gebhart/patrepeval huggingface dataset:
Cutting Edge: Contrasting Roles of TNF Receptor-Associated Factor 2 (TRAF2) and TRAF3 in CD40-Activated B Lymphocyte Differentiation (1999)

In B lymphocytes, CD40 signals contribute to the activation of Ab secretion, isotype switching, T cell costimulation, and immunological memory. TRAF proteins appear to be important components of the CD40 signal transduction complex, but their roles in the activation of B cell effector functions are poorly understood. We examined the contributions of TNF receptor-associated factor 2 (TRAF2) and TRAF3 to CD40-activated differentiation in mouse B cells transfected with inducible TRAF and dominant-negative TRAF cDNAs. We find that binding of TRAF2 and TRAF3 to CD40 is not required for the induction of Ab secretion, but that both TRAF molecules can regulate the activation process. We demonstrate a negative regulatory role for TRAF3 and that this activity is dependent on the availability of an intact TRAF3-binding site in the cytoplasmic domain of CD40. In contrast, TRAF2 appears to play a positive role in B cell differentiation, and this activity is apparent even when its binding site on CD40 is disrupted.
CdS/CdSe core/sheath nanostructures obtained from CdS nanowires (1999)

CdS/CdSe core/sheath nanowires with diameters of 7.7/0.75 nm were prepared by treating CdS nanowires with selenium in tributylphosphine (TBP) at 100 °C for 24 h and were characterized by X-ray powder diffraction, transmission electron microscopy, high resolution TEM, UV–VIS absorption spectra, photoluminescence spectra and X-ray photoelectron spectroscopy.
Efficient log authentication for forensic computing (2005)

In this paper, an efficient log authentication scheme for forensic computing is proposed. To conduct reliable forensic computing, it is required that the logs as digital evidences be verified. To verify them, digital signatures issued by authorities are needed. However, if many logging hosts connect to the server that issues the signatures, the traffic of the server will increase. Therefore, the authors proposed an efficient log authentication scheme for forensic computing. The scheme reduces the traffic of the sign server, which signs the logs of the logging hosts, by using distributed Merkle tree algorithm among the logging hosts. The scheme's effectiveness was shown through evaluation experiments.
Generalized Epilepsy with Febrile Seizures Plus (GEFS+): Clinical Spectrum in Seven Italian Families Unrelated to SCN1A, SCN1B, and GABRG2 Gene Mutations (2004)

The most frequently observed phenotypes matched those reported in families with mutations of the SCN1A, SCN1B, and GABRG2 genes. IGE and GEFS+ may overlap in some families, suggesting a shared genetic mechanism. The observation that 13% of affected individuals had focal epilepsy confirms previously reported rates and should prompt a reformulation of the "GEFS+" concept to include focal epileptogenesis.
A bio-inspired system for spatio-temporal recognition in static and video imagery (2007)

This paper presents a bio-inspired method for spatio-temporal recognition in static and video imagery. It builds upon and extends our previous work on a bio-inspired Visual Attention and object Recognition System (VARS). The VARS approach locates and recognizes objects in a single frame. This work presents two extensions of VARS. The first extension is a Scene Recognition Engine (SCE) that learns to recognize spatial relationships between objects that compose a particular scene category in static imagery. This could be used for recognizing the category of a scene, e.g., office vs. kitchen scene. The second extension is the Event Recognition Engine (ERE) that recognizes spatio-temporal sequences or events in sequences. This extension uses a working memory model to recognize events and behaviors in video imagery by maintaining and recognizing ordered spatio-temporal sequences. The working memory model is based on an ARTSTORE<sup>1</sup> neural network that combines an ART-based neural network with a cascade of sustained temporal order recurrent (STORE)<sup>1</sup> neural networks. A series of Default ARTMAP classifiers ascribes event labels to these sequences. Our preliminary studies have shown that this extension is robust to variations in an object's motion profile. We evaluated the performance of the SCE and ERE on real datasets. The SCE module was tested on a visual scene classification task using the LabelMe<sup>2</sup> dataset. The ERE was tested on real world video footage of vehicles and pedestrians in a street scene. Our system is able to recognize the events in this footage involving vehicles and pedestrians.
Mechanism of TNF-α modulation of Caco-2 intestinal epithelial tight junction barrier: role of myosin light-chain kinase protein expression (2005)

TNF-alpha plays a central role in the intestinal inflammation of various inflammatory disorders including Crohn's disease (CD). TNF-alpha-induced increase in intestinal epithelial tight junction (TJ) permeability has been proposed as one of the proinflammatory mechanisms contributing to the intestinal inflammation. The intracellular mechanisms involved in the TNF-alpha-induced increase in intestinal TJ permeability remain unclear. The purpose of this study was to investigate the possibility that the TNF-alpha-induced increase in intestinal epithelial TJ permeability was regulated by myosin light-chain kinase (MLCK) protein expression, using an in vitro intestinal epithelial model system consisting of the filter-grown Caco-2 intestinal epithelial monolayers. TNF-alpha (10 ng/ml) produced a time-dependent increase in Caco-2 MLCK expression. The TNF-alpha increase in MLCK protein expression paralleled the increase in Caco-2 TJ permeability, and the inhibition of the TNF-alpha-induced MLCK expression (by cycloheximide) prevented the increase in Caco-2 TJ permeability, suggesting that MLCK expression may be required for the increase in Caco-2 TJ permeability. The TNF-alpha increase in MLCK protein expression was preceded by an increase in MLCK mRNA expression but not an alteration in MLCK protein degradation. Actinomycin-D prevented the TNF-alpha increase in MLCK mRNA expression and the subsequent increase in MLCK protein expression and Caco-2 TJ permeability, suggesting that the increase in MLCK mRNA transcription led to the increase in MLCK expression. The TNF-alpha increase in MLCK protein expression was also associated with an increase in Caco-2 MLCK activity. The cycloheximide inhibition of MLCK protein expression prevented the TNF-alpha increase in MLCK activity and Caco-2 TJ permeability. Moreover, inhibitors of MLCK, Mg(2+)-myosin ATPase, and metabolic energy prevented the TNF-alpha increase in Caco-2 TJ permeability, suggesting that the increase in MLCK activity was required for the TNF-alpha-induced opening of the Caco-2 TJ barrier. In conclusion, our results indicate for the first time that 1) the TNF-alpha increase in Caco-2 TJ permeability was mediated by an increase in MLCK protein expression, 2) the increase in MLCK protein expression was regulated by an increase in MLCK mRNA transcription, and 3) the increase in Caco-2 TJ permeability required MLCK protein expression-dependent increase in MLCK activity.
A Simple Capacitive Charge-Division Readout for Position-Sensitive Solid-State Photomultiplier Arrays (2013)

A capacitive charge-division readout method for reading out a 2 × 2 array of 5 mm × 5 mm position-sensitive solid-state photomultipliers (PS-SSPM) was designed and evaluated. Using this analog multiplexing method, the 20 signals (16 position, 4 timing) from the PS-SSPM array are reduced to 5 signals (4 position, 1 timing), allowing the PS-SSPM array to be treated as an individual large-area PS-SSPM module. A global positioning approach can now be used, instead of individual positioning for each PS-SSPM in the array, ensuring that the entire light signal is utilized. The signal-to-noise ratio (SNR) and flood histogram quality at different bias voltages (27.5 V to 32.0 V at 0.5 V intervals) and a fixed temperature of 0 °C were evaluated by coupling a 6 × 6 array of 1.3 mm × 1.3 mm × 20 mm polished LSO crystals to the center of the PS-SSPM array. The timing resolution was measured at a fixed bias voltage of 31.0 V and a fixed temperature of 0 °C. All the measurements were evaluated and compared using capacitors with different values and tolerances. Capacitor values ranged from 0.051 nf to 10 nf, and the capacitance tolerance ranged from 1% to 20%. The results show that better performance was achieved using capacitors with smaller values and better capacitance tolerance. Using 0.2 nf capacitors, the SNR, energy resolution and timing resolution were 24.3, 18.2% and 8.8 ns at a bias voltage 31.0 V, respectively. The flood histogram quality was also evaluated by using a 10 × 10 array of 1 mm × 1 mm × 10 mm polished LSO crystals and a 10 × 10 array of 0.7 mm × 0.7 mm × 20 mm unpolished LSO crystals to determine the smallest crystal size resolvable. These studies showed that the high spatial resolution of the PS-SSPM was preserved allowing for 0.7 mm crystals to be identified. These results show that the capacitive charge-division analog signal processing method can significantly reduce the number of electronic channels, from 20 to 5, while retaining the excellent performance of the detector.
Why Can Smart Cut® Change the Future of Microelectronics? (2000)

Deposition techniques like chemical vapor deposition (CVD) offer to the semiconductor industry the initial flexibility to deposit thin films of key materials on many kinds of substrates. The homoepitaxy or hetroepitaxy techniques using CVD or molecular beam epitaxy (MBE) add the flexibility to get a pure monocrystalline thin film but with a major limitation: the starting substrate has to be monocrystalline. The missing technology has always been the one which allows the growth of a thin monocrystalline film on any kind of substrate. Hydrogen induced splitting (known today as Smart Cut®), discovered at the LETI laboratory in 1991, provides a unique opportunity to get crystalline layers on any kind of substrate. Therefore, a new tool is offered to the semiconductor industry, for new material developments and new structures. This technique is in use in production today on a first application: silicon-on-insulator (SOI) wafers which consist of a monocrystalline film of silicon on a thin amorphous silicon dioxide layer, on top of a silicon wafer. We will discuss the SOI application of the Smart Cut® technology and present other recently demonstrated breakthroughs in new material development, including SiC, compound semiconductor or 3D structures.
Transcriptome mining, functional characterization, and phylogeny of a large terpene synthase gene family in spruce (Piceaspp.) (2011)

The functional diversity of these characterized TPSs parallels the diversity of terpenoids found in the oleoresin and volatile emissions of Sitka spruce and provides a context for understanding this chemical diversity at the molecular and mechanistic levels. The comparative characterization of Sitka spruce and Norway spruce diterpene synthases revealed the natural occurrence of TPS sequence variants between closely related spruce species, confirming a previous prediction from site-directed mutagenesis and modelling.
Mode of action of the yeastSaccharomyces cerevisiaeas a feed additive for ruminants (1996)

Two suggested modes of action of yeast in stimulating rumen fermentation were investigated. The first, that yeast respiratory activity protects anaerobic rumen bacteria from damage by O2, was tested using different strains of yeast that had previously been shown to have differing abilities to increase the viable count of rumen bacteria. Saccharomyces cerevisiae NCYC 240, NCYC 1026, and the commercial product Yea-Sacc, added to rumen fluid in vitro at 1.3 mg/ml, increased the rate of O2 disappearance by between 46 and 89%. The same three preparations also stimulated bacterial numbers in an in vitro fermenter (Rusitec). S. cerevisiae NCYC 694 and NCYC 1088, which had no influence on the viable count in Rusitec, also had no effect on O2 uptake. Respiration-deficient (RD) mutants of S. cerevisiae NCYC 240 and NCYC 1026 were enriched by repeated culturing in the presence of ethidium bromide. S. cerevisiae NCYC 240 and NCYC 1026 stimulated the total and cellulolytic bacterial populations in Rusitec, while the corresponding RD mutants did not. Rigorous precautions to exclude air from Rusitec resulted in S. cerevisiae NCYC 240 no longer stimulating total bacterial numbers, although it still increased numbers of cellulolytic bacteria. The second hypothesis, that yeast provides malic and other dicarboxylic acids which stimulate the growth of some rumen bacteria, was examined by comparing the effects of yeast and malic acid on rumen fermentation in sheep. Three mature sheep were given 0.85 kg barley/d plus 0.55 kg chopped ryegrass hay/d either unsupplemented, or supplemented with 4 g S. cerevisiae NCYC 240/d or 100 mg L-malic acid/d either mixed with the diet or in aqueous solution infused continuously into the rumen. Yeast increased the total viable count of bacteria (P < 0.05) whereas malic acid did not, and no other effect of the treatments reached statistical significance. It was concluded, therefore, that the stimulation of rumen bacteria by S. cerevisiae is at least partly dependent on its respiratory activity, and is not mediated by malic acid.
The digital transducer, new sonar technology (2002)

The new digital architecture in sonar/echosounders designed and produced by BioSonics, Inc. is very different compared to traditional analog architecture. The acoustic signal received by the transducer is digitized inside the transducer unit just on the face of the transducer's ceramic element or elements, then the digitized echo signal is sent further to other units of the instrument, which removes problems associated with sending an analog echo signal through long cable lines. Traditional analog sonar/echo sounder systems suffer from high noise, excessive signal loss and signal distortion. Besides that, the wide dynamic range of the digital transducer allows simultaneous recording without saturation of very low echo signals from plankton particles and large bottom returns. The digital echo samples can be recorded on a PC computer hard drive. Digital design allows simplicity of operation (no controls such as gain knobs and switches) and a direct link between the echosounder and data processing and analysis software making the process of data acquisition simple and versatile. New digital technology allows new applications such as: (a) simple turnkey echosounder for mobile or fixed location surveying of aquatic resources, bottom typing and bathymetry, (b) deployment of unmanned platforms such as buoys, remote sensing stations on the surface or underwater for data storage and telemetering, (c) single or multiplexed transducers (single beam, dual beam, split beam), (d) wide range of frequencies (from 38 kHz to 1 MHz).
A Quick Guide for Developing Effective Bioinformatics Programming Skills (2009)

DOAJ is a unique and extensive index of diverse open access journals from around the world, driven by a growing community, committed to ensuring quality content is freely available online for everyone.
Secreted Glycoproteins Of Human Kidney Tumour Cells Contain Sulphated Complextype Oligosaccharides (1984)

Human kidney tumour cells in culture incorporated [3H]glucosamine and 35SO4 into glycoprotein products, which were secreted into the culture medium. The effects of sodium butyrate, a known differentiation-inducing agent, on the production of these sulphated glycoproteins were studied. Cells were cultured in the absence or presence of butyrate (2 mM) in serum-containing medium, for various times, and the labelled glycoproteins were partially purified by DEAE-cellulose chromatography. Treatment of these cells with butyrate resulted in an increase in the synthesis of secreted [3H]glucosamine- and 35SO4-labelled glycoproteins over several days of culture. This same increase in levels of 35SO4 incorporation was not observed with B16 melanoma cells. Sodium dodecyl sulphate (SDS)/polyacrylamide gel electrophoresis revealed that five major glycoproteins labelled with [3H]glucosamine also were labelled with 35SO4. The major secreted glycoproteins from cells cultured in the absence or presence of butyrate over a 3-day period were similar by SDS/polyacrylamide gel electrophoresis. Analyses of Pronase-derived glycopeptides indicated that these secreted 3H/35S-labelled glycoproteins contained sulphated oligosaccharides with terminal sialic acid----Gal----GlcNAc residues similar to glycoproteins secreted by vascular endothelial cells.
The Role of Post-translational Modifications of the CXCR4 Amino Terminus in Stromal-derived Factor 1α Association and HIV-1 Entry (2002)

The chemokine receptor CXCR4 plays critical roles in development, immune function, and human immunodeficiency virus type 1 (HIV-1) entry. Here we demonstrate that, like the CC-chemokine receptors CCR5 and CCR2b, CXCR4 is posttranslationally modified by sulfation of its amino-terminal tyrosines. The sulfate group at tyrosine 21 contributes substantially to the ability of CXCR4 to bind its ligand, stromal derived factor 1 alpha. Tyrosine sulfation plays a less significant role in CXCR4-dependent HIV-1 entry than in CCR5-dependent HIV-1 entry. In some cell lines, CXCR4 is efficiently modified by a chondroitin sulfate chain at serine 18, but neither HIV-1 entry nor stromal derived factor 1 alpha binding was affected by loss of this glycosaminoglycan. These data demonstrate a functional role for tyrosine sulfate in the CXC-chemokine receptor family and underscore a general difference in HIV-1 utilization of CCR5 and CXCR4.
Preclinical assessments of 90Y-labeled C110 anti-carcinoembryonic antigen immunotoxin: a therapeutic immunoconjugate for human colon cancer. (1991)

We have synthesized 90Y-labeled immunotoxin (IT) containing ricin A chain and C110 anti-carcinoembryonic antigen monoclonal antibody (MAb) to produce a therapeutic immunoconjugate for human colon cancer. The C110 IT was labeled with 90Y via a benzylisothiocyanate derivative of diethylenetriaminepentaacetic acid. The efficiency of 90Y labeling was consistently 90 to 98%, with a specific activity of about 1 microCi/microgram. In in vitro stability studies, more than 80% of 90Y remained bound to the C110 IT for up to 5 days after incubation. The percentage of binding of 90Y-labeled C110 IT to carcinoembryonic antigen-coated microbeads was 86%, indicating good retention of the initial immunoreactivity of the C110 MAb. In in vitro protein synthesis inhibition assays, 90Y-labeled C110 IT was approximately 3.7-fold more toxic to the LS174T human colon carcinoma cell line than unmodified C110 IT and 1380-fold more toxic than 90Y-labeled C110 MAb. Biodistribution studies of 90Y-labeled C110 IT in LS174T tumor-bearing mice showed that, at 24 h following i.p. injection, high accumulation of radioactivity was seen in the i.p. tumor and liver and, thereafter, high accumulation in these tissues remained almost unchanged until up to 168 h, with percentage of injected dose/g ranging from 15 to 18% in the tumor and 10 to 15% in the liver. The radioactivity in the spleen and bone gradually increased with time and reached their highest levels (approximately 8% of injected dose/g) at 168 h. Estimation of absorbed radiation doses to the tissues showed that i.p. tumor would have received an approximately 1.5 to 7 times higher radiation dose than normal organs. In in vivo therapeutic trials, 90Y-labeled C110 IT provided survival prolongation of LS174T tumor-bearing mice superior to that with either unmodified C110 IT or 90Y-labeled C110 MAb (4 less than 0.01; Mann-Whitney U test). These results indicate that 90Y-labeled C110 anti-carcinoembryonic antigen IT may be a potent therapeutic immunoconjugate for human colon cancer and that it may have direct relevance for i.p. treatment of peritoneal carcinomatosis from colon cancers.
Integrated optics N*N multiplexer on silicon (1991)

The authors report the measured performance of an integrated N*N multiplexer fabricated using SiO/sub 2//Si waveguides. The insertion loss for N=7 was typically lower than 2.5 dB, and crosstalk was less than -25 dB. The multiplexer response is approximately periodic. In each period the multiplexer accepts, from each input waveguide, a total of N channels, and it efficiently transmits each channel to a particular output port. Similarly, each output port receives N channels, one from each input port. Thus, the total number of channels that can be transmitted simultaneously is N/sup 2/, which requires N optical frequencies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Diode laser‐induced thermal damage evaluation on the retina with a liposome dye system (1999)

Background and Objectives The aim of the study was to evaluate the feasibility of retinal thermal damage assessment in a rabbit eye model by using laser-induced release of liposome-encapsulated dye. Study Design/Materials and Methods After anesthesia, thermosensitive liposomes (DiStearoyl Phosphatidyl Choline: DSPC) loaded with 5,6-carboxyfluorescein were injected intravenously to pigmented rabbits. Retinal photocoagulations were performed with a 810nm diode laser (P=100–400 mW, Ø=500 μm, 1s) (OcuLight®, IRIS Medical Instruments, Mountain View, CA). Fluorescence measurements in the area of the laser exposures were then realized with a digitized angiograph (CF-60UVi®, Canon-Europe, The Netherlands ; OcuLab®, Life Science Resources,® UK). Results Fluorescent spots were observed for power ranging from 100 ± 5 mW to 400 ± 5 mW. The fluorescence intensity increased linearly with the power and reached a plateau at 280 ± 5 mW. The fluorescence intensity was correlated to the maximum temperature at the center of the laser spot with a linear increase from 42 ± 3°C to 65 ± 3°C. These results are in agreement with our two previous studies with DSPC liposomes for temperature measurements in a tissue model and then in a vascular model. Conclusion This preliminary study demonstrates the possibility of a laser-induced release of liposome-encapsulated dye for a quantification of diode laser induced thermal damage in ophthalmology. Such a method could be useful for a real-time monitoring of laser photocoagulation for conditions such as choroidal neovascular membranes when a precise thermal damage is required near the foveolar area. Lasers Surg. Med. 24:61–68, 1999. © 1999 Wiley-Liss, Inc.
Screening and characterization of yeasts for xylitol production (2006)

Microbial species are of importance for xylitol production. Xylitol production involves complicated metabolic regulation including xylose transport, production of key enzymes and cofactor regeneration. Thus, screening of naturally occurring xylose-utilizing micro-organisms is a viable and effective mean to obtain xylitol producing organisms with industrial application. Moreover, the research on selected strains will contribute to a better understanding of regulatory properties of xylose metabolism in different yeasts.