gebhart/patrepeval huggingface dataset:
Combination treatment in the management of type 2 diabetes: focus on vildagliptin and metformin as a single tablet (2008)

Vildagliptin is a potent and selective inhibitor of dipeptidyl peptidase-IV (DPP-4), orally active, that improves glycemic control in patients with type 2 diabetes (T2DM) primarily by enhancing pancreatic (alpha and beta) islet function. Thus vildagliptin has been shown both to improve insulin secretion and to suppress the inappropriate glucagon secretion seen in patients with T2DM. Vildagliptin reduces HbA(1c) when given as monotherapy, without weight gain and with minimal hypoglycemia, or in combination with the most commonly prescribed classes of oral hypoglycemic drugs: metformin, a sulfonylurea, a thiazolidinedione, or insulin. Metformin, with a different mode of action not addressing beta-cell dysfunction, has been used for about 50 years and still represents the universal first line therapy of all guidelines. However, given the multiple pathophysiological abnormalities in T2DM and the progressive nature of the disease, intensification of therapy with combinations is typically required over time. Recent guidelines imply that patients will require pharmacologic combinations much earlier to attain and sustain the increasingly stringent glycemic targets, with careful drug selection to avoid unwanted adverse events, especially hypoglycemia. The combination of metformin and vildagliptin offers advantages when compared to currently used combinations with additive efficacy and complimentary mechanisms of action, since it does not increase the risk of hypoglycemia and does not promote weight gain. Therefore, by specifically combining these agents in a single tablet, there is considerable potential to achieve better blood glucose control and to improve compliance to therapy.
Fast Keypoint Recognition in Ten Lines of Code (2007)

While feature point recognition is a key component of modern approaches to object detection, existing approaches require computationally expensive patch preprocessing to handle perspective distortion. In this paper, we show that formulating the problem in a Naive Bayesian classification framework makes such preprocessing unnecessary and produces an algorithm that is simple, efficient, and robust. Furthermore, it scales well to handle large number of classes. To recognize the patches surrounding keypoints, our classifier uses hundreds of simple binary features and models class posterior probabilities. We make the problem computationally tractable by assuming independence between arbitrary sets of features. Even though this is not strictly true, we demonstrate that our classifier nevertheless performs remarkably well on image datasets containing very significant perspective changes.
Verifying the performance of the PCI local bus using symbolic techniques (2002)

Symbolic model checking is a successful technique for checking properties of large finite-state systems. This method has been used to verify a number of real-world hardware designs; however it is not able to determine timing or performance properties directly. Since these properties are extremely important in the design of high-performance systems and in time-critical applications, we have extended model checking techniques to produce timing information. Our results allow a more detailed analysis of a model than is possible with tools that simply determine whether a property is satisfied or not. We present algorithms that determine the exact bounds on the time interval between two specified events and the number of occurrences of another event in such an interval. To demonstrate how our method works, we have modelled the PCI local bus and analyzed its temporal behavior. The results demonstrate the usefulness of our technique in analyzing complex modem designs.
A microfluidic bioreactor with integrated transepithelial electrical resistance (TEER) measurement electrodes for evaluation of renal epithelial cells (2010)

We have developed a bilayer microfluidic system with integrated transepithelial electrical resistance (TEER) measurement electrodes to evaluate kidney epithelial cells under physiologically relevant fluid flow conditions. The bioreactor consists of apical and basolateral fluidic chambers connected via a transparent microporous membrane. The top chamber contains microfluidic channels to perfuse the apical surface of the cells. The bottom chamber acts as a reservoir for transport across the cell layer and provides support for the membrane. TEER electrodes were integrated into the device to monitor cell growth and evaluate cell-cell tight junction integrity. Immunofluorescence staining was performed within the microchannels for ZO-1 tight junction protein and acetylated α-tubulin (primary cilia) using human renal epithelial cells (HREC) and MDCK cells. HREC were stained for cytoskeletal F-actin and exhibited disassembly of cytosolic F-actin stress fibers when exposed to shear stress. TEER was monitored over time under normal culture conditions and after disruption of the tight junctions using low Ca(2+) medium. The transport rate of a fluorescently labeled tracer molecule (FITC-inulin) was measured before and after Ca(2+) switch and a decrease in TEER corresponded with a large increase in paracellular inulin transport. This bioreactor design provides an instrumented platform with physiologically meaningful flow conditions to study various epithelial cell transport processes.
Branched-chain amino acids suppress the cumulative recurrence of hepatocellular carcinoma under conditions of insulin-resistance (2013)

Branched-chain amino acids (BCAAs) reportedly inhibit the incidence of hepatocellular carcinoma (HCC) in patients with liver cirrhosis and obesity that is frequently associated with insulin resistance (IR). We previously reported that BCAAs exert a chemopreventive effect against HCC under IR conditions in rats. The aim of the present study was to examine the effect of BCAAs on the cumulative recurrence of HCC under IR conditions in the clinical practice. BCAA granules (Livact®, 12 g/day) were administered for 60 months following the local curative therapy for HCC, and several indices were determined. Treatment with BCAAs markedly inhibited the cumulative recurrence of HCC in patients with a high IR index [homeostasis model assessment (HOMA)-IR >2.5], but not in patients with HOMA-IR of ≤2.5. BCAA also improved the HOMA-IR, and the inhibitory effect was observed regardless of the serum albumin (Alb) levels. Similarly, BCAA treatment revealed a marked suppressive effect in patients with high fasting insulin [immune reactive insulin (IRI)>15 U/ml], but not with IRI of ≤15. BCAA treatment did not result in differences in HCC recurrence in patients with high and low glucose levels [fasting blood sugar (FBS)>110 and ≤110, respectively]. Furthermore, serum levels of the soluble form of vascular endothelial growth factor receptor 2 (sVEGFR2) were significantly inhibited along with these clinical effects. Our findings indicate that the inhibitory effect of BCAAs was achieved, at least partly, by coordinated effects of anti-angiogenesis and IR improvement. Since BCAAs are widely and safely used in clinical practice to treat patients with chronic liver diseases, BCAAs may represent a new strategy for secondary chemoprevention for HCC patients with IR. Moreover, our findings suggest that sVEGFR2 may be a useful clinical predictive marker for BCAA treatment under IR conditions.
Molecular Mechanisms Controlling the Fibrotic Repair Phenotype in Cornea: Implications for Surgical Outcomes (2003)

These data suggest that integrity of the basement membrane is a deciding factor in determining the regenerative character of corneal repair.
The voltage-gated sodium channel Scn8a is a genetic modifier of severe myoclonic epilepsy of infancy (2007)

The mammalian genome contains four voltage-gated sodium channel genes that are primarily expressed in the central nervous system: SCN1A, SCN2A, SCN3A and SCN8A. Mutations in SCN1A and SCN2A are responsible for several dominant idiopathic epilepsy disorders, including generalized epilepsy with febrile seizures plus (GEFS+) and severe myoclonic epilepsy of infancy (SMEI). Mutations in SCN8A are associated with cognitive deficits and neuropsychiatric illness in humans and movement disorders in mice; however, a role for SCN8A (Na(v)1.6) in epilepsy has not been investigated. To determine the relationship between Na(v)1.6 dysfunction and seizure susceptibility, we examined the thresholds of two Scn8a mouse mutants, Scn8a(med) and Scn8a(med-jo), to flurothyl- and kainic acid (KA)-induced seizures. Both mutants were more seizure resistant than wild-type littermates, suggesting that altered Na(v)1.6 function reduces neuronal excitability. To determine whether impaired Na(v)1.6 function could ameliorate seizure severity in a mouse model of SMEI, we generated Scn1a(+/-); Scn8a(med-jo/+) double heterozygous mice. Unlike Scn1a(+/-) mice that are more susceptible to flurothyl-induced seizures, Scn1a(+/-); Scn8a(med-jo/+) mice displayed thresholds that were comparable to wild-type littermates. The Scn8a(med-jo) allele was also able to rescue the premature lethality of Scn1a(+/-) mice and extend the lifespan of Scn1a(-/-) mutants. These results demonstrate that genetic interactions can alter seizure severity and support the hypothesis that genetic modifiers contribute to the clinical variability observed in SMEI and GEFS+.
Chemoprevention by perillyl alcohol coupled with viral gene therapy reduces pancreatic cancer pathogenesis (2008)

Pancreatic cancer is one of the deadliest of cancers. Even with aggressive therapy, the 5-year survival rate is <5%, mandating development of more effective treatments. Melanoma differentiation-associated gene-7/interleukin-24 (mda-7/IL-24) shows potent antitumor activity against most cancers displaying safety with significant clinical efficacy. However, pancreatic cancer cells display inherent resistance to mda-7/IL-24 that is the result of a "protein translational block" of mda-7/IL-24 mRNA in these tumor cells. We now show that a dietary supplement perillyl alcohol (POH) has significant chemopreventive effects for pancreatic cancer and, when coupled with adenovirus-mediated mda-7/IL-24 gene therapy (Ad.mda-7), effectively eliminates s.c. and i.p. xenografts of human pancreatic cancer cells in nude mice, promoting enhanced survival. The combination of POH and Ad.mda-7 efficiently abrogates the mda-7/IL-24 protein translational block, resulting in MDA-7/IL-24 protein production and growth suppression. Of direct translational relevance, clinically achievable concentrations of POH with Ad.mda-7, both of which have been found safe and without toxic effects in human trials, were used. This novel and innovative approach combining a dietary agent and a virally delivered therapeutic cytokine provides a means of both preventing and treating human pancreatic cancer with significant clinical translational potential.
Telcordia's Database Reconciliation and Data Quality Analysis Tool (2000)

This demonstration illustrates how a comprehensive database reconciliation tool can provide the ability to charactenze data-quality and data-reconciliation issues in complex real-world applications. Telcordia's data reconciliation and data quality analysis tool includes rapid generation of appropriate pre-processing and matching rules applied to a training set created from samples of the data. Once tuned, the appropriate rules can be applied efficiently to the complete data sets. The tool uses a modular JavaBeans-based architecture that allows for customized matching functions and iterative runs that build upon previously learned information. Telcordia has been able to provide significant insights to clients who recognize that they have data reconciliation problems but cannot determine root causes effectively when using currently available off-the-shelf tools. A description of the analysis of a duplicate-record problem in a set of taxpayer databases is included in this report to illustrate the effective use of the tool.
Deep learning-based classification for brain-computer interfaces (2017)

Brain-computer interface (BCI) is an emerging area of research that aims to improve the quality of human-computer applications. It has enormous scope in biomedical applications, neural rehabilitation, biometric authentication, educational programmes, and entertainment applications. A BCI system has four major components: signal acquisition, signal preprocessing, feature extraction, and classification. In this study, we provide a comparison of various traditional classification algorithms to the newer methods of deep learning. We explore two different types of deep learning methods, namely, convolutional neural networks (CNN) and recurrent neural networks (RNN) with long short-term memory (LSTM) architecture. We test the classification accuracies on a recent 5-dass steady-state visual evoked potential (SSVEP) dataset. The results prove the superiority of deep learning methods in comparison with the traditional classification algorithms. Amongst the traditional classifiers, support vector machine (SVM) with Gaussian kernel employing sequential forward selection (SFS) of features provided a better classification accuracy of 66.09%, while CNN provided the highest classification accuracy of 69.03%.
Staphylococcus aureusCapsular Polysaccharides (2004)

Serotype 5 and 8 capsular polysaccharides predominate among clinical isolates of Staphylococcus aureus. The results of experiments in animal models of infection have revealed that staphylococcal capsules are important in the pathogenesis of S. aureus infections. The capsule enhances staphylococcal virulence by impeding phagocytosis, resulting in bacterial persistence in the bloodstream of infected hosts. S. aureus capsules also promote abscess formation in rats. Although the capsule has been shown to modulate S. aureus adherence to endothelial surfaces in vitro, animal studies suggest that it also promotes bacterial colonization and persistence on mucosal surfaces. S. aureus capsular antigens are surface associated, limited in antigenic specificity, and highly conserved among clinical isolates. With the emergence of vancomycin-resistant S. aureus in the United States in 2002, new strategies are needed to combat staphylococcal infections. Purified serotype 5 and 8 capsular polysaccharides offer promise as target antigens for a vaccine to prevent staphylococcal infections, although the inclusion of other antigens is likely to be essential in the development of an effective S. aureus vaccine. The genetics and mechanisms of capsule biosynthesis are complex, and much work remains to enhance our understanding of capsule biosynthesis and its regulation.
Circulating levels of interleukin 1 beta and of interleukin 1 receptor antagonist in systemic juvenile chronic arthritis. (1995)

To measure circulating interleukin 1 beta (IL-1 beta) and IL-1 receptor antagonist (IL-1Ra) levels in patients with systemic juvenile chronic arthritis (JCA) and to evaluate their correlation with disease activity.IL-1 beta and IL-1Ra levels were measured by ELISA in 45 patients with JCA (20 systemic, 10 polyarticular and 15 pauciarticular) and in 15 healthy controls.Plasma IL-1 beta levels were undetectable in the majority of patients with systemic JCA, and detectable levels were not associated with different treatments or with parameters of disease severity. Serum IL-1Ra levels were markedly increased in patients with systemic JCA and significantly correlated with the persistence of systemic features, the extent and severity of joint involvement, and with C-reactive protein concentrations. Serum IL-1Ra levels were also significantly correlated with IL-6 levels.These results argue against a relevant role of IL-1 in systemic JCA. The increase in IL-1Ra levels does not appear to reflect an increase in IL-1 production, but may rather be induced by IL-6.
Soluble expression and one-step purification of recombinant bacillus anthracis protective antigen (1998)

Abstract: We have greatly simplified production of the Bacillus anthracis protective antigen (PA), the immunoprotective antigen of the anthrax vaccine. By varying induction conditions, we have expressed stable, soluble PA in E. coli, affinity-tagged to facilitate rapid, single-step purification. Recombinant PA exhibited identical properties to B. anthracis PA. Our approach is an attractive strategy for generating purified vaccine antigens that are difficult to express recombinantly.
Augmented acetylcholine‐induced, Rho‐mediated Ca2+ sensitization of bronchial smooth muscle contraction in antigen‐induced airway hyperresponsive rats (1999)

Treatment with acetylcholine (ACh) of a beta-escin-permeabilized intrapulmonary bronchial smooth muscle of the rat induced force when the Ca2+ concentration was clamped at 1 microM. The ACh-induced Ca2+ sensitization of myofilaments was significantly greater in antigen-induced airway hyperresponsive rats than in control rats. The ACh-induced Ca2+ sensitization was completely blocked by treatment with Clostridium botulinum C3 exoenzyme, an inactivator of Rho family of proteins. Moreover, the protein level of RhoA in the intrapulmonary bronchi was significantly increased in the airway hyperresponsive rats. Thus, increased airway smooth muscle contractility observed in asthmatics may be related to augmented agonist-induced, Rho-mediated Ca2+ sensitization of myofilaments.
The role of activated cytotoxic T cells in inflammatory bowel disease. (2000)

The role of cell-mediated cytotoxicity in the pathogenesis of ulcerative colitis and Crohn's disease has been controversial since reports indicating either a decreased, or an increased, activity of cytotoxic T cells in active stages of inflammatory bowel disease exist. Some of these discrepancies may be attributed to the fact that so far mostly peripheral blood lymphocytes rather than intestinal T cells have been examined. To overcome some of these limitations we performed in situ hybridizations for the detection of perforin and granzyme A mRNA expressing cells, i.e. of cytotoxic cells activated in situ, in the affected intestinal mucosa. These studies revealed increased frequencies of activated, cytotoxic T cells in active stages of ulcerative colitis and Crohn's disease. Interestingly, activated perforin mRNA expressing T cells are present both in the CD4 and in the CD8 T cell subsets. In the latter T cell subset up to 60% of the mucosal T cells isolated from the affected sites express perforin mRNA at detectable levels. The elevated frequency of activated cytotoxic cells and their histological distribution also in close proximity to the epithelial cells may thus indicate an important role for cytotoxic cells in the pathogenesis of inflammatory bowel disease since activated cytotoxic T cells may further exacerbate the inflammatory process through the production of pro-inflammatory cytokines such as interferon-gamma or tumor necrosis factor-alpha, but also through the release of pro-inflammatory cytokines and chemokines upon lysis of epithelial cells and the increased influx of luminal antigens at the site of epithelial erosions.
A HaemAtlas: characterizing gene expression in differentiated human blood cells (2009)

Hematopoiesis is a carefully controlled process that is regulated by complex networks of transcription factors that are, in part, controlled by signals resulting from ligand binding to cell-surface receptors. To further understand hematopoiesis, we have compared gene expression profiles of human erythroblasts, megakaryocytes, B cells, cytotoxic and helper T cells, natural killer cells, granulocytes, and monocytes using whole genome microarrays. A bioinformatics analysis of these data was performed focusing on transcription factors, immunoglobulin superfamily members, and lineage-specific transcripts. We observed that the numbers of lineage-specific genes varies by 2 orders of magnitude, ranging from 5 for cytotoxic T cells to 878 for granulocytes. In addition, we have identified novel coexpression patterns for key transcription factors involved in hematopoiesis (eg, GATA3-GFI1 and GATA2-KLF1). This study represents the most comprehensive analysis of gene expression in hematopoietic cells to date and has identified genes that play key roles in lineage commitment and cell function. The data, which are freely accessible, will be invaluable for future studies on hematopoiesis and the role of specific genes and will also aid the understanding of the recent genome-wide association studies.
Surface plasmon resonance imaging‐based protein arrays for high‐throughput screening of protein‐protein interaction inhibitors (2005)

The E7 protein produced by high-risk human papillomavirus (HPV) induces a degradation of the retinoblastoma tumor suppressor RB through direct interaction, which suggests that an inhibitor for the interaction can be a potential anticancer drug. A surface plasmon resonance (SPR) imaging-based protein array chip was developed for the high-throughput screening of inhibitor molecules targeting RB-E7 interaction. The glutathione S-transferase-fused E7 protein (GST-E7) was first layered onto a glutathionylated gold chip surface that had been designed to specifically bind to GST-fused proteins. Subsequently, a microarrayer was used to spot the hexa-histidine-tagged RB proteins (His(6)-RB) onto the GST-E7-layered gold chip surface, and the resulting SPR image was analyzed. Upon increased His(6)-RB concentration in the spotting solution, the SPR signal intensity increased proportionally, indicating that His(6)-RB bound to GST-E7 in a concentration-dependent manner. The His(6)-RB/GST-E7 interaction was challenged by spotting the His(6)-RB solution in the presence of a RB binding peptide (PepC) derived from a motif on E7. The SPR imaging data showed that PepC inhibited the His(6)-RB/GST-E7 interaction in a concentration-dependent manner. Our results show that the SPR imaging-based protein array chip can be applied to screen small molecule inhibitors that target protein-protein interaction.
Circulating Tumor Cells (2013)

Much remains to be learned about CTCs and their clinical potential as biomarkers and therapeutic targets.
Alpha-2 adrenoceptor agonist protects retinal function after acute retinal ischemic injury in the rat (2002)

Alpha-2 adrenoceptor agonists have previously been shown to enhance neuronal survival in an optic nerve mechanical injury model and to protect photoreceptors in a light-induced degeneration model. The purpose of this study was to examine the effect of the alpha-2 adrenoceptor agonist in a pressure-induced retinal ischemia model. Brown-Norway rats were treated systemically or topically with alpha-2 adrenoceptor specific agonist brimonidine. Retinal ischemia was induced by increasing the intraocular pressure to 110 mm Hg for 50 min. The effect of brimonidine on retinal ischemic injury was functionally assessed in the rats 7 d later using electroretinography (ERG). Ischemia-induced retinal cell death was studied using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) staining. We found that brimonidine treatment significantly protected the retina from retinal ischemic injury in a dose- and time-dependent manner. This protection can be achieved either by systemic or topical application and can be blocked by pretreatment with the alpha-2 adrenoceptor antagonist, yohimbine. Using reverse transcription-polymerase chain reaction (RT-PCR) and Western blot analysis, we found that brimonidine can up-regulate the expression of basic fibroblast growth factor, bcl-2 and bcl-xl in the retina. The drug also can activate two major cell survival signaling pathways in the retina: the extracellular-signal-regulated kinases (ERKs) and phosphatidylinositol-3' kinase/protein kinase Akt pathways. All these aforementioned factors may potentially contribute in mediating brimonidine's protective effect in this acute retinal ischemia model.