gebhart/patrepeval huggingface dataset:
LC‐MS/MS‐based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma (2015)

Associating changes in protein levels with the onset of cancer has been widely investigated to identify clinically relevant diagnostic biomarkers. In the present study, we analyzed sera from 205 patients recruited in the United States and Egypt for biomarker discovery using label-free proteomic analysis by LC-MS/MS. We performed untargeted proteomic analysis of sera to identify candidate proteins with statistically significant differences between hepatocellular carcinoma (HCC) and patients with liver cirrhosis. We further evaluated the significance of 101 proteins in sera from the same 205 patients through targeted quantitation by MRM on a triple quadrupole mass spectrometer. This led to the identification of 21 candidate protein biomarkers that were significantly altered in both the United States and Egyptian cohorts. Among the 21 candidates, ten were previously reported as HCC-associated proteins (eight exhibiting consistent trends with our observation), whereas 11 are new candidates discovered by this study. Pathway analysis based on the significant proteins reveals upregulation of the complement and coagulation cascades pathway and downregulation of the antigen processing and presentation pathway in HCC cases versus patients with liver cirrhosis. The results of this study demonstrate the power of combining untargeted and targeted quantitation methods for a comprehensive serum proteomic analysis, to evaluate changes in protein levels and discover novel diagnostic biomarkers. All MS data have been deposited in the ProteomeXchange with identifier PXD001171 (http://proteomecentral.proteomexchange.org/dataset/PXD001171).
Characterization of a heparan sulfate and a peculiar chondroitin 4-sulfate proteoglycan from platelets. Inhibition of the aggregation process by platelet chondroitin sulfate proteoglycan (1991)

A high molecular weight chondroitin sulfate proteoglycan (Mr 240,000) is released from platelet surface during aggregation induced by several pharmacological agents. Some details on the structure of this compound are reported. beta-Elimination with alkali and borohydride produces chondroitin sulfate chains with a molecular weight of 40,000. The combined results indicate a proteoglycan molecule containing 5-6 chondroitin sulfate chains and a protein core rich in serine and glycine residues. Degradation with chondroitinase AC shows that a 4-sulfated disaccharide is the only disaccharide released from this chondroitin sulfate, characterizing it as a chondroitin 4-sulfate homopolymer. It is shown that this proteoglycan inhibits the aggregation of platelets induced by ADP. Analysis of the sulfated glycosaminoglycans not released during aggregation revealed the presence of a heparan sulfate in the platelets. Degradation by heparitinases I and II yielded the four disaccharide units of heparan sulfates: N,O-disulfated disaccharide, N-sulfated disaccharide, N-acetylated 6-sulfated disaccharide, and N-acetylated disaccharide. The possible role of the sulfated glycosaminoglycans on cell-cell interaction is discussed in view of the present findings.
Simultaneous tracking of head poses in a panoramic view (2002)

In this paper we present an approach to simultaneously estimate gaze directions of multiple people in the view of a panoramic camera. Human faces are located and tracked using a probabilistic skin-color model and motion detection. Neural networks are used to estimate head poses of the detected faces. With this approach, it is possible to simultaneously track the locations of multiple people around a meeting table and estimate their gaze directions using only a panoramic camera. We have achieved an accuracy of 9 degrees for head pan estimation and 6 degrees for tilt estimation for a multi-user system.
A design framework of Orchestrator for computing systems (2010)

An Orchestrator is a system which is used for coordinating and sequencing the services, processes and threads in the number of applications. Orchestrator is a coordinator which provides controlling of different computational services or processes or threads. It manages services and data processing in distributed environment at the same time considering priorities, timeouts and failures of services. In this paper a design framework of Orchestrator is developed and presented. This design considers an Orchestrator as super class for the different type of concurrent computing systems- Service Oriented Architecture (SOA) based computing, parallel distributed computing and sequential distributed computing. These systems can be derived as the special classes of the Orchestrator design framework given in this paper. The same framework can also be used in robotics and control systems.
Design methodology for FPGA implementation of lattice piecewise-affine functions (2011)

This paper describes a design methodology to implement on FPGAs piecewise-affine (PWA) functions based on representation methods from the lattice theory. An off-line automatic processing starts at the algorithmic formulation of the problem, obtains the parameters required by a parameterized digital architecture, and ends with the bitstream to program an FPGA. The methodology has been proven to implement PWA functions on Xilinx FPGAs. The results are compared with other approaches for FPGA implementations of PWA functions.
The fabrication of sub-10 nm planar electrodes and their use for a molecule-based transistor (2004)

The typical size of a single molecule is of the order of a few nanometres; for this reason metal electrodes separated by a nanometre-scale channel are required to make molecule-based electronic devices. In this work, we report on the fabrication of metallic (Cr/Au, Ti/Au or Ti/Pt) arrow-shaped electrodes on Si/SiO2 substrates, with tip separation between 100 and less than 10 nm. They can be used to implement two and three terminal molecular devices, just by connecting them by the chosen molecules and adding an Ag electrode on the back of the Si substrate. Electron beam lithography (EBL) allowed us to obtain electrodes with separation around 40 nm. In order to reduce the tip separation down to 20 nm, before the EBL process, we used a defocused e-beam to brush the poly(methyl methacrylate) (PMMA) layer for a short time (from 10 to 40 s). The smallest gap between the electrodes (less than 10 nm) was obtained with standard EBL and lift-off followed by Au electroplating deposition. The fabricated devices were inspected by plan-view scanning electron microscopy (SEM) and electrically tested by I/V measurements in the range ± 2 V. Open-circuit characteristics gave very low currents (in the range −10 to 10 pA) and a resistance . As a typical example, we demonstrate a field effect transistor (FET) based on a deoxyguanosine derivative (a DNA base) placed between the fabricated planar electrodes by room temperature (RT) cast deposition. The FET device tested at RT and ambient pressure exhibited a maximum voltage gain as high as 0.76.
Towards Transparent Introspection (2016)

There is a growing need for the dynamic analysis of sensitive systems thatdo not support traditional debugging or emulation environments. Analysiscan alter program behavior, necessitating transparency. For example, asthe cat and mouse game between malware authors and malware analystsprogresses, malicious software can increasingly detect and confounddebuggers. Analysts must understand variable values, stack traces, andfactors influencing dynamic behavior, but recent malware samples leverageany piece of information or artifact available that signals the presence ofa debugger or emulator. In this work, we advance the state-of-the-art for transparent programanalysis by introducing a low-artifact introspection technique. Ourapproach uses hardware-assisted live memory snapshots ofprocess execution on native targets (e.g., x86 processors), coupledwith static reasoning about programs. We produce high-fidelity data and control flow information with minimaldetectable artifacts that could influence benign subject behavior or beleveraged for anti-analysis. We evaluate our system using two hardwareimplementations (x86-supported System Management Mode and PCI-basedSlotScreamer devices) and two software configurations (benign and evasiveprograms). We also analyze the theoretical and practical limitations of our technique. We discuss an expert case study in which we apply our technique to amalware reverse engineering task. Finally, we present results of a human study in which 30 participantsperformed debugging tasks using information provided by our approach, ourtool was as useful as a gdb baseline, but applies transparently. Our dynamic analysis approach permitstransparent introspection to access previously-unavailable informationabout a process's internal state with minimal instrumentation artifacts.
Specific configuration of a four-pass laser amplifier with a stimulated Brillouin scattering mirror (1984)

A four-pass configuration of a laser amplifier with a stimulated Brillouin scattering mirror but without a Faraday isolator was proposed and investigated experimentally. The dependence of the output radiation energy on the energy of the light beam at the amplifier input was determined.
Learning to Learn Programs from Examples: Going Beyond Program Structure (2017)

Programming-by-example technologies let end users construct and run new programs by providing examples of the intended program behavior. But, the few provided examples seldom uniquely determine the intended program. Previous approaches to picking a program used a bias toward shorter or more naturally structured programs. Our work here gives a machine learning approach for learning to learn programs that departs from previous work by relying upon features that are independent of the program structure, instead relying upon a learned bias over program behaviors, and more generally over program execution traces. Our approach leverages abundant unlabeled data for semisupervised learning, and incorporates simple kinds of world knowledge for common-sense reasoning during program induction. These techniques are evaluated in two programming-by-example domains, improving the accuracy of program learners.
Distributed database management model and validation (1986)

The authors describe a simple, yet effective, distributed database model that simulates database usage and buffer management in the distributed data processing environment. The model is table driven such that database access requirements, file location, and other information defining the database environment are set up internally in several tables, and linked lists represent the directory and data blocks. Each database transaction is defined and represented by a transaction flow diagram (TFD), and a sequence of TFDs representing an operational scenario is input to the model. The model `executes' input TFDs by looking up tables, and performs buffer management for directory and file data while logging history and gathering various statistics on database usage and buffer management. The performance data are used for database access overhead measurement, database workload characterization, and buffer allocation. Disk access frequency and response time are used to validate the simulation results.
An Effective Method for Producing a Nutritive Protein Extract Powder from Shrimp-head Waste (2005)

Enzymatic hydrolysis has been widely applied for production of protein hydrolysate from shrimp waste and for purification of chitin. In the present study, shrimp (P. semisulcatus) head waste was hydrolysed, using a commercial proteolytic enzyme, Alcalase. In order to improve protein extraction efficiency, certain chemicals such as sodium sulphite and Triton x-100 were used along with the enzyme. When Alcalase (12 AU/kg) used alone, the yield of protein extraction was 45.1% and by using Triton x-100 (0.01 g/kg) together with Alcalase, the yield was decreased to 39%, whereas the presence of sodium sulphite (200 mmol/L) with the enzyme or with the enzyme and Triton x-100 increased the level of protein extraction to 62% and 65.1%, respectively. The resulting protein powder contained sufficient amounts of essential amino acids to be used in feed formulations. By precipitating proteins from the resulting protein extract at pH 3.1, the residual sulphite in protein powder was decreased by 97% and thus the powder can be considered suitable for animal and/or aquaculture feed formulations.
Active tumor cell resistance to human natural killer lymphocyte attack. (1981)

Inhibition of protein synthesis by cycloheximide, puromycin, or emetine increased tumor lysis mediated by human natural killer (NK) cells to "slow" but not "fast" tumor targets. Human T24 bladder carcinoma cells were used as slow targets which are killed after a approximately 3-hr lag period, and K562 cells derived from a patient with myelogenous leukemia were used as fast targets which are killed without a lag period. This enhancement of killing exceeded that which would have been expected simply from a reduction of tumor cell growth during the time of assay. Pretreatment of the NK effector cells and the tumor cells separately showed that the effect was on the tumor cells and not due to enhancement of NK cell activity. These observations imply that some tumor cells can actively resist NK attack. The discovery that some but not all human tumor cells actively resist cellular immune attack, perhaps by repair mechanisms dependent upon protein synthesis, provides a new model for evaluation of tumor cells in their resistance to host defenses.
Regulation of the <i>sol</i> Locus Genes for Butanol and Acetone Formation in <i>Clostridium acetobutylicum</i> ATCC 824 by a Putative Transcriptional Repressor (1999)

A gene (orf1, now designated solR) previously identified upstream of the aldehyde/alcohol dehydrogenase gene aad (R. V. Nair, G. N. Bennett, and E. T. Papoutsakis, J. Bacteriol. 176:871-885, 1994) was found to encode a repressor of the sol locus (aad, ctfA, ctfB and adc) genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824. Primer extension analysis identified a transcriptional start site 35 bp upstream of the solR start codon. Amino acid comparisons of SolR identified a potential helix-turn-helix DNA-binding motif in the C-terminal half towards the center of the protein, suggesting a regulatory role. Overexpression of SolR in strain ATCC 824(pCO1) resulted in a solvent-negative phenotype owing to its deleterious effect on the transcription of the sol locus genes. Inactivation of solR in C. acetobutylicum via homologous recombination yielded mutants B and H (ATCC 824 solR::pO1X) which exhibited deregulated solvent production characterized by increased flux towards butanol and acetone formation, earlier induction of aad, lower overall acid production, markedly improved yields of solvents on glucose, a prolonged solvent production phase, and increased biomass accumulation compared to those of the wild-type strain.
Effects of content and time of delivery on receptivity to mobile interruptions (2010)

In this paper we investigate effects of the content of interruptions and of the time of interruption delivery on mobile phones. We review related work and report on a naturalistic quasi-experiment using experience-sampling that showed that the receptivity to an interruption is influenced by its content rather than by its time of delivery in the employed modality of delivery - SMS. We also examined the underlying variables that increase the perceived quality of content and found that the factors interest, entertainment, relevance and actionability influence people's receptivity significantly. Our findings inform system design that seeks to provide context-sensitive information or to predict interruptibility and suggest the consideration of receptivity as an extension to the way we think and reason about interruptibility.
A Single-Amino-Acid Mutation in Hepatitis C Virus NS5A Disrupting FKBP8 Interaction Impairs Viral Replication (2008)

Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) regulates viral replication through its interaction with host and other viral proteins. We have previously shown that FK506-binding protein 8 (FKBP8) binds to NS5A and recruits Hsp90 to form a complex that participates in the replication of HCV. In this study, we examined the biochemical characteristics of the interaction and the intracellular localization of NS5A and FKBP8. Surface plasmon resonance analysis revealed that the dissociation constant of the interaction between the purified FKBP8 and NS5A expressed in bacteria was 82 nM. Mutational analyses of NS5A revealed that a single amino acid residue of Val or Ile at position 121, which is well conserved among all genotypes of HCV, is critical for the specific interaction with FKBP8. Substitution of the Val(121) to Ala drastically impaired the replication of HCV replicon cells, and the drug-resistant replicon cells emerging after drug selection were shown to have reverted to the original arrangement by replacing Ala(121) with Val. Examination of individual fields of the replicon cells by both fluorescence microscopy and electron microscopy (the correlative fluorescence microscopy-electron microscopy technique) revealed that FKBP8 is partially colocalized with NS5A in the cytoplasmic structure known as the membranous web. These results suggest that specific interaction of NS5A with FKBP8 in the cytoplasmic compartment plays a crucial role in the replication of HCV.
<title>Robust least-square-baseline finding using a branch and bound algorithm</title> (2001)

Many document analysis and OCR systems depend on precise identification of page rotation, as well as the reliable identification of text lines. This paper presents a new algorithm to address both problems. It uses a branch-and-bound approach to globally optimal line finding and simultaneously models the baseline and the descender line under a Gaussian error/robust least square model. Results of applying the algorithm to documents in the University of Washington Database 2 are presented.
Regulation of the sarcoplasmic reticulum ryanodine receptor by inorganic phosphate. (1994)

To better understand the mechanisms regulating myoplasmic Ca2+ during muscle activity, we have examined the effect of inorganic phosphate (P(i)) on the ryanodine receptor (RyR) Ca2+ release channel of the sarcoplasmic reticulum (SR). We report that P(i) at concentrations reached in exercising skeletal muscle (3-30 mM) produced a dose-dependent stimulation of ryanodine binding to skeletal muscle SR. Ryanodine binding was increased by 84% in the presence of 30 mM P(i) with half-maximal stimulation at 4 mM P(i). In contrast to its effect on skeletal muscle SR, ryanodine binding to cardiac muscle SR was not stimulated by P(i) (3-30 mM). Stimulation of ryanodine binding to skeletal muscle SR was maximal in the presence of micromolar Ca2+ and was associated with an increased affinity of the RyR for ryanodine (Kd = 204 nM in the absence, versus 107 nM in the presence of 10 mM P(i)). P(i) (10 mM) also increased the rate of Ca2+ release from 45Ca(2+)-filled skeletal muscle SR vesicles by 50% in the presence of micromolar Ca2+. Conversely, arsenate and sulfate (10 mM) had no effect on either ryanodine binding or Ca(2+)-induced Ca2+ release, demonstrating the specificity of the P(i) effect. Single-channel recordings of purified skeletal muscle SR RyR incorporated into planar lipid bilayers showed that addition of 10 mM P(i) to the cis chamber increased the open probability of the channel by 91%. These results demonstrate that concentrations of P(i) which occur in vivo during exercise significantly stimulate the in vitro activity of the skeletal muscle RyR Ca2+ release channel.
Signal peptide replacements enhance expression and secretion of hepatitis C virus envelope glycoproteins (2011)

A large number of researches focused on glycoproteins E1 and E2 of hepatitis C virus (HCV) aimed at the development of anti-HCV vaccines and inhibitors. Enhancement of E1/E2 expression and secretion is critical for the characterization of these glycoproteins and thus for subunit vaccine development. In this study, we designed and synthesized three signal peptide sequences based on online programs SignalP, TargetP, and PSORT, then removed and replaced the signal peptide preceding E1/E2 by overlapping the polymerase chain reaction method. We assessed the effect of this alteration on E1/E2 expression and secretion in mammalian cells, using western blot analysis, dot blot, and Galanthus nivalis agglutinin lectin capture enzyme immunoassay. Replacing the peptides preceding E1 and E2 with the signal peptides of the tissue plasminogen activator and Gaussia luciferase resulted in maximum enhancement of E1/E2 expression and secretion of E1 in mammalian cells, without altering glycosylation. Such an advance would help to facilitate both the research of E1/E2 biology and the development of an effective HCV subunit vaccine. The strategy used in this study could be applied to the expression and production of other glycoproteins in mammalian cell line-based systems.
Detection of a spinning object using lights orbital angular momentum (2013)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. P. J. Lavery, F. C. Speirits, S. M. Barnett, and M. J. Padgett, "Detection of a spinning object using lights orbital angular momentum," in Frontiers in Optics 2013, I. Kang, D. Reitze, N. Alic, and D. Hagan, eds., OSA Technical Digest (online) (Optica Publishing Group, 2013), paper FTu1F.5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Glass reinforced plastic waste characterisation and recycling potential (2009)

The aim of the study reported herein, which is part of an ongoing industry and government funded project, was to characterise GRP waste and to assess its recycling potential in concrete composites and polymer-rubber composites. Detailed characterisation studies of GRP waste were carried out in terms of physical, and chemical properties. The physical characterisation results showed that the GRP waste polyester resin powder had a wide particle size distribution ranging from 0.02 micro meter to 600 micro meter. The particle size analysis and scanning electron microscopy (SEM) studies showed that the GRP waste powder particles were different in size and were irregular in shape. Using the energy dispersive X-ray spectroscopy (EDX) spectrum, the chemical characterisation of the GRP powder showed that the major chemical constituents in the GRP powder were silica (Si), calcium (Ca), aluminium (Al) and oxygen (O).