gebhart/patrepeval huggingface dataset:
Accumulation of DNA methylation is associated with tumor stage in gastric cancer (2006)

The average number of methylated genes per tumor was 4.83. DNA methylation of each gene was correlated with low expression of the respective mRNA. High methylation (GC with 5 or more methylated genes) was detected in 39 (52.0%) of 75 GCs. Twenty-nine (37.8%) of 75 GCs were CIMP-positive. DNA methylation of each of the 12 genes was observed more frequently in the high-methylation group than in the low-methylation group. Methylation of 6 specific genes occurred more frequently in CIMP-positive GC than in CIMP-negative GC. Methylation of the remaining 6 genes was not correlated with CIMP-status. High methylation was found more frequently in Stage III/IV GC (26 of 40 cases, 65.0%) than in Stage I/II GC (13 of 35 cases, 37.1%, P = 0.029).CONCLUSIONS.These findings indicate that GCs with higher numbers of methylated genes have more distinct DNA methylation profiles than the originally defined CIMP-positive GCs. DNA methylation of tumor-related genes accumulates in conjunction with tumor progression.
Selection of secure single sign-on solutions for heterogeneous computing environments (1997)

Secure Single Sign-on (SSSO) is the concept of minimizing the number of different userids and passwords required to access various host systems in a distributed computing environment, while providing a consistently secure environment which also provides confidentiality and integrity services. In its purest form, Single Sign-on (SSO) allows a user to sign -on once to the enterprise computing environment and be granted access to participating host systems across the enterprise. In a wider context, extending the concept to SSSO, it impacts on the enforcement of security policies, security management and administration, security services, and overall productivity. Selecting and implementing SSSO solutions may present interesting challenges, and may lead to increased risk, if not done carefully and properly. This paper discusses the concepts of SSSO, user requirements, and presents a reference framework for selection of Secure Single Sign-on solutions in heterogeneous computing environments, which can assist in SSSO requirements specification and product evaluation.
Ex-vivo crystalline lens optical quality measurements during simulated accommodation using a single pass PSF measurement system (2005)

Purpose: To design and test an optical system to measure the optical quality of post mortem lenses during simulated accommodation. Methods: An optical bench top system was designed to measure the point spread function and calculate the modulation transfer function (MTF) of monkey and human ex-vivo crystalline lenses. The system consists of a super luminescent diode emitting at 850nm, collimated into a 3mm beam which is focused by the ex-vivo lens under test. The intensity distribution at the focus (point spread function) is re-imaged and magnified onto a beam profiler CCD camera. The optical quality in terms of spatial frequency response (modulation transfer function) is calculated by Fourier transform of the point spread function. The system was used on ex-vivo lenses with attached zonules, ciliary body and sclera. The sclera was glued to 8 separate PMMA segments and stretched radial by 5mm on an accommodation simulating lens stretching device. The point spread function was measured for each lens in the relaxed and stretched state for 5 human (ages 38-86 years) and 5 cynomolgus monkey (ages 53 - 67 months) fresh post mortem crystalline lenses. Results: Stretching induced measurable changes in the MTF. The cutoff frequency increased from 54.4±13.6 lp/mm unstretched to 59.5±21.4 lp/mm stretched in the post-presbyopic human and from 51.9±24.7 lp/mm unstretched to 57.7±18.5 lp/mm stretched cynomolgus monkey lenses. Conclusion: The results demonstrate the feasibility of measuring the optical quality of ex-vivo human and cynomolgus monkey lenses during simulated accommodation. Additional experiments are underway to quantify changes in optical quality induced by stretching.
How Many Variables Can Humans Process? (2005)

The conceptual complexity of problems was manipulated to probe the limits of human information processing capacity. Participants were asked to interpret graphically displayed statistical interactions. In such problems, all independent variables need to be considered together, so that decomposition into smaller subtasks is constrained, and thus the order of the interaction directly determines conceptual complexity. As the order of the interaction increases, the number of variables increases. Results showed a significant decline in accuracy and speed of solution from three-way to four-way interactions. Furthermore, performance on a five-way interaction was at chance level. These findings suggest that a structure defined on four variables is at the limit of human processing capacity.
Human serum amyloid A protein. Behaviour in aqueous and urea-containing solutions and antibody production (1989)

Human serum amyloid A protein (apo-SAA) can be prepared by gel filtration of delipidated acute-phase high-density lipoprotein in the presence of urea. The resultant apo-SAA is soluble (greater than 90% solubility) in a wide range of buffer solutions, with all of the six major isoforms of apo-SAA being equally soluble. In urea-containing solutions the isoforms behave qualitatively differently in various urea concentrations, probably reflecting subtle primary-structure variations. The higher-pI isoforms are only completely unfolded at greater than 7 M-urea. By immunizing with apo-SAA adsorbed to acid-treated bacteria (Salmonella minnesota R595), high-titre antibodies can easily be elicited in rabbits.
Phase- and polarization-diversity coherent optical techniques (1989)

Progress in phase- and polarization-diversity coherent optical techniques has led to impressive receivers able to tolerate wide laser linewidth and large polarization fluctuations. The advantages and the drawbacks of diversity receivers, and recent experimental and theoretical research results are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Engineering tissues and organs (1999)

Genitourinary tissues can be engineered in-vitro and in-vivo for reconstruction using selective cell transplantation in combination with acellular matrices. This technology involves an interdisciplinary approach combining techniques of cell biology and materials sciences towards the development of functional tissues or organs. Tissues and organs in urology, such as the bladder, clitoris, corpus cavermosum, kidney, testis, ureter and urethra have been created in the laboratory, with varying degrees of functionality. Cells have also been recently used in patients as bulking agents for the treatment of vesicoureteral reflux and urinary incontinence. As the science of tissue engineering evolves, one can expect a wider application of this technology to the armamentarium of urologic surgery.
Short related sequences in the cytoplasmic domains of CD4 and CD8 mediate binding to the amino-terminal domain of the p56lck tyrosine protein kinase. (1990)

We report that the cytoplasmic domains of the T-lymphocyte glycoproteins CD4 and CD8 alpha contain short related amino acid sequences that are involved in binding the amino-terminal domain of the intracellular tyrosine protein kinase, p56lck. Transfer of as few as six amino acid residues from the cytoplasmic domain of the CD8 alpha protein to the cytoplasmic domain of an unrelated protein conferred p56lck binding to the hybrid protein in HeLa cells. The common sequence motif shared by CD4 and CD8 alpha contains two cysteines, and mutation of either cysteine in the CD4 sequence eliminated binding of p56lck.p56lck also contains two cysteine residues within its CD4-CD8 alpha-binding domain, and both are critical to the interaction with CD4 or CD8 alpha. Because the interaction does not involve disulfide bond formation, a metal ion could stabilize the complex.
PCR Assay To Detect Bacillus anthracis Spores in Heat-Treated Specimens (2003)

Recent interest in anthrax is due to its potential use in bioterrorism and as a biowarfare agent against civilian populations. The development of rapid and sensitive techniques to detect anthrax spores in suspicious specimens is the most important aim for public health. With a view to preventing exposure of laboratory workers to viable Bacillus anthracis spores, this study evaluated the suitability of PCR assays for detecting anthrax spores previously inactivated at 121 degrees C for 45 min. The results indicate that heat treatment ensures the complete inactivation of B. anthracis spores without significantly affecting the efficiency of PCR assays.
Microtubule Binding and Clustering of Human Tau-4R and Tau-P301L Proteins Isolated from Yeast Deficient in Orthologues of Glycogen Synthase Kinase-3β or cdk5 (2006)

Phosphorylation of Tau protein and binding to microtubules is complex in neurons and was therefore studied in the less complicated model of humanized yeast. Human Tau was readily phosphorylated at pathological epitopes, but in opposite directions regulated by kinases Mds1 and Pho85, orthologues of glycogen synthase kinase-3beta and cdk5, respectively (1). We isolated recombinant Tau-4R and mutant Tau-P301L from wild type, Delta mds1 and Delta pho85 yeast strains and measured binding to Taxol-stabilized mammalian microtubules in relation to their phosphorylation patterns. Tau-4R isolated from yeast lacking mds1 was less phosphorylated and bound more to microtubules than Tau-4R isolated from wild type yeast. Paradoxically, phosphorylation of Tau-4R isolated from kinase Pho85-deficient yeast was dramatically increased resulting in very poor binding to microtubules. Dephosphorylation promoted binding to microtubules to uniform high levels, excluding other modifications. Isolated hyperphosphorylated, conformationally altered Tau-4R completely failed to bind microtubules. In parallel to Tau-4R, we expressed, isolated, and analyzed mutant Tau-P301L. Total dephosphorylated Tau-4R and Tau-P301L bound to microtubules very similarly. Surprisingly, Tau-P301L isolated from all yeast strains bound to microtubules more extensively than Tau-4R. Atomic force microscopy demonstrated, however, that the high apparent binding of Tau-P301L was due to aggregation on the microtubules, causing their deformation and bundling. Our data explain the pathological presence of granular Tau aggregates in neuronal processes in tauopathies.
Serpins 2005 – fun between the β‐sheets (2005)

Serpins are the largest family of protease inhibitors and are fundamental for the control of proteolysis in multicellular eukaryotes. Most eukaryote serpins inhibit serine or cysteine proteases, however, noninhibitory members have been identified that perform diverse functions in processes such as hormone delivery and tumour metastasis. More recently inhibitory serpins have been identified in prokaryotes and unicellular eukaryotes, nevertheless, the precise molecular targets of these molecules remains to be identified. The serpin mechanism of protease inhibition is unusual and involves a major conformational rearrangement of the molecule concomitant with a distortion of the target protease. As a result of this requirement, serpins are susceptible to mutations that result in polymerization and conformational diseases such as the human serpinopathies. This review reports on recent major discoveries in the serpin field, based upon presentations made at the 4th International Symposium on Serpin Structure, Function and Biology (Cairns, Australia).
Decoupled Optimal Load Flow Using Linear or Quadratic Programming (1986)

The Optimal Load Flow problem is a constrained optimization problem of large size and great complexity. For on-line implementation fast execution times and minimum computer storage are required. The proposed iterative scheme, reported in this paper, decomposes the Optimal Load Flow problem into real and reactive subproblems. At each iteration the two subproblems are solved using quadratic programming. If the valve point loading is to be considered, the two subproblems are solved using linear programming. In our scheme, linearization of the non-linear constraints of the problem is succeeded by utilizing Z-matrix techniques and sensitivity analysis.
Development of Industrial‐Medium‐Required Elimination of the 2,3‐Butanediol Fermentation Pathway To Maintain Ethanol Yield in an Ethanologenic Strain of Klebsiellaoxytoca (2005)

Fermentation efficiency and nutrient costs are both significant factors in process economics for the microbial conversion of cellulosic biomass to commodity chemicals such as ethanol. In this study, we have developed a more industrial medium (OUM1) composed of 0.5% corn steep liquor (dry weight basis) supplemented with mineral salts (0.2%), urea (0.06%), and glucose (9%). Although the growth of strain P2 was vigorous in this medium, approximately 14% of substrate carbon was diverted into 2,3-butanediol and acetoin under the low pH conditions needed for optimal cellulase activity during simultaneous saccharification. Deleting the central region of the budAB genes encoding alpha-acetolactate synthase and alpha-acetolactate decarboxylase eliminated the butanediol and acetoin coproducts and increased ethanol yields by 12%. In OUM1 medium at pH 5.2, strain BW21 produced over 4% ethanol in 48 h (0.47 g ethanol per g glucose). Average productivity (48 h), ethanol titer, and ethanol yield for BW21 in OUM1 medium (pH 5.2) exceeded that of the parent (strain P2) in rich laboratory medium (Luria broth).
Catalytic Enantioselective Cr-Mediated Propargylation: Application to Halichondrin Synthesis (2009)

A catalytic enantioselective propargylation in the presence of 10 mol % of Cr catalyst prepared from Cr(III) bromide and (R)-sulfonamide E furnishes homopropargyl alcohol 8 in 78% yield with 90% ee. Coupled with the workup based on Amano-lipase, this method provides a practical synthesis of optically pure 8 on a multigram scale. With maintenance of its optical purity, 8 has been converted to 1b, the C14-C19 building block of halichondrins and E7389, in two steps.
Prediction of chemical–protein interactions: multitarget-QSAR versus computational chemogenomic methods (2012)

Elucidation of chemical-protein interactions (CPI) is the basis of target identification and drug discovery. It is time-consuming and costly to determine CPI experimentally, and computational methods will facilitate the determination of CPI. In this study, two methods, multitarget quantitative structure-activity relationship (mt-QSAR) and computational chemogenomics, were developed for CPI prediction. Two comprehensive data sets were collected from the ChEMBL database for method assessment. One data set consisted of 81 689 CPI pairs among 50 924 compounds and 136 G-protein coupled receptors (GPCRs), while the other one contained 43 965 CPI pairs among 23 376 compounds and 176 kinases. The range of the area under the receiver operating characteristic curve (AUC) for the test sets was 0.95 to 1.0 and 0.82 to 1.0 for 100 GPCR mt-QSAR models and 100 kinase mt-QSAR models, respectively. The AUC of 5-fold cross validation were about 0.92 for both 176 kinases and 136 GPCRs using the chemogenomic method. However, the performance of the chemogenomic method was worse than that of mt-QSAR for the external validation set. Further analysis revealed that there was a high false positive rate for the external validation set when using the chemogenomic method. In addition, we developed a web server named CPI-Predictor, , which is available for free. The methods and tool have potential applications in network pharmacology and drug repositioning.
Overview: Translating Hsp90 Biology into Hsp90 Drugs (2003)

The Hsp90 molecular chaperone has emerged as one of the most exciting targets for cancer drug development. Hsp90 is overexpressed in many malignancies, very likely as a result of the stress that is induced both by the hostile cancer microenvironment and also by the mutation and abberant expression of oncoproteins. A particularly attractive feature of Hsp90 as a cancer drug target is that it is required for the conformational stability and function of a wide range of oncogenic 'client' proteins, including c-Raf-1, Cdk4, ErbB2, mutant p53, c-Met, Polo-1 and telomerase hTERT. Inhibition of Hsp90 should therefore block multiple mission critical oncogenic pathways in the cancer cell, leading to inhibition of all the hallmark traits of malignancy. This combinatorial blockade of oncogenic targets should give rise to board spectrum antitumour activity across multiple cancer types. The 'druggability' of Hsp90 was confirmed by the discovery that the natural products geldanamycin and radicicol, which have anticancer activity, exert their biological effects by inhibiting the essential ATPase activity associated with the N-terminal domain of the protein. The first-in-class Hsp90 inhibitor has entered clinical trial and provided proof of concept that Hsp90 can be inhibited and clinical benefit seen at non-toxic doses. Further development is underway and a related analogue 17DMAG also shows promise in preclinical models. In addition, novel Hsp90 inhibitors have been identified using methods such as high throughput screening and x-ray crystallography. The opportunities and challenges involved in translating the fast moving biology of Hsp90 into patient benefit is discussed.
Fast Mode Decision for H.264 Based on Rate-Distortion Cost Estimation (2007)

A fast mode decision algorithm for an H.264 encoder is proposed which reduces computation by using a statistical dependency of macroblock rate-distortion (RD) costs. The algorithm skips the motion estimation and/or intra prediction mode decision with an adaptive threshold. The simulation results show that the proposed algorithm achieves an almost 2X speedup with negligible degradation in coding efficiency.
A methodology for high-level synthesis of communication on multicomputers (1992)

Freeing the user from the tedious task of generating explicit communication is one of the primary goals of numerous research projects on compilers for distributed memory machines. In the process of synthesis of communication, the effective use of collective communication routines offers a considerable scope for improving the program performance. This paper presents a methodology for determining the collective communication primitives that should be used for implementing the data movement at various points in the program. We introduce the notion of certain synchronous properties between array references in statements inside loops, and present tests to determine the presence of these properties. These tests enable the compiler to analyze quite precisely the communication requirements of those statements, and implement communication using appropriate primitives. These results not only lay down a framework for synthesis of communication on multicomputers, they also form the basis of our implementation of a system that statically estimates the communication costs of programs on multicomputers.
Nutritional therapy improves function and complements corticosteroid intervention in mdx mice (2005)

Corticosteroid therapy for Duchenne muscular dystrophy is effective but associated with long-term side effects. To determine the potential therapeutic benefit from four nutritional compounds (creatine monohydrate, conjugated linoleic acid, alpha-lipoic acid, and beta-hydroxy-beta-methylbutyrate) alone, in combination, and with corticosteroids (prednisolone), we evaluated the effects on several variables in exercising mdx mice. Outcome measures included grip strength, rotarod performance, serum creatine kinase levels, muscle metabolites, internalized myonuclei, and retroperitoneal fat pad weight. In isolation, each nutritional treatment showed some benefit, with the combination therapy showing the most consistent benefits. Prednisolone and the combination therapy together provided the most consistent evidence of efficacy; increased peak grip strength (P < 0.05), decreased grip strength fatigue (P < 0.05), decreased number of internalized myonuclei (P < 0.01), and smaller retroperitoneal fat pad stores (P < 0.001). This study provided evidence for therapeutic benefit from a four-compound combination therapy alone, and in conjunction with corticosteroids in the mdx model of DMD.
Induction of ovalbumin-specific cytotoxic T cells by in vivo peptide immunization. (1989)

CTL recognize peptide forms of processed, foreign antigens in association with class I molecules encoded by the MHC and are usually directed against endogenously synthesized "cellular antigens," such as those expressed by virus-infected cells. In vitro studies have shown that small exogenous peptides can directly associate with class I molecules on the cell surface and mimic the target complex derived by intracellular processing and presentation. We have recently generated OVA-specific, H-2Kb-restricted CTL by immunizing C57BL/6 mice with a syngeneic tumor line transfected with the OVA cDNA. The CTL recognize the OVA transfectant E.G7-OVA and the synthetic peptide OVA258-276, but fail to recognize the native protein. We reasoned that given the potential for direct peptide/class I association observed in vitro, OVA258-276 may induce CTL after in vivo priming. However, we found that this is not the case. OVA258-276 and peptides of increasing lengths up to OVA242-276 and OVA242-285, which are all able to form the target complex in vitro, are inefficient at priming E.G7-OVA-specific CTL responses after intravenous injection. This is also true for both native and denatured OVA. In contrast to these results the synthetic peptide OVA229-276 corresponding to a peptide in a partial tryptic digestion of OVA can efficiently prime C57BL/6 mice in vivo after intravenous injection. This peptide elicits CTL that appear identical to those derived from animals immunized with syngeneic cells producing OVA endogenously. These results are discussed in terms of separate class I and class II antigen presentation pathways and the ability of only certain, exogenous antigens to enter the cytoplasmic, class I pathway.
Step-by-Step Assembly of Self-Patterning Polyelectrolyte Films Violating (Almost) All Rules of Layer-by-Layer Deposition (2010)

Because of its versatility, the layer-by-layer (LBL) assembly method has become a popular tool for preparing multimaterial films, yet astonishingly little is known about the fundamental rules governing their deposition. Here we show an unusual case of self-patterning LBL films made from poly(allylamine hydrochloride) and poly(sodium phosphate). In such films, both the film thickness and the film roughness increase linearly with the number of deposition steps up to a thickness of approximately 60 nm. Even more surprising is the fact that the adsorption of individual "layers" of polyanions and polycations proceeds without a regular inversion of the zeta potential and with the occurrence of a growth instability at approximately 75 layers. These findings underline the need to reconsider the fundamentals of polyelectrolyte multilayer film deposition.
The Pioneers of NMR and Magnetic Resonance in Medicine: The Story of MRI (1997)

Share Icon Share Twitter Facebook Reddit LinkedIn Reprints and Permissions Cite Icon Cite Search Site Citation James Mattson, Merrill Simon, Paul R. Moran; The Pioneers of NMR and Magnetic Resonance in Medicine: The Story of MRI. Physics Today 1 January 1997; 50 (1): 66–67. https://doi.org/10.1063/1.881661 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentPhysics Today Search Advanced Search