gebhart/patrepeval huggingface dataset:
Centralized Molecular Testing for Oncogenic Gene Mutations Complements the Local Cytopathologic Diagnosis of Thyroid Nodules (2014)

Centralized and standardized molecular testing for genetic alterations associated with a high risk of malignancy efficiently complements the local cytopathologic diagnosis of thyroid nodule aspirates in the clinical setting. Actionable molecular cytology can improve the personalized surgical and medical management of patients with thyroid cancers, facilitating one-stage total thyroidectomy and reducing the number of unnecessary diagnostic surgeries.
Transonics: a speech to speech system for English-Persian interactions (2003)

In this paper, we describe the first phase of development of our speech-to-speech system between English and Modem Persian under the DARPA Babylon program. We give an overview of the various system components: the front end ASR, the machine translation system and the speech generation system. Challenges such as the sparseness of available spoken language data and solutions that have been employed to maximize the obtained benefits from using these limited resources are examined. Efforts in the creation of the user interface and the underlying dialog management system for mediated communication are described.
High-Throughput Comparative Proteome Analysis Using a Quantitative Cysteinyl-peptide Enrichment Technology (2004)

A new quantitative cysteinyl-peptide enrichment technology (QCET) was developed to achieve higher efficiency, greater dynamic range, and higher throughput in quantitative proteomics that use stable-isotope labeling techniques combined with high-resolution liquid chromatography (LC)-mass spectrometry (MS). This approach involves (18)O labeling of tryptic peptides, high-efficiency enrichment of cysteine-containing peptides, and confident protein identification and quantification using the accurate mass and time tag strategy. Proteome profiling of naïve and in vitro-differentiated human mammary epithelial cells using QCET resulted in the identification and quantification of 603 proteins in a single LC-Fourier transform ion cyclotron resonance MS analysis. Advantages of this technology include the following: (1) a simple, highly efficient method for enriching cysteinyl-peptides; (2) a high-throughput strategy suitable for extensive proteome analysis; and (3) improved labeling efficiency for better quantitative measurements. This technology enhances both the functional analysis of biological systems and the detection of potential clinical biomarkers.
3D Motion of DNA-Au Nanoconjugates in Graphene Liquid Cell Electron Microscopy (2013)

Liquid-phase transmission electron microscopy (TEM) can probe and visualize dynamic events with structural or functional details at the nanoscale in a liquid medium. Earlier efforts have focused on the growth and transformation kinetics of hard material systems, relying on their stability under electron beam. Our recently developed graphene liquid cell technique pushed the spatial resolution of such imaging to the atomic scale but still focused on growth trajectories of metallic nanocrystals. Here, we adopt this technique to imaging three-dimensional (3D) dynamics of soft materials instead, double strand (dsDNA) connecting Au nanocrystals as one example, at nanometer resolution. We demonstrate first that a graphene liquid cell can seal an aqueous sample solution of a lower vapor pressure than previously investigated well against the high vacuum in TEM. Then, from quantitative analysis of real time nanocrystal trajectories, we show that the status and configuration of dsDNA dictate the motions of linked nanocrystals throughout the imaging time of minutes. This sustained connecting ability of dsDNA enables this unprecedented continuous imaging of its dynamics via TEM. Furthermore, the inert graphene surface minimizes sample-substrate interaction and allows the whole nanostructure to rotate freely in the liquid environment; we thus develop and implement the reconstruction of 3D configuration and motions of the nanostructure from the series of 2D projected TEM images captured while it rotates. In addition to further proving the nanoconjugate structural stability, this reconstruction demonstrates 3D dynamic imaging by TEM beyond its conventional use in seeing a flattened and dry sample. Altogether, we foresee the new and exciting use of graphene liquid cell TEM in imaging 3D biomolecular transformations or interaction dynamics at nanometer resolution.
Biochemical and Biophysical Aspects of Water Deficits and the Predisposition to Disease (1995)

Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for ...Read More
The kinetics of azaserine and phosphinothricin inhibition of glutamate synthase cycle enzymes from barley leaves (1994)

The interaction of chemical inhibitors with the enzymes of the glutamate synthase cycle extracted from barley (Hordeum vulgare) leaves has been examined. Azaserine, a potent inhibitor of glutamine amide transfer reactions, behaves initially as a competitive (with respect to glutamine) inhibitor of ferredoxin glutamate synthase (EC 1.4.7.1). With respect to 2-oxoglutarate, the other substrate, it is an uncompetitive inhibitor. It rapidly becomes tightly bound to the enzyme, and cannot be removed by dilution or gel filtration. From the initial inhibition kinetics an apparent Ki was determined of between 5-12.5 μM. The rate limiting step appears to be the initial formation of the enzyme-inhibitor complex
From Combs to Comb-g-Comb Centipedes (2005)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTFrom Combs to Comb-g-Comb CentipedesMichel Schappacher and Alain DeffieuxView Author Information Laboratoire de Chimie des Polymères Organiques, UMR 5629 CNRS-ENSCPB-Université Bordeaux 1, 16 Avenue Pey Berland, 33607 Pessac Cedex, France Cite this: Macromolecules 2005, 38, 17, 7209–7213Publication Date (Web):July 23, 2005Publication History Received26 May 2005Revised4 July 2005Published online23 July 2005Published inissue 1 August 2005https://pubs.acs.org/doi/10.1021/ma051076ohttps://doi.org/10.1021/ma051076orapid-communicationACS PublicationsCopyright © 2005 American Chemical SocietyRequest reuse permissionsArticle Views475Altmetric-Citations48LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Chemical structure,Copolymers,Ethers,Macromolecules,Polymers Get e-Alerts
Defining the Importance of Mitochondrial Gene Defects in Maternally Inherited Diabetes by Sequencing the Entire Mitochondrial Genome (2002)

For any mitochondrial DNA (mtDNA) mutation, the ratio of mutant to wild-type mtDNA (% heteroplasmy) varies across tissues, with low levels in leukocytes and high levels in postmitotic tissues (e.g., skeletal muscle). Direct sequencing is the gold-standard method used to detect novel mutations, but can only reliably detect % heteroplasmy >25%, which is rare in leukocytes. Therefore, we investigated the role of mtDNA defects in maternally inherited diabetes by first screening for the A3243G tRNA(Leu(UUR)) mutation by restriction assay, followed by sequencing of the entire mitochondrial genome using skeletal muscle derived mtDNA. A total of 28 patients had maternally inherited diabetes either alone (group 1, n = 17) or with one or more additional features of mitochondrial disease, including bilateral sensori-neural deafness and neuromuscular disease (group 2, n = 11). Three patients (all from group 2) carried the A3243G mutation. Skeletal muscle mtDNA from eight group 1 patients and six more group 2 patients was sequenced. No pathogenic mutations were found in the group 1 patients, while two patients from group 2 had mutations at positions 12258 and 14709 in the tRNA serine and glutamic acid genes, respectively. We conclude, therefore, that screening for mtDNA mutations should be considered in patients with maternally inherited diabetes, but only when additional features of mitochondrial disease are present.
Effect of lattice anharmonicity on high-amplitude phonon dynamics in photoexcited bismuth (2005)

Separate theoretical and experimental investigations of the effect of lattice anharmonicity on the ${A}_{1g}$ phonon dynamics in photoexcited bismuth are presented. First-principles density functional calculations show that the anharmonic contribution to the phonon period is negligible for an excitation of 1.25% or less of the valence electrons, corresponding to electronic frequency softening from $2.9\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}2.3\phantom{\rule{0.3em}{0ex}}\mathrm{THz}$. Experiments using optical double-pump-probe excitation of coherent phonon motion clearly separate the role of lattice anharmonicity from electron-hole plasma and other dynamics, confirming that the effect of anharmonicity on the phonon period is much smaller than the observed softening.
Application of Adoptive T-Cell Therapy Using Tumor Antigen-Specific T-Cell Receptor Gene Transfer for the Treatment of Human Leukemia (2010)

The last decade has seen great strides in the field of cancer immunotherapy, especially the treatment of melanoma. Beginning with the identification of cancer antigens, followed by the clinical application of anti-cancer peptide vaccination, it has now been proven that adoptive T-cell therapy (ACT) using cancer antigen-specific T cells is the most effective option. Despite the apparent clinical efficacy of ACT, the timely preparation of a sufficient number of cancer antigen-specific T cells for each patient has been recognized as its biggest limitation. Currently, therefore, attention is being focused on ACT with engineered T cells produced using cancer antigen-specific T-cell receptor (TCR) gene transfer. With regard to human leukemia, ACT using engineered T cells bearing the leukemia antigen-specific TCR gene still remains in its infancy. However, several reports have provided preclinical data on TCR gene transfer using Wilms' tumor gene product 1 (WT1), and also preclinical and clinical data on TCR gene transfer involving minor histocompatibility antigen, both of which have been suggested to provide additional clinical benefit. In this review, we examine the current status of anti-leukemia ACT with engineered T cells carrying the leukemia antigen-specific TCR gene, and discuss the existing barriers to progress in this area.
An Empirical Understanding of the Glycosylation Reaction (2018)

Reliable glycosylation reactions that allow for the stereo- and regioselective installation of glycosidic linkages are paramount to the chemical synthesis of glycan chains. The stereoselectivity of glycosylations is exceedingly difficult to control due to the reaction's high degree of sensitivity and its shifting, simultaneous mechanistic pathways that are controlled by variables of unknown degree of influence, dominance, or interdependency. An automated platform was devised to quickly, reproducibly, and systematically screen glycosylations and thereby address this fundamental problem. Thirteen variables were investigated in as isolated a manner as possible, to identify and quantify inherent preferences of electrophilic glycosylating agents (glycosyl donors) and nucleophiles (glycosyl acceptors). Ways to enhance, suppress, or even override these preferences using judicious environmental conditions were discovered. Glycosylations involving two specific partners can be tuned to produce either 11:1 selectivity of one stereoisomer or 9:1 of the other by merely changing the reaction conditions.
Storage of saline‐adenine‐glucose‐mannitol‐suspended red cells in a new plastic container: polyvinylchloride plasticized with butyryl‐n‐ trihexyl‐citrate (1991)

Blood collection and component preparation have been performed in integrally connected multiple plastic containers made with a new plastic. This polyvinylchloride (PVC) container plasticized with butyryl-n-trihexyl-citrate (BTHC) is a new material for blood storage; it contains no di(2-ethylhexyl)phthalate (DEHP). After removal of plasma and buffy coat, the red cells were suspended in saline-adenine-glucose-mannitol (SAGM) medium. After 42-day refrigerator storage, the total adenine nucleotide concentration remained the same as the initial concentration in the red cells, whereas ATP levels had decreased to 61 percent of the initial value. The 2,3 DPG concentration was 62 percent of normal on Day 7 and 21 percent on Day 14. Glucose consumption, lactate production, potassium leakage from red cells, and pH levels were similar to those found after storage in DEHP-plasticized containers under the same conditions. After 42 days, hemolysis levels were 0.56 +/- 0.21 percent and 0.42 +/- 0.17 percent in two series of units mixed weekly and 0.70 +/- 0.27 percent in units stored unmixed. Although even higher levels of hemolysis were observed in the units stored unmixed and used for 24-hour posttransfusion survival, the autologous red cell recovery results were excellent (83.2 +/- 5.1%, n = 8). BTHC-plasticized PVC is found to be a suitable material for 42-day storage of red cells in SAGM solution.
Methyl jasmonate alters polyamine metabolism and induces systemic protection against powdery mildew infection in barley seedlings (2002)

Treatment of the first leaves of barley (Hordeum vulgare L. cv. Golden Promise) seedlings with methyl jasmonate (MJ) led to small, but significant increases in levels of free putrescine and spermine 1 d later and to significant increases in levels of free putrescine, spermidine and spermine by 4 d following treatment. MJ-treated first leaves also exhibited significant increases in the amounts of soluble conjugates of putrescine and spermidine 1, 2 and 4 d after treatment. In second leaves of plants where the first leaves had been treated with MJ, no significant changes in levels of free polyamines were observed, but significant increases in levels of soluble conjugates of putrescine and spermidine were detected. These changes were accompanied by increased activities of soluble ornithine decarboxylase (ODC), soluble and particulate arginine decarboxylase (ADC), and S-adenosylmethionine decarboxylase (AdoMetDC), in first and second leaves following treatment of the first leaves with MJ. Activities of soluble and particulate diamine oxidase (DAO) were also higher in first and second leaves following treatment of the first leaves with MJ. Treatment of the first leaves with MJ led to a significant reduction in powdery mildew (Blumeria graminis f. sp. hordei) infection on the second leaves and also resulted in significant increases in activities of the plant defence-related enzymes, phenylalanine ammonia lyase (PAL) and peroxidase.
Arterial smooth muscle. A multifunctional mesenchymal cell. (1988)

In 1968, Professor Robert Wissler published a landmark review on the role of smooth muscle cells in atherogenesis. He suggested that in future studies more attention should be given to the cytologic and metabolic characteristics of these multifunctional mesenchymal cells. This article summarizes some of our studies inspired by these words and indicates a few of the many questions that still need to be addressed. We have shown that smooth muscle cells of different phenotypes from that expressed in normal arterial media exist in regions of diffuse intimal thickenings adjacent to atheroma and also in vessels following injury. Cells of equivalent phenotype can exist in cell culture, and we have shown that they have all the characteristics of smooth muscle in atherogenesis, ie, they proliferate in response to mitogens, readily synthesize increased amounts of extracellular matrix, and accumulate large amounts of lipid. In contrast, smooth muscle cells of the phenotype that normally exists in the unaffected artery do not express these characteristics and their major function is maintenance of vessel tone. Thus a deeper knowledge of the factors that control smooth muscle phenotype is essential to an understanding of the mechanisms underlying the pathogenesis of atherosclerosis.
Risperidone alone versus risperidone plus valproate in the treatment of patients with schizophrenia and hostility (2007)

The objective of the study was to compare the antiaggressive efficacy of risperidone monotherapy versus risperidone plus valproate in patients with schizophrenia. This was an 8-week open-label randomized parallel group clinical trial in hospitalized adults diagnosed with schizophrenia and with hostile behavior. Patients were randomly assigned to receive risperidone alone (n=16) or risperidone plus valproate (n=17). To minimize bias, raters were blinded to the assigned treatment arm. Outcome measures included the Positive and Negative Syndrome Scale (PANSS), Buss-Durkee Hostility Inventory (BDHI), Barratt Impulsiveness Scale (BIS), Nurses Observation Scale for Inpatient Evaluation (NOSIE), and the Overt Aggression Scale (OAS). Although significantly fewer patients randomized to monotherapy completed the study (chi(2)=8.62, d.f.=1, P=0.003), no significant differences between monotherapy or combination treatment were observed in change of the BDHI, BIS, NOSIE, PANSS total scores, OAS measures of aggressive behavior or the hostility item of the PANSS. In conclusion, although patients receiving combination treatment were more likely to complete the study, we were unable to detect a meaningful advantage for combination therapy as measured by rating scales.
Surface Generation-Recombination Processes of Gate and STI Oxide Interfaces Responsible For Junction Leakage on SOI (2009)

Carrier generation-recombination at the top, corner and trench surfaces of silicon-on-insulator (SOI) diode bodies have been studied using the standard gated-diode methodology and new test structures with independent trench-side gates. The influences of top or trench gate voltage, temperature and junction bias have been elucidated. Four distinct diode current peaks are observed during top-gate voltage sweeps. Qualitative analysis has assigned these peaks to surface recombination at the different surface areas of SOI bodies. The coexistence of multiple recombination current peaks might be related to silicon faceting at top trench corners. During top-gate voltage sweeps, STI-gate voltage causes a larger recombination current peak shift for interface traps at the SOI trench corners and walls than those at top SOI interface. A new model involving an oxide trap within the STI oxide has been proposed to interpret the random telegraphic signal (RTS) noise of a gated-diode at high carrier injection and temperature.
Modification of Arg‐13 of μ‐conotoxin GIIIA with piperidinyl‐Arg analogs and their relation to the inhibition of sodium channels (2001)

mu-Conotoxin GIIIA, a peptide toxin isolated from the marine snail Conus geographus, preferentially blocks skeletal muscle sodium channels in vertebrates. In this study, analogs of mu-conotoxin GIIIA in which essential Arg-13 was replaced with arginine analogs consisting of a piperidyl framework to regulate length and direction of the side chain were synthesized. Synthesized analogs exhibited similar CD and NMR spectra to that of GIIIA, suggesting a three-dimensional structure identical to that of the native toxin. The biological activities of piperidyl analogs were decreased or lost despite the small change in the side chain of Arg-13. The investigated structure-activity relationships in inhibiting electrically stimulated muscle contraction suggest that the guanidinium group at amino acid position 13 interacts best when spaced with three to four carbons and placed in a vertical direction from the peptide loop. Thus, the position of the guanidinium group at Arg-13 of GIIIA must be located in a certain range for its strong interaction with the channel protein.
Overexpression of HER-2/neu is associated with poor survival in advanced epithelial ovarian cancer. (1990)

Previous studies have suggested that overexpression of HER-2/neu oncogene occurs in 15-40% of breast cancers and that overexpression is associated with poor prognosis. In the present report, we have used an immunohistochemical technique involving a monoclonal antibody specifically reactive with the external domain of HER-2/neu to study expression of HER-2/neu in frozen sections of normal ovary and advanced epithelial ovarian cancer. The intensity of staining for HER-2neu was always moderate or less (0-2+) in normal ovarian epithelium. Among 73 ovarian cancers, 50 (68%) had staining similar to that for normal ovarian epithelium (0-2+) while 23 (32%) stained heavily (3+). Survival of the 23 patients with high HER-2/neu expression (median, 15.7 months) was significantly worse (P = 0.001) than that of the 50 patients (median, 32.8 months) with normal HER-2/neu expression. In addition, patients whose tumors had high HER-2/neu expression were significantly less likely to have a complete response to primary therapy (P less than 0.05) or have a negative second-look laparotomy when serum CA 125 levels were normal preoperatively (P less than 0.05). These findings suggest that HER-2/neu deserves further evaluation as a prognostic marker in epithelial ovarian cancer.
A technique for fault diagnosis of defects in scan chains (2002)

In this paper, we present a scan chain fault diagnosis procedure. The diagnosis for a single scan chain fault is performed in three steps. The first step uses special chain test patterns to determine both the faulty chain and the fault type in the faulty chain. The second step uses a novel procedure to generate special test patterns to identify the suspect scan cell within a range of scan cells. Unlike previously proposed methods that restrict the location of the faulty scan cell only from the scan chain output side, our method restricts the location of the faulty scan cell from both the scan chain output side and the scan chain input side. Hence the number of suspect scan cells is reduced significantly in this step. The final step further improves the diagnostic resolution by ranking the suspect scan cells inside this range. The proposed technique handles both stuck-at and timing failures (transition faults and hold time faults). The extension of the procedure to diagnose multiple faults is discussed. The experimental results show the effectiveness of the proposed method.