gebhart/patrepeval huggingface dataset:
EGFR Exon 20 Insertion Mutations in Lung Adenocarcinomas: Prevalence, Molecular Heterogeneity, and Clinicopathologic Characteristics (2013)

In contrast to other primary epidermal growth factor receptor (EGFR) mutations in lung adenocarcinomas, insertions in exon 20 of EGFR have been generally associated with resistance to EGFR-tyrosine kinase inhibitors. Their molecular spectrum, clinicopathologic characteristics, and prevalence are not well established. Tumors harboring EGFR exon 20 insertions were identified through an algorithmic screen of 1,500 lung adenocarcinomas. Cases were first tested for common mutations in EGFR (exons 19 and 21) and KRAS (exon 2) and, if negative, further analyzed for EGFR exon 20 insertions. All samples underwent extended genotyping for other driver mutations in EGFR, KRAS, BRAF, ERBB2/HER2, NRAS, PIK3CA, MEK1, and AKT by mass spectrometry; a subset was evaluated for ALK rearrangements. We identified 33 EGFR exon 20 insertion cases [2.2%, 95% confidence interval (CI), 1.6-3.1], all mutually exclusive with mutations in the other genes tested (except PIK3CA). They were more common among never-smokers (P < 0.0001). There was no association with age, sex, race, or stage. Morphologically, tumors were similar to those with common EGFR mutations but with frequent solid histology. Insertions were highly variable in position and size, ranging from 3 to 12 bp, resulting in 13 different insertions, which, by molecular modeling, are predicted to have potentially different effects on erlotinib binding. EGFR exon 20 insertion testing identifies a distinct subset of lung adenocarcinomas, accounting for at least 9% of all EGFR-mutated cases, representing the third most common type of EGFR mutation after exon 19 deletions and L858R. Insertions are structurally heterogeneous with potential implications for response to EGFR inhibitors.
Repellency of Milled Aromatic Eastern Red Cedar to Domiciliary Cockroaches (Dictyoptera: Blattellidae and Blattidae) (1989)

Journal Article Repellency of Milled Aromatic Eastern Red Cedar to Domiciliary Cockroaches (Dictyoptera: Blattellidae and Blattidae) Get access A. G. Appel, A. G. Appel Department of Entomology and Alabama Agricultural Experiment Station, Auburn University, Auburn, Alabama 36849 Search for other works by this author on: Oxford Academic PubMed Google Scholar T. P. Mack T. P. Mack Department of Entomology and Alabama Agricultural Experiment Station, Auburn University, Auburn, Alabama 36849 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 82, Issue 1, 1 February 1989, Pages 152–155, https://doi.org/10.1093/jee/82.1.152 Published: 01 February 1989 Article history Received: 14 January 1988 Accepted: 03 August 1988 Published: 01 February 1989
Gene expression profiling of taxol-resistant nasopharyngeal carcinoma cells with siRNA-mediated FOLR1 downregulation. (2015)

The suppression of FOLR1 by RNA interference altered gene expression profile of taxol-resistant nasopharyngeal carcinoma cell lines. The apoptosis-related genes and the gene alterations in viral carcinogenesis, MAPK signaling pathways might be important in FOLR1 siRNA-induced taxol-resistant reversal.
Nutritional deficiencies in patients with Crohnʼs disease in remission (2006)

In CD patients in remission, macronutrient needs are usually covered by food intake. However, micronutrient deficiencies are frequent and call for specific screening and treatment.
Automatic recognition and understanding of spoken language - a first step toward natural human-machine communication (2000)

The promise of a powerful computing device to help people in productivity as well as in recreation can only be realized with proper human-machine communication. Automatic recognition and understanding of spoken language is the first step toward natural human-machine interaction. Research in this field has produced remarkable results, leading to many exciting expectations and new challenges. We summarize the development of the spoken language technology from both a vertical (chronology) and a horizontal (spectrum of technical approaches) perspective. We highlight the introduction of statistical methods in dealing with language-related problems, as this represents a paradigm shift in the research field of spoken language processing. Statistical methods are designed to allow the machine to learn structural regularities in the speech signal, directly from data, for the purpose of automatic speech recognition and understanding. Research results in spoken language processing have led to a number of successful applications, ranging from dictation software for personal computers and telephone-call processing systems for automatic call routing, to automatic sub-captioning for television broadcasts. We analyze the technical successes that support these applications. Along with an assessment of the state of the art in this broad technical field, we also discuss the limitations of the current technology, and point out the challenges that are ahead. This paper presents an accurate overview of spoken language technology as a basis to inspire future advances.
Psychological autopsy studies of suicide: a systematic review (2003)

The results indicated that mental disorder was the most strongly associated variable of those that have been studied. Further studies should focus on specific disorders and psychosocial factors. Suicide prevention strategies may be most effective if focused on the treatment of mental disorders.
Antibody to a 39-kilodalton Borrelia burgdorferi antigen (P39) as a marker for infection in experimentally and naturally inoculated animals (1991)

Borrelia burgdorferi expresses a conserved, species-specific 39-kDa protein (P39) that can stimulate antibodies during human infection. To confirm that anti-P39 antibodies are produced consistently in animals exposed to infectious spirochetes, white-footed mice, Peromyscus leucopus, and laboratory white mice, Mus musculus (strain BALB/c), were experimentally inoculated with either infectious or noninfectious B. burgdorferi and the antibody response to P39 was determined by immunoblot at 21 days postinoculation. All mice inoculated with approximately 10(7) infectious B. burgdorferi produced anti-P39 antibodies and were cultured positive for this spirochete. Mice inoculated with similar numbers of inactivated or viable noninfectious B. burgdorferi still producing P39 did not induce anti-P39 antibodies. By contrast, putative antiflagellin antibodies were detected in less than 18% of the infected animals, which supports the notion that antibody reactive with flagellin may not be reliable as a marker for B. burgdorferi exposure as was originally thought. Mice infected with B. burgdorferi following exposure to ticks (Ixodes dammini) produced anti-P39 antibodies no later than 7 days postinfection, indicating that P39 is an effective immunogen in natural infections. Notably, anti-P39 antibodies were the predominant B. burgdorferi reactive antibodies detected early in the infection. Our results indicate that anti-P39 antibodies are produced in response to an active infection and are therefore reliable markers for infection in experimentally and naturally inoculated animals.
Synthesis and biological properties of novel phosphotriesters: a new approach to the introduction of biologically active nucleotides into cells (1990)

A series of aryl bis(3'-O-acetylthymidin-5'-yl) phosphate derivatives have been synthesized in order to find a suitable aryl derivative which would hydrolyze to the bis(nucleosid-5'-yl) phosphate under physiological conditions. The 4-(methylsulfonyl)phenyl derivative was selected and 4-(methylsulfonyl)phenyl bis[(E)-5-(2-bromovinyl)-2'-deoxyuridin-5'-yl] phosphate (6d) and bis[2-(guanin-9-ylmethoxy)ethoxy]-4-(methylsulfonyl)phenyl phosphate (7b) were prepared. The former compound (6d) was stable in human serum and only following hydrolysis to the 5'-5'-linked diester (half-life of 17 h at pH 7.7) was it enzymatically degraded very rapidly by phosphodiesterases. Compounds 6d and 7b were evaluated for antiherpesvirus effects, both in vitro and in vivo. Their antiviral spectrum and potency was remarkably similar to that of (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) and 9-[(2-hydroxyethoxy)-methyl]guanine (ACV), suggesting that they only act as prodrugs of BVDU and ACV, respectively. However, compound 6d did show unexpected toxicity, which could be explained by the liberation of BVDUMP following penetration of the triester into the cell.
Magnetic properties and spin polarization ofCo2MnSiHeusler alloy thin films epitaxially grown on GaAs(001) (2005)

Single-crystalline ${\mathrm{Co}}_{2}\mathrm{MnSi}$ Heusler alloy films have been grown on GaAs(001) substrates by pulsed laser deposition (PLD). The best crystallographic quality of the ${\mathrm{Co}}_{2}\mathrm{MnSi}$ films has been achieved after deposition at 450 K. The films exhibit in-plane uniaxial magnetic anisotropy with the easy axis of magnetization along the [1-10] direction superimposed with a fourfold anisotropy with the easy axis along ⟨110⟩. Spin-resolved photoemission measurements of the single-crystalline ${\mathrm{Co}}_{2}\mathrm{MnSi}$ films reveal a spin-resolved density of states that is in qualitative agreement with recent band structure calculations. The spin polarization of photoelectrons close to the Fermi level is found to be at most 12%, in contrast to the predicted half-metallic behavior. We suggest that these discrepancies may be attributed to a partial chemical disorder in the ${\mathrm{Co}}_{2}\mathrm{MnSi}$ lattice.
Optical coherence microscopy in scattering media (1994)

We describe a novel technique, based on optical coherence tomography, for enhanced optical sectioning in confocal microscopy. Confocal imaging deep into highly scattering media is demonstrated and compared with the predictions of a single-backscatter theory.
Peroxisome proliferator-activated receptor gamma and cancers. (2003)

The peroxisome proliferator-activated receptor gamma (PPARgamma) ligands have anticancer activity against a wide variety of neoplastic cells in vitro. Animal studies have chronicled their in vivo anticancer effects and chemopreventive capabilities. In addition, moderate anticancer activities of PPARgamma ligands with minimal toxicities have been observed in patients with liposarcomas and prostate cancers. These compounds can slow growth and induce partial differentiation of selected cancer cells. They can decrease levels of cyclin D(1) and E, inflammatory cytokines, and nuclear factor kappaB and increase expression of p21(waf1) and p27(kip1). Surprisingly, some or many of these effects may occur independently of PPARgamma. Other data suggest that PPARgamma may behave as a tumor suppressor gene, although several compelling murine models, paradoxically, suggest that under selected circumstances, PPARgamma ligands may stimulate cancer formation. Nevertheless, the bulk of studies showed that PPARgamma ligands do have antiproliferative activity against many transformed cells and may be helpful in the setting of adjuvant and chemopreventive treatments of several common tumors, including colon, prostate, and breast cancers.
Terahertz imaging with nanometer resolution (2003)

We report on the application of scanning near-field optical microscopy for terahertz imaging. We demonstrate a spatial resolution of 150 nm for 2.0 THz pulses. Our experiments show the feasibility of submicron THz microscopy for imaging of biologic tissues on the cell level or for the investigation of individual submicron semiconductor devices.
Dynamic Wetting and Spreading Characteristics of a Liquid Droplet Impinging on Hydrophobic Textured Surfaces (2011)

We report on the wetting dynamics of a 4.3 μL deionized (DI) water droplet impinging on microtextured aluminum (Al 6061) surfaces, including microhole arrays (hole diameter 125 μm and hole depth 125 μm) fabricated using a conventional microcomputer numerically controlled (μ-CNC) milling machine. This study examines the influence of the texture area fraction ϕ(s) and drop impact velocity on the spreading characteristics from the measurement of the apparent equilibrium contact angle, dynamic contact angle, and maximum spreading diameter. We found that for textured surfaces the measured apparent contact angle (CA) takes on values of up to 125.83°, compared to a CA of approximately 80.59° for a nontextured bare surface, and that the spreading factor decreases with the increased texture area fraction because of increased hydrophobicity, partial penetration of the liquid, and viscous dissipation. In particular, on the basis of the model of Ukiwe and Kwok (Ukiwe, C.; Kwok, D. Y. Langmuir 2005, 21, 666), we suggest a modified equation for predicting the maximum spreading factor by considering various texturing effects and wetting states. Compared with predictions by using earlier published models, the present model shows better agreement with experimental measurements of the maximum spreading factor.
Brightly photoluminescent phosphor materials based on silicon quantum dots with oxide shell passivation (2011)

We demonstrate silicon-based phosphor materials which exhibit bright photoluminescence from near-infra-red to green. The colloidal composites which are composed of silicon quantum dots (SiQDs) attached on micro-size silicon particles are synthesized by electrochemical etching of silicon wafers and then dispersed in ethanol. Subsequently, isotropic etching by HF/HNO3 mixture controls the size so as the emission wavelength of SiQDs, and forms an oxide passivating shell. The phosphors can further react with alkoxysilanes to form a stable suspension in non-polar solvents for solution-processing. The resulting red-light-emitting SiQD-based phosphors in chloroform exhibit photoluminescence external quantum efficiency of 15.9%. Their thin films can be efficiently excited by InGaN light-emitting diodes and are stable in room condition.
Rapid identification and typing of Staphylococcus aureus by nested PCR amplified ribosomal DNA spacer region (1997)

We designed a polymerase chain reaction (PCR) assay for rapid detection of prokaryotic 16S-23S spacer regions. This PCR assay consisted of nested DNA amplifications. The first-step PCR was able to detect the general presence of eubacteriales with a unified set of universal primers. The universal primers were selected from highly conserved regions in 16S and 23S ribosomal RNA (rRNA) genes and amplified DNAs from all 62 different species of bacteria tested. In the second-step PCR, the identification primers could detect four important bacterial species through amplification of the rRNA spacer regions between the 16S-23S rRNA genes. For Staphylococcus aureus, intraspecies variation in spacer amplification products was observed with S. aureus specific primers. We suggest that the nested PCR assay could be used as a novel method for the identification and typing in epidemiological studies of S. aureus.
On the asymptotic eigenvalue distribution of Toeplitz matrices (1972)

Since covariance matrices of weakly stationary random processes are Toeplitz, much of the theory involving asymptotic results for such processes is simply the theory of the asymptotic behavior of Toeplitz forms. The fundamental theorem of this type is the Szegö theorem on the asymptotic eigenvalue distribution of Toeplitz matrices. This theorem is often quoted but relatively little understood in the engineering literature. In this tutorial paper we prove the Szegiö theorem for the special case of finite-order Toeplitz matrices. In this setting the mathematical sophistication of the classical proofs is not required and the proof is both simple and intuitive--yet it contains the important concepts involved in the most general case.
The Poor Prognosis of Central Nervous System Cryptococcosis among Nonimmunosuppressed Patients: A Call for Better Disease Recognition and Evaluation of Adjuncts to Antifungal Therapy (2006)

We describe 9 nonimmunosuppressed patients with central nervous system cryptococcosis. Morbidity and mortality were high, especially among patients with cerebral infarcts. This was attributed to delayed diagnosis and apparent sequelae of overwhelming host immune responses. We present clues suggesting the diagnosis. Increased recognition and timely diagnosis of this condition may improve outcomes.
The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data (2010)

The JCVI metagenomics analysis pipeline provides for the efficient and consistent annotation of shotgun metagenomics sequencing data for sampling communities of prokaryotic organisms. The process can be equally applied to individual sequence reads from traditional Sanger capillary electrophoresis sequences, newer technologies such as 454 pyrosequencing, or sequence assemblies derived from one or more of these data types. It includes the analysis of both coding and non-coding genes, whether full-length or, as is often the case for shotgun metagenomics, fragmentary. The system is designed to provide the best-supported conservative functional annotation based on a combination of trusted homology-based scientific evidence and computational assertions and an annotation value hierarchy established through extensive manual curation. The functional annotation attributes assigned by this system include gene name, gene symbol, GO terms, EC numbers, and JCVI functional role categories.
High Bronchoalveolar Levels of Tumor Necrosis Factor and Its Inhibitors, Interleukin-1, Interferon, and Elastase, in Patients with Adult Respiratory Distress Syndrome after Trauma, Shock, or Sepsis (1992)

Intrapulmonary activation of leukocytes and release of cellular mediators and enzymes are involved in the pathophysiology of the adult respiratory distress syndrome (ARDS). To investigate a possible role of local cytokines, we measured bronchoalveolar fluid (BALF) and plasma levels of tumor necrosis factor alpha (TNF-alpha) and its soluble inhibitors (sTNF-RI + RII), interleukin-1 beta (IL-1 beta), interferon-alpha (IFN-alpha), and granulocyte elastase in 14 patients at risk for ARDS and in 35 patients developing ARDS after trauma, sepsis, or shock. During clinical development of severe ARDS, BALF cytokines increased markedly: TNF-alpha from 116 +/- 36 to 10,731 +/- 5,048 pg/ml (mean +/- SEM), p = 0.001; sTNF-RI + RII from 3.7 +/- 1.4 to 24.6 +/- 2.6 ng/ml, p less than 0.05; and IL-1 beta from 7,746 +/- 5,551 to 42,255 +/- 19,176 pg/ml, p = 0.01. Plasma cytokines were not increased in most patients, nor were they correlated with the development or severity of ARDS. BALF elastase was higher in patients developing ARDS than in those at risk but not going into pulmonary failure (0.97 +/- 0.26 versus 0.28 +/- 0.13 U/ml, p = 0.026), and the highest values were observed in the early stages of severe ARDS (1.85 +/- 0.39 U/ml). BALF elastase levels correlated with IFN-alpha (r = 0.72, p less than 0.001). In conclusion, local release of TNF-alpha and IL-1 beta, possibly by pulmonary macrophages or other cells, and/or accumulation in the lung is associated with the development of ARDS.(ABSTRACT TRUNCATED AT 250 WORDS)
Protection and communication abstractions for web browsers in MashupOS (2007)

Web browsers have evolved from a single-principal platform on which one site is browsed at a time into a multi-principal platform on which data and code from mutually distrusting sites interact programmatically in a single page at the browser. Today's "Web 2.0" applications (or mashups ) offer rich services, rivaling those of desktop PCs. However, the protection andcommunication abstractions offered by today's browsers remain suitable onlyfor a single-principal system--either no trust through completeisolation between principals (sites) or full trust by incorporating third party code as libraries. In this paper, we address this deficiency by identifying and designing the missing abstractions needed for a browser-based multi-principal platform. We have designed our abstractions to be backward compatible and easily adoptable. We have built a prototype system that realizes almost all of our abstractions and their associated properties. Our evaluation shows that our abstractions make it easy to build more secure and robust client-side Web mashups and can be easily implemented with negligible performance overhead.
Spectrum of Mutations in BRCA1, BRCA2, CHEK2, and TP53 in Families at High Risk of Breast Cancer (2006)

The mutational spectra of BRCA1 and BRCA2 include many high-penetrance, individually rare genomic rearrangements. Among patients with breast cancer and severe family histories of cancer who test negative (wild type) for BRCA1 and BRCA2, approximately 12% can be expected to carry a large genomic deletion or duplication in one of these genes, and approximately 5% can be expected to carry a mutation in CHEK2 or TP53. Effective methods for identifying these mutations should be made available to women at high risk.
Application of Solvent‐Directed Assembly of Block Copolymers to the Synthesis of Nanostructured Materials with Low Dielectric Constants (2006)

An inverse relationship: Mixtures of poly(dimethylacrylamide)-block-polylactide copolymer (PDMA-b-PLA) with organosilicate oligomers (PMSSQ) selectively sequestered into the PDMA phase form micelles and inverse micelles in solution depending on the solvent. The micellar structures are imprinted into the resulting cured organosilicate to give monoliths or assemblies of densely packed organosilicate nanoparticles, respectively. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z601888_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Chloropolysporins A, B and C, novel glycopeptide antibiotics from Faenia interjecta sp. nov. II. Fermentation, isolation and physico-chemical characterization. (1987)

New antibiotics, chloropolysporins A, B and C, were found in the culture broth of an actinomycete identified as Faenia interjecta sp. nov. They were isolated from the culture filtrate by column chromatography on various resinous adsorbents, followed by preparative reverse phase HPLC. Chloropolysporins A, B and C possessed all the same new aglycone composed of actinoidic acid, 3-chloro-4-hydroxyphenylglycine, N-methyl-p-hydroxyphenylglycine and vancomycinic acid. From elementary analyses and mass spectroscopic measurements, the molecular formulae of chloropolysporins A, B and C appear to be C89H99O39N8Cl3 (MW 2,008), C83H89O34N8Cl3 (MW 1,846) and C77H79O30N8Cl3 (MW 1,700), respectively. Their physico-chemical characterizations including molecular formulae revealed that chloropolysporins A, B and C were new members of glycopeptide antibiotics.
Therapy With Immunoglobulin Suppresses Myocarditis in a Murine Coxsackievirus B3 Model (1995)

Immunoglobulin therapy completely suppressed acute CB3 myocarditis by transferring the neutralizing antibody into the host in the acute viremic stage and induced an anti-inflammatory effect in the subsequent aviremic stage; the reduction of the splenic B-cell population may be closely associated with an anti-inflammatory effect.
Photophysical characterization of the 9,10-disubstituted anthracene chromophore and its applications in triplet–triplet annihilation photon upconversion (2015)

Eight 9,10-disubstituted anthracenes have been synthesized, photochemically characterized and used for triplet–triplet annihilation photon upconversion.