gebhart/patrepeval huggingface dataset:
Molecular cloning of the B-CAM cell surface glycoprotein of epithelial cancers: a novel member of the immunoglobulin superfamily. (1994)

The human F8/G253 antigen, B-CAM, is a cell surface glycoprotein that is expressed with restricted distribution pattern in normal fetal and adult tissues, and is up-regulated following malignant transformation in some cell types. We have isolated a complementary DNA for B-CAM using an expression cloning technique. The complementary DNA (EMBL accession number X80026) encodes a 588-amino acid protein which is a novel member of the immunoglobulin superfamily with a characteristic V-V-C2-C2-C2 immunoglobulin domain structure. This structure has been described previously for the human MUC18 melanoma antigen (31% amino acid identity) and chicken and rat versions of a neural adhesion molecule referred to as SC1/DM-GRASP/BEN or KG-CAM, respectively (26% amino acid identity). This homology is suggestive of a role for B-CAM in cell-cell or cell-matrix adhesion. The gene for B-CAM has been mapped by fluorescence in situ hybridization to chromosome 19q13.2-13.3.
Slowly conducting afferents activated by innocuous low temperature in human skin (2001)

1. Microneurography was used to search for primary afferents responsive to innocuous low temperature in human nerves supplying the hairy skin of the hand or foot. Eighteen units were identified as cold-specific units: they displayed a steady-state discharge at skin temperatures in the range 28-30 degrees C, they were sensitive to small changes in temperature, and they responded vigorously when a cool metal probe touched their receptive fields (RFs). They were insensitive to mechanical stimuli and sympathetic activation. Their RFs comprised one, or at most two, spots less than 5 mm in diameter. 2. Nine units were characterised in detail by a series of 10 s cooling and warming pulses from a holding temperature of 35 degrees C. The threshold temperature for activation by cooling was 29.4 +/- 2.0 degrees C (mean +/- S.D.). Adaptation of the responses to supra-threshold cooling pulses was partial: mean peak and plateau firing rates were maximal on steps to 15 degrees C (35.9 and 19.9 impulses x s(-1), respectively). Three of these units also displayed a paradoxical response to warming, with a mean threshold of 42.3 degrees C. 3. Sixteen of the eighteen cold-specific units were also studied by electrical stimulation of their RFs. They conducted in the velocity range 0.8-3.0 m x s(-1). When stimulated at 2 Hz, their latency increased according to a characteristic time course, reaching a plateau within 3 min (mean slowing (+/- S.D.) 5.2 +/- 1.1 %) and recovering quickly (50 % recovery in 17.8 +/- 4.5 s). 4. To reconcile these findings with previous studies of reaction times and the effects of nerve compression on sensation, it is concluded that either human cold-specific afferent fibres are incompletely myelinated 'BC' fibres, or else there are C as well as A(delta) cold fibres, with the C fibre group contributing little to sensation.
Toward simulation-time data analysis and I/O acceleration on leadership-class systems (2011)

The performance mismatch between computing and I/O components of current-generation HPC systems has made I/O the critical bottleneck for scientific applications. It is therefore critical to make data movement as efficient as possible, and, to facilitate simulation-time data analysis and visualization to reduce the data written to storage. These will be of paramount importance to enabling us to glean novel insights from simulations. We present our work in GLEAN, a flexible framework for data-analysis and I/O acceleration at extreme scale. GLEAN leverages the data semantics of applications, and fully exploits the diverse system topologies and characteristics. We discuss the performance of GLEAN for simulation-time analysis and I/O acceleration with simulations at scale on leadership class systems.
Anti-Epidermal Growth Factor Receptor Antibodies Inhibit the Autocrine-Stimulated Growth of MDA-468 Human Breast Cancer Cells (1989)

The response of malignant and nonmalignant human breast cell lines to the growth inhibitory effects of monoclonal antibodies against the epidermal growth factor (EGF) receptor was studied. A series of human breast cell lines, which express EGF receptor, were used: MDA-468, MDA-231, and Hs578T human breast cancer cells and the transformed human mammary epithelial cell lines 184A1N4 and 184A1N4-T that have been benzo[a]pyrene immortalized and further transformed with SV40T, respectively. Four antibodies of two different classes were tested: 225 immunoglobulin G (IgG), 108.4 IgG, 96 immunoglobulin M (IgM), and 42 IgM. All four antibodies inhibited the anchorage-dependent and -independent, EGF-stimulated growth of 184A1N4 and 184A1N4-T cells, respectively, and this growth inhibition could be reversed by the addition of increasing concentrations of EGF. In contrast, the antibodies inhibited the anchorage-dependent and -independent growth of MDA-468 cells in the absence of exogenous EGF suggesting that the antibodies were acting to block access of an endogenously produced ligand to the EGF receptor. In the presence of antibody and increasing concentrations of EGF, MDA-468 cell growth was first stimulated then inhibited as the EGF concentration increased, thus, uncovering the growth stimulatory potential of low concentrations of EGF in these cells. Data is presented that indicates MDA-468 cells secrete a transforming growth factor with autocrine growth stimulatory capabilities. The growth of MDA-231 and Hs578T cells, which contain activated ras oncogenes, was not inhibited by the antibodies and the growth of these cell lines was not stimulated by EGF. Of the cell lines studied only MDA-468 cells appear to possess an autocrine growth stimulatory capacity.
Magnavox Automatic Vehicle Location Pilot System for the Toronto Department of Ambulance Services (2003)

The AVLS integrates several technologies in a manner that permits satisfaction of demanding requirements, and allows for significant growth and application customizing. Principal examples of this integration are the navigation subsystem, communication subsystem, and AVLS base station dispatch software. Each of these subsystems is described, and how they address the specific needs of the application is illustrated. The ability to tailor the system to other AVLS requirements is also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Capped mRNA Degradation Intermediates Accumulate in the Yeast spb8-2 Mutant (1998)

mRNA in the yeast Saccharomyces cerevisiae is primarily degraded through a pathway that is stimulated by removal of the mRNA cap structure. Here we report that a mutation in the SPB8 (YJL124c) gene, initially identified as a suppressor mutation of a poly(A)-binding protein (PAB1) gene deletion, stabilizes the mRNA cap structure. Specifically, we find that the spb8-2 mutation results in the accumulation of capped, poly(A)-deficient mRNAs. The presence of this mutation also allows for the detection of mRNA species trimmed from the 3' end. These data show that this Sm-like protein family member is involved in the process of mRNA decapping, and they provide an example of 3'-5' mRNA degradation intermediates in yeast.
Comparison of the nasal bacterial floras in two groups of healthy subjects and in patients with acute maxillary sinusitis (1989)

The nasal bacterial flora was studied in 183 healthy men entering military service (entry group), 103 healthy recruits in service (service group), and 185 recruits with acute maxillary sinusitis. The 267 nasal and ipsilateral sinus aspirate findings in the same patients with acute maxillary sinusitis were compared pairwise. In the entry group presumed sinus pathogens were only rarely isolated from the nasal cavities: Haemophilus influenzae in 4%, Streptococcus pneumoniae in 1%, Branhamella catarrhalis in 3%, and Streptococcus pyogenes in 0%. The corresponding isolation frequencies in the service group were 19, 13, 3, and less than 1%, respectively, and those in the group with acute maxillary sinusitis were 61, 25, 7, and 6%, respectively. Suppression of the major components of the normal nasal flora, Corynebacterium sp., coagulase-negative staphylococci, Propionibacterium acnes, and Staphylococcus aureus, was seen in the group with acute maxillary sinusitis and also occasionally in the service group. When a sinus aspirate culture yielded a presumed sinus pathogen, the same pathogen was found in the nasal samples in 91% of the cases. The predictive value of a pathogen-positive nasal finding was highest (93.8%) for S. pyogenes, followed by 77.7% for H. influenzae and 68.7% for S. pneumoniae, and lowest (20%) for B. catarrhalis.
Interactions of target-sensitive immunoliposomes with herpes simplex virus. The foundation of a sensitive immunoliposome assay for the virus. (1987)

Interactions between target-sensitive (TS) immunoliposomes and herpes simplex virus (HSV) were investigated. Target sensitivity of phosphatidylethanolamine (PE) immunoliposomes is a result of the ability of acylated monoclonal anti-HSV glycoprotein D (gD) to stabilize the bilayer phase of PE, whereas by itself, PE does not form stable liposomes (Ho, R. J. Y., Rouse, B. T., and Huang, L. (1986) Biochemistry 25, 5500-5506). Upon binding of these immunoliposomes to HSV antigen-containing gD, destabilization of PE immunoliposomes was observed. By encapsulating either a self-quenching fluorescent dye, calcein, or alkaline phosphatase inside the liposomal compartment, the HSV-induced destabilization of TS immunoliposomes was shown to be target-specific. Neither Sendai, Semliki Forest, nor Sindbis virus could significantly destabilize the TS immunoliposomes. Moreover, HSV-induced liposome destabilization could be inhibited by free anti-gD (the same antibody used in TS immunoliposomes) but not by monoclonal anti-HSV glycoprotein B, indicating that the interaction was antigen-specific. Destabilization could also be induced by binding to truncated gD (tgD), but only when in a multivalent form immobilized on latex beads. Truncated gD is a cloned, 312-amino acid fragment of HSV-gD that lacks the transmembrane segment. Preincubation of soluble tgD with the TS immunoliposomes failed to induce destabilization and, in addition, abolished the tgD-bead-induced destabilization. This finding strongly indicated that multivalent binding is essential for TS immunoliposome destabilization. Using alkaline phosphatase encapsulated in the liposomes, TS immunoliposomes could be used to detect HSV in fluid phase with 50% signal recorded at 5 microliters of 3.2 x 10(3) pfu/ml; at least 10-fold more sensitive than the standard double-antibody sandwich enzyme-linked immunosorbent assay. The interactions described here may be useful in designing a homogeneous and sensitive immunoliposome assay.
Direct Measurement of the Wigner Function of a One-Photon Fock State in a Cavity (2002)

We have measured the complete Wigner function W of the vacuum and of a single-photon state for a field stored in a high-Q cavity. This experiment implements the direct Lutterbach and Davidovich method [L. G. Lutterbach and L. Davidovich, Phys. Rev. Lett. 78, 2547 (1997)]] and is based on the dispersive interaction of a single circular Rydberg atom with the cavity field. The nonclassical nature of the single-photon field is exhibited by a region of negative W values. Extensions to other nonclassical cavity field states are discussed.
Model Transformation Chains in Model-Driven Performance Engineering: Experiences and Future Research Needs (2010)

Abstract: We gained experiences in implementing rule based model transformations within an industrial
Immunotherapy of cancer by IL-12-based cytokine combinations (2007)

Cancer is a multi-faceted disease comprising complex interactions between neoplastic and normal cells. Over the past decade, there has been considerable progress in defining the molecular, cellular and environmental contributions to the pathophysiology of tumor development. Despite these advances, the conventional treatment of patients still generally involves surgery, radiotherapy and/or chemotherapy, and the clinical outcome for many of these efforts remains unsatisfactory. Recent studies have highlighted the feasibility of using immunotherapeutic approaches that seek to enhance host immune responses to developing tumors. These strategies include immunomodulatory cytokines, with TNF-alpha, type I or type II IFNs, IL-2, IL-12, IL-15 and IL-18 being among the most potent inducers of anti-tumor activity in a variety of preclinical studies. More recently, some exciting new cytokines have been characterized, such as IL-21, IL-23, IL-27 and their immunomodulatory and antitumor effects in vitro and in vivo suggest that they may have considerable promise for future immunotherapy protocols. The promise of cytokine therapy does indeed derive from the identification of these novel cytokines but even more fundamentally, the field is greatly benefiting from the ever-expanding amount of preclinical data that convincingly demonstrate synergistic and/or novel biologic effects, which may be achieved through the use of several combinations of cytokines with complementary immune-stimulating capabilities. One cytokine in particular, IL-12, holds considerable promise by virtue of the fact that it plays a central role in regulating both innate and adaptive immune responses, can by itself induce potent anticancer effects, and synergizes with several other cytokines for increased immunoregulatory and antitumor activities. This review discusses the antitumor activity of IL-12, with a special emphasis on its ability to synergize with other cytokines for enhancement of immune effector cell populations and regulation of host-tumor cell interactions and the overall tumor microenvironment.
GSTP1 CpG island hypermethylation as a molecular biomarker for prostate cancer (2003)

Somatic hypermethylation of CpG island sequences at GSTP1, the gene encoding the pi-class glutathione S-transferase, appears to be characteristic of human prostatic carcinogenesis. To consider the potential utility of this epigenetic alteration as a biomarker for prostate cancer, we present here a comprehensive review of the literature describing somatic GSTP1 changes in DNA from prostate cells and tissues. GSTP1 CpG island hypermethylation has been detected in prostate cancer DNA using a variety of assay techniques, including (i) Southern blot analysis (SB), after treatment with (5-m)C-sensitive restriction endonucleases, (ii) the polymerase chain reaction, following treatment with (5-m)C-sensitive restriction endonucleases (RE-PCR), (iii) bisulfite genomic sequencing (BGS), and (iv) bisulfite modification followed by the polymerase chain reaction, using primers selective for target sequences containing (5-m)C (MSP). In the majority of the case series so far reported, GSTP1 CpG island hypermethylation was present in DNA from at least 90% of prostate cancer cases. When analyses have been carefully conducted, GSTP1 CpG island hypermethylation has not been found in DNA from normal prostate tissues, or from benign prostatic hyperplasia (BPH) tissues, though GSTP1 CpG island hypermethylation changes have been detected in DNA from candidate prostate cancer precursor lesions proliferative inflammatory atrophy (PIA) and prostatic intraepithelial neoplasia (PIN). Using PCR methods, GSTP1 CpG island hypermethylation has also been detected in urine, ejaculate, and plasma from men with prostate cancer. GSTP1 CpG island hypermethylation, a somatic epigenetic alteration, appears poised to serve as a molecular biomarker useful for prostate cancer screening, detection, and diagnosis.
A flow cytometric method using Hoechst 33342 and propidium iodide for simultaneous cell cycle analysis and apoptosis determination in unfixed cells (1994)

A flow cytometric method to detect apoptotic cells is described. This method is based on the detection of differences in chromatin condensation with Hoechst 33342 as a probe and the detection of dead cells with propidium iodide as a probe for membrane damage. By this method it was possible to detect, in the same sample and at the same time, intact cells, cells undergoing apoptosis, and dead cells resulting from apoptotic and/or necrotic processes. The method was successfully applied to the detection of apoptotic cells in two human cell models: cultured polymorphonuclear cells and the U937 cell line treated with antitumoral drugs. Staining specificity for apoptotic cells was controlled by cell sorting of the presumed apoptotic population, followed by morphologic examination or DNA analysis of the sorted populations. The usefulness of such a method is discussed in terms of applications in the analysis of heterogeneous clinical samples, populations with low DNA degradation during apoptosis, and cell cycle position of the apoptotic cells.
Enantioselective Total Synthesis of Epothilones A and B Using Multifunctional Asymmetric Catalysis (2000)

An enantioselective total synthesis of epothilones A (1) and B (2) using multifunctional asymmetric catalysis such as a cyanosilylation of an aldehyde, an aldol reaction of an unmodified ketone with an aldehyde, and a protonation in the conjugate addition of a thiol to an α,β-unsaturated thioester has been achieved. We divided 1 and 2 into fragment A, fragment B, and fragment C. A catalytic asymmetric synthesis of fragments A and B was accomplished using a catalytic asymmetric cyanosilylation as a key step. An enantiocontrolled synthesis of fragment C was achieved in two ways. One is the use of a direct catalytic asymmetric aldol reaction of an unmodified ketone with an aldehyde as a key step, and the other utilizes a catalytic asymmetric protonation in the conjugate addition of a thiol to an α,β-unsaturated thioester as a key step. Suzuki cross-coupling of fragment A with fragment C followed by Yamaguchi lactonization as key steps led to an enantiocontrolled synthesis of epothilone A (1). On the other hand, Suzuki cross-coupling of fragment B with fragment C followed by Yamaguchi lactonization accomplished an enantiocontrolled synthesis of epothilone B (2).
Segmental Arteriography in Pulmonary Embolism (1969)

FOR THE PAST several years we have pursued with vigor the arteriographic investigation of pulmonary emboli and have chanced upon a number of features not previously described or poorly documented. Demonstration of these features is largely attributable to the use of segmental pulmonary injections, as well as the sometime application of bronchial arteriography, in the study of embolism. Arteriographic manifestations of pulmonary embolism include arterial occlusions, stenoses, and filling defects (5). Indirect signs such as slowed flow and regional disparities in vascularity are associated but less reliable findings. These manifestations are readily apparent when emboli involve major pulmonary branches. However, embolic involvement of small pulmonary branches, 0.5 to several millimeters in diameter, usually occurs in pulmonary embolism (11). Indeed, emboli may be lodged exclusively in such small branches. These emboli cause the same fundamental arteriographic manifestations as large vessel emboli, but segmental arteriography is required for precise demonstration. Furthermore, segmental injections may demonstrate embolic sequelae which have otherwise escaped in vivo detection. Technic Segmental arteriography refers to the selective injection of contrast medium into pulmonary branches which supply a pulmonary segment or lobe. These injections might also be termed super-selective or subwedge, but the immodesty of the former term and the inaccuracy of the latter prompt acceptance of “segmental” as the preferred designation. Although pulmonary arteriography is one of the oldest angiographic procedures, the technic has not kept pace with angiographic developments elsewhere in the body. While selectivity is pursued in catheterizing most vessels, it seems to be generally assumed that adequate pulmonary arteriograms may be obtained with main pulmonary artery injections. Although such injections offer a decided improvement over the intravenous route, main pulmonary artery injections do not provide clear visualization of small peripheral vessels because: (a) there is marked dilution of contrast medium during cardiac systole, (b) there is obscuration of detail by overlapping of vessels, and (c) blood flow is diverted from areas of emboli. Segmental arteriography overcomes these disadvantages. Of singular importance, it enables diversion of contrast medium into, rather than away from, areas of greatest embolic obstruction. Our technic routinely incorporates segmental arteriography and is performed in the following manner. A large woven nylon side-hole catheter, usually a No. 8 Eppendorf,3 is passed via antecubital cut-down into the pulmonary artery, and pulmonary artery pressure is recorded. If the pressure is not markedly elevated,40–50 ml of 75 per cent Hypaque or equivalent is injected at the rate of 25 ml per second, and serial anteroposterior films of the chest are obtained.
Genes encoding putative effector proteins of the type III secretion system of Salmonella pathogenicity island 2 are required for bacterial virulence and proliferation in macrophages (1998)

The type III secretion system of Salmonella pathogenicity island 2 (SPI-2) is required for systemic infection of this pathogen in mice. Cloning and sequencing of a central region of SPI-2 revealed the presence of genes encoding putative chaperones and effector proteins of the secretion system. The predicted products of the sseB, sseC and sseD genes display weak but significant similarity to amino acid sequences of EspA, EspD and EspB, which are secreted by the type III secretion system encoded by the locus of enterocyte effacement of enteropathogenic Escherichia coli. The transcriptional activity of an sseA::luc fusion gene was shown to be dependent on ssrA, which is required for the expression of genes encoding components of the secretion system apparatus. Strains carrying nonpolar mutations in sseA, sseB or sseC were severely attenuated in virulence, strains carrying mutations in sseF or sseG were weakly attenuated, and a strain with a mutation in sseE had no detectable virulence defect. These phenotypes were reflected in the ability of mutant strains to grow within a variety of macrophage cell types: strains carrying mutations in sseA, sseB or sseC failed to accumulate, whereas the growth rates of strains carrying mutations in sseE, sseF or sseG were only modestly reduced. These data suggest that, in vivo, one of the functions of the SPI-2 secretion system is to enable intracellular bacterial proliferation.
Diffracted evanescent wave model for enhanced and suppressed optical transmission through subwavelength hole arrays (2004)

Transmission enhancements of order 1000 have been reported for subwavelength hole arrays in metal films and attributed to surface plasmon (SP) resonance. We show that the properly normalized enhancement factor is consistently less than 7, and that similar enhancements occur in nonmetallic systems that do not support SPs. We present a new model in which the transmission is modulated not by coupling to SPs but by interference of diffracted evanescent waves generated by subwavelength features at the surface, leading to transmission suppression as well as enhancement. This mechanism accounts for the salient optical properties of subwavelength apertures surrounded by periodic surface corrugations.