gebhart/patrepeval huggingface dataset:
HDL Mimetics Inhibit Tumor Development in Both Induced and Spontaneous Mouse Models of Colon Cancer (2012)

Recent studies suggest that high-density lipoprotein (HDL) levels are inversely related to colon cancer risk. HDL mimetics constructed from a number of peptides and proteins with varying structures possess anti-inflammatory and antioxidant properties reminiscent of HDL. In this article, we examined whether HDL mimetics, L-4F (an apolipoprotein A-I mimetic peptide) and G* (an apolipoprotein J mimetic peptide) affect tumor growth and development in mouse models of colon cancer. HDL mimetics reduced viability and proliferation of CT26 cells, a mouse colon adenocarcinoma cell line, and decreased CT26 cell-mediated tumor burden in BALB/c mice when administered subcutaneously or orally. Plasma levels of lysophosphatidic acid (LPA), a serum biomarker for colon cancer, were significantly reduced in mice that received HDL mimetics, suggesting that binding and removal of proinflammatory lipids is a potential mechanism for the inhibition of tumor development by HDL mimetics. Furthermore, L-4F significantly reduced size and number of polyps in APC(min/+) mice, a mouse model for human familial adenomatous polyposis, suggesting that HDL mimetics are effective in inhibiting the development of both induced and spontaneous cancers of the colon. Our results, for the first time, identify HDL mimetics as a novel therapeutic strategy for the treatment of colon cancer.
Photochemical transition of 5-methylcytosine to thymine by DNA photoligation (2007)

We report that deamination coupled with 5-carboxyvinyl-2'-deoxyuridine-mediated photoligation causes the heat-induced transition of 5-methylcytosine to thymine with high selectivity and efficiency without any side reaction. The difference of deamination rate between 5-methylcytosine and cytosine is useful for evaluation of DNA methylation status and the study of gene expression and stability.
Aperture averaging of optical scintillations in the turbulent atmosphere (1991)

We have developed approximate expressions for the aperture-averaging factor of optical scintillation in the turbulent atmosphere. For large apertures and weak path-integrated turbulence with a small inner scale, the variance of signal fluctuations is proportional to the −7/3 power of the ratio of the aperture diameter to the Fresnel zone size. If the inner scale is large, the variance is proportional to the −7/3 power of the ratio of the aperture diameter to the inner scale. In strong path-integrated turbulence, two scales develop. That portion of the variance associated with the smaller scale is proportional to the −2 power of the ratio of the aperture diameter to the phase coherence length. That portion of the variance associated with the larger scale is proportional to the −7/3 power of the ratio of the aperture diameter to the scattering disk. These simple approximations are within a factor of 2 of the measurements.
CD8 T Cell Responses to Myelin Oligodendrocyte Glycoprotein-Derived Peptides in Humanized HLA-A*0201-Transgenic Mice (2007)

Multiple sclerosis (MS) is a demyelinating inflammatory disease of the CNS. Though originally believed to be CD4-mediated, additional immune effector mechanisms, including myelin-specific CD8(+) T cells, are now proposed to participate in the pathophysiology of MS. To study the immunologic and encephalitogenic behavior of HLA-A*0201-binding myelin-derived epitopes in vivo, we used a humanized HLA-A*0201-transgenic mouse model. Eight HLA-A*0201-binding peptides derived from myelin oligodendrocyte glycoprotein (MOG), an immunodominant myelin self-Ag, were identified in silico. After establishing their relative affinity for HLA-A*0201 and their capacity to form stable complexes with HLA-A*0201 in vitro, their immunological characteristics were studied in HLA-A*0201-transgenic mice. Five MOG peptides, which bound stably to HLA-A*0201 exhibited strong immunogenicity by inducing a sizeable MOG-specific HLA-A*0201-restricted CD8(+) T cell response in vivo. Of these five candidate epitopes, four were processed by MOG-transfected RMA target cells and two peptides proved immunodominant in vivo in response to a plasmid-encoding native full-length MOG. One of the immunodominant MOG peptides (MOG(181)) generated a cytotoxic CD8(+) T cell response able to aggravate CD4(+)-mediated EAE. Therefore, this detailed in vivo characterization provides a hierarchy of candidate epitopes for MOG-specific CD8(+) T cell responses in HLA-A*0201 MS patients identifying the encephalitogenic MOG(181) epitope as a primary candidate.
32-Parallel SAD Tree Hardwired Engine for Variable Block Size Motion Estimation in HDTV1080P Real-Time Encoding Application (2007)

H.264/AVC coding standard incorporates variable block size (VBS) motion estimation (ME) to improve the compression efficiency. For HDTV-1080p application, the massive computation and huge memory bandwidth by the large video frame size and the wide search range are two critical impediments to the real-time hardwired VB-SME engine design. In this paper, we present six techniques to circumvent these difficulties. First, the inter modes bellow 8 × 8 are eliminated in our design to reduce the hardware cost. Second, the low-pass filter based 4:1 down-sampling algorithm successfully reduces about 75% arithmetic computation in each search position. Third, the coarse to fine search scheme is made use of to reduce 25%-50% search candidates. Fourth, C+ memory organization is adopted to reduce the external IO bandwidth. Fifth, horizontal zigzag scan mode optimizes the search window memories. Finally, in circuit design, 4:2 compressor based CSA tree, multi-cycle path delay and 2 pipeline stage SAD tree techniques are utilized to improve the speed and reduce the hardware of each SAD tree. The hardwired integer motion estimation (IME) engine with 192 × 128 search range for HDTVl080p@30Hz is demonstrated in this paper. With TSMC 0.18μm 1P6M CMOS technology, it is implemented with 485.7k gates standard cells and 327.68k bit on chip memories. The power dissipation is 729mw at 200MHz clock speed.
Sulfoxides as Ligands. I. A Preliminary Survey of Methyl Sulfoxide Complexes (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSulfoxides as Ligands. I. A Preliminary Survey of Methyl Sulfoxide ComplexesF. A. Cotton and R. FrancisCite this: J. Am. Chem. Soc. 1960, 82, 12, 2986–2991Publication Date (Print):June 1, 1960Publication History Published online1 May 2002Published inissue 1 June 1960https://pubs.acs.org/doi/10.1021/ja01497a003https://doi.org/10.1021/ja01497a003research-articleACS PublicationsRequest reuse permissionsArticle Views1328Altmetric-Citations288LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Fiber-optic sensing of pressure and temperature (1979)

The use of a fiber-optic Mach-Zehnder interferometer to measure differences in temperature or pressure between two single-mode fiber arms is described. Temperature or pressure changes are observed as a motion of an optical interference fringe pattern. Values are calculated for the pressure and temperature dependence of the fringe motion. Pressure and temperature measurements are made with the interferometer, and the experimental values for sensitivity are in good agreement with those calculated.
Subcarrier-multiplexed signaling based add/drop multiplexer in optical FDM networks (1996)

To guarantee the transparency of optical FDM networks, both the link and node are fully operated in optical domain. This requires true sense of optical node, of which both the function and the signaling for the control are optically realized. Compared with a dedicated signaling channel on a common wavelength, subcarrier multiplexing (SCM) offers higher cost-savings as well as wavelength resource efficiency. An optical implementation of SCM-controlled add/drop multiplexer, which performs one of the fundamental node functions, is proposed and experimentally demonstrated. It is composed of a pair of arrayed-waveguide-gratings and optical switches driven by SCM-control signals. It is shown that this configuration is suitable for multigigabits optical FDM networks due to the capability of high-speed operation.
Improved gene delivery to human saphenous vein cells and tissue using a peptide-modified adenoviral vector (2004)

The establishment of efficient gene delivery to target human tissue is a major obstacle for transition of gene therapy from the pre-clinical phases to the clinic. The poor long-term patency rates for coronary artery bypass grafting (CABG) is a major clinical problem that lacks an effective and proven pharmacological intervention. Late vein graft failure occurs due to neointima formation and accelerated atherosclerosis. Since CABG allows a clinical window of opportunity to genetically modify vein ex vivo prior to grafting it represents an ideal opportunity to develop gene-based therapies. Adenoviral vectors have been frequently used for gene delivery to vein ex vivo and pre-clinical studies have shown effective blockade in neointima development by overexpression of candidate therapeutic genes. However, high titers of adenovirus are required to achieve sufficient gene delivery to provide therapeutic benefit. Improvement in the uptake of adenovirus into the vessel wall would therefore be of benefit. Here we determined the ability of an adenovirus serotype 5 vector genetically-engineered with the RGD-4C integrin targeting peptide inserted into the HI loop (Ad-RGD) to improve the transduction of human saphenous vein smooth muscle cells (HSVSMC), endothelial cells (HSVEC) and intact saphenous vein compared to a non-modified virus (Ad-CTL). We exposed each cell type to virus for 10, 30 or 60 mins and measured transgene at 24 h post infection. For both HSVSMC and HSVEC Ad-RGD mediated increased transduction, with the largest increases observed in HSVSMC. When the experiments were repeated with intact human saphenous vein (the ultimate clinical target for gene therapy), again Ad-RGD mediated higher levels of transduction, at all clinically relevant exposures times (10, 30 and 60 mins tissue:virus exposure). Our study demonstrates the ability of peptide-modified Ad vectors to improve transduction to human vein graft cells and tissue and has important implications for gene therapy for CABG.
Improvement of Usable Capacity and Cyclability of Silicon-Based Anode Materials for Lithium Batteries by Sol-Gel Graphite Matrix (2002)

High capacity silicon-graphite composite anode materials were made by dispersing silicon in a sol-gel graphite (SGG) matrix. The capacity increased with increasing Si content and the best application performance was delivered by a composite containing 19.2 wt % Si, where the first cycle discharge and charge capacities were 1033.7 mAh composite (or 4311 mAh Si) and composite (or Si), respectively (80.5% coulombic efficiency). Capacity fading was less than 12% in 25 cycles, which is a substantial improvement over unsupported silicon anodes where precipitous drop in capacity occurs within a few cycles. The improvement is attributed to the presence of the SGG matrix, which, with its extensive open 3D network, effectively cushioned the volume change in the electrode during charging and discharging reactions, hence raising the usability in applications. © 2002 The Electrochemical Society. All rights reserved.
Genomic Fingerprinting by Arbitrarily Primed PCR: Strain Classification and Genetic Mapping (1991)

Journal Article Genomic Fingerprinting by Arbitrarily Primed PCR: Strain Classification and Genetic Mapping Get access John Welsh, John Welsh California Inst. of Biol. Res., 11099 North Torrey Pines Rd., La Jolla, CA 92037 Search for other works by this author on: Oxford Academic Google Scholar Michael McClelland Michael McClelland California Inst. of Biol. Res., 11099 North Torrey Pines Rd., La Jolla, CA 92037 Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 37, Issue 4, 1 April 1991, Pages 605–606, https://doi.org/10.1093/clinchem/37.4.605 Published: 01 April 1991
Bioanalysis without Sample Cleanup or Chromatography: The Evaluation and Initial Implementation of Direct Analysis in Real Time Ionization Mass Spectrometry for the Quantification of Drugs in Biological Matrixes (2008)

Two key bottlenecks in pharmaceutical bioanalysis are sample cleanup and chromatographic separations. Although multiple approaches have been developed in the past decade to either shorten or multiplex these steps, they remain the rate limiting steps as ADME (Absorption, Distribution, Metabolism, and Excretion) property screening is being routinely incorporated into the drug discovery process. In this work, a novel system incorporating an automated Direct Analysis in Real Time (DART) ionization source coupled with a triple-quadrupole mass spectrometer has been developed and evaluated for quantitative bioanalysis. This system has the capability of directly analyzing samples from their biological matrixes and therefore potentially eliminating the need for sample cleanup and chromatographic separations. A LEAP Technologies autosampler was customized to perform the automated sample introduction into the DART beam with high precision, which significantly improved the reproducibility of the method. Additional pumping was applied to the atmospheric pressure inlet on the mass spectrometer to compensate for the increased vacuum load because of the use of high-flow helium by the DART. This resulted in an improvement of detection sensitivity by a factor of 10 to 100 times. Matrix effects for a diversified class of compounds were evaluated directly from untreated raw plasma and were found to range from approximately 0.05 to 0.7. Precision and accuracy were also tested for multiple test compounds over a dynamic range of four orders of magnitude. The system has been used to analyze biological samples from both in vivo pharmacokinetic studies and in vitro microsomal/S9 stability studies, and the results generated were similar to those obtained with conventional LC/MS/MS methods. Overall, this new automated DART-triple quadrupole mass spectrometer system has demonstrated significant potential for high-throughput bioanalysis.
Prebiotic Effect of Fructooligosaccharide in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME ® Model) (2014)

Maintaining "gut health" is a goal for scientists throughout the world. Therefore, microbiota management models for testing probiotics, prebiotics, and synbiotics have been developed. The SHIME(®) model was used to study the effect of fructooligosaccharide (FOS) on the fermentation pattern of the colon microbiota. Initially, an inoculum prepared from human feces was introduced into the reactor vessels and stabilized over 2 weeks using a culture medium. This stabilization period was followed by a 2-week control period during which the microbiota was monitored. The microbiota was then subjected to a 4-week treatment period by adding 5 g/day-1 FOS to vessel one (the "stomach" compartment). Plate counts, Denaturing Gradient Gel Electrophoresis (DGGE), short-chain fatty acid (SCFA), and ammonium analyses were used to observe the influence of FOS treatment in simulated colon compartments. A significant increase (P<.01) in the Lactobacillus spp. and Bifidobacterium spp. populations was observed during the treatment period. The DGGE obtained showed the overall microbial community was changed in the ascending colon compartment of the SHIME reactor. FOS induced increase of the SCFA concentration (P<.05) during the treatment period, mainly due to significant increased levels of acetic and butyric acids. However, ammonium concentrations increased during the same period (P<.01). This study indicates the usefulness of in vitro methods that simulate the colon region as part of research towards the improvement of human health.
Cereblon expression is required for the antimyeloma activity of lenalidomide and pomalidomide (2011)

The precise molecular mechanism of action and targets through which thalidomide and related immunomodulatory drugs (IMiDs) exert their antitumor effects remains unclear. We investigated the role of cereblon (CRBN), a primary teratogenic target of thalidomide, in the antimyeloma activity of IMiDs. CRBN depletion is initially cytotoxic to human myeloma cells, but surviving cells with stable CRBN depletion become highly resistant to both lenalidomide and pomalidomide, but not to the unrelated drugs bortezomib, dexamethasone, and melphalan. Acquired deletion of CRBN was found to be the primary genetic event differentiating isogenic MM1.S cell lines cultured to be sensitive or resistant to lenalidomide and pomalidomide. Gene expression changes induced by lenalidomide were dramatically suppressed in the presence of CRBN depletion, further demonstrating that CRBN is required for lenalidomide activity. Downstream targets of CRBN include interferon regulatory factor 4 (IRF4) previously reported to also be a target of lenalidomide. Patients exposed to, and putatively resistant to, lenalidomide had lower CRBN levels in paired samples before and after therapy. In summary, CRBN is an essential requirement for IMiD activity and a possible biomarker for the clinical assessment of antimyeloma efficacy.
All‐in‐one silicon photonic polarization processor (2018)

Abstract With the great developments in optical communication technology and large‐scale optical integration technology, it is imperative to realize the traditional functions of polarization processing on an integration platform. Most of the existing polarization devices, such as polarization multiplexers/demultiplexers, polarization controllers, polarization analyzers, etc., perform only a single function. Definitely, integrating all these polarization functions on a chip will increase function flexibility and integration density and also cut the cost. In this article, we demonstrate an all‐in‐one chip‐scale polarization processor based on a linear optical network. The polarization functions can be configured by tuning the array of phase shifters on the chip. We demonstrate multiple polarization processing functions, including those of a multiple‐input‐multiple‐output polarization descrambler, polarization controller, and polarization analyzer, which are the basic building blocks of polarization processing. More functions can be realized by using an additional two‐dimensional output grating. A numerical gradient descent algorithm is employed to self‐configure and self‐optimize these functions. Our demonstration suggests great potential for chip‐scale, reconfigurable, and fully programmable photonic polarization processors with the artificial intelligence algorithm.
Characteristics of Animal Models for Scleroderma (2005)

Scleroderma is a fibrotic condition characterized by immunologic abnormalities, vascular injury and increased accumulation of matrix proteins in the affected dermis. Although the etiology of scleroderma is not fully elucidated, numerous studies suggest that extracellular matrix overproduction by activated fibroblasts and myofibroblasts results from a complex interactions among endothelial cells, lymphocytes, macrophages, and fibroblasts, via a number of mediators. Animal models which exhibit all the aspects of human scleroderma are not currently available, however, several spontaneous or experimental animal models, such as tight skin (Tsk) mouse, Tsk2 mouse, bleomycin-induced scleroderma, sclerodermatous graft-versus-host disease (Scl GvHD) model, UCD chicken, and fibrosis model by exogenous injections of TGF-β/CTGF have been investigated. This review describes different animal models for scleroderma, paying the most attention to the recent progress in bleomycin-induced experimental murine scleroderma. Each model exhibits unique characteristics of dermal fibrosis/sclerosis which can be of great help in exploring the pathogenesis as well as therapeutic strategies of scleroderma. Keywords: scleroderma, animal model, bleomycin, tsk mouse, gvhd, ucd chicken
Efficient implementation of suffix trees (1995)

Abstract We study the problem of string searching using the traditional approach of storing all unique substrings of the text in a suffix tree. The methods of path compression, level compression and data compression are combined to build a simple, compact and efficient implementation of a suffix tree. Based on a comparative discussion and extensive experiments, we argue that our new data structure is superior to previous methods in many practical situations.
Preliminary Design and Evaluation of a B-Scan OCT-Guided Needle (2014)

Real-time intraoperative B-scan optical coherence tomography (OCT) visualization of intraocular tissues is a desired ophthalmic feature during retinal procedures. A novel intraocular 25-gauge B-mode forward-imaging OCT probe was combined with a 36-gauge needle into a prototype instrument. Imaging of the needle tip itself and the effects of saline injection into a gelatin phantom were performed. A combined B-scan forward-imaging OCT-needle prototype was capable of real-time-imaging of saline injection into a gelatin phantom. Additional future miniaturization may permit this instrument to be an adjunctive realtime imaging and procedure tool for vitreoretinal surgery.
Knowledge-Based Intelligent Techniques in Industry (1998)

From the Publisher:
In one volume, Knowledge-Based Intelligent Techniques in Industry comprehensively addresses the more important developments in the use of intelligent techniques in solving industrial problems. Its primary readership includes electrical engineers in industry as well as researchers working in computational intelligence research labs - outlining state-of-the-art techniques and cost-effective solutions.
Low-Temperature Damage and Subsequent Recovery of fab1 Mutant Arabidopsis Exposed to 2[deg]C (1997)

The fab1 mutant of Arabidopsis thaliana, which contains increased levels of saturated fatty acids, was indistinguishable from the wild type when it was grown at 22 or 12 degrees C. During the first 7 to 10 d after transfer to 2 degrees C, the growth and photosynthetic characteristics of the fab1 plants remained indistinguishable from the wild type, with values for the potential quantum efficiency of photosystem II decreasing from 0.8 to 0.7 in plants of both lines. Whereas wild-type plants maintained quantum efficiency of photosystem II at approximately 0.7 for at least 35 d at 2 degrees C, this parameter declined rapidly in the mutant after 7 d and reached a value of less than 0.1 after 28 d at 2 degrees C. This decline in photosynthetic capacity was accompanied by reductions in chlorophyll content and the amount of chloroplast glycerolipids per gram of leaf. Electron microscopic examination of leaf samples revealed a rapid and extensive disruption of the thylakoid and chloroplast structure in the mutant, which is interpreted here as a form of selective autophagy. Despite the almost complete loss of photosynthetic function and the destruction of photosynthetic machinery, fab1 plants retained a substantial capacity for recovery following transfer to 22 degrees C. These results provide a further demonstration of the importance of chloroplast membrane unsaturation to the proper growth and development of plants at low temperature.