gebhart/patrepeval huggingface dataset:
Expression of an ATP-Binding Cassette Transporter-Encoding Gene (YOR1) Is Required for Oligomycin Resistance in Saccharomyces cerevisiae (1995)

Semidominant mutations in the PDR1 or PDR3 gene lead to elevated resistance to cycloheximide and oligomycin. PDR1 and PDR3 have been demonstrated to encode zinc cluster transcription factors. Cycloheximide resistance mediated by PDR1 and PDR3 requires the presence of the PDR5 membrane transporter-encoding gene. However, PDR5 is not required for oligomycin resistance. Here, we isolated a gene that is necessary for PDR1- and PDR3-mediated oligomycin resistance. This locus, designated YOR1, causes a dramatic elevation in oligomycin resistance when present in multiple copies. A yor1 strain exhibits oligomycin hypersensitivity relative to an isogenic wild-type strain. In addition, loss of the YOR1 gene blocks the elevation in oligomycin resistance normally conferred by mutant forms of PDR1 or PDR3. The YOR1 gene product is predicted to be a member of the ATP-binding cassette transporter family of membrane proteins. Computer alignment indicates that Yor1p shows striking sequence similarity with multidrug resistance-associated protein, Saccharomyces cerevisiae Ycf1p, and the cystic fibrosis transmembrane conductance regulator. Use of a YOR1-lacZ fusion gene indicates that YOR1 expression is responsive to PDR1 and PDR3. While PDR5 expression is strictly dependent on the presence of PDR1 or PDR3, control of YOR1 expression has a significant PDR1/PDR3-independent component. Taken together, these data indicate that YOR1 provides the link between transcriptional regulation by PDR1 and PDR3 and oligomycin resistance of yeast cells.
Performance Assessment of Cross-Directional Control for Paper Machines (2016)

The minimum variance controller has been extensively used as a benchmark in the performance assessment of both univariate and multivariate control loops when time delay is the fundamental performance limitation. In this paper, the spatial and temporal performance limitations in the cross-directional (CD) control of paper machines are analyzed. The idea of minimum variance benchmarking is extended to the CD process based on these performance limitations. Based on an industrial CD controller, a user-specified benchmark, which is more practical and less aggressive, is also proposed. In addition, several related performance indices are proposed for the CD process based on both the minimum variance benchmark and the user-specified benchmark. Illustrative examples from a paper machine simulator and industrial data sets are provided to show the effectiveness of the proposed performance indices.
Continuous Electricity Generation from Domestic Wastewater and Organic Substrates in a Flat Plate Microbial Fuel Cell (2004)

A microbial fuel cell (MFC) is a device that converts organic matter to electricity using microorganisms as the biocatalyst. Most MFCs contain two electrodes separated into one or two chambers that are operated as a completely mixed reactor. In this study, a flat plate MFC (FPMFC) was designed to operate as a plug flow reactor (no mixing) using a combined electrode/proton exchange membrane (PEM) system. The reactor consisted of a single channel formed between two nonconductive plates that were separated into two halves by the electrode/PEM assembly. Each electrode was placed on an opposite side of the PEM, with the anode facing the chamber containing the liquid phase and the cathode facing a chamber containing only air. Electricity generation using the FPMFC was examined by continuously feeding a solution containing wastewater, or a specific substrate, into the anode chamber. The system was initially acclimated for 1 month using domestic wastewater orwastewater enriched with a specific substrate such as acetate. Average power density using only domestic wastewater was 72+/-1 mW/m2 at a liquid flow rate of 0.39 mL/min [42% COD (chemical oxygen demand) removal, 1.1 h HRT (hydraulic retention time)]. At a longer HRT = 4.0 h, there was 79% COD removal and an average power density of 43+/-1 mW/m2. Power output was found to be a function of wastewater strength according to a Monod-type relationship, with a half-saturation constant of Ks = 461 or 719 mg COD/L. Power generation was sustained at high rates with several organic substrates (all at approximately 1000 mg COD/L), including glucose (212+/-2 mW/ m2), acetate (286+/-3 mW/m2), butyrate (220+/-1 mW/ m2), dextran (150+/-1 mW/m2), and starch (242+/-3 mW/ m2). These results demonstrate the versatility of power generation in a MFC with a variety of organic substrates and show that power can be generated at a high rate in a continuous flow reactor system.
Hydrogen plasma enhancement of boron activation in shallow junctions (2004)

The ability to activate large concentrations of boron at lower temperatures is a persistent contingency in the continual drive for device scaling in Si microelectronics. We report on our experimental observations offering evidence for enhancement of electrical activation of implanted boron dopant in the presence of atomic hydrogen in silicon. This increased electrical activity of boron at lower anneal temperature is attributed to the creation of vacancies in the boron-implanted region, lattice-relaxation caused by the presence of atomic hydrogen, and the effect of atomic hydrogen on boron-interstitial cluster formation.
Microbiological diagnosis of streptococcal pharyngitis: Lacunae and their implications (2006)

Post-streptococcal sequelae, especially acute rheumatic fever/rheumatic heart disease continue to occur in significant proportions in many parts of the world. Despite several attempts with various intervention strategies, little success has been achieved in the control of acute rheumatic fever/rheumatic heart disease in India. The success of the control programmes depends upon timely primary prophylaxis with benzathine penicillin for which a microbiological confirmation of group A streptococcal pharyngitis is essential. Isolation of beta hemolytic streptococci from throat cultures and their identification as GAS in the laboratory, clinches the microbiological diagnosis while demonstration of a 'significant rise' in antibody titers such as Anti-streptolysin O and Anti-deoxyribonuclease B differentiates it from a group A streptococcal carrier state or pharyngitis of a viral etiology. Despite the easiness with which these can be achieved, many laboratories in India are not equipped to do so. Enhancing bacteriological and serological facilities in laboratories across the country will drastically improve the clinician's ability to diagnose bona fide GAS pharyngitis and help to institute penicillin prophylaxis at the appropriate time. This will go a long way in enhancing the compliance to penicillin prophylaxis which is the cornerstone of any RF/RHD control program.
Gene Expression from a Transcriptionally Disabled Retroviral Vector (1986)

It is very likely that a variety of viruses will become useful as vectors for the introduction of foreign genes into human patients suffering from a variety of genetic diseases. Such gene therapy requires not only that the vector be efficient for transferring and expressing the transduced gene in human cells and tissues, but also that the introduction of the virus be safe (Friedmann 1983; Anderson 1984). Without a doubt, a number of classes of viruses will eventually be used for this purpose, but the best understood and most highly developed model systems at the moment involve defective forms of murine and avian retroviruses.
Ancient DNA From Frozen Hair May Untangle Eskimo Roots (2008)

Humans began to brave the frozen northern reaches of Alaska, Canada, and Greenland about 4500 years ago, according to archaeological evidence. Researchers have long pondered the family history of these so-called Paleo-Eskimos, who were skillful hunters. Did they descend from the same Asian peoples who 10 millennia earlier crossed the Bering Strait and headed south, giving rise to Native Americans? And were they the ancestors of modern Eskimos? Now DNA recovered from an ancient clump of hair suggests that the answer to both questions is no.
Blockade of T Cell Activation Using a Surface-Linked Single-Chain Antibody to CTLA-4 (CD152) (2000)

CTLA-4 (CD152) engagement can down-regulate T cell activation and promote the induction of immune tolerance. However, the strategy of attenuating T cell activation by engaging CTLA-4 has been limited by sharing of its natural ligands with the costimulatory protein CD28. In the present study, a CTLA-4-specific single-chain Ab (scFv) was developed and expressed on the cell surface to promote selective engagement of this regulatory molecule. Transfectants expressing anti-CTLA-4 scFv at their surface bound soluble CTLA-4 but not soluble CD28. Coexpression of anti-CTLA-4 scFv with anti-CD3epsilon and anti-CD28 scFvs on artificial APCs reduced the proliferation and IL-2 production by resting and preactivated bulk T cells as well as CD4+ and CD8+ T cell subsets. Importantly, expression of anti-CTLA-4 scFv on the same cell surface as the TCR ligand was essential for the inhibitory effects of CTLA-4-specific ligation. CTLA-4-mediated inhibition of tyrosine phosphorylation of components of the proximal TCR signaling apparatus was similarly dependent on coexpression of TCR and CTLA-4 ligands on the same surface. These findings support a predominant role for CTLA-4 function in the modification of the proximal TCR signal. Using T cells from DO11.10 and 2C TCR transgenic mice, negative regulatory effects of selective CTLA-4 ligation were also demonstrated during the stimulation of Ag-specific CD4+ and CD8+ T cells by MHC/peptide complexes. Together these studies demonstrate that selective ligation of CTLA-4 using a membrane-bound scFv results in attenuated T cell responses only when coengaged with the TCR during T cell/APC interaction and define an approach to harnessing the immunomodulatory potential of CTLA-4-specific ligation.
2-Phenyl-4-quinolinecarboxamides:  A Novel Class of Potent and Selective Non-Peptide Competitive Antagonists for the Human Neurokinin-3 Receptor (1996)

ADVERTISEMENT RETURN TO ISSUELetterNEXT2-Phenyl-4-quinolinecarboxamides: A Novel Class of Potent and Selective Non-Peptide Competitive Antagonists for the Human Neurokinin-3 ReceptorGiuseppe A. M. Giardina, Henry M. Sarau, Carlo Farina, Andrew D. Medhurst, Mario Grugni, James J. Foley, Luca F. Raveglia, Dulcie B. Schmidt, Roberto Rigolio, Marco Vassallo, Vittorio Vecchietti, and Douglas W. P. HayView Author Information Department of Chemistry, SmithKline Beecham S.p.A., Via Zambeletti, 20021 Baranzate, Milano, Italy, Department of Pulmonary Pharmacology, SmithKline Beecham Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406-0939, and Department of Neurology Research, SmithKline Beecham Pharmaceuticals, New Frontiers Science Park, Third Avenue, Harlow, Essex, England CM19 5AW Cite this: J. Med. Chem. 1996, 39, 12, 2281–2284Publication Date (Web):June 7, 1996Publication History Received27 March 1996Published online7 June 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jm9602423https://doi.org/10.1021/jm9602423rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views357Altmetric-Citations40LEARN 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 SUBJECTS:Antagonists,Quinolines,Receptors,Screening assays,Selectivity Get e-Alerts
N-Terminal Derivatization of Peptides with Isothiocyanate Analogues Promoting Edman-Type Cleavage and Enhancing Sensitivity in Electrospray Ionization Tandem Mass Spectrometry Analysis (2009)

N-terminal derivatization of peptides with Edman's reagent, phenyl isothiocyanate (PITC), promotes gas-phase Edman cleavage that yields abundant complementary b(1) and y(n-1) ion pairs by tandem mass spectrometry (MS/MS). The formation of b(1) ions can be utilized as a mass tag to enhance the interpretation of MS/MS spectra and increase the confidence of peptide identification during mass spectrometry analysis. Derivatization of tryptic peptides with another isothiocyanate analogue, 4-sulfophenyl isothiocyanate, also produces signature ions resulting from Edman cleavage and facilitates peptide sequencing on linear or branched peptides. The limitation of these derivatizations, however, is reduced MS signal intensities of modified peptides, due presumably to the tags themselves. Here we have demonstrated that several other isothiocyanate analogues bearing basic moieties can derivatize peptides and significantly improve the MS sensitivity of tagged analytes, while promoting Edman fragmentation and maintaining other sequence fragments as well.
Adhesion and signaling by B cell‐derived exosomes: the role of integrins (2004)

Exosomes are nanometer-sized vesicles secreted by various cells, with potentially diverse roles in physiology. Although emphasis has been placed on their involvement in immune modulation, their potential for more wide-ranging biological effects has not been appreciated. A common exosome feature is the expression of adhesion molecules, which include the integrin family. We have for the first time addressed the possible function of B cell-derived exosome-integrins by examining adhesive interactions of exosomes (immobilized onto beads) with extracellular matrix (ECM) components and cytokine-treated fibroblasts. Integrin (beta1 and beta2) expression was demonstrated by Western blotting and flow cytometry. Binding studies (with blocking antibodies) demonstrated their function in adhesion to collagen-I, fibronectin, and tumor necrosis factor (TNF)-alpha-activated fibroblasts. Exosome adhesion to TNF-alpha-activated fibroblasts also triggered integrin-dependent changes in cytosolic calcium, measured by single cell imaging. Thus, B cell-derived exosomes express functional integrins, which are capable of mediating anchorage to ECM and cell-surface adhesion molecules, and may be a novel mode of delivering adhesion signals at distances beyond that of direct cell-cell contact during inflammation.
Approaches explored for producing a variety of ion-assisted deposited thin film coatings using an end-Hall ion source (1996)

The variety of optical components produced using this ion- assisted-deposition (IAD) technique, spans a wide ken of applications: immersed beamsplitters; band pass and edge filters; laser filters; IR windows; durable anti-reflection filters, fiber optics, and enhanced metals. Each product type has a specific set of constraints that establishes the design and production strategy: substrate type, material indices, intrinsic stress, temperature, distribution, uniformity, thickness monitoring, spectral performance specification, and environmental requirements. The end-Hall IAD processes were performed using an ion-beam current of approximately one Ampere over a range of 40 to 120eV, providing a uniform ion current density impinging on a large substrate area. Compared to films deposited using either conventional physical vapor deposition, or standard gridded ion sources, this process produces optically stable films with abroad ion-beam that is well suited for volume manufacturing of complex optical coatings.
Optimization methodology for designing 2-CPAs exploiting pattern diversity in clustered MIMO channels (2008)

Arrays designed for multiple-input multiple-output (MIMO) communication systems must provide good performance in terms of information theoretic and microwave theoretic performance measures for a large number of channel scenarios. Consequently, the general MIMO array design problem is challenging. This paper proposes a novel optimization methodology for designing circular patch arrays (CPAs), under a clustered MIMO channel model assumption. Based on the ergodic capacity, it is found that the single-cluster scenario can approximate CPA performance in clustered channels, reducing the number of channel scenarios that need to be considered. Using a new definition of channel spatial correlation that allows for pattern diversity, metrics are derived for evaluating average and outage capacity performance of CPAs, which can be expressed as a function of only the antenna parameters. With this expression, an optimization is formulated and solved numerically for optimizing the parameters of a 2-CPA on a capacity based objective function and microwave theory performance constraints. An example design is given corresponding to a 2-CPA in the 2.4 GHz unlicensed frequency band.
Photoprotection by Sunscreens with Topical Antioxidants and Systemic Antioxidants to Reduce Sun Exposure (2004)

Skin cancer is the most common cancer diagnosed in the United States, and its incidence continues to rise. Epidemiological studies have documented that excessive sun exposure increases the risk of developing nonmelanoma skin cancer. Consequently, it is mandatory that the skin be protected from the damage that occurs from ultraviolet (UV) exposure. It is the purpose of this report to review the scientific basis for photoprotection by sunscreens, topical antioxidants, and systemic antioxidants to minimize the harmful effect of sun exposure. The US Food and Drug Administration regulates sunscreen products as over-the-counter drugs. Sunscreens are chemical or organic UV absorbers and nonchemical or inorganic UV absorbers. Other important sunscreen considerations include the sunscreen vehicle, sunscreen photostability, sunscreen preservatives, and sunscreen photoallergy and phototoxicity. Topical and systemic antioxidants have now been shown to supplement the photoprotective effects of sunscreen. The Skin Cancer Foundation, the only national and international nonprofit organization concerned exclusively with cancer of the skin, is playing a leadership role in eliminating skin cancer in our world.
Casein kinase 2-dependent serine phosphorylation of MuSK regulates acetylcholine receptor aggregation at the neuromuscular junction (2006)

The release of Agrin by motoneurons activates the muscle-specific receptor tyrosine kinase (MuSK) as the main organizer of subsynaptic specializations at the neuromuscular junction. MuSK downstream signaling is largely undefined. Here we show that protein kinase CK2 interacts and colocalizes with MuSK at post-synaptic specializations. We observed CK2-mediated phosphorylation of serine residues within the kinase insert (KI) of MuSK. Inhibition or knockdown of CK2, or exchange of phosphorylatable serines by alanines within the KI of MuSK, impaired acetylcholine receptor (AChR) clustering, whereas their substitution by residues that imitate constitutive phosphorylation led to aggregation of AChRs even in the presence of CK2 inhibitors. Impairment of AChR cluster formation after replacement of MuSK KI with KIs of other receptor tyrosine kinases correlates with potential CK2-dependent serine phosphorylation within KIs. MuSK activity was unchanged but AChR stability decreased in the presence of CK2 inhibitors. Muscle-specific CK2beta knockout mice develop a myasthenic phenotype due to impaired muscle endplate structure and function. This is the first description of a regulatory cross-talk between MuSK and CK2 and of a role for the KI of the receptor tyrosine kinase MuSK for the development of subsynaptic specializations.
Finding security vulnerabilities in java applications with static analysis (2005)

This paper proposes a static analysis technique for detecting many recently discovered application vulnerabilities such as SQL injections, cross-site scripting, and HTTP splitting attacks. These vulnerabilities stem from unchecked input, which is widely recognized as the most common source of security vulnerabilities in Web applications. We propose a static analysis approach based on a scalable and precise points-to analysis. In our system, user-provided specifications of vulnerabilities are automatically translated into static analyzers. Our approach finds all vulnerabilities matching a specification in the statically analyzed code. Results of our static analysis are presented to the user for assessment in an auditing interface integrated within Eclipse, a popular Java development environment. Our static analysis found 29 security vulnerabilities in nine large, popular open-source applications, with two of the vulnerabilities residing in widely-used Java libraries. In fact, all but one application in our benchmark suite had at least one vulnerability.Context sensitivity, combined with improved object naming, proved instrumental in keeping the number of false positives low. Our approach yielded very few false positives in our experiments: in fact, only one of our benchmarks suffered from false alarms.
Assessment of Th1/Th2 Bias of STING Agonists Coated on Microneedles for Possible Use in Skin Allergen Immunotherapy (2018)

Microneedle-based skin allergen-specific immunotherapy (AIT) can benefit from adjuvants that can stimulate a stronger Th1 response against the allergen. We evaluated two stimulator of interferon genes (STING) agonists, namely, cyclic diguanylate monophosphate (c-di-GMP) and cyclic diadenylate monophosphate (c-di-AMP), as skin adjuvants using coated microneedles (MNs). For comparison, the approved subcutaneous (SC) hypodermic injection containing alum was used. Ovalbumin (Ova) was used as a model allergen. Ova-specific IgG2a antibody in serum, which is a surrogate marker for Th1 type immune response was significantly higher when STING agonists were used with coated MNs as compared to SC injection of Ova+alum in mice. In contrast, IgG1 antibody, a surrogate marker for Th2 type immune response, was at comparable levels in the MN and SC groups. Restimulation of splenocytes with Ova produced higher levels of Th1 cytokines (IFN-γ and IL-2) in the STING agonists MN groups as compared to the SC group. In conclusion, delivery of STING agonists into the skin using coated MNs activated the Th1 pathway better than SC- and MN-based delivery of alum. Thus, STING agonists could fulfill the role of adjuvants for skin AIT and even for infectious disease vaccines, where stimulation of the Th1 pathway is of interest.