gebhart/patrepeval huggingface dataset:
Mixture excitations and finite-state CELP speech coders (1992)

Code excited linear prediction (CELP) coding and its derivatives are currently the most frequently used techniques for speech compression at medium-to-low rate range. Until this study, the excitation vectors were always selected from a codebook generated by a Gaussian source or by the ensemble of residual signals collected from the used speech database. To the best of the author's knowledge, there is no study in which the excitation vectors were formed from a mixture of sources, a notion very successfully used by the speech recognition community within the hidden Markov model (HMM) framework. The authors proposed an improvement to the excitation model of CELP coders by embedding a labeled-state finite state vector quantization (FSVQ) and a mixture density approach in constructing 5-ms-long excitation vectors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Low-cost fabrication of submicron all polymer field effect transistors (2006)

All polymer field effect transistors have been fabricated combining nanoimprint lithography and inkjet printing. Trenches with hydrophilic bottoms confined by hydrophobic walls with considerable height are patterned by nanoimprint lithography. Conducting polymer solutions were then delivered into these trench liquid containers by inkjet printing. Dried conducting polymer in nearby trenches forms source-drain electrodes with the channel length accurately defined by the gap in between the designed two trenches. Top-gate all polymer field effect transistors with submicron channel lengths were successfully realized by such low-cost process.
Herpes simplex virus 1 helicase-primase: a complex of three herpes-encoded gene products. (1989)

In an earlier report, we described a DNA helicase that is specifically induced upon infection of Vero cells with herpes simplex virus 1. We have purified this enzyme to near homogeneity and found it to consist of three polypeptides with molecular weights of 120,000, 97,000, and 70,000. Immunochemical analysis has shown these polypeptides to be the products of three of the genes UL52, UL5, and UL8 that are required for replication of a plasmid containing a herpes simplex 1 origin (oriS). In addition to helicase activity, the enzyme contains a tightly associated DNA primase. Thus, the three-subunit enzyme is a helicase-primase complex that may prime lagging-strand synthesis as it unwinds DNA at the viral replication fork.
CD46 Is a Cellular Receptor for All Species B Adenoviruses except Types 3 and 7 (2005)

The 51 human adenovirus serotypes are divided into six species (A to F). Adenovirus serotypes from all species except species B utilize the coxsackie-adenovirus receptor for attachment to host cells in vitro. Species B adenoviruses primarily cause ocular and respiratory tract infections, but certain serotypes are also associated with renal disease. We have previously demonstrated that adenovirus type 11 (species B) uses CD46 (membrane cofactor protein) as a cellular receptor instead of the coxsackie-adenovirus receptor (A. Segerman et al., J. Virol. 77:9183-9191, 2003). In the present study, we found that transfection with human CD46 cDNA rendered poorly permissive Chinese hamster ovary cells more permissive to infection by all species B adenovirus serotypes except adenovirus types 3 and 7. Moreover, rabbit antiserum against human CD46 blocked or efficiently inhibited all species B serotypes except adenovirus types 3 and 7 from infecting human A549 cells. We also sequenced the gene encoding the fiber protein of adenovirus type 50 (species B) and compared it with the corresponding amino acid sequences from selected serotypes, including all other serotypes of species B. From the results obtained, we conclude that CD46 is a major cellular receptor on A549 cells for all species B adenoviruses except types 3 and 7.
Immunology at the Maternal-Fetal Interface: Lessons for T Cell Tolerance and Suppression (2000)

Mammalian reproduction poses an immunological paradox because fetal alloantigens encoded by genes inherited from the father should provoke responses by maternal T cells leading to fetal loss. Current understanding of T cell immunobiology and the critical role of inflammatory processes during pregnancy is reviewed and discussed. Lessons derived from studies on the regulation of T cell responsiveness during mammalian gestation are considered in the wider context of T cell tolerance toward some microbial infections and tumors, avoidance of autoimmunity, and tissue allograft rejection.
Quantification of Gene Expression with a Secreted Alkaline Phosphatase Reporter System (1997)

The cDNA encoding secreted alkaline phosphatase (SEAP) is a useful tool for investigating the function of known or putative enhancer/promoter elements. SEAP has the unusual properties of extreme heat stability and resistance to the phosphatase inhibitor L-homoarginine. Therefore, endogenous alkaline phosphatase activity in transfected cells can be minimized by pretreatment of samples at 65 degrees C and incubation with the inhibitor. With the use of the chemiluminescent substrate CSPD, 10(-13) g of enzyme can be detected in culture medium, and the enzyme activity can be detected as early as 24 h after transfection. The chemiluminescence-based SEAP assay is about 10-fold more sensitive than similar assays using firefly luciferase as the reporter enzyme. The SEAP activity can also be assayed with a fluorescent substrate MUP, which provides sensitivity comparable to luciferase. Since the enzyme is secreted to culture medium, the enzyme assay can be performed on small samples of the culture supernatant. Because preparation of cell lysates is not required, assaying for SEAP activity is faster and more convenient than assaying for intracellular reporters. Furthermore, because the transfected cells are not disturbed by the sampling procedure, the same cultures can be repeatedly sampled for time-course studies or used for further investigations.
The regulation of T cell-dependent antibody formation in vitro by CD40 ligand and IL-2 (1993)

Our study demonstrates the central role for the murine CD40 ligand and IL-2 in contact-dependent T cell help for Ag-specific primary antibody responses in vitro. Helper T cell clones were found to express CD40 ligand after activation with CD3 mAb. Membrane-bound recombinant CD40 ligand expressed on fixed CV1/EBNA cells had similar B cell-activating properties as T cell clones that had been activated and then fixed. These activities include the induction of B cell proliferation, induction of polyclonal secretion of multiple Ig isotypes in a cytokine-dependent manner, and induction of Ag-specific antibody responses by purified B cells. The induction of polyclonal Ig secretion by the recombinant CD40 ligand required IL-4 and IL-5 although optimal Ag-specific antibody formation required IL-2. Finally, soluble CD40.Fc inhibited the induction of Ag-specific antibody responses by fixed, activated Th cell clones. The requirement for both CD40 ligand and IL-2 for induction of Ag-specific antibody responses was mediated, in part, by the induction of B cell IL-2R expression by CD40 ligand. We conclude that the interaction of CD40 on B cells with its ligand on activated T cells is an integral event in the early activation of B cells to grow and differentiate to antibody formation.
The SDL Language Weaver Systems in the WMT12 Quality Estimation Shared Task (2012)

We present in this paper the system submissions of the SDL Language Weaver team in the WMT 2012 Quality Estimation shared-task. Our MT quality-prediction systems use machine learning techniques (M5P regression-tree and SVM-regression models) and a feature-selection algorithm that has been designed to directly optimize towards the official metrics used in this shared-task. The resulting submissions placed 1st (the M5P model) and 2nd (the SVM model), respectively, on both the Ranking task and the Scoring task, out of 11 participating teams. 1
Dendritic Nucleic Acid Probes for DNA Biosensors (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDendritic Nucleic Acid Probes for DNA BiosensorsJoseph Wang, Mian Jiang, Thor W. Nilsen, and Robert C. GettsView Author Information Department of Chemistry and Biochemistry New Mexico State University Las Cruces, New Mexico 88003 Polyprobe Inc., 4170 City Avenue Philadelphia, Pennsylvania 19131 Cite this: J. Am. Chem. Soc. 1998, 120, 32, 8281–8282Publication Date (Web):July 30, 1998Publication History Received24 February 1998Published online30 July 1998Published inissue 1 August 1998https://pubs.acs.org/doi/10.1021/ja980619phttps://doi.org/10.1021/ja980619prapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views1109Altmetric-Citations115LEARN 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 (2)»Supporting Information Supporting Information SUBJECTS:Biotechnology,Dendrons,Genetics,Hybridization,Sensors Get e-Alerts
Rapid antibiotic susceptibility phenotypic characterization of Staphylococcus aureus using automated microscopy of small numbers of cells (2014)

Staphylococcus aureus remains a leading, virulent pathogen capable of expressing complex drug resistance that requires up to 2-4 days for laboratory analysis. In this study, we evaluate the ability of automated microscopy of immobilized live bacterial cells to differentiate susceptible from non-susceptible responses of S. aureus isolates (MRSA/MSSA, clindamycin resistance/susceptibility and VSSA/hVISA/VISA) to an antibiotic based on the characterization of as few as 10 growing clones after 4 h of growth, compared to overnight growth required for traditional culture based methods. Isolates included 131 characterized CDC isolates, 3 clinical isolates and reference strains. MRSA phenotype testing used 1 h of 1 μg/mL cefoxitin induction followed by 3 h of 6 μg/mL cefoxitin. Clindamycin susceptibility testing used 1h of induction by 0.1 μg/mL erythromycin followed by 3h of 0.5 μg/mL clindamycin. An automated microscopy system acquired time-lapse dark-field images, and then computed growth data for individual immobilized progenitor cells and their progeny clones while exposed to different test conditions. Results were compared to concurrent cefoxitin disk diffusion and D-test references. For CDC organisms, microscopy detected 77/77 MRSA phenotypes and 54/54 MSSA phenotypes, plus 53/56 clindamycin-resistant and 75/75 clindamycin susceptible strains. Automated microscopy was used to characterize heterogeneous and inducible resistance, and perform population analysis profiles. Microscopy-based hVISA population analysis profiles (PAPs) were included as an extended proof of concept, and successfully differentiated VSSA from hVISA and VISA phenotypes compared to plate-based PAP.
Bile acid-induced rat hepatocyte apoptosis is inhibited by antioxidants and blockers of the mitochondrial permeability transition (2001)

The accumulation of hydrophobic bile acids plays a role in the induction of apoptosis and necrosis of hepatocytes during cholestasis. The aim of this study was to determine in freshly isolated rat hepatocytes the roles of oxidant stress and the mitochondrial permeability transition (MPT) in bile acid-induced apoptosis. Hepatocytes isolated from adult male Sprague-Dawley rats were incubated for 4 hours in buffer containing the hydrophobic bile acid, glycochenodeoxycholic acid (GCDC, 0-500 micromol/L) or the hydrophilic bile acid, glycocholic acid (GCA), and either the antioxidants, alpha tocopherol, ebselen, or idebenone (a coenzyme Q analogue); or the MPT blockers, cyclosporin A, or bongkrekic acid, or a caspase-8 inhibitor. Apoptosis was assessed hourly by nuclear morphologic changes of fixed cells by DAPI fluorescence microscopy and reactive oxygen species (ROS) generation by dichlorofluorescein fluorescence of hepatocytes. The percent of cells undergoing apoptosis increased in a time- and concentration-dependent manner in cells exposed to GCDC, and to a much lesser extent to GCA. ROS generation preceded the onset of apoptosis. MPT blockers, caspase-8 inhibition, and antioxidants prevented apoptosis and reduced ROS generation by hepatocytes. Flow cytometry analysis showed that MPT occurred within 1 hour of exposure of cells to 100 micromol/L GCDC, prior to onset of significant apoptosis. In conclusion, ROS generation, MPT induction, and cytochrome c release are critical steps in the induction of apoptosis by bile acids. Antioxidants may reduce liver injury caused by low levels of bile acids by preventing the generation of oxidant stress and subsequent stimulation of the MPT and release of cytochrome c from mitochondria.
A sphingosine 1-phosphate receptor 2 selective allosteric agonist (2013)

Molecular probe tool compounds for the Sphingosine 1-phosphate receptor 2 (S1PR2) are important for investigating the multiple biological processes in which the S1PR2 receptor has been implicated. Amongst these are NF-κB-mediated tumor cell survival and fibroblast chemotaxis to fibronectin. Here we report our efforts to identify selective chemical probes for S1PR2 and their characterization. We employed high throughput screening to identify two compounds which activate the S1PR2 receptor. SAR optimization led to compounds with high nanomolar potency. These compounds, XAX-162 and CYM-5520, are highly selective and do not activate other S1P receptors. Binding of CYM-5520 is not competitive with the antagonist JTE-013. Mutation of receptor residues responsible for binding to the zwitterionic headgroup of sphingosine 1-phosphate (S1P) abolishes S1P activation of the receptor, but not activation by CYM-5520. Competitive binding experiments with radiolabeled S1P demonstrate that CYM-5520 is an allosteric agonist and does not displace the native ligand. Computational modeling suggests that CYM-5520 binds lower in the orthosteric binding pocket, and that co-binding with S1P is energetically well tolerated. In summary, we have identified an allosteric S1PR2 selective agonist compound.
CodeHint: dynamic and interactive synthesis of code snippets (2014)

There are many tools that help programmers find code fragments, but most are inexpressive and rely on static information. We present a new technique for synthesizing code that is dynamic (giving accurate results and allowing programmers to reason about concrete executions), easy-to-use (supporting a wide range of correctness specifications), and interactive (allowing users to refine the candidate code snippets). Our implementation, which we call CodeHint, generates and evaluates code at runtime and hence can synthesize real-world Java code that involves I/O, reflection, native calls, and other advanced language features. We have evaluated CodeHint in two user studies and show that its algorithms are efficient and that it improves programmer productivity by more than a factor of two.
Query Adaptive Instance Search using Object Sketches (2016)

Sketch-based object search is a challenging problem mainly due to two difficulties: (1) how to match the binary sketch query with the colorful image, and (2) how to locate the small object in a big image with the sketch query. To address the above challenges, we propose to leverage object proposals for object search and localization. However, instead of purely relying on sketch features, e.g., Sketch-a-Net, to locate the candidate object proposals, we propose to fully utilize the appearance information to resolve the ambiguities among object proposals and refine the search results. Our proposed query adaptive search is formulated as a sub-graph selection problem, which can be solved by maximum flow algorithm. By performing query expansion using a smaller set of more salient matches as the query representatives, it can accurately locate the small target objects in cluttered background or densely drawn deformation intensive cartoon (Manga like) images. Our query adaptive sketch based object search on benchmark datasets exhibits superior performance when compared with existing methods, which validates the advantages of utilizing both the shape and appearance features for sketch-based search.
Adaptive Evolution ofEscherichia coliK-12 MG1655 during Growth on a Nonnative Carbon Source,l-1,2-Propanediol (2010)

Laboratory adaptive evolution studies can provide key information to address a wide range of issues in evolutionary biology. Such studies have been limited thus far by the inability of workers to readily detect mutations in evolved microbial strains on a genome scale. This limitation has now been overcome by recently developed genome sequencing technology that allows workers to identify all accumulated mutations that appear during laboratory adaptive evolution. In this study, we evolved Escherichia coli K-12 MG1655 with a nonnative carbon source, l-1,2-propanediol (l-1,2-PDO), for approximately 700 generations. We found that (i) experimental evolution of E. coli for approximately 700 generations in 1,2-PDO-supplemented minimal medium resulted in acquisition of the ability to use l-1,2-PDO as a sole carbon and energy source so that the organism changed from an organism that did not grow at all initially to an organism that had a growth rate of 0.35 h(-1); (ii) six mutations detected by whole-genome resequencing accumulated in the evolved E. coli mutant over the course of adaptive evolution on l-1,2-PDO; (iii) five of the six mutations were within coding regions, and IS5 was inserted between two fuc regulons; (iv) two major mutations (mutations in fucO and its promoter) involved in l-1,2-PDO catabolism appeared early during adaptive evolution; and (v) multiple defined knock-in mutant strains with all of the mutations had growth rates essentially matching that of the evolved strain. These results provide insight into the genetic basis underlying microbial evolution for growth on a nonnative substrate.
Thiazolidinediones in the treatment of Type 2 diabetes (2002)

In the last few years there has been an explosion of research that has improved our understanding of the pathogenesis of Type 2 diabetes mellitus (DM-2) and has led to the development of new oral antidiabetic drugs. Thiazolidinediones (TZDs) are the newest of these antidiabetic agents. TZDs are insulin sensitisers that depend on the presence of insulin for their action. They target insulin resistance, which is thought to play a central role in DM-2 and the associated metabolic syndrome characterised by central obesity, hypertension, dyslipidemia and hypercoagulability, all leading to increased cardiovascular morbidity and mortality. As a result, TZDs have the potential to improve other conditions associated with the metabolic syndrome, in addition to their glycaemic action. TZDs act by activating peroxisome proliferator-activated receptor (PPAR) phi a nuclear receptor implicated not only in lipid and glucose metabolism but other physiological functions as well. TZDs may have wide clinical applications beyond DM-2, as they can potentially be used to treat other conditions associated with insulin resistance and PPAR-phi receptors, such as impaired glucose tolerance, polycystic ovarian syndrome and HIV lipodystrophy.
Efficiently using graphics hardware in volume rendering applications (1998)

OpenGL and its extensions provide access to advanced per-pixel operations available in the rasterization stage and in the frame buffer hardware of modern graphics workstations. With these mechanisms, completely new rendering algorithms can be designed and implemented in a very particular way. In this paper we extend the idea of extensively using graphics hardware for the rendering of volumetric data sets in various ways. First, we introduce the concept of clipping geometries by means of stencil buffer operations, and we exploit pixel textures for the mapping of volume data to spherical domains. We show ways to use 3D textures for the rendering of lighted and shaded iso-surfaces in real-time without extracting any polygonal representation. Second, we demonstrate that even for volume data on unstructured grids, where only software solutions exist up to now, both methods, iso-surface extraction and direct volume rendering, can be accelerated to new rates of interactivity by simple polygon drawing and frame buffer operations.
Interaction of Diabetes and Hypertension on Determinants of Endothelial Adhesiveness (1998)

Epidemiological studies have established that diabetes mellitus and hypertension are independent risk factors for atherosclerosis. One of the earliest abnormalities seen in atherogenesis is enhanced monocyte adherence to the endothelium. The mechanisms by which diabetes mellitus or hypertension enhances monocyte-endothelial cell interactions are incompletely characterized. It is not known whether there are additive interactions between these risk factors on endothelial adhesiveness for monocytes. Male Wistar-Kyoto (WKY) and spontaneously hypertensive (SHR) rats were fed a normal or fructose-enriched diet. In some cases, animals were injected with streptozotocin (35 mg/kg body weight) to induce diabetes. After 2 weeks, plasma was drawn for biochemical measurements, and thoracic aortas were harvested, opened longitudinally, and exposed to fluorescently labeled mouse monocytoid cells (WEHI 78/24, 2 x 10(6)/mL) for 30 minutes on a rocking platform. Adherent cells were counted by epifluorescence microscopy. WEHI 78/24 binding to aortic segments from SHR animals was elevated compared with segments from WKYs. Fructose feeding alone had no effect on endothelial adhesiveness. When WKYs were made hyperglycemic by STZ injection, monocyte binding was 160% of the control value. Elevated monocyte binding was also observed in aortas derived from SHR animals injected with STZ, indicating an additive effect of hypertension and hyperglycemia. To determine whether alterations in oxidative state played a role in the endothelial adhesiveness, aortic segments were exposed to lucigenin (250 micromol/L) for measurement of superoxide anion. Aortic segments from SHR elaborated 120% more superoxide anion than did controls. Elevated free-radical production was also observed in aortas from diabetic WKYs. Furthermore, thoracic aortas derived from diabetic SHR animals elaborated more superoxide anion than did any of the other groups (374%, P<0.05). Immunohistochemical staining for monocyte chemotactic protein-1 demonstrated increased expression in aortas isolated from diabetic WKY and SHR compared with control vessels. These studies demonstrate that both diabetes and hypertension lead to increased monocyte adherence to the endothelium. This abnormality is associated with increased vascular superoxide production and monocyte chemotactic protein-1 expression. Furthermore, there appears to be an additive interaction between hyperglycemia and hypertension in their effects on endothelial adhesiveness and its determinants.