gebhart/patrepeval huggingface dataset:
Generalizing prosodic prediction of speech recognition errors (2000)

Since users of spoken dialogue systems have difficulty correcting system misconceptions, it is important for automatic speech recognition (ASR) systems to know when their best hypothesis is incorrect. We compare results of previous experiments which showed that prosody improves the detection of ASR errors to experiments with a new system and new domain, the W99 conference registration system. Our new results again show that prosodic features can improve prediction of ASR misrecognitions over the use of other standard techniques for ASR rejection.
Antibody production by molecular farming in plants. (2000)

"Molecular farming" is the production of pharmaceutical proteins in transgenic plants and has great potential for the production of therapeutic anti-cancer antibodies and recombinant therapeutic proteins. Plants make fully functional recombinant human or animal antibodies. Cultivating transgenic plants on an agricultural scale will produce almost unlimited supplies of recombinant proteins for uses in medicine. Combinatorial library technology is a key tool for the generation and optimisation of therapeutic antibodies ahead of their expression in plants. Optimised antibody expression can be rapidly verified using transient expression assays in plants before creation of transgenic suspension cells or plant lines. Subcellular targeting signals that increase expression levels and optimise protein stability can be identified and exploited using transient expression to create high expresser plant lines. When high expresser lines have been selected, the final step is the development of efficient purification methods to retrieve functional antibody. Antibody production on an industrial scale is then possible using plant suspension cell culture in fermenters, or by the propagation of stably transformed plant lines in the field. Recombinant proteins can be produced either in whole plants or in seeds and tubers, which can be used for the long-term storage of both the protein and its production system. The review will discuss these developments and how we are moving toward the molecular farming of therapeutic antibodies becoming an economic and clinical reality.
Efficient Conversion of CO2 to Methanol Catalyzed by Three Dehydrogenases Co-encapsulated in an Alginate−Silica (ALG−SiO2) Hybrid Gel (2006)

In this study, the conversion of carbon dioxide to methanol was realized through a novel biochemical approach that was catalyzed by three dehydrogenases: formate dehydrogenase (FateDH), formaldehyde dehydrogenase (FaldDH), and alcohol dehydrogenase (ADH). The dehydrogenases were encapsulated in an alginate−silica (ALG−SiO2) hybrid gel, which was prepared through in situ growth of the silica precursor within an alginate solution, which was followed by Ca2+ cross-linking. Methanol yields that were catalyzed by free dehydrogenases, and by dehydrogenases immobilized in pure alginate (ALG) gel and in ALG−SiO2 hybrid gel, were 98.8%, 71.3%, and 98.1%, respectively. Furthermore, methanol yield that was catalyzed by dehydrogenases in an ALG−SiO2 composite could be retained as high as 76.2% after 60 days storage and as high as 78.5% after 10 times recycling. The significantly improved catalytic properties of the dehydrogenases in the ALG−SiO2 composite were attributed to the creation of the appropriate immobilizing microenvironment: high hydrophilicity, moderate rigidity and flexibility, ideal diffusion characteristics, and optimized cage confinement effect.
Inducible Costimulator Protein Controls the Protective T Cell Response Against Listeria monocytogenes (2002)

The inducible costimulator protein (ICOS) was recently identified as a costimulatory molecule for T cells. Here we analyze the role of ICOS for the acquired immune response of mice against the intracellular bacterium Listeria monocytogenes. During oral L. monocytogenes infection, low levels of ICOS expression were detected by extracellular and intracellular Ab staining of Listeria-specific CD4(+) and CD8(+) T cells. Blocking of ICOS signaling with a soluble ICOS-Ig fusion protein markedly impaired the Listeria-specific T cell responses. Compared with control mice, the ICOS-Ig treated mice generated significantly reduced numbers of Listeria-specific CD8(+) T cells in spleen and liver, as determined by tetramer and intracellular cytokine staining. In contrast, the specific CD8(+) T cell response in the intestinal mucosa did not appear to be impaired by the ICOS-Ig treatment. Analysis of the CD4(+) T cell response revealed that ICOS-Ig treatment also affected the specific CD4(+) T cell response. When restimulated with listerial Ag in vitro, reduced numbers of CD4(+) T cells from infected and ICOS-Ig-treated mice responded with IFN-gamma production. The impaired acquired immune response in ICOS-Ig treated mice was accompanied by their increased susceptibility to L. monocytogenes infection. ICOS-Ig treatment drastically enhanced bacterial titers, and a large fraction of mice succumbed to the otherwise sublethal dose of infection. Thus, ICOS costimulation is crucial for protective immunity against the intracellular bacterium L. monocytogenes.
Vaccination of Small Cell Lung Cancer Patients with Polysialic Acid orN-Propionylated Polysialic Acid Conjugated to Keyhole Limpet Hemocyanin (2004)

Vaccination with NP-polySA-KLH, but not polySA-KLH, resulted in a consistent high titer antibody response. We are now conducting a de-escalation dosing study with NP-polySA-KLH to better assess the immunogenicity, toxicities, and optimal dose of this vaccine. We plan to incorporate this vaccine as a component of a polyvalent vaccine with GM2, fucosylated GM1, and Globo H to target SCLC.
The synthesis of amines by the homogeneous hydrogenation of secondary and primary amides (2007)

Amides can be hydrogenated to amines using a catalyst prepared in situ from [Ru(acac)(3)] and 1,1,1-tris(diphenylphosphinomethyl)ethane; water is required to stabilize the catalyst and primary amines can only be formed (selectivity up to 85%) if ammonia is also present.
Separation of Organic Pollutants by Reverse Osmosis and Nanofiltration Membranes:  Mathematical Models and Experimental Verification (1999)

Predictive reverse osmosis (RO) models have been well-developed for many systems. However, the applications to dilute organic−water systems require the modification of transport models and the understanding of solute−polymer interactions. Studies with various substituted, nonionized phenolic compounds showed that these could cause substantial membrane water flux drop, even in dilute solutions with negligible osmotic pressure. Further, the organics could significantly adsorb on the cross-linked aromatic polyamide active layer. In some cases, even concentrations as low as 0.2 mM, 2,4-dinitrophenol (solution in particle-free, double-distilled water) can cause as much as a 70% flux drop with an aromatic polyamide membrane. Two models are presented in this paper: a modified steady-state solution diffusion model and an unsteady-state diffusion adsorption model which are able to predict flux and permeate concentrations from a single RO experiment. Further, the development of these models allows for the understanding of the mechanisms of organic−membrane interactions. For instance, it has been proposed that increased adsorption inherently leads to an increase in flux drop. However, we have found, on one hand, that due to specific interactions with membrane water transport groups, chloro- and nitro-substituted phenols cause significant flux drops. On the other hand, benzene had a high physical adsorption but caused negligible flux drop. The results were further extended to nanofiltration experiments with an aromatic pollutant containing two types of charge groups. The adsorption and separation results are explained according to an ionization model.
Luminescent Chemodosimeters for Bioimaging (2012)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTLuminescent Chemodosimeters for BioimagingYuming Yang†, Qiang Zhao‡, Wei Feng†, and Fuyou Li*†View Author Information† Department of Chemistry and State Key Laboratory of Molecular Engineering of Polymers and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China‡ Key Laboratory for Organic Electronics and Information Displays (KLOEID) and Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210046, P. R. China.*Fax: 86-21-55664621. Tel.: 86-21-55664185. E-mail: [email protected]Cite this: Chem. Rev. 2013, 113, 1, 192–270Publication Date (Web):June 18, 2012Publication History Received27 October 2011Published online18 June 2012Published inissue 9 January 2013https://pubs.acs.org/doi/10.1021/cr2004103https://doi.org/10.1021/cr2004103review-articleACS PublicationsCopyright © 2012 American Chemical SocietyRequest reuse permissionsArticle Views31453Altmetric-Citations2087LEARN 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:Fluorescence,Fluorescence detection,Ions,Luminescence,Mercury Get e-Alerts
Context-aware Language Modeling for Conversational Speech Translation. (2011)

Context plays a critical role in the understanding of language, especially conversational speech. However, few approaches exist to utilize the external contextual knowledge which is readily available to practical speech translation systems deployed in the field. In this work, we propose a novel framework to integrate context in the language models used for conversational speech translation. The proposed approach takes into account the contextual distance between a test utterance and the training corpus, a measure obtained from the external context in which the utterances were spoken. Language model probabilities are adjusted through a sentence-level weighting scheme based on this context-distance measure. When incorporated into our English-Iraqi Arabic speech-to-speech translation system, the proposed approach obtains improvements in both speech recognition accuracy and translation quality compared to the baseline system. 1
Tunicamycin inhibits ganglioside biosynthesis in rat liver Golgi apparatus by blocking sugar nucleotide transport across the membrane vesicles. (1983)

The synthesis of ganglioside GM1 in intact rat liver Golgi-derived vesicles is stimulated by phosphatidylglycerol as much (about 20-fold) as by Triton X-100. The antibiotic tunicamycin inhibits strongly the synthesis, in the presence as well as in the absence of the phospholipid, but has no effect when Golgi membranes are solubilized with detergent. In Pronase-treated Golgi vesicles, which retain full enzyme activity, both phospholipid dependence and tunicamycin inhibition of the synthesis disappear completely. When freshly prepared Golgi vesicles are incubated with 125 microM UDP-[3H]Gal for 10 min at 30 degrees C, the nucleotide sugar is found to be transported into the vesicles at an approximate rate of about 85 pmol/mg of protein per min, 92% of which remains firmly bound to the membrane. Tunicamycin inhibits this transport in a concentration-dependent manner. These results indicate the existence of carrier proteins in rat liver Golgi vesicles, which mediate the transport of the sugar nucleotide UDP-Gal, and that the carriers face the cytoplasmic side of the vesicles. The results also show that, although the mechanism of phosphatidylglycerol-induced stimulation of the synthetic activity remains unclear, tunicamycin inhibits ganglioside biosynthesis by blocking the transport of the nucleotide sugar and not by inhibiting the transferase directly.
Nicotinamide is a potent inducer of endocrine differentiation in cultured human fetal pancreatic cells. (1993)

The effects of nicotinamide (NIC) on human fetal and adult endocrine pancreatic cells were studied in tissue culture. Treatment of the fetal cells with 10 mM NIC resulted in a twofold increase in DNA content and a threefold increase in insulin content. This was associated with the development of beta cell outgrowths from undifferentiated epithelial cell clusters and an increase in the expression of the insulin, glucagon, and somatostatin genes. DNA synthesis was stimulated only in the undifferentiated cells. Half-maximal doses for the insulinotropic and mitogenic effects of NIC were 5-10 and 1-2 mM, respectively. Islet-like cell clusters cultured with NIC responded to glucose stimulation with a biphasic increase in insulin release (fourfold peak), whereas control cells were unresponsive to glucose. Both control and NIC-treated cells developed into functional islet tissue after transplantation into athymic nude mice. As compared with adult islets, the insulinotropic action of NIC could only be demonstrated in the fetal cells. Our results indicate that NIC induces differentiation and maturation of human fetal pancreatic islet cells. This model should be useful for the study of molecular mechanisms involved in beta cell development.
Macrophage Tropism of HIV-1 Depends on Efficient Cellular dNTP Utilization by Reverse Transcriptase (2004)

Retroviruses utilize cellular dNTPs to perform proviral DNA synthesis in infected host cells. Unlike oncoretroviruses, which replicate in dividing cells, lentiviruses, such as human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus, are capable of efficiently replicating in non-dividing cells (terminally differentiated macrophages) as well as dividing cells (i.e. activated CD4+ T cells). In general, non-dividing cells are likely to have low cellular dNTP content compared with dividing cells. Here, by employing a novel assay for cellular dNTP content, we determined the dNTP concentrations in two HIV-1 target cells, macrophages and activated CD4+ T cells. We found that human macrophages contained 130-250-fold lower dNTP concentrations than activated human CD4+ T cells. Biochemical analysis revealed that, unlike oncoretroviral reverse transcriptases (RTs), lentiviral RTs efficiently synthesize DNA even in the presence of the low dNTP concentrations equivalent to those found in macrophages. In keeping with this observation, HIV-1 vectors containing mutant HIV-1 RTs, which kinetically mimic oncoretroviral RTs, failed to transduce human macrophages despite retaining normal infectivity for activated CD4+ T cells and other dividing cells. These results suggest that the ability of HIV-1 to infect macrophages, which is essential to establishing the early pathogenesis of HIV-1 infection, depends, at least in part, on enzymatic adaptation of HIV-1 RT to efficiently catalyze DNA synthesis in limited cellular dNTP substrate environments.
Fine mapping association study and functional analysis implicate a SNP in MSMB at 10q11 as a causal variant for prostate cancer risk (2009)

A single nucleotide polymorphism (SNP) at 10q11 (rs10993994) in the 5' region of the MSMB gene was recently implicated in prostate cancer risk in two genome-wide association studies. To identify possible causal variants in the region, we genotyped 16 tagging SNPs and imputed 29 additional SNPs in approximately 65 kb genomic region at 10q11 in a Swedish population-based case-control study (CAncer of the Prostate in Sweden), including 2899 cases and 1722 controls. We found evidence for two independent loci, separated by a recombination hotspot, associated with prostate cancer risk. Among multiple significant SNPs at locus 1, the initial SNP rs10993994 was most significant. Importantly, using an MSMB promoter reporter assay, we showed that the risk allele of this SNP had only 13% of the promoter activity of the wild-type allele in a prostate cancer model, LNCaP cells. Curiously, the second, novel locus (locus 2) was within NCOA4 (also known as ARA70), which is known to enhance androgen receptor transcriptional activity in prostate cancer cells. However, its association was only weakly confirmed in one of the three additional study populations. The observations that rs10993994 is the strongest associated variant in the region and its risk allele has a major effect on the transcriptional activity of MSMB, a gene with previously described prostate cancer suppressor function, together suggest the T allele of rs10993994 as a potential causal variant at 10q11 that confers increased risk of prostate cancer.
THE EXTRA-INTESTINAL COMPLICATIONS OF CROHNʼS DISEASE AND ULCERATIVE COLITIS: A STUDY OF 700 PATIENTS (1976)

The records of a series of 700 patients with inflammatory bowel disease, 498 with Crohn's disease and 202 with ulcerative colitis, have been analyzed to determine the relative incidence and characteristic features of their extra-intestinal manifestations. The group with Crohn's disease included 62 with colitis, 223 with ileocolitis, and 213 with regional enteritis. A consideration of the clinical patterns and an understanding of their pathophysiology suggested a subdivision into two main groups: one "colitis related" and one related to the pathophysiology of the small nonspecific third group. Group A, colitis related, comprises joint, skin, mouth, and eye disease. The complications might be immunologically determined, were closely associated with active inflammation, and often responded to medical or surgical treatment of the underlying bowel disease. They occurred in 36% of the entire series of patients: joints were involved in 23%, skin in 15%, and mouth and eye each in 4%. Pyoderma gangrenosum was observed most often in ulcerative colitis and erythema nodosum most often in granulomatous colitis. The incidence of Group A complications was higher in disease involving the colon (42%) than in disease restricted exclusively to the small bowel (23%). There were interrelationships among the various members of Group A, with multiple manifestations occurring in a third of affected patients. Group B, related to small bowel pathophysiology, includes malabsorption, gallstones, kidney stones, and non-calculous hydronephrosis and hydroureter. Disorders in this group were generally related to the severity of the disease in the small bowel and tended to persist even in the absence of active inflammation. In contrast to Group A, this group occurred most frequently in small bowel disease, and least in colonic disease. Malabsorption was virtually confined to the patients with small bowel disease (10% incidence), while gallstones and renal stones were also both more frequent in Crohn's disease (11% and 9% respectively), the latter usually in association with small bowel resection or ileostomy. Group C, found in a small percentage of patients, consists of nonspecific complications, including osteoporosis (3%), liver disease (5%), peptic ulcer (10%), and amyloidosis (1%).
Mental Rotation in Unipolar Major Depression (2002)

Mental rotation (MR) performance may be used as an index of mental slowing or bradyphrenia, and may reflect, in particular, speed of motor preparation. MR was employed with a sample of both melancholic (n=8) and non-melancholic (n=9) unipolar depressed patients and healthy controls (n=10) to determine if motor slowing associated with depression might be reflected in slowed motor preparation (as reflected in slope of the MR function) independent of actual motor slowing (overall response time). Both melancholic and non-melancholic patients showed a generalised slowing relative to controls, perhaps reflecting bradykinesia and akinesia. This effect was significantly greater in the melancholic group than in the non-melancholic group. Relative to both the controls and the non-melancholic groups, the melancholic patients showed a progressive slowing with increasing angle of orientation indicating a specific slowing of MR. This deficit suggests a role of slowed motor planning in the psychomotor retardation of patients with melancholic depression.
The penetration of cefoxitin into peritoneal fluid (1981)

Journal Article The penetration of cefoxitin into peritoneal fluid Get access R. Wise, R. Wise Departments of Microbiology and Surgery, Dudley Road HospitalBirmingham B18 7QH, England Search for other works by this author on: Oxford Academic PubMed Google Scholar I. A. Donovan, I. A. Donovan Departments of Microbiology and Surgery, Dudley Road HospitalBirmingham B18 7QH, England Search for other works by this author on: Oxford Academic PubMed Google Scholar N. S. Ambrose, N. S. Ambrose Departments of Microbiology and Surgery, Dudley Road HospitalBirmingham B18 7QH, England Search for other works by this author on: Oxford Academic PubMed Google Scholar J. E. Allcock J. E. Allcock Departments of Microbiology and Surgery, Dudley Road HospitalBirmingham B18 7QH, England Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Antimicrobial Chemotherapy, Volume 8, Issue 6, December 1981, Pages 453–457, https://doi.org/10.1093/jac/8.6.453 Published: 01 December 1981 Article history Accepted: 10 June 1981 Published: 01 December 1981
Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines (2011)

In this study, we used both single-end and paired-end sequencing strategies to discover gene fusions in breast cancer transcriptomes with BRCA1 mutations. We found that the use of paired-end reads is an effective tool for transcriptome profiling of gene fusions. Our findings suggest that while gene fusions are present in some BRCA1-mutated breast cancers, they are infrequent and not recurrent. However, private fusions may still be valuable as potential patient-specific biomarkers for diagnosis and treatment.
Biological and chemical sensors based on graphene materials (2011)

Owing to their extraordinary electrical, chemical, optical, mechanical and structural properties, graphene and its derivatives have stimulated exploding interests in their sensor applications ever since the first isolation of free-standing graphene sheets in year 2004. This article critically and comprehensively reviews the emerging graphene-based electrochemical sensors, electronic sensors, optical sensors, and nanopore sensors for biological or chemical detection. We emphasize on the underlying detection (or signal transduction) mechanisms, the unique roles and advantages of the used graphene materials. Properties and preparations of different graphene materials, their functionalizations are also comparatively discussed in view of sensor development. Finally, the perspective and current challenges of graphene sensors are outlined (312 references).