gebhart/patrepeval huggingface dataset:
Amplification of human B cell activation by a monoclonal antibody to the B cell-specific antigen CD22, Bp 130/140. (1987)

Abstract The B cell-specific antigen CD22 is a 130/140-Kd complex and is unique among human B cell antigens, since its surface expression is restricted to a subpopulation of Ig+ B cells. Here the function of the CD22 antigen was evaluated by using the mAb HD6, directed against one of the epitopes on the molecule. The HD6 antibody was constimulatory with anti-Ig in inducing small, dense tonsillar cells to proliferate; however, the antibody by itself was devoid of stimulatory activity. Anti-CD22 antibody also induced more anti-Ig-treated B cells to leave G0 and enter the G1 phase of the cell cycle. It also was constimulatory with low-m.w. BCGF and with an antibody to a 50-Kd polypeptide, Bp50, which mediates a BCGF-like activity. Results of kinetic experiments and analysis of different B cell fractions suggested that anti-CD22 acts during an early phase of B cell activation, probably by amplifying the anti-Ig signal. F(ab’)2 fragments of anti-CD22 HD6 were as effective as the whole antibody in inducing augmentation of B cell proliferation, showing that the Fc portion of the molecule was not required for the activity. The results of these experiments, together with the intriguing distribution of the Bp 130/140 antigen in B cell ontogeny, suggest that this molecule plays an important role in the process that leads to B cell activation and proliferation.
Hybrid-WSI: a massively parallel computing technology? (1993)

It is argued that although it is not yet clear which of the two wafer scale integration (WSI) forms, monolithic or hybrid, will gain the lead to an enabling technology for second-generation massively parallel computers (MPCs), there are noticeably more backers for hybrid-WSI. The application requirements, implementation problems, and engineering issues of MPCs are discussed. In particular, the associative string processor (ASP) modules, which comprise building blocks for second-generation MPC configurations, are described. The progress reported in developing ASP modules is quantitatively extrapolated to other MPC implementations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Three-dimensional planning and virtual radiographs in revision total hip arthroplasty for instability. (2006)

Instability is one of the most challenging complications of total hip arthroplasty. The cause of instability is not always clear and treatment outcome is not always satisfactory. Treatment can be optimized by accurate identification of the cause of instability and precise surgical technique. In this case report, we illustrate the use of a three-dimensional (3-D) preoperative planner and virtual radiographic system to improve component position in revision total hip arthroplasty required because of recurrent dislocation. Using this technique, we identified common problems seen in patients with unstable hips after previous revision surgery including impingement, cup malpositioning, bone deficiency in the medial wall, and integrity of fixation screws. The computer-assisted system allowed preoperative planning with range of motion simulation and optimization of the acetabular cup position. The virtual radiographic system provided 3-D measurement of the cup position using a postoperative plane radiograph.
Development of a Nanoparticle-Labeled Microfluidic Immunoassay for Detection of Pathogenic Microorganisms (2005)

The light-scattering properties of submicroscopic metal particles ranging from 40 to 120 nm in diameter have recently been investigated. These particles scatter incident white light to generate monochromatic light, which can be seen either by the naked eye or by dark-field microscopy. The nanoparticles are well suited for detection in microchannel-based immunoassays. The goal of the present study was to detect Helicobacter pylori- and Escherichia coli O157:H7-specific antigens with biotinylated polyclonal antibodies. Gold particles (diameter, 80 nm) functionalized with a secondary antibiotin antibody were then used as the readout. A dark-field stereomicroscope was used for particle visualization in poly(dimethylsiloxane) microchannels. A colorimetric quantification scheme was developed for the detection of the visual color changes resulting from immune reactions in the microchannels. The microchannel immunoassays reliably detected H. pylori and E. coli O157:H7 antigens in quantities on the order of 10 ng, which provides a sensitivity of detection comparable to those of conventional dot blot assays. In addition, the nanoparticles within the microchannels can be stored for at least 8 months without a loss of signal intensity. This strategy provides a means for the detection of nanoparticles in microchannels without the use of sophisticated equipment. In addition, the approach has the potential for use for further miniaturization of immunoassays and can be used for long-term archiving of immunoassays.
Identification of extracellular siderophores of pathogenic strains ofAspergillus fumigatus (1990)

Clinical and environmental isolates of Aspergillus fumigatus synthesized extracellular siderophores when grown in defined medium. Six hydroxamate siderophores were purified from culture filtrates and identified by thin layer chromatography. The most prominent siderophore was identified as N,N',N"-triacetylfusarinine C and the second most prominent siderophore was identified as ferricrocin. In addition, a hydrolytic product of N,N',N"-triacetylfusarinine C was identified. Three other siderophores were present in smaller amounts and were not identified. Since the same siderophores were produced by isolates from diseases of varying severity and from environmental material, it is unlikely that the extracellular siderophores function as virulence factors during infection. However, they may function as growth factors by mediating iron uptake by the fungus in the micro-environment of the inflammatory focus.
Expression of survivin is associated with malignant potential in epithelial ovarian carcinoma (2002)

Survivin is a new member of the inhibitor of apoptosis family of anti-apoptotic proteins. It has been reported that survivin is expressed during fetal development and in cancer tissues. Because suppression of apoptosis is important for carcinogenesis and tumor growth, we investigated the expression of survivin in human endometrial carcinomas. We analyzed serial frozen sections for survivin protein expression in 26 patients with ovarian epithelial carcinoma and 10 patients with benign cystadenoma of the ovary by fluorescent immunohistochemistry. We analyzed the relationship between the percentages of survivin-stained cells and the characteristics of the patient including histological classification, clinical stage, histological grade, and clinical outcome. Survivin was weakly detected in some benign ovarian cystadenomas (0-12.1%). There was, however, abundant survivin immunoreactivity in the nucleus and/or cytoplasm of the epithelial ovarian carcinoma cells. Scoring on the basis of the percentage of positive cells indicated that survivin expression was significantly associated with PCNA-labeling index, clinical stage, histological grade, clinical outcome, and survival rate (p<0.01, respectively). We conclude that the survivin protein is a defining diagnostic marker for epithelial ovarian carcinomas that may also yield prognostic information.
Impact of Antibiotic Resistance on the Treatment of Sepsis (2003)

Antibiotics are essential to the treatment of bacterial sepsis as they reduce the bacterial burden. The impact of bacterial resistance has recently been studied and found to be important in a range of conditions. Resistance to antibiotics can be defined genotypically, phenotypically and clinically through pharmacokinetic/pharmacodynamic studies and their correlations with clinical outcomes. Although the kinetics of antibiotics has been shown to be favourably altered in sepsis, a range of studies in sepsis has revealed that for most pathogens resistance contributes to significant increases in mortality. This has been clearly demonstrated in bacteraemia, including community- and hospital-acquired infection, and with bacteraemia caused by vancomycin-resistant enterococci, methicillin-resistant staphylococci and extended-spectrum producing Gram-negative bacteria. Significant mortality increases have also been seen with ventilator-associated pneumonia and serious infections requiring admission to intensive care. Gentotypic and phenotypic resistance in coagulase-negative staphylococci causing bacteraemia, and in invasive pneumococcal disease has not shown differences in mortality. In the latter case, dosage regimens have to date been adequate to overcome laboratory-defined resistance. Early indications are that de-escalating therapy from broad-spectrum initial coverage after results of cultures and susceptibility tests become available does not jeopardize outcomes, and further prospective studies are warranted. There is now convincing evidence that broad-spectrum initial therapy to cover the likely pathogens and their resistances pending culture results is mandatory in sepsis to minimize adverse outcomes.
Biventricular pacing in congestive heart failure. (2002)

Congestive heart failure (CHF) is a common, debilitating and usually lethal condition responsible for enormous burden on health care. The recent trials have shown improvement in morbidity and mortality with ACE inhibitors and beta blockers1,2,3. However, despite this the overall prognosis remains dismal. The other alternative of cardiac transplantation has several limitations including the donor organ scarcity. In view of this gloomy prognosis, several alternative strategies are being explored, one of which has been pacing for heart failure. In this form of therapy pacing is used in absence of the conventional bradyarrhthymic indications with an attempt to lead to optimization of AV delay and co-ordination of ventricular contraction.
Chemokine receptor signaling in mast cells (89.27) (2007)

Abstract Mast cells play an important role in IgE-associated allergic disorders and immune response to parasites. In a former study, we demonstrated that chemokine CCL3 (MIP-1α) acted as a co-stimulator for FcεRI-mediated activation on mast cells. To advance our understanding on this finding, we studied gene profiles in Rat Basophilic Leukaemia mast cells after co-activation of CCR1 (a receptor of CCL3) and FcεRI using the Affymetrix GeneChip Arrays. Emp1 (Epithelial Membrane protein 1), RT1-S3 (non-classical type 1 MHC gene), and Slc35e4 (solute carrier family 35, member E4) were found to be the top possible synergy-related genes. Validations of this data are being carried out using real time PCR, western-blotting and siRNA technologies. Further to our in vivo findings of the inhibition of the immediate hypersensitivity reactions in the conjunctiva and the attenuation of mast cell degranulation in MIP-1α deficient mice, we would like to check if MIP-1α and CCR1 play a critical role to produce these effects. We reconstituted the bone marrow-derived mice mast cells (BMMC) from naïve mice into mast cell-deficient mice and confirmed that the reconstituted BMMC home to their eye. The next step is to examine whether CCR1 and CCL3 are critical for mast cell activation and allergic conjunctivitis-like symptoms following induction of murine allergic conjunctivitis using CCR1- and CCL3- deficient mice.
Infectious enveloped RNA virus antigenic chimeras. (1992)

Random insertion mutagenesis has been used to construct infectious Sindbis virus structural protein chimeras containing a neutralization epitope from a heterologous virus, Rift Valley fever virus. Insertion sites, permissive for recovery of chimeric viruses with growth properties similar to the parental virus, were found in the virion E2 glycoprotein and the secreted E3 glycoprotein. For the E2 chimeras, the epitope was expressed on the virion surface and stimulated a partially protective immune response to Rift Valley fever virus infection in vivo. Besides providing a possible approach for developing live attenuated vaccine viruses, insertion of peptide ligands into virion surface proteins may ultimately allow targeting of virus infection to specific cell types.
56 Gb/s Germanium Waveguide Electro-Absorption Modulator (2015)

We report a Germanium waveguide electro-absorption modulator with electro-optic bandwidth substantially beyond 50 GHz. The device is implemented in a fully integrated Si photonics platform on 200 mm silicon-on-insulator wafers with 220 nm top Si thickness. Wide open eye diagrams are demonstrated at 1610 nm operation wavelength for nonreturn-to-zero on-off keying (NRZ-OOK) modulation at data rates as high as 56 Gb/s. Dynamic extinction ratios up to 3.3 dB are obtained by applying drive voltages of 2 V peak-to-peak, along with an optical insertion loss below 5.5 dB. The device has a low junction capacitance of just 12.8 fF, resulting in 12.8 fJ/bit of dynamic and ~1.2 mW of static power consumption in typical operating conditions. Wafer-scale performance data are presented and confirm the manufacturability of the device. The demonstrated modulator shows great potential for realizing high-density and low-power silicon photonic transceivers targeting short-reach optical interconnects at serial data rates of 56 Gb/s and beyond.
Detection of multiple gains and losses of genetic material in ten glioma cell lines by comparative genomic hybridization (1995)

A protocol for comparative genomic hybridization by use of nucleotides directly labeled with fluorochromes was used to map regions of deletion and amplification in ten glioma cell lines. The protocol greatly reduced experimental artifacts. We detected several genetic aberrations, including whole chromosome loss and gain, partial loss and gain, possible isochromosome, and higher level DNA amplification. The most frequent losses (in order of frequency) occurred on chromosomes 10, 18, 13, 11, 9, 14, 4, 6, 1, and X. The most common gain occurred on chromosome 7. Several sites of previously known and unknown amplifications were observed.
Proteins on ribosome surface: Measurements of protein exposure by hot tritium bombardment technique (1997)

The hot tritium bombardment technique [Goldanskii, V. I., Kashirin, I. A., Shishkov, A. V., Baratova, L. A. & Grebenshchikov, N. I. (1988) J. Mol. Biol. 201,567-574] has been applied to measure the exposure of proteins on the ribosomal surface. The technique is based on replacement of hydrogen by high energy tritium atoms in thin surface layer of macromolecules. Quantitation of tritium radioactivity of each protein has revealed that proteins S1, S4, S5, S7, S18, S20, and S21 of the small subunit, and proteins L7/L12, L9, L10, L11, L16, L17, L24, and L27 of the large subunit are well exposed on the surface of the Escherichia coli 70 S ribosome. Proteins S8, S10, S12, S16, S17, L14, L20, L29, L30, L31, L32, L33, and L34 have virtually no groups exposed on the ribosomal surface. The remaining proteins are found to be exposed to lesser degree than the well exposed ones. No additional ribosomal proteins was exposed upon dissociation of ribosomes into subunits, thus indicating the absence of proteins on intersubunit contacting surfaces.
FOLFOX/FOLFIRI pharmacogenetics: The call for a personalized approach in colorectal cancer therapy (2014)

While 5-fluorouracil used as single agent in patients with metastatic colorectal cancer has an objective response rate around 20%, the administration of combinations of irinotecan with 5-fluorouracil/folinic acid or oxaliplatin with 5-fluorouracil/folinic acid results in significantly increased response rates and improved survival. However, the side effects of systemic therapy such as myelotoxicity, neurotoxicity or gastrointestinal toxicity may lead to life-threatening complications and have a major impact on the quality of life of the patients. Therefore, biomarkers that would be instrumental in the choice of optimal type, combination and dose of drugs for an individual patient are urgently needed. The efficacy and toxicity of anticancer drugs in tumor cells is determined by the effective concentration in tumor cells, healthy tissues and by the presence and quantity of the drug targets. Enzymes active in drug metabolism and transport represent important determinants of the therapeutic outcome. The aim of this review was to summarize published data on associations of gene and protein expression, and genetic variability of putative biomarkers with response to therapy of colorectal cancer to 5-fluorouracil/leucovorin/oxaliplatin and 5-fluorouracil/leukovorin/irinotecan regimens. Gaps in the knowledge identified by this review may aid the design of future research and clinical trials.
Lipid modulation of membrane‐bound epitope recognition and blocking by HIV‐1 neutralizing antibodies (2008)

The conserved, aromatic-rich membrane-proximal external region (MPER) of gp41 is functional in human immunodeficiency virus (HIV)-cell fusion by perturbing membrane integrity. Broadly-neutralizing 2F5 and 4E10 monoclonal antibodies (MAb-s) recognize amino- and carboxy-terminal epitope sequences within this domain, respectively. An MPER peptide overlapping 2F5 and 4E10 epitope sequences was capable of breaching the permeability barrier of lipid vesicles. Cholesterol and sphingomyelin raft-lipids, present at high quantities in the HIV-1 envelope, promoted exposure or occlusion of 4E10 epitope, respectively. Conversely, 2F5 epitope accessibility was affected to a lesser extent by these envelope lipids. These observations support the idea that MPER epitopes on membranes are segmented in terms of how they are affected by envelope lipids, which may have implications for MPER-based vaccine development.
Ethanol from biomass by enzymatic hydrolysis (1988)

Haemonchus contortus is a parasite species that affects the health and production of grazing small ruminants in different parts of the world. Scanning electron microscopy (SEM) is an important tool for the study of parasites' morphology and taxonomy as it generates images that appear 3D and are generally easier to interpret than optical microscopy images. This study used the SEM to describe the vulval types of adult H. contortus from a Mexican isolate. A total of 14 adult H. contortus females were obtained from two artificially infected goats. Females were fixed and processed by critical point drying and observed with SEM. A collection of SEM images was obtained from these parasites and those images were used to identify the structures previously described by optical microscopy studies. Two different types of vulval structures were described in this Mexican H. contortus isolate: Type 1 (vulval flap), Type 2 (epiptygma). An unusual vulval structure was reported in a single individual. The Type 1 included vulval flaps of different sizes and spatial dispositions, as well as one or more knobs in different positions around the vulva. The Type 2 shows differences in the epiptygma. The present study suggests that the Mexican H. contortus isolate used in donor animals possess intraspecific polymorphism in vulval structures.
α-Synuclein–induced Aggregation of Cytoplasmic Vesicles inSaccharomyces cerevisiae (2008)

Aggregated alpha-synuclein (alpha-syn) fibrils form Lewy bodies (LBs), the signature lesions of Parkinson's disease (PD) and related synucleinopathies, but the pathogenesis and neurodegenerative effects of LBs remain enigmatic. Recent studies have shown that when overexpressed in Saccharomyces cerevisiae, alpha-syn localizes to plasma membranes and forms cytoplasmic accumulations similar to human alpha-syn inclusions. However, the exact nature, composition, temporal evolution, and underlying mechanisms of yeast alpha-syn accumulations and their relevance to human synucleinopathies are unknown. Here we provide ultrastructural evidence that alpha-syn accumulations are not comprised of LB-like fibrils, but are associated with clusters of vesicles. Live-cell imaging showed alpha-syn initially localized to the plasma membrane and subsequently formed accumulations in association with vesicles. Imaging of truncated and mutant forms of alpha-syn revealed the molecular determinants and vesicular trafficking pathways underlying this pathological process. Because vesicular clustering is also found in LB-containing neurons of PD brains, alpha-syn-mediated vesicular accumulation in yeast represents a model system to study specific aspects of neurodegeneration in PD and related synucleinopathies.
Localization of a minimal binding domain and activation regions in yeast regulatory protein ADR1. (1989)

ADR1 is a transcription factor required for activation of the glucose-repressible alcohol dehydrogenase 2 (ADH2) gene in Saccharomyces cerevisiae. ADR1 has two zinc finger domains between amino acids 102 and 159, and it binds to an upstream activation sequence (UAS1) in the ADH2 promoter. A functional dissection of ADR1 was performed by using a series of amino- and carboxy-terminal deletion mutants of ADR1, most of which were fused to the Escherichia coli beta-galactosidase. These deletion mutants were assayed for binding to UAS1 in vitro, for the ability to activate ADH2 transcription in vivo, and for level of expression. Deletion of ADR1 amino acids 150 to 172 and 76 to 98 eliminated DNA binding in vitro, which accounted for the loss of transcriptional activation in vivo. Results with the former deletion mutant indicated that both of the ADR1 zinc fingers are necessary for sequence-specific DNA binding. Results with the latter deletion mutant suggested that at least part of the sequence between amino acids 76 to 98, in addition to the two finger domains, is required for high-affinity DNA binding. The smallest fusion protein able to activate ADH2 transcription, containing ADR1 amino acids 76 to 172, was much less active in vivo than was the longest fusion protein containing amino acids 1 to 642 of ADR1. In addition, multiple regions of the ADR1 polypeptide (including amino acids 40 to 76, 260 to 302, and 302 to 505), which are required for full activation of ADH2, were identified. An ADR1-beta-galactosidase fusion protein containing only the amino-terminal 16 amino acids of ADR1 was present at a much higher level than were larger fusion proteins, which suggested that the sequences within ADR1 influence the expression of the gene fusion.
Progress in Oncology (2002)

This inaugural volume in a series of annual updates in oncology summarizes basic science, clinical applications, and controversies in the field. Topics include gene analysis using DNA microarrays, progress in the molecular diagnostics of cancer, thalidomide for cancer therapy, rolling circle amplifi
Vascular Endothelial Growth Factor Receptor 1 Morpholino Decreases Angiogenesis in a Murine Corneal Suture Model (2011)

Flt morpholinos decrease mFlt-1 and increase sFlt-1 levels, resulting in decreased neovascularization in a murine corneal suture model.
An 8Mbit DRAM Design Using a 1TBulk Cell (2005)

An 8 Mbit memory chip featuring a floating body one transistor cell on bulk substrate is characterized for the first time. A high-speed and high accuracy current sense-amplifier with a large common mode reference current is proposed. It achieves a reading time of 10 ns and a current read margin lower than 5 /spl mu/A. A bit fail rate of 0.017% was measured on a 1 Mbit module. Data retention shows that 1 Tbulk cell concept has the potential to be used as a future eDRAM memory cell.
VLSI Design of High-Rate Quasi-Cyclic LDPC Codes for Magnetic Recording Channel (2006)

By implementing an FPGA-based simulator, this paper investigates the semi-random construction of high-rate regular QC-LDPC codes with low error floor for the magnetic recording channel. Then a new QC-LDPC decoder hardware architecture is proposed. Finally, a read channel signal processing datapath consisting of a parallel Max-Log-MAP detector and the proposed QC-LDPC decoder is implemented in 0.13 mum CMOS. This design achieves a throughput up to 1.8Gbps under 16 iterations of LDPC decoding