gebhart/patrepeval huggingface dataset:
Remote reservoir monitoring in oil sands: From feasibility study to baseline datasets (2013)

Summary A joint research project between Statoil and Schlumberger is focusing on permanent cross-well geophysical methods for reservoir monitoring during steam assisted gravity drainage (SAGD). In 2009, a feasibility study indicated detectable differences in seismic and electrical reservoir properties based on expected changes in temperature and fluid saturation during oil production. Based on these results, several geophysical reservoir monitoring methods were evaluated. These included cross-well seismic, vertical seismic profiling (VSP), and electrical resistivity tomography (ERT). The modeling study was followed by an installation of a permanent cross-well system at Statoil’s Leismer Demonstration Area (LDA) in Alberta, Canada, in 2010. After the system was successfully installed and tested, baseline datasets were acquired through an established data link, also allowing for remote monitoring throughout the calendar year. ERT datasets can now be acquired without personnel on site, while seismic acquisitions require a moving source on the surface or a cross-well seismic source and receiver array deployed on wireline. Comparisons of
Structural Analysis of Botulinum Neurotoxin Type E Catalytic Domain and Its Mutant Glu212→Gln Reveals the Pivotal Role of the Glu212 Carboxylate in the Catalytic Pathway, (2004)

The seven serotypes of botulinum neurotoxins (A-G) produced by Clostridium botulinum share significant sequence homology and structural similarity. The functions of their individual domains and the modes of action are also similar. However, the substrate specificity and the peptide bond cleavage selectivity of their catalytic domains are different. The reason for this unique specificity of botulinum neurotoxins is still baffling. If an inhibitor leading to a therapeutic drug common to all serotypes is to be developed, it is essential to understand the differences in their three-dimensional structures that empower them with this unique characteristic. Accordingly, high-resolution structures of all serotypes are required, and toward achieving this goal the crystal structure of the catalytic domain of C. botulinum neurotoxin type E has been determined to 2.1 A resolution. The crystal structure of the inactive mutant Glu212-->Gln of this protein has also been determined. While the overall conformation is unaltered in the active site, the position of the nucleophilic water changes in the mutant, thereby causing it to lose its ability to activate the catalytic reaction. The structure explains the importance of the nucleophilic water and the charge on Glu212. The structural differences responsible for the loss of activity of the mutant provide a common model for the catalytic pathway of Clostridium neurotoxins since Glu212 is conserved and has a similar role in all serotypes. This or a more nonconservative mutant (e.g., Glu212-->Ala) could provide a novel, genetically modified protein vaccine for botulinum.
The Cellular Trafficking of the Secretory Proprotein Convertase PCSK9 and Its Dependence on the LDLR (2007)

Mutations in the proprotein convertase PCSK9 gene are associated with autosomal dominant familial hyper- or hypocholesterolemia. These phenotypes are caused by a gain or loss of function of proprotein convertase subtilisin kexin 9 (PCSK9) to elicit the degradation of the low-density lipoprotein receptor (LDLR) protein. Herein, we asked whether the subcellular localization of wild-type PCSK9 or mutants of PCSK9 and the LDLR would provide insight into the mechanism of PCSK9-dependent LDLR degradation. We show that the LDLR is the dominant partner in regulating the cellular trafficking of PCSK9. In cells lacking the LDLR, PCSK9 localized in the endoplasmic reticulum (ER). In cells expressing the LDLR, PCSK9 sorted to post-ER compartments (i.e. endosomes in cell lines and Golgi apparatus in primary hepatocytes), where it colocalized with the LDLR. In cell lines, PCSK9 also colocalized with the LDLR at the cell surface, requiring the presence of the C-terminal Cys/His-rich domain of PCSK9. We provide evidence that PCSK9 promotes the degradation of the LDLR by an endocytic mechanism, as small interfering RNA-mediated knockdown of the clathrin heavy chain reduced the functional activity of PCSK9. We also compared the subcellular localization of natural mutants of PCSK9 with that of the wild-type enzyme in human hepatic (HuH7) cells. Whereas the mutants associated with hypercholesterolemia (S127R, F216L and R218S) localized to endosomes/lysosomes, those associated with hypocholesterolemia did not reach this compartment. We conclude that the sorting of PCSK9 to the cell surface and endosomes is required for PCSK9 to fully promote LDLR degradation and that retention in the ER prevents this activity. Mutations that affect this transport can lead to hyper- or hypocholesterolemia.
History of Reading Struggles Linked to Enhanced Learning in Low Spatial Frequency Scenes (2012)

People with dyslexia, who face lifelong struggles with reading, exhibit numerous associated low-level sensory deficits including deficits in focal attention. Countering this, studies have shown that struggling readers outperform typical readers in some visual tasks that integrate distributed information across an expanse. Though such abilities would be expected to facilitate scene memory, prior investigations using the contextual cueing paradigm failed to find corresponding advantages in dyslexia. We suggest that these studies were confounded by task-dependent effects exaggerating known focal attention deficits in dyslexia, and that, if natural scenes were used as the context, advantages would emerge. Here, we investigate this hypothesis by comparing college students with histories of severe lifelong reading difficulties (SR) and typical readers (TR) in contexts that vary attention load. We find no differences in contextual-cueing when spatial contexts are letter-like objects, or when contexts are natural scenes. However, the SR group significantly outperforms the TR group when contexts are low-pass filtered natural scenes [F(3, 39) = 3.15, p<.05]. These findings suggest that perception or memory for low spatial frequency components in scenes is enhanced in dyslexia. These findings are important because they suggest strengths for spatial learning in a population otherwise impaired, carrying implications for the education and support of students who face challenges in school.
A synthetic peptide induces long-term protection from lethal infection with herpes simplex virus 2. (1987)

Immunization against viral pathogens is generally directed toward the induction of virus neutralizing antibody (VNA) and the maintenance of the potential for a second-set (IgG) response. Indeed, an elevated level of specific antibody is considered a reliable clinical indicator that a state of immunity exists in the host. However, in the case of herpes simplex virus (HSV), the presence of circulating VNA does not necessarily correlate with protection. Thus, it has been found that secondary infections occur in individuals even with high neutralizing titers to HSV, suggesting that antibody to the virus may be useless or even deleterious. In consideration of these facts, we were interested in inducing a T cell response to HSV. We had already shown that synthetic peptides corresponding to the NH3-terminal region of the glycoprotein D (gD) molecule of HSV could induce a strong T cell response when injected into mice, but did not, by themselves, confer protection. In this report, we examined the ability of peptides, covalently coupled to palmitic acid and incorporated into liposomes, to induce virus-specific T cell responses that confer protection against a lethal challenge of HSV-2. We have demonstrated that long-term protective immunity is achieved with a single immunization in the absence of neutralizing antibody when antigen is presented in this form. Furthermore, T cells but not serum from such immune mice can adoptively transfer this protection.
Halitosis: the multidisciplinary approach (2012)

Halitosis, bad breath or oral malodour are all synonyms for the same pathology. Halitosis has a large social and economic impact. For the majority of patients suffering from bad breath, it causes embarrassment and affects their social communication and life. Moreover,halitosis can be indicative of underlying diseases. Only a limited number of scientific publications were presented in this field until 1995. Ever since, a large amount of research is published, often with lack of evidence. In general, intraoral conditions, like insufficient dental hygiene, periodontitis or tongue coating are considered to be the most important cause (85%) for halitosis. Therefore, dentists and periodontologists are the first-line professionals to be confronted with this problem. They should be well aware of the origin, the detection and especially of the treatment of this pathology. In addition, ear-nose-throat-associated (10%) or gastrointestinal/endocrinological (5%) disorders may contribute to the problem. In the case of halitophobia, psychiatrical or psychological problems may be present. Bad breath needs a multidisciplinary team approach: dentists, periodontologists, specialists in family medicine, ear-nose-throat surgeons, internal medicine and psychiatry need to be updated in this field, which still is surrounded by a large taboo.Multidisciplinary bad breath clinics offer the best environment to examine and treat this pathology that affects around 25% of the whole population. This article describes the origin, detection and treatment of halitosis, regarded from the different etiological origins.
Nobiletin suppresses cell viability through AKT Pathways in PC-3 and DU-145 prostate cancer cells (2014)

Taken together, our results show that nobiletin suppresses cell viability through AKT pathways, with a more profound effect against the more metastatic PC-3 line. Due to this enhanced action against a more malignant cell type, nobiletin may be used to improve prostate cancer survival rates.
Effect of Biological and Synthetic Polymers on BK Virus Infectivity and Hemagglutination (1992)

The effect of several biological and synthetic polymers, chosen on the basis of different physical and chemical properties, was investigated on BK virus infectivity and hemagglutination. It was observed that polyanions like mucin, dextran sulfate and heparin depressed the viral binding, whereas polycations had no significant activity, with the exception of poly-L-lysine, which enhanced it. The effect of the active polymers was studied in different experimental conditions and the results obtained suggested that polyanions may act directly on the virus particle, whereas the target of polycations could be at the level of cell membranes. However, the effect shown by the active compounds did not appear to be simply related to the electric charge since neutral compounds, such as tamarind gum and locust bean gum, showed a marked inhibitory effect on BK virus binding to the cells.
A Staphylococcus aureus autolysin that has an N-acetylmuramoyl-L-alanine amidase domain and an endo-beta-N-acetylglucosaminidase domain: cloning, sequence analysis, and characterization. (1995)

The Tn551 insertion site of the autolysis-deficient Staphylococcus aureus mutant RUSAL2 was cloned and used to identify the autolysis gene atl in the parent strain, RN450. The open reading frame for atl was 3768 bp in length, encoding a deduced protein of 1256 amino acids and molecular size of 137,381 Da. The atl gene product is a bifunctional protein that has an amidase domain and an endo-beta-N-acetylglucosaminidase domain which must undergo proteolytic processing to generate the two extracellular lytic enzymes found in the culture broth of S. aureus.
"Micro-Bubbles": New Aphron Drill-In Fluid Technique Reduces Formation Damage in Horizontal Wells (1998)

Tom Brookey, SPE, Acti Systems, Inc. Abstract Horizontal drilling technology has enhanced production through increased ability to expose formation openings. In most cases, these openings are fractured, vugular, or otherwise highly permeable. Many are drilled through low-pressure reservoirs where drilling fluid losses occur and often cause severe formation damage. The use of conventional lost circulation control materials are restricted due to the downhole tools required, and borehole sealing techniques are mostly ineffective in this type of application. A novel new drill-in fluid is being used to drill horizontal and high angle wells through these damage-prone reservoirs. This fluid combines certain surfactants and polymers to create a system of "micro-bubbles" known as aphrons encapsulated in a uniquely viscosified system. These aphrons are non- coalescing and recirculatable so that density reduction is accomplished without expensive air or gas injection. A unique feature of the micro-bubble network, stopping or slowing the entry of fluids into the formation, creates downhole bridging. The unique viscosity builds to create a resistance to movement into and through the zone so that a true noninvasive, at-balance fluid is achieved. Test data shows the enhanced hole cleaning and suspension properties. Case histories show that drilling problems are reduced, mud losses are prevented, and completions are simplified. Natural production was achieved in many cases. No problems with formation damage or inhibited production were seen. P. 645
Antibodies to cellular antigens in Sjögren's syndrome. (1975)

An extract of human lymphocytes from continous cell culture was used as the antigen source to detect antibodies in sera of patients with Sjögren's syndrome (SS). Using double diffusion in agarose, 85 per cent of a selected group of patients had precepating antibodies. Three precipitating antigen-antibody systems were detected and were shown to be different from those described previously in othe systemic rheumatic diseases. The SS precipitating antibodies were temporarily classified as precipitins, A, B, and C. SS patinets with sicca syndrome but without clinical rheumatoid arthritis had precipitin systems A and/or B, and SS patients with associated rheumatoid arthritis had precipitin system C. Serum reactants were demonstrated by immuno-electrophoresis to migrate in the gamma globulin region. The precipitating activity of the serum factors was not destroyed by treatment with 2-mercaptoethanol and was not removed by absorption of rheumatoid factor from the sera. The reactivity of the lympuocyte antigens was destroyed by treatment with trypsin but not by deoxyribonuclease or ribonuclease.
Strand transfer is enhanced by mismatched nucleotides at the 3' primer terminus: a possible link between HIV reverse transcriptase fidelity and recombination (1996)

Strand transfer catalyzed by HIV reverse transcriptase (RT) was examined. The system consisted of a 142 nt RNA (donor) to which a 50 nt DNA primer was hybridized. The primer bound such that its 3' terminal nucleotide hybridized to the 12th nt from the 5' end of the donor. The 3' terminal nucleotide on the primer was either a G, A or T residue. Since the corresponding nucleotide of the donor was a C, the G formed a matched terminus and the A or T a mismatched terminus. The efficiency with which DNA bound to the donor transferred to a second RNA, termed acceptor, was monitored. The acceptor was homologous to the donor for all but the last 9 nt at the 5' end of the donor. Therefore, homologous strand transfer could occur at any point prior to the DNA being extended into the nonhomologous region on the donor. Strand transfer occurred approximately twice as efficiently with the mismatched versus matched substrates. The mismatched nucleotide was fixed into transfer products indicating that excision of the mismatch was not required for RT extension or transfer. Results suggest that base misincorporations by RT may promote recombination by enhancing strand transfer.
Neutrophil function in ischemic heart disease. (1989)

Neutrophils contribute to the healing of and scar formation in myocardium after ischemic injury. Many recent studies indicate that neutrophils may be involved in the genesis and propagation of myocardial ischemia. To characterize neutrophil function in ischemic heart disease, neutrophil chemotaxis, leukotriene B4 (LTB4) generation, and elastase release in plasma were measured in 20 patients with stable angina, 17 patients with unstable angina or acute myocardial infarction (AMI), and 20 age-matched control subjects. Neutrophils from patients with stable angina exhibited markedly increased chemotactic activity and LTB4 generation as compared with the age-matched control subjects (p less than 0.01). Neutrophils of nine of 17 patients with unstable angina or AMI clumped spontaneously ex vivo and exhibited marked pseudopod formation and granule extrusion on electron microscopy. Subsequent chemotactic activity and LTB4 generation by neutrophils from these patients was less than in patients with stable angina, suggesting previous in vivo activation. Plasma levels of peptide B beta, a product of fibrin degradation by human neutrophil elastase, were approximately 15-fold higher (p less than 0.001) in patients with unstable angina or AMI (588 +/- 171 pmol/l, mean +/- SEM) compared with those in patients with stable angina (37 +/- 25 pmol/l) or control subjects (40 +/- 22 pmol/l), confirming intense in vivo neutrophil activation. Our study shows enhanced neutrophil function in patients with ischemic heart disease. The increased neutrophil chemotactic activity and LTB4 generation may be markers of stable angina pectoris. Intense neutrophil activation in unstable angina or AMI, as manifested by morphologic changes in neutrophils and elastase release, may relate to ongoing in vivo cellular activation.
Angiogenesis in B Cell Lymphoproliferative Diseases. Biological and Clinical Studies (1995)

Angiogenesis is a necessary step in solid tumor progression (growth, invasion and metastasis) with which it correlates and is indicative of an unfavourable prognosis. We observed bone marrow angiogenesis in patients with active multiple myeloma (MM), though not in patients with non-active MM nor with monoclonal gammopathies of undetermined significance (MGUS). Microvessel density increased in parallel with the labeling index (LI%)--an indicator of plasma cell proliferating activity that correlates with prognosis--and defined a risk of MM progression in much the same way as LI% itself. Consequently, bone marrow angiogenesis could be an indication for unfavourable prognosis in MGUS and MM. Angiogenesis has also been demonstrated in lymph nodes involved by B cell non Hodgkin's lymphoma (B-NHL) belonging to the Working Formulation intermediate-grade (diffuse subtypes), and high-grade categories, but not in the low-grade and intermediate-grade (follicular subtype) categories. It correlated with the B-NHL cell proliferating activity, since large increments in this activity have already been demonstrated in intermediate- and high-grade vs low-grade tumors. Active MM, intermediate-grade, diffuse subtypes, and high-grade B-NHLs correspond to the vascular phases of B cell lymphoproliferative diseases, and could thus be assimilated to locally invasive and metastatic solid tumors. Similarly to solid tumors during these stages of progression, tumor B cells are also capable of inducing angiogenesis, both directly and indirectly by activating the inflammation infiltrate--a possibility that was first demonstrated by means of B-NHL implants onto the chick embryo chorioallantoic membrane. Anti-angiogenic therapy can be envisaged as a possible future development.
The top-transmon: a hybrid superconducting qubit for parity-protected quantum computation (2011)

Qubits constructed from uncoupled Majorana fermions are protected from decoherence, but to perform a quantum computation this topological protection needs to be broken. Parity-protected quantum computation breaks the protection in a minimally invasive way, by coupling directly to the fermion parity of the system --- irrespective of any quasiparticle excitations. Here we propose to use a superconducting charge qubit in a transmission line resonator (a socalled transmon) to perform parity-protected rotations and read-out of a topological (top) qubit. The advantage over an earlier proposal using a flux qubit is that the coupling can be switched on and off with exponential accuracy, promising a reduced sensitivity to charge noise.
Effects of K-877, a novel selective PPARα modulator (SPPARMα), in dyslipidaemic patients: A randomized, double blind, active- and placebo-controlled, phase 2 trial (2016)

In dyslipidaemic patients with high TG and low HDL-C, K-877 improved TG, HDL-C, and other lipid parameters without increasing AEs or ADRs, compared to placebo and fenofibrate. K-877 can be expected to improve atherogenicity and to be a new beneficial treatment for dyslipidaemic patients.
Humoral immune responses in L-selectin-deficient mice (1996)

L-selectin regulates lymphocyte migration by mediating lymphocyte attachment to high endothelial venules of peripheral lymph nodes (PLN). L-selectin-deficient mice display a 70 to 90% reduction in the number of lymphocytes within PLNs and a 30 to 55% increase in spleen cellularity. The altered distribution of lymphocyte subpopulations in L-selectin-deficient mice resulted in significantly elevated serum IgM and IgG1 levels and augmented humoral immune responses to T cell-independent and T cell-dependent Ags following i.p. immunization. By contrast, s.c. immunization of L-selectin-deficient mice with a T cell-dependent Ag resulted in serum IgM responses that were 40% lower when compared with wild-type littermates on day 7, while primary IgG responses were essentially absent. Most serum Ig responses were normal by day 14 and secondary responses were higher in L-selectin-deficient mice. Although lymphocytes from L-selectin-deficient mice were unable to enter Ag-stimulated lymph nodes through high endothelial venules, the cellularity of draining lymph nodes increased significantly following immunization. Germinal centers developed rapidly following immunization, although PLNs of L-selectin-deficient mice contained few follicles. Germinal centers within PLNs and the spleen were also consistently much larger and more well defined in L-selectin-deficient mice when compared with wild-type littermates. These results confirm that lymphocyte migration plays an important role in the initiation of humoral responses and demonstrate complementary and overlapping roles for the spleen and other peripheral lymphoid tissues in the generation of immune responses.
Cancer and the Complement Cascade (2010)

Despite significant research on the role of inflammation and immunosurveillance in the immunologic microenvironment of tumors, little attention has been given to the oncogenic capabilities of the complement cascade. The recent finding that complement may contribute to tumor growth suggests an insidious relationship between complement and cancer, especially in light of evidence that complement facilitates cellular proliferation and regeneration. We address the hypothesis that complement proteins promote carcinogenesis and suggest mechanisms by which complement can drive the fundamental features of cancer. Evidence shows that this diverse family of innate immune proteins facilitates dysregulation of mitogenic signaling pathways, sustained cellular proliferation, angiogenesis, insensitivity to apoptosis, invasion and migration, and escape from immunosurveillance. Given that the traditionally held functions for the complement system include innate immunity and cancer defense, our review suggests a new way of thinking about the role of complement proteins in neoplasia.