gebhart/patrepeval huggingface dataset:
Electrowetting on dielectric-based microfluidics for integrated lipid bilayer formation and measurement (2009)

We present a microfluidic platform for the formation and electrical measurement of lipid bilayer membranes. Using electrowetting on dielectric (EWOD), two or more aqueous droplets surrounded by a lipid-containing organic phase were manipulated into contact to form a lipid bilayer at their interface. Thin-film Ag/AgCl electrodes integrated into the device enabled electrical measurement of membrane formation and the incorporation of gramicidin channels of two bilayers in parallel.
New life for greenbacks (1994)

A \\"green\\" movement is underway at several Federal Reserve Banks.
Stochastic language adaptation over time and state in natural spoken dialog systems (2000)

We are interested in adaptive spoken dialog systems for automated services. Peoples' spoken language usage varies over time for a given task, and furthermore varies depending on the state of the dialog. Thus, it is crucial to adapt automatic speech recognition (ASR) language models to these varying conditions. We characterize and quantify these variations based on a database of 30 K user-transactions with AT&T's experimental How May I Help You? spoken dialog system. We describe a novel adaptation algorithm for language models with time and dialog-state varying parameters. Our language adaptation framework allows for recognizing and understanding unconstrained speech at each stage of the dialog, enabling context-switching and error recovery. These models have been used to train state-dependent ASR language models. We have evaluated their performance with respect to word accuracy and perplexity over time and dialog states. We have achieved a reduction of 40% in perplexity and of 8.4% in word error rate over the baseline system, averaged across all dialog states.
IL-4 is an essential factor for the IgE synthesis induced in vitro by human T cell clones and their supernatants. (1988)

The property of 109 CD4+ T cell clones (TCC) to induce IgE synthesis in vitro in human B cells was compared with their ability to produce IL-2, IL-4, and IFN-gamma in their supernatants (SUP) after 24-h stimulation with PHA. A significant positive correlation was found between the property of TCC to induce or enhance spontaneous IgE synthesis and their ability to release IL-4. In contrast, there was an inverse relationship between the IgE helper activity of TCC and their ability to release IFN-gamma, whereas no statistical correlation between the property to induce IgE synthesis and to produce IL-2 was observed. The ability of PHA-SUP from 71 CD4+ TCC to induce IgE synthesis in B cells was also investigated. Twenty-nine SUP (all derived from TCC active on IgE synthesis) induced production of substantial amounts of IgE in target B cells. There was a correlation between the amount of IgE synthesized by B cells in response to these SUP and their IL-4 content. An even higher correlation was found between the IgE synthesis induced by these SUP and the ratio between the amount of IL-4 and IFN-gamma present in the same SUP. Like IL-4-containing SUP, rIL-4 also showed the ability to induce IgE production in B cells from both atopic and nonatopic donors. The addition to B cell cultures of anti-IL-4 antibody virtually abolished not only the IgE synthesis induced by rIL-4, but also that stimulated by TCC and their SUP. In contrast, the IgG synthesis induced by TCC SUP was not or only slightly inhibited by the anti-IL-4 antibody. These data indicate that IL-4 is an essential mediator for the IgE synthesis induced in vitro by human TCC and their SUP in the absence of a polyclonal activator, whereas IFN-gamma seems to exert a negative regulatory effect on the production of IgE.
Shielding the front-strand β3 of the von Willebrand factor A1 domain inhibits its binding to platelet glycoprotein Ibα (2003)

Platelet adhesion to damaged vessel wall and shear-induced platelet aggregation necessitate binding of the von Willebrand factor (VWF) A1 domain to platelet GPIbalpha. Blocking this interaction represents a promising approach to the treatment of arterial thrombosis. Comparison of amino acid sequences of the VWF A1 domain in several species, expressing VWF recognized by the blocking monoclonal antibody AJvW-2, suggested 9 residues (His563, Ile566, Asp570, Ala581, Val584, Ala587, Arg616, Ala618, and Met622) to contribute to the epitope for AJvW-2 or to be part of the GPIbalpha-binding site. Glutathione-S-transferase (GST)-human VWF A1 fusion proteins, in which these amino acids were mutated to their murine counterparts, were tested for their capacity to bind AJvW-2 or heparin, to interfere with botrocetin- or ristocetin-mediated VWF binding to GPIb, or to induce flow-dependent platelet tethering in a perfusion chamber. Thus, mutations His563Arg, Ile566Leu, Asp570Ala, and Ala587Thr, clustered on the outer surface of the A1 domain, dramatically impaired binding of AJvW-2 to A1. The His563Arg, Ile566Leu, and Asp570Ala mutations also impaired the binding of heparin, which competes with AJvW-2 for binding to A1. Perfusion studies revealed that His563, Ile566, Asp570, Arg616, and Ala618 take part in GPIbalpha binding, their mutation-impairing platelet recruitment. In agreement with the surface distribution of VWF type 2M mutations, this study demonstrates overlapping of the epitope for AJvW-2 and the GPIbalpha-binding site, located around the front pocket of the A1 domain and defined by strands beta3, beta4, and helix alpha3, and it provides a mechanistic basis for VWF neutralization by this antibody.
Comparative Effects of Cerivastatin and Fenofibrate on the Atherogenic Lipoprotein Phenotype in Proteinuric Renal Disease (2001)

Patients with nephrotic-range proteinuria have impaired clearance of triglyceride-rich lipoproteins. This results in the atherogenic lipoprotein phenotype (mild hypertriglyceridemia, low high-density lipoproteins [HDL], and excess small, dense low-density lipoproteins [LDLIII]). Excess remnant lipoproteins (RLP) are linked to hypertriglyceridemia and may contribute to the atherogenicity of nephrotic dyslipidemia. A randomized crossover study compared the effects of a statin (cerivastatin) and a fibrate (fenofibrate) on LDLIII and RLP in 12 patients with nephrotic-range proteinuria. Cerivastatin reduced cholesterol (21%, P: < 0.01), triglyceride (14%, P: < 0.05), LDL cholesterol (LDL-C; 23%, P: < 0.01), total LDL (18%, P: < 0.01), and LDLIII concentration (27% P: < 0.01). %LDLIII, RLP-C, and RLP triglyceride (RLP-TG) were unchanged. Plasma LDLIII reduction with cerivastatin treatment correlated with LDL-C reduction (r(2) = 34%, P: < 0.05). Fenofibrate lowered cholesterol (19%), triglyceride (41%), very low-density lipoprotein cholesterol (52%), LDLIII concentration (49%), RLP-C (35%), and RLP-TG (44%; all P: < 0.01). Fenofibrate also reduced %LDLIII from 60 to 33% (P: < 0.01). HDL-C (19%, P: < 0.01) increased with fenofibrate treatment; LDL-C and total LDL were unchanged. The reduction in LDLIII concentration and RLP-C with fenofibrate treatment correlated with plasma triglyceride reduction (LDLIII r(2) = 67%, P: < 0.001; RLP cholesterol r(2) = 58%, P: < 0.005). Serum creatinine increased with fenofibrate treatment (14%, P: < 0.01); however, creatinine clearance was unchanged. LDLIII concentration was 187 +/- 85 mg/dl after cerivastatin treatment and 133 +/- 95 mg/dl after fenofibrate treatment. Cerivastatin and fenofibrate reduce LDLIII concentration in nephrotic-range proteinuria. However, atherogenic concentrations of LDLIII remain prevalent after either treatment. Fenofibrate but not cerivastatin reduces remnant lipoproteins. The two treatments seem to reduce LDLIII by different mechanisms, suggesting a potential role for combination therapy to optimize lowering of LDLIII and RLP.
Phase Dependence of Intense Field Ionization: A Study Using Two Colors (1994)

We present the first measurement of the ionization rate from above-threshold ionization (ATI) in an optical field whose phase dependence is known and controllable. Our method uses a harmonic two-color light field with a calibrated phase difference between the $1\ensuremath{\omega}$ and $2\ensuremath{\omega}$ fields. Our measurements confirm many of the predictions of recent semiclassical theories, but show an important discrepancy: An asymmetry in the ATI rates relative to the sign of the two-color phase difference supports recently suggested modifications to the models to include electron-core rescattering during ionization.
Clinical utility of colon cancer molecular subtypes: Validation of two main colorectal molecular classifications on the PETACC-8 phase III trial cohort. (2017)

3509 Background: The molecular subtyping of colon cancers (CC) has been the subject of several recent publications, leading to an international consensus. The clinical relevance of these molecular classifications remains to be evaluated on large prospective patient cohorts using a tool that can be widely used on formalin-fixed paraffin-embedded (FFPE) samples. Methods: We aimed to evaluate the clinical relevance of two molecular subtyping systems, CMS (Guinney et al. 2015) and CCMST (Marisa et al. 2013), on the PETACC-8 cohort, a randomized phase III trial comparing adjuvant FOLFOX with or without cetuximab in patients with stage III CC. For each of these two classification systems, a predictor tool was developed and adapted to FFPE samples. The NanoString nCounter platform was used to screen 196 genes. Predictors were built from 249 frozen tumor samples previously used to build our classification system and 61 new paired FFPE/frozen samples. Both predictors were then applied to 1781 PETACC-8 FFPE samples. Subtypes associations to clinical and molecular features were analyzed. Results: The CMS predictor assigned 297 samples to CMS1 (17%), 585 to CMS2 (34%), 68 to CMS3 (4%) and 770 to CMS4 (45%). CMS were significantly associated with several molecular and clinical features, including MSI status (49% in CMS1, p &lt; 0.001), CIMP status (47% in CMS1, p &lt; 0.001), KRAS mutation (75% in CMS3, p &lt; 0.001), BRAF mutation (34% in CMS1, p &lt; 0.001), tumor location (less proximal tumors in CMS2, p &lt; 0.001), validating the predictor tool developed. The classification was significantly associated to prognosis in multivariate analysis, CMS4 subtype having a shorter overall survival (hazard ratio = 1.7, p= 0.021). A deleterious effect of cetuximab was observed in CMS1 (p &lt; 0.05). Similar results were obtained with the CCMST classification. Conclusions: We validated molecular CC subtyping predictors for both CMS and CCMST classifications on PETACC-8 FFPE samples. The prognostic value of CMS and CCMST classifications was confirmed, stem-like tumors being associated with a poor prognosis. These results pave the avenue for widely use of the CC molecular classification in clinical routine.
Object-based multiresolution watermarking of images and video (2000)

This paper proposes a new approach to digital watermarking of image and video objects with arbitrary regions of support (AROS) based on the 2D and 3D shape adaptive wavelet transforms. The hierarchical nature of the wavelet representation of objects allows detection of the digital watermark at various resolutions. We show that, when subjected to image/video compression, the corresponding watermark of objects can still be correctly identified at each resolution (excluding the lowest one) in the wavelet domain. Such a multiresolution watermarking scheme for objects has computational advantage, especially for the video case. Potential applications of our proposed scheme include watermark-based object searching and indexing.
Multilevel hypergraph partitioning: applications in VLSI domain (1999)

In this paper, we present a new hypergraph-partitioning algorithm that is based on the multilevel paradigm. In the multilevel paradigm, a sequence of successively coarser hypergraphs is constructed. A bisection of the smallest hypergraph is computed and it is used to obtain a bisection of the original hypergraph by successively projecting and refining the bisection to the next level finer hypergraph. We have developed new hypergraph coarsening strategies within the multilevel framework. We evaluate their performance both in terms of the size of the hyperedge cut on the bisection, as well as on the run time for a number of very large scale integration circuits. Our experiments show that our multilevel hypergraph-partitioning algorithm produces high-quality partitioning in a relatively small amount of time. The quality of the partitionings produced by our scheme are on the average 6%-23% better than those produced by other state-of-the-art schemes. Furthermore, our partitioning algorithm is significantly faster, often requiring 4-10 times less time than that required by the other schemes. Our multilevel hypergraph-partitioning algorithm scales very well for large hypergraphs. Hypergraphs with over 100 000 vertices can be bisected in a few minutes on today's workstations. Also, on the large hypergraphs, our scheme outperforms other schemes (in hyperedge cut) quite consistently with larger margins (9%-30%).
Mirk protein kinase is a mitogen-activated protein kinase substrate that mediates survival of colon cancer cells. (2000)

We have cloned a novel gene mirk (minibrain-related kinase) encoding a protein kinase that enables colon carcinoma cells to survive under certain stress conditions. Mirk is a mitogen-activated protein kinase substrate but is down-regulated by activated extracellular signal-regulated kinases (erks) in vivo. Mirk contains a PEST region characteristic of rapidly turned over proteins and is broken down to a Mr 57,000 form only in the nucleus. In each of three colon carcinoma cell lines, mirk levels were increased 20-fold when erk activation was blocked by the MEK inhibitor PD98059 in serum-free medium. Addition of IGF-I to activate erks blocked this increase. Mirk was stably overexpressed in two colon carcinoma cell lines to attain levels seen in colon cancers. Each of five mirk transfectants proliferated when switched to serum-free medium and regained rapid growth when serum was restored, whereas five vector control transfectants and three kinase-dead mutant mirk transfectants did not. mirk mRNA levels were elevated in several types of carcinomas, and mirk protein was detected in each of seven colon carcinoma cell lines. mirk was expressed at a higher protein level in Western blots from three of eight colon cancers compared with paired normal colon tissue, suggesting that mirk plays a role in the evolution of a subset of colon cancers. mirk is not mutated in colon carcinomas. Mirk may mediate tumor cell survival in mitogen-poor environments or early in colon cancer development before many autocrine growth factors have been induced.
Merging path and gshare indexing in perceptron branch prediction (2005)

We introduce the hashed perceptron predictor, which merges the concepts behind the gshare, path-based and perceptron branch predictors. This predictor can achieve superior accuracy to a path-based and a global perceptron predictor, previously the most accurate dynamic branch predictors known in the literature. We also show how such a predictor can be ahead pipelined to yield one cycle effective latency. On the SPECint2000 set of benchmarks, the hashed perceptron predictor improves accuracy by up to 15.6% over a MAC-RHSP and 27.2% over a path-based neural predictor.
Therapeutic efficacy of prosaposin-derived peptide on different models of allodynia (2006)

We have previously demonstrated that the prosaposin-derived 14-mer peptide TX14(A) prevents structural and functional abnormalities associated with peripheral neuropathy in diabetic rats. Unusually, this neuroprotective peptide also exhibited acute anti-hyperalgesic properties in the same model, suggesting a dual action of TX14(A) that could allow therapeutic targeting of both degenerative neuropathy and neuropathic pain. In the present study, we have extended investigation of the anti-allodynic properties of TX14(A) to a range of models in which allodynia is induced using metabolic, physical, neurotoxic or chemical/inflammatory damage to the peripheral nerve. Single systemic doses of TX14(A) rapidly alleviated tactile allodynia in rats in which nerve injury was induced by diabetes, sciatic nerve hemiligation, systemic paclitaxel treatment or paw formalin injection. Further, TX14(A) pre-treatment prevented onset of allodynia in the paclitaxel and formalin injection models. These results indicate that TX14(A) has anti-allodynic properties in diverse models of neuropathic pain and support further exploration of its potential as a therapeutic agent for a wide range of peripheral neuropathies and neuropathic pain states.
Epstein-Barr virus vectors for gene delivery to B lymphocytes. (1996)

Basic research in Epstein-Barr virus (EBV) molecular genetics has provided means to maintain episomes in human cells, to efficiently deliver episomes with up to 150 kbp of heterologous DNA to human B lymphocytes, and to immortalize human B lymphocytes with EBV recombinants that can maintain up to 120 kbp of heterologous DNA. Episome maintenance requires an EBV nuclear protein, EBNA1, whereas immortalization of cells with EBV recombinants requires EBNA1, EBNA2, EBNA3A, EBNA3C, EBNALP, and LMP1. EBV-derived vectors are useful for experimental genetic reconstitution in B lymphocytes, a cell type frequently used in establishing repositories of human genetic deficiencies. The ability of EBV-infected cells to establish a balanced state of persistence in normal humans raises the possibility that cells infected with EBV recombinants could be useful for genetic reconstitution, in vivo.
Ten key issues in modern flow chemistry (2011)

Ten essentials of synthesis in the flow mode, a new enabling technology in organic chemistry, are highlighted as flashlighted providing an insight into current and future issues and developments in this field.
Colocalization of antisense RNAs and ribozymes with their target mRNAs (1997)

The use of complementary RNA sequences such as antisense RNAs and ribozymes to regulate the expression of specific genes in eukaryotic cells has been well-documented, particularly with their application to both human gene therapy and plant biotechnology. Despite the simplicity of this approach, this technique usually results in only partial suppression of gene expression and, in some instances, even fails to regulate the gene of interest. The variation observed with antisense RNA and ribozyme-mediated regulation is further complicated by the many factors with the potential to impact on the effectiveness of these RNAs. Recent advances in the understanding of the global architecture of the nucleus, chromatin structure, and RNA metabolism provide useful and necessary information for designing novel approaches to improving antisense RNA and ribozyme regulation. These studies predict that the position of genes within the nucleus is not random and that transcripts produced from these genes follow specific tracks in migrating to the cell cytoplasm. These observations have the potential to impact significantly on the ways in which RNA-mediated forms of gene regulation are applied. The purpose of this review is to discuss the concept of colocalizing antisense RNAs and ribozymes with their target mRNAs and to introduce a variety of approaches aimed at achieving this goal.
Acoustic Surgery (2001)

Bursts of focused ultrasound energy three orders of magnitude more intense than diagnostic ultrasound are emerging as a noninvasive option for treating cancer and other medical procedures.
C9orf72 repeat expansions cause neurodegeneration in Drosophila through arginine-rich proteins (2014)

An expanded GGGGCC repeat in C9orf72 is the most common genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis. A fundamental question is whether toxicity is driven by the repeat RNA itself and/or by dipeptide repeat proteins generated by repeat-associated, non-ATG translation. To address this question, we developed in vitro and in vivo models to dissect repeat RNA and dipeptide repeat protein toxicity. Expression of pure repeats, but not stop codon-interrupted "RNA-only" repeats in Drosophila caused adult-onset neurodegeneration. Thus, expanded repeats promoted neurodegeneration through dipeptide repeat proteins. Expression of individual dipeptide repeat proteins with a non-GGGGCC RNA sequence revealed that both poly-(glycine-arginine) and poly-(proline-arginine) proteins caused neurodegeneration. These findings are consistent with a dual toxicity mechanism, whereby both arginine-rich proteins and repeat RNA contribute to C9orf72-mediated neurodegeneration.
Normal pre-B cells express a receptor complex of mu heavy chains and surrogate light-chain proteins. (1991)

Precursors of B cells, which constitute a subpopulation of the lymphocytes in bone marrow, can be identified by their surface expression of nonimmunoglobulin markers and the absence of immunoglobulin kappa and lambda light chains. Most pre-B cells synthesize mu heavy chains but, without light-chain partners, these undergo rapid cytoplasmic degradation. In the present study, we demonstrate that late stage pre-B cells, like their neoplastic counterparts, express low levels of a surface receptor composed of mu chains paired with a surrogate light-chain complex formed by Vpre-B and lambda 5-like proteins. The data define a previously suspected but unrecognized stage in normal pre-B-cell differentiation. Expression of a clonally diverse receptor renders this population of immature B-lineage cells potentially vulnerable to clonal selection by antigens and idiotypic interactions.
Screening for mutations in the peripheral myelin genesPMP22,MPZ andCx32 (GJB1) in Russian Charcot-Marie-Tooth neuropathy patients (2000)

Charcot-Marie-Tooth disease (CMT) and related inherited peripheral neuropathies, including Dejerine-Sottas syndrome, congenital hypomyelination, and hereditary neuropathy with liability to pressure palsies (HNPP), are caused by mutations in three myelin genes: PMP22, MPZ and Cx32 (GJB1). The most common mutations are the 1.5 Mb CMT1A tandem duplication on chromosome 17p11.2-p12 in CMT1 patients and the reciprocal 1.5 Mb deletion in HNPP patients. We performed a mutation screening in 174 unrelated CMT patients and three HNPP families of Russian origin. The unrelated CMT patients included 108 clinically and electrophysiologically diagnosed CMT1 cases, 32 CMT2 cases, and 34 cases with unspecified CMT. Fifty-nine CMT1A duplications were found, of which 58 belonged to the CMT1 patient group. We found twelve distinct mutations in Cx32, six mutations in MPZ, and two mutations in PMP22. Of these respectively, eight, five, and two lead to a CMT1 phenotype. Eight mutations (Cx32: Ile20Asn/Gly21Ser, Met34Lys, Leu90Val, and Phe193Leu; MPZ: Asp134Gly, Lys138Asn, and Thr139Asn; PMP22: ValSer25-26del) were not reported previously. Phenotype-genotype correlations were based on nerve conduction velocity studies and mutation type.
Photodynamic therapy for Barrett's esophagus: Cardiac effects (1997)

No permanent electrocardiographic changes or significant abnormalities in cardiac enzymes were detected following esophageal photodynamic therapy in patients with or without histories of cardiac disease. Delivery of esophageal PDT is not associated with permanent adverse cardiac effects.