gebhart/patrepeval huggingface dataset:
Suppression subtractive hybridization profiles of radial growth phase and metastatic melanoma cell lines reveal novel potential targets (2008)

This study identifies two populations of genes differentially expressed between melanoma cell lines from two tumor stages and suggests that these sets of genes represent profiles of less aggressive versus metastatic melanomas. A search for expression profiles of melanoma in available expression study databases allowed us to point to a great potential of involvement in tumor progression for several of the genes identified here. A few sequences obtained here may also contribute to extend annotated mRNAs or to the identification of novel transcripts.
Using hardware transactional memory for data race detection (2009)

Widespread emergence of multicore processors will spur development of parallel applications, exposing programmers to degrees of hardware concurrency hitherto unavailable. Dependable multithreaded software will have to rely on the ability to dynamically detect non-deterministic and notoriously hard to reproduce synchronization bugs manifested through data races. Previous solutions to dynamic data race detection have required specialized hardware, at additional power, design and area costs. We propose RaceTM, a novel approach to data race detection that exploits hardware that will likely be present in future multiprocessors, albeit for a different purpose. In particular, we show how emerging hardware support for transactional memory can be leveraged to aid data race detection. We propose the concept of lightweight debug transactions that exploit the conflict detection mechanisms of transactional memory systems to perform data race detection. We present a proof-of-concept simulation prototype, and evaluate it on data races injected into applications from the SPLASH-2 suite. Our experiments show that this technique is effective at discovering data races and has low performance overhead.
Field Monitoring Using Sensor-Nodes with a Web Server (2005)

In order to realize field and environment monitoring over long periods, we propose remote monitoring that responds flexibly and dynamically to change. Field Servers are one of the small monitoring sensor-nodes having a Web server accessed via the Internet and using a wireless LAN to provide a high-speed transmission network differing from traditional sensor-nodes. Monitoring with Field Servers enables easy installation, monitoring field information, and remote operation in any field. By providing a Web server for all modules, we can treat them collectively via the Internet. To evaluate this monitoring, we managed numerous Field Servers in different countries using an agent program. Field experiments show the system is safe and effective for remote monitoring applications.
Extracellular mRNA Induces Dendritic Cell Activation by Stimulating Tumor Necrosis Factor-α Secretion and Signaling through a Nucleotide Receptor (2002)

We previously demonstrated that dendritic cell (DC) pulsing with antigen-encoded mRNA resulted in the loading of both major histocompatibility complex class I and II antigen presentation pathways and the delivery of an activation signal. Coculture of mRNA-pulsed DC with T cells led to the induction of a potent primary immune response. DC, in addition to recognizing foreign antigens through pattern recognition receptors, also must respond to altered self, transformed, or intracellularly infected cells. This occurs through cell surface receptors that recognize products of inflammation and cell death. In this report, we characterize two signaling pathways utilized by extracellular mRNA to activate DC. In addition, a novel ligand, poly(A), is identified that mediates signaling through a receptor that can be inhibited by pertussis toxin and suramin and can be desensitized by ATP and ADP, suggesting a P2Y type nucleotide receptor. The role of this signaling activity in vaccine design and the potential effect of mRNA released by damaged cells in the induction of immune responsiveness is discussed.
Natural co‐occurrence of <i>Fusarium toxins</i> and aflatoxin B<sub>1</sub> in com for feed in North Vietnam (1995)

Natural occurrence of Fusarium mycotoxins (trichothecenes and fumonisins) and aflatoxin B1 (AFB1) were surveyed in 32 corn samples, harvested in 1993 and randomly sampled in 1994 in several districts of Hanoi, Vietnam. Corn samples were first milled into fine powder, extracted with methanol-water (3:1) and the crude extracts obtained from the same samples were used for the simultaneous analysis of the trichothecenes such as nivalenol (NIV), deoxynivalenol (DON), and T-2 toxin (T-2) by gas chromatography/mass spectrometry (GC/NS); fumonisins B1 (FB1), B2 (FB2), and B3 (FB3) by high-performance liquid chromatography (HPLC) with a flourescence detector; and AFB1 by and ELISA kit based on a monoclonal antibody. The data revealed that 14, 8, 4, 3, and 2 out of 15 corn kernel samples were positive for AFB1, FB1, FB2, FB3, and NIV with the average levels being 28, 1, 101, 276, 232, and 858 ppb, respectively, and neither DON nor T-2 were detected. As for the other 17 samples of corn powder, 13, 15, 12, 10, 4 and 2 were positive for AFB1, FB1, FB2, FB3, DON, and NIV with the average being 30, 780, 289, 176, 3, 170, and 1,365 ppb, respectively, and T-2 was not detected. Although their positive rates and levels fell in the ranges reported elsewhere, it was found for the first time that the Fusarium toxins (NIV, DON, and fumonisins) and an Aspergillus toxin (AFB1) were naturally co-contaminated in selected samples of corn produced in north Vietnam.
On T Cell Memory: Arguments for Antigen Dependence (1996)

Memory is a hallmark of the immune system. Considerable progress has been made towards understanding B cell memory, but T cell memory remains poorly understood and its nature is controversial. There is good evidence that B cell memory is driven by antigen, but the antigen dependence of T cell memory is still being debated. For several years we have investigated the nature, duration and antigen dependence of different aspects of CD8+ T cell memory and this review will discuss our findings as well as how and why they differ from some other results. As others, we find that antigen, due to proliferation of antigen-specific T cell clones, induces a shift in the T cell repertoire which remains detectable for years as an elevated cytotoxic T cell precursor frequency (CTLp) in lymphoid organs. Also in the absence of antigen, in vitro assays for T cell memory which invariably isolate memory T cells from these lymphoid organs therefore remain positive. In contrast, immunity against reinfection with a pathogen requires more than just elevated numbers of CTLp in lymphoid organs. Since reinfection usually takes place via peripheral nonlymphoid tissue, these CTLp have to a) efficiently extravasate and patrol through such tissues, and b) be immediately able to exert effector function in case of reinfection. Both functions, require a certain level of activation which critically depends on T cell stimulation by persisting antigen.
Decoding accuracy in eRF1 mutants and its correlation with pleiotropic quantitative traits in yeast (2010)

Translation termination in eukaryotes typically requires the decoding of one of three stop codons UAA, UAG or UGA by the eukaryotic release factor eRF1. The molecular mechanisms that allow eRF1 to decode either A or G in the second nucleotide, but to exclude UGG as a stop codon, are currently not well understood. Several models of stop codon recognition have been developed on the basis of evidence from mutagenesis studies, as well as studies on the evolutionary sequence conservation of eRF1. We show here that point mutants of Saccharomyces cerevisiae eRF1 display significant variability in their stop codon read-through phenotypes depending on the background genotype of the strain used, and that evolutionary conservation of amino acids in eRF1 is only a poor indicator of the functional importance of individual residues in translation termination. We further show that many phenotypes associated with eRF1 mutants are quantitatively unlinked with translation termination defects, suggesting that the evolutionary history of eRF1 was shaped by a complex set of molecular functions in addition to translation termination. We reassess current models of stop-codon recognition by eRF1 in the light of these new data.
Organizational Change Models In Small And Medium Sized Enterprises (Smes) (2011)

Bringing forward the concepts of change and change management is no longer surprising nowadays. Small and Medium Enterprises (SMEs) face unique and difficult challenges in the business environment. Challenges to the growth and viability of Small and Medium Enterprises (SMEs) are arising from several external factors, like globalization, increased customer expectations or competition, technological advances, all of the factors being determined by the change. SMEs need to successfully deal with the prevalent forces for change if they are to survive and grow and meet the expectations to create investment and employment opportunities. For organizations to develop, they often must undergo significant change at various points in their development. That's why the topic of organizational change and development has become widespread in communications about business, organizations, leadership and management.
Experience With Candida Infections in the Burn Patient (1972)

A review of 427 acutely burned patients reveals that<i>Candida</i>organisms were cultured in 271 patients. The organism was found in the wound in 233 patients and in the urine in 131. Positive blood cultures were present in 22 instances. Disseminated candidiasis was demonstrated at autopsy in 14 of the 65 patients who died. The presence of the organism in the wound may not be of clinical significance, but disseminated systemic infection does occur in a significant number of cases. Discontinuing antibiotic therapy, the removal of intravenous catheters, and, where appropriate, intravenous administration of amphotericin B is advised. While<i>Candida albicans</i>has long been recognized as a pathogen, other species of<i>Candida</i>are also capable of causing systemic disease.
A Comprehensive Map of the Human Urinary Proteome (2011)

The study of the human urinary proteome has the potential to offer significant insights into normal physiology as well as disease pathology. The information obtained from such studies could be applied to the diagnosis of various diseases. The high sensitivity, resolution, and mass accuracy of the latest generation of mass spectrometers provides an opportunity to accurately catalog the proteins present in human urine, including those present at low levels. To this end, we carried out a comprehensive analysis of human urinary proteome from healthy individuals using high-resolution Fourier transform mass spectrometry. Importantly, we used the Orbitrap for detecting ions in both MS (resolution 60 000) and MS/MS (resolution 15 000) modes. To increase the depth of our analysis, we characterized both unfractionated as well as lectin-enriched proteins in our experiments. In all, we identified 1,823 proteins with less than 1% false discovery rate, of which 671 proteins have not previously been reported as constituents of human urine. This data set should serve as a comprehensive reference list for future studies aimed at identification and characterization of urinary biomarkers for various diseases.
Iterative Closest Normal Point for 3D Face Recognition (2013)

The common approach for 3D face recognition is to register a probe face to each of the gallery faces and then calculate the sum of the distances between their points. This approach is computationally expensive and sensitive to facial expression variation. In this paper, we introduce the iterative closest normal point method for finding the corresponding points between a generic reference face and every input face. The proposed correspondence finding method samples a set of points for each face, denoted as the closest normal points. These points are effectively aligned across all faces, enabling effective application of discriminant analysis methods for 3D face recognition. As a result, the expression variation problem is addressed by minimizing the within-class variability of the face samples while maximizing the between-class variability. As an important conclusion, we show that the surface normal vectors of the face at the sampled points contain more discriminatory information than the coordinates of the points. We have performed comprehensive experiments on the Face Recognition Grand Challenge database, which is presently the largest available 3D face database. We have achieved verification rates of 99.6 and 99.2 percent at a false acceptance rate of 0.1 percent for the all versus all and ROC III experiments, respectively, which, to the best of our knowledge, have seven and four times less error rates, respectively, compared to the best existing methods on this database.
Preclinical considerations and results with the combination of verapamil and trandolapril: blood pressure reduction and beyond. (1997)

Two weeks after occlusion of the left anterior descending artery, surviving rats were randomly allocated to no treatment or to verapamil at 20 or 40 mg/kg per day or to trandolapril at 0.3 or 0.7 mg/kg per day or to combinations of both drugs, orally for 24 weeks. (ABSTRACT TRUNCATED)
Effects of Anemarrhena asphodeloides on Focal Ischemic Brain Injury Induced by Middle Cerebral Artery Occlusion in Rats (2007)

The preventive effect of Anemarrhena asphodeloides Bunge (Liliaceae), a traditional Chinese medicine, on ischemia-reperfusion-induced brain injury was evaluated in the rat brain. Ischemia was induced by intraluminal occlusion of the right middle cerebral artery for 2 h and reperfusion was continued for 22 h. Water extract of Anemarrhena asphodeloides (WEAA) was orally administered promptly prior to and 2 h after reperfusion. Total infarct volume and edema in the ipsilateral hemispheres of ischemia-reperfusion rats were significantly reduced by treatment with WEAA in a dose-dependent manner (p<0.05). The therapeutic time window of WEAA was 3 h in this ischemia-reperfusion rat model. WEAA also significantly inhibited increased neutrophil infiltration of ischemic brain tissue as estimated by myeloperoxidase (MPO) activity and immunohistochemical analysis. MPO-positive cells were markedly reduced by WEAA administration in striatal and cortical areas. These findings suggest that WEAA plays a crucial protective role in ischemia-induced brain injury, and suggest that WEAA could serve as a lead medicinal herb for the development of neuroprotective agents following transient focal ischemic brain injury.
Innovative VDI Standards: Moving an Industry Forward (2009)

Effective self-service automation requires data sharing among non-proprietary system components. Historically, the original self-service provider, the vending industry, has failed to develop and implement open architecture standards that enable seamless data sharing among disparate devices and servers in a network. This lack of interoperability among the main entities in a sophisticated vending system (e.g. vending machine controller, telemetry device, vending management software, and cashless payment equipment) has contributed to a lack of innovation and creativity in the evolution of unattended point-ofsale retailing. Recently crafted Vending Data Interchange (VDI) standards from the National Automatic Merchandising Association (NAMA) provide a non-proprietary means by which to share machine-level data among diverse technology providers. The VDI standards are designed to ensure reliability, continuity, and longevity among installed hardware, software, and netware. In essence, VDI standards contain technical specifications that bundle vending machine-level data for easy distribution throughout a vending operator’s technology network and can be implemented by a qualified provider without operator involvement.
Migration velocity analysis from locally coherent events in 2-D laterally heterogeneous media, Part II: Applications on synthetic and real data (2002)

Abstract We demonstrate a method for estimating 2-D velocity models from synthetic and real seismic reflection data in the framework of migration velocity analysis (MVA). No assumption is required on the reflector geometry or on the unknown background velocity field, provided that the data only contain primary reflections/diffractions. In the prestack depth-migrated volume, locations where the reflectivity exhibits local coherency are automatically picked without interpretation in two panels: common image gathers (CIGs) and common offset gathers (COGs). They are characterized by both their positions and two slopes. The velocity is estimated by minimizing all slopes picked in the CIGs. We test the applicability of the method on a real data set, showing the possibility of an efficient inversion using (1) the migration of selected CIGs and COGs, (2) automatic picking on prior uncorrelated locally coherent events, (3) efficient computation of the gradient of the cost function via paraxial ray tracing from the picked events to the surface, and (4) a gradient-type optimization algorithm for convergence.
Single-mode MxN star couplers fabricated using fused biconical taper techniques (1991)

Over the last few years the fused biconical taper (FBT) process has been the technology of choice for fabricating passive fiber optic couplers. The FBT couplers can be made with a wide variety of fiber types and exhibit excellent optical and envirornnental characteristics. Recently much attention has been given to the fabrication of compact MxN singlemode star couplers for future local subscriber loop applications. Some of the systems being considered utilize passive star architectures which require singlemnode star couplers to split the light to a multiple number of ports or residences. In this paper we report the fabrication of true lxN and MxN singlemnode tree and star couplers using the fused biconical taper techniques. In addition to good optical uniformity and insertion loss the fused couplers offer the same environmental stability and long term reliability that are characteristic of standard FBT couplers. A discussion of the optical and environmental data will be presented.
Using Search Methods for Selecting and Combining Software Sensors to Improve Fault Detection in Autonomic Systems (2010)

Fault-detection approaches in autonomic systems typically rely on runtime software sensors to compute metrics for CPU utilization, memory usage, network throughput, and so on. One detection approach uses data collected by the runtime sensors to construct a convex-hull geometric object whose interior represents the normal execution of the monitored application. The approach detects faults by classifying the current application state as being either inside or outside of the convex hull. However, due to the computational complexity of creating a convex hull in multi-dimensional space, the convex-hull approach is limited to a few metrics. Therefore, not all sensors can be used to detect faults and so some must be dropped or combined with others. This paper compares the effectiveness of genetic-programming, genetic-algorithm, and random-search approaches in solving the problem of selecting sensors and combining them into metrics. These techniques are used to find 8 metrics that are derived from a set of 21 available sensors. The metrics are used to detect faults during the execution of a Java-based HTTP web server. The results of the search techniques are compared to two hand-crafted solutions specified by experts.
Dissociative recombination cross section and branching ratios of protonated dimethyl disulfide and <i>N</i>-methylacetamide (2004)

Dimethyl disulfide (DMDS) and N-methylacetamide are two first choice model systems that represent the disulfide bridge bonding and the peptide bonding in proteins. These molecules are therefore suitable for investigation of the mechanisms involved when proteins fragment under electron capture dissociation (ECD). The dissociative recombination cross sections for both protonated DMDS and protonated N-methylacetamide were determined at electron energies ranging from 0.001 to 0.3 eV. Also, the branching ratios at 0 eV center-of-mass collision energy were determined. The present results give support for the indirect mechanism of ECD, where free hydrogen atoms produced in the initial fragmentation step induce further decomposition. We suggest that both indirect and direct dissociations play a role in ECD.
Invariant measures for some one-dimensional attractors (1982)

Abstract We consider certain non-invertible maps of the square which are extensions of the quadratic maps of the interval and their small perturbations. We show that several maps of the type possess attractors which are not hyperbolic but have invariant measures similar to Bowen-Ruelle measures for hyperbolic attractors.
Breed differences in boar taint: relationship between tissue levels boar taint compounds and sensory analysis of taint. (1996)

A total of 228 intact male pigs form Duroc, Hampshire, Landrace, and Yorkshire breeds were used in the experiment. Samples of salivary gland and backfat were collected at slaughter for colorimetric assay of salivary and fat 16-androstene levels and fat skatole levels. Fat levels also were tested by a sensory panel using an R-index technique for detecting the presence of boar taint. The proportion of tainted carcasses determined by the sensory panel was 5.0% for androstenone and 11.4% for skatole, with a combined total of 15.0% tainted from either source. Sensory analysis of taint showed a lower proportion (P < .05) of tainted carcasses in Hampshire, with no difference in taint across the other three breeds. Analysis of taint compounds indicated that overall 14.5% of pigs had salivary gland 16-androstene levels and 20.9% had fat 16-androstene levels above acceptable limits. There was a higher (P < .05) proportion of Duroc pigs above the threshold levels for 16-androstenes in both salivary gland and fat. Landrace pigs had the lowest (P < .05) average tissue concentrations of steroids and skatole. Across breeds, only 1.8% of pigs had fat skatole concentrations above .25 ppm, which has been suggested as threshold levels of skatole for taint. The canonical correlation coefficient between fat compound levels and the R-indices of fat 16-androstenes and skatole was .40 (P < .001). Our results indicate breed differences in tissue levels of taint compounds and in taint assessed by a sensory panel. Levels of 16-androstene steroids were highly associated with taint, but more pigs had measured levels above the threshold than those identified as tainted by sensory analysis. Levels of fat skatole were low overall and did not account for all the pigs judged as tainted from skatole by sensory analysis.
A microfabricated deformability-based flow cytometer with application to malaria (2011)

Malaria resulting from Plasmodium falciparum infection is a major cause of human suffering and mortality. Red blood cell (RBC) deformability plays a major role in the pathogenesis of malaria. Here we introduce an automated microfabricated "deformability cytometer" that measures dynamic mechanical responses of 10(3) to 10(4) individual RBCs in a cell population. Fluorescence measurements of each RBC are simultaneously acquired, resulting in a population-based correlation between biochemical properties, such as cell surface markers, and dynamic mechanical deformability. This device is especially applicable to heterogeneous cell populations. We demonstrate its ability to mechanically characterize a small number of P. falciparum-infected (ring stage) RBCs in a large population of uninfected RBCs. Furthermore, we are able to infer quantitative mechanical properties of individual RBCs from the observed dynamic behavior through a dissipative particle dynamics (DPD) model. These methods collectively provide a systematic approach to characterize the biomechanical properties of cells in a high-throughput manner.