gebhart/patrepeval huggingface dataset:
An unsupervised approach to recognizing discourse relations (2001)

We present an unsupervised approach to recognizing discourse relations of CONTRAST, EXPLANATION-EVIDENCE, CONDITION and ELABORATION that hold between arbitrary spans of texts. We show that discourse relation classifiers trained on examples that are automatically extracted from massive amounts of text can be used to distinguish between some of these relations with accuracies as high as 93%, even when the relations are not explicitly marked by cue phrases.
Critical role of the group A streptococcal capsule in pharyngeal colonization and infection in mice. (1994)

To study the role of the group A streptococcal capsule in pharyngeal colonization, we used two acapsular mutants derived from a type 24 strain of group A Streptococcus by transposon mutagenesis. One mutant had a stable acapsular phenotype due to a transposon-associated chromosomal deletion of essential capsule synthetic genes, while the second mutant could revert to the encapsulated phenotype at a low frequency (< 10(-4)) upon spontaneous excision of the transposon from the capsule-synthesis region of the chromosome. Both acapsular mutants were sensitive to phagocytic killing in vitro and had reduced virulence in mice after intraperitoneal challenge. Mice inoculated intranasally with the stable acapsular mutant rapidly cleared the organisms from the pharynx, and no mice died. In contrast, throat cultures of animals challenged with the revertible mutant yielded many encapsulated revertants, and mortality was similar to that of animals challenged with the parent strain. The rapid emergence of a population of encapsulated revertants in the pharynx implies that the capsule conferred a powerful selective advantage in this environmental niche. Together with the complete avirulence of the stable acapsular mutant, these observations indicate that the hyaluronic acid capsule plays a critical role in colonization and infection of the pharynx by group A streptococci.
Deep Colorization (2015)

This paper investigates into the colorization problem which converts a grayscale image to a colorful version. This is a very difficult problem and normally requires manual adjustment to achieve artifact-free quality. For instance, it normally requires human-labelled color scribbles on the grayscale target image or a careful selection of colorful reference images (e.g., capturing the same scene in the grayscale target image). Unlike the previous methods, this paper aims at a high-quality fully-automatic colorization method. With the assumption of a perfect patch matching technique, the use of an extremely large-scale reference database (that contains sufficient color images) is the most reliable solution to the colorization problem. However, patch matching noise will increase with respect to the size of the reference database in practice. Inspired by the recent success in deep learning techniques which provide amazing modeling of large-scale data, this paper re-formulates the colorization problem so that deep learning techniques can be directly employed. To ensure artifact-free quality, a joint bilateral filtering based post-processing step is proposed. Numerous experiments demonstrate that our method outperforms the state-of-art algorithms both in terms of quality and speed.
An application of the theory of electrocyclic reactions to bioluminescence (1968)

The first page of this article is displayed as the abstract.
Gene-set approach for expression pattern analysis (2008)

Recently developed gene set analysis methods evaluate differential expression patterns of gene groups instead of those of individual genes. This approach especially targets gene groups whose constituents show subtle but coordinated expression changes, which might not be detected by the usual individual gene analysis. The approach has been quite successful in deriving new information from expression data, and a number of methods and tools have been developed intensively in recent years. We review those methods and currently available tools, classify them according to the statistical methods employed, and discuss their pros and cons. We also discuss several interesting extensions to the methods.
First Human Trial of a DNA-Based Vaccine for Treatment of Human Immunodeficiency Virus Type 1 Infection: Safety and Host Response (1998)

A DNA-based vaccine containing human immunodeficiency virus type 1 (HIV-1) env and rev genes was tested for safety and host immune response in 15 asymptomatic HIV-infected patients who were not using antiviral drugs and who had CD4+ lymphocyte counts of > or = 500 per microliter of blood. Successive groups received three doses of vaccine (30, 100, or 300 microg) at 10-week intervals in a dose-escalation trial. Vaccine administration induced no local or systemic reactions, and no laboratory abnormalities were detected. Specifically, no patient developed anti-DNA antibody or muscle enzyme elevations. No consistent change occurred in CD4 or CD8 lymphocyte counts or in plasma HIV concentration. Antibody against gp120 increased in individual patients in the 100- and 300-/microg groups. Some increases were noted in cytotoxic T lymphocyte activity against gp160-bearing targets and in lymphocyte proliferative activity. The safety and potential immunogenicity of an HIV-directed DNA-based vaccine was demonstrated, a finding that should encourage further studies.
Novel Nickel‐ and Palladium‐Complexes with Aminobis(imino)phosphorane Ligands for the Polymerization of Ethylene (1981)

The new ethylene polymerization catalyst (2), which is formed from bis(η3-allyl)nickel and (1) in situ, arises from a migration of an allyl group from nickel to phosphorus. Moreover, the catalyst awakens the hope that the expensive preparation of high-pressure polyethylene can be simplified.
A Quantitative Exploration of Surface Antigen Expression in Common B-Cell Malignancies Using Flow Cytometry (2006)

The use of flow cytometry to diagnose hematological malignancies has become routine due to its ability to often differentiate between morphologically similar diseases based on antigens expressed on the surface of malignant cells. In an attempt to expand on the utility of flow cytometry in the study of B-cell malignancies we have used the most reliable quantitative methodology, QIFI (quantitative indirect immunofluorescence assay), to study the expression of CD5, CD10, CD11c, CD19, CD20, CD22, CD23, and CD79b in 384 cases of several common B-lineage malignancies, including: B-ALL, CLL, SLL, hairy cell leukemia, diffuse large B-cell lymphoma, and follicular lymphoma. The impetus behind this extensive, single institution study of surface antigens was two-fold: evaluating similarities and differences of antigen expression between B-cell neoplasms and finding additional clinical utility for the quantitative flow cytometric data generated. Our results show that each distinct malignant histology has its own quantitative pattern of surface antigen expression. In most cases, these quantitative patterns do not increase the ability of flow cytometry to distinguish between them. However, a high expression of specific antigens on a given B-cell malignancy may potentially identify optimal therapeutic targets for current and/or future monoclonal antibody-based therapies.
Design and testing of a multi-output 300 kV prototype induction cell pulsed power supply for DARHT (2002)

Technology demonstrations of key components at LANL for the dual-axis radiographic hydro test (DARHT) facility including the turnkey induction cell pulsed power supply (ICPPS) delivered by Maxwell have been in progress at the DARHT integrated test stand (ITS) for over three years. The prototype system has accumulated >35000 shots to date with no component failures and only minor system malfunctions. The eight induction cells in the ITS are driven by four water insulated Blumleins at 250 kV nominal, >67 ns wide negative polarity pulses with /spl plusmn/1% flat-top deviation. Each Blumlein drives two cells and is switched by an SF/sub 6/-insulated, coaxial triggered spark gap. The Blumlein is charged using a pulse transformer via two electrically isolated primary power capacitors switched by their respective thyratrons. The timing adjustment between the respective Blumlein output pulses is controlled via Maxwell's turnkey DARHT HV triggering system. Four switching supplies provide independent control of each Blumlein output pulse voltage. The ICPPS prototype system is provided with a single integrated control console capable of remote operation via a MODICON programmable logic controller. Details of the ICPPS and the results obtained during this extensive testing are described.
Functional expression of a single-chain antibody to ErbB-2 in plants and cell-free systems (2006)

ScFv800E6 is a useful reagent for in vitro biochemical and immunodiagnostic applications in oncology, and a candidate for future in vivo studies.
Characterization of C‐terminal domains of Arabidopsis heat stress transcription factors (Hsfs) and identification of a new signature combination of plant class A Hsfs with AHA and NES motifs essential for activator function and intracellular localization (2004)

Heat stress transcription factors (Hsfs) are the major regulators of the plant heat stress (hs) response. Sequencing of the Arabidopsis genome revealed the existence of 21 open-reading frames (ORFs) encoding putative Hsfs assigned to classes A-C. Here we present results of a functional genomics approach to the Arabidopsis Hsf family focused on the analysis of their C-terminal domains (CTDs) harboring conserved modules for their function as transcription factors and their intracellular localization. Using reporter assays in tobacco protoplasts and yeast as well as glutathione-S-transferase (GST) pull-down assays, we demonstrate that short peptide motifs enriched with aromatic and large hydrophobic amino acid (aa) residues embedded in an acidic surrounding (AHA motifs) are essential for transcriptional activity of class A Hsfs. In contrast to this, class B and C Hsfs lack AHA motifs and have no activator function on their own. We also provide evidence for the function of a leucine (Leu)-rich region centered around a conserved QMGPhiL motif at the very C-terminus as a nuclear export signal (NES) of class A Hsfs. Sequence comparison indicates that the combination of a C-terminal AHA motif with the consensus sequence FWxxF/L,F/I/L as well as the adjacent NES represents a signature domain for plant class A Hsfs, which allowed to identify more than 60 new Hsfs from the expressed sequence tag (EST) database.
Cytogenetic analysis of 63 non‐small cell lung carcinomas: Recurrent chromosome alterations amid frequent and widespread genomic upheaval (1994)

A detailed cytogenetic analysis of 63 non-small cell lung carcinomas (NSCLCs) was carried out for identification of recurrent chromosomal alterations. Most specimens displayed very complex karyotypes with multiple numerical and structural changes (median number, 31). Losses of chromosomes 9 (65% of cases) and 13 (71%) were the most frequent numerical changes. Loss of the Y was often observed in tumors from males. Gain of chromosome 7 was also frequent (41%). Chromosome arms 1p, 1q, 3p, 3q, 6q, 7q, 8q, 9p, 11q, 17p, and 19q were particularly prone to rearrangement. The chromosome arm most often contributing to losses was 9p (79%). Other arms that were frequently lost included 3p, 6q, 8p, 9q, 13q, 17p, 18q, 19p, 21q, 22q, and the short arm of each acrocentric chromosome. The percentage of cases with loss of 3p was significantly higher in squamous cell carcinomas (94%) than in adenocarcinomas (60%). There was also a statistically significant increase in the proportion of cases with gains of 1q, 7p, and 11q in adenocarcinomas compared to squamous cell carcinomas. Several recurrent isochromosomes and unbalanced exchanges were found. Among these was i(5p), which was observed in nine tumors, eight of which displayed adenomatous features. An i(8q) was identified in six cases, including five adenocarcinomas. Double minutes and/or homogeneously staining regions were seen in seven specimens. These data indicate that numerous chromosome alterations contribute to the pathogenesis of NSCLC and that, amid this widespread genomic disarray, recurrent abnormalities exist that could have biological and clinical implications.
Ubiquitin-dependent Degradation of p73 Is Inhibited by PML (2004)

p73 has been identified recently as a structural and functional homologue of the tumor suppressor p53. Here, we report that p73 stability is directly regulated by the ubiquitin-proteasome pathway. Furthermore, we show that the promyelocytic leukemia (PML) protein modulates p73 half-life by inhibiting its degradation in a PML-nuclear body (NB)-dependent manner. p38 mitogen-activated protein kinase-mediated phosphorylation of p73 is required for p73 recruitment into the PML-NB and subsequent PML-dependent p73 stabilization. We find that p300-mediated acetylation of p73 protects it against ubiquitinylation and that PML regulates p73 stability by positively modulating its acetylation levels. As a result, PML potentiates p73 transcriptional and proapoptotic activities that are markedly impaired in Pml-/- primary cells. Our findings demonstrate that PML plays a crucial role in modulating p73 function, thus providing further insights on the molecular network for tumor suppression.
Characterization of Mycobacterium smegmatis Expressing the Mycobacterium tuberculosis Fatty Acid Synthase I ( fas1 ) Gene (2004)

Unlike most other bacteria, mycobacteria make fatty acids with the multidomain enzyme eukaryote-like fatty acid synthase I (FASI). Previous studies have demonstrated that the tuberculosis drug pyrazinamide and 5-chloro-pyrazinamide target FASI activity. Biochemical studies have revealed that in addition to C(16:0), Mycobacterium tuberculosis FASI synthesizes C(26:0) fatty acid, while the Mycobacterium smegmatis enzyme makes C(24:0) fatty acid. In order to express M. tuberculosis FASI in a rapidly growing Mycobacterium and to characterize the M. tuberculosis FASI in vivo, we constructed an M. smegmatis Deltafas1 strain which contained the M. tuberculosis fas1 homologue. The M. smegmatis Deltafas1 (attB::M. tuberculosis fas1) strain grew more slowly than the parental M. smegmatis strain and was more susceptible to 5-chloro-pyrazinamide. Surprisingly, while the M. smegmatis Deltafas1 (attB::M. tuberculosis fas1) strain produced C(26:0), it predominantly produced C(24:0). These results suggest that the fatty acid elongation that produces C(24:0) or C(26:0) in vivo is due to a complex interaction among FASI, FabH, and FASII and possibly other systems and is not solely due to FASI elongation, as previously suggested by in vitro studies.
Primary structure of tyrosinase from Streptomyces glaucescens (1985)

The complete amino acid sequence of Streptomyces glaucescens tyrosinase is reported. The molecule consists of 273 amino acids and has a Mr of 30 900 including two copper atoms. The primary structure was determined by a combination of amino acid and DNA sequence analysis. Peptide sequence information was derived from the cyanogen bromide, tryptic, and thermolytic fragments of apotyrosinase by automated Edman degradation and aminopeptidase M and carboxypeptidase C digestions. The nucleotide sequence of the tyrosinase gene cloned into the PvuII site of pBR322 was determined. The enzyme contains no apparent leader peptide despite the fact that it is secreted into the culture medium. As observed for a number of different Streptomyces genes, the tyrosinase gene shows a strong preference (97%) for codons ending in G or C. A comparison of the amino acid sequence of Streptomyces glaucescens tyrosinase with that of Neurospora crassa tyrosinase reveals an overall sequence homology of only 24.2%. However, the sequence homology is much higher in those regions thought to be involved in metal binding of the binuclear active site copper of this monooxygenase.
The Flavonoid Quercetin Inhibits Proinflammatory Cytokine (Tumor Necrosis Factor Alpha) Gene Expression in Normal Peripheral Blood Mononuclear Cells via Modulation of the NF-κβ System (2006)

The flavonoids comprise a large class of low-molecular-weight plant metabolites ubiquitously distributed in food plants. These dietary antioxidants exert significant antitumor, antiallergic, and anti-inflammatory effects. The molecular mechanisms of their biological effects remain to be clearly understood. We investigated the anti-inflammatory potentials of a safe, common dietary flavonoid component, quercetin, for its ability to modulate the production and gene expression of the proinflammatory cytokine tumor necrosis factor alpha (TNF-alpha) by human peripheral blood mononuclear cells (PBMC). Our results showed that quercetin significantly inhibited TNF-alpha production and gene expression in a dose-dependent manner. Our results provide direct evidence of the anti-inflammatory effects of quercetin by PBMC, which are mediated by the inhibition of the proinflammatory cytokine TNF-alpha via modulation of NF-kappabeta1 and Ikappabeta.
Study of 15&#x00B5;m pitch solder microbumps for 3D IC integration (2009)

Developments of ultra fine pitch and high density solder microbumps and assembly process for low cost 3D stacking technologies are discussed in this paper. The solder microbumps developed in this work consist of Cu and Sn, which are electroplated in sequential with total thickness of 10µm; The under bump metallurgy (UBM) pads used here is electroless plated nickel and immersion gold (ENIG) with thickness of 2µm. Accordingly, joining of the two Si chips can be conducted by joining CuSn solder microbumps to ENIG UBM pads or CuSn solder microbumps to CuSn solder microbumps. The first joining can only be done with chip to chip assembly whereas the second joining has the potential for chip to wafer assembly. Assembly of the Si chips is conducted with the FC150 flip chip bonder at different temperatures, times, and pressures and the optimized bonding conditions are obtained. After assembly, underfill process is carried out to fill the gap and a void free underfilling is achieved using an underfill material with fine filler size.
Intracellular retention of membrane-anchored v-sis protein abrogates autocrine signal transduction. (1992)

An important question regarding autocrine transformation by v-sis is whether intracellularly activated PDGF receptors are sufficient to transform cells or whether activated receptor-ligand complexes are required at the cell surface. We have addressed this question by inhibiting cell surface transport of a membrane-anchored v-sis protein utilizing the ER retention signal of the adenoviral transmembrane protein E3/19K. A v-sis fusion protein containing this signal was retained within the cell and not transported to the cell surface as confirmed by immunofluorescent localization experiments. Also, proteolytic maturation of this protein was suppressed, indicating inefficient transport to post-Golgi compartments of the secretory pathway. When compared with v-sis proteins lacking a functional retention signal, the ER-retained protein showed a diminished ability to transform NIH 3T3 cells, as measured by the number and size of foci formed. In newly established cell lines, the ER-retained protein did not down-regulate PDGF receptors. However, continued passage of these cells selected for a fully transformed phenotype exhibiting downregulated PDGF receptors and proteolytically processed v-sis protein. These results indicate that productive autocrine interactions occur in a post-ER compartment of the secretory pathway. Transport of v-sis protein beyond the Golgi correlated with acquisition of the transformed phenotype. Furthermore, suramin treatment reversed transformation and upregulated the expression of cell surface PDGF receptors, suggesting an important role for receptor-ligand complexes localized to the cell surface.
On the performance of selenium rich lead-salt heterostructure lasers with remote p-n junction (1987)

In order to increase the operating temperature of lasers emitting in the mid-IR, various lead chalcogenide diode lasers have been fabricated and examined: Pb <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.95</inf> Sn <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.05</inf> Se/PbSe and PbSe/PbS double heterostructure and funnel-type Pb <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</inf> Eu <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> Se lasers (the Eu content in the cladding layers increased steadily from <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x = 0.01</tex> near the active layer up to <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x = 0.03</tex> ). All the lasers were grown by molecular beam epitaxy on PbSe substrates. The p-n junctions were located not on the (lattice mismatched) interfaces, but at various distances (2000-6000 A) within the confinement layer. The highest operation temperatures (CW operation up to 165 K at 5.3 μm and pulsed operation up to 220 K at 4.4 μm) were attained by the PbSe/Pb <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</inf> Eu <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> Se funnel-type laser. The experimental results were compared to theoretical computer-assisted calculations, which accounted in a self-consistent way for the distributions of light, charge carriers, and temperature within the lasers. The agreement between theory and measurements for the temperature dependence of the threshold current and wavelength and for maximal operation temperatures was quite good. We found that the main contributions to the current come from interface recombination and from overbarrier leakage of nonconfined carriers (both minority and majority). Ways to improve the lasers are discussed.
Evaluation of Smartphone Menstrual Cycle Tracking Applications Using an Adapted APPLICATIONS Scoring System (2016)

Most free smartphone menstrual cycle tracking apps for patient use are inaccurate. Few cite medical literature or health professional involvement. We list accurate apps to aid health care providers in understanding the key components they can use to evaluate and recommend apps for patients.