gebhart/patrepeval huggingface dataset:
Stimuli-Responsive Properties of Peptide-Based Copolymers Studied via Directional Growth of Self-Assembled Patterns on Solid Substrate (2009)

We studied the self-assembly of peptide-based ABA and CBC triblock-copolymers (obtained by bacterial expression) containing random coiled hydrophilic central B blocks flanked with helical A or C blocks. The A and C blocks were of different compositions with respect to the fraction of lysine residues which provided a higher pH sensitivity of the copolymer solutions. The interchain interactions of the copolymers driven by external stimuli (pH and temperature) were explored in the process of macromolecular self-assembling in the thin films of the copolymer solutions deposited on the solid substrate. The interactions involved in the macromolecular association affected the morphology of the developed patterns. The polypeptide of the B block was not involved in the formation of the secondary structures, while the A and C blocks demonstrated helical folding responsible for the intermolecular association. The mechanism of the responsive behavior of the copolymers is based on the reversible assembling of the helices into coiled-coil structures upon the change of pH or temperature. It was found that at low pH values, when electrostatic repulsion was strong and the A/C blocks unfolded, assembling yielded fractal dendrites. Increasing the pH resulted in the recovery of the helical conformation of the A/C blocks and caused a transition from the fractal to compact structures. An elevation of temperature resulted in the disruption of the dendritic structures. The reported here approach to the evaluation of the intermolecular interactions, based on the analysis of the dendritic patterns, provides a rapid and simple method for the characterization of complex processes of self-assembling biomacromolecules.
Using Formal Grammars to Predict I/O Behaviors in HPC: The Omnisc'IO Approach (2015)

The increasing gap between the computation performance of post-petascale machines and the performance of their I/O subsystem has motivated many I/O optimizations including prefetching, caching, and scheduling. In order to further improve these techniques, modeling and predicting spatial and temporal I/O patterns of HPC applications as they run has become crucial. In this paper we present Omnisc'IO, an approach that builds a grammar-based model of the I/O behavior of HPC applications and uses it to predict when future I/O operations will occur, and where and how much data will be accessed. To infer grammars, Omnisc'IO is based on StarSequitur, a novel algorithm extending Nevill-Manning's Sequitur algorithm. Omnisc'IO is transparently integrated into the POSIX and MPI I/O stacks and does not require any modification in applications or higher-level I/O libraries. It works without any prior knowledge of the application and converges to accurate predictions of any N future I/O operations within a couple of iterations. Its implementation is efficient in both computation time and memory footprint.
Digital Waveguide Mesh for Room Acoustic Modeling (2001)

The two main approaches for room acoustic modeling are the wave-based and the ray-based techniques. In this paper we briefly overview the digital waveguide mesh method which is a wave-based model operating in the time domain. As a case study we show visualizations of edge diffraction modeled with the waveguide mesh technique. Some preliminary analysis of computational requirements for real-time auralizations are also presented, and the idea of frequency domain hybrid model is revisited.
Genome-Wide Association Scan for Diabetic Nephropathy Susceptibility Genes in Type 1 Diabetes (2009)

We identified genetic associations for susceptibility to diabetic nephropathy at two novel candidate loci near the FRMD3 and CARS genes. Their identification implicates previously unsuspected pathways in the pathogenesis of this important late complication of type 1 diabetes.
A mechanism for persistently naming topological entities in history-based parametric solid models (1995)

Abstract One of the fundamental problems in history-based parametric solid modelling systems is to identify topological entities (faces, edges, vertices) of solid models in such a way that the same entities can still be identified after the models have been reevaluated from the sequential history of modelling steps. The Topological ID System, presented in this paper, systematically assigns IDs (names, labels) to topological entities in solid models. When the history of modelling steps is edited and then automatically re-evaluated to produce a new version of the solid model, the IDs of topological entities in the old version of the solid model are mapped to IDs of the corresponding topological entities in the new version of the solid model. This mapping defines the correspondence between topological entities in both models.
Multiwavelength fluorescence lifetime imaging by TCSPC (2006)

We present an approach which monitors both time- and spectral information of the fluorescence in order to receive the full information content of the light emitted from a sample. Our instrumentation covers a combination of the TCSPC technique extended by a multi-wavelength detection scheme. Based on the spectral properties of the participating chromophores their relative contributions to the fluorescence within each wavelength channel can be derived. This information serves as an additional parameter for the decay curve analysis which allows us to identify emission patterns for both lifetime and wavelength. Potential applications of the multi-wavelength TCSPC technique are FRET experiments, new marker techniques based on environment-dependent lifetime, and the separation of fluorophores in autofluorescence images of tissue.
Mechanisms of estrogen action on the proliferation of MCF-7 human breast cancer cells in an improved culture medium. (1989)

The effects of 17 beta-estradiol and tamoxifen (TAM) on the proliferation of responsive MCF-7 and unresponsive HBC-4 human breast cancer cells were studied in a defined culture medium containing insulin (2 micrograms/ml), transferrin (2 micrograms/ml), ethanolamine (2 microM), and selenite (25 nM). MCF-7 cells grew at a population-doubling rate of 2.0 days in serum-free medium and at a rate of 1.7 days in the medium containing 1 mg/ml of the 55-70% ammonium sulfate fraction of bovine serum or 1% dextrancoated charcoal-treated fetal bovine serum. Increasing concentrations of the ammonium sulfate fraction and/or dextran-coated charcoal-treated fetal bovine serum increasingly inhibited the growth of MCF-7 cells but did not inhibit HBC-4 cell growth, indicating that such serum preparations contain some growth inhibitor specific for estradiol-responsive MCF-7 cells. A sufficiently high concentration of exogenous estradiol (100 pM) had the dual action of neutralizing the growth inhibition by the 55-70% ammonium sulfate fraction of bovine serum and dextran-treated charcoal-treated fetal bovine: serum and enhancing directly the MCF-7 cell growth maximally 2-fold. Bovine serum albumin fraction V containing globulin remnants also inhibited growth, but globulin-free bovine serum albumin did not. Eliminating growth inhibition by the use of globulin-free bovine serum albumin enabled us to develop an ideal medium for assaying the direct effects of estradiol and TAM on MCF-7 cells. With this medium, we clearly identified (a) a direct mitogenic effect of exogenous estradiol on MCF-7 cells which was initiated at 3 pM and maximized at 0.2 to 10 nM, (b) an acute lethal effect of 1 microM TAM and its prevention by 100 pM estradiol, and (c) a nearly 50-fold increase in the concentration of exogenous estradiol (10 nM) required for maximum growth enhancement in the presence of 1 microM TAM than without TAM (0.2-0.3 nM).
Studies on the role of angiotensin in experimental renovascular hypertension: an immunologic approach (1969)

The role of angiotensin in three forms of experimental hypertension was assessed in rats. First, the acute blood pressure response to injected angiotensin amide and angiotensin acid was determined. Rats made hypertensive with deoxycorticosterone and saline showed exaggerated responses; rats made hypertensive by clipping one renal artery showed depressed responses; and rats made hypertensive by clipping one renal artery and contralateral nephrectomy showed normal responsivity to angiotensin amide but depressed responsivity to angiotensin acid. These findings suggested that different mechanisms may be involved in the three types of hypertension studied. To assess the role of angiotensin in these hypertensive rats the blood pressure response, the presence of antibodies determined by radioimmune techniques, and the degree of refractoriness to injected angiotensin after immunization with angiotensin were studied. None of six rats made hypertensive by deoxycorticosterone and saline, and none of five mock immunized rats with renal hypertension of both types had a fall in blood pressure. By contrast, of the 20 rats with both types of renal hypertension in which antibody determinations were made, 11 had developed a significant antibody titer, of which seven showed a significant reduction in blood pressure at the time of antibody determination, and three of the remaining four had a significant blood pressure reduction earlier in their course. None of the nine renal hypertensive rats without demonstrable antibodies had a reduced blood pressure at the time of antibody determination, and only one had an earlier reduction in blood pressure. The renal hypertensive rats were all refractory to injected angiotensin after immunization. These results suggest a primary role for angiotensin in both forms of renal hypertension.
Nucleotide sequence of a mutant acetolactate synthase gene from an imidazolinone-resistantArabidopsis thalianavar. Columbia (1990)

Journal Article Nucleotide sequence of a mutant acetolactate synthase gene from an imidazolinone-resistant Arabidopsis thaliana var. Columbia Get access Kanagasabapathi Sathasivan, Kanagasabapathi Sathasivan Search for other works by this author on: Oxford Academic PubMed Google Scholar George W. Haughn, George W. Haughn 1Department of Biology, University of SaskatchewanSaskatoon, S7N 0W0, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Norimoto Murai Norimoto Murai * * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 8, 25 April 1990, Page 2188, https://doi.org/10.1093/nar/18.8.2188 Published: 25 April 1990 Article history Received: 19 February 1990 Published: 25 April 1990
Protection against Nitric Oxide Toxicity by Tea (2000)

It is found that green tea and black tea are able to protect against nitric oxide (NO(*)) toxicity in several ways. Both green tea and black tea scavenge NO(*) and peroxynitrite, inhibit the excessive production of NO(*) by the inducible form of nitric oxide synthase (iNOS), and suppress the LPS-mediated induction of iNOS. The NO(*) scavenging activity of tea was less than that of red wine. The high activity found in the polyphenol fraction of black tea (BTP) could not be explained by the mixed theaflavin fraction (MTF) or catechins [epicatechin, epigallocatechin, epicatechin gallate, epigallocatechin gallate (EGCG)], which were tested separately. Synergistic effects between the compounds, or the presence of a potent, unidentified NO(*) scavenger, may explain the high activity of BTP. The peroxynitrite scavenging of tea was comparable to that of red wine. The main activity was found in the polyphenol fraction. MTF and the catechins were found to be potent peroxynitrite scavengers. Tea and tea components were effective inhibitors of iNOS. Of the tea components tested, only MTF had an activity higher than that of the tea powders. The polyphenol fractions of tea were much more active than the tea powders in suppressing the induction of iNOS. On the basis of its abundance and activity, EGCG was the most active inhibitor. The protective effect of tea on NO(*) toxicity is discussed in relation to the beneficial effect of flavonoid intake on the occurrence of cardiovascular heart disease.
Models, algorithms, and measurements for underwater acoustic positioning (2001)

Several problems in underwater acoustic position estimation are investigated within the context of their associated models, algorithms, and measurements. The first appendix provides a detailed discussion of these concepts and demonstrates the fact that simultaneous consideration of all three is necessary in order to properly address a particular position estimation problem. The particular problems addressed herein stem from the so-called long baseline underwater acoustic positioning method whose principle of operation is hyperbolic multilateration; a technique employed in the now common Global Positioning System and its predecessor systems such as Long Range Navigation (LORAN), Decca and Omega. Although motivated by this application, many of the results are quite general and can be applied to other types of positioning systems and other types of problems. The first manuscript investigates the problem of position estimation in an inhomogeneous medium. The second manuscript treats the problem of geodetic position estimation of underwater acoustic sensors placed at fixed but unknown locations on the seafloor where the goal is to obtain the most accurate positions possible from the available measurements. The third manuscript addresses the problem of optimal recursive non-linear estimation for non-linear measurement models by application of a newly proposed algorithm to underwater acoustic positioning. It is referred to as the two-step estimator and is shown to work well with certain models but has difficulty with the newer models developed in the previous manuscript. The last manuscript develops an approach to obtaining the covariance matrix for an estimate when there are multiple input parameters with error, multiple output variables to be estimated, and the functional relationship is non-linear. To accomplish this, a novel two-step procedure is developed that linearizes with respect to the parameters and then with respect to the variables. The method is quite general and is presented in a general form. An example is provided by applying the method to the hyperbolic underwater acoustic positioning model. The accuracy of the method is verified by numerical study using Monte Carlo simulation.
Solution composition and thermal denaturation for the production of single-stranded PCR amplicons: Piperidine-induced destabilization of the DNA duplex? (2002)

Strategies to produce single-stranded PCR amplicons for detection by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) were investigated using modified electrospray solutions and by thermally denaturing the duplex structures with a resistively heated electrospray ionization source. A synthetic 20-mer oligonucleotide annealed to its complementary strand was used as a model system for initial experiments. Electrospray solutions were altered by varying the relative proportion of aqueous phase in efforts to induce destabilization of the double helix. When the electrospray solution contains a 25% aqueous content, the 20-mer oligonucleotide is detected in its double-stranded form. Increasing the proportion of aqueous phase in the electrospray solution to 60% destabilized the double helix, resulting in the detection of only single-stranded species. This strategy was extended to an 82-bp polymerase chain reaction (PCR) product derived from the human tyrosine hydroxylase gene (HUMTH01). In efforts to destabilize the 82-bp PCR product, electrospray solutions reaching 70% aqueous content were necessary to promote the detection of only single-stranded amplicons. Implementation of the resistively heated transfer line and an electrospray solution in which the oligonucleotide is on the threshold of duplex stability allowed for double-stranded and single-stranded species to be generated from the same ESI solutions at both ambient and elevated transfer line temperatures, respectively, without disruption of the electrospray process. The volatile base piperidine, present at 20 mM concentrations in the electrospray solution, was found to play a critical role in the formation of single-stranded species at the higher aqueous percentages and a duplex destabilization mechanism has been proposed.
Porous Interpenetrated Zirconium–Organic Frameworks (PIZOFs): A Chemically Versatile Family of Metal–Organic Frameworks (2011)

We present the synthesis and characterization of porous interpenetrated zirconium-organic frameworks (PIZOFs), a new family of metal-organic frameworks obtained from ZrCl(4) and the rodlike dicarboxylic acids HO(2)C[PE-P(R(1),R(2))-EP]CO(2) H that consist of alternating phenylene (P) and ethynylene (E) units. The substituents R(1),R(2) were broadly varied (alkyl, O-alkyl, oligo(ethylene glycol)), including postsynthetically addressable substituents (amino, alkyne, furan). The PIZOF structure is highly tolerant towards the variation of R(1) and R(2). This together with the modular synthesis of the diacids offers a facile tuning of the chemical environment within the pores. The PIZOF structure was solved from single-crystal X-ray diffraction analysis. The PIZOFs are stable under ambient conditions. PIZOF-2, the PIZOF prepared from HO(2)C[PE-P(OMe,OMe)-EP]CO(2)H, served as a prototype to determine thermal stability and porosity. It is stable up to 325 °C in air as determined by using thermogravimetry and powder X-ray diffraction. Argon sorption isotherms on PIZOF-2 revealed a Brunauer-Emmett-Teller (BET) surface area of 1250 m(2) g(-1) and a total pore volume of 0.68 cm(3) g(-1).
Analysis of Essential Oil of Coridothymus capitatus (L.) and Its Antibacterial and Antifungal Activity (2003)

The water-distilled essential oil the leaves of Coridothymus capitatus were analyzed by GC/MS and also analyzed by direct thermal desorption GC/MS. Comparison was made between two analyses techniques. The essential oil consisted mainly of monoterpenes 98.9%, while oxygenated hydrocarbons were identified as 55.6 % and non-oxygenated hydrocarbons as 43.6%. As major components were found carvacrol (35.6%), p-cymene (21.0%), thymol (18.6%), gamma-terpinene (12.3%), alpha-terpinene (3.2%), beta-myrcene (3.0%) and alpha-thujene (1.3%) by hydrodistillation and by the GC/MS method. The direct thermal desorption GC/MS analysis also showed the same major components, namely carvacrol (51.6%), thymol (21.7%), p-cymene (9.7%) gamma-terpinene (8.2%), alpha-terpinene (1.64%). The essential oil of C. capitatus showed strong activity against S. aureus, P. vulgaris, P. aeruginosa, E. coli, K. pneumonia, B.
Il-6 signaling in inflammatory bowel disease: Pathophysiological role and clinical relevance (2007)

Crohn's disease (CD) and ulcerative colitis (UC) are chronic inflammatory bowel diseases (IBDs) occurring in the gut of genetically susceptible individuals independent of a specific pathogen. The interaction between antigen-presenting cells and the local bacterial flora contributes to an uncontrolled activation of mucosal CD4+ T lymphocytes with the consecutive release of proinflammatory cytokines such as tumor necrosis factor (TNF), interleukin (IL)-6, IL-12, IL-23, IL-27, and also IL-17, which is attributed to a specific, differentiated CD4+ lineage called Th17 (TH-IL17, THi). Recent data suggest that IL-6 contributes to Th17 differentiation. However, to clarify the importance of Th17 cells in IBD further data are needed. So far, CD has been attributed to a Th1-mediated disease, whereas UC exhibits a modified Th2 cytokine response. In both diseases CD4+ T cells at the site of inflammation are critically dependent on antiapoptotic IL-6 signaling. Thereby, IL-6 induces the transcription factor STAT-3 via transsignaling (activation of a cell lacking membrane-bound IL-6 receptor via soluble IL-6 receptor). STAT-3 itself induces the antiapoptotic factors bcl-2 and bcl-xL, thus resulting in T-cell resistance against apoptosis. This vicious circle of T-cell accumulation, mediated by apoptosis resistance, finally leading to chronic inflammation, can be blocked by anti-IL-6 receptor antibodies. This review highlights the role of IL-6 in IBD immunopathogenesis and its clinical relevance in IBD therapy and diagnostics.
cDNA cloning and expression analysis of a novel human F-box only protein. (2002)

F-box proteins are an expanding family of eukaryotic proteins that are characterized by an approximately 40 amino acid motif. Some F-box proteins are critical for the controlled degradation of cellular regulatory proteins. During a large-scale sequencing analysis of a human fetal brain cDNA library, we isolated a cDNA clone that encodes a novel F-box protein. It showed a 90.0% identity with the previously isolated mouse F-box protein16 at the amino acid level. Northern blot analysis showed no detectable expression, while reverse transcription-polymerase chain reaction analysis indicated that FBXO16 was expressed in the heart, spleen, and colon. By mapping, we localized the FBXO16 gene to the human chromosome 8p12. The FBXO16 gene consisted of 9 exons that spanned 67,816 bp of human genomic DNA.
Two-Locus Sampling Distributions and Their Application (2001)

Methods of estimating two-locus sample probabilities under a neutral model are extended in several ways. Estimation of sample probabilities is described when the ancestral or derived status of each allele is specified. In addition, probabilities for two-locus diploid samples are provided. A method for using these two-locus probabilities to test whether an observed level of linkage disequilibrium is unusually large or small is described. In addition, properties of a maximum-likelihood estimator of the recombination parameter based on independent linked pairs of sites are obtained. A composite-likelihood estimator, for more than two linked sites, is also examined and found to work as well, or better, than other available ad hoc estimators. Linkage disequilibrium in the Xq28 and Xq25 region of humans is analyzed in a sample of Europeans (CEPH). The estimated recombination parameter is about five times smaller than one would expect under an equilibrium neutral model.
Obesity Increases Risk of Organ Failure after Severe Trauma (2006)

Obese patients are at increased risk of postinjury MOF. Study of the obesity-related inflammatory profile could provide additional insight into the pathogenesis of organ dysfunction and identify therapeutic targets for both obese and nonobese patients. Increased morbidity and length of stay in obese trauma patients implies greater resource allocation for this population.
Identification and characterization of RET fusions in advanced colorectal cancer (2015)

There is an unmet clinical need for molecularly directed therapies available for metastatic colorectal cancer. Comprehensive genomic profiling has the potential to identify actionable genomic alterations in colorectal cancer. Through comprehensive genomic profiling we prospectively identified 6 RET fusion kinases, including two novel fusions of CCDC6-RET and NCOA4-RET, in metastatic colorectal cancer (CRC) patients. RET fusion kinases represent a novel class of oncogenic driver in CRC and occurred at a 0.2% frequency without concurrent driver mutations, including KRAS, NRAS, BRAF, PIK3CA or other fusion tyrosine kinases. Multiple RET kinase inhibitors were cytotoxic to RET fusion kinase positive cancer cells and not RET fusion kinase negative CRC cells. The presence of a RET fusion kinase may identify a subset of metastatic CRC patients with a high response rate to RET kinase inhibition. This is the first characterization of RET fusions in CRC patients and highlights the therapeutic significance of prospective comprehensive genomic profiling in advanced CRC.
The Sunnybrook Stroke Study (1998)

Depressive symptoms and functional outcome are correlated. In view of the prevalence of depressive symptoms in this population, diagnosis and treatment of depression are important in optimizing recovery.