gebhart/patrepeval huggingface dataset:
Mutated tumor alleles are expressed according to their DNA frequency (2014)

The transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency.
Sorption and diffusion in ethyl cellulose. Part III. Comparison between ethyl cellulose and rubber (1958)

Abstract Sorption and diffusion of C 4 and C 5 hydrocarbons have been studied in thin films of ethyl cellulose in the temperature range 30 to 80°C. Only regions of low penetrant concentration were chosen in order to minimize hysteresis effects associated with slow relaxation of polymer chains. The data have been quantitatively compared with those for the same penetrants in rubber, since ethyl cellulose and rubber are examples of stiff and flexible chain polymers, respectively. In both solution and diffusion some major differences were found between the two types of medium. In rubber the heats of dilution were small and the corresponding positive entropies close to those predicted by the lattice theory of solutions. On the other hand, in ethyl cellulose at low penetrant concentrations the heats of dilution were strongly exothermal and the entropies negative. For both polymers diffusion coefficients of penetrants were dependent upon concentration, but whereas in rubber this concentration dependent decreased rapidly with rising temperature, in ethyl cellulose it was largely independent of temperature. Energy barriers involved in each unit diffusion process were comparable for a given hydrocarbon in rubber and in ethyl cellulose, while the molecular shape of the penetrant molecule substantially influenced the diffusion coefficients in each polymer. Further interpretation of the diffusion coefficients suggested that the involvement of polymer chains in each unit diffusion is much less for ethyl cellulose than for rubber. Explanations are offered, based upon the nature of the chains composing the two media and upon the existence of holes in the ethyl cellulose network, for the essential differences indicated above. The relative efficiency of ethyl cellulose and rubber membranes for gas separation is discussed.
Nanostructured polystyrene films engineered by plasma processes: Surface characterization and stem cell interaction (2014)

ABSTRACT In this work we showed the promising perspectives offered by the radiofrequency plasma processes on polymeric substrates. Polystyrene (PS) films with micropatterned grooves and nanostructured roughness were developed by Oxygen plasma treatment coupled with mask, and t process parameters, as power supply and treatment time were modulated. Then, hydrogenated amorphous carbon (a‐C:H) coatings (∼30 nm thickness) were deposited by methane radiofrequency plasma enhanced chemical vapor deposition (rf‐PECVD) on the polymer surface. Oxygen modified PS surface showed improved wettability, roughness and etching rate by increasing the power supply and the treatment time. Uniform and patterned bi‐layer films show a regular surface morphology, uniform chemical properties, with a contact angle to water of 77°, a surface energy of 51.15 mN m −1 and good stability in physiological conditions. Nanoindentation measurements revealed a decrease of the bi‐layer friction coefficient from 0.76 of PS to 0.17, highlighting the improvement of the nanomechanical properties of the novel developed system. Interaction with human bone‐marrow mesenchymal stem cells demonstrates that uniform and patterned PS based films are biocompatible surfaces and remarkable, that groove patterned substrates induce stem cell alignment and elongation. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131 , 40427.
An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences (1982)

This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is displayed on a simple graphics terminal. Use of a graphics terminal allows the user to display the whole of the two sequences in one screenful or to home-in on regions of interest to examine them in more detail. The program is interactive and so the user can easily see the effect of changes to variables and can use inbuilt editing functions to make insertions to produce alignments of the two sequences. These aligned sequences can then be saved on disk files for further processing.
A Multiagent Swarming System for Distributed Automatic Target Recognition Using Unmanned Aerial Vehicles (2008)

Over the past few years, automatic target recognition (ATR) has emerged as an essential image analysis tool to identify objects from temporally and spatially disjoint possibly noisy image data. For many current applications, ATR is performed by unmanned aerial vehicles (UAVs) that fly within a reconnaissance area to collect image data through sensors and upload the data to a central ground control station for analyzing and identifying potential targets. The centralized approach to ATR introduces several problems, including scalability with the number of UAVs, network delays in communicating with the central location, and the susceptibility of the system to malicious attacks on the central location. These challenges can be addressed by using a distributed system for performing ATR. In this paper, we describe a multiagent-based prototype system that uses swarming techniques inspired from insect colonies to perform ATR using UAVs in a distributed manner within simulated scenarios. We assume that UAVs are constrained in the resources available onboard and in their capabilities for performing ATR due to payload limitations. Our focus in this paper is on the coordination aspects between UAVs to efficiently decide how they are to act by using a swarming mechanism. We describe algorithms for the different operations performed by the UAVs in the system and for different swarming strategies, which are embedded within software agents located on the UAVs. We provide empirical simulations of our system within a simulated area of interest to determine its behavior in different scenarios with varying operational constraints. Our experimental results indicate that swarming strategies for distributed ATR perform favorably compared with centralized ATR strategies.
Rational Expectations, Information Acquisition, and Competitive Bidding (1981)

Most rational expectations market equilibrium models are not models of price formation, and naive mechanisms leading to such equilibria can be severely manipulable. In this paper, a bidding model is developed which has the market-like features that bidders act as price takers and that prices convey information. Higher equilibrium prices convey more favorable information about the quality of the objects being sold than do lower prices. Bidders can benefit from trading only if they have a transactions motive or if they have access to inside information. Apart from exceptional cases, prices are not fully revealing. A two stage model is developed in which bidders may acquire information at a cost before bidding and for which the equilibrium price is fully revealing, resolving a well-known paradox.
Effects of ligand activation of peroxisome proliferator-activated receptor γ in human prostate cancer (2000)

Peroxisome proliferator-activated receptor gamma (PPARgamma) is a nuclear hormone receptor that plays a key role in the differentiation of adipocytes. Activation of this receptor in liposarcomas and breast and colon cancer cells also induces cell growth inhibition and differentiation. In the present study, we show that PPARgamma is expressed in human prostate adenocarcinomas and cell lines derived from these tumors. Activation of this receptor with specific ligands exerts an inhibitory effect on the growth of prostate cancer cell lines. Further, we show that prostate cancer and cell lines do not have intragenic mutations in the PPARgamma gene, although 40% of the informative tumors have hemizygous deletions of this gene. Based on our preclinical data, we conducted a phase II clinical study in patients with advanced prostate cancer using troglitazone, a PPARgamma ligand used for the treatment of type 2 diabetes. Forty-one men with histologically confirmed prostate cancer and no symptomatic metastatic disease were treated orally with troglitazone. An unexpectedly high incidence of prolonged stabilization of prostate-specific antigen was seen in patients treated with troglitazone. In addition, one patient had a dramatic decrease in serum prostate-specific antigen to nearly undetectable levels. These data suggest that PPARgamma may serve as a biological modifier in human prostate cancer and its therapeutic potential in this disease should be further investigated.
Expression of vascular endothelial growth factors A, B, C, and D and their relationships to lymph node status in lung adenocarcinoma. (2000)

Vascular endothelial growth factors (VEGFs) C and D are novel members of the VEGF family that show some selectivity toward lymphatic endothelial cells. Recent studies suggest that VEGF-C may be involved in lymphangiogenesis and spread of cancer cells via lymphatic vessels. However, whether other VEGF family members play a role in lymph node metastasis is largely unknown. The aim of the present study was to explore whether expressions of VEGF-A, VEGF-B, VEGF-C, and VEGF-D are correlated with lymph node status in lung adenocarcinoma. Total RNA was isolated from 60 surgical specimens of lung adenocarcinoma with (n = 27) or without (n = 33) lymph node metastasis. The relative mRNA abundance of VEGF-A, VEGF-B, VEGF-C, and VEGF-D was measured by real-time reverse transcription-PCR analysis based on TaqMan fluorescence methodology. We found that, as single factors, expression of none of the four VEGF family members clearly correlated with the presence of lymph node metastasis. The only tendency noted was for higher VEGF-B and VEGF-C and lower VEGF-D levels in the node-positive group. However, two-way scatterplot analysis revealed that tumors with lymph node metastasis were associated with a pattern of low VEGF-D and high VEGF-A, VEGF-B, or VEGF-C, such that the ratios of VEGF-D:VEGF-A, VEGF-D:VEGF-B, or VEGF-D:VEGF-C were significantly lower in the node-positive group. Strikingly, none of the 11 tumors with high VEGF-D levels metastasized to lymph nodes. Furthermore, a low VEGF-D:VEGF-C ratio correlated with the presence of lymphatic invasion, and six of seven tumors with a pattern of very high expression of VEGF-C and low expression of VEGF-D displayed lymph vessel invasion that extended along the bronchovascular tree beyond the main tumor. Finally, levels of VEGF-A, but not VEGF-B or VEGF-C, were higher in tumors with large nodal metastasis (> or = 1 cm) than in those with small (< 1 cm) nodal metastasis. These results support the hypothesis that two VEGF family members are involved in lymph node metastasis at two distinct steps; VEGF-C facilitates entry of cancer cells into the lymph vasculature, whereas VEGF-A promotes the growth of metastatic tumor through angiogenesis. The results also suggest that the balance between VEGF-C and VEGF-D could be important rather than the level of VEGF-C alone. Whether a low VEGF-D level plays a causative role in lymph node metastasis requires further investigation.
Ecology and Metabolism of Plant Lipids (1987)

Lipids are distinguished by their high solubility in non-polar organic solvents and their low solubility in water. Lipids can be classified as derivatives of fatty acids or other compounds not containing a fatty acid moiety. Quantitatively, the acyl glycerides, polar and non-polar, make up the bulk of plant lipids. These include the neutral triglycerides, found in seed storage lipids, and the polar acyl glycerides such as the phosphatides, glycolipids and sulfolipids. There are a variety of non-glyceride lipids which embrace waxes, sterols, terpenes and their derivatives, hydrocarbons, and even some phenolics. Many organisms do not synthesize all their required lipids de novo, but obtain them from other species. Some plants are able to synthesize lipids which modify behavior in and help to protect against pests and pathogenic organisms. Hence, a variety of interactions have evolved which are the subject matter of this volume.
Molecular Epidemiology of Pneumococcal Colonization in Response to Pneumococcal Conjugate Vaccination in Children with Recurrent Acute Otitis Media (2005)

A randomized double-blind trial with a 7-valent pneumococcal conjugate vaccine was conducted in The Netherlands among 383 children, aged 1 to 7 years, with a history of recurrent acute otitis media. No effect of vaccination on the pneumococcal colonization rate was found. However, a shift in serotype distribution was clearly observed (R. Veenhoven et al., Lancet 361:2189-2195, 2003). We investigated the molecular epidemiology of 921 pneumococcal isolates retrieved from both the pneumococcal vaccine (PV) and control vaccine (CV) groups during the vaccination study. Within individuals a high turnover rate of pneumococcal restriction fragment end labeling genotypes, which was unaffected by vaccination, was observed. Comparison of the genetic structures before and after completion of the vaccination scheme revealed that, despite a shift in serotypes, there was clustering of 70% of the pneumococcal populations. The remaining isolates (30%) were equally observed in the PV and CV groups. In addition, the degree of genetic clustering was unaffected by vaccination. However, within the population genetic structure, nonvaccine serotype clusters with the serotypes 11, 15, and 23B became predominant over vaccine-type clusters after vaccination. Finally, overall pneumococcal resistance was low (14%), and, albeit not significant, a reduction in pneumococcal resistance as a result of pneumococcal vaccination was observed. Molecular surveillance of colonization in Dutch children shows no effect of pneumococcal conjugate vaccination on the degree of genetic clustering and the genetic structure of the pneumococcal population. However, within the genetic pneumococcal population structure, a clear shift toward nonvaccine serotype clusters was observed.
Enzyme catalysis in water pools (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzyme catalysis in water poolsF. M. Menger and K. YamadaCite this: J. Am. Chem. Soc. 1979, 101, 22, 6731–6734Publication Date (Print):October 1, 1979Publication History Published online1 May 2002Published inissue 1 October 1979https://pubs.acs.org/doi/10.1021/ja00516a039https://doi.org/10.1021/ja00516a039research-articleACS PublicationsRequest reuse permissionsArticle Views436Altmetric-Citations241LEARN 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-Alertsclose Get e-Alerts
Optical coherence and Doppler tomography for monitoring tissue changes induced by laser thermal therapy—An in vivo feasibility study (2003)

A high-speed optical coherence and Doppler tomography system suitable for real-time monitoring of the microstructural and microvascular tissue changes induced by laser thermal therapy is described. The performance of the system is demonstrated experimentally in vivo by noting the morphological change, manifest as an increase in the optical extinction coefficient, and the reduction in the blood flow during and after laser thermal therapy in an animal model.
Peripheral Mechanisms of Neuropathic Pain — Involvement of Lysophosphatidic Acid Receptor-Mediated Demyelination (2008)

Recent advances in pain research provide a clear picture for the molecular mechanisms of acute pain; substantial information concerning plasticity that occurs during neuropathic pain has also become available. The peripheral mechanisms responsible for neuropathic pain are found in the altered gene/protein expression of primary sensory neurons. With damage to peripheral sensory fibers, a variety of changes in pain-related gene expression take place in dorsal root ganglion neurons. These changes, or plasticity, might underlie unique neuropathic pain-specific phenotype modifications - decreased unmyelinated-fiber functions, but increased myelinated A-fiber functions. Another characteristic change is observed in allodynia, the functional change of tactile to nociceptive perception. Throughout a series of studies, using novel nociceptive tests to characterize sensory-fiber or pain modality-specific nociceptive behaviors, it was demonstrated that communication between innocuous and noxious sensory fibers might play a role in allodynia mechanisms. Because neuropathic pain in peripheral and central demyelinating diseases develops as a result of aberrant myelination in experimental animals, demyelination seems to be a key mechanism of plasticity in neuropathic pain. More recently, we discovered that lysophosphatidic acid receptor activation initiates neuropathic pain, as well as possible peripheral mechanism of demyelination after nerve injury. These results lead to further hypotheses of physical communication between innocuous Abeta- and noxious C- or Adelta-fibers to influence the molecular mechanisms of allodynia.
The Integrin-Extracellular Matrix Axis in Pancreatic Cancer (2007)

Pancreatic cancer is the fifth leading cause of adult cancer death in the United States, with 5-year survival rates of only 1% to 4%. Current therapeutic strategies generally result in only a few months of extended life. Recent evidence from several independent laboratories in vitro and in vivo indicate that integrin-mediated cell attachment to the extracellular matrix (ECM), components of which are highly up-regulated in pancreatic cancer, evokes phenotypes and signaling pathways that regulate tumor cell growth and migration. In this review, we will discuss our current understanding of the role of the ECM in directing pancreatic cancer growth, progression, and metastasis. Topics covered include a survey of the existing literature regarding the in vivo and in vitro expression of the ECM and its cell surface receptors, the integrins, in pancreatic cancer; mechanisms involved in the integrin-ECM-mediated malignant phenotype; and future directions for the study of the integrin-ECM axis and its role in pancreatic cancer progression, including potential therapeutic strategies.
DNA methylation biomarkers of prostate cancer: Confirmation of candidates and evidence urine is the most sensitive body fluid for non‐invasive detection (2009)

Analysis of the biomarkers in urine DNA significantly discriminated PCa from biopsy negative patients. The biomarkers provided information independent of PSA and may warrant inclusion in nomograms for predicting prostate biopsy outcome. The biomarkers' PCa sensitivity was greater for urine than plasma DNA. The biomarker performances in urine DNA should next be validated in formal training and test studies.
Managing trust between collaborating companies using outsourced role based access control (1999)

In this document we describe an approach for modelling large organisations applying an RBAC-schema to control access to remote services of the organisation.
Role of the Tau N-terminal region in microtubule stabilization revealed by newendogenous truncated forms (2015)

Tau is a central player in Alzheimer's disease (AD) and related Tauopathies, where it is found as aggregates in degenerating neurons. Abnormal post-translational modifications, such as truncation, are likely involved in the pathological process. A major step forward in understanding the role of Tau truncation would be to identify the precise cleavage sites of the several truncated Tau fragments that are observed until now in AD brains, especially those truncated at the N-terminus, which are less characterized than those truncated at the C-terminus. Here, we optimized a proteomics approach and succeeded in identifying a number of new N-terminally truncated Tau species from the human brain. We initiated cell-based functional studies by analyzing the biochemical characteristics of two N-terminally truncated Tau species starting at residues Met11 and Gln124 respectively. Our results show, interestingly, that the Gln124-Tau fragment displays a stronger ability to bind and stabilize microtubules, suggesting that the Tau N-terminal domain could play a direct role in the regulation of microtubule stabilization. Future studies based on our new N-terminally truncated-Tau species should improve our knowledge of the role of truncation in Tau biology as well as in the AD pathological process.
Crystallization and preliminary X-ray crystallographic analysis of Ca2+-independent and Ca2+-dependent species of the type II antifreeze protein (2006)

Ca2+-independent and Ca2+-dependent species of the type II antifreeze protein (AFP) were both crystallized using the hanging-drop vapour-diffusion method. It appeared that the crystal of the Ca2+-independent species from Brachyosis rostratus belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 43.3, b = 48.4, c = 59.7 A, and diffraction data were collected to 1.34 A resolution. For the Ca2+-dependent type II AFP species from Hypomesus nipponensis, crystallization was carried out for its Ca2+-free and Ca2+-bound states. 1.25 A resolution data were collected from the crystal in the Ca(2+)-free state, which exhibited P3(1)21 (or P3(2)21) symmetry, with unit-cell parameters a = b = 66.0, c = 50.3 A. Data collection could be extended to 1.06 A resolution for the crystal in the Ca2+ -bound state, which appeared to be isomorphous to the crystal in the Ca2+-free state (unit-cell parameters a = b = 66.0, c = 49.8 A). These data will allow us to determine the high-resolution structures of the two species of type II AFP.