gebhart/patrepeval huggingface dataset:
Urinary proteomics as a novel tool for biomarker discovery in kidney diseases (2010)

Urine has become one of the most attractive biofluids in clinical proteomics, for its procurement is easy and noninvasive and it contains sufficient proteins and peptides. Urinary proteomics has thus rapidly developed and has been extensively applied to biomarker discovery in clinical diseases, especially kidney diseases. In this review, we discuss two important aspects of urinary proteomics in detail, namely, sample preparation and proteomic technologies. In addition, data mining in urinary proteomics is also briefly introduced. At last, we present several successful examples on the application of urinary proteomics for biomarker discovery in kidney diseases, including diabetic nephropathy, IgA nephropathy, lupus nephritis, renal Fanconi syndrome, acute kidney injury, and renal allograft rejection.
Soft Computing for diagnostics in equipment service (2001)

We present methods and tools from the Soft Computing (SC) domain, which is used within the diagnostics and prognostics framework to accommodate imprecision of real systems. SC is an association of computing methodologies that includes as its principal members fuzzy, neural, evolutionary, and probabilistic computing. These methodologies enable us to deal with imprecise, uncertain data and incomplete domain knowledge typically encountered in real-world applications. We outline the advantages and disadvantages of these methodologies and show how they can be combined to create synergistic hybrid SC systems. We conclude the paper with a description of successful SC case study applications to equipment diagnostics.
Area-efficient pulse-shaping 1:4 interpolated FIRfilterbased on LUT partitioning (1999)

The design of an area-efficient pulse-shaping 1:4 interpolation FIR filter with a partitioned LUT structure is described. Since the LUT block of the FIR filter occupies a large area relative to that of other blocks, in the proposed FIR filter design the LUT size is reduced by partitioning, exploiting coefficient symmetry, and sharing the partitioned LUTs by multiplexing input data streams. Experiments show that in the proposed filter the area is reduced by >40% compared to the popular single-architecture dual-channel filter. The proposed FIR filter produces optimised results in the QPSK modulator.
TARGETgene: A Tool for Identification of Potential Therapeutic Targets in Cancer (2012)

The vast array of in silico resources and data of high throughput profiling currently available in life sciences research offer the possibility of aiding cancer gene and drug discovery process. Here we propose to take advantage of these resources to develop a tool, TARGETgene, for efficiently identifying mutation drivers, possible therapeutic targets, and drug candidates in cancer. The simple graphical user interface enables rapid, intuitive mapping and analysis at the systems level. Users can find, select, and explore identified target genes and compounds of interest (e.g., novel cancer genes and their enriched biological processes), and validate predictions using user-defined benchmark genes (e.g., target genes detected in RNAi screens) and curated cancer genes via TARGETgene. The high-level capabilities of TARGETgene are also demonstrated through two applications in this paper. The predictions in these two applications were then satisfactorily validated by several ways, including known cancer genes, results of RNAi screens, gene function annotations, and target genes of drugs that have been used or in clinical trial in cancer treatments. TARGETgene is freely available from the Biomedical Simulations Resource web site (http://bmsr.usc.edu/Software/TARGET/TARGET.html).
Usefulness of three probes in typing isolates of methicillin-resistant Staphylococcus aureus (MRSA) (1991)

Fifty-nine epidemiologically unrelated methicillin-resistant Staphylococcus aureus (MRSA) isolates from different geographical areas and 23 phage-type 77 MRSA isolates from France were investigated. Cellular DNA, digested with restriction endonucleases EcoRI or HindIII, was probed with plasmids carrying the gene encoding 16S rRNA (pBA2), the gene aacA-aphD (pSF815A) and the gene aacA-aphD plus part of IS256 (pIP1307). When probed with pBA2, most of the unrelated isolates displayed the same hybridisation pattern. A greater diversity in patterns was detected in gentamicin-resistant strains with the two other probes. The most accurate fingerprinting of these isolates was obtained with the probe pIP1307. Moreover, this probe appeared to be useful for tracing the phage-type 77 epidemic MRSA isolates widespread in French hospitals.
Recombinant Activated Factor VII in Obstetric Hemorrhage (2011)

Phillips, L.E.; McLintock, C.; Pollock, W.; Gatt, S.; Popham, P.; Jankelowitz, G.; Ogle, R.; Cameron, P.A. Author Information
The Evaluation of an Abdominal Aortic Tourniquet for the Control of Pelvic and Lower Limb Hemorrhage (2013)

Despite improved body armor, hemorrhage remains the leading cause of preventable death on the battlefield. Trauma to the junctional areas such as pelvis, groin, and axilla can be life threatening and difficult to manage. The Abdominal Aortic Tourniquet (AAT) is a prehospital device capable of preventing pelvic and proximal lower limb hemorrhage by means of external aortic compression. The aim of the study was to evaluate the efficacy of the AAT. Serving soldiers under 25 years old were recruited. Basic demographic data, height, weight, blood pressure, and abdominal girth were recorded. Doppler ultrasound was used to identify blood flow in the common femoral artery (CFA). The AAT was applied while the CFA flow was continuously monitored. The balloon was inflated until flow in the CFA ceased or the maximum pressure of the device was reached. A total of 16 soldiers were recruited. All participants tolerated the device. No complications were reported. Blood flow in the CFA was eliminated in 15 out of 16 participants. The one unsuccessful subject was above average height, weight, body mass index, and abdominal girth. This study shows the AAT to be effective in the control of blood flow in the pelvis and proximal lower limb and potentially lifesaving.
Identification of a Potential Receptor That Couples Ion Transport to Protein Kinase Activity (2010)

In our previous studies, we have demonstrated that the Src-coupled α1 Na/K-ATPase works as a receptor for cardiotonic steroids, such as ouabain, to regulate cellular protein kinase cascades. Here, we explore further the structural determinants of the interaction between the α1 Na/K-ATPase and Src and demonstrate that the Src-coupled α1 Na/K-ATPase allows the cell to decode the transmembrane transport activity of the Na/K-ATPase to turn on/off protein kinases. The α1 Na/K-ATPase undergoes E1/E2 conformational transition during an ion pumping cycle. The amount of E1 and E2 Na/K-ATPase is regulated by extracellular K(+) and intracellular Na(+). Using purified enzyme preparations we find that the E1 Na/K-ATPase can bind both the Src SH2 and kinase domains simultaneously and keep Src in an inactive state. Conversely, the E1 to E2 transition releases the kinase domain and activates the associated Src. Moreover, we demonstrate that changes in E1/E2 Na/K-ATPase by either Na(+) or K(+) are capable of regulating Src and Src effectors in live cells. Together, the data suggest that the Src-coupled α1 Na/K-ATPase may act as a Na(+)/K(+) receptor, allowing salt to regulate cellular function through Src and Src effectors.
Detecting and correcting user activity switches (2009)

The TaskTracer system allows knowledge workers to define a set of activities that characterize their desktop work. It then associates with each user-defined activity the set of resources that the user accesses when performing that activity. In order to correctly associate resources with activities and provide useful activity-related services to the user, the system needs to know the current activity of the user at all times. It is often convenient for the user to explicitly declare which activity he/she is working on. But frequently the user forgets to do this. TaskTracer applies machine learning methods to detect undeclared activity switches and predict the correct activity of the user. This paper presents TaskPredictor2, a complete redesign of the activity predictor in TaskTracer and its notification user interface. TaskPredictor2 applies a novel online learning algorithm that is able to incorporate a richer set of features than our previous predictors. We prove an error bound for the algorithm and present experimental results that show improved accuracy and a 180-fold speedup on real user data. The user interface supports negotiated interruption and makes it easy for the user to correct both the predicted time of the task switch and the predicted activity.
Spacecraft Multiple Array Communication System Performance Analysis (2010)

The Communication Systems Simulation Laboratory (CSSL) at the NASA Johnson Space Center is tasked to perform spacecraft and ground network communication system simulations, design validation, and performance verification. The CSSL has developed simulation tools that model spacecraft communication systems and the space and ground environment in which the tools operate. In this paper, a spacecraft communication system with multiple arrays is simulated. Multiple array combined technique is used to increase the radio frequency coverage and data rate performance. The technique is to achieve phase coherence among the phased arrays to combine the signals at the targeting receiver constructively. There are many technical challenges in spacecraft integration with a high transmit power communication system. The array combining technique can improve the communication system data rate and coverage performances without increasing the system transmit power requirements. Example simulation results indicate significant performance improvement can be achieved with phase coherence implementation.
Which app will you use next? (2013)

The application a smart phone user will launch next intuitively depends on the sequence of apps used recently. More generally, when users interact with systems such as shopping websites or online radio, they click on items that are of interest in the current context. We call the sequence of clicks made in the current session interactional context. It is desirable for a recommender system to use the context set by the user to update recommendations. Most current context-aware recommender systems focus on a relatively less dynamic representational context defined by attributes such as season, location and tastes. In this paper, we study the problem of collaborative filtering with interactional context, where the goal is to make personalized and dynamic recommendations to a user engaged in a session. To this end, we propose the methodname algorithm that works in two stages. First, users are clustered by their transition behavior (one-step Markov transition probabilities between items), and cluster-level Markov models are computed. Then personalized PageRank is computed for a given user on the corresponding cluster Markov graph, with a personalization vector derived from the current context. We give an interpretation of the second stage of the algorithm as adding an appropriate context bias, in addition to click bias (or rating bias), to a classical neighborhood-based collaborative filtering model, where the neighborhood is determined from a Markov graph. Experimental results on two real-life datasets demonstrate the superior performance of our algorithm, where we achieve at least 20% (up to 37%) improvement over competitive methods in the recall level at top-20.
Microengineered hydromechanical cochlear model (2005)

Micromachined fluid-filled variable impedance waveguides intended to mimic the mechanics of the passive mammalian cochlea have been fabricated and experimentally examined. The structures were microfabricated with dimensions similar to those of the biological system. Experimental tests demonstrate acoustically excited traveling fluid-structure waves with phase accumulations between 1.5 and 3 pi radians at the location of maximum response. The resulting measured frequency-position mapping function, with similarities to that observed in the cochlea, is presented. Results for both isotropic and orthotropic membranes are reported, demonstrating that the achieved orthotropy ratio of 8:1 in tension is insufficient to produce the sharp filtering observed in animal experiments and many computational models that use higher ratios. It is also shown experimentally that high viscosity fluids must be used to provide sufficient damping to avoid the formation of a nonphysiological standing wave pattern. A mathematical model incorporating a thin-layer viscous, compressible fluid approximation coupled to an orthotropic membrane model is validated against experimental results. The work presented herein is motivated by the possibility of producing microfabricated cochlear-like filters, thus the structure is designed for production in a scalable microfabrication process.
Competitive exclusion treatment reduces the mortality and fecal shedding associated with enterotoxigenic Escherichia coli infection in nursery-raised neonatal pigs. (2000)

We have previously reported that the administration of a competitive exclusion culture (PCF-1), derived from the cecal microflora of a young, healthy pig and maintained in a continuous flow fermentation system to neonatal pigs resulted in a decrease in the incidence of fecal shedding and cecal colonization by Salmonella choleraesuis in pigs at weaning. In the present experiment, we describe the effects of the administration of a derivative of the PCF-1 culture, RPCF, against an enterotoxigenic E. coli infection in neonatal pigs raised off-sow. The administration of RPCF at 12 and 24 hours after birth resulted in significant (P < 0.05) reductions in mortality, incidence of fecal shedding, and in gut colonization by E. coli when compared to control values. The RPCF reduced mortality from 17.5%, observed in untreated pigs, to 4.4% in RPCF-treated pigs. Fecal shedding of E. coli was reduced significantly (P < 0.05) in RPCF-treated pigs between Days 1 and 3 post-challenge. These results indicate that the RPCF culture is effective against one of the most important causes of neonatal scours (E. coli infections) in piglets.
Purification and Characterization of an Inhibitor of Calcium- Activated Neutral Protease from Rabbit Skeletal Muscle (1981)

An endogenous inhibitor of calcium-activated neutral protease was purified to homogeneity from rabbit skeletal muscle using ion-exchange chromatography on DEAE-cellulose and QAE-Sephadex A-50 columns, chromatofocusing, and hydro phobic interaction chromatography on a phenyl-Sepharose CL-4B column. The purified inhibitor was shown to be a dimer of identical subunits and each subunit has a molecular weight of about 34,000. This inhibitor was remarkably thermo and acid-stable. It was specific for calcium-activated neutral protease and had no effect on any other protease examined (trypsin, papairi, cr-chymotrypsin, bromelain, etc.). It is demonstrated that the inhibition is due to the formation of a stoichio metric complex between two enzyme molecules and one inhibitor molecule.
Helping TicketMaster: Changing the Economics of Ticket Robots with Geographic Proof-of-Work (2010)

When tickets for popular events such as Hannah Montana concerts go on sale online, they sell out almost instantly. Unfortunately, a significant number of them are purchased by world-wide networks of ticket purchasing robots run by scalpers looking to turn a quick profit. Ticket outlets currently employ CAPTCHAs to slow down fully automated purchasing robots. Since the profit associated with scalping tickets is several orders of magnitude larger than the cost associated with paying humans to solve the CAPTCHAs, this approach has been ineffective. CAPTCHAs have a fundamental flaw when used to protect online tickets: the cost to solve them using humans is fixed and small. To address this problem, this paper explores a novel alternative based on geographically-driven proof-of-work. The crux of the approach exploits the observation that most legitimate clients are located geographically close to the event. By requiring every client to solve a cryptographic puzzle whose difficulty is based on their distance to the event, ticket purchasing robots must be placed close to each event in order to monopolize the tickets. This requirement significantly increases the cost of operating such networks. Using emulation and simulation, we demonstrate the utility of our approach in tackling the online ticketing problem.
Tumour necrosis factor (1989)

Tumour necrosis factor, TNF, possesses the attributes of a typical cytokine, being a pleiotropic cell regulatory protein whose activity is largely determined by the cell type to which it binds and the presence of other protein regulators. Thus TNF can be a growth factor, cytotoxin, cytostatic agent or inducer of differentiation. This cytokine is also an important inflammatory mediator regulating the activity of neutrophils, eosinophils, T and B lymphocytes and modulating the properties of the vascular endothelium. All of these actions may play a role in the ability of TNF to induce necrosis of experimental animal tumours, but the potential of this cytokine in therapy of human cancer is uncertain. The increasing evidence for a role for TNF in the pathophysiology of acute and chronic disease makes the use of specific TNF antagonists an equally interesting therapeutic possibility.
Human Progesterone Receptor Complexed with the Antagonist RU 486 Binds to Hormone Response Elements in a Structurally Altered Form (1989)

Structural and functional properties of human progesterone receptors (PR) bound with the antiprogestin, RU 486, and the progestin agonist, R5020, were compared in order to identify receptor mechanisms responsible for the inability of RU 486 to activate the transcriptional capacity of receptors. RU 486 interaction with human PR did not inhibit receptor transformation as assessed by dissociation of nontransformed 8-10S oligomeric receptors (in vitro and in vivo) and by tight binding of PR to nuclei/chromatin in whole cells. Assays based on immunoprecipitation of PR-DNA complexes with an antibody to human PR and gel retardation were used to analyze the effect of RU 486 on receptor binding to the hormone response element (HRE) of the mouse mammary tumor virus (MMTV). RU 486 did not impair PR recognition of the MMTV HRE. Quantitative affinity constants and kinetic parameters of PR binding to these specific DNA sites were similar for receptors complexed with either agonist or antagonist. However, PR-RU 486 complexes exhibited an altered sedimentation rate on sucrose gradients and a faster mobility when bound to the MMTV HRE as assessed by gel retardation. These results indicate that human PR transformed by RU 486 exhibit no impairment in binding to specific DNA sites of target genes, but when bound to DNA assumes a structural form different from that of the receptor-agonist complexes to activate transcription results from this structural alteration in PR, which does not permit protein-protein interactions required for receptor-mediated induction of gene transcription.
Suppression of the critical angle of diffraction in thin-film colloidal photonic crystals (2010)

We present an experimental and numerical investigation of the polarization anisotropy of the zero-order backdiffracted light from three-dimensional thin-film photonic crystals assembled from colloidal spheres. In particular, we compare simulations of reflectance spectra from perfectly ordered fcc lattice of spheres with measured reflectance data from self-organized opal films and forced-assembled Langmuir-Blodgett crystal films. We identify cross-polarization couplings and interactions between photonic crystal eigenmodes as the major physical mechanisms for resonance depolarization effects. Based on this, we find that a necessary condition for the observation of critical angles of diffraction in three-dimensional lattices is that the orientation of the light's plane of incidence coincides with a high-symmetry plane of the crystal lattice. We further show that for currently achievable colloidal photonic crystals with moderate refractive index contrast, this resonance depolarization mechanisms together with the destructive influence of lattice disorder effectively renders the meaning of a critical angle of diffraction obsolete.
Regulation of T cell proliferation by anti-CD49d and anti-CD29 monoclonal antibodies (1992)

The beta 1 integrin VLA-4 (alpha 4 beta 1, CD49d/CD29), which is expressed on a large subpopulation of peripheral blood T lymphocytes, functions as a receptor for the endothelial adhesion protein VCAM-1 and the extracellular matrix protein fibronectin. Previous studies showed that immobilized fibronectin enhanced anti-CD3 monoclonal antibody (mAb)-induced T cell proliferation through binding to the integrins VLA-4 and VLA-5 (alpha 5 beta 1, CD49e/CD29). We studied the ability of the anti-CD49d mAb L25 to potentiate proliferation. T cell proliferation was induced by subthreshold concentrations of anti-CD3 mAb (mAb OKT3) coimmobilized with mAb L25 but not with coimmobilized anti-CD29 (beta 1) mAb. Soluble anti-CD29 mAb inhibited the proliferation induced by coimmobilized mAb OKT3 and L25 but not proliferation induced by mAb OKT3 with PMA or coimmobilized anti-CD26 mAb.
PAD4 is not essential for disease in the K/BxN murine autoantibody-mediated model of arthritis (2012)

PAD4 WT and KO mice develop disease in the K/BxN serum transfer model of arthritis with similar severity and kinetics, indicating that PAD4 is dispensable in this effector phase model of disease.
A Generalized Model of Plain Woven Fabric (1985)

A generalized model of plain woven fabric is proposed, based on a more realistic approximation of yarn bending behavior than that previously used. Peirce's rigid thread model is a special case. Approximate formulae for calculating the ratio of crimp height to thread spacing and weave angle are developed.
A New Preferential Etch for Defects in Silicon Crystals (1977)

A new preferential etch for (100) and (111) oriented, p‐ and n‐type silicon has been developed. Oxidation‐induced stacking faults, dislocations, swirl, and striations are clearly defined with minimum surface roughness or extraneous pitting. A relatively slow etch rate (∼1 μm per min) at room temperature provides etch control. The long shelf life of this etch allows the solution to be stored in large quantities.
Improvement of the KrF(<i>B</i>→<i>X</i>) excimer lamp with 248 and 193 nm dual wavelength emission using an Ar buffer (1990)

A quasi-continuous KrF(248 nm:B→X)fluorescence of over 8 ms pulse duration with a 100 Hz operation frequency was observed in a microwave-discharge-pumped KrF lamp with an Ar buffer gas in place of the He/Ne buffer. With an average microwave power deposition of 517.1 W, the maximum average KrF fluorescence power was 58.2 W obtained at a KrF intrinsic efficiency of 11.2% with the lamp gas mixture of F2/Kr/Ar=4/2/94(%) at 50 Torr and simultaneously an average ArF(193 nm:B→X) fluorescence power of 17.4 W with over 8 ms pulse duration at a 100 Hz operation frequency was also obtained. Based on the total fluorescence power of ArF and KrF, the intrinsic efficiency becomes as high as 14.6%. The maximum KrF intrinsic efficiency was 13.8% obtained with a lamp gas mixture of F2/Kr/Ar=2/2/96(%) at 50 Torr. The maximum average KrF fluorescence power and KrF intrinsic efficiency with the Ar buffer has exceeded the maximum average KrF fluorescence of 53 W and the corresponding KrF intrinsic efficiency of 8.3% achieved previously with the lamp gas mixture of F2/Kr/He/Ne=2/1/48.5/48.5(%) at 50 Torr. Dual wavelength emission should be useful for those that need both the 248 and 193 nm wavelengths.