gebhart/patrepeval huggingface dataset:
Quantitative determination of surface antibody binding capacities of immune subsets present in peripheral blood of healthy adult donors (1996)

The objective of this study was to quantitate the antibody binding capacity (ABC) of CD3, CD4, CD8, CD16, and CD19 on lymphocytes and CD4 on monocytes from healthy adult donors. Peripheral blood was collected over three consecutive days and repeated in the same format two weeks later for comparison to initial measurements. Immune subsets were labeled by direct single or two-color staining in whole blood followed by lysis of erythrocytes. Fluorescence intensity measurements were made by carefully calibrating the flow cytometer and then measuring the intensity of monoclonal antibody staining on labeled cells and on Quantum Simply Cellular Microbeads. The effect of paraformaldehyde fixation on intensity measurements and coefficient of variation of thirty replicates for each phenotype were also studied. We found a small change in calculated ABC following overnight fixation with a greater change following 48 h of fixation prior to flow cytometric analysis. We found excellent precision could be achieved for measuring the ABC of most markers with some improvement desirable for expression of CD4 on monocytes and CD16+ lymphocytes. Between donors we found a high-low range of CD3+ = 134,349-45,905; CD4+ (lymphocytes) = 54,174-36,106; CD4+ (monocytes) = 9,246-3094; CD8+ = 268,868-190,622; CD3+CD8+ = 269,858-212,024; CD16+ = 38,307-336; and CD19+ = 25,252-11,689. For the total donor group, the observations at week 1 and week 2 were not significantly different (alpha = .05) for any of the immunophenotypes we studied. The data presented here continue to show that it is possible to perform quantitative intensity measurements of immune subsets when performing immunophenotyping studies.
Prevention of Travellers Diarrhoea by Lactobacillus GG (1990)

A placebo-controlled double-blind study was conducted on the efficacy of Lactobacillus GG in preventing travellers' diarrhoea. Altogether 820 persons travelling on holiday to southern Turkey to two destinations were randomized into two groups receiving either Lactobacillus GG or placebo in identical sachets. On the return flight each participant completed a questionnaire indicating the incidence of diarrhoea and related symptoms during the trip. Of the original group 756 (92%) subjects completed the study acceptably. The overall incidence of diarrhoea was 43.8% (331 cases). The total incidence of diarrhoea in the placebo group was 46.5% and in the Lactobacillus GG 41.0% indicating an overall protection of 11.8%. Protection rates varied between two different destinations with the maximum protection rate reported as 39.5%. Among older age groups there was significantly less diarrhoea when compared to younger travellers. Lactobacillus GG appeared to be effective in reducing the occurrence of travellers' diarrhoea in one of the two destinations with no side effects.
Clara cell adhesion and migration to extracellular matrix (2008)

Thus, Clara cells resemble alveolar type II and bronchiolar ciliated epithelial cells by showing integrin mediated pro-migratory changes to extracellular matrix components that are present in tissues after injury.
Suppression of c-Src activity by C-terminal Src kinase involves the c-Src SH2 and SH3 domains: analysis with Saccharomyces cerevisiae. (1993)

The kinase activity of c-Src is normally repressed in vertebrate cells by extensive phosphorylation of Y-527. C-terminal Src kinase (CSK) is a candidate for the enzyme that catalyzes this phosphorylation. We have used budding yeast to study the regulation of c-Src activity by CSK in intact cells. Expression of c-Src in Saccharomyces cerevisiae, which lacks endogenous c-Src and Y-527 kinases, induces a kinase-dependent growth inhibition. Coexpression of CSK in these cells results in phosphorylation of c-Src on Y-527 and suppression of the c-Src phenotype. CSK does not fully suppress the activity of c-Src mutants lacking portions of the SH2 or SH3 domains, even though these mutant proteins are phosphorylated on Y-527 by CSK both in vivo and in vitro. These results suggest that both the SH2 and SH3 domains of c-Src are required for the suppression of c-Src activity by Y-527 phosphorylation.
BLIMP‐1 is a target of cellular stress and downstream of the unfolded protein response (2006)

B lymphocyte-induced maturation protein-1 (BLIMP-1) acts during differentiation of B cells and monocytes, but was originally identified as a repressor of the IFN-beta promoter induced during viral infection. A central regulator of the intracellular response to viral infection is the interferon-inducible double-stranded RNA activated protein kinase (PKR). PKR belongs to a family of kinases that phosphorylate the eukaryotic translation initiation factor 2-alpha (eIF2alpha) and activate common downstream signaling pathways. PERK, the endoplasmic reticulum resident PKR-homologue, is activated during the unfolded protein response (UPR), a stress response involved in both macrophage activation and terminal B-cell differentiation. This suggested that BLIMP-1 might be a target of stress responses involving PERK. We demonstrate that BLIMP-1 is rapidly up-regulated during the UPR in human myeloid and B-cell lines. This response is conserved in murine B-cells and murine macrophages, in which mimics of physiological stress and classical activation stimuli also induce Blimp-1. During the UPR, BLIMP-1 mRNA is induced at the level of transcription. This response is dependent on an intact PERK signaling pathway, independent of new protein synthesis and blocked by an inhibitor of NF-kappaB. Our data provide evidence for a novel pathway linking cellular stress to BLIMP-1, a regulator of differentiation in macrophages and B cells.
Sampling with Hammersley and Halton Points (1997)

Abstract The Hammersley and Halton point sets, two well-known, low discrepancy sequences, have been used for quasi-Monte Carlo integration in previous research. A deterministic formula generates a uniformly distributed and stochasticlooking sampling pattern at low computational cost. The Halton point set is also useful for incremental sampling. In this paper, we discuss detailed implementation issues and our experience of choosing suitable bases for the point sets, not just on the two-dimensional plane but also on a spherical surface. The sampling scheme is also applied to ray tracing, with a significant improvement in error over standard sampling techniques.
DATABASE SUPPORT FOR DATA-DRIVEN SCIENTIFIC APPLICATIONS IN THE GRID (2003)

In this paper we describe a services oriented software system to provide basic database support for efficient execution of applications that make use of scientific datasets in the Grid. This system supports two core operations: efficient selection of the data of interest from distributed databases and efficient transfer of data from storage nodes to compute nodes for processing. We present its overall architecture and main components and describe preliminary experimental results.
A 1-GHz 6-bit ADC system (1987)

A two-rank GaAs sample-and-hold (S/H) chip and four 250-MHz silicon digitizers form a 1-GHz 6-b analog-to-digital converter (ADC) system. The two rank S/H architecture avoids dynamic errors inherent to interleaved ADCs; accuracy exceeds 5.2 effective bits, up to 1-GHz input frequency. Special attention is paid to avoiding GaAs slow transient errors.
Inhibition of tumor growth and metastasis by a self-therapeutic nanoparticle (2013)

Although biomedical applications of nanotechnology, which typically involve functionalized nanoparticles, have taken significant strides, biological characterization of unmodified nanoparticles remains underinvestigated. Herein we demonstrate that unmodified gold nanoparticles (AuNPs) inhibit the proliferation of cancer cells in a size- and concentration-dependent manner by abrogating MAPK-signaling. In addition, these AuNPs reverse epithelial-mesenchymal transition (EMT) in cancer cells by reducing secretion of a number of proteins involved in EMT, up-regulating E-Cadherin, and down-regulating Snail, N-Cadherin, and Vimentin. Inhibition of MAPK signaling and reversal of EMT upon AuNP treatment inhibits tumor growth and metastasis in two separate orthotopic models of ovarian cancer. Western blot analyses of tumor tissues reveal up-regulation of E-Cadherin and down-regulation of Snail and phospho-MAPK, confirming the reversal of EMT and inhibition of MAPK signaling upon AuNP treatment. The ability of a single self-therapeutic nanoparticle to abrogate signaling cascades of multiple growth factors is distinctive and purports possible medical applications as potential antitumor and antimetastatic agent.
The human papillomavirus E7 oncoprotein can uncouple cellular differentiation and proliferation in human keratinocytes by abrogating p21Cip1-mediated inhibition of cdk2 (1997)

The high risk human papillomaviruses (HPVs) are associated etiologically with the majority of human cervical carcinomas. These HPVs encode two viral oncoproteins, E6 and E7, which are expressed consistently in cervical cancers. The function of these viral oncoproteins during a productive infection is to ensure viral replication in cells that have normally withdrawn from the cell division cycle and are committed to terminal differentiation. Expression of the E7 oncoprotein has been shown to lead to the abrogation of various negative growth regulatory signals, including a p53-mediated G1 growth arrest, TGFbeta-mediated growth inhibition, and quiescence of suprabasal keratinocytes. Here we describe a novel mechanism by which E7 can uncouple cellular proliferation and differentiation. In contrast to normal, differentiating keratinocytes, HPV-16 E7-expressing keratinocytes show delayed cellular differentiation and elevated cdk2 kinase activity despite high levels of p21(Cip1) and association of p21(Cip1) with cdk2. We show that the HPV E7 protein can interact with p21(Cip1) and abrogate p21(Cip1)-mediated inhibition of cyclin A and E-associated kinase activities. Based on these findings, we propose that this capacity of the HPV E7 oncoprotein to overcome p21(Cip1)-mediated inhibition of cdk2 activity during keratinocyte differentiation contributes to the ability of E7 to allow for cellular DNA synthesis in differentiated keratinocytes.
Crystal structure of non‐allosteric L‐lactate dehydrogenase from Lactobacillus pentosus at 2.3 Å resolution: Specific interactions at subunit interfaces (2001)

L-Lactate dehydrogenase (LDH) from Lactobacillus pentosus is a non-allosteric enzyme, which shows, however, high sequence similarity to allosteric LDHs from certain bacteria. To elucidate the structural basis of the absence of allostery of L. pentosus LDH (LPLDH), we determined the crystal structure of LPLDH at 2.3 A resolution. Bacterial LDHs are tetrameric enzymes composed of identical subunits and exhibit 222 symmetry. The quaternary structure of LPLDH was similar to the active conformation of allosteric LDHs. Structural analysis revealed that the subunit interfaces of LPLDH are optimized mainly through hydrophilic interactions rather than hydrophobic interactions, compared with other LDHs. The subunit interfaces of LPLDH are more specifically stabilized by increased numbers of intersubunit salt bridges and hydrogen bonds, and higher geometrical complementarity. Such high specificity at the subunit interfaces should hinder the rearrangement of the quaternary structure needed for allosteric regulation and thus explain the "non-allostery" of LPLDH.
Simplifying concurrent algorithms by exploiting hardware transactional memory (2010)

We explore the potential of hardware transactional memory (HTM) to improve concurrent algorithms. We illustrate a number of use cases in which HTM enables significantly simpler code to achieve similar or better performance than existing algorithms for conventional architectures. We use Sun's prototype multicore chip, code-named Rock, to experiment with these algorithms, and discuss ways in which its limitations prevent better results, or would prevent production use of algorithms even if they are successful. Our use cases include concurrent data structures such as double ended queues, work stealing queues and scalable non-zero indicators, as well as a scalable malloc implementation and a simulated annealing application. We believe that our paper makes a compelling case that HTM has substantial potential to make effective concurrent programming easier, and that we have made valuable contributions in guiding designers of future HTM features to exploit this potential.
Increase in Neuroendocrine Cells in the Duodenal Mucosa of Patients with Refractory Celiac Disease (2014)

Serotonin-producing neuroendocrine cells are increased in RCD mucosa. IFN-γ upregulation induced by serotonin suggests that this monoamine may have a role in sustaining the local inflammatory response in CD.
Amygdala norepinephrine levels after training predict inhibitory avoidance retention performance in rats (2002)

Previous findings indicate that footshock and several drugs that modulate memory consolidation alter norepinephrine (noradrenaline) release in the amygdala, as assessed by in vivo microdialysis and high-performance liquid chromatography. Such findings suggest that norepinephrine release in the amygdala may be critical for regulating memory consolidation. The present study was the first to examine the relationship between norepinephrine release in the amygdala assessed after inhibitory avoidance training and 24-h retention performance within individual animals. Norepinephrine levels increased to > 300% of pretraining baseline 30 min after training and remained elevated for 2 h. In individual rats, the increase in norepinephrine levels after training correlated highly with 24-h retention performance. These findings indicate that the degree of activation of the noradrenergic system within the amygdala in response to a novel, emotionally arousing experience predicts the extent of long-term memory for that experience.
A Cockcroft-Walton for FELTRON: the new mu -wave source for TeV colliders (1992)

A pulsed powerful Cockcroft-Walton generator for an electrostatic accelerator is presented. The electrostatic accelerator is designed to provide a pulsed electron beam of 5.5 MeV, 100 A, and 0.5 mu s with a repetition rate of 1 kHz. The output voltage has a descending staircase waveform. This voltage provides an electron beam made up of ten sections having different energies. Two adjacent pieces have a relative energy variation Delta gamma ij/ gamma of 1%. A dispersive system spatially separates those sections into ten 50-ns-long electron beam pulses.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
TUMOR NECROSIS FACTOR: A Pleiotropic Cytokine and Therapuetic Target (1994)

Advances in the molecular biology of human diseases indicate that the most striking manifestations of illness may be caused not by exogenous pathogenic or tumor products, but rather by toxic peptides produced by the host itself. Tumor necrosis factor (TNF), a polypeptide cytokine produced during infection, injury, or invasion, has proved pivotal in triggering the lethal effects of septic shock syndrome, cachexia, and other systemic manifestations of disease. Because removing TNF from the diseased host may prevent development of the illness, this factor has recently been the focus of intensive research. This review discusses the biology of this cytokine, with particular emphasis on its potential therapeutic role in septic shock and cachexia.
Giant Liposome Microreactors for Controlled Production of Calcium Phosphate Crystals (2004)

Calcium phosphates are among the most important biominerals in living organisms, where they play both a mechanical and a calcium storage role. Their growth in vivo is under strong biological control, and this process occurs in closed spaces. Our aim in this paper is to describe a microreactor system able to control the mineralization process within closed spaces. To this aim we produce giant liposomes containing calcium ions as active ions in the mineralization process, spermine as an activator of crystal growth, and alkaline phosphatase as a catalyst to convert phosphate esters into phosphates. These phosphate esters are provided in the form of p-nitrophenyl phosphate outside of the liposomes. It is demonstrated that these amphiphilic molecules are able to diffuse through the lipidic container and to be subsequently hydrolyzed under enzymatic catalysis into active phosphate species which interact with the already available calcium and spermine to produce calcium phosphates only in the interior of the liposomes. This opens the route to control the calcium phosphate particle size in biomimetic systems.
Direct visualization of copper-metallothionein in LEC rat kidneys: application of autofluorescence signal of copper-thiolate cluster. (1996)

We report on the histochemistry of copper-metallothionein (Cu-MT) in the kidneys of Long Evans Cinnamon (LEC) rats. We used the visualization principle of histochemistry based on the autofluorescence emission from the fluorophore of Cu(+)-thiolate clusters in proteins. Intense autofluorescence signals were observed with a ring at the outer stripe of the outer medulla. Orange fluorescence signals were observed in the nuclei and cytoplasm of proximal straight tubular (PST) cells of segment 3 (S3) at the outer stripe of the outer medulla, and yellow-orange signals were detected in lysosome-like organelles in the proximal convoluted tubule (PCT) cells of segments 1 and 2 (S1 and S2) adjacent to the glomeruli in the cortex. These fluorescent materials were identified as Cu-MT because both signals were quenched by withdrawing Cu+ or by blocking cysteine residues, the distributions of cysteine residues and immunoreactive MT showed identical patterns to the localization of the fluorescence signals, and the fluorescent proteins containing Cu were eluted at the same Kd value of purified Cu-MT by gel filtration chromatography. However, a high level of MT mRNA was detected only in the outer stripe of the outer medulla where the orange fluorescence signals were detected, but not in the cortex. This difference in localization between the protein and the mRNA suggested that synthesis of renal MT occurs do novo in the outer stripe of the outer medulla. The yellow-orange fluorescent Cu-MT located in the lysosomal organelles at S1 and S2 of the PCT cells in the cortex could be Cu-MT of nonrenal origin, i.e., Cu-MT transported from other organs.
Cetuximab in the treatment of head and neck cancer (2006)

Approaches to the treatment of locally advanced and recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) have been limited by their toxicity. Effective, better tolerated approaches are urgently required. Cetuximab is an immunoglobulin G(1) monoclonal antibody that specifically targets the epidermal growth factor receptor (EGFR), which is commonly expressed in a number of solid tumors, including SCCHN, where it is associated with poor prognosis. Cetuximab is approved in 56 countries for use in the treatment of EGFR-expressing metastatic colorectal cancer that has progressed on irinotecan-containing therapy and has recently received approval in Europe and the USA for use in the treatment of SCCHN. A randomized Phase III study has demonstrated that cetuximab plus radiotherapy can significantly improve locoregional control and prolong overall survival compared with radiotherapy alone. Cetuximab has also been confirmed to be effective as monotherapy in recurrent and/or metastatic SCCHN that has progressed on platinum-containing therapy. Clinical studies have demonstrated that cetuximab is well tolerated and does not significantly increase the side effects associated with radiotherapy or chemotherapy. This article presents the rationale for EGFR inhibition in the management of head and neck cancers, and the preclinical and clinical evidence for the use of cetuximab in the treatment of SCCHN.
An S -nitrosothiol (SNO) synthase function of hemoglobin that utilizes nitrite as a substrate (2006)

Red blood cells (RBCs) act as O(2)-responsive transducers of vasodilator and vasoconstrictor activity in lungs and tissues by regulating the availability of nitric oxide (NO). Vasodilation by RBCs is impaired in diseases characterized by hypoxemia. We have proposed that the extent to which RBCs constrict vs. dilate vessels is, at least partly, controlled by a partitioning between NO bound to heme iron and to Cysbeta93 thiol of hemoglobin (Hb). Hemes sequester NO, whereas thiols deploy NO bioactivity. In recent work, we have suggested that specific micropopulations of NO-liganded Hb could support the chemistry of S-nitrosohemoglobin (SNO-Hb) formation. Here, by using nitrite as the source of NO, we demonstrate that a (T state) micropopulation of a heme-NO species, with spectral and chemical properties of Fe(III)NO, acts as a precursor to SNO-Hb formation, accompanying the allosteric transition of Hb to the R state. We also show that at physiological concentrations of nitrite and deoxyHb, a S-nitrosothiol precursor is formed within seconds and produces SNO-Hb in high yield upon its prompt exposure to O(2) or CO. Deoxygenation/reoxygenation cycling of oxyHb in the presence of physiological amounts of nitrite also efficiently produces SNO-Hb. In contrast, high amounts of nitrite or delays in reoxygenation inhibit the production of SNO-Hb. Collectively, our data provide evidence for a physiological S-nitrosothiol synthase activity of tetrameric Hb that depends on NO-Hb micropopulations and suggest that dysfunction of this activity may contribute to the pathophysiology of cardiopulmonary and blood disorders.
Commensal bacteria can enter colonic epithelial cells and induce proinflammatory cytokine secretion: a possible pathogenic mechanism of ulcerative colitis (2009)

Interleukin 2 (IL-2)- and IL-10-knockout mice develop spontaneous colitis under conventional but not germ-free conditions, suggesting that commensal bacteria play an important role in the pathogenesis of colitis. However, interactions between commensal bacteria and colonic epithelial cells have not been fully investigated. We therefore assessed the ability of various commensal bacteria and probiotics to adhere to and invade colonic epithelial cells. Effects of the bacteria on production of proinflammatory cytokines were also measured. Commensal bacteria, including mucosal organisms isolated from ulcerative colitis (UC) patients, such as Fusobacterium varium, reported as a possible pathogen in UC, Bacteroides vulgatus, Escherichia coli and Clostridium clostridioforme, as well as their type strains and probiotics, were assessed for their ability to adhere to and invade colonic epithelial cells using two cell lines, SW-480 and HT-29. Our experiments employed co-incubation, a combination of scanning and transmission electron microscopy and recovery of bacteria from infected-cell lysates. F. varium and several other commensal bacteria, but not probiotics, adhered to colonic epithelial cells and invaded their cytoplasm. ELISA and real-time PCR revealed that the host cells, particularly those invaded by F. varium, showed significant increases in IL-8 and TNF-alpha concentrations in supernatants, with elevation of IL-8, TNF-alpha, MCP-1 and IL-6 mRNAs. Furthermore, IL-8 and TNF-alpha expression and nuclear phosphorylated NF-kappaB p65 expression could be immunohistochemically confirmed in inflamed epithelium with cryptitis or crypt abscess in UC patients. Certain commensal bacteria can invade colonic epithelial cells, activating early intracellular signalling systems to trigger host inflammatory reactions.