gebhart/patrepeval huggingface dataset:
Composition of the Wax Secreted by a Scale Insect, Drosicha corpulenta KUWANA (Homoptera : Margarodidae) (1982)

White wax secreted by the adult female of Drosicha corpulenta was examined under scanning electron microscope. The dorsal surface this insect body was covered by numerous waxy threads, mostly in coil form and semi-tubular in shape. The wax was comprised of hydrocarbons (18%) and wax esters (82%); there were no unsaturated molecules. The hydrocarbon consisted of straight chain alkanes (70.5%) and 2-methylalkanes (27.6%); the major components were octacosane, 2-methyloctacosane and nonacosane, with a range of carbon numbers from CX27 to CX33. The principal wax ester was of chain length CX52, formed by 1-hexacosanol esterified with hexacosanoic acid.
A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature (2010)

The most important way of conveying new findings in biomedical research is scientific publication. Extraction of protein-protein interactions (PPIs) reported in scientific publications is one of the core topics of text mining in the life sciences. Recently, a new class of such methods has been proposed - convolution kernels that identify PPIs using deep parses of sentences. However, comparing published results of different PPI extraction methods is impossible due to the use of different evaluation corpora, different evaluation metrics, different tuning procedures, etc. In this paper, we study whether the reported performance metrics are robust across different corpora and learning settings and whether the use of deep parsing actually leads to an increase in extraction quality. Our ultimate goal is to identify the one method that performs best in real-life scenarios, where information extraction is performed on unseen text and not on specifically prepared evaluation data. We performed a comprehensive benchmarking of nine different methods for PPI extraction that use convolution kernels on rich linguistic information. Methods were evaluated on five different public corpora using cross-validation, cross-learning, and cross-corpus evaluation. Our study confirms that kernels using dependency trees generally outperform kernels based on syntax trees. However, our study also shows that only the best kernel methods can compete with a simple rule-based approach when the evaluation prevents information leakage between training and test corpora. Our results further reveal that the F-score of many approaches drops significantly if no corpus-specific parameter optimization is applied and that methods reaching a good AUC score often perform much worse in terms of F-score. We conclude that for most kernels no sensible estimation of PPI extraction performance on new text is possible, given the current heterogeneity in evaluation data. Nevertheless, our study shows that three kernels are clearly superior to the other methods.
Synthesis of dithiols as reducing agents for disulfides in neutral aqueous solution and comparison of reduction potentials (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of dithiols as reducing agents for disulfides in neutral aqueous solution and comparison of reduction potentialsGuy V. Lamoureux and George M. WhitesidesCite this: J. Org. Chem. 1993, 58, 3, 633–641Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/jo00055a015https://doi.org/10.1021/jo00055a015research-articleACS PublicationsRequest reuse permissionsArticle Views1656Altmetric-Citations63LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
The National Economic Burden of Cancer: An Update (1990)

Journal Article The National Economic Burden of Cancer: An Update Get access Martin L. Brown Martin L. Brown * Applied Research Branch, Surveillance Program, Division of Cancer Prevention and Control, National Cancer InstituteBethesda, Md * Correspondence to: Martin Brown, PhD, Executive Plaza North, Room 313, National Institutes of Health, Bethesda, MD 20892. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 82, Issue 23, 5 December 1990, Pages 1811–1814, https://doi.org/10.1093/jnci/82.23.1811 Published: 05 December 1990 Article history Received: 12 July 1990 Revision received: 13 September 1990 Accepted: 25 September 1990 Published: 05 December 1990
Digital Microfluidics with In-Line Sample Purification for Proteomics Analyses with MALDI-MS (2004)

An in-line sample purification method for MALDI-MS, which relies on the electrowetting-on-dielectric (EWOD)-based technique for digital microfluidics, is reported. In this method, a droplet containing peptides and impurities is moved by EWOD and deposited onto a Teflon-AF surface. A droplet of water is subsequently moved over the spot, where it dissolves and removes the impurities. A droplet containing MALDI matrix is then moved to the spot, which is analyzed by MALDI-MS. This purification method reduces the number of salt adduct peaks caused by low concentrations of impurities (e.g., 20 mM sodium phosphate), and reduces or eliminates the catastrophic effects of high concentrations of impurities (e.g., 8 M urea). The method was used to purify spots made by depositing multiple droplets of contaminated peptides. Spectra from the purified spots showed an increase in the S/N ratio as a function of the number of droplets deposited; when not purified, the S/N ratio remained constant regardless of the number of droplets. Finally, the method was used to purify protein digests for peptide mass fragment (PMF) searches, and was shown to be more efficient than the conventional method of purification with reversed-phase-packed pipet tips. We anticipate this new, in-line sample purification technique for EWOD-MALDI-MS will enable development of integrated high-throughput proteomics analysis methodologies.
A double-blind comparison of topical clindamycin and oral minocycline in the treatment of acne vulgaris. (1990)

Sixty-six patients with moderate to severe facial acne vulgaris were entered in a 12-week double-blind study to compare the efficacy of topical clindamycin phosphate 1% twice daily and oral minocycline 50 mg twice daily. Both treatments gave significant overall improvements from baseline observations in acne grade and inflamed lesion counts, but not in noninflamed lesion counts. There were no significant differences between the two treatment groups in respect of acne grade, inflamed or non-inflamed lesion counts. Both treatment regimes were well tolerated. This study has shown that topical clindamycin twice daily is an effective alternative to oral minocycline 50 mg twice daily in the treatment of moderate to severe facial acne vulgaris.
Investigation into the Origin and Tumoral Mass Correlation of Plasma Epstein–Barr Virus DNA in Nasopharyngeal Carcinoma (2005)

Despite the increasing number of clinical applications of circulating Epstein–Barr virus (EBV) DNA analysis for the detection (1)(2), monitoring(3)(4), and prognostication(5)(6) of nasopharyngeal carcinoma (NPC), several fundamental questions concerning plasma EBV DNA, including its tissue origin and relationship with tumor mass, remain unanswered.

In the first part of this study, we investigated the relative contributions of tumor cells and other latently EBV-infected lymphoid tissues to the pool of circulating EBV DNA. Previous studies have shown that different EBV genotypes are harbored by latently EBV-infected lymphoid tissues and blood cells (7)(8)(9)(10) in healthy persons and patients with malignancies. On the other hand, it is well established that the EBV is monoclonal in NPC tumor tissues and other EBV-associated cancers(11)(12)(13)(14). Therefore, investigation of the genotype of plasma EBV DNA should reveal the relative contributions of tumor cells and other latently EBV-infected lymphoid tissues to the pool of circulating EBV DNA in NPC patients.

For this study, 25 patients with newly diagnosed NPC, 15 patients with systemic lupus erythematosus, and 13 renal transplant recipients were recruited and gave informed consent. This study was approved by the ethics committee of the Prince of Wales Hospital, Hong Kong. Plasma samples were collected from all patients, and tumor specimens for microdissection were obtained from 14 of the 25 NPC patients. DNA extracted from the plasma samples and the microdissected tumor tissues was used for the amplification of EBV DNA, targeting a region encoding the carboxy terminus of latent membrane protein (LMP-1), using the primers 5′-ATGGTAATGCCTAGAAGTAAAGAAAGG-3′ (LMP1f) and 5′-CATAGCCCTAGCGACTCTGCTG-5′ (R2b). The PCR products were ligated to the pGEM®-T Easy Vectors (Promega), and the ligation products were transformed into competent Escherichia coli cells. Twelve bacterial clones were …
Extracellular ATP triggers IL-1 beta release by activating the purinergic P2Z receptor of human macrophages (1997)

Extracellular ATP (ATPe) is known to cause release of processed IL-1 beta from LPS-treated macrophages and microglial cells. IL-1 beta release is fast and thought to be associated with cell death. We have reinvestigated this process to identify 1) the purinergic receptor involved; 2) the relationship to cell death; and 3) pharmacologic agonists or antagonists able to modulate IL-1 beta release. Our data confirm that ATPe is a powerful stimulus for IL-1 beta release from LPS-treated human macrophages; however, we also show that IL-1 beta release is not necessarily associated with cell death, as it occurs at lower ATP concentrations and much earlier than leakage of cytoplasmic markers. The selective purinergic P2Z receptor agonist benzoylbenzoyl ATP was at least one order of magnitude more powerful than ATP, but also had a strong cytotoxic effect. 2-Methylthio-ATP was equipotent as ATPe at the optimal concentration of 1 mM, but markedly inhibitory at higher concentrations. The irreversible P2Z blocker-oxidized ATP completely inhibited ATPe-induced IL-1 beta release. IL-1 beta release also was inhibited by increasing the K+ concentration of the incubation medium. These data suggest that ATPe triggers IL-1 beta via the purinergic P2Z receptor recently shown to be expressed by human macrophages and identified as a new member of the P2X family (P2X7), and provide pharmacologic tools for the modulation of IL-1 beta release in vitro and, possibly, in vivo.
A 300 MHz, 3.3 V 1 Mb SRAM fabricated in a 0.5 μm CMOS process (2002)

A 300 MHz, 1 Mb SRAM with 5.4 ns access in 3.3 V, 0.5 /spl mu/m CMOS uses self-timed and self-resetting circuits. A dual-clock, flow-through read protocol optimizes data window control and a 750 ps setup-and-hold window for all input signals is achieved through floorplanning, receiver design and localized input-signal registering. The SRAM interfaces with high-speed transceiver logic (HSTL) levels through high-speed, noise-tolerant receivers. Programmable impedance output drivers for HSTL interfaces match transmission line impedance to within 10% tolerances over process, voltage and temperature variations.
Erratum: “Layer-by-layer growth of Ag on a GaN(0001) surface” [Appl. Phys. Lett. 82, 1389 (2003)] (2003)

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Magnetic resonance imaging during dobutamine stress for detection and localization of coronary artery disease. Quantitative wall motion analysis using a modification of the centerline method. (1994)

Dobutamine MRI clearly identifies wall motion abnormalities by quantitative analysis using a modification of the centerline method. Dobutamine MRI is an accurate method for detection and localization of myocardial ischemia and may emerge as a new noninvasive approach for evaluation of patients with known or suspected coronary artery disease.
Cytoplasmic Tail-Dependent Localization of CD1b Antigen-Presenting Molecules to MIICs (1996)

CD1 proteins have been implicated as antigen-presenting molecules for T cell-mediated immune responses, but their intracellular localization and trafficking remain uncharacterized. CD1b, a member of this family that presents microbial lipid antigens of exogenous origin, was found to localize to endocytic compartments that included the same specialized subset of endosomes in which major histocompatibility complex (MHC) class II molecules are proposed to bind endocytosed antigens. Unlike MHC class II molecules, which traffic to antigen-loading endosomal compartments [MHC class II compartments (MIICs)] primarily as a consequence of their association with the invariant chain, localization of CD1b to these compartments was dependent on a tyrosine-based motif in its own cytoplasmic tail.
Issues in predicting protein function from sequence (2001)

Identifying homologues, defined as genes that arose from a common evolutionary ancestor, is often a relatively straightforward task, thanks to recent advances made in estimating the statistical significance of sequence similarities found from database searches. The extent by which homologues possess similarities in function, however, is less amenable to statistical analysis. Consequently, predicting function by homology is a qualitative, rather than quantitative, process and requires particular care to be taken. This review focuses on the various approaches that have been developed to predict function from the scale of the atom to that of the organism. Similarities in homologues' functions differ considerably at each of these different scales and also vary for different domain families. It is argued that due attention should be paid to all available clues to function, including orthologue identification, conservation of particular residue types, and the co-occurrence of domains in proteins. Pitfalls in database searching methods arising from amino acid compositional bias and database size effects are also discussed.
Crystal structure of 2-(bis(4-fluorophenyl)methylsulfonyl)acetamide, C15H13F2NO2S (2010)

Article Crystal structure of 2-(bis(4-fluorophenyl)methylsulfonyl)acetamide, C15H13F2NO2S was published on December 1, 2010 in the journal Zeitschrift für Kristallographie - New Crystal Structures (volume 225, issue 4).
Slug, a Unique Androgen-Regulated Transcription Factor, Coordinates Androgen Receptor to Facilitate Castration Resistance in Prostate Cancer (2012)

Prostate cancer (PCa) becomes lethal when cancer cells develop into castration-resistant PCa (CRPC). Androgen receptor (AR) gene mutation, altered AR regulation, or overexpression of AR often found in CRPC is believed to become one of the key factors to the lethal phenotype. Here we identify Slug, a member of the Snail family of zinc-finger transcription factors associated with cancer metastasis, as a unique androgen-responsive gene in PCa cells. In addition, the presence of constitutively active AR can induce Slug expression in a ligand-independent manner. Slug overexpression will increase AR protein expression and form a complex with AR. In addition, Slug appears to be a novel coactivator to enhance AR transcriptional activities and AR-mediated cell growth with or without androgen. In vivo, elevated Slug expression provides a growth advantage for PCa cells in androgen-deprived conditions. Most importantly, these observations were validated by several data sets from tissue microarrays. Overall, there is a reciprocal regulation between Slug and AR not only in transcriptional regulation but also in protein bioactivity, and Slug-AR complex plays an important role in accelerating the androgen-independent outgrowth of CRPC.
Simvastatin reduces human atrial myofibroblast proliferation independently of cholesterol lowering via inhibition of RhoA (2004)

Simvastatin reduced proliferation of cultured human atrial myofibroblasts independently of cholesterol synthesis via a mechanism involving inhibition of RhoA geranylgeranylation. Statins may therefore have an important role in preventing adverse myocardial remodeling associated with cardiac myofibroblast proliferation.
Fine needle aspiration biopsy in the diagnosis of intrathoracic masses. (1992)

During a 3.5-year period (January 1, 1987, to June 30, 1990) 420 percutaneous fine needle aspiration (FNA) biopsies were performed on 390 patients (309 males, 81 females) suffering from one or more intrathoracic, radiologically visible lesions. Aspirations were carried out using 21- or 23-gauge Chiba needles under fluoroscopic or computed tomographic control. The aspirates were used to make minibiopsies and cytologic smears. Diagnosis was possible in 373 cases (95.64%): on the first pass in 344 cases, on the second in 28 cases and on the third in 1. In 17 cases (4.36%) the aspirate was inadequate for diagnosis. There were complications in 10 cases (2.56%) (9 pneumothorax and 1 hemophtysis) requiring intensive care. The 373 percutaneous FNA biopsy diagnoses included 256 malignant tumors (68.63%), of which 234 were primary and 22 were secondary, and 117 benign lesions (31.37%), 5 of them neoplastic and 112 nonneoplastic. Three hundred two of 373 percutaneous FNA biopsy diagnoses were followed (80.96%). One hundred twenty-three follow-ups were histologic (40.73%), including secondary tumors, which could be compared with the primary histotype. Twenty-eight follow-ups were cytologic (9.27%), and 151 were clinical (50.00%), using progression of the disease or the beginning of chemoradiotherapy as a criterion for malignancy and a stable condition or regression of the lesion with nononcologic medical treatment as a criterion for benignity. Percutaneous FNA biopsy diagnoses were confirmed in 288 cases (221 true positives and 67 true negatives) and unconfirmed in 14 (1 false positive and 13 false negatives). Specificity, sensitivity, negative predictive value, positive predictive value and total diagnostic accuracy were, respectively, 98.52, 94.44, 83.75, 99.54 and 95.36%. The histologic typing accuracy of percutaneous FNA biopsy on 70 specimens of surgically removed malignant epithelial neoplasias was 70.00%. These results confirm that percutaneous FNA biopsy is a reliable method of diagnosing intrathoracic masses and reduces the need for diagnostic thoracotomy.
Constitutive activity of signal transducer and activator of transcription 3 protein in acute myeloid leukemia blasts is associated with short disease-free survival (2002)

Signal transducer and activator of transcription (STAT) proteins are involved in hematopoietic cytokine receptor signaling pathways that regulate cell proliferation, differentiation, and survival. STATs are dysregulated in acute myeloid leukemia (AML); mechanisms of dysregulation include constitutive activation and truncation of the C-terminal transactivation domain; the latter results in a beta isoform that has a trans-dominant negative effect on gene induction mediated by the full-length STAT alpha form. It was hypothesized that constitutive STAT activity might correlate with unfavorable treatment outcome in AML. Pretreatment bone marrow samples from 63 adult patients with AML were analyzed by electrophoretic mobility shift assay for the presence of STAT DNA-binding activity. Isoforms and relative levels of STAT proteins were determined by immunoblotting. Constitutive STAT3 activity was detected in samples from 28 (44%) patients. Pretreatment clinical characteristics, expression of STAT alpha/beta isoforms, and treatment regimens did not differ significantly between patients with and without constitutive STAT3 activity. Disease-free survival (DFS) was significantly shorter in patients with than in patients without constitutive STAT3 activity (median 8.7 vs 20.6 months; P =.01). Overall survival did not differ significantly. The subgroup of patients with constitutive STAT3 activity and the STAT3 beta isoform had the shortest DFS (P =.006) and shorter overall survival (P =.049) than all other patients. Whether adverse treatment outcome is attributable to constitutive STAT activity itself or to a process that leads to constitutive STAT activity remains to be determined. This is the first demonstration of a prognostic significance for STAT proteins in a malignancy.
Preliminary13C measurements using a gas chromatograph interfaced to an isotope ratio mass spectrometer (1985)

Stable isotope tracer methods are gaining popularity in many fields, including environmental science, agriculture and medicine. This is particularly true in the clinical sciences, where the use of radioisotopes can be precluded on ethical grounds and 13C and 15N tracers are being used more frequently for metabolic studies. Mass spectrometry is the preferred technique for isotope analysis. Sample preparation techniques for classical isotope ratio mass spectrometry are often tedious and can involve the use of complex vacuum apparatus that is quite foreign to the biological chemist. Organic gas chromatography/mass spectrometry (GC/MS) overcomes many sample preparation problems but may lack the performance needed for isotope analysis. This paper describes the analysis of 13C using an automatic elemental gas chromatograph interfaced to an isotope ratio mass spectrometer, a system which was developed initially for the analysis of 15N. Details of the residual gas background, peak broadening due to high carrier gas pressures, mass spectral linearity and response to changing sample peak heights and variations of the measured isotope ratio with sample pressure are described. Sensitivity and performance data (reproducibility ± 0.62% at natural abundance) are also given. The potential of this system for other gas chromatographic applications, automatic data handling and the possible simultaneous analysis of 13C and 15N are also discussed.
Differentiation of Human Embryonic Stem Cells into Insulin‐Producing Clusters (2004)

Type I diabetes mellitus is caused by an autoimmune destruction of the insulin-producing beta cells. The major obstacle in using transplantation for curing the disease is the limited source of insulin-producing cells. The isolation of human embryonic stem (hES) cells introduced a new prospect for obtaining a sufficient number of beta cells for transplantation. We present here a method for forming immature islet-like clusters of insulin-producing cells derived from hES cells. The protocol consisted of several steps. Embryoid bodies were first cultured and plated in insulin-transferrin-selenium-fibronectin medium, followed by medium supplemented with N2, B27, and basic fibroblast growth factor (bFGF). Next, the glucose concentration in the medium was lowered, bFGF was withdrawn, and nicotinamide was added. Dissociating the cells and growing them in suspension resulted in the formation of clusters which exhibited higher insulin secretion and had longer durability than cells grown as monolayers. Reverse transcription-polymerase chain reaction detected an enhanced expression of pancreatic genes in the differentiated cells. Immunofluorescence and in situ hybridization analyses revealed a high percentage of insulin-expressing cells in the clusters. In addition to insulin, most cells also coexpressed glucagon or somatostatin, indicating a similarity to immature pancreatic cells. Further improvement of this insulin-producing cell protocol may lead to the formation of an unlimited source of cells suitable for transplantation.