gebhart/patrepeval huggingface dataset:
The interaction between staphylococcal superantigen-like proteins and human dendritic cells (2005)

Staphylococcus aureus produce a family of exotoxins (staphylococcal superantigen like proteins, SSLs) with structural, but not functional, homology to superantigens. These proteins have previously been shown to interact selectively with antigen presenting cells, including dendritic cells. The functional consequences of this interaction are now explored. SSL7 and 9 had no effect on viability or morphology of dendritic cells. The proteins did not induce dendritic cell maturation, as measured by cell surface phenotype. Exposure to SSL did not alter the ability of dendritic cells to take up FITC-dextran. Finally, exposure to SSLs did not impair the ability of the dendritic cells to stimulate allogeneic or antigen specific T cell responses. However, dendritic cells loaded with SSL7 or 9 were able to stimulate a T cell proliferative response in 3/8 healthy individuals tested. Sera from nine out of 10 individuals tested contained antibodies against both SSL7 and SSL9, and the response to each SSL was specific and not cross-reactive. The results demonstrate that SSLs are immunogenic in humans at both the B and T cell level, but it remains unclear whether this response is to the benefit of the bacterium or the host.
Autonomic denervation for the treatment of atrial fibrillation. (2011)

The influence of the autonomic nervous system (ANS) on triggering and perpetuation of atrial fibrillation (AF) is well established. Ganglionated plexi (GP) ablation achieves autonomic denervation by affecting both the parasympathetic and sympathetic components of the ANS. An anatomic approach for GP ablation at relevant atrial sites appears to be safe, and improves the results of PV isolation in patients with paroxysmal and persistent AF. GP ablation can be accomplished endocardially or epicardially, ie, during the maze procedure or thoracoscopic approaches. Further experience is needed to assess the clinical value of this promising technique.
Neutralizing monoclonal antibodies to hepatocyte growth factor/scatter factor (HGF/SF) display antitumor activity in animal models (2001)

The hepatocyte growth factor (HGF/SF) receptor, Met, regulates mitogenesis, motility, and morphogenesis in a cell type-dependent fashion. Activation of Met via autocrine, paracrine, or mutational mechanisms can lead to tumorigenesis and metastasis and numerous studies have linked inappropriate expression of this ligand-receptor pair to most types of human solid tumors. To prepare mAbs to human HGF/SF, mice were immunized with native and denatured preparations of the ligand. Recloned mAbs were tested in vitro for blocking activity against scattering and branching morphogenesis. Our results show that no single mAb was capable of neutralizing the in vitro activity of HGF/SF, and that the ligand possesses a minimum of three epitopes that must be blocked to prevent Met tyrosine kinase activation. In vivo, the neutralizing mAb combination inhibited s.c. growth in athymic nu/nu mice of tumors dependent on an autocrine Met-HGF/SF loop. Importantly, growth of human glioblastoma multiforme xenografts expressing Met and HGF/SF were markedly reduced in the presence of HGF/SF-neutralizing mAbs. These results suggest interrupting autocrine and/or paracrine Met-HGF/SF signaling in tumors dependent on this pathway is a possible intervention strategy.
Stimulation of HIV Expression by Intracellular Calcium Pump Inhibition (1995)

We have studied the role of intracellular calcium sequestration on human immunodeficiency virus (HIV) production by latently infected T-lymphocytic cells. Inhibition of the sarco-endoplasmic reticulum-type calcium transport ATPases by thapsigargin or cyclopiazonic acid induced activation of HIV production in the CEM-derived ACH-2 cells. An approximately 50% depletion of the thapsigargin-sensitive calcium pools as measured fluorimetrically of Indo-loaded cells fully activated virus production. Viral activation was manifest by increases in soluble viral core p24 production, increases in cellular immunofluorescent staining for viral antigens, and increased viral transcription as measured by HIV long terminal repeat-directed expression of the chloramphenicol acetyltransferase reporter gene. Virus induction could be blocked in a dose-dependent manner by the calcium channel blocker econazole. Virus production by the Jurkat-derived HIV-1-inducible J1.1 cells was not significantly stimulated by thapsigargin. These data indicate that intracellular calcium pool function is involved in the control of the transcription of proviral HIV in a cell type-specific manner within the T-lymphoid lineage and that ACH-2 cells represent a useful model for the study of calcium dependent activation of the transcription of proviral HIV.
Cryopreservation characteristics of adipose-derived stem cells: maintenance of differentiation potential and viability (2007)

With the emergence of regenerative medicine, many researchers have turned to fat tissue as a source of adipose-derived stem cells (ASCs). Because freshly collected adipose tissue is not always readily available, there will be a need for improved cryopreservation methods to reproducibly maintain ASC viablility and multipotentiality in long-term storage. This study examines the efficiency of conventional dimethyl sulphoxide cryopreservation methods by measuring the maintenance of differentiation potential after one freeze cycle. Additionally, we analysed the viability of ASCs as a function of varying cell concentrations in cryopreservation media. We evaluated four distinct colony-forming unit assays (fibroblast, alkaline phosphatase, adipocyte and osteoblast) to monitor quantitatively the differentiation potential in ASCs after one freeze cycle. We found that the post-thaw viability was a function of storage concentration and that an optimal viability was observed for a concentration of 0.5 x 10(6) cells/ml cryopreservation medium.
Dynamically stable 0° phase mode operation of a grating-surface-emitting diode-laser array (1988)

A coherent grating-surface-emitting diode-laser array has demonstrated dynamically stable operation in the 0 degrees phase mode. The array was operated under pulsed conditions, had a peak power output of 44 mW and a large central lobe on axis in the far field, and exhibited single-mode spectral output with better than 18-dB side-mode rejection.
The Structure of Scientific Revolutions (2017)

Thomas Kuhn’s The Structure of Scientific Revolutions can be seen, without exaggeration, as a landmark text in intellectual history. In his analysis of shifts in scientific thinking, Kuhn questioned the prevailing view that science was an unbroken progression towards the truth. Progress was actually made, he argued, via "paradigm shifts", meaning that evidence that existing scientific models are flawed slowly accumulates – in the face, at first, of opposition and doubt – until it finally results in a crisis that forces the development of a new model. This development, in turn, produces a period of rapid change – "extraordinary science," Kuhn terms it – before an eventual return to "normal science" begins the process whereby the whole cycle eventually repeats itself. This portrayal of science as the product of successive revolutions was the product of rigorous but imaginative critical thinking. It was at odds with science’s self-image as a set of disciplines that constantly evolve and progress via the process of building on existing knowledge. Kuhn’s highly creative re-imagining of that image has proved enduringly influential – and is the direct product of the author’s ability to produce a novel explanation for existing evidence and to redefine issues so as to see them in new ways.
Dynamic Behavioral Data Collection Using an Instrumented Vehicle (1999)

A significant problem that has become increasingly apparent in the development of models of driver behavior over the last few years is the absence of reliable data with which simulated processes, such as car following, may be compared. Obtaining such data, and the associated increase in model validity that this would allow, is clearly becoming of greater importance since a reliable baseline is required against which improvements in traffic flow and safety produced by many advanced transport telematics systems can be judged. One source of such data is an instrumented vehicle; a vehicle equipped with relative distance- and speed-measuring sensors that may be deployed in the traffic stream to collect data that are realistic, accurate, and dynamic. The opportunities for data collection afforded by instrumented vehicles are examined, in particular, the construction and testing of a new facility fitted with an optical speedometer, a radar rangefinder (capable of measuring the distance to, and relative speed of, the next vehicle in the traffic stream), and forward- and rear-looking video camera. Examples are given of the use of the vehicle in several current research projects, the operational strategies for which will be presented and discussed along with output. These include experiments on close-following, lane-changing, and the perception of relative speed. In conclusion, future areas of research and development are examined.
A New Pathway of Staphylococcal Pathogenesis: Apoptosis-Like Death Induced by Staphopain B in Human Neutrophils and Monocytes (2008)

Circulating neutrophils and monocytes form the first line of cellular defense against invading bacteria. Here, we describe a novel and specific mechanism of disabling and eliminating phagocytes by Staphylococcus aureus. Staphopain B (SspB) selectively cleaved CD11b on phagocytes, which rapidly acquired features of cell death. SspB-treated phagocytes expressed phosphatidylserine as well as annexin I and became permeable to propidium iodide, thus demonstrating distinctive features of both apoptosis and necrosis, respectively. The cell death observed was caspase and Syk tyrosine kinase independent, whilst cytochalasin D efficiently inhibited the staphopain-induced neutrophil killing. Neutrophil and monocyte cell death was not affected by integrin clustering ligands (ICAM-1 or fibrin) and was prevented, and even reversed, by IgG. This protective effect was dependent on the Fc fragment, collectively suggesting cooperation of the CD16 receptor and integrin Mac-1 (CD11b/CD18). We conclude that SspB, particularly in the presence of staphylococcal protein A, may reduce the number of functional phagocytes at infection sites, thus facilitating colonization and dissemination of S. aureus.
Sorafenib and Sunitinib in the Treatment of Advanced Non-Small Cell Lung Cancer (2007)

Despite the optimization of chemotherapy regimens, treatment outcomes for advanced non-small cell lung cancer (NSCLC) are still considered to be disappointing. Thus, clinical research of new treatment strategies is warranted. Several targeted agents have been introduced into clinical trials in NSCLC, but to date, only a few of these new agents can offer hope of a substantial impact on the natural history of the disease. One of the main reasons for the failure of several clinical trials of targeted therapy in lung cancer is that there is multilevel cross-stimulation among the targets of the new biological agents along several pathways of signal transduction that lead to neoplastic events; blocking only one of these pathways, as most first-generation targeted agents do, allows others to act as salvage or escape mechanisms for cancer cells. Sorafenib and sunitinib are two oral multitargeted receptor tyrosine kinase inhibitors. Sorafenib is a multikinase inhibitor that inhibits the kinase activity of both C-RAF and B-RAF and targets the vascular endothelial growth factor receptor family (VEGFR-2 and VEGFR-3) and platelet-derived growth factor receptor family (PDGFR-beta and stem cell factor receptor [KIT]). Sunitinib is a multitargeted inhibitor of PDGFR, KIT, fms-like tyrosine kinase 3, and VEGFR. The kinases targeted and inhibited by sorafenib and sunitinib directly and indirectly regulate tumor growth, survival, and angiogenesis, and this might be expected to result in broad antitumor efficacy. Sorafenib and sunitinib have been approved by the U.S. Food and Drug Administration for the treatment of metastatic renal cell carcinoma; sunitinib has also been approved for the treatment of gastrointestinal stromal tumors. Their mechanism of action, preclinical data, and phase II studies suggest efficacy in the treatment of advanced NSCLC.
Accelerated 3D carotid MRI using compressed sensing and parallel imaging (2010)

Introduction Imaging of the carotid artery with black-blood MRI can be used to identify plaques that are vulnerable for rupture [1,2]. 3D imaging is particularly interesting to overcome the SNR and volumetric coverage limitations of 2D multislice techniques. However, 3D scans are more susceptible to motion artifacts, particularly swallowing-related artifacts, due to the longer acquisition times [3]. Parallel imaging can be used to accelerate the acquisition, but acceleration is limited by noise amplification. An alternative acceleration technique is compressed sensing (CS) [4], where image compressibility can be exploited to undersample k-space without losing image information. 3D imaging is a natural candidate for CS, since higher dimensional data sets increase sparsity. We propose to combine CS and parallel imaging to increase the acceleration rate for 3D carotid imaging.
Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data (2004)

MDAT v1.0 is a Matlab toolbox and requires Matlab to run. MDAT is freely available at http://microarray.omrf.org/publications/2004/knowlton/MDAT.zip.
Nitric Oxide Inhibits Rhinovirus-Induced Cytokine Production and Viral Replication in a Human Respiratory Epithelial Cell Line (1998)

To better understand the early biochemical events that occur in human rhinovirus (HRV) infections, we examined the kinetics and mechanisms of interleukin-8 (IL-8) and IL-6 production from infected epithelial cells. Several HRV strains caused IL-8 and IL-6 production, but HRV-16 induced maximal IL-8 and IL-6 mRNA expression and protein production more rapidly than did HRV-14, despite similar rates of replication of the two viral strains. Viral induction of cytokine mRNA does not require new protein synthesis, since it was unaffected by cycloheximide treatment. The potent glucocorticoid budesonide did not affect viral replication or cytokine mRNA induction but modestly inhibited cytokine protein production. Interestingly, the nitric oxide donor 3-(2-hydroxy-2-nitroso-1-propylhydrazino)-1-propanamine (NONOate) inhibited both rhinovirus replication and cytokine production in a dose-dependent fashion without reducing levels of cytokine mRNA. The NONOate effects were due to release of nitric oxide, because NONOate that had been depleted of its nitric oxide content had no effect. Thus, nitric oxide may play an important anti-inflammatory and antiviral role in colds and nitric oxide donors may represent a novel therapeutic approach.
Mitogen-Activated Protein Kinase Signal Transduction in Solid Tumors (2014)

Mitogen-activated protein kinase (MAPK) is an important signaling pathway in living beings in response to extracellular stimuli. There are 5 main subgroups manipulating by a set of sequential actions: ERK(ERK1/ ERK2), c-Jun N(JNK/SAPK), p38 MAPK(p38α, p38β, p38γ and p38δ), and ERK3/ ERK4/ ERK5. When stimulated, factors of upstream or downstream change, and by interacting with each other, these groups have long been recognized to be related to multiple biologic processes such as cell proliferation, differentiation, death, migration, invasion and inflammation. However, once abnormally activated, cancer may occur. Several components of the MAPK network have already been proposed as targets in cancer therapy, such as p38, JNK, ERK, MEK, RAF, RAS, and DUSP1. Among them, alteration of the RAS-RAF-MEK-ERK-MAPK(RAS-MAPK) pathway has frequently been reported in human cancer as a result of abnormal activation of receptor tyrosine kinases or gain-of-function mutations in genes. The reported roles of MAPK signaling in apoptotic cell death are controversial, so that further in-depth investigations are needed to address these controversies. Based on an extensive analysis of published data, the goal of this review is to provide an overview on recent studies about the mechanism of MAP kinases, and how it generates certain tumors, as well as related treatments.
Development of a Vaccine for Celiac Disease (2008)

Celiac disease is the result of an immune response to gluten. Gluten exclusion removes the antigen that stimulates CD4 T-cell-mediated tissue damage in the gut, but does not remove the immune response. In fact, gluten exclusion may heighten the immune response stimulated by gluten since regulatory T cells are typically not maintained unless antigen exposure continues. This may explain why gluten exposure triggers more dramatic symptoms following adoption of a gluten-free diet than during chronic gluten exposure associated with untreated celiac disease. Peptide-based therapeutic vaccines aim to strengthen the antigen-specific regulatory T-cell response to suppress proinflammatory adaptive and innate immunity in an antigen-specific and nonspecific fashion. Peptide-based therapeutic vaccines require detailed understanding of the peptides derived from pathogenic antigens that stimulate pathogenic CD4 T cells. The present knowledge of gluten peptides recognized by CD4 T cells largely derives from T-cell clones and lines isolated from celiac-disease-affected intestinal tissue. In this chapter, it is argued that T cells mobilized into blood by acute gluten exposure facilitate a more reliable mapping of gluten peptides recognized by relevant CD4 T cells. Understanding not only the specificity, but also the hierarchy (immunodominance) of peptides is critical to the practical design of a peptide-based therapeutic vaccine. The effort is worthwhile and the debate important since peptide- based therapeutic vaccines offer the possibility of a qualitative change in the pathogenic immune response to gluten and for patients to return to a virtually normal lifestyle.
Ingestion and carbon budget of juvenile Portunus trituberculatus (2004)

The ingestion and carbon budget of juvenile Portunus trituberculatus (Stimpson) feeding on shelled shrimp (Trachypenaeus curvirostris) were determined at natural temperatures (24.0 ℃,24.9 ℃ and 26.3 ℃) from June to September, 2002. The crabs used in experiments were divided into three groups (Group I, Group II and Group III) according to their body weights, their weights were 0.73±0.15 g,1.55±35 g and 3.75±0.52 g, respectively. Experimental results show that the ingestion of crabs was significantly affected by the water temperature and body weight, and the effect by body weights were much more than that by water temperature. The special growth rate (SGR) and ecological transform efficiency (Eg) obtained from wet weight and dry weight were 2.5±1.33～3.0±0.95 and 19.4±4.8～59.4±22.9,2.8±0.73～4.3±2.28 and 10.1±2.3～29.1±12.4, respectively.The equations of carbon budget of the juvenile crab indicate that the carbon consumption through metabolism made up the biggest part of the total intake carbon (more than 50%), the second was that comsumptious allocated to growth (about 28%), the carbon consumptions allocated to exuviation and ejection both were less than 5%. The proportions of carbon allocation were affected more obviously by water temperature than by body weight.
Bacterial Retention on Superhydrophobic Titanium Surfaces Fabricated by Femtosecond Laser Ablation (2011)

Two-tier micro- and nanoscale quasi-periodic self-organized structures, mimicking the surface of a lotus Nelumbo nucifera leaf, were fabricated on titanium surfaces using femtosecond laser ablation. The first tier consisted of large grainlike convex features between 10 and 20 μm in size. The second tier existed on the surface of these grains, where 200 nm (or less) wide irregular undulations were present. The introduction of the biomimetic surface patterns significantly transformed the surface wettabilty of the titanium surface. The original surface possessed a water contact angle of θ(W) 73 ± 3°, whereas the laser-treated titanium surface became superhydrophobic, with a water contact angle of θ(W) 166 ± 4°. Investigations of the interaction of S. aureus and P. aeruginosa with these superhydrophobic surfaces at the surface-liquid interface revealed a highly selective retention pattern for two pathogenic bacteria. While S. aureus cells were able to successfully colonize the superhydrophobic titanium surfaces, no P. aeruginosa cells were able to attach to the surface (i.e., any attached bacterial cells were below the estimated lower detection limit).
Identification of Thermobacteria and Homofermentative, Thermophilic, Pentose‐utilizing Lactobacilli from High Temperature Fermenting Grape Musts (1978)

Eight strains belonging to Thermobacterium have been isolated from high temperature (between 40° and 43°C) fermenting grape musts. They resemble Lactobacillus acidophilus very closely. Four other thermophilic homofermentative strains are somewhat different: they ferment arabinose and ribose with production of more than 90% of the end product carbon as lactate. This last result involves a metabolic pathway undescribed among lactic acid bacteria.
Chronic Treatment With 5-Aminoimidazole-4-Carboxamide-1- -D-Ribofuranoside Increases Insulin-Stimulated Glucose Uptake and GLUT4 Translocation in Rat Skeletal Muscles in a Fiber Type--Specific Manner (2001)

Recent studies have demonstrated that chronic administration of AICAR (5-aminoimidazole-4-carboxamide- 1-beta-D-ribofuranoside), an activator of the AMP-activated protein kinase, increases hexokinase activity and the contents of total GLUT4 and glycogen in rat skeletal muscles. To explore whether AICAR also affects insulin-stimulated glucose transport and GLUT4 cell surface content, Wistar rats were subcutaneously injected with AICAR for 5 days in succession (1 mg/g body wt). Maximally insulin-stimulated (60 nmol/l) glucose uptake was markedly increased in epitrochlearis (EPI) muscle (average 63%, P < 0.001, n = 18-19) and in extensor digitorum longus muscle (average 26%, P < 0.001, n = 26-30). In contrast, administration of AICAR did not maximally influence insulin-stimulated glucose transport in soleus muscle. Studies of EPI muscle with the 4,4'-O-[2-[2-[2-[2-[2-[6-(biotinylamino)hexanoyl]amino]ethoxy]ethoxy] ethoxy]-4-(1-azi-2,2,2,-trifluoroethyl)benzoyl]amino-1,3-propanediyl]bis-D-mannose photolabeling technique showed a concomitant increase (average 68%, P < 0.02) in cell surface GLUT4 content after insulin exposure in AICAR-injected rats when compared with controls. In conclusion, 5 days of AICAR administration induces a pronounced fiber type-specific increase in insulin-stimulated glucose uptake and GLUT4 cell surface content in rat skeletal muscle with the greatest effect observed on white fast-twitch glycolytic muscles (EPI). These results are comparable with the effects of chronic exercise training, and it brings the AMP-activated protein kinase into focus as a new interesting target for future pharmacological intervention in insulin-resistant conditions.
The specific direct interaction of helper T cells and antigen-presenting B cells. (1986)

Cell couples have been formed by mixing an antigen- and Ia-specific cloned helper T-cell line with a B-cell hybridoma presenting the antigen. By immunofluorescence observations, we have shown that the microtubule-organizing center (MTOC) inside the helper T cell, but not in the bound antigen-presenting cell, becomes oriented to face the area of specific cell-cell contact. This MTOC orientation is antigen- and Ia-specific, and thus provides direct evidence for the specific interaction of a helper T cell with a B cell. It is presumed that the function served by this MTOC orientation, which is accompanied by the coordinate reorientation of the Golgi apparatus, is to target Golgi apparatus-derived secretory vesicles, containing putative lymphokines and/or growth factors, from the helper T cell directly to the antigen-presenting cell.