gebhart/patrepeval huggingface dataset:
Identification of a Glyphosate-Resistant Mutant of Rice 5-Enolpyruvylshikimate 3-Phosphate Synthase Using a Directed Evolution Strategy (2005)

5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) is a key enzyme in the shikimate pathway and is targeted by the wide-spectrum herbicide glyphosate. Here, we describe the use of a selection system based on directed evolution to select glyphosate-resistant mutants of EPSPS. Using this system, the rice (Oryza sativa) EPSPS gene, mutagenized by Error-Prone polymerase chain reaction, was introduced into an EPSPS-deficient Escherichia coli strain, AB2829, and transformants were selected on minimal medium by functional complementation. Three mutants with high glyphosate resistance were identified in three independent glyphosate selection experiments. Each mutant contained a C(317)-->T transition within the EPSPS coding sequence, causing a change of proline-106 to leucine (P106L) in the protein sequence. Glyphosate resistance assays indicated a 3-fold increase in glyphosate resistance of E. coli expressing the P106L mutant. Affinity of the P106L mutant for glyphosate and phosphoenolpyruvate was decreased about 70-fold and 4.6-fold, respectively, compared to wild-type EPSPS. Analysis based on a kinetic model demonstrates that the P106L mutant has a high glyphosate resistance while retaining relatively high catalytic efficiency at low phosphoenolpyruvate concentrations. A mathematical model derived from the Michaelis-Menten equation was used to characterize the effect of expression level and selection conditions on kinetic (Ki and Km) variation of the mutants. This prediction suggests that the expression level is an important aspect of the selection system. Furthermore, glyphosate resistance of the P106L mutant was confirmed in transgenic tobacco (Nicotiana tabacum), demonstrating the potential for using the P106L mutant in transgenic crops.
Epipolythiodioxopiperazines from Fungi: Chemistry and Bioactivities (2011)

Epipolythiodioxopiperazines (ETPs), characterized by a unique bridged disulfide or polysulfide dioxopiperazine six-membered ring, occur in many fungi. Due to its broad spectra of bioactivities, ETPs have drawn wide attention in recent years. This review covers diverse natural sources that produce ETPs, the synthetic chemistry of ETPs and an overview of promising bioactivities exhibited by some well studied ETPs. The plausible biosynthetic hypotheses of ETPs and some new results on antitumor activity of ETPs are also reviewed.
Silicon-Based Polymer Science (1989)

The chapter gives a brief overview of organosilicon chemistry and serves as an introduction to the rest of the material in the volume.
A diagnostic-prognostic test for bladder cancer using a monoclonal antibody-based enzyme-linked immunoassay for detection of urinary fibrin(ogen) degradation products. (1984)

An enzyme-linked immunosorbent assay (ELISA) using a monoclonal antibody was developed to determine the clinical value of urinary fibrinogen/fibrin degradation product levels for the identification and management of patients with bladder cancer. Assays were performed on 286 serial urine specimens from 56 bladder carcinoma patients. Specimens were grouped according to whether the patient had an evident tumor at the time of specimen collection (134 specimens, 41 patients) or was clinically disease-free following treatment (152 specimens, 38 patients). Many patients contributed specimens to both groups as determined by their clinical status at the time of collection. In addition, 45 specimens from 33 patients with inflammation of the urogenital tract and 81 specimens from 19 patients with renal or prostatic cancer were assayed for urinary fibrin degradation products. The ELISA, using a high-sensitivity procedure, identified 83% of the specimens from bladder cancer-positive patients with an overall accuracy with all specimens of 78% and a false-negative rate of 5% for all specimens tested. The high-sensitivity ELISA appeared most appropriate for monitoring bladder cancer patients for recurrence of tumor after surgery. The ELISA using a high-specificity procedure appeared most appropriate for screening. The high-specificity ELISA accurately identified 96% of urine specimens from non-bladder cancer patients with a false-positive rate of only 5%. These results demonstrate that the ELISA is an efficient, reliable, quantitative, and noninvasive immunoassay that can be useful both for the identification of bladder cancer patients and for monitoring the course of the disease.
Gaze computer interaction on stereo display (2006)

There are several researches on 2D gaze tracking techniques on the 2D screen. However, the researches for the gaze-based interaction to the stereo images or contents are not reported. This paper addresses gaze-based 3D interaction techniques on stereo display, such as parallax barrier display. This paper presents our researches on two issues for gaze-based 3D interaction, one is eye-vergence based 3D interaction, and the other is gaze vector based 3D interaction.
CD8 T-Cell Infiltration in Extravascular Tissues of Patients With Human Immunodeficiency Virus Infection. Interleukin-15 Upmodulates Costimulatory Pathways Involved in the Antigen-Presenting Cells–T-Cell Interaction (1999)

Abstract Interleukin (IL)-15 regulates the proliferative activity of the CD8+ T-cell pool in human immunodeficiency virus (HIV)-infected patients, thereby contributing to the maintenance of the CD8+ T-cell–mediated immune response against HIV in extravascular tissues, including the lung. However, the effects of IL-15 on antigen-presenting cells (APC) during HIV infection are still unclear. In this study, we evaluated whether IL-15 regulates the macrophage stimulatory pathways governing inflammatory events that take place in the lung of patients with HIV infection. As a first step we evaluated the in vitro effects of IL-15 on lung macrophages retrieved from the respiratory tract of eight normal subjects. Although macrophages from uninfected individuals expressed the IL-15 binding proteins (IL-15R and the common γc) at resting conditions, they did not express IL-15 messenger RNA (mRNA). However, a 24-hour stimulation with IL-15 induced the expression of interferon-γ (IFN-γ) and IL-15 itself, suggesting a role for this cytokine in the activation of the pulmonary macrophage pool during inflammation. As a confirmation of the role of IL-15 in this setting, at resting conditions, alveolar macrophages of patients with HIV infection and T-cell alveolitis expressed IL-15, IFN-γ, and IL-15 binding proteins; showed an upmodulation of costimulatory molecules, B7 and CD72, which are involved in the APC of macrophages; and behaved as effective accessory cells because they elicited a strong proliferation of T cells. The accessory effect was inhibited by pretreatment with anti-CD72, anti-B7 (CD80 and CD86), and anti–IL-15 monoclonal antibodies (MoAb). We then investigated the relationship between IL-15 and the expression of costimulatory molecules by macrophages. A 24-hour stimulation of IL-15R+/γc+ macrophages with IL-15 upregulated the expression of CD80 and CD86. The evidence that IL-15 upregulates the expression of coligands that favor the contact between T cells and APC, per se, triggers T-cell activation and proliferation and acts as a chemoattractant for T cells, suggests that IL-15 plays a key role in Tc1-mediated defense mechanisms taking place in extravascular tissues of patients with HIV disease.
Tissue-Engineered Bone Using Mesenchymal Stem Cells and a Biodegradable Scaffold (2002)

Warren, Stephen M. MD; Nacamuli, Randall P. MD; Song, HanJoon M. MD; Longaker, Michael T. MD, FACS Author Information
Rationalizable Strategic Behavior and the Problem of Perfection (1984)

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Effects of increasing hydrophobicity on the physical-chemical and biological properties of a class A amphipathic helical peptide (2001)

We have recently shown that a class A amphipathic peptide 5F with increased amphipathicity protected mice from diet-induced atherosclerosis (Garber et al. J. Lipid Res. 2001. 42: 545–552). We have now examined the effects of increasing the hydrophobicity of a series of homologous class A amphipathic peptides, including 5F, on physical and functional properties related to atherosclerosis inhibition by systematically replacing existing nonpolar amino acids with phenylalanine. The peptides, based on the sequence Ac-D-W-L-K-A-F-Y-D-K-V-A-E-K-L-K-E-A-F-NH2 (Ac-18A-NH2 or 2F) were: 3F3(Ac-F318A-NH2), 3F14(Ac-F1418A-NH2), 4F(Ac-F3,1418A-NH2), 5F(Ac-F11,14,17 18A-NH2), 6F(Ac-F10,11,14,17 18A-NH2), and 7F(Ac-F3,10,11,14,17 18A-NH2). Measurements of aqueous solubility, HPLC retention time, exclusion pressure for penetration into an egg phosphatidylcholine (EPC) monolayer, and rates of EPC solubilization revealed an abrupt increase in the hydrophobicity between peptides 4F and 5F; this was accompanied by increased ability to associate with phospholipids. The peptides 6F and 7F were less effective, indicating a limit to increased hydrophobicity for promoting lipid interaction in these peptides. Despite this marked increase in lipid affinity, these peptides were less effective than apoA-I in activating the plasma enzyme, lecithin:cholesterol acyltransferase, with 5F activating LCAT the best (80% of apoA-I). Peptides 4F, 5F, and 6F were equally potent in inhibiting LDL-induced monocyte chemotactic activity.These studies suggest that an appropriate balance between peptide-peptide and peptide-lipid interactions is required for optimal biological activity of amphipathic peptides. These studies provide a rationale for the design of small apoA-I-mimetics with increased potency for atherosclerosis inhibition.—Datta, G., M. Chaddha, S. Hama, M. Navab, A. M. Fogelman, D. W. Garber, V. K. Mishra, R. M. Epand, R. F. Epand, S. Lund-Katz, M. C. Phillips, J. P. Segrest, and G. M. Anantharamaiah. Effects of increasing hydrophobicity on the physical-chemical and biological properties of a class A amphipathic helical peptide. J. Lipid Res. 2001. 42: 1096–1104.
The reconstructive ladder. An orthoplastic approach. (1993)

The reconstructive ladder has many rungs. The reconstructive surgeon may go from one level to another and, in many instances, simultaneously employ different aspects of the ladder for different problems (i.e., a free-muscle transplant to a large lower extremity defect being covered by split-thickness skin grafts uses two rungs on the ladder). Familiarly with local as well as distant tissue options ensures success when the soft-tissue envelope is treated using this reconstructive ladder.
Transcription Factors in Long-Term Memory and Synaptic Plasticity (2009)

Transcription is a molecular requisite for long-term synaptic plasticity and long-term memory formation. Thus, in the last several years, one main interest of molecular neuroscience has been the identification of families of transcription factors that are involved in both of these processes. Transcription is a highly regulated process that involves the combined interaction and function of chromatin and many other proteins, some of which are essential for the basal process of transcription, while others control the selective activation or repression of specific genes. These regulated interactions ultimately allow a sophisticated response to multiple environmental conditions, as well as control of spatial and temporal differences in gene expression. Evidence based on correlative changes in expression, genetic mutations, and targeted molecular inhibition of gene expression have shed light on the function of transcription in both synaptic plasticity and memory formation. This review provides a brief overview of experimental work showing that several families of transcription factors, including CREB, C/EBP, Egr, AP-1, and Rel, have essential functions in both processes. The results of this work suggest that patterns of transcription regulation represent the molecular signatures of long-term synaptic changes and memory formation.
Identification and Characterization of a Novel Heme-Associated Cell Surface Protein Made by Streptococcus pyogenes (2002)

Analysis of the genome sequence of a serotype M1 group A Streptococcus (GAS) strain identified a gene encoding a previously undescribed putative cell surface protein. The gene was cloned from a serotype M1 strain, and the recombinant protein was overexpressed in Escherichia coli and purified to homogeneity. The purified protein was associated with heme in a 1:1 stoichiometry. This streptococcal heme-associated protein, designated Shp, was produced in vitro by GAS, located on the bacterial cell surface, and accessible to specific antibody raised against the purified recombinant protein. Mice inoculated subcutaneously with GAS and humans with invasive infections and pharyngitis caused by GAS seroconverted to Shp, indicating that Shp was produced in vivo. The blood of mice actively immunized with Shp had significantly higher bactericidal activity than the blood of unimmunized mice. The shp gene was cotranscribed with eight contiguous genes, including homologues of an ABC transporter involved in iron uptake in gram-negative bacteria. Our results indicate that Shp is a novel cell surface heme-associated protein.
Microchip isoelectric focusing using a miniature scanning detection system (2001)

A miniature scanning fluorescent detector has been developed for plastic microchannel isoelectric focusing (mIEF) analysis. The detector, comprised of a lamp and photomultiplier tube (PMT) on a moving stage, measured the real-time distribution of fluorescently labeled peptides subjected to gel-free mIEF. During the run, the effective length of the 6-cm channel was scanned every 9 s. Analysis was completed within 5 min while still obtaining high resolution and sensitivity. In addition, the scanning detector was used to characterize peptide migration properties within the channel by providing simultaneous temporal and spatial measurements.
Small Heat-Shock Protein Family: Function in Health and Disease (1998)

In summary, several important issues were discussed at the workshop. These included the importance of oligomer size for different functions of the sHsps, the highly significant observation that the sHsps can block apoptosis; and that some mechanisms of sHsps protection involve glutathione while others may be related to microfilament stability. Further evidence was presented for the chaperone functions of sHsps, and structural studies provided additional information relating sHsps' large oligomeric structure to chaperone function. Regulation of oligomer size by phosphorylation was also a prominent topic of discussion, as was the importance of the relationship of oligomer size to differing functions of Hsp27. An interesting contrast was noted between Hsp27, whose oligomer size is regulated by phosphorylation, and alpha beta-crystallin, whose large oligomer structure is unaffected by phosphorylation. This may prove to be of physiological significance, particularly in cell types that express both of these proteins. Observations of the translocation of MAPKAP kinase 2 from the nucleus to the cytoplasm in live cells suggest that the dynamics of phosphorylation of the sHsps may be more complex than previously thought. One topic that seems to have been settled is that the binding site of at least dimers of sHsps resides in the carboxyl-terminal region of the proteins. Ever-increasing numbers of studies are reporting interesting patterns of sHsp expression, phosphorylation, and subcellular localizations of the sHsps in various cells or tissues in normal and diseased states. Unfortunately, very little is understood about what these observations may mean. It can be expected, however, that as more is learned about the function and regulation of sHsps, the relationships between sHsps and cellular response to disease will become better understood. Lastly, the discovery that specific Hsp27-binding proteins may exist should open completely new avenues of investigation into the functions of sHsps. If the observations of unique subcellular localizations of sHsps in various cells types (e.g., striated muscle and Sertoli cells) can be related to expression of specific Hsp-binding proteins, considerable advances in our understanding of sHsps should result. It was abundantly clear from results presented and from ensuing discussions in the workshop that the study of sHsps is an exceedingly dynamic area of research (FIG. 2) with an ever-expanding significance for a number of other areas of current biological research.
Anti-tumor necrosis factor alpha-associated multiple sclerosis. (2005)

A case of multiple sclerosis presenting during anti-tumor necrosis factor treatment for rheumatoid arthritis is discussed. This association has been reported in the nonradiological literature, but is an important association for radiologists to be aware of, as they may be in a position to first suggest the diagnosis.
Effect of Route of Administration on the Efficacy of a Recombinant Fowlpox Virus against H5N2 Avian Influenza (1992)

A recombinant fowlpox vaccine virus containing the H5 hemagglutinin gene of avian influenza virus was administered to susceptible chickens via wing-web puncture, eye drop, instillation into the nares, and drinking water. Even though there was a negligible hemagglutination-inhibition (HI) serologic response, all 10 chickens vaccinated by wing-web puncture remained without obvious signs of disease and survived challenge with a highly pathogenic strain of H5N2 avian influenza virus. All unvaccinated chickens and those vaccinated by nasal and drinking-water routes died following challenge. Eight of 10 chickens vaccinated with the recombinant by eyedrop died. All vaccinates were negative on the agar gel precipitin (AGP) test, and only one chicken had a positive HI titer before challenge. All chickens that survived challenge had high levels of HI antibody and were positive on the AGP test, indicating that they were infected by the challenge virus.
Adrenoleukodystrophy: Survey of 303 cases: Biochemistry, diagnosis, and therapy (1984)

Adrenoleukodystrophy (ALD) is a genetically determined disorder associated with progressive central demyelination and adrenal cortical insufficiency. All affected persons show increased levels of saturated unbranched very-long-chain fatty acids, particularly hexacosanoate (C26:0), because of impaired capacity to degrade these acids. This degradation normally takes place in a subcellular organelle called the peroxisome, and ALD, together with Zellweger's cerebrohepatorenal syndrome, is now considered to belong to the newly formed category of peroxisomal disorders. Biochemical assays permit prenatal diagnosis, as well as identification of most heterozygotes. We have identified 303 patients with ALD in 217 kindreds. These patients show a wide phenotypic variation. Sixty percent of patients had childhood ALD and 17% adrenomyeloneuropathy, both of which are X-linked, with the gene mapped to Xq28. Neonatal ALD, a distinct entity with autosomal recessive inheritance and points of resemblance to Zellweger's syndrome, accounted for 7% of the cases. Although excess C26:0 in the brain of patients with ALD is partially of dietary origin, dietary C26:0 restriction did not produce clear benefit. Bone marrow transplant lowered the plasma C26:0 level but failed to arrest neurological progression.
Comparison of Three Amyloid Assembly Inhibitors: The Sugar scyllo-Inositol, the Polyphenol Epigallocatechin Gallate, and the Molecular Tweezer CLR01 (2012)

Many compounds have been tested as inhibitors or modulators of amyloid β-protein (Aβ) assembly in hope that they would lead to effective, disease-modifying therapy for Alzheimer’s disease (AD). These compounds typically were either designed to break apart β-sheets or selected empirically. Two such compounds, the natural inositol derivative scyllo-inositol and the green-tea-derived flavonoid epigallocatechin gallate (EGCG), currently are in clinical trials. Similar to most of the compounds tested thus far, the mechanism of action of scyllo-inositol and EGCG is not understood. Recently, we discovered a novel family of assembly modulators, Lys-specific molecular tweezers, which act by binding specifically to Lys residues and modulate the self-assembly of amyloid proteins, including Aβ, into formation of nontoxic oligomers by a process-specific mechanism (Sinha, S., Lopes, D. H., Du, Z., Pang, E. S., Shanmugam, A., Lomakin, A., Talbiersky, P., Tennstaedt, A., McDaniel, K., Bakshi, R., Kuo, P. Y., Ehrmann, M., Benedek, G. B., Loo, J. A., Klarner, F. G., Schrader, T., Wang, C., and Bitan, G. (2011) Lysine-specific molecular tweezers are broad-spectrum inhibitors of assembly and toxicity of amyloid proteins. J. Am. Chem. Soc.133, 16958–16969). Here, we compared side-by-side the capability of scyllo-inositol, EGCG, and the molecular tweezer CLR01 to inhibit Aβ aggregation and toxicity. We found that EGCG and CLR01 had comparable activity whereas scyllo-inositol was a weaker inhibitor. Exploration of the binding of EGCG and CLR01 to Aβ using heteronuclear solution-state NMR showed that whereas CLR01 bound to the two Lys and single Arg residues in Aβ monomers, only weak, nonspecific binding was detected for EGCG, leaving the binding mode of the latter unresolved.
Comparação do uso de drogas entre acadêmicos do curso de Medicina da Pontifícia Universidade Católica de São Paulo (2007)

Introdução - Sabe-se há muito tempo que a utilização de drogas está relacionada com prejuízos à saúde humana, no entanto, sua utilização vem aumentando nos últimos anos, principalmente pela população universitária em geral. Alguns meios propiciam a utilização de drogas, como o afastamento dos pais e a ausência de religiosidade. A utilização de drogas está relacionada diretamente com prejuízos econômicos, sociais e intelectuais. Objetivo - Comparar a utilização de drogas entre acadêmicos recém-ingressados e entre aqueles que já apresentam maior tempo de permanência na Faculdade de Medicina da Pontifícia Universidade Católica de São Paulo (PUC-SP). Material e Método - Um questionário com 161 questões de múltipla escolha - das quais apenas uma alternativa era considerada válida - foi aplicado, separadamente, entre todos os acadêmicos do primeiro e quarto ano, em 2002. Os alunos responderam ao questionário através de uma folha anônima de respostas. Para a análise dos dados utilizou-se como auxílio o método de Kruskal-Wallis. Resultados - Um total de 192 questionários foram respondidos, sendo 96 do primeiro ano e 96 do quarto ano. A análise dos resultados permitiu identificar uma discrepância entre as respostas dos alunos das duas séries. Os resultados mostraram diferenças de até dois pontos na média das respostas dos alunos dos dois anos, sendo maior para os do quarto ano, em uma escala de 0 até 4 pontos (p &lt; 0,05), sendo considerada uma variação com significância estatística. Discussão - Os alunos que freqüentam uma escola médica conhecem todos os efeitos negativos das drogas, entretanto, o estudo em questão verificou um aumento do uso de drogas mesmo após a inserção do aluno na faculdade. Conclusão - O meio universitário, provavelmente, exerça influência sobre os acadêmicos em relação à utilização de drogas. Esse fato reflete a importância de se pensar em uma estratégia para diminuição do uso de drogas entre os jovens e os universitários.