gebhart/patrepeval huggingface dataset:
Engineering Substrate Preference in Subtilisin: Structural and Kinetic Analysis of a Specificity Mutant (2008)

Bacillus subtilisin has been a popular model protein for engineering altered substrate specificity. Although some studies have succeeded in increasing the specificity of subtilisin, they also demonstrate that high specificity is difficult to achieve solely by engineering selective substrate binding. In this paper, we analyze the structure and transient state kinetic behavior of Sbt160, a subtilisin engineered to strongly prefer substrates with phenylalanine or tyrosine at the P4 position. As in previous studies, we measure improvements in substrate affinity and overall specificity. Structural analysis of an inactive version of Sbt160 in complex with its cognate substrate reveals improved interactions at the S4 subsite with a P4 tyrosine. Comparison of transient state kinetic behavior against an optimal sequence (DFKAM) and a similar, but suboptimal, sequence (DVRAF) reveals the kinetic and thermodynamic basis for increased specificity, as well as the limitations of this approach. While highly selective substrate binding is achieved in Sbt160, several factors cause sequence specificity to fall short of that observed with natural processing subtilisins. First, for substrate sequences which are nearly optimal, the acylation reaction becomes faster than substrate dissociation. As a result, the level of discrimination among these substrates diminishes due to the coupling between substrate binding and the first chemical step (acylation). Second, although Sbt160 has 24-fold higher substrate affinity for the optimal substrate DFKAM than for DVRAF, the increased substrate binding energy is not translated into improved transition state stabilization of the acylation reaction. Finally, as interactions at subsites become stronger, the rate-determining step in peptide hydrolysis changes from acylation to product release. Thus, the release of the product becomes sluggish and leads to a low k(cat) for the reaction. This also leads to strong product inhibition of substrate turnover as the reaction progresses. The structural and kinetic analysis reveals that differences in the binding modes at subsites for substrates, transition states, and products are subtle and difficult to manipulate via straightforward protein engineering. These findings suggest several new strategies for engineering highly sequence selective enzymes.
Interleukin-13 Upregulates Eotaxin Expression in Airway Epithelial Cells by a STAT6-Dependent Mechanism (2001)

Interleukin (IL)-13 is a T helper 2-derived cytokine that has recently been implicated in allergic airway responses. We hypothesized that IL-13 may regulate expression of eotaxin in airway epithelium. We found that IL-13 upregulated eotaxin messenger RNA and protein synthesis in the airway epithelial cell line BEAS-2B; this effect showed synergy with tumor necrosis factor (TNF)-alpha and also was inhibited by the glucocorticoid budesonide. To establish the mechanisms of eotaxin upregulation by IL-13, cells were transfected with an eotaxin promoter-luciferase reporter plasmid and transcription was activated by IL-13 (1.7-fold) and TNF-alpha (2.8-fold). The combination of IL-13 and TNF-alpha additively activated the promoter constructs (4.1-fold). Activation of signal transducer and activator of transcription (STAT) 6 by IL-13 was confirmed by nuclear protein binding to a DNA probe derived from the eotaxin promoter. Activation of eotaxin transcription by IL-13 and the additive effect with TNF-alpha were lost in plasmids mutated at a putative STAT6 binding site. Cotransfection with a wild-type STAT6 expression vector significantly enhanced activation of the eotaxin promoter after IL-13 stimulation (6-fold induction). A significant increase of eotaxin protein secretion in the supernatant of STAT6 wild-type-transfected cells was observed after IL-13 stimulation. Cotransfection with a dominant negative STAT6 mutant expression vector inhibited activation of the eotaxin promoter by IL-13. These results indicate that IL-13 stimulates eotaxin expression in airway epithelial cells and that STAT6 plays a pivotal role in this response.
Vascular effects of dietary nitrate (as found in green leafy vegetables and beetroot) via the nitrate‐nitrite‐nitric oxide pathway (2012)

The discovery that dietary (inorganic) nitrate has important vascular effects came from the relatively recent realization of the 'nitrate-nitrite-nitric oxide (NO) pathway'. Dietary nitrate has been demonstrated to have a range of beneficial vascular effects, including reducing blood pressure, inhibiting platelet aggregation, preserving or improving endothelial dysfunction, enhancing exercise performance in healthy individuals and patients with peripheral arterial disease. Pre-clinical studies with nitrate or nitrite also show the potential to protect against ischaemia-reperfusion injury and reduce arterial stiffness, inflammation and intimal thickness. However, there is a need for good evidence for hard endpoints beyond epidemiological studies. Whilst these suggest reduction in cardiovascular risk with diets high in nitrate-rich vegetables (such as a Mediterranean diet), others have suggested possible small positive and negative associations with dietary nitrate and cancer, but these remain unproven. Interactions with other nutrients, such as vitamin C, polyphenols and fatty acids may enhance or inhibit these effects. In order to provide simple guidance on nitrate intake from different vegetables, we have developed the Nitrate 'Veg-Table' with 'Nitrate Units' [each unit being 1 mmol of nitrate (62 mg)] to achieve a nitrate intake that is likely to be sufficient to derive benefit, but also to minimize the risk of potential side effects from excessive ingestion, given the current available evidence. The lack of data concerning the long term effects of dietary nitrate is a limitation, and this will need to be addressed in future trials.
Fc? receptor IIa polymorphism in caucasian patients with systemic lupus erythematosus: Association with clinical symptoms (1998)

The FcgammaRIIa polymorphism constitutes an additional factor that might influence the clinical manifestations and course of SLE, but does not represent a genetic risk factor for the occurrence of SLE.
Diffraction methods for biological macromolecules. Part A. (1985)

This book contains three sections, each consisting of several papers. Some of the paper titles are: Crystallization in Capillary Tubes; Determination of Protein Molecular Weight, Hydration and Packing from Crystal Density; Photographic Science and Microdensitometry in X-Ray Diffraction Data Collection; X-Ray Sources; and Measuring X-Ray Diffraction Data from Large Proteins with X-Ray Diffractometry.
Low-cost rapid prototyping of flexible plastic paper based microfluidic devices (2013)

This research presents a novel rapid prototyping method for paper-based flexible microfluidic devices. The microchannels were fabricated using laser ablation on a piece of plastic paper (permanent paper), the dimensions of the microchannels was carefully studied for various laser powers and scanning speeds. After laser ablation of the microchannels on the plastic paper, a transparent poly (methyl methacrylate)(PMMA) film was thermally bonded to the plastic paper to enclose the channels. After connection of tubing, the device was ready to use. An example microfluidic device (droplet generator) was also fabricated using this technique. Due to the flexibility of the fabricated device, this technique can be used to fabricate 3D microfluidic devices. The fabrication process was simple and rapid without any requirement of cleanroom facilities.
Ondansetron versus Promethazine to Treat Acute Undifferentiated Nausea in the Emergency Department: A Randomized, Double‐blind, Noninferiority Trial (2008)

Promethazine and ondansetron have similar efficacy in reducing nausea among ED patients. Change in anxiety was similar, but promethazine was associated with greater sedation.
The Legionnaires' disease bacterium (Legionella pneumophila) inhibits phagosome-lysosome fusion in human monocytes. (1983)

The interactions between the L. pneumophila phagosome and monocyte lysosomes were investigated by prelabeling the lysosomes with thorium dioxide, an electron-opaque colloidal marker, and by acid phosphatase cytochemistry. Phagosomes containing live L. pneumophila did not fuse with secondary lysosomes at 1 h after entry into monocytes or at 4 or 8 h after entry by which time the ribosome-lined L. pneumophila replicative vacuole had formed. In contrast, the majority of phagosomes containing formalin-killed L. pneumophila, live Streptococcus pneumoniae, and live Escherichia coli had fused with secondary lysosomes by 1 h after entry into monocytes. Erythromycin, a potent inhibitor of bacterial protein synthesis, at a concentration that completely inhibits L. pneumophila intracellular multiplication, had no influence on fusion of L. pneumophila phagosomes with secondary lysosomes. However, coating live L. pneumophila with antibody or with antibody and complement partially overcame the inhibition of fusion. Also activating the monocytes promoted fusion of a small proportion of phagosomes containing live L. pneumophila with secondary lysosomes. Acid phosphatase cytochemistry revealed that phagosomes containing live L. pneumophila did not fuse with either primary or secondary lysosomes. In contrast to phagosomes containing live bacteria, the majority of phagosomes containing formalin-killed L. pneumophila were fused with lysosomes by acid phosphatase cytochemistry. The capacity of L. pneumophila to inhibit phagosome-lysosome fusion may be a critical mechanism by which the bacterium resists monocyte microbicidal effects.
Prolonged Expression and Effective Readministration of Erythropoietin Delivered with a Fully Deleted Adenoviral Vector (2000)

Helper-dependent (HD) adenoviral (Ad) vectors, in which all viral coding sequences are deleted, have been generated. We show here that intravenous delivery of a mouse EPO (mEPO) expression cassette cloned in an HD vector in immunocompetent mice is effective and long lasting, but not permanent. A precise dose-response relationship between the dose of injected virus and stable EPO serum levels was observed, together with a 100-fold increase in gene expression per infectious particle when compared with a first-generation Ad vector bearing the same cassette. As a direct consequence, therapeutic increases in hematocrit that lasted more than 6 months were achieved with minute amounts of virus, which caused no detectable production of neutralizing antibodies. Intravenous readministration of the HD-mEPO vector in the same mice was as effective as in naive animals without any need for prior immunosuppression. Finally, HD-mEPO injection in subtotally nephrectomized rats improved the anemic status induced by surgery. HD Ad vectors are thus excellent tools for EPO gene therapy.
Unbound free fatty acid levels in human serum. (1995)

Total serum free fatty acids (FFAt) levels provide an important measure of the physiologic state. Most of the FFA in serum is bound to albumin; a small portion, however, is unbound. This study presents the first measurements of serum unbound free fatty acid (FFAu) concentrations. These measurements were made possible by the development of the fluorescence probe ADIFAB (acrylodated intestinal fatty acid binding protein). In the present study ADIFAB was shown to provide the correct value of the sum of the [FFAu] of each molecular species of long chain FFA: 1) in aqueous mixtures of FFA and ADIFAB; 2) in mixtures of FFA, human serum albumin, and ADIFAB; and 3) in serum and ADIFAB. Human serum [FFAu] were measured in 283 samples from healthy donors and yielded a mean value of 7.5 nM with a standard deviation of 2.5 nM. This measured value is as much as 1000-fold smaller than [FFAu] values previously estimated. The distribution of [FFAu] values was found to be invariant with donor gender and age. Average [FFAu] values do, as expected, exhibit a small (1.5 nM) but significant (P < 0.001) increase after overnight fasting. FFAu levels were found to be well correlated with total serum FFA or, equivalently, [FFAt]/[HSA]. Given their ease and accuracy, and because [FFAu] values increase exponentially with [FFAt]/[HSA], [FFAu] measurements could provide a sensitive method for assessing the physiologic state.
Prohibitin, an evolutionarily conserved intracellular protein that blocks DNA synthesis in normal fibroblasts and HeLa cells. (1991)

Genes that act inside the cell to negatively regulate proliferation are of great interest because of their implications for such processes as development and cancer, but these genes have been difficult to clone. This report details the cloning and analysis of cDNA for prohibitin, a novel mammalian antiproliferative protein. Microinjection of synthetic prohibitin mRNA blocks entry into S phase in both normal fibroblasts and HeLa cells. Microinjection of an antisense oligonucleotide stimulates entry into S phase. By sequence comparison, the prohibitin gene appears to be the mammalian analog of Cc, a Drosophila gene that is vital for normal development.
Fine dissection of a nine amino acid glycoprotein epitope, a major determinant recognized by lymphocytic choriomeningitis virus-specific class I-restricted H-2Db cytotoxic T lymphocytes. (1988)

We define a nine-amino acid (aa) sequence of VAL-GLU-ASN-PRO-GLY-GLY-TYR-CYS-LEU as a major epitope for immunologic recognition of lymphocytic choriomeningitis virus (LCMV) by H-2b-restricted CTL. The epitope was characterized using molecular genetics to bracket broadly and chemistry to precisely identify aa residues 278-286 of the viral glycoprotein. The epitope's composition is characteristic of a reverse (beta turn) but not an amphipathic alpha helix. A series of peptides with a single aa substitution in position 278 of VAL with other nonpolar (hydrophobic) amino acids (LEU, ILE, ALA, or GLY) coat targets that are recognized and lysed by CTL clones recognizing this epitope. In contrast, substitution of VAL with either large aromatic amino acids (that add bulk: PHE, TYR) or polar side chains (SER, THR) segregates CTL clones normally recognizing aa 278-286 into two groups, one that remains lytic (permissive) despite these changes and another that fails to lyse, indicating CTL can discriminate at a single aa. A change in charge at this position (VAL----ASP or GLU), in general, reduces CTL lysis while a change of VAL to LYS or ASN has minimal affect for four of the five CTL clones analyzed. CTL reactivity with the viral epitope is restricted by the Db but not the Kb of the murine MHC haplotype. A 16-aa peptide of Db that spans alpha 1 residues 37-52 blocks CTL lysis, whereas the corresponding Kb peptide that differs from Db in a single aa in position 50 does not.
The impact of backoff, EIFS, and beacons on the performance of IEEE 802.11 wireless LANs (2002)

In late 1997, IEEE standardized the physical layers and the medium access for wireless local area networks. This paper presents a performance study of the distributed coordination function, the fundamental contention based access mechanism. Most performance studies adopt unchecked simplifying assumptions or do not reveal all details of the simulation model. We develop a stochastic Petri net model, which captures all relevant system aspects in a concise way. Simulation allows to quantify the influence of many mandatory features of the standard on performance, especially the backoff procedure, extended interframe spaces, and the timing synchronisation function. This study also serves to identify conditions when simplifying assumptions commonly used in analytical modeling are justified.
Differential expression of Mr 70,000 heat shock protein in normal, premalignant, and malignant human uterine cervix. (1995)

Transformed cells differ from normal cells in their pattern of heat shock protein expression. Here, we report differential expression of a Mr 70,000 heat shock protein (HSP70) in squamous cell carcinomas of the uterine cervix compared to normal or premalignant uterine cervix. Expression of HSP70 was measured using a mouse mAb against HSP70 by an ELISA. A significant increase in the level of expression of HSP70 was observed in fresh tumor cells as compared to normal or dysplastic ones (P < 0.001). The induction of HSP70 in tumor cells subjected to hyperthermia was less than that in normal or premalignant cells. Strong cytoplasmic and nuclear immunostaining was observed in cancerous tissues using anti-HSP70 mAb, biotinylated rabbit antimouse immunoglobulins, avidin combined in vitro with biotinylated horseradish peroxidase, and diaminobenzidine tetrachloride. HSP70 immunostaining was not detected in normal or dysplastic tissue sections. The results were confirmed by immunoprecipitation using anti-HSP70 mAb. These results are the first demonstration of overexpression of HSP70 in squamous cell carcinomas of the uterine cervix as compared to that in dysplastic or normal uterine cervix cells. We conclude that tumor cells differ from normal cells in their pattern of HSP70 expression, and increased levels of HSP70 correlate with an increase in tumor size.
Effects of Synthesis Conditions on the Properties of a Superconducting Bi-Sr-Ca-Cu-O System (1988)

With the aim of preparing a single, high- T c phase in the Bi-Sr-Ca-Cu-O system, optimization of the composition and heat treatment have been studied. It was found that the temperature range at which the high- T c phase forms, was very narrow (865–880°C) and a process of furnace-cooling was required to reduce a residual resistance due to the low- T c phase. The high- T c phase in this oxide system can easily form from a limited starting composition around Bi 1 Sr 1 Ca 1 Cu 2 O x . T c values for the high- T c phase do not change much from the initial composition or the heat treatment, while that for the low- T c phase moves considerably from about 88 K down to below 20 K. Existence of new superconducting phases in the Sr-Ca-Cu-O system is mentioned.
Macrophage‐induced cytotoxicity and anti‐metastatic activity of a 43‐kDa human urinary protein against the lewis tumor (1993)

Resident, inflammatory or bone-marrow macrophages from C57Bl/6 mice incubated in vitro with a pure human urinary protein (HGP.43) decreased the growth rate of Lewis tumor cells (3LL). This inhibition of 3LL growth was the result of a cytotoxic activity of these macrophages which was independent of oxygen metabolites and nitrous oxide. Murine monoclonal antibodies (MAbs) against HGP.43 inhibited macrophage-mediated cytotoxicity. This cytotoxic activity was not due to the release of cytotoxic factors in the culture supernatant, showing that a contact between macrophages and tumor cells was required to express cytotoxicity. The presence of HGP.43 was absolutely necessary during the incubation of macrophages with target cells. In vivo, in HGP.43-treated mice, the growth of the primary tumor was not delayed but the size and number of lung metastases were significantly reduced 21 days after tumor inoculation.
Intrinsic Hippocampal Activity as a Biomarker for Cognition and Symptoms in Schizophrenia (2014)

These findings suggest that greater intrinsic hippocampal activity is a characteristic feature of schizophrenia that is broadly associated with cognitive dysfunction, and they support hippocampal activity as a candidate biomarker for therapeutic development.
Gene Mutation Provides More Meat on the Hoof (1997)

Scientists have for the first time identified a gene that influences an economically important trait in beef cattle. When mutated, the gene, which codes for a protein called myostatin, leads to a phenomenon called doubling muscling in which the muscles grow much larger than normal, while still retaining their tenderness. Because the gene has also been found in nine additional animals, including the pig, turkey, and chicken, the discovery may lead to development not only of meatier strains of cattle but of other domestic animals as well.
Generative Programming of graphical user interfaces (2004)

Generative Programming (GP) is a computing paradigm allowing automatic creation of entire software families utilizing the configuration of elementary and reusable components. GP can be projected on different technologies, e.g. C++-templates, Java-Beans, Aspect-Oriented Programming (AOP), or Frame technology. This paper focuses on Frame Technology, which aids the possible implementation and completion of software components. The purpose of this paper is to introduce the GP paradigm in the area of GUI application generation. It demonstrates how automatically customized executable applications with GUI parts can be generated from an abstract specification.
Proteolysis in human breast and colorectal cancer (1999)

Proteolysis occurs when proteinase activity exceeds inhibitor activity. Proteolysis is normally tightly regulated and is involved in cancer invasion and metastasis. The aim of this study was to compare proteolysis in breast and colorectal cancer. Proteinase and inhibitor expression were analysed in paired tumour and normal tissue samples from 43 breast and 24 colorectal cancer patients using substrate zymography, Western blotting and quenched fluorescence substrate hydrolysis. The expression of the latent forms of matrix metalloproteinase-2 (MMP-2), MMP-3 and MMP-9, urokinase plasminogen activator (uPA), tissue inhibitor of metalloproteinase-1 (TIMP-1) and TIMP-2 expression were observed in both tumour and normal tissue samples from breast and colorectal tissue; however, expression was greater in the tumour tissue. Expression of active MMP-2 and MMP-9 and the total MMP activity were greater in tumour compared to normal samples in both tissues (P < 0.05). The expression of all proteinases and total MMP activity was greater in colorectal tissue than breast tissue samples. Breast and colorectal cancer demonstrated different proteinase profiles, however proteolysis in both tissues was greater in tumour tissue than normal tissue.
Photochemical Reactions in Sunlight. Experiments with 2-N-Phenyl-α,β-naphtho-1,2,3-triazolequinone and Monoxime Derivative in Sunlight and in Dark (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemical Reactions in Sunlight. Experiments with 2-N-Phenyl-α,β-naphtho-1,2,3-triazolequinone and Monoxime Derivative in Sunlight and in DarkAHMED MUSTAFA, ABDEL KADER MANSOUR, and HUSSEIN ABDEL AZIM ZAHERCite this: J. Org. Chem. 1960, 25, 6, 949–950Publication Date (Print):June 1, 1960Publication History Published online1 May 2002Published inissue 1 June 1960https://pubs.acs.org/doi/10.1021/jo01076a021https://doi.org/10.1021/jo01076a021research-articleACS PublicationsRequest reuse permissionsArticle Views69Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts