gebhart/patrepeval huggingface dataset:
Yacc : Yet Another Compiler Compiler (1978)

Computer program input generally has some structure; in fact, every computer program that does input can be thought of as defining an &amp;quot;input language&amp;quot; which it accepts. An input language may be as complex as a programming language, or as simple as a sequence of numbers. Unfortunately, usual input facilities are limited, difficult to use, and often are lax about checking their inputs for validity. Yacc provides a general tool for describing the input to a computer program. The Yacc user specifies the structures of his input, together with code to be invoked as each such structure is recognized. Yacc turns such a specification into a subroutine that handles the input process; frequently, it is convenient and appropriate to have most of the flow of control in the user&amp;apos;s application handled by this subroutine. The input subroutine produced by Yacc calls a user-supplied routine to return the next basic input item. Thus, the user can specify his input in terms of individual input characters, or in terms of higher level constructs such as names and numbers. The usersupplied routine may also handle idiomatic features such as comment and continuation conventions, which typically defy easy grammatical specification. Yacc is written in portable C. The class of specifications accepted is a very general one: LALR(1) grammars with disambiguating rules. In addition to compilers for C, APL, Pascal, RATFOR, etc., Yacc has also been used for less conventional languages, including a phototypesetter language, several desk calculator languages, a document retrieval system, and a Fortran debugging system.
Rapid detection of Staphylococcus aureus by a combination of monoclonal antibody‐coated latex and capillary electrophoresis (2006)

The rapid detection of pathogenic bacteria is extremely important in biotechnology and clinical diagnosis. CE has been utilized in the field of bacterial analysis for many years, but to some extent, simultaneous separation and identification of certain microbes from complex samples by CE coupled with UV detector is still a challenge. In this paper, we propose a new strategy for rapid separation and identification of Staphylococcus aureus (S. aureus) in bacterial mixtures by means of specific mAb-coated latex coupled with CZE. An appropriate set of conditions that selectively isolated S. aureus from the microorganisms Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae were established. S. aureus could be differentiated from the others by unique peaks in the electropherograms. The validity was also confirmed by LIF with antibodies specific to both the latex and the microbial cells. The LOD is as low as 9.0 x 10(5) colony forming unit/mL. We have also utilized this technology to identify S. aureus in a stool sample coming from a healthy volunteer spiked successfully with S. aureus. This CZE-UV technique can be applied to rapid diagnosis of enteritis caused by S. aureus or other bacterial control-related fields needing rapid identification of target pathogens from microbial mixtures. In theory, this method is suitable for the detection of any bacterium as long as corresponding bacterium-specific antibody-coated latex is available.
CpG Oligodeoxynucleotides Increase the Susceptibility of Normal Mice to Infection byCandida albicans (2005)

Synthetic oligodeoxynucleotides containing CpG motifs trigger an innate immune response that typically increases host resistance to infection. Yet CpG treatment reduces the resistance of normal mice to Candida albicans infection. This effect is mediated by CpG-induced interleukin-12, indicating that CpG-dependent cytokine production may have adverse consequences for the host.
Time without end: exploring the temporal experience of wong kar-wai's 2046 through Walter Benjamin (2009)

Beyond their beautifully crafted and mesmerising images revered by international audience and critics, the works of Hong Kong filmmaker, Wong Kar-wai, present melancholic tales of missed opportunities, repetition, regrets, lamentations, and mis-recognition. Time plays a central role in these works. At their hearts, Wong's films mourn for the loss of a potential humanity in a hyper-capitalist city - super-modernity that produces a disconnected space governed by a timeless time. In this paper, I present an analysis of Wong's films focusing on his 2005 work, 2046, through the prism of Walter Benjamin's philosophical writings. In particular, Benjamin's works on the Trauerspeils (or German mourning plays) and the German Romantics are used to formulate three main points: 1. Trauerspiel is a product of capitalism where the Messianic end is forever postponed and time is incomplete; this is fundamental for an interpretation of Wong Kar-wai's works; 2. Benjamin's speculative or immanent critique (developed from his in-depth engagement with the works of the German Romantics) allows an effective analysis of Wong's films that exposes their latent content (or Wahrheitsgehalt); 3. accessing the truth content of Wong's films presents a key to the practice of making perceptible elusive experiences - which Ackabar Abbas describes as these experiences that, 'the more you try to make [them] hold still in a reflective gaze, the more it moves under you'. Through this analysis, I identify strategies that form part of the practice of making the hidden perceptible as means to pursue and reveal truths: a task that is very pertinent to our present cultural politics.
Phosphorylation of the endothelial nitric oxide synthase at Ser‐1177 is required for VEGF‐induced endothelial cell migration (2000)

Vascular endothelial growth factor (VEGF) stimulates endothelial cell (EC) migration. The protein kinase Akt activates the endothelial NO synthase (eNOS) by phosphorylation of Ser-1177. Therefore, we investigated the contribution of Akt-mediated eNOS phosphorylation to VEGF-induced EC migration. Inhibition of NO synthase or overexpression of a dominant negative Akt abrogated VEGF-induced cell migration. In contrast, overexpression of constitutively active Akt was sufficient to induce cell migration. Moreover, transfection of an Akt site phospho-mimetic eNOS (S1177D) potently stimulated EC migration, whereas a non-phosphorylatable mutant (S1177A) inhibited VEGF-induced EC migration. Our data indicate that eNOS activation via phosphorylation of Ser-1177 by Akt is necessary and sufficient for VEGF-mediated EC migration.
Challenging nickel-catalysed amine arylations enabled by tailored ancillary ligand design (2016)

Palladium-catalysed C(sp(2))-N cross-coupling (that is, Buchwald-Hartwig amination) is employed widely in synthetic chemistry, including in the pharmaceutical industry, for the synthesis of (hetero)aniline derivatives. However, the cost and relative scarcity of palladium provides motivation for the development of alternative, more Earth-abundant catalysts for such transformations. Here we disclose an operationally simple and air-stable ligand/nickel(II) pre-catalyst that accommodates the broadest combination of C(sp(2))-N coupling partners reported to date for any single nickel catalyst, without the need for a precious-metal co-catalyst. Key to the unprecedented performance of this pre-catalyst is the application of the new, sterically demanding yet electron-poor bisphosphine PAd-DalPhos. Featured are the first reports of nickel-catalysed room temperature reactions involving challenging primary alkylamine and ammonia reaction partners employing an unprecedented scope of electrophiles, including transformations involving sought-after (hetero)aryl mesylates for which no capable catalyst system is known.
Cancer gene therapy: challenges and opportunities. (2004)

Understanding the molecular basis of human disease has been the corner-stone of rationally designed molecular therapies. Medicine has a long history of treating patients with cell therapies (i.e., blood transfusions) and protein therapies (i.e., growth factors and cytokines). Gene therapies are the newest therapeutic strategy for treating human diseases. Where will gene therapy be in five years after the euphoria and frustrations of the last 14 years? This is a complex question, but the primary challenge for gene therapy will be to successfully deliver an efficacious dose of a therapeutic gene to the defective tissue. Will the delivery systems return to the early clinical trials of ex vivo gene therapy or will there still be a high demand for systemic therapy? Will systemic therapy continue to depend on viral vectors, or will non-viral and nano-particles become the new mode for gene delivery? The future success of gene therapy will be built on achievements in other fields, such as medical devices, cell therapy, protein therapy and nano-particle technology. This review describes the advances being made in the gene therapy field, as well as addressing the challenges of the near future for cancer gene therapy.
Plasmonic Properties of Concentric Nanoshells (2004)

The plasmonic properties of a concentric nanoshell, or “nanomatryushka”, are investigated. The plasmon resonant modes are analyzed in terms of the plasmon hybridization model, where new resonances occur due to a hybridization of the plasmon modes of the inner metallic shell with those of the outer metallic shell. The plasmon resonant spectra of experimentally realized concentric nanoshells are analyzed in terms of dipolar and higher order multipolar hybridized plasmon modes. A size-dependent asymmetry in the splitting of the hybridized plasmon states is observed, which is related to phase retardation effects due to the nanostructure's finite size.
Vedolizumab: an α4β7 integrin antagonist for ulcerative colitis and Crohn’s disease (2015)

Ulcerative colitis (UC) and Crohn's disease (CD) are chronic, relapsing inflammatory bowel diseases associated with significant morbidity. Conventional therapies for these diseases include corticosteroids, aminosalicylates, immunomodulators, and monoclonal antibodies. Over the years tumor necrosis factor (TNF)-α antagonists alone or in combination with other therapies have emerged as the cornerstone of treatment for induction and maintenance of remission of moderate to severe UC and CD. Unfortunately, some patients with moderate to severe UC and CD are unable to attain or maintain remission with TNF-α antagonist treatment. Vedolizumab, a humanized monoclonal antibody, is the first integrin receptor antagonist approved that selectively antagonizes α4β7 gastrointestinal integrin receptors. US Food and Drug Administration approval is for treatment of patients with moderate to severe active UC and CD who have inadequate response with, lost response to, or are intolerant to a TNF-α antagonist or an immunomodulator; or have inadequate response with, are intolerant to, or demonstrate dependence on corticosteroids. When administered according to approved dosing in patients with moderate to severe CD and UC, vedolizumab induces clinical response rates up to 31.4% and 47.1% at week 6, and clinical remission rates up to 39% and 41.8% at week 52, respectively. Serious adverse events reported with vedolizumab include serious infections, malignancies, and anaphylaxis. Since vedolizumab is gastrointestinal selective, to date, it has not shown evidence of causing progressive multifocal leukoencephalopathy; however, postmarketing studies monitoring for this adverse effect are ongoing. Further assessment of vedolizumab earlier in the course of these diseases and in combination with other therapies is warranted.
Regulation of cystatin C activity by serine proteinases. (1991)

The effect of four human serine proteinases on the human cysteine proteinase inhibitor, cystatin C, has been studied in vitro. Neutrophil elastase in catalytic amounts was observed to rapidly cleave cystatin C at neutral pH, thereby giving rise to a modified form of the inhibitor lacking the N-terminal Ser1-Val10 decapeptide. The two other leukocyte serine proteinases, cathepsin G and neutrophil proteinase 4, did not catalytically hydrolyse cystatin C bonds. Neither had the seminal plasma serine proteinase, prostate-specific antigen, any effect on cystatin C. The physiological implications of neutrophil elastase catalysed modification of cystatin C are discussed, and recent findings indicating that this reaction also occurs in vivo are reviewed.
A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence (1998)

We address the problem of efficiently aligning a transcribed and spliced DNA sequence with a genomic sequence containing that gene, allowing for introns in the genomic sequence and a relatively small number of sequencing errors. A freely available computer program, described herein, solves the problem for a 100-kb genomic sequence in a few seconds on a workstation.
Cancer of the prostate and aging: An autopsy study in black men from Washington, DC, and selected African cities (1982)

Age-related changes of arteries, veins, glands, and stroma in the prostate of black men from Washington, DC, and from Ibadan, Nigeria, and Accra, Ghana, West AFrica, were studied in a total of 795 consecutive, unselected prostate specimens removed at autopsy during a 7-year period (1973-1980). Except for age group 80 and over, aging changes in the prostate were more severe in all age groups in black men from Washington, DC, than in black men from Ibadan and Accra (P less than 0.01). However, when the intensity of age-dependent alterations was compared in either US or African black men with carcinoma and with no carcinoma, no significant differences were found. These findings do not support the idea that the aging process per se increases susceptibility to cancer.
Optimal spliced alignments of short sequence reads (2008)

Datasets for training and evaluation, additional results and a stand-alone alignment tool implemented in C++ and python are available at http://www.fml.mpg.de/raetsch/projects/qpalma.
The Olfactory Responses of Flies in a New Type of Insect Olfactometer1 (1934)

Journal Article The Olfactory Responses of Flies in a New Type of Insect Olfactometer Get access W. M. Hoskins, W. M. Hoskins Search for other works by this author on: Oxford Academic PubMed Google Scholar R. Craig R. Craig Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 27, Issue 5, 1 October 1934, Pages 1029–1036, https://doi.org/10.1093/jee/27.5.1029 Published: 01 October 1934
EVOLUTION OF IV IRON COMPOUNDS OVER THE LAST CENTURY (2009)

Administration of intravenous (IV) iron has become pivotal in the management of anaemia in patients with chronic kidney disease (CKD). Since parenteral iron was first introduced for human use in the 1930s, things have come a long way. Seventy years ago, iron was toxic, administered as an iron oxyhydroxide complex. This problem was circumvented with the introduction of compounds containing iron in a core surrounded by a carbohydrate shell. The carbohydrate shell consists of molecules such as dextran, sucrose, dextrin or gluconate. The first dextran-containing IV iron preparations carried a small risk of anaphylaxis, but the more recently introduced low molecular weight iron dextran preparation has significantly less risk of this. Iron reactions occur with all IV iron preparations, but are generally not thought to be immune based. Recently, newer IV iron preparations have appeared in the market, including Ferumoxytol (Feraheme) and ferric carboxymaltose (Ferinject). These latest IV iron preparations do not contain a requirement for a test dose, and a much higher dose of iron can be delivered as a single administration. Thus, giving supplemental iron to man has come a long way since 1930s; we are now in an era when we are able to administer higher doses of iron with acceptable safety and without significant adverse effects. However, the long-term safety of the newer IV iron preparations is not yet established.
Radiation-induced crystallinity changes in pressure-crystallized ultrahigh molecular weight polyethylene (1983)

Abstract Exposure to high-energy radiation has been known to induce structural changes in linear polyethylene (LPE) [1–7]. For instance, it has been reported to cause cross-linking in LPE in the amorphous as well as in the crystalline phases [8–15]. Loss of crystallinity has been observed to result, especially at high radiation doses [16–20].
Recombinant human interleukin-11 stimulates multilineage hematopoietic recovery in mice after a myelosuppressive regimen of sublethal irradiation and carboplatin (1994)

Interleukin-11 (IL-11) is a novel multifunctional hematopoietic cytokine capable of stimulating cells of the myeloid, lymphoid, erythroid, and megakaryocytic lineages in vitro. We have tested the pleiotropic properties of this cytokine on the hematopoietic recovery of mice after a combined regimen of sublethal irradiation and carboplatin administration. This regimen results in severe myelosuppression, characterized by a prolonged period of thrombocytopenia and severe anemia. Administration of recombinant human IL-11 (rhIL-11; 250 micrograms/kg/d) had multilineage effects on bone marrow and spleen hematopoietic activity, increasing the number of megakaryocyte, erythroid, granulocyte, and macrophage progenitors compared with the vehicle-treated controls. This was reflected in the peripheral circulation by a reduction of both the platelet and hematocrit nadirs and a significantly reduced period of thrombocytopenia and anemia in the rhIL-11-treated mice. The results from this study support the broad spectrum of biologic activities that have been attributed to rhIL-11 in vitro and suggest that this cytokine may be an effective agent in the treatment of myelosuppression associated with cancer chemotherapy and bone marrow transplantation.
Modifications of cellulose synthase confer resistance to isoxaben and thiazolidinone herbicides in Arabidopsis Ixr1 mutants (2001)

In many higher plants, cellulose synthesis is inhibited by isoxaben and thiazolidinone herbicides such as 5-tert-butyl-carbamoyloxy-3-(3-trifluromethyl) phenyl-4-thiazolidinone. Semidominant mutations at the IXR1 and IXR2 loci of Arabidopsis confer isoxaben and thiazolidinone resistance. Isolation of the IXR1 gene by map-based cloning revealed that it encodes the AtCESA3 isoform of cellulose synthase. The two known mutant alleles contain point mutations that replace glycine 998 with aspartic acid, and threonine 942 with isoleucine, respectively. The mutations occur in a highly conserved region of the enzyme near the carboxyl terminus that is well separated from the proposed active site. Although the IXR1 gene is expressed in the same cells as the structurally related RSW1 (AtCESA1) cellulose synthase gene, these two CESA genes are not functionally redundant.
Aluminum Neurotoxicity in Preterm Infants Receiving Intravenous-Feeding Solutions (1997)

In preterm infants, prolonged intravenous feeding with solutions containing aluminum is associated with impaired neurologic development.
An iodine-doped polymer light-emitting diode (1997)

The performance of polymer light-emitting diodes (LEDs) having the configuration Al/MEH–PPV/ITO, where MEH–PPV=poly(2-methoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylene-vinylene) has been improved by light iodine doping of the emissive MEH–PPV polymer layer whereby the turn-on voltage is reduced and the external quantum efficiency is increased by an order of magnitude. It differs from nondoped MEH–PPV LEDs in that light emission is observed in both forward and reverse bias modes. It is believed that the mobility of the I3− anions in the (MEH–PPV)x+y(I3)xy− species formed on doping the MEH–PPV compensate for injected charges at the electrodes, thus reducing the electron and hole injection barriers.
A CMOS RF Programmable-Gain Amplifier for Digital TV With a $+$9-dBm IIP3 Cross-Coupled Common-Gate LNA (2012)

A CMOS RF programmable-gain amplifier (RFPGA) is designed for a digital television receiver. In order to obtain high linearity with wide bandwidth, a common-gate (CG) low-noise amplifier (LNA) with transconductance nonlinearity cancellation is proposed for the RFPGA. The proposed LNA achieves high linearity while maintaining low-noise and low-power characteristics by applying a g" <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> nonlinearity cancellation technique to the cross-coupled CG configuration. The proposed RFPGA is designed with a 0.13-μm CMOS process and measured. The measurement result at maximum gain mode shows a gain of 17.5-19.8 dB, a noise figure of 1.9-3.9 dB, an input-referred third-order intercept point of 6-9.1 dBm, an input-referred second-order intercept point of 22.4-25 dBm, and an input impedance matching of less than -10 dB over the range of 48-860 MHz with 5.4-mW power consumption at a 1.8-V supply voltage. The total gain range of the proposed RFPGA covers 55 dB with a 1-dB resolution.
Immunotherapy with PI3K Inhibitor and Toll-Like Receptor Agonist Induces IFN-γ+IL-17+ Polyfunctional T Cells That Mediate Rejection of Murine Tumors (2011)

The immunosuppressive microenvironment in tumors hampers the induction of antitumor immunity by vaccines or immunotherapies. Toll-like receptor (TLR) ligands have the potential to treat tumors, but they can exert a mixture of positive and negative effects on inflammation in the tumor microenvironment. In this study, we show that specific small molecule inhibitors of phosphoinositide 3-kinase (PI3K) relieve immunosuppression to heighten the proinflammatory effects of TLR ligands that support antitumor immunity. Multiple strategies to inhibit PI3K in dendritic cells (DC) each led to suppression of interleukin (IL)-10 and TGF-β but did affect IL-12 or IL-1β induction by the TLR5 ligand flagellin. In three different mouse models of cancer, combining flagellin with a class I PI3K inhibitor, either with or without a DC vaccine, delayed tumor growth and increased survival, with some animals exhibiting complete rejection and resistance to secondary challenge. Tumor growth suppression was associated with increased accumulation of polyfunctional T cells that secreted multiple effector cytokines, including IFN-γ, IL-17, and IL-2. Therapeutic protection was abolished in mice deficient in IL-17 or deprived of IFN-γ. Together, our results indicate that PI3K inhibition heighten the antitumor properties of TLR ligands, eliciting tumor regression directly but also indirectly by relieving suppressive signals that restrict potent antitumor T-cell responses. These findings suggest important uses for PI3K inhibitors in heightening responses to cancer immunotherapy and immunochemotherapy.
Classification analysis of the transcriptosome of nonlesional cultured dermal fibroblasts from systemic sclerosis patients with early disease (2005)

Fibroblasts cultured from nonlesional skin of patients with SSc already have detectable abnormalities in a variety of genes and cellular processes, including those involved in extracellular matrix formation, fibrillogenesis, complement activation, and angiogenesis.
Effect on product specificity of cyclodextrin glycosyltransferase by site‐directed mutagenesis (1997)

Cyclodextrin glycosyltransferase (CGTase; EC 2.4.1.19) catalyzes the degradation of starch into cyclodextrins through an intramolecular transglycosylation reaction. Tyr-89, Asn-94, and Tyr-100 are located near the putative active center. To analyze their roles in product specificity, Tyr-89, Asn-94, and Tyr-100 of CGTase from alkalophilic Bacillus sp. I-5 were replaced with different amino acids. Among the mutants, the N94S mutant protein produced about two times more alpha-cyclodextrin than the wild-type at all incubation times. The Y89F and Y100F mutant proteins were changed to more beta-specific enzymes. From these results it is suggested that the changing of the residues located at the near active site can change the product specificity of CGTase.