gebhart/patrepeval huggingface dataset:
ATMPK4, an Arabidopsis Homolog of Mitogen-Activated Protein Kinase, Is Activated in Vitro by AtMEK1 through Threonine Phosphorylation (2000)

The modulation of mitogen-activated protein kinase (MAPK) activity regulates many intracellular signaling processes. In animal and yeast cells, MAP kinases are activated via phosphorylation by the dual-specificity kinase MEK (MAP kinase kinase). Several plant homologs of MEK and MAPK have been identified, but the biochemical events underlying the activation of plant MAPKs remain unknown. We describe the in vitro activation of an Arabidopsis homolog of MAP kinase, ATMPK4. ATMPK4 was phosphorylated in vitro by an Arabidopsis MEK homolog, AtMEK1. This phosphorylation occurred principally on threonine (Thr) residues and resulted in elevated ATMPK4 kinase activity. A second Arabidopsis MEK isoform, ATMAP2Kalpha, failed to phosphorylate ATMPK4 in vitro. Tyr dephosphorylation by the Arabidopsis Tyr-specific phosphatase AtPTP1 resulted in an almost complete loss of ATMPK4 activity. Immunoprecipitates of Arabidopsis extracts with anti-ATMPK4 antibodies displayed myelin basic protein kinase activity that was sensitive to treatment with AtPTP1. These results demonstrate that a plant MEK can phosphorylate and activate MAPK, and that Tyr phosphorylation is critical for the catalytic activity of MAPK in plants. Surprisingly, in contrast to the animal enzymes, AtMEK1 may not be a dual-specificity kinase but, rather, the required Tyr phosphorylation on ATMPK4 may result from autophosphorylation.
Immunolocalization of endothelial and leukocyte adhesion molecules in human rheumatoid and osteoarthritic synovial tissues. (1991)

Leukocyte adhesion to endothelium plays an important role in the development and perpetuation of chronic inflammatory diseases such as rheumatoid arthritis (RA). In order to help define the role of adhesion molecules in arthritic disorders, we have studied the expression of CD11c, endothelial leukocyte adhesion molecule-1 (ELAM-1), vascular cell adhesion molecule-1 (VCAM-1), and intercellular adhesion molecule-1 in synovial tissues from patients with RA and osteoarthritis (OA) by immunohistochemistry. CD11c is expressed predominantly on macrophages deep within RA and OA synovial tissues, as well as on some synovial tissue lining cells. ELAM-1 has endothelial reactivity, being present mainly on venules and capillaries and staining more blood vessels in RA than OA. VCAM-1 is present predominantly on synovial tissue macrophages and, to a lesser degree, on synovial tissue endothelial cells of venules, capillaries, and arterioles in both RA and OA. Like ELAM-1, VCAM-1 appears to be present more often on endothelial cells in RA than in OA tissues. VCAM-1 is present on macrophages isolated from RA synovium as well as macrophages in situ. Intercellular adhesion molecule-1 is more broadly distributed than the other adhesion molecules, being found on endothelium, macrophages, some fibroblasts, and some lymphocytes in both RA and OA tissues. This study shows that ELAM-1, a molecule that was previously thought to be important mainly in acute inflammatory reactions, is also found in RA, a chronic inflammatory disease, as well as in OA. Thus, ELAM-1 as well as VCAM-1 and intercellular adhesion molecule-1 may be involved in mediating the leukocyte traffic into RA and OA synovium.
Assessing the feasibility of subepidermal moisture to predict erythema and stage 1 pressure ulcers in persons with spinal cord injury: A pilot study (2011)

Preliminary results of using SEM to detect early PrU damage may translate from nursing home (NH) residents to persons with SCI. This study provides a foundation for a larger study to implement and assess SEM use as a method of prevention of PrUs.
Regulation ofStaphylococcus aureusα‐Toxin Gene(hla)Expression byagr, sarA,andsaeIn Vitro and in Experimental Infective Endocarditis (2006)

These results indicate that, although several distinct regulatory circuits can affect hla expression in vitro and in vivo, sae appears to play a crucial role in this context.
Toxicologists Brace for Genomics Revolution (2000)

According to researchers who gathered here at a high-powered summit this month, toxicology may be on the verge of changing the way it collects raw data--adopting a process that could reduce animal use and improve test results. The new approach, called "toxicogenomics," uses DNA arrays to profile gene expression in cells exposed to test compounds. But some leaders in the field warn against rushing too quickly to embrace DNA tests, which are still difficult to interpret.
Electronic Interactions and Polymer Effect in the Functionalization and Solvation of Carbon Nanotubes by Pyrene- and Ferrocene-Containing Poly(1-alkyne)s (2008)

4-[3-(1-Pyrenyl)propylcarbonyloxy]-1-butyne (PyB) and 4- ferrocenylcarbonyloxy-1-butyne (FcB) were effectively polymerized by zwitterionic rhodium complex Rh<sup>+</sup>(nbd)[C<sub>6</sub>H <sub>5</sub>B<sup>-</sup>(C<sub>6</sub>H<sub>5</sub>)<sub>3</sub>], giving corresponding polymers PPyB and PFcB with high molecular weights (M<sub>w</sub> up to 33300) in high yields (up to 83%). The polymers are excellent solvating agents in making carbon nanotubes (CNTs) soluble in common organic solvents. The salvation is aided by the wrapping or coating of CNTs by the polymers through strong electronic interactions between the aromatic pendants and the CNT shells. A pronounced "polymer effect" was observed in the solvating process: the polymers showed much higher solvating power than their monomers. The polymers endowed the CNTs with functional properties: the PPyB/CNT and PFcB/CNT hybrids were light-emitting and redox-active, respectively.
Film Properties of Low-k Silicon Nitride Films Formed by Hexachlorodisilane and Ammonia (2000)

A low‐temperature process with good step coverage of silicon nitride (SiN) formed by low‐pressure chemical vapor deposition (LPCVD) has been successfully developed by using hexachlorodisilane (HCD). HCD‐SiN showed a higher deposition rate than the conventional LPCVD technique performed at temperatures above 700°C. SiN films can be deposited down to 250°C using HCD. Deposition characteristics, film composition, and film properties under integrated circuit fabrication processes are measured mainly in terms of deposition temperature dependence. A low‐k HCD‐SiN film, formed at 450°C with a permittivity of 5.4, was applied on Cu films as an oxidation and diffusion barrier layer. The film shows excellent barrier properties and is advantageous for realizing high‐performance very large scale integrated devices with Cu interconnects. © 2000 The Electrochemical Society. All rights reserved.
The disposition of three phosphodiesterase type 5 inhibitors, vardenafil, sildenafil, and udenafil, is differently influenced by the CYP3A5 genotype (2011)

These results suggest that the disposition of these PDE5Is are differently influenced by the CYP3A5*3 genotype of individual participants. The CYP3A5*3 genotype affects the oral disposition of vardenafil significantly. The pharmacokinetic diversity of PDE5Is in relation to CYP3A5 genotype may lead to the clinical response variation and remains to be evaluated.
Carborane Complexes of Ruthenium: A Convenient Synthesis of [Ru(CO)3(.eta.5-7,8-C2B9H11)] and a Study of Reactions of This Complex (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarborane Complexes of Ruthenium: A Convenient Synthesis of [Ru(CO)3(.eta.5-7,8-C2B9H11)] and a Study of Reactions of This ComplexStephen Anderson, Donald F. Mullica, Eric L. Sappenfield, and F. Gordon A. StoneCite this: Organometallics 1995, 14, 7, 3516–3526Publication Date (Print):July 1, 1995Publication History Published online1 May 2002Published inissue 1 July 1995https://pubs.acs.org/doi/10.1021/om00007a059https://doi.org/10.1021/om00007a059research-articleACS PublicationsRequest reuse permissionsArticle Views244Altmetric-Citations52LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Synthesis of the Parent and Substituted Tetracyclic ABCD Ring Cores of Camptothecins via 1-(3-Aryl-2-propynyl)- 1,6-dihydro-6-oxo-2-pyridinecarbonitriles (2006)

A new synthetic pathway to the parent and substituted ABCD ring cores of the camptothecin family of alkaloids was developed. The N-alkylation of 1,6-dihydro-6-oxo-2-pyridinecarbonitrile (2) with 3-bromo-1-phenylpropyne provided 3a using Curran's protocol. Treatment of 3a with a catalytic amount of DBU (5 mol %) at 110 degrees C for 12 h produced indolizino[1,2-b]quinolin-9(11H)-one (6a), the parent ABCD ring core of camptothecin, in essentially quantitative yield.
N-gram-based text categorization (1994)

Text categorization is a fundamental task in doc-ument processing, allowing the automated han-dling of enormous streams of documents in electronic form. One difficulty in handling some classes of documents is the presence of different kinds of textual errors, such as spelling and grammatical errors in email, and character rec-ognition errors in documents that come through OCR. Text categorization must work reliably on all input, and thus must tolerate some level of these kinds of problems. We describe here an N-gram-based approach to text categorization that is tolerant of textual errors. The system is small, fast and robust. This system worked very well for language classifica-tion, achieving in one test a 99.8 % correct clas-sification rate on Usenet newsgroup articles written in different languages. The system also worked reasonably well for classifying articles from a number of different computer-oriented newsgroups according to subject, achieving as high as an 80 % correct classification rate. There are also several obvious directions for improving the system’s classification performance in those cases where it did not do as well. The system is based on calculating and com-paring profiles of N-gram frequencies. First, we use the system to compute profiles on training set data that represent the various categories, e.g., language samples or newsgroup content sam-ples. Then the system computes a profile for a particular document that is to be classified. Finally, the system computes a distance measure between the document’s profile and each of the
Effects of two major activating lesions on the structure and conformation of human ras oncogene products. (1985)

ras oncogenes are frequently activated in human tumors by mutations at codon 12 or 61 in their coding sequences. To investigate how these subtle alterations exert such profound effects on the biologic activities of these genes, we studied structural and conformational properties of human ras-oncogene-encoded 21-kDa proteins (p21s). We observed striking differences in the electrophoretic mobilities of the proteins under reducing and nonreducing conditions. These findings imply that intramolecular disulfide bonds affect native p21 conformation. The two activating lesions were shown to induce distinctly different alterations in p21 electrophoretic mobility that were unmasked only under reducing conditions. These results suggest that regions of the molecule containing such alterations are either not exposed or under conformational constraints in the native p21 molecule. We confirmed the opposing effects on protein mobility induced by the two activating lesions by using a recombinant gene containing both lesions. The recombinant gene's high-titer transforming activity further established that the two lesions do not negatively complement one another with respect to transforming-gene function. Our findings of distinct alterations in electrophoretic mobilities of position-12- and position-61-altered p21 molecules should be applicable to the rapid immunologic diagnosis of ras oncogenes in human malignancies.
Genetic Suppression of Polyglutamine Toxicity in Drosophila (2000)

A Drosophila model for Huntington's and other polyglutamine diseases was used to screen for genetic factors modifying the degeneration caused by expression of polyglutamine in the eye. Among 7000 P-element insertions, several suppressor strains were isolated, two of which led to the discovery of the suppressor genes described here. The predicted product of one, dHDJ1, is homologous to human heat shock protein 40/HDJ1. That of the second, dTPR2, is homologous to the human tetratricopeptide repeat protein 2. Each of these molecules contains a chaperone-related J domain. Their suppression of polyglutamine toxicity was verified in transgenic flies.
Paclitaxel Resistance: Molecular Mechanisms and Pharmacologic Manipulation (2003)

It has been approximately ten years since the Food and Drug Administration (FDA) approved paclitaxel for the treatment of platinum resistant epithelial ovarian carcinoma. Since the approval, the drug has found therapeutic applications in a variety of schedules and in a wide variety of epithelial malignancies. Its novel mechanism of action provided the hope that it would demonstrate anti-neoplastic activity in multidrug resistant tumor cells. Unfortunately, as with other chemotherapeutic drugs, resistance is commonly seen. Laboratory investigation has defined a wide variety of resistance mechanisms including overexpression of multidrug resistance (MDR-1) gene, molecular changes in the target molecule (betatubulin), changes in apoptotic regulatory and mitosis checkpoint proteins, and more recently changes in lipid composition and potentially the overexpression of interleukin 6 (IL-6). This review describes the in vitro molecular data that define and support the various mechanisms of resistance and critically evaluates the evidence for the participation of these mechanisms in clinically relevant paclitaxel resistance. This review also explores pharmacologic attempts to modulate paclitaxel resistance, principally through inhibition of the MDR-1 drug efflux pump. Future avenues for drug resistance research and its pharmacologic manipulation in the clinic are discussed.
Mitochondria‐Targeted Antioxidants in the Treatment of Disease (2008)

Mitochondrial oxidative damage is thought to contribute to a wide range of human diseases; therefore, the development of approaches to decrease this damage may have therapeutic potential. Mitochondria-targeted antioxidants that selectively block mitochondrial oxidative damage and prevent some types of cell death have been developed. These compounds contain antioxidant moieties, such as ubiquinone, tocopherol, or nitroxide, that are targeted to mitochondria by covalent attachment to a lipophilic triphenylphosphonium cation. Because of the large mitochondrial membrane potential, the cations are accumulated within the mitochondria inside cells. There, the conjugated antioxidant moiety protects mitochondria from oxidative damage. Here, we outline some of the work done to date on these compounds and how they may be developed as therapies.
A generic approach to engineer antibody pH-switches using combinatorial histidine scanning libraries and yeast display (2014)

There is growing interest in the fast and robust engineering of protein pH-sensitivity that aims to reduce binding at acidic pH, compared to neutral pH. Here, we describe a novel strategy for the incorporation of pH-sensitive antigen binding functions into antibody variable domains using combinatorial histidine scanning libraries and yeast surface display. The strategy allows simultaneous screening for both, high affinity binding at pH 7.4 and pH-sensitivity, and excludes conventional negative selection steps. As proof of concept, we applied this strategy to incorporate pH-dependent antigen binding into the complementary-determining regions of adalimumab. After 3 consecutive rounds of separate heavy and light chain library screening, pH-sensitive variants could be isolated. Heavy and light chain mutations were combined, resulting in 3 full-length antibody variants that revealed sharp, reversible pH-dependent binding profiles. Dissociation rate constants at pH 6.0 increased 230- to 780-fold, while high affinity binding at pH 7.4 in the sub-nanomolar range was retained. Furthermore, binding to huFcRn and thermal stability were not affected by histidine substitutions. Overall, this study emphasizes a generalizable strategy for engineering pH-switch functions potentially applicable to a variety of antibodies and further proteins-based therapeutics.
Wireless Power Transfer via Subterahertz-Wave (2018)

Research on wireless power transmission by a rectenna using millimeter waves and subterahertz waves is gaining attention. It is expected that energy harvesters at high frequencies will be developed for use with future 5 G. High-power wireless power supply to various applications will be possible because of miniaturization of the rectenna. As described herein, we investigate earlier studies of millimeter-wave wireless power supply, selecting and explaining salient examples of millimeter-wave high power wireless power supply.
The impact of thrombocytopenia from temozolomide and radiation in newly diagnosed adults with high-grade gliomas1 (2006)

Temozolomide (TMZ) administered daily with radiation therapy (RT) for six weeks, followed by adjuvant TMZ for six months, has become standard therapy for patients with glioblastoma multiforme (GBM). After several newly diagnosed patients at our institution developed severe (grade 3-4), prolonged thrombocytopenia, we conducted a retrospective review to define the incidence, depth, and duration of thrombocytopenia associated with this therapy. We reviewed the medical records and laboratory data of all adult patients with newly diagnosed high-grade gliomas who started treatment with this regimen between June 2004, when the regimen was first used at our institution, and August 2005. Of the 52 patients who met the criteria for this review, grade 3-4 thrombocytopenia occurred in 10 (19%; 95% CI, 10%-33%). In eight patients, the thrombocytopenia was attributable to concurrent daily TMZ and RT. The median duration of grade 3-4 thrombocytopenia was 32 days (range, 1-389 days). Five patients (10%) required platelet transfusions, two (4%) have required continued biweekly platelet transfusions for over six months, and nine (17%) discontinued therapy because of thrombocytopenia. Grade 3-4 thrombocytopenia occurred in 25% of women and 14% of men. Grade 3-4 neutropenia and anemia were noted in 10% and 8% of patients, respectively, and were not clinically significant. Between 15% and 20% of our newly diagnosed patients receiving TMZ and RT developed severe (grade 3-4) and potentially irreversible thrombocytopenia. The factors that predispose patients to this toxicity have yet to be determined. This toxicity should be considered when (1) prescribing this regimen to patient populations where a clinical benefit has yet to be shown, (2) contemplating empirical escalations of the dose or duration of TMZ, or (3) combining it with other potentially myelosuppressive therapies.
Therapeutic Potential of Janus-activated Kinase-2 Inhibitors for the Management of Myelofibrosis (2010)

Myelofibrosis (either primary or postpolycythemia vera/essential thrombocythemia) is a chronic and debilitating myeloproliferative neoplasm for which there is no well-accepted standard of care. Clinical manifestations of this disease (e.g., cytopenias, splenomegaly, bone marrow fibrosis) and constitutional symptoms (e.g., hypercatabolic state, fatigue, night sweats, fever) create significant treatment challenges. For example, progressive splenomegaly increases the risk for more serious clinical sequelae (e.g., portal hypertension, splenic infarction). Myelofibrosis arises from hematopoietic stem cells or early progenitor cells. However, the molecular mechanisms underlying its pathogenesis and clinical presentation are poorly understood, delaying the development of effective and targeted treatments. Recent studies have implicated mutations that directly or indirectly lead to the deregulated activation of Janus-activated kinase 2 (JAK2). Appreciation for the activation of JAK2 and the importance of increased levels of circulating proinflammatory cytokines in the pathogenesis and clinical manifestations of myelofibrosis has led to novel therapeutic agents targeting JAKs. This review will briefly discuss the origins of the JAK2 hypothesis, the clinical relevance of JAK2 mutations in myelofibrosis, and recent clinical progress in targeting JAKs as a therapeutic intervention for patients with this chronic and debilitating disease.
Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities (2003)

Assessing soil microbial community structure by the use of molecular techniques requires a satisfactory sampling strategy that takes into account the high microbial diversity and the heterogeneous distribution of microorganisms in the soil matrix. The influence of the sample size of three different soil types (sand, silt and clay soils) on the DNA yield and analysis of bacterial and fungal community structure were investigated. Six sample sizes from 0.125 g to 4 g were evaluated. The genetic community structure was assessed by automated ribosomal intergenic spacer analysis (A-RISA fingerprint). Variations between bacterial (B-ARISA) and fungal (F-ARISA) community structure were quantified by using principal component analysis (PCA). DNA yields were positively correlated with the sample size for the sandy and silty soils, suggesting an influence of the sample size on DNA recovery, whereas no correlation was observed in the clay soil. B-ARISA was shown to be consistent between the different sample sizes for each soil type indicating that the sampling procedure has no influence on the assessment of bacterial community structure. On the contrary for F-ARISA profiles, strong variations were observed between replicates of the smaller samples (<1 g). Principal component analysis analysis revealed that sampling aliquots of soil > or =1 g are required to obtain robust and reproducible fingerprinting analysis of the genetic structure of fungal communities. However, the smallest samples could be adequate for the detection of minor populations masked by dominant ones in larger samples. The sampling strategy should therefore be different according to the objectives: rather large soil samples (> or =1 g) for a global description of the genetic community structure, or a large number of small soil samples for a more complete inventory of microbial diversity.
Transforming biomass conversion with ionic liquids: process intensification and the development of a high-gravity, one-pot process for the production of cellulosic ethanol (2015)

Producing concentrated sugars and minimizing water usage are key elements in the economics and environmental sustainability of advanced biofuels.