gebhart/patrepeval huggingface dataset:
Detecting errors in Chinese spoken dialog system using ngram and dependency parsing (2008)

In this paper, a hybrid method of detecting ASR error in spoken turns is developed. The erroneous text is locally analyzed first by neighbouring co-occurrence relations using ngram model. Then the text is globally analyzed by long distance dependency relations using a dependency parser. Our experiments show that we can use information from a dependency parsing phase together with n-gram language model not only to detect erroneous ASR hypotheses that can cause understanding errors, but also reliably locate errors and sometimes correct them as the hypotheses are being processed.
CUG Repeats Present in Myotonin Kinase RNA Form Metastable “Slippery” Hairpins (1997)

We show that CUG repeats form "slippery" hairpins in their natural sequence context of the myotonin kinase gene transcript. This novel type of RNA structure is characterized by strong S1 and T1 nuclease and lead cleavages in the terminal loop and by mild lead cleavages in the hairpin stem. The latter effect indicates a relaxed metastable structure of the stem. (CUG)5 repeats do not form any detectable secondary structure, whereas hairpins of increasing stability are formed by (CUG)11, (CUG)21, and (CUG)49. The potential role of the RNA hairpin structure in the pathogenesis of myotonic dystrophy is discussed.
Frequency of multi-drug resistance and mutations in Mycobacterium tuberculosis isolates from Punjab state of India (2017)

Data regarding prevalence of multi-drug resistant tuberculosis (MDR-TB) and associated common mutations is scarce from Punjab region. The study was designed to determine rate of MDR-TB among presumptive MDR-TB from Punjab and mutation patterns using GenoType MTBDRplus assay. Total of 812 consecutive sputum samples were received from January 2012 to July 2013, from 14 districts of Punjab at the National Reference Laboratory at New Delhi for diagnosis of MDR-TB as hand holding activity. Presumptive MDR-TB patients were identified on basis of criterion B defined by the programme. Smear positive and negatives patients were found to be 636/798 (79.7%) and 162/ 798 (20.3%) respectively. Total of 606 GenoType MTBDRplus tests were conducted and mutations in rpoB, kat G and inhA genes analyzed. Total of 94/606 (15.5%), 43/606 (7.1%) and 40/606 (6.6%) were found to be RIF and INH resistant, mono-RIF resistant and 40/606 (6.6%) mono-INH resistant respectively. Commonest known mutation for RIF in rpoB gene and INH in kat G gene was S531L (80/ 137; 58.4%) and S315T1 (119/134; 88.8%) respectively. Mutations in inhA were found in 21/134 (15.7%) strains. Average turn-around time (TAT) for dispatch of result toPunjab was 4.6days. Prevalence of RIF resistance in Punjab was found to be 22.6%. Common mutations for RIF and INH were similar to that in other regions of country. GenoType MTBDRplus was found to be useful assay for rapid detection of MDR-TB, responsible for determining better management of MDR-TB patients under the programme.
Prevalence of Antibodies in Human Sera against JC Virus, an Isolate from a Case of Progressive Multifocal Leukoencephalopathy (1973)

Sera from 406 people of various ages throughout the state of Wisconsin were assayed for antibodies against IC virus, a new human papova-like virus isolated from a patient with progressive multifocal leukoencephalopathy. The hemagglutination-inhibition (HAl) test was used after it was determined that a linear relationship existed between the titers of HAI and neutralizing antibodies in human sera. About 69% (191/277) of the adults tested had significant levels of antibodies against IC virus in their serum. The highest rate of conversion to seropositivity occurred during the first 14 years of life. No sex difference in the incidence of antibodies against IC virus was found.
Integration of retroviral vectors induces minor changes in the transcriptional activity of T cells from ADA-SCID patients treated with gene therapy (2009)

Gene transfer into hematopoietic stem cells by gamma-retroviral vectors (RVs) is an effective treatment for inherited blood disorders, although potentially limited by the risk of insertional mutagenesis. We evaluated the genomic impact of RV integration in T lymphocytes from adenosine deaminase-deficient severe combined immunodeficiency (ADA-SCID) patients 10 to 30 months after infusion of autologous, genetically corrected CD34(+) cells. Expression profiling on ex vivo T-cell bulk population revealed no difference with respect to healthy controls. To assess the effect of vector integration on gene expression at the single-cell level, primary T-cell clones were isolated from 2 patients. T-cell clones harbored either 1 (89.8%) or 2 (10.2%) vector copies per cell and displayed partial to full correction of ADA expression, purine metabolism, and T-cell receptor-driven functions. Analysis of RV integration sites indicated a high diversity in T-cell origin, consistently with the polyclonal T-cell receptor-Vbeta repertoire. Quantitative transcript analysis of 120 genes within a 200-kb window around RV integration sites showed modest (2.8- to 5.2-fold) dysregulation of 5.8% genes in 18.6% of the T-cell clones compared with controls. Nonetheless, affected clones maintained a stable phenotype and normal in vitro functions. These results confirm that RV-mediated gene transfer for ADA-SCID is safe, and provide crucial information for the development of future gene therapy protocols. The trials described herein have been registered at http://www.clinicaltrials.gov as #NCT00598481 and #NCT00599781.
The Requirement for DNAM-1, NKG2D, and NKp46 in the Natural Killer Cell-Mediated Killing of Myeloma Cells (2007)

Recent evidence suggests a role for natural killer (NK) cells in the control of multiple myeloma. We show that expression of the NK cell receptor DNAM-1 (CD226) is reduced on CD56(dim) NK cells from myeloma patients with active disease compared with patients in remission and healthy controls. This suggested that this receptor might play a role in NK-myeloma interactions. The DNAM-1 ligands Nectin-2 (CD112) and the poliovirus receptor (PVR; CD155) were expressed by most patient myeloma samples analyzed. NK killing of patient-derived myelomas expressing PVR and/or Nectin-2 was DNAM-1 dependent, revealing a functional role for DNAM-1 in myeloma cell killing. In myeloma cell lines, cell surface expression of PVR was associated with low levels of NKG2D ligands, whereas cells expressing high levels of NKG2D ligands did not express PVR protein or mRNA. Furthermore, NK cell-mediated killing of myeloma cell lines was dependent on either DNAM-1 or NKG2D but not both molecules. In contrast, the natural cytotoxicity receptor NKp46 was required for the killing of all myeloma cell lines analyzed. Thus, DNAM-1 is important in the NK cell-mediated killing of myeloma cells expressing the cognate ligands. The importance of NKp46, NKG2D, and DNAM-1 in myeloma killing mirrors the differential expression of NK cell ligands by myeloma cells, reflecting immune selection during myeloma disease progression.
Autolytic Processing of Dimeric Plant Virus Satellite RNA (1986)

Associated with some plant viruses are small satellite RNA's that depend on the plant virus to provide protective coat protein and presumably at least some of the proteins necessary for satellite RNA replication. Multimeric forms of the satellite RNA of tobacco ringspot virus are probable in vivo precursors of the monomeric satellite RNA. Evidence is presented for the in vitro autolytic processing of dimeric and trimeric forms of this satellite RNA. The reaction generates biologically active monomeric satellite RNA, apparently is reversible to form dimeric RNA from monomeric RNA, and does not require an enzyme for its catalysis.
Optochemogenetics (OCG) Allows More Precise Control of Genetic Engineering in Mice with CreER regulators (2012)

New approaches that allow precise spatiotemporal control of gene expression in model organisms at the single cell level are necessary to better dissect the role of specific genes and cell populations in development, disease, and therapy. Here, we describe a new optochemogenetic switch (OCG switch) to control CreER/loxP-mediated recombination via photoactivatable ("caged") tamoxifen analogues in individual cells in cell culture, organoid culture, and in vivo in adult mice. This approach opens opportunities to more fully exploit existing CreER transgenic mouse strains to achieve more precise temporal- and location-specific regulation of genetic events and gene expression.
Innate Lymphoid Cells: Emerging Insights in Development, Lineage Relationships, and Function (2012)

Innate lymphoid cells (ILCs) are immune cells that lack a specific antigen receptor yet can produce an array of effector cytokines that in variety match that of T helper cell subsets. ILCs function in lymphoid organogenesis, tissue remodeling, antimicrobial immunity, and inflammation, particularly at barrier surfaces. Their ability to promptly respond to insults inflicted by stress-causing microbes strongly suggests that ILCs are critical in first-line immunological defenses. Here, we review current data on developmental requirements, lineage relationships, and effector functions of two families of ILCs: (a) Rorγt-expressing cells involved in lymphoid tissue formation, mucosal immunity, and inflammation and (b) type 2 ILCs that are important for helminth immunity. We also discuss the potential roles of ILCs in the pathology of immune-mediated inflammatory and infectious diseases including allergy.
Bulged-out nucleotides protect an antisense RNA from RNase III cleavage (1995)

Bulged-out nucleotides or internal loops are present in the stem-loop structures of several antisense RNAs. We have used the antisense/target RNA system (CopA/CopT) that controls the copy number of plasmid R1 to examine the possible biological function of bulged-out nucleotides. Two regions within the major stem-loop of the antisense RNA, CopA, carry bulged-out nucleotides. Base pairing in either one or both of these regions of the stem was restored by site-specific mutagenesis and in one case a new internal loop was introduced. The set of mutant and wild-type CopA variants was characterized structurally in vitro. The results reported here indicate a possible function of the bulges: their presence protects CopA RNA from being a substrate for the double-strand-specific enzyme RNase III. In vitro cleavage rates were drastically increased when either the lower or both bulges were absent. This is paralleled by a similar, but not identical, effect of the bulges on metabolic stability of the CopA RNAs in vivo. The degradation pathways of wild-type and mutant CopA in various strain backgrounds are discussed. In the accompanying paper, we address the significance of bulges in CopA for binding to the target RNA in vitro and for its inhibitory efficiency in vivo.
Updating the 97% identity threshold for 16S ribosomal RNA OTUs (2018)

Supplementary data are available at Bioinformatics online.
A randomized trial of plasma exchange in acute central nervous system inflammatory demyelinating disease (1999)

There are no established treatments for patients with acute, severe neurological deficits caused by multiple sclerosis or other inflammatory demyelinating diseases of the central nervous system who fail to recover after treatment with high-dose corticosteroids. We conducted a randomized, sham-controlled, double-masked study of plasma exchange without concomitant immunosuppressive treatment in patients with recently acquired, severe neurological deficits resulting from attacks of inflammatory demyelinating disease, who failed to recover after treatment with intravenous corticosteroids. Patients who did not achieve moderate or greater improvement after the first treatment phase crossed over to the opposite treatment. Moderate or greater improvement in neurological disability occurred during 8 of 19 (42.1%) courses of active treatment compared with 1 of 17 (5.9%) courses of sham treatment. The primary analysis was positive. Improvement occurred early in the course of treatment, and was sustained on follow-up. However, 4 of the patients who responded to the active treatment experienced new attacks of demyelinating disease during 6 months of follow-up. Moderate or greater improvement occurred during follow-up in only 2 of 13 patients who failed to improve during the treatment phase. Plasma exchange leads to functionally important neurological recovery in an important proportion of severely disabled patients with acute attacks of idiopathic inflammatory demyelinating disease.
Microcontact Printing of Palladium Colloids:  Micron-Scale Patterning by Electroless Deposition of Copper (1996)

This paper describes a new method for forming micron- and submicron-scale patterns of copper on surfaces. This method uses microcontact printing (μCP) to deposit colloids that serve as catalysts for the selective electroless deposition of copper. A patterned elastomeric stamp fabricated from poly(dimethylsiloxane) was used to deliver the catalystpalladium colloids stabilized with tetraalkylammonium bromidesto the substrate surface. The electroless deposition of the copper on the sample occurred only where palladium colloid was transferred to the substrate. Electroless deposition catalyzed by the colloids resulted in the formation of metal structures with features having submicron dimensions, with an edge resolution in the range of 100 nm. This technique of activating substrates for electroless metalization was successfully used to pattern glass, (Si/SiO2), and polymers; both flat and curved substrates were used. Microcontact printing of colloids was also used to fabricate metal structures whose thicknesses were varied in different regions of the sample (multilevel metal structures). Free-standing metal structures were produced by dissolving the substrate after the metal film had reached the desired thickness.
Validation of non-invasive central blood pressure devices: ARTERY Society task force consensus statement on protocol standardization (2016)

&lt;p&gt;The original Riva-Rocci method to measure blood pressure (BP) using a cuff at the upper arm assumed the pressure obtained by this technique was a good proxy for central aortic BP. The clinical (prognostic) importance of brachial cuff BP is undeniable for both the assessment of cardiovascular risk associated with elevated BP and the benefits of treatment-induced BP reduction. However, it is also generally appreciated that peripheral artery systolic BP (SBP; brachial or radial artery) may be an inaccurate substitute for central SBP. This has been reported in human studies using intra-arterial catheterization of peripheral and central arteries. There may also be a discrepancy between peripheral and central BP responses to vasoactive drugs. These findings are corroborated in larger studies using non-invasive central aortic BP methods, and, while yet to be fully adopted in clinical practice, an independent prognostic value of central BP has been demonstrated. Altogether, there is a growing interest among clinicians towards improving risk estimates by using devices that provide more accurate measures of central aortic BP than those provided by current brachial cuff BP methods.&lt;/p&gt;&lt;p&gt;Many non-invasive devices have been developed that purport to estimate central BP from different peripheral artery sites (e.g. radial, brachial, carotid arteries) using different principles of recording the pressure or surrogate signals (e.g. applanation tonometry, oscillometry, ultrasound, or magnetic resonance imaging) and different calibration methods to derive central BP. Since upper arm cuff-based devices to estimate central BP are more clinically appealing, in recent years several companies have developed such devices using a variety of techniques (e.g. oscillometric sub-diastolic or supra-systolic waveform analysis with generalized transfer functions), which employ a variety of signal processing steps to estimate central BP from peripheral signals. Yet, with no standardized guidelines, the accuracy testing of these new devices (as well as the preceding devices) has not been undertaken in a uniform fashion with comparable protocols, emphasizing the need for guidance in this field. An international task force was convened to address this situation.&lt;/p&gt;
Constructing star polymersvia modular ligation strategies (2011)

Over recent years, modular ligation reactions—some of which adhere to the click criteria—have enabled the synthesis of a variety of star polymers <italic>via</italic> efficient polymer–polymer conjugations. The copper catalyzed azide–alkyne cycloaddition (CuAAC), Diels–Alder (DA), and Hetero Diels–Alder (HDA) reactions are reviewed here in detail for the facile generation of various macromolecular star topologies.
Computer mail meeting notes (1982)

This RFC consists of notes from a meeting that was held at USC
Information Sciences Institute on 11 January 1982, to discuss
addressing issues in computer mail. The major conclusion reached at
the meeting is to extend the username@hostname mailbox format to
username@host.domain, where the domain itself can be further
strutured.
Sex Hormones Determine Immune Response (2018)

OPINION article Front. Immunol., 27 August 2018Sec. Cytokines and Soluble Mediators in Immunity Volume 9 - 2018 | https://doi.org/10.3389/fimmu.2018.01931
Memory for spatial location in children, adults, and mentally retarded persons. (1989)

Two experiments extended earlier research showing age- and intelligence-invariance in memory for spatial location. Second and sixth graders, college students, and mildly retarded persons relocated pictures after looking through a 100-picture book. There were no differences due to age, IQ, or instruction (intentional or incidental) in location memory; there were differences in picture recall. In a second experiment persons with Down syndrome, as a group, were less accurate in location memory than were college students, but many individuals performed as accurately. A 3-month follow-up on the subjects with Down syndrome revealed greater consistency in location memory than in recall. Overall, the results show that young children and mildly mentally retarded persons process spatial location information as well as do college students. Some, but not all, of the more severely mentally retarded persons had deficits in processing memory for location. All persons with mental retardation had deficits in effortful processing as reflected by free recall.
Carbon nanotubes as non-contact optical strain sensors in smart skins (2015)

Progress is reported in the development of a novel non-contact strain measurement technology in which the sensors are single-walled carbon nanotubes. This approach exploits the characteristic short-wave infrared fluorescence signatures of semiconducting single-walled carbon nanotubes and the systematic shifts of their fluorescence wavelengths when the nanotubes are axially strained. A strain-sensing smart skin is prepared by coating the surface to be monitored with a thin film of a composite containing well-dispersed single-walled carbon nanotubes embedded in a urethane varnish host. Strain in the surface transfers through the host polymer to the embedded nanotubes. The nanotube strains are then quantitatively monitored by exciting the region of interest with a visible laser beam and capturing and analyzing the resulting single-walled carbon nanotube fluorescence spectrum. High-quality spectra are shown for strain-sensing smart skin films in which the nanotubes were pre-processed by selective extraction with the organic polymer poly(9,9-dioctylfluorenyl-2,7-diyl) and purification by centrifugation. The design of a compact, field-portable optical system for exciting, collecting, and interpreting strain-sensing smart skin spectral data is also described. This system is used to validate the linear dependence of peak shifts with strain in test specimens subjected to multiple tension cycles inducing strains from 0 to 5000 µε. Adequate linearity is found up to 1500 µε; however, minor hysteresis is observed above this level. The gage length for these measurements can be as small as several micrometers, and the strain resolution is currently between 10 and 100 µε (depending on strain magnitude). Cyclic reversible strain measurements are demonstrated, with minor hysteresis being attributed to imperfect adhesion between nanotube sidewalls and the surrounding polymer host.
Identification of the sites of action for regulatory genes controlling the amdS gene of Aspergillus nidulans. (1988)

The amdS gene of Aspergillus nidulans, which encodes an acetamidase enzyme, is positively regulated by the trans-acting genes amdR, facB, amdA, and areA. Sequence changes in several cis-acting mutations in the 5' region of the gene which specifically affect amdS regulation were determined. The amdI9 mutation, which results in increased facB-dependent acetate induction, is due to a single-base change at base pair -210 relative to the start point of translation. The amdI93 mutation, which abolishes amdR-dependent omega-amino acid induction, is a deletion of base pairs -181 to -151. The amdI66 mutation, which causes increased gene activation in strains carrying amdA regulatory gene mutations, is a duplication of base pairs -107 to -90. Transformation of A. nidulans can generate transformants containing multiple integrated copies of plasmid sequences. When these plasmids carry a potential binding site for a regulatory gene product, growth on substrates whose catabolism requires genes activated by that regulatory gene can be reduced, apparently because of titration of the regulatory gene product. Introduction of 5' amdS sequences via cotransformation into strains of various genotypes was used to localize sequences apparently involved in binding of the products of the amdR, amdA, and facB genes. The position of these sequences is in agreement with the positions of the specific cis-acting mutations. Consistent with these results, a transformant of A. nidulans derived from a plasmid deleted for sequences upstream from -111 was found to have lost amdR- and facB-mediated control but was still regulated by the amdA gene. In addition, amdS expression in this transformant was still dependent on the areA gene.
Medical treatment of advanced non-small cell lung cancer: progress in 2014 (2015)

Non-small cell lung cancer is the most common pathological type of lung cancer. Along with the rising incidence in recent years, lung cancer has been the leading cause of death due to malignancies both in our country and worldwide. Due to simplistic therapeutic approach for lung cancer decades ago, those patients suffering from advanced lung cancer had short lifetime, and it was difficult to ensure their life quality. In recent years, many molecular targeted drugs, such as Gefitinib, Erlotinib and Crizotinib etc., have been successively applied in clinical use, and they bring about a substantial prolongation of survival life and improvement in life quality of those patients with advanced lung cancer. In 2014, there was a number of important reports concerning the diagnosis and treatment of non-small cell lung cancer in the annual meetings of either American Society of Clinical Oncology or European Society for Medical Oncology. On the basis of the relevant reports delivered in the conferences, it is our attempt to summarize the recent advances in regard to chemotherapy, molecular targeted therapy, measures to treat TKI therapy resistant cases, and immune therapy, followed by a comment regarding recent advances in the treatment of non-small cell lung cancer in 2014.
		
		DOI: 10.11855/j.issn.0577-7402.2015.01.03