gebhart/patrepeval huggingface dataset:
V(D)J Recombination: RAG Proteins, Repair Factors, and Regulation (2002)

V(D)J recombination is the specialized DNA rearrangement used by cells of the immune system to assemble immunoglobulin and T-cell receptor genes from the preexisting gene segments. Because there is a large choice of segments to join, this process accounts for much of the diversity of the immune response. Recombination is initiated by the lymphoid-specific RAG1 and RAG2 proteins, which cooperate to make double-strand breaks at specific recognition sequences (recombination signal sequences, RSSs). The neighboring coding DNA is converted to a hairpin during breakage. Broken ends are then processed and joined with the help of several factors also involved in repair of radiation-damaged DNA, including the DNA-dependent protein kinase (DNA-PK) and the Ku, Artemis, DNA ligase IV, and Xrcc4 proteins, and possibly histone H2AX and the Mre11/Rad50/Nbs1 complex. There may be other factors not yet known. V(D)J recombination is strongly regulated by limiting access to RSS sites within chromatin, so that particular sites are available only in certain cell types and developmental stages. The roles of enhancers, histone acetylation, and chromatin remodeling factors in controlling accessibility are discussed. The RAG proteins are also capable of transposing RSS-ended fragments into new DNA sites. This transposition helps to explain the mechanism of RAG action and supports earlier proposals that V(D)J recombination evolved from an ancient mobile DNA element.
Meeting the Challenges of Opioid-Induced Constipation in Chronic Pain Management – A Novel Approach (2008)

Opioid analgesics are the cornerstone of pain management for moderate-to-severe cancer pain and, increasingly, chronic noncancer pain. Despite proven analgesic efficacy, the use of opioids is commonly associated with frequently dose-limiting constipation that seriously impacts on patients' quality of life. Agents currently used to manage opioid-induced constipation (OIC), such as laxatives, do not address the underlying opioid receptor-mediated cause of constipation and are often ineffective. A significant need therefore exists for more effective treatment options. A novel approach for selectively and locally antagonizing the gastrointestinal effects of opioids involves the coadministration of a mu-opioid receptor antagonist with negligible systemic availability, such as oral naloxone. Combination therapy with prolonged-release (PR) oxycodone plus PR naloxone has been shown to provide effective analgesia while preventing or reducing constipation. The current article highlights this novel strategy in its potential to significantly improve the quality of life of patients suffering from chronic pain, affording patients the benefit of full analgesia, without the burden of OIC.
A digital background calibration technique for time-interleaved analog-to-digital converters (1998)

A 10-bit 40-Msample/s two-channel parallel pipelined ADC with monolithic digital background calibration has been designed and fabricated in a 1 /spl mu/m CMOS technology. Adaptive signal processing and extra resolution in each channel are used to carry out digital background calibration. Test results show that the ADC achieves a signal-to-noise-and-distortion ratio of 55 dB for a 0.8-MHz sinusoidal input, a peak integral nonlinearity of 0.34 LSB, and a peak differential nonlinearity of 0.14 LSB, both at a 10-bit level. The active area is 42 mm/sup 2/, and the power dissipation is 565 mW from a 5 V supply.
Boosting Algorithms as Gradient Descent (1999)

Much recent attention, both experimental and theoretical, has been focussed on classification algorithms which produce voted combinations of classifiers. Recent theoretical work has shown that the impressive generalization performance of algorithms like AdaBoost can be attributed to the classifier having large margins on the training data. We present an abstract algorithm for finding linear combinations of functions that minimize arbitrary cost functionals (i.e functionals that do not necessarily depend on the margin). Many existing voting methods can be shown to be special cases of this abstract algorithm. Then, following previous theoretical results bounding the generalization performance of convex combinations of classifiers in terms of general cost functions of the margin, we present a new algorithm (DOOM II) for performing a gradient descent optimization of such cost functions. Experiments on several data sets from the UC Irvine repository demonstrate that DOOM II generally outper...
High Levels of Exosomes Expressing CD63 and Caveolin-1 in Plasma of Melanoma Patients (2009)

We describe a new non-invasive assay allowing detection and quantification of human exosomes in plasma of melanoma patients. Our results suggest that the Exotest for detection of plasma exosomes carrying tumor-associated antigens may represent a novel tool for clinical management of cancer patients.
Altered synaptic plasticity and memory formation in nitric oxide synthase inhibitor-treated rats. (1993)

Nitric oxide (NO) is a messenger molecule that is produced in the brain from the metabolism of L-arginine to L-citrulline. Growing evidence suggests a physiological role for NO in long-term potentiation (LTP). Since LTP is a form of synaptic plasticity thought to be involved in learning and memory, we have tested whether inhibition of endogenous NO production affects memory capacities of rats. We found that the NO synthase [L-arginine, NADPH:oxygen oxidoreductase (nitric oxide-forming), EC 1.14.13.39] inhibitor N omega-nitro-L-arginine, at doses blocking LTP in hippocampal slices, impairs spatial learning in a radial arm maze and olfactory memory in a social recognition test. In contrast, N omega-nitro-L-arginine left shock-avoidance learning unaffected. These results indicate that NO is involved in some but not all forms of memory and further support the existence of a causal link between LTP and spatial learning.
Pulsations and absorbing defects in (Al,Ga)As injection lasers (1979)

Forty-seven strip-buried-heterostructure (Al,Ga)As lasers have been examined for pulsations and absorbing defects in the active volume. All 18 pulsating lasers were found to have defects while only one of the 29 nonpulsating lasers had a visible defect. These results show conclusively that absorbing defects can cause pulsations in double-heterostructure injection lasers and support a recently published model for the origin of these pulsations. The presence of absorbing defects and pulsations also correlates with structure in the functional dependence of −I2 d2V/dI2 upon I above threshold. Lasers not exhibiting pulsations were aged, and the same correlation was found between the development of defects (particularly mirror darkening), the change in −I d2V/dI2, and the development of pulsations.
Bandwidth-limited subpicosecond pulse generation in mode-locked cw dye lasers (1976)

A cw Rhodamine 6G dye laser with a thin optically contacted saturable absorber cell has been mode locked over an operating frequency range of 598–615 nm to produce pulses with durations as short as 0.3 ps. The pulses, with sech2 intensity profiles, are practically bandwidth limited.
Target epitope in the Tax protein of human T-cell leukemia virus type I recognized by class I major histocompatibility complex-restricted cytotoxic T cells (1992)

A trans-acting regulatory gene product p40tax (Tax) of human T-cell leukemia virus type I (HTLV-I) is one of the main target antigens recognized by cytotoxic T lymphocytes (CTL) specific for HTLV-I. A CTL epitope within the Tax protein was identified in this report. HTLV-I-specific CD8+ CTL lines established from two HTLV-I carriers with HTLV-I-associated myelopathy or Sjögren syndrome were previously demonstrated to kill predominantly the target cells expressing HTLV-I Tax. The CTL from two patients showed significant levels of cytotoxicity to autologous target cells pulsed with a synthetic peptide of 24 amino acids corresponding to the amino-terminal sequences of the Tax protein. Allogeneic target cells were also sensitized for CTL by this peptide when the target cells have HLA-A2. Tax-specific cytotoxicity, detected as cytolysis of the target cells infected with vaccinia virus-HTLV-I recombinant expressing Tax protein, was almost completely inhibited by competitor cells pulsed with the synthetic peptide. This indicates that a major CTL epitope is present in this peptide. Further analysis using shorter peptides revealed that the core sequence of the CTL epitope was LLFGYPVYV at positions 11 through 19. This sequence can be aligned with the HLA-A2-specific motifs reported recently.
FRVT 2006 and ICE 2006 large-scale results (2007)

This report describes the large-scale experimental results from the Face Recognition Vendor Test (FRVT) 2006 and the Iris Challenge Evaluation (ICE) 2006. The FRVT 2006 looks at recognition from high-resolution still images and three-dimensional (3D) face images, and measures performance for still images taken under controlled and uncontrolled illumination. The ICE 2006 reports iris recognition performance from left and right iris images. The FRVT 2006 results from controlled still images and 3D images document an order-of-magnitude improvement in recognition performance over the FRVT 2002. This order-of-magnitude improvement was one of the goals of the preceding technology development effort, the Face Recognition Grand Challenge (FRGC). The FRVT 2006 and the ICE 2006 compared recognition performance from very-high resolution still face images, 3D face images, and single-iris images. On the FRVT 2006 and the ICE 2006 datasets, recognition performance was comparable for all three biometrics. In an experiment comparing human and algorithm performance, the best-performing face recognition algorithms were more accurate than humans. These and other results are discussed in detail.
PAM-Blox: high performance FPGA design for adaptive computing (2002)

PAM-Blox are object-oriented circuit generators on top of the PCI Pamette design environment, PamDC. High-performance FPGA design for adaptive computing is simplified by using a hierarchy of optimized hardware objects described in C++. PAM-Blox consist of two major layers of abstraction. First, PamBlox are parameterizable simple elements such as counters and adders. Automatic placement of carry chains and flexible shapes are supported. PaModules are more complex elements possibly instantiating PamBlox. PaModules have fixed shapes and are usually optimized for a specific data-width. Examples for PaModules are multipliers, Coordinate Rotations (CORDICs), and special arithmetic units for encryption. The key difference of our approach to most other design tools for FPGAs is that the designer has total control over placement at each level of the design hierarchy, which is the key to high-performance FPGA design. Second, the object interface was chosen carefully to encourage code-reuse and simplify code-sharing between designers. PAM-Blox are intended to be part of an open library that allows design sharing between members of the adaptive computing community.
Ueber Verbindungen des Thiazols (Pyridins der Thiophenreihe) (1887)

NH Endlich
Human immunodeficiency virus contains an epitope immunoreactive with thymosin alpha 1 and the 30-amino acid synthetic p17 group-specific antigen peptide HGP-30. (1987)

We have reported that an antiserum prepared against thymosin alpha 1 [which shares a region of homology with the p17 protein of the acquired immunodeficiency syndrome (AIDS)-associated human immunodeficiency virus] effectively neutralized the AIDS virus and prevented its replication in H9 cells. Using HPLC and immunoblot analysis, we have identified from a clone B, type III human T-lymphotropic virus (HTLV-IIIB) extract a protein with a molecular weight of 17,000 that is immunoreactive with thymosin alpha 1. In contrast, no immunoreactivity was found in retroviral extracts from a number of nonhuman species including feline, bovine, simian, gibbon, and murine retroviruses. Heterologous antiserum prepared against a 30-amino acid synthetic peptide analogue (HGP-30) does not cross-react with thymosin alpha 1 but does react specifically with the p17 protein of the AIDS virus in a manner identical to that seen with an HTLV-IIIB p17-specific monoclonal antibody. The demonstration that this synthetic analogue is immunogenic and that antibodies to HGP-30 cross-react not only with the synthetic peptide but also with the HTLV-IIIB p17 viral protein provides an additional, and potentially more specific, candidate for development of a synthetic peptide vaccine for AIDS. In addition, the p17 synthetic peptide (HGP-30) may prove to be useful in a diagnostic assay for the detection of AIDS virus infection in seronegative individuals.
Interstitial fluid flow induces myofibroblast differentiation and collagen alignment in vitro (2005)

The differentiation of fibroblasts to contractile myofibroblasts, which is characterized by de novo expression of alpha-smooth muscle actin (alpha-SMA), is crucial for wound healing and a hallmark of tissue scarring and fibrosis. These processes often follow inflammatory events, particularly in soft tissues such as skin, lung and liver. Although inflammatory cells and damaged epithelium can release transforming growth factor beta1 (TGF-beta1), which largely mediates myofibroblast differentiation, the biophysical environment of inflammation and tissue regeneration, namely increased interstitial flow owing to vessel hyperpermeability and/or angiogenesis, may also play a role. We demonstrate that low levels of interstitial (3D) flow induce fibroblast-to-myofibroblast differentiation as well as collagen alignment and fibroblast proliferation, all in the absence of exogenous mediators. These effects were associated with TGF-beta1 induction, and could be eliminated with TGF-beta1 blocking antibodies. Furthermore, alpha1beta1 integrin was seen to play an important role in the specific response to flow, as its inhibition prevented fibroblast differentiation and subsequent collagen alignment but did not block their ability to contract the gel in a separate floating gel assay. This study suggests that the biophysical environment that often precedes fibrosis, such as swelling, increased microvascular permeability and increased lymphatic drainage--all which involve interstitial fluid flow--may itself play an important role in fibrogenesis.
A member of the ras gene superfamily is expressed specifically in T, B and myeloid hemopoietic cells. (1990)

A 1.26 kb murine cDNA having 31% homology with human ras and 55% homology with human rho proteins was isolated using an oligonucleotide probe homologous to catalytic subdomain of a tyrosine kinase subfamily. Northern blot analysis indicates that the expression of the murine gene is restricted to the cells of hemopoietic lineages and the mRNA levels increase with the terminal differentiation of hemopoietic cells into granulocytes.
Polymer-Assisted Direct Deposition of Uniform Carbon Nanotube Bundle Networks for High Performance Transparent Electrodes (2009)

Flexible transparent electrodes are crucial for touch screen, flat panel display, and solar cell technologies. While carbon nanotube network electrodes show promise, characteristically poor dispersion properties have limited their practicality. We report that addition of small amounts of conjugated polymer to nanotube dispersions enables straightforward fabrication of uniform network electrodes by spin-coating and simultaneous tuning of parameters such as bundle size and density. After treatment in thionyl chloride, electrodes have sheet resistances competitive with other reported carbon nanotube based transparent electrodes to date.
High-quality InAsyP1−y step-graded buffer by molecular-beam epitaxy (2003)

Relaxed, high-quality, compositionally step-graded InAsyP1−y layers with an As composition of y=0.4, corresponding to a lattice mismatch of ∼1.3% were grown on InP substrates using solid-source molecular-beam epitaxy. Each layer was found to be nearly fully relaxed observed by triple axis x-ray diffraction, and plan-view transmission electron microscopy revealed an average threading dislocations of 4×106 cm−2 within the InAs0.4P0.6 cap layer. Extremely ordered crosshatch morphology was observed with very low surface roughness (3.16 nm) compared to cation-based In0.7Al0.3As/InxAl1−xAs/InP graded buffers (10.53 nm) with similar mismatch and span of lattice constants on InP. The results show that InAsyP1−y graded buffers on InP are promising candidates as virtual substrates for infrared and high-speed metamorphic III–V devices.
GAL1-GAL10 divergent promoter region of Saccharomyces cerevisiae contains negative control elements in addition to functionally separate and possibly overlapping upstream activating sequences. (1987)

The upstream activating sequence (UASG) of the adjacent and divergently transcribed GAL1 and GAL10 promoters of Saccharomyces cerevisiae regulates the induction of the corresponding genes in response to the presence of galactose. We constructed chimeric yeast promoters in which a different UAS, UASC from the iso-1-cytochrome c (CYC1) gene of S. cerevisiae, was fused at different locations upstream of GAL1 (UASC-GAL1 promoters) or GAL10 (UASC-GAL10 promoters) and used to monitor the activity of UASG in cells grown in the presence or absence of galactose. Though the CYC1 promoter is fully induced in yeast grown in glycerol medium, UASC-GAL chimeric promoters containing UASG were repressed as much as 400-fold (UASC-GAL1) or 1350-fold (UASC-GAL10) in this growth medium. Several distinct portions of the GAL1-GAL10 divergent promoter region blocked the UASC-induced expression of the GAL1 and GAL10 promoters, whereas others did not, suggesting that several distinct negative control elements are present that may repress transcription of GAL1 and GAL10 in the absence of galactose. The approximate locations of these negative control elements were delimited to sites adjacent to or possibly overlapping the sites at which the positive control protein GAL4 binds in UASG. Deletion derivatives of GAL4 that fail to induce transcription from the wild-type GAL promoters but retain the DNA binding domain significantly derepressed the expression of the UASC-GAL chimeric promoters. These results, combined with those of earlier studies, suggest the possibility that GAL4 normally induces transcription of GAL1 and GAL10 by blocking the activity of these negative control elements, in addition to stimulating transcription by a mechanism of positive control.
<title>Self-contained off-line media for exchanging medical images using DICOM-compliant standard</title> (2000)

The goal of this project is to develop and implement off-line DICOM-compliant CD ROMs that contain the necessary software tools for displaying the images and related data on any personal computer. We implemented a hybrid recording technique allowing CD-ROMs for Macintosh and Windows platforms to be fully DICOM compliant. A public domain image viewing program (OSIRIS) is recorded on the CD for display and manipulation of sequences of images. The content of the disk is summarized in a standard HTML file that can be displayed on any web-browser. This allows the images to be easily accessible on any desktop computer, while being also readable on high-end commercial DICOM workstations. The HTML index page contains a set of thumbnails and full-size JPEG images that are directly linked to the original high-resolution DICOM images through an activation of the OSIRIS program. Reports and associated text document are also converted to HTML format to be easily displayable directly within the web browser. This portable solution provides a convenient and low cost alternative to hard copy images for exchange and transmission of images to referring physicians and external care providers without the need for any specialized software or hardware.
Peroxisomal Impairment in Niemann-Pick Type C Disease (1997)

Niemann-Pick type C disease (NPC) belongs to the group of lysosomal storage diseases characterized by an accumulation of cholesterol and sphingomyelin. Using a mutant mouse strain, enzymatic markers for lysosomes, mitochondria, microsomes, and peroxisomes were investigated in the liver and brain. Aside from lysosomal changes, we found a sizable decrease of peroxisomal beta-oxidation of fatty acids and catalase activity in the brain and liver. Isolated peroxisomes displayed a significant decrease of these enzyme activities. Furthermore, the only phospholipid change in brain was a decreased content of the plasmalogen form of phosphatidylethanolamine, and the dimethylacetal pattern was also modified. The electron microscopical appearance of peroxisomes did not display any large changes. The defect of peroxisomal enzymes was already present 18 days before the onset of the disease. In contrast, the lysosomal marker enzyme increased in activity only 6 days after appearance of the symptoms. The events of the studied process have previously been considered to be elicited by a lysosomal deficiency, but this study demonstrates disturbances similar to those in a number of peroxisomal diseases. It appears that the peroxisomal impairment is an early event in the process and could be a factor in the development of Niemann-Pick type C disease.
Transcriptional repression ofADH2-regulated Î²-xylanase production by ethanol in recombinant strains ofSaccharomyces cerevisiae (2001)

The regulation of endo-beta-(1,4)-xylanase production by two different strains of Saccharomyces cerevisiae, each transformed with the XYN2 gene from Trichoderma reesei under control of the promoter of the alcohol dehydrogenase II (ADH2) gene of S. cerevisiae, was investigated. In batch culture, the rate of xylanase production was severely reduced by the pulse addition of 390 mmol ethanol l(-1). Pulses of 190-630 mmol ethanol l(-1) into aerobic glucose-limited steady-state continuous cultures reduced the xylanase activity about five-fold and showed that ethanol repressed the ADH2 promoter, as was evident from Northern blot analyses. Derepression of the ADH2-regulated xylanase gene occurred at ethanol concentrations below approximately 50 mmol l(-1).
A synthetic entry in the Aristotelia alkaloids (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA synthetic entry in the Aristotelia alkaloidsCatherine Mirand, Georges Massiot, and Jean LevyCite this: J. Org. Chem. 1982, 47, 21, 4169–4170Publication Date (Print):October 1, 1982Publication History Published online1 May 2002Published inissue 1 October 1982https://pubs.acs.org/doi/10.1021/jo00142a034https://doi.org/10.1021/jo00142a034research-articleACS PublicationsRequest reuse permissionsArticle Views314Altmetric-Citations26LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts