gebhart/patrepeval huggingface dataset:
Anti-CD3-stimulated Ca2+ signal in individual human peripheral T cells. Activation correlates with a sustained increase in intracellular Ca2+1 (1993)

The changes in [Ca2+]i after mitogen stimulation of individual human peripheral T cells were examined by single cell image analysis to determine the relationship between the Ca2+ signal and functional outcome. Marked heterogeneity in the magnitude of increase in [Ca2+]i, in the lag time of the responses, and in the percentage of T cells that responded to mAb to CD3 and to PHA was observed. However, mitogenic stimuli that induced IL-2 production or DNA synthesis consistently generated increases in [Ca2+]i in individual T cells that were sustained for 1 to 2 h. Soluble mAb to CD3 induced an increase in [Ca2+]i that remained elevated at 60 min and led to IL-2 production and proliferation upon costimulation by phorbol ester. In contrast, cross-linking anti-CD3 with a secondary antibody foreshortened the increase in [Ca2+]i, and IL-2 production and DNA synthesis were inhibited. Immobilized anti-CD3, which can stimulate T cell proliferation and IL-2 production in the absence of phorbol ester, produced a constant sustained elevation in [Ca2+]i that lasted more than 2 h. Similarly, functional responses could be generated by concentrations of PHA that resulted in only a slow increase in [Ca2+]i that continued to rise for 1 to 2 h. Examination of the mitogen-induced sustained increases in [Ca2+]i suggested that an elevation in [Ca2+]i as small as 50 to 100 nM above control mean [Ca2+]i was associated with evidence of T cell activation. Spontaneous oscillatory changes in [Ca2+]i were observed in a small percentage of peripheral T cells although they were noted to occur frequently in Jurkat cells. Mitogenic stimulation did not consistently increase oscillations in peripheral T cells, and neither their frequency nor their magnitude correlated with IL-2 production or DNA synthesis. These observations suggest that oscillatory changes in [Ca2+]i are not a primary determinant of T cell activation. Rather, the data indicate that functional activation of T cells by PHA and anti-CD3 is correlated with the induction of a small, but sustained increase in [Ca2+]i.
Virtual Training of the Myosignal (2015)

Three different virtual training methods showed comparable results when learning myocontrol. Continuous myocontrol was improved by training while discrete myocontrol was not. Myocontrol ability could not be predicted by the manual motor control tests.
Deep learning and 3D-DESI imaging reveal the hidden metabolic heterogeneity of cancer (2017)

Visual inspection of tumour tissues does not reveal the complex metabolic changes that differentiate cancer and its sub-types from healthy tissues. Mass spectrometry imaging, which quantifies the underlying chemistry, represents a powerful tool for the molecular exploration of tumour tissues. A 3-dimensional topological description of the chemical properties of the tumour permits the formulation of hypotheses about the biological composition and interactions and the possible causes of its heterogeneous structure. The large amount of information contained in such datasets requires powerful tools for its analysis, visualisation and interpretation. Linear methods for unsupervised dimensionality reduction, such as PCA, are inadequate to capture the complex non-linear relationships present in these data. For this reason, a deep unsupervised neural network based technique, parametric t-SNE, is adopted to map a 3D-DESI-MS dataset from a human colorectal adenocarcinoma biopsy onto a 2-dimensional manifold. This technique allows the identification of clusters not visible with linear methods. The unsupervised clustering of the tumour tissue results in the identification of sub-regions characterised by the abundance of identified metabolites, making possible the formulation of hypotheses to account for their significance and the underlying biological heterogeneity in the tumour.
Effectiveness of Fluticasone Furoate–Vilanterol for COPD in Clinical Practice (2016)

In patients with COPD and a history of exacerbations, a once-daily treatment regimen of combined fluticasone furoate and vilanterol was associated with a lower rate of exacerbations than usual care, without a greater risk of serious adverse events. (Funded by GlaxoSmithKline; Salford Lung Study ClinicalTrials.gov number, NCT01551758 .).
Characteristics of stacking faults in AlN thin films (1997)

We have investigated growth characteristics and atomic structure of defects in AlN thin films grown by the metalorganic chemical vapor deposition technique on the (101̄2) r plane of α-Al2O3. The AlN films were single crystal and exhibited the following epitaxial relationship: (112̄0)AlN∥(101̄2)sap with the in-plane alignment of [0001]AlN∥[1̄011]sap. Using high-resolution electron microscopy and multislice image simulation, the predominant defects in AlN thin films grown on the r plane of α-Al2O3 were found to be low-energy intrinsic stacking faults of type I1 lying in the basal plane. This fault, with a 1/6[202̄3] resultant displacement vector, can be formed by removing one (0002) plane and then shearing the remaining half-crystal by displacement of 1/3[101̄0]. The faults appear as a single face-centered-cubic stack ABC inserted into the normal …ABAB… hexagonal sequence. We discuss the possible role of these defects in optical properties of semiconductor devices.
Fluid effects in vibrating micromachined structures (2005)

Squeeze film damping and hydrodynamic lift for a micromechanical perforated proof mass are calculated and measured. This paper has resulted in closed-form expressions that can be used to design accelerometers, tuning-fork gyroscopes (TFGs), and other micromechanical devices. The fluid damping and lift are determined using finite-element analyses of the normalized and linearized governing equations where the boundary condition of the pressure relief holes is derived using pipe flow analysis. The rarefaction of gas is incorporated in the governing equations based on slip flow condition. As a further check, a one-dimensional (1-D) network model is developed to account for the boundary condition of the holes on a tilted proof mass. Both closed-form and numerical solutions are compared against experimental data over a range of pressures.
Intranet security with micro-firewalls and mobile agents for proactive intrusion response (2002)

We propose a distributed multi-level architecture to solve the intranet security problem. The basic idea is to build micro firewalls on all hosts in the intranet, as a second line of defense behind the gateway firewall. A distributed intrusion detection system (IDS) is developed to achieve proactive intrusion responses with dynamic policy changes. Mobile agents, CORBA, and RMI are evaluated for dynamic policy update. We find that mobile agents are most scalable and robust for policy update, but prone to attacks by other agents and hosts. CORBA has the best speed performance. The Java-based RMI has the highest security based on the sandbox model. Key concepts, preliminary results, and continued research challenges are presented.
Oncogenic and nononcogenic human genital papillomaviruses generate the E7 mRNA by different mechanisms (1989)

A new promoter located within E6 was mapped in human papillomavirus type 6b (HPV6b)- and HPV11-containing benign genital condylomata (genital warts). The RNA transcribed from this promoter represented the major RNA species colinear with open reading frames E6 and E7 and can encode the E7 protein. No equivalent promoter was active in HPV16-containing cancers and cancer-derived cell lines. In those, the major transcripts contained one of two different introns within E6 and the RNAs could encode two different E6 proteins and E7.
DISC1 (Disrupted-In-Schizophrenia 1) is a centrosome-associated protein that interacts with MAP1A, MIPT3, ATF4/5 and NUDEL: regulation and loss of interaction with mutation (2003)

Disrupted-In-Schizophrenia 1 (DISC1) is a novel gene associated with schizophrenia by multiple genetic studies. In order to determine how mutations in DISC1 might cause susceptibility to schizophrenia, we undertook a comprehensive study of the cellular biology of DISC1 in its full-length and disease-associated mutant forms. DISC1 interacts by yeast two-hybrid, mammalian two-hybrid, and co-immunoprecipitation assays with multiple proteins of the centrosome and cytoskeletal system, including MIPT3, MAP1A and NUDEL; proteins which localize receptors to membranes, including alpha-actinin2 and beta4-spectrin; and proteins which transduce signals from membrane receptors, including ATF4 and ATF5. Truncated mutant DISC1 fails to interact with ATF4, ATF5 or NUDEL. Deletion mapping demonstrated that DISC1 has distinct interaction domains: MAP1A interacts via its LC2 domain with the N-terminus of DISC1, whereas MIPT3 and NUDEL bind via their C-terminal domains to the central coiled-coil domain of DISC1, and ATF4/5 bind via their C-terminal domains to the C-terminus of DISC1. In its full-length form, DISC1 protein localizes to predominantly perinuclear punctate structures which extend into neurites in some cells; mutant truncated DISC1, by contrast, is seen in a diffuse pattern throughout the cytoplasm and abundantly in neurites. Both forms co-localize with the centrosomal complex, although truncated less abundantly than full-length DISC1. Although both full-length and mutant DISC1 are found in microtubule fractions, neither form of DISC1 appears to bind directly to microtubules, but rather do so in a MIPT3-dependent fashion that is stabilized by taxol. Based on these data, we propose that DISC1 is a multifunctional protein whose truncation contributes to schizophrenia susceptibility by disrupting intracellular transport, neurite architecture and/or neuronal migration, all of which have been hypothesized to be pathogenic in the schizophrenic brain.
Systematic Analysis of Reportedly Distinct Populations of Multipotent Bone Marrow-Derived Stem Cells Reveals a Lack of Distinction (2002)

Adult human bone marrow-derived stem cells, having the ability to differentiate into cells of multiple lineages, have been isolated and propagated by varied protocols, including positive (CD105(+))/negative (CD45(-)GlyA(-)) selection with immunomagnetic beads, or direct plating into selective culture media. Each substratum-adherent cell population was subjected to a systematic analysis of their cell surface markers and differentiation potential. In the initial stages of culture, each cell population proliferated slowly, reaching confluence in 10-14 days. Adherent cells proliferated at similar rates whether cultured in serum-free medium supplemented with basic fibroblast growth factor, medium containing 2% fetal bovine serum (FBS) supplemented with epidermal growth factor and platelet-derived growth factor, or medium containing 10% FBS alone. Cell surface marker analysis revealed that more than 95% of the cells were positive for CD105/endoglin, a putative mesenchymal stem cell marker, and negative for CD34, CD31, and CD133, markers of hematopoietic, endothelial, and neural stem cells, respectively, regardless of cell isolation and propagation method. CD44 expression was variable, apparently dependent on serum concentration. Functional similarity of the stem cell populations was also observed, with each different cell population expressing the cell type-specific markers beta-tubulin, type II collagen, and desmin, and demonstrating endothelial tube formation when cultured under conditions favoring neural, cartilage, muscle, and endothelial cell differentiation, respectively. On the basis of these data, adult human bone marrow-derived stem cells cultured in adherent monolayer are virtually indistinguishable, both physically and functionally, regardless of the method of isolation or proliferative expansion.
Differential effects of sodium butyrate, dimethyl sulfoxide, and retinoic acid on membrane-associated antigen, enzymes, and glycoproteins of human rectal adenocarcinoma cells. (1982)

The effects of sodium butyrate, dimethyl sulfoxide (DMSO), and retinoic acid on the growth, morphology, carcinoembryonic antigen content, cell surface membrane-associated enzyme activities, and glycoprotein profiles of a human rectal adenocarcinoma cell line (HRT-18) in culture were compared. All three agents reversibly caused a marked increase in doubling times, a decrease in saturation densities, and a markedly reduced colony-forming efficiency in soft agar. Only butyrate caused gross morphological changes including cell enlargement, flattening, and increased membranous process formation. Carcinoembryonic antigen content was increased during culture in butyrate, while it was reduced by DMSO and unchanged by retinoic acid. The activities of membrane-associated enzymes were altered significantly in the butyrate-treated cells. For example, an increase in the activities of alkaline phosphatase (10-fold), gamma-glutamyl transpeptidase activity (3-fold) and sucrase activity (2-fold) was observed, while those of aminooligopeptidase and K+-stimulated phosphatase actually showed slight decreases. DMSO- or retinoic acid-treated cells showed a marked decrease in alkaline phosphatase activity, but other enzyme activities remained unchanged. Surface protein-labeling patterns of lactoperoxidase-catalyzed iodinated HRT-18 cells showed no significant change from the control cells following treatment with DMSO or retinoic acid. The most prominent change caused by butyrate treatment was the appearance of a major glycoprotein band with an apparent molecular weight of 60,000. These data indicate that the use of butyrate, DMSO, and retinoic acid may provide useful information concerning the identification of differentiation-associated markers of human rectal cancer cells. Furthermore, these agents, although having similar effects on the growth properties, have different effects on the morphology and on the biochemical properties of human rectal cancer cells.
An empirical study on configuration errors in commercial and open source systems (2011)

Configuration errors (i.e., misconfigurations) are among the dominant causes of system failures. Their importance has inspired many research efforts on detecting, diagnosing, and fixing misconfigurations; such research would benefit greatly from a real-world characteristic study on misconfigurations. Unfortunately, few such studies have been conducted in the past, primarily because historical misconfigurations usually have not been recorded rigorously in databases.
0409 LES of Gasturbine Combustor (2007)

To investigate turbulent combustion phenomena in a gas-turbine combustor, we conduct a numerical simulation of a partially premixed turbulent combustion in a practical combustor. Large-Eddy simulation and 2-scalar flamelet approach are coupled and applied to the unsteady turbulent combustion simulation in the combustor geometry for modeling turbulent and combustion reaction phenomena, and also their interactions. This paper reports an application of the LES to a 1700 degree class of new-Generation gasturbine combustor and discusses their feasibility to the practical combustor design.
Suppression of the floating-body effects in SOI MOSFETs by bandgap engineering (2002)

The floating-body effects, which are regarded as the most critical issues in applying Silicon-On-Insulator (SOI) devices to actual LSIs, can be suppressed by the reduction in bandgap energy in the source region. In addition to an increase in the drain breakdown voltage, the suppression of both kinks in I/sub d/-V/sub d/ characteristics and threshold voltage shift with an increase in drain voltage are achieved in sub-quarter micron Nch thin-film SOI MOSFETs.
β‐Cells at the crossroads: choosing between insulin granule production and proliferation (2009)

Pancreatic beta-cells are the sole source of insulin, the major hormonal regulator of glycaemia. In physiological and pathological conditions with increased insulin demand, beta-cells adjust their insulin output either through increased insulin secretory granule (ISG) biogenesis and secretion, or hyperplasia. Failure of these compensatory mechanisms eventually results in hyperglycaemia and diabetes mellitus. Both of these major adaptive behaviours are positively regulated by several extrinsic factors, such as glucose, GLP-1, insulin and growth hormones (GH). Still unclear, however, it is how beta-cells in response to these stimuli opt for one or the other strategy at a given time. Here we review recent advances concerning the factors and pathways that enhance ISG biogenesis and beta-cell replication, and propose the existence of 'switch factors' that play a key role in regulating the shift between these two adaptive responses.
Flame-Made Titania/Silica Epoxidation Catalysts:  Toward Large-Scale Production (2002)

Titania/silica catalysts were made continuously in flame reactors and evaluated for the demanding epoxidation of 2-cyclohexenol with tert-butylhydroperoxide. Silica- and titania-precursors were evaporated separately and mixed prior to feeding into a hydrogen-air diffusion flame. Upon reaction, the corresponding oxides formed highly agglomerated nanoparticles with titania confined to the surface of silica particles. The epoxidation activity was strongly dependent on the titania content of the catalyst. Scaling-up the production rate of these catalysts (6−500 g/h) in the flame did not affect their exceptionally high catalytic performance. Sample composition and homogeneity were determined by local analysis using laser ablation inductively coupled plasma mass spectroscopy. Large-scale flame-made catalysts (100−500 g/h) were compared to similar catalysts made in a laboratory flame microreactor (6 g/h) and to conventional ones prepared by wet-phase chemistry. Compared to classical catalysts (65−80% selectivity), the flame-made titania/silica showed excellent selectivity (up to 90%) at 80% conversion.
Perfluoropolyether structures as surface modifying agents of UV-curable systems (1998)

New functionalised macromers containing perfluoropolyether (PFPE) structures and methacrylic end groups were synthesised and used as modifying additives for acrylic UV-curable systems. Their chemical structure is Rh-Rf-Rh, where and with p ≈ q. Notwithstanding their very low concentration, below 0.5 wt.-%, the fluorinated macromers cause a dramatic change of the surface properties of the films, without changing their curing conditions and their bulk properties. X-ray photoelectron spectroscopy (XPS) measurements showed that the macromers are able to concentrate selectively at the surfaces of the films, depending on their chemical structure and on the kind of substrate employed.
Immunization of low density lipoprotein (LDL) receptor-deficient rabbits with homologous malondialdehyde-modified LDL reduces atherogenesis. (1995)

Atherosclerotic lesions contain oxidized LDL (OxLDL), immunoglobulins, and immune-competent cells. Low levels of circulating autoantibodies against malondialdehyde (MDA)-modified lysine, an epitope of OxLDL, occur in several species, and immune complexes between such autoantibodies and OxLDL are present in lesions. To study the potential role of autoantibodies against OxLDL in the atherogenic process, we prospectively hyperimmunized LDL receptor-deficient rabbits with homologous MDA-LDL and determined the effects of this intervention on the development of atherosclerosis. Immunization with MDA-LDL generated high titers of antibodies with similar specificity as naturally occurring autoantibodies. Immunized animals showed a significant reduction in the extent of atherosclerotic lesions in the aortic tree after 6.5 months, compared with "saline"-immunized controls (48% vs. 68%, P < 0.005). Immunization with keyhole limpet hemocyanin produced no change in lesion formation. Although the mechanisms by which immunization led to a protective effect are unknown, these results suggest an important role for the immune system in modulating the atherogenic process and may indicate a novel approach for inhibiting the progression of atherosclerosis.
Identification of LFA-1 as a Candidate Autoantigen in Treatment-Resistant Lyme Arthritis (1998)

Treatment-resistant Lyme arthritis is associated with immune reactivity to outer surface protein A (OspA) of Borrelia burgdorferi, the agent of Lyme disease, and the major histocompatibility complex class II allele DRB1*0401. The immunodominant epitope of OspA for T helper cells was identified. A homology search revealed a peptide from human leukocyte function-associated antigen-1 (hLFA-1) as a candidate autoantigen. Individuals with treatment-resistant Lyme arthritis, but not other forms of arthritis, generated responses to OspA, hLFA-1, and their highly related peptide epitopes. Identification of the initiating bacterial antigen and a cross-reactive autoantigen may provide a model for development of autoimmune disease.
Whole-Genome Amplification by Adaptor-Ligation PCR of Randomly Sheared Genomic DNA (PRSG) (2008)

INTRODUCTIONPCR-based whole-genome amplification (WGA) has the goal of generating microgram quantities of genome-representative DNA from picogram or nanogram amounts of starting material. This amplification should introduce little, or ideally no, representational bias. In contrast to other techniques for WGA, PCR-based methods are generally less affected by DNA quality and are more applicable to DNA extracted from various sources (fixed and fresh tissues). Ligation-mediated PCR techniques involve ligating an adaptor sequence onto a "representation" of DNA molecules, generated following enzymatic digestion, random shearing, or chemical cleavage. Adaptor-ligation PCR of randomly sheared genomic DNA (PRSG), described here, is based on ligation-mediated PCR and was designed to improve genome coverage. Rather than using enzymatically generated fragments, this method uses randomly fragmented DNA as the template. The process involves three steps: (1) the hydrodynamic shearing of genomic DNA to a 0.5-2-kb size range, (2) end filling and adaptor ligation, and (3) high-stringency PCR for faithful replication of the resulting fragments.
Adenovirus-Mediated Gene Transfer into Isolated Mouse Adult Pancreatic Islets: Normal β -Cell Function Despite Induction of an Anti-Adenovirus Immune Response (1997)

The in vitro purification of pancreatic islets offers an opportunity for their modification by ex vivo gene transfer. We investigated the efficiency and functional consequences of adenovirus-mediated gene transfer into adult murine pancreatic islets with a recombinant adenovirus encoding for the beta-galactosidase (beta-Gal) reporter gene. At 10(6) pfu/islet, almost all of the islets were transduced, but maximal transduction was obtained at 10(7) pfu/islet. Histochemical analysis of frozen islet sections showed that transduced cells were only located at the periphery of islets. Transduced islets showed normal insulin secretion in vitro, and were able to normalize in vivo the glycemia of streptozotocin-induced diabetes in syngeneic and allogeneic mice. beta-Gal expression in transduced islets was observed for at least 6 weeks in naive normal recipients and in immunodeficient mice, but was shortened in mice preimmunized to adenovirus. Nevertheless, islets maintained normal control of glycemia in all mice. An early leukocyte infiltrate was observed in syngeneic grafts of transduced islets, but no acceleration in rejection of fully MHC-incompatible islet grafts occurred. In summary, adenovirus-mediated gene transfer in adult mouse islets, although sparing most of the beta-cells, was highly efficient and did not impair insulin secretion by islets. The immune response to the adenovirus and/or to the transgene might be only partially responsible for the decreased expression over time of the transduced gene. Accordingly, adenovirus-mediated gene transfer might allow efficient expression of vectorized sequences with potential immunosuppressive effects in the islet microenvironment.