gebhart/patrepeval huggingface dataset:
Docking sites on mitogen-activated protein kinase (MAPK) kinases, MAPK phosphatases and the Elk-1 transcription factor compete for MAPK binding and are crucial for enzymic activity (2003)

Mitogen-activated protein kinase (MAPK) cascades control gene expression patterns in response to extracellular stimuli. MAPK/ERK (extracellular-signal-regulated kinase) kinases (MEKs) activate MAPKs by phosphorylating them; activated MAPKs, in turn, phosphorylate target transcription factors, and are deactivated by phosphatases. One mechanism for maintaining signal specificity and efficiency is the interaction of MAPKs with their substrates and regulators through high-affinity docking sites. In the present study, we show that peptides corresponding to the MAPK-docking sites of MEK1, MEK2, Ste7, Elk-1 and MAPK phosphatase (MKP)-2 potently inhibit MEK2 phosphorylation of ERK2, ERK2 phosphorylation of Elk-1, and MKP-1 dephosphorylation of ERK2. Each peptide inhibited multiple reactions; for example, the MEK2 peptide inhibited not only MEK2, but also ERK2 and MKP-1. In addition, these docking-site peptides inhibited MEK2-ERK2 binding. The MAPK-docking site of MEK1 also potently stimulated ERK2-mediated phosphorylation of a target site on the same peptide. Control peptides with mutations of conserved basic and hydrophobic residues of the MAPK-docking site consensus lacked biological activity. We conclude that MEKs, MKPs and the Elk-1 transcription factor compete for binding to the same region of ERK2 via protein-protein interactions that are crucial for kinase/phosphatase activity.
An approach for the fabrication of hexagonally ordered arrays of cylindrical nanoholes in crystalline and amorphous silicon based on the self-organization of polymer micelles (2006)

A nanolithographic process is introduced based on the self-organization of gold salt loaded inverse micelles formed by poly(styrene)-block-poly(2-vinylpyridine) di-block-copolymers in toluene. The developed procedure allows the fabrication of hexagonally arranged cylindrical nanoholes (diameters ≥20 nm, aspect ratios ∼7) in crystalline as well as in amorphous Si. In the latter case, applying the concept to amorphous Si layers evaporated onto any substrate results in nanomasks allowing the transfer of the hole pattern into the substrate.
TaintDroid (2014)

Today’s smartphone operating systems frequently fail to provide users with visibility into how third-party applications collect and share their private data. We address these shortcomings with TaintDroid, an efficient, system-wide dynamic taint tracking and analysis system capable of simultaneously tracking multiple sources of sensitive data. TaintDroid enables realtime analysis by leveraging Android’s virtualized execution environment. TaintDroid incurs only 32% performance overhead on a CPU-bound microbenchmark and imposes negligible overhead on interactive third-party applications. Using TaintDroid to monitor the behavior of 30 popular third-party Android applications, in our 2010 study we found 20 applications potentially misused users’ private information; so did a similar fraction of the tested applications in our 2012 study. Monitoring the flow of privacy-sensitive data with TaintDroid provides valuable input for smartphone users and security service firms seeking to identify misbehaving applications.
Expression of hepcidin is down-regulated in TfR2 mutant mice manifesting a phenotype of hereditary hemochromatosis (2004)

Transferrin receptor 2 (TfR2) is a membrane glycoprotein that mediates cellular iron uptake from holotransferrin. Homozygous mutations of this gene cause one form of hereditary hemochromatosis in humans. We recently reported that homozygous TfR2(Y245X) mutant mice, which correspond to the TfR2(Y250X) mutation in humans, showed a phenotype similar to hereditary hemochromatosis. In this study, we further analyzed the phenotype as well as iron-related gene expression in these mice by comparing the TfR2-mutant and wild-type siblings. Northern blot analyses showed that the levels of expression of hepcidin mRNA in the liver were generally lower, whereas those of duodenal DMT1, the main transporter for uptake of dietary iron, were higher in the TfR2-mutant mice as compared to the wild-type siblings. Expression of hepcidin mRNA in the TfR2 mutant mice remained low even after intraperitoneal iron loading. In isolated hepatocytes from both wild-type and TfR2 mutant mice, interleukin-6 and lipopolysaccharide each induced expression of hepcidin mRNA. These results suggest that up-regulation of hepcidin expression by inflammatory stimuli is independent of TfR2 and that TfR2 is upstream of hepcidin in the regulatory pathway of body iron homeostasis.
Prevention and control of influenza with vaccines: recommendations of the Advisory Committee on Immunization Practices (ACIP), 2010. (2009)

This report updates the 2008 recommendations by CDC's Advisory Committee on Immunization Practices (ACIP) regarding the use of influenza vaccine for the prevention and control of seasonal influenza (CDC. Prevention and control of influenza: recommendations of the Advisory Committee on Immunization Practices [ACIP]. MMWR 2008;57[No. RR-7]). Information on vaccination issues related to the recently identified novel influenza A H1N1 virus will be published later in 2009. The 2009 seasonal influenza recommendations include new and updated information. Highlights of the 2009 recommendations include 1) a recommendation that annual vaccination be administered to all children aged 6 months-18 years for the 2009-10 influenza season; 2) a recommendation that vaccines containing the 2009-10 trivalent vaccine virus strains A/Brisbane/59/2007 (H1N1)-like, A/Brisbane/10/2007 (H3N2)-like, and B/Brisbane/60/2008-like antigens be used; and 3) a notice that recommendations for influenza diagnosis and antiviral use will be published before the start of the 2009-10 influenza season. Vaccination efforts should begin as soon as vaccine is available and continue through the influenza season. Approximately 83% of the United States population is specifically recommended for annual vaccination against seasonal influenza; however, <40% of the U.S. population received the 2008-09 influenza vaccine. These recommendations also include a summary of safety data for U.S. licensed influenza vaccines. These recommendations and other information are available at CDC's influenza website (http://www.cdc.gov/flu); any updates or supplements that might be required during the 2009-10 influenza season also can be found at this website. Vaccination and health-care providers should be alert to announcements of recommendation updates and should check the CDC influenza website periodically for additional information.
The Role of the Cytochrome P450-Dependent Metabolites of Arachidonic Acid in Blood Pressure Regulation and Renal Function A Review (1997)

Arachidonic acid metabolism through the cytochrome P450-dependent monooxygenase system has been the subject of considerable research interest over the last several years. This article reviews the biological actions of the metabolites generated through this pathway and explores their role in the regulation of renal function and systemic blood pressure. Arachidonic acid is metabolized by the cytochrome P450-dependent monooxygenase system in three ways: epoxidation, resulting in the formation of 5,6-, 8,9-, 11,12-, 14,15-epoxyeicosatrienoic acids; allylic oxidation, resulting in the formation of 5,8,9,11,12,15-hydroxyeicosatetraenoic acids (HETE); and hydroxylation, resulting in the formation of 19,20-HETEs and 20-carboxyl arachidonic acid. Elements of this pathway have been localized in the kidney and several extrarenal sites. Vasodilation, vasoconstriction, inhibition of Na+,K+-ATPase, inhibition of ion transport and modulation of cell growth have been some of the diverse physiological actions demonstrated by metabolites produced by this pathway. As a physiological correlate of these properties, considerable evidence has accumulated regarding the role of the cytochrome P450-dependent metabolites of arachidonic acid in the pathogenesis of hypertension in the spontaneously hypertensive rat. Data in humans are limited, but in small studies increased production of these metabolites has been shown in hypertensive persons. In summary, several properties of products of this "third" pathway of arachidonic acid metabolism suggest a role in cardiovascular and renal function. Additional studies are needed to precisely define the role of this pathway in human hypertension.
Unified Approach to Cycloid Drive Profile, Stress, and Efficiency Optimization (2010)

Cycloid drives are compact, efficient speed reducers. In this paper, a unified set of equations is presented to optimize their design. The conceptual framework and profile design are described. Sources and effects of tolerance are then introduced, including profile reduction, backlash and torque ripple, and maximum gear-ratio. Equations for stress, efficiency, and moment of inertia are provided.
Sublingual apomorphine (APL‐130277) for the acute conversion of OFF to ON in Parkinson's disease (2016)

This was the first study of a new sublingual apomorphine formulation in PD patients. In this open-label study, APL-130277 appeared to provide a convenient, rapid, and reliable method for treating OFF episodes. © 2016 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
Antigen-specific immature dendritic cell vaccine ameliorates anti-dsDNA antibody-induced renal damage in a mouse model (2011)

iDCs were generated from haemopoietic stem cells in bone marrow and then pulsed in vitro with nuclear antigen. The iDC vaccine and corresponding controls were injected into mice with lupus-like renal damages. The evaluation of disease was monitored by biochemical parameters and histological scores. Anti-dsDNA antibody isotypes and T-lymphocyte-produced cytokines were analysed for elucidating therapeutic mechanisms. RESULTS; The mice treated with antigen-pulsed iDCs had a sustained remission of renal damage compared with those injected with non-pulsed iDCs or other controls, including decreased anti-dsDNA antibody level, less proteinuria, lower blood urea nitrogen and serum creatinine values, and improved histological evaluation. Analysis on isotypes of anti-dsDNA antibody showed that iDC vaccine preferentially inhibited the production of IgG3, IgG2b and IgG2a. Furthermore, administration of antigen-treated iDCs to mice resulted in significantly reduced IL-2, IL-4 and IL-12 and IFN-γ produced by T-memory cells. Conversely, the vaccination of antigen-pulsed mature DCs led to increased anti-dsDNA antibody production and an aggravation of lupus-like disease in the model. CONCLUSIONS; These results suggested the high potency of iDC vaccine in preventing lupus-like renal injuries induced by pathogenic autoantibodies.
BIONOMICS OF THE FACE FLY, MUSCA AUTUMNALIS (1997)

The face fly was introduced from the Palearctic region and spread across North America in 20 years after World War II. Adults feed on cattle and horses, and larvae develop in fresh cattle dung. Little genetic differentiation appears between European and North American populations and among regions within North America. After an autumnally initiated diapause, overwintered flies emerge in spring and reproduce through late spring and summer. Generations after the first overlap, and age structure develops toward a stable age distribution. After three to ten generations, depending on weather, facultative diapause interrupts host feeding and oogenesis, and flies with hypertrophied fat body enter overwintering hibernaculae. Life table statistics and factors affecting population growth and diapause are reviewed. Early views on the fly's effects on animal productivity may have been exaggerated. On-farm control by conventional means has not been effective because of the fly's population dynamics and mobility. We suggest that the alternatives of classical biological control and area-wide control with the sterile insect technique should be considered.
MOFs as Adsorbents for Low Temperature Heating and Cooling Applications (2009)

The 3D metal-organic framework (MOF) (3)(infinity){[Ni(3)(mu(3)-btc)(2)(mu(4)-btre)(2)(mu-H(2)O)(2)]. approximately 22H(2)O} is found to be a reversibly dehydratable-hydratable water-stable MOF material with a large loading spread of 210 g/kg as a candidate for solid adsorbents in heat transformation cycles for refrigeration, heat pumping, and heat storage.
Identification of a dehydrogenase acting on D-2-hydroxyglutarate (2004)

Extracts of frozen rat liver were found to catalyse the formation of 3H2O from DL-2-hydroxy[2-3H]glutarate. Three peaks of enzyme activities were observed on separation by chromatography on DEAE-Sepharose. The first and second peaks corresponded to an enzyme acting on L-2-hydroxyglutarate and the third peak corresponded to an enzyme acting on D-2-hydroxyglutarate, as indicated by competitive inhibition of the detritiation of the racemic radioactive compound by the unlabelled L- and D-isomers respectively. The enzyme acting on the D-form was further characterized. It was independent of NAD or NADP and it converted D-2-hydroxyglutarate into a-ketoglutarate, transferring electrons to artificial electron acceptors. It also oxidized D-lactate, D-malate and meso-tartrate and was stimulated by Zn2+, Co2+ and Mn2+, but not by Mg2+ or Ca2+. Subcellular fractionation indicated that it was present in the mitochondrial fraction. The enzyme was further purified by chromatography on Blue Trisacryl and phenyl-Sepharose, up to a stage where only a few bands were still visible by SDS/PAGE. Among the four candidate polypeptides that were identified by MS, one corresponded to a predicted mitochondrial protein homologous with FAD-dependent D-lactate dehydrogenase. The corresponding human protein was expressed in HEK-293 cells and it was shown to catalyse the detritiation of DL-2-hydroxy[2-3H]glutarate with similar properties as the purified rat enzyme.
Mycology – an update. Part 1: Dermatomycoses: Causative agents, epidemiology and pathogenesis (2014)

Dermatomycoses are caused most commonly by dermatophytes. The anthropophilic dermatophyte Trichophyton rubrum is still the most frequent causative agent worldwide. Keratinolytic enzymes, e.g. hydrolases and keratinases, are important virulence factors of T. rubrum. Recently, the cysteine dioxygenase was found as new virulence factor. Predisposing host factors play a similarly important role for the development of dermatophytosis of the skin and nails. Chronic venous insufficiency, diabetes mellitus, disorders of cellular immunity, and genetic predisposition should be considered as risk factors for onychomycosis. A new alarming trend is the increasing number of cases of onychomycosis - mostly due to T. rubrum - in infancy. In Germany, tinea capitis is mostly caused by zoophilic dermatophytes, in particular Microsporum canis. New zoophilic fungi, primarily Trichophyton species of Arthroderma benhamiae, should be taken into differential diagnostic considerations of tinea capitis, tinea faciei, and tinea corporis. Source of infection are small household pets, particularly rodents, like guinea pigs. Anthropophilic dermatophytes may be introduced by families which immigrate from Africa or Asia to Europe. The anthropophilic dermatophytes T. violaceum, T. tonsurans (infections occurring in fighting sports clubs as "tinea gladiatorum capitis et corporis") and M. audouinii are causing outbreaks of small epidemics of tinea corporis and tinea capitis in kindergartens and schools. Superficial infections of the skin and mucous membranes due to yeasts are caused by Candida species. Also common are infections due to the lipophilic yeast fungus Malassezia. Today, within the genus Malassezia more than 10 different species are known. Malassezia globosa seems to play the crucial role in pityriasis versicolor. Molds (also designated non-dermatophyte molds, NDM) are increasingly found as causative agents in onychomycosis. Besides Scopulariopsis brevicaulis, several species of Fusarium and Aspergillus are found.
Inhibition of radiation induced migration of human head and neck squamous cell carcinoma cells by blocking of EGF receptor pathways (2011)

Our results demonstrate that the EGFR is involved in radiation induced migration of HNSCC cells. Therefore EGFR or the downstream pathways might be a target for the treatment of HNSCC to improve the efficacy of radiotherapy.
Preparation of .alpha.,.alpha.-difluoro-.beta.-hydroxy esters via a modified Reformatsky reaction (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of .alpha.,.alpha.-difluoro-.beta.-hydroxy esters via a modified Reformatsky reactionTimothy T. CurranCite this: J. Org. Chem. 1993, 58, 23, 6360–6363Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/jo00075a033https://doi.org/10.1021/jo00075a033research-articleACS PublicationsRequest reuse permissionsArticle Views401Altmetric-Citations35LEARN 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 (1)»Supporting Information Supporting Information Get e-Alerts
Generation of 21-fs millijoule-energy pulses by use of Ti:sapphire (1994)

We have demonstrated the generation of 21 ± 2 fs duration pulses, with an energy of 0.5 mJ, a bandwidth of 44 nm, and a repetition rate of 10 Hz, using a chirped-pulse amplification scheme in Ti:sapphire. We use 11-fs, 5-nJ pulses from a Ti:sapphire oscillator as the input for an eight-pass Ti:sapphire amplifier. A broadband, low-dispersion chirped-pulse stretcher-and-amplifier design was used for propagation and amplification of the ultrashort pulses. By the addition of a prism pair to the stretcher, both the second- and third-order dispersions are minimized, permitting us to generate near-transform-limited amplified pulses at a duration near the theoretical limit imposed by gain narrowing in Ti:sapphire.
InGaN-Based Blue Light-Emitting Diodes Grown on Epitaxially Laterally Overgrown GaN Substrates (1998)

InGaN single-quantum-well-structure blue light-emitting diodes (LEDs) were grown on epitaxially laterally overgrown GaN (ELOG) and sapphire substrates. The emission spectra showed the similar blue shift with increasing forward currents for both LEDs. The output power of both LEDs was almost the same, as high as 6 mW at a current of 20 mA. The LED on sapphire had a considerable amount of leakage current in comparison with that on ELOG. These results indicate that the In composition fluctuation is not caused by dislocations, the dislocations do not act as nonradiative recombination centers in the InGaN, and the dislocations forms the leakage current pathway in InGaN.
Effects of Bacteria Associated with Pine Wood Nematode (Bursaphelenchus xylophilus) on Development and Egg Production of the Nematode (2006)

We tested the effects of four bacterial strains carried on the surface of the pine wood nematode (PWN), Bursaphelenchus xylophilus, on egg hatch, development rate and egg production. Strains GcM5-1A (Pseudomonas fluorescens) and ZpB1-2A (P. putida), were strong phytotoxin producers, while strains JnB1B (Pantoea sp.) and AcB1C (Peptostreptococcus asaccharalyticus) did not produce phytotoxins. None of the strains had any effect on egg hatch. GcM5-1A and ZpB1-2A promoted egg production, developmental rate, body length and diameter growth in both male and female PWN, whereas JnB1B and AcB1C had no such effects on the nematode. Indeed, the latter two strains completely inhibited egg production of the nematode. The results suggest that GcM5-1A and ZpB1-2A may provide PWN with food and/or essential nutrients for development and egg production. These results provide further evidence for our previous finding of a mutualistic symbiosis between the PWN and certain strains of bacteria carried by this nematode (Zhao et al., 2003, 2005).
Trends in Antimicrobial Prescribing Rates for Children and Adolescents (2002)

The rate of antimicrobial prescribing overall and for respiratory tract infections by office-based physicians for children and adolescents younger than 15 years decreased significantly between 1989-1990 and 1999-2000.
Tetracycline-inducible expression systems with reduced basal activity in mammalian cells (1999)

We describe a modification of the tetracycline-inducible eukaryotic gene expression system with decreased basal levels of expression in HeLa cells. It employs the tetracycline-inducible transactivator and a tetracycline-regulated repressor fusion acting on the same promoter. To avoid heterodimerization or competition for the same DNA site, each was provided with different DNA recognition and/or protein dimerization specificities. We achieved active silencing in the uninduced state resulting in approximately 6-fold reduced levels of basal transcription and several hundred-fold activation of gene expression upon addition of tetracycline.
The serine-aspartate repeat (Sdr) protein family in Staphylococcus epidermidis The GenBank accession numbers for the sequences determined in this work are AF245041 (sdrF), AF245042 (sdrG) and AF245043 (sdrH). (2000)

Staphylococcus epidermidis can express three different cell-surface-associated proteins, designated SdrF, SdrG and SdrH, that contain serine-aspartate dipeptide repeats. Proteins SdrF and SdrG are similar in sequence and structural organization to the Sdr proteins of Staphylococcus aureus and comprise unique 625- and 548-residue A regions at their N termini, respectively, followed by 110-119-residue B-repeat regions and SD-repeat regions. The C termini contain LPXTG motifs and hydrophobic amino acid segments characteristic of surface proteins covalently anchored to peptidoglycan. In contrast, SdrH has a short 60-residue A region at its N terminus followed by a SD-repeat region, a unique 277-residue C region and a C-terminal hydrophobic segment. SdrH lacks a LPXTG motif. Recombinant proteins representing the A regions of SdrF, SdrG and SdrH were expressed and purified from Escherichia coli. Antisera specific to these proteins were raised in rabbits and used to identify Sdr proteins expressed by S. epidermidis. Only SdrF was released from lysostaphin-generated protoplasts of cells grown to late-exponential phase. SdrG and SdrH remained associated with the protoplast fraction and thus appear to be ineffectively sorted along the conventional pathway used for cell-wall-anchored proteins. In Southern hybridization analyses, the sdrG and sdrH genes were present in all 16 strains tested, whilst sdrF was present in 12 strains. Antisera from 16 patients who had recovered from S. epidermidis infections contained antibodies that reacted with recombinant A regions of SdrG and SdrH, suggesting that these proteins can be expressed during infection.