation of the role of context in a contemporary, challenging object detection task - the PASCAL VOC 2008. Previous experiments with context have mostly been done on home-grown datasets, often with non-standard baselines, making it difficult to isolate the contribution of contextual information. In this work, we present our analysis on a standard dataset, using top-performing local appearance detectors as baseline. We evaluate several different sources of context and ways to utilize it. While we employ many contextual cues that have been used before, we also propose a few novel ones including the use of geographic context and a new approach for using object spatial support.
Cross-reactivity between the pollens of Cupressus sempervirens (common cypress) and of Cryptomeria japonica (Japanese cedar). (1986)

A clinical and immunologic study was performed comparing a group of French patients allergic to the pollens of cypress (Cupressus sempervirens, which belongs to the Cupressaceae family) and a group of Japanese patients allergic to the pollens of Sugi (Cryptomeria japonica, which belongs to the Taxodiaceae family). By skin testing, RAST, and RAST inhibition, clear cross-reactivity was detected between the two pollens. No cross-reactivity was detected between the pollens of Cupressus sempervirens and Sugi and the Pinaceae family. In addition, one can speculate that an antigen in Cupressus sempervirens is cross-reactive with SBP, the major allergen of Sugi, suggesting that there is a closer relationship between the Taxodiaceae family and the Cupressaceae family than between these two families and the other families of the gymnosperms. This finding throws new light on the taxonomy of the gymnosperms.
Sodium Channels, Inherited Epilepsy, and Antiepileptic Drugs (2014)

Voltage-gated sodium channels initiate action potentials in brain neurons, mutations in sodium channels cause inherited forms of epilepsy, and sodium channel blockers-along with other classes of drugs-are used in therapy of epilepsy. A mammalian voltage-gated sodium channel is a complex containing a large, pore-forming α subunit and one or two smaller β subunits. Extensive structure-function studies have revealed many aspects of the molecular basis for sodium channel structure, and X-ray crystallography of ancestral bacterial sodium channels has given insight into their three-dimensional structure. Mutations in sodium channel α and β subunits are responsible for genetic epilepsy syndromes with a wide range of severity, including generalized epilepsy with febrile seizures plus (GEFS+), Dravet syndrome, and benign familial neonatal-infantile seizures. These seizure syndromes are treated with antiepileptic drugs that offer differing degrees of success. The recent advances in understanding of disease mechanisms and sodium channel structure promise to yield improved therapeutic approaches.
A rapid and efficient one-tube PCR-based mutagenesis technique usingPfuDNA polymerase (1994)

A rapid method for efficiently generating site-directed mutations on a clean sequence background is described. This modification of the megaprimer PCR mutagenesis approach can be performed in one tube in less than 4.5 hours, and does not require purification of intermediate products. High fidelity of DNA sequence replication is obtained by employing Pfu DNA polymerase and limiting the total number of amplification cycles to 30. The mutagenesis efficiency of the procedure is high enough to allow rapid, direct identification of mutants by restriction digest or sequencing techniques.
Arrayed Primer Extension: Solid-Phase Four-Color DNA Resequencing and Mutation Detection Technology (2000)

The technology and application of arrayed primer extension (APEX) is presented. We describe an integrated system with DNA chip and template preparation, multiplex primer extension on the array, fluorescence imaging, and data analysis. The method is based upon an array of oligonucleotides, immobilized via the 5' end on a glass surface. A patient DNA is amplified by PCR, digested enzymatically, and annealed to the immobilized primers, which promote sites for template-dependent DNA polymerase extension reactions using four unique fluorescently labeled dideoxy nucleotides. A mutation is detected by a change in the color code of the primer sites. The technology was applied to the analysis of 10 common beta-thalassemia mutations. Nine patient DNA samples, each of which carries a different mutation, and four wild-type DNA samples were correctly identified. The signal-to-noise ratio of this technology is, on the average, 40:1, which enables the identification of heterozygous mutations with a high confidence level. The APEX method can be applied to any DNA target for efficient analysis of mutations and polymorphisms.
Noninvasive Molecular Detection of Head and Neck Squamous Cell Carcinoma (2009)

Noninvasive high-throughput multiplex ligation-dependent probe amplification identified discrete gene signatures that differentiated HNSCC patients from normal controls providing proof-of-concept for noninvasive HNSCC detection.
Characterization of defined ompR mutants of Salmonella typhi: ompR is involved in the regulation of Vi polysaccharide expression (1994)

The ompB operon, comprising the ompR and envZ genes, was cloned from a Salmonella typhi Ty2 cosmid bank and characterized by DNA sequence analysis. The S. typhi ompR and envZ genes contained open reading frames encoding proteins of 240 and 451 amino acids, respectively. Comparison with the Salmonella typhimurium OmpB protein sequences revealed 99.5% homology. The DNA sequence data were used to identify appropriate restriction sites for generating a defined deletion of 517 bp within the open reading frame of the ompR gene. This deletion was introduced by homologous recombination into the chromosomes of two S. typhi strains which already harbored defined deletions in both the aroC and aroD genes. The presence of the deletions within ompR was confirmed by Southern hybridization and sequencing of the DNA fragments surrounding the deleted regions by PCR. The S. typhi ompR mutants displayed a marked decrease in OmpC and OmpF porin expression as demonstrated by examination of outer membrane preparations. It was also found that S. typhi strains harboring the defined ompR deletions no longer agglutinated with Vi antiserum. However, when a functional ompB operon was introduced back into the S. typhi ompR mutants, either on a multicopy plasmid or as a single-copy chromosomal replacement, the Vi+ phenotype was restored. The levels of Vi synthesis were also found to be sensitive to different concentrations of sodium chloride present in the growth medium, although the levels of sensitivity varied between different isolates of S. typhi. It is therefore concluded that the ompR-envZ two component regulatory system plays an important role in the regulation of Vi polysaccharide synthesis in S. typhi and that one of the environmental signals for this regulation may be osmolarity.
ALK and NSCLC: Targeted therapy with ALK inhibitors (2011)

For many years treatment for advanced or metastatic non-small cell lung cancer (NSCLC) has employed chemotherapy regimens for patient care, with limited effect. Five-year survival rates for these patients are not encouraging. However, for a subgroup of these patients, there have been radical changes over recent years. Our understanding of the basic pathology behind NSCLC at the molecular level has offered up a host of new molecularly targeted therapies, which are revolutionizing this area of cancer care. Results from recent clinical trials provide hope for NSCLC patients harboring oncogenic translocations involving the anaplastic lymphoma kinase (ALK) receptor tyrosine kinase. Just as inhibition of the breakpoint cluster region-ABL complex has changed the face of chronic myeloid leukemia diagnosis, oncogenic ALK fusions offer a step forward in the diagnosis and treatment of ALK-positive NSCLC. This article discusses the current knowledge and potential implications concerning ALK inhibitors and NSCLC.
Nitric oxide production and inducible nitric oxide synthase expression in inflammatory arthritides. (1995)

In this study, we have identified the source of nitric oxide (NO) produced in the human inflammatory joints by analyzing expression of inducible NO synthase. In ex vivo organ cultures, both inflammatory synovium and cartilage from patients with rheumatoid arthritis produced NO. The NO production was suppressed by NG-monomethyl-L-arginine, an inhibitor of NO synthase. The amount of NO produced by the synovium correlated with the proportion of CD14+ cells in the corresponding tissue (r = 0.8, P < 0.05). Immunohistochemical analysis as well as in situ hybridization showed that inducible NO synthase was predominantly expressed in synovial lining cells, endothelial cells, chondrocytes, and to a lesser extent, in infiltrating mononuclear cells and synovial fibroblasts. The synovial lining cells and the infiltrating cells expressing inducible NO synthase were identified where CD14+ cells were located. Together with morphological features, this suggests that they are type A synoviocytes. NO production from freshly isolated synoviocytes and chondrocytes was up-regulated by in vitro stimulation with a combination of IL-TNF-beta, TNF-alpha, and LPS. In summary, the present results suggest that NO is produced primarily by CD14+ synoviocytes, chondrocytes, and endothelial cells in inflammatory joints of arthritides. NO production can be upregulated by cytokines present in inflamed joints. The increased NO production may thus contribute to the pathological features in inflammatory arthritides.
Cellular Basis of Physiological and Pathological Myocardial Growth (2002)

The sections in this article are: 1 Morphometric Analysis of Cell Size and Number in the Ventricular Myocardium 1.1 Myocyte Dimensional Properties and Number: Methodological Considerations 1.2 Confocal Microscopic Measurements of Myocyte Cell Volume 2 Morphometric Analysis of the Coronary Vasculature 3 Physiological Myocardial Growth: Maturation of the Heart 3.1 Ventricular Remodeling 3.2 Myocyte Adaptations 3.3 Cytoplasmic Adaptations in Myocytes 3.4 Capillary Adaptations 3.5 Conclusions 4 Aging of the Heart 4.1 Aging and Ventricular Remodeling 4.2 Aging and Myocyte Number 4.3 Aging and Myocyte Reactive Hypertrophy 4.4 Aging and the Coronary Arterial and Capillary Tree 4.5 Conclusions 5 Pressure and Volume Overload Hypertrophy 5.1 Cardiac Hypertrophy and Ventricular Remodeling 5.2 Cardiac Hypertrophy and Myocyte Size, Shape, and Number 5.3 Cardiac Hypertrophy and Volume Composition of Myocytes 5.4 Cardiac Hypertrophy and the Coronary Arterial and Capillary Tree 5.5 Conclusions 6 Ischemic Cardiomyopathy 6.1 Ischemic Cardiomyopathy and Ventricular Remodeling 6.2 Ischemic Cardiomyopathy, Myocyte Cell Loss, and Ventricular Function 6.3 Ischemic Cardiomyopathy and Myocyte Cellular Hypertrophy and Hyperplasia 6.4 Ischemic Cardiomyopathy and Volume Composition of Myocytes 6.5 Ischemic Cardiomyopathy and the Coronary Capillary Tree 6.6 conclusion6.6 Conclusions
Efficient alias-free rendering using bit-masks and look-up tables (1985)

We demonstrate an efficient method of rendering alias-free synthetic images using precomputed convolution integrals. The method is based on the observation that a visible polygon fragment's contribution to an image is solely a function of its position and shape, and that within a reasonable level of accuracy, a limited number of shapes represent the majority of cases encountered in images commonly rendered .The convolution integral is precomputed for all pixels affected by the polygon fragment and is stored in a table. Completely visible fragments which are either triangular or trapezoidal produce two indices into the table. Most other fragments which are represented as differences of simple fragments. The remaining cases are characterized by a bit-mask for which each bit has a corresponding set of look up tables.The basic technique has been applied to several fundamentally different rendering algorithms. In addition, we illustrate a version of the newly introduced nonuniform sampling technique implemented in the same program, but with different table values.
The correlation between heart rate turbulence of pediatric viral myocarditis and other indexes (2009)

Objective To study the value of heart rate turbulence(HRT) of acute pediatric viral myocarditis (VMC) ,and the relationship between HRT and other indexes. Methods We randomly assigned 75 acute pediatric VMC and 77 health enfant those all received holter. We calculated the heart rate turbulence(To) and turbulence slope (Ts) respectively,and compared the difference between them. Simultaneously, record the number of ventricular pre-mature complex(VPC) ,whether with ventricular tachycardia(VT) and the SDNN index of HRV. Then we analyzed the association between them and To,Ts. Results The difference of To between pediatric VMC and control group is significant in statistics, as follows [ (1.47±2.03 ) %, (-0.78±2.55) %, P<0.01; (3.05±2.12) ms/RR, (8.82±3.42) ms/RR,P<0.01]. There are no correlation between To and the number of VPC. And the number of VPC is interrelated to Ts. To and Ts are not correlative with whether with VT and heart rate variability(HRV). Conclusions The HRT of pediatric VMC is significanty reduced,so HRT can be a new index that to evaluate the heart parasym-pathetic function state in pediatric VMC and it is independent from traditional HRV. Therefore we can evaluate the heart parasympathetic function state of the sufferers after analyzed their HRT. This technique can help to discover pathological changes of heart parasympathetic system in forepart and guide clinical therapy in time,and avoid heart ill event.

Key words: 
Heart rate; Myocarditis;  Ventricular premature complexs; Child
177. The synthesis and reactions of certain 6-substituted benzimidazo[1,2-c]quinazolines (1962)

M. Davis and F. G. Mann, J. Chem. Soc., 1962, 945 DOI: 10.1039/JR9620000945
Standardised Parenteral Nutrition (2013)

Parenteral nutrition (PN) has become an integral part of clinical management of very low birth weight premature neonates. Traditionally different components of PN are prescribed individually considering requirements of an individual neonate (IPN). More recently, standardised PN formulations (SPN) for preterm neonates have been assessed and may have advantages including better provision of nutrients, less prescription and administration errors, decreased risk of infection, and cost savings. The recent introduction of triple-chamber bag that provides total nutrient admixture for neonates may have additional advantage of decreased risk of contamination and ease of administration.
A novel human T-leukemia virus type 1 cell-to-cell transmission assay permits definition of SU glycoprotein amino acids important for infectivity (1997)

Human T-leukemia virus type 1 (HTLV-1) envelope glycoproteins play a major role in viral transmission, which in the case of this virus occurs almost exclusively via cell-to-cell contact. Until very recently, the lack of an HTLV-1 infectivity assay precluded the determination of the HTLV-1 protein domains required for infectivity. Here, we describe an assay which allows the quantitative evaluation of HTLV-1 cell-to-cell transmission in a single round of infection. Using this assay, we demonstrate that in this system, cell-to-cell transmission is at least 100 times more efficient than transmission with free viral particles. We have examined 46 surface (SU) glycoprotein mutants in order to define the amino acids of the HTLV-1 SU glycoprotein required for full infectivity. We demonstrate that these amino acids are distributed along the entire length of the SU glycoprotein, including the N-terminus and C-terminus regions, which have not been previously defined as being important for HTLV-1 glycoprotein function. For most of the mutated glycoproteins, the capacity to mediate cell-to-cell transmission is correlated with the ability to induce formation of syncytia. This result indicates that the fusion capacity is the main factor responsible for infectivity mediated by the HTLV-1 SU envelope glycoprotein, as is the case for other retroviral glycoproteins. However, other factors must also intervene, since two of the mutated glycoproteins were correctly fusogenic but could not mediate cell-to-cell transmission. Existence of this phenotype shows that capacity for fusion is not sufficient to confer infectivity, even in cell-to-cell transmission, and could suggest that postfusion events involve the SU.
Comparative Genomics of the IncA/C Multidrug Resistance Plasmid Family (2009)

Multidrug resistance (MDR) plasmids belonging to the IncA/C plasmid family are widely distributed among Salmonella and other enterobacterial isolates from agricultural sources and have, at least once, also been identified in a drug-resistant Yersinia pestis isolate (IP275) from Madagascar. Here, we present the complete plasmid sequences of the IncA/C reference plasmid pRA1 (143,963 bp), isolated in 1971 from the fish pathogen Aeromonas hydrophila, and of the cryptic IncA/C plasmid pRAx (49,763 bp), isolated from Escherichia coli transconjugant D7-3, which was obtained through pRA1 transfer in 1980. Using comparative sequence analysis of pRA1 and pRAx with recent members of the IncA/C plasmid family, we show that both plasmids provide novel insights into the evolution of the IncA/C MDR plasmid family and the minimal machinery necessary for stable IncA/C plasmid maintenance. Our results indicate that recent members of the IncA/C plasmid family evolved from a common ancestor, similar in composition to pRA1, through stepwise integration of horizontally acquired resistance gene arrays into a conserved plasmid backbone. Phylogenetic comparisons predict type IV secretion-like conjugative transfer operons encoded on the shared plasmid backbones to be closely related to a group of integrating conjugative elements, which use conjugative transfer for horizontal propagation but stably integrate into the host chromosome during vegetative growth. A hipAB toxin-antitoxin gene cluster found on pRA1, which in Escherichia coli is involved in the formation of persister cell subpopulations, suggests persistence as an early broad-spectrum antimicrobial resistance mechanism in the evolution of IncA/C resistance plasmids.
Association of protein-tyrosine phosphatase PTP-BAS with the transcription-factor-inhibitory protein IκBα through interaction between the PDZ1 domain and ankyrin repeats (1999)

PTP-BAS is a membrane-associated protein tyrosine phosphatase containing a band-4.1 homology region and five PDZ (PSD-95 Dlg ZO-1) [discs-large homology region (‘DHR’)/Gly-Leu-Gly-Phe (‘GLGF’)] domains. The second and fourth PDZ domains were reported to associate with Fas/CD95. By using the first PDZ domain as a bait in yeast two-hybrid screening, we have identified IκBα as a binding protein. IκBα associated with PDZ1 through the stretch of the N-terminal three ankyrin repeats. The association was also confirmed in HeLa cells by co-immunoprecipitation experiments. Inhibition of PTP-BAS by expression of dominant-negative PTP-BAS mutant resulted in tyrosine-phosphorylation of IκBα. Tyrosine-phosphorylation of IκBα is a key event in activation of nuclear factor (NF)-κB during reoxygenation. PTP-BAS may thus play a regulatory role in activation of NF-κB under high oxidative stress.
Catalog of the tobacco introductions in the U.S. Department of Agriculture's tobacco germplasm collection (Nicotiana tabacum) / (1982)

This catalog describes the over 1,000 tobacco introductions (Nicotiana tabacum L.) in the U.S.