gebhart/patrepeval huggingface dataset:
Lexical Chains and Sliding Locality Windows in Content-based Text Similarity Detection (2005)

We present a system to determine content similarity of documents. More specifi-cally, our goal is to identify book chapters that are translations of the same original chapter; this task requires identification of not only the different topics in the docu-ments but also the particular flow of these topics. We experiment with different rep-resentations employing n-grams of lexical chains and test these representations on a corpus of approximately 1000 chapters gathered from books with multiple paral-lel translations. Our representations in-clude the cosine similarity of attribute vectors of n-grams of lexical chains, the cosine similarity of tf*idf-weighted key-words, and the cosine similarity of un-weighted lexical chains (unigrams of lexical chains) as well as multiplicative combinations of the similarity measures produced by these approaches. Our results identify fourgrams of unordered lexical chains as a particularly useful representa-tion for text similarity evaluation. 1
High Capacity Poly(ethylene glycol) Based Amino Polymers for Peptide and Organic Synthesis (2004)

Abstract A beaded, chemically stable, high capacity amino resin for solid phase synthesis under polar and non‐polar conditions is described. By exhaustive reduction of amide carbonyl groups in PEG cross linked poly(ethylene glycol)‐poly(acrylamide) copolymer (PEGA) a significant increase in functional amino groups is obtained. Furthermore, a resin containing 90% PEG which is free of amide carbonyl groups is produced. The polymer was characterized by IR spectroscopy and the macroscopic properties of the beads were analyzed by microscopy. Excellent swelling properties in various solvents ranging from water to DCM were demonstrated. The chemical stability of the polymer in various reagents and solvents was investigated and changes in resin properties monitored by IR spectroscopy. The mechanical stability of the resin was analyzed by measurement of compressive strain. The unique three dimensional structure of the swelled polyethylene glycol network facilitate fast and unhindered diffusion of reagents and the support is excellent for synthesis of peptides or peptide mimetics, which can be produced in high yield/reaction volume. The efficacy of the new resin in solid phase synthesis was demonstrated by synthesizing an α‐MSH peptide fragment. A cyclic peptide mimetic was also synthesized on the new resin by the Cu (1) catalyzed intra molecular cyclo addition of alkyne and azide to form a triazole acting as a disulphide mimetic entity in very high yield and purity.
Efficacy of desciclovir in the treatment of Epstein-Barr virus infection in oral hairy leukoplakia. (1990)

The efficacy of desciclovir, an analog of acyclovir, in eliminating lesions of oral hairy leukoplakia (HL) and suppressing Epstein-Barr virus (EBV) infection was evaluated in a double-blind, placebo-controlled study of 14 patients. Patients were randomized to receive either the active drug, 250 mg three times a day for 14 days, or placebo. In all eight patients receiving desciclovir, lesions of HL were either completely resolved or significantly reduced during the treatment period, whereas lesions in patients receiving placebo showed no change. The histological features of HL were significantly diminished in patients on desciclovir, and cytochemical, in situ hybridization, and ultrastructural studies showed that EBV infection was eliminated or dramatically reduced in the desciclovir group only. Four patients on desciclovir reported side effects, but none required withdrawal from the study. The reappearance of HL in all eight subjects on desciclovir within 1-4 months after therapy was discontinued suggests the need for additional study.
Cardiac Aging: From Molecular Mechanisms to Significance in Human Health and Disease (2012)

Cardiovascular diseases (CVDs) are the major causes of death in the western world. The incidence of cardiovascular disease as well as the rate of cardiovascular mortality and morbidity increase exponentially in the elderly population, suggesting that age per se is a major risk factor of CVDs. The physiologic changes of human cardiac aging mainly include left ventricular hypertrophy, diastolic dysfunction, valvular degeneration, increased cardiac fibrosis, increased prevalence of atrial fibrillation, and decreased maximal exercise capacity. Many of these changes are closely recapitulated in animal models commonly used in an aging study, including rodents, flies, and monkeys. The application of genetically modified aged mice has provided direct evidence of several critical molecular mechanisms involved in cardiac aging, such as mitochondrial oxidative stress, insulin/insulin-like growth factor/PI3K pathway, adrenergic and renin angiotensin II signaling, and nutrient signaling pathways. This article also reviews the central role of mitochondrial oxidative stress in CVDs and the plausible mechanisms underlying the progression toward heart failure in the susceptible aging hearts. Finally, the understanding of the molecular mechanisms of cardiac aging may support the potential clinical application of several "anti-aging" strategies that treat CVDs and improve healthy cardiac aging.
Characterization of Interferon Messenger RNA from Human Lymphoblastoid Cells (1979)

After treatment with Sendai virus, Namalwa cells form large amounts of interferon. RNA extracted from treated whole cells or from their polysomes was injected into Xenopus laevis oocytes and the interferon formed was titrated. The results show that the amount of interferon mRNA was maximal by 9 h after treatment of the cells with Sendai virus and then declined. Sucrose gradient centrifugation of the mRNA gave substantial purification and showed that its size was 12 S.
Overlapping binding sites for the virulence gene regulators AphA, AphB and cAMP‐CRP at the Vibrio cholerae tcpPH promoter (2001)

The expression of the Vibrio cholerae virulence factors, toxin-co-regulated pilus (TCP) and cholera toxin (CT), are dependent on the ability of the LysR regulator AphB to co-operate with a second protein, AphA, to activate the expression of the membrane-bound transcription factors TcpP and TcpH. To gain insights into the mechanism by which AphA and AphB co-operate to activate the expression of tcpPH, we have purified these two proteins to near homogeneity and show that they are each capable of interacting with the classical tcpPH promoter at distinct binding sites. As shown by tcpP-lacZ promoter deletion experiments, gel shift and DNase I footprinting, AphA binds to and activates from a region of the promoter between -101 and -71 from the start of transcription. AphB binds to and activates from a partially overlapping downstream site between -78 and -43, and these functions are dependent upon a region of partial dyad symmetry that resembles the well-characterized LysR-binding motif. A single basepair difference in this region of dyad symmetry has been shown previously to play a critical role in the expression of virulence genes between the two disease-causing biotypes of V. cholerae, classical and El Tor. We also show here that the tcpPH promoter is negatively influenced by the global regulator cAMP-CRP. Purified CRP binds to a near-consensus sequence in the tcpPH promoter in a cAMP-dependent manner and protects from DNase I digestion a region that is completely within the region protected by AphA and AphB. These findings raise the possibility that the negative effect of cAMP-CRP on virulence gene expression is the result of its ability to influence AphA- and AphB-dependent transcriptional activation of tcpPH under various conditions.
In Vitro Activity of the Type II Anti-CD20 Antibody GA101 in Refractory, Genetic High-Risk CLL. (2009)

Abstract Abstract 2379 Poster Board II-356 Introduction: Anti-CD20 (i.e. rituximab) based immuno-chemotherapies are now considered standard of care in CLL. However, addition of rituximab does not appear to decisively alter the dismal clinical outcome for 17p- / TP53 mutated CLL. Relatively little is known about activity of different anti-CD20 antibodies in genetic subgroups of CLL. Methods: In an effort to assess the activity of the next generation mAb GA101 in vitro, we studied B cell depletion / apoptosis in a set of CLL patients. CLL samples were genetically characterized with respect to genetics (genomic aberrations, TP53 mutation, IGHV mutation status), as well as clinical course and immunophenotype. To study the effect on CLL cells, we assessed GA101, Rituximab and Alemtuzumab by in vitro treatment after ficoll separation with FACS (7-AAD) for viability. In addition, in order to maintain ADCC and to mirror the in vivo situation, we studied the effect of GA101 in a whole blood culture (n=10). Results: With increasing concentrations (0.01-100mg/ml) of GA101 we observed significant cell death as measured by a B cell depletion assay (whole blood) after GA101 exposure (n=10). After 3 hours the maximum effect was observed at a concentration of 10mg/ml with a reduction of CLL cells to 43% of untreated cells. The results after 8h were similar, again showing the profound effect in GA101 treated samples (mean B-cell depletion to 34.6% remaining cells). Interestingly, further increasing the dose to 100mg/ml did not increase the B-cell depletion by the antibody, but appeared to decrease the ability to deplete CLL cells (Fig. 1). In contrast treatment with control antibodies (isotype control, rituximab, alemtuzumab) did not lead to similar B-cell depletion (101%, 69%, and 73% of control cells at 3h). We were particularly interested in any potential effect in cases with TP53 mutation. While the sample number is still low (TP53 mutation / 17p deletion n=3), currently we have no indication of differential response in different genetic subgroups. Conclusion: Compared to the currently most widely used mAb in CLL (Rituximab), GA101 appears more potent at equivalent concentration in depleting CLL cells. Further in vitro studies are currently ongoing to assess this antibody in particular in genetic high-risk, refractory CLL. Disclosures: Zenz: Roche: Honoraria. Klein:Roche: Employment, Equity Ownership, Patents &amp; Royalties. Umana:Roche: Employment, Equity Ownership, Patents &amp; Royalties. Döhner:Roche: Research Funding. Stilgenbauer:Roche, Bayer Schering Pharma: Honoraria, Research Funding.
Low-Dose Adenovirus Vaccine Encoding Chimeric Hepatitis B Virus Surface Antigen-Human Papillomavirus Type 16 E7 Proteins Induces Enhanced E7-Specific Antibody and Cytotoxic T-Cell Responses (2005)

Induction of effective immune responses may help prevent cancer progression. Tumor-specific antigens, such as those of human papillomaviruses involved in cervical cancer, are targets with limited intrinsic immunogenicity. Here we show that immunization with low doses (10(6) infectious units/dose) of a recombinant human adenovirus type 5 encoding a fusion of the E7 oncoprotein of human papillomavirus type 16 to the carboxyl terminus of the surface antigen of hepatitis B virus (HBsAg) induces remarkable E7-specific humoral and cellular immune responses. The HBsAg/E7 fusion protein assembled efficiently into virus-like particles, which stimulated antibody responses against both carrier and foreign antigens, and evoked antigen-specific kill of an indicator cell population in vivo. Antibody and T-cell responses were significantly higher than those induced by a control adenovirus vector expressing wild-type E7. Such responses were not affected by preexisting immunity against either HBsAg or adenovirus. These data demonstrate that the presence of E7 on HBsAg particles does not interfere with particle secretion, as it occurs with bigger proteins fused to the C terminus of HBsAg, and results in enhancement of CD8(+)-mediated T-cell responses to E7. Thus, fusion to HBsAg is a convenient strategy for developing cervical cancer therapeutic vaccines, since it enhances the immunogenicity of E7 while turning it into an innocuous secreted fusion protein.
Body Iron Stores in Relation to Risk of Type 2 Diabetes in Apparently Healthy Women (2004)

Higher iron stores (reflected by an elevated ferritin concentration and a lower ratio of transferrin receptors to ferritin) are associated with an increased risk of type 2 diabetes in healthy women independent of known diabetes risk factors.
Extracellular melibiose and fructose are intermediates in raffinose catabolism during fermentation to ethanol by engineered enteric bacteria (1997)

Contrary to general concepts of bacterial saccharide metabolism, melibiose (25 to 32 g/liter) and fructose (5 to 14 g/liter) accumulated as extracellular intermediates during the catabolism of raffinose (O-alpha-D-galactopyranosyl-1, 6-alpha-D-glucopyranosyl-beta-D-fructofuranoside) (90 g/liter) by ethanologenic recombinants of Escherichia coli B, Klebsiella oxytoca M5A1, and Erwinia chrysanthemi EC16. Both hydrolysis products (melibiose and fructose) were subsequently transported and further metabolized by all three organisms. Raffinose catabolism was initiated by beta-fructosidase; melibiose was subsequently hydrolyzed to galactose and glucose by alpha-galactosidase. Glucose and fructose were completely metabolized by all three organisms, but galactose accumulated in the fermentation broth with EC16(pLOI555) and P2. MM2 (a raffinose-positive E. coli mutant) was the most effective biocatalyst for ethanol production (38 g/liter) from raffinose. All organisms rapidly fermented sucrose (90 g/liter) to ethanol (48 g/liter) at more than 90% of the theoretical yield. During sucrose catabolism, both hydrolysis products (glucose and fructose) were metabolized concurrently by EC16(pLOI555) and P2 without sugar leakage. However, fructose accumulated extracellularly (27 to 28 g/liter) at early stages of fermentation with KO11 and MM2. Sequential utilization of glucose and fructose correlated with a diauxie in base utilization (pH maintenance). The mechanism of sugar escape remains unknown but may involve downhill leakage via permease which transports precursor saccharides or novel sugar export proteins. If sugar escape occurs in nature with wild organisms, it could facilitate the development of complex bacterial communities which are based on the sequence of saccharide catabolism and the hierarchy of sugar utilization.
Serum Anti-BPAG1 Auto-Antibody Is a Novel Marker for Human Melanoma (2010)

Malignant melanoma is one of the most aggressive types of tumor. Because malignant melanoma is difficult to treat once it has metastasized, early detection and treatment are essential. The search for reliable biomarkers of early-stage melanoma, therefore, has received much attention. By using a novel method of screening tumor antigens and their auto-antibodies, we identified bullous pemphigoid antigen 1 (BPAG1) as a melanoma antigen recognized by its auto-antibody. BPAG1 is an auto-antigen in the skin disease bullous pemphigoid (BP) and anti-BPAG1 auto-antibodies are detectable in sera from BP patients and are used for BP diagnosis. However, BPAG1 has been viewed as predominantly a keratinocyte-associated protein and a relationship between BPAG1 expression and melanoma has not been previously reported. In the present study, we show that bpag1 is expressed in the mouse F10 melanoma cell line in vitro and F10 melanoma tumors in vivo and that BPAG1 is expressed in human melanoma cell lines (A375 and G361) and normal human melanocytes. Moreover, the levels of anti-BPAG1 auto-antibodies in the sera of melanoma patients were significantly higher than in the sera of healthy volunteers (p<0.01). Furthermore, anti-BPAG1 auto-antibodies were detected in melanoma patients at both early and advanced stages of disease. Here, we report anti-BPAG1 auto-antibodies as a promising marker for the diagnosis of melanoma, and we discuss the significance of the detection of such auto-antibodies in cancer biology and patients.
Electrical current distribution across a metal–insulator–metal structure during bistable switching (2001)

Combining scanning electron microscopy and electron-beam-induced current imaging with transport measurements, it is shown that the current flowing across a two-terminal oxide-based capacitor-like structure is preferentially confined in areas localized at defects. As the thin-film device switches between two different resistance states, the distribution and intensity of the current paths, appearing as bright spots, change. This implies that switching and memory effects are mainly determined by the conducting properties along such paths. A model based on the storage and release of charge carriers within the insulator seems adequate to explain the observed memory effect.
Interaction of mouse sperm with purified sperm receptors covalently linked to silica beads (1989)

We describe a solid-phase assay that has permitted further analysis of zona pellucida glycoprotein, ZP3, as sperm receptor and acrosome reaction-inducer during fertilization in mice. The assay employs silica beads that contain epoxy groups to which purified, mouse oocyte ZP3 is covalently linked (ZP3-beads). ZP3-beads were characterized, e.g. by whole-mount autoradiography and flow cytofluorometry, incubated with capacitated mouse sperm under a variety of conditions, and the extent of sperm binding determined by light microscopy. Results of experiments presented suggest the following: (1) sperm bind specifically to ZP3-beads, but not to silica beads either exposed to 2-aminoethanol or derivatized with oocyte ZP2, fetuin or bovine serum albumin. (2) In nearly all cases, only one sperm binds per ZP3-bead and binding occurs via the sperm head. (3) The extent of sperm binding to ZP3-beads is dependent on ZP3 and sperm concentrations, as well as on incubation time and temperature. (4) Sperm binding to ZP3-beads is unaffected by antibodies directed against ZP3, but is inhibited in a reversible manner by treatment of ZP3-beads with galactose oxidase. (5) Only acrosome-intact sperm bind to ZP3-beads but, once bound, sperm can undergo the acrosome reaction, which results in their release from ZP3-beads. (6) Islet-activating protein and 3-quinuclidinyl benzilate, two inhibitors of the zona pellucida-induced acrosome reaction, prevent sperm bound to ZP3-beads from undergoing the acrosome reaction. These results confirm and extend previous studies of sperm-egg interaction in mice, and suggest that the solid-phase assay will be useful for both cellular and biochemical analyses of mammalian fertilization.
Interactive Deep Colorization With Simultaneous Global and Local Inputs (2018)

Colorization methods using deep neural networks have become a recent trend. However, most of them do not allow user inputs, or only allow limited user inputs (only global inputs or only local inputs), to control the output colorful images. The possible reason is that it's difficult to differentiate the influence of different kind of user inputs in network training. To solve this problem, we present a novel deep colorization method, which allows simultaneous global and local inputs to better control the output colorized images. The key step is to design an appropriate loss function that can differentiate the influence of input data, global inputs and local inputs. With this design, our method accepts no inputs, or global inputs, or local inputs, or both global and local inputs, which is not supported in previous deep colorization methods. In addition, we propose a global color theme recommendation system to help users determine global inputs. Experimental results shows that our methods can better control the colorized images and generate state-of-art results.
Pexelizumab: A novel therapy for mycardial ischemia-reperfusion (2005)

Despite significant advances in the study of myocardial reperfusion, patients with epicardial coronary reperfusion still have adverse clinical outcomes. This is in part due to an inflammatory reaction in the injured tissue. Inflamed myocardial tissue after ischemia and reperfusion releases several cytokines and toxic metabolites that lead to reperfusion injury and cellular apoptosis. Complement activation appears to mediate myocardial damage through both these pathways. Recently, pexelizumab, a novel C5 complement monoclonal antibody fragment, has been developed to prevent the complement-mediated myocardial damage from myocardial ischemia and reperfusion. In animal studies, pexelizumab decreased the amount of myocardial damage with ischemia and reperfusion. Pexelizumab has been studied in phase II and phase III clinical trials involving patients undergoing coronary artery bypass grafting and in patients with acute myocardial infarction as an adjunct to reperfusion therapy. Two large clinical trials are currently underway in coronary artery bypass surgery and acute myocardial infarction patients undergoing primary percutaneous revascularization. This review will cover the pathophysiological role of complement activation with regards to ischemia-reperfusion injury, the novel compound pexelizumab, and both the preclinical and clinical data for pexelizumab use in coronary artery bypass surgery and acute myocardial infarction patients.
Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens (2004)

The gastrointestinal tract is a complex ecosystem that associates a resident microbiota and cells of various phenotypes lining the epithelial wall expressing complex metabolic activities. The resident microbiota in the digestive tract is a heterogeneous microbial ecosystem containing up to 1 x 10(14) colony-forming units (CFUs) of bacteria. The intestinal microbiota plays an important role in normal gut function and maintaining host health. The host is protected from attack by potentially harmful microbial microorganisms by the physical and chemical barriers created by the gastrointestinal epithelium. The cells lining the gastrointestinal epithelium and the resident microbiota are two partners that properly and/or synergistically function to promote an efficient host system of defence. The gastrointestinal cells that make up the epithelium, provide a physical barrier that protects the host against the unwanted intrusion of microorganisms into the gastrointestinal microbiota, and against the penetration of harmful microorganisms which usurp the cellular molecules and signalling pathways of the host to become pathogenic. One of the basic physiological functions of the resident microbiota is that it functions as a microbial barrier against microbial pathogens. The mechanisms by which the species of the microbiota exert this barrier effect remain largely to be determined. There is increasing evidence that lactobacilli and bifidobacteria, which inhabit the gastrointestinal microbiota, develop antimicrobial activities that participate in the host's gastrointestinal system of defence. The objective of this review is to analyze the in vitro and in vivo experimental and clinical studies in which the antimicrobial activities of selected lactobacilli and bifidobacteria strains have been documented.
Depth Reconstruction Filter and Down/Up Sampling for Depth Coding in 3-D Video (2009)

A depth image represents three-dimensional (3-D) scene information and is commonly used for depth image-based rendering (DIBR) to support 3-D video and free-viewpoint video applications. The virtual view is generally rendered by the DIBR technique and its quality depends highly on the quality of depth image. Thus, efficient depth coding is crucial to realize the 3-D video system. In this letter, we propose a depth reconstruction filter and depth down/up sampling techniques to improve depth coding performance. Experimental results demonstrate that the proposed methods reduce the bit-rate for depth coding and achieve better rendering quality.