gebhart/patrepeval huggingface dataset:
E2 Proteins of High Risk Human Papillomaviruses Down-Modulate STING and IFN-κ Transcription in Keratinocytes (2014)

In the early stages of human papillomavirus (HPV) infection, the viral proteins elicit specific immune responses that can participate to regression of ano-genital lesions. HPV E6 protein for instance can reduce type I interferon (IFN) including IFN-κ that is involved in immune evasion and HPV persistence. To evaluate the role of E2 protein in innate immunity in HPV16-associated cervical lesions, genome-wide expression profiling of human primary keratinocytes (HPK) transduced by HPV16 E2 was investigated using microarrays and innate immunity associated genes were specifically analyzed. The analyses showed that the expression of 779 genes was modulated by HPV16E2 and 92 of them were genes associated with innate immunity. Notably IFN-κ and STING were suppressed in HPK expressing the E2 proteins of HPV16 or HPV18 and the trans-activation amino-terminal domain of E2 was involved in the suppressive effect. The relationship between STING, IFN-κ and interferon stimulated genes (ISGs) in HPK was confirmed by gene silencing and real time PCR. The expression of STING and IFN-κ were further determined in clinical specimens by real time PCR. STING and IFN-κ were down-modulated in HPV positive low grade squamous intraepithelial lesions compared with HPV negative controls. This study demonstrates that E2 proteins of high risk HPV reduce STING and IFN-κ transcription and its downstream target genes that might be an immune evasion mechanism involved in HPV persistence and cervical cancer development.
Ni(II) Specifically Cleaves the C-Terminal Tail of the Major Variant of Histone H2A and Forms an Oxidative Damage-Mediating Complex with the Cleaved-Off Octapeptide (2000)

The acetyl-TESHHK-amide peptide, modeling a part of the C-terminal "tail" of histone H2A, was found previously by us to undergo at pH 7. 4 a Ni(II)-assisted hydrolysis of the E-S peptide bond with formation of a stronger Ni(II) complex with the SHHK-amide product [Bal, W., et al. (1998) Chem. Res. Toxicol. 11, 1014-1023]. To further characterize the hydrolysis and test the resulting Ni(II) complex for redox activity, bovine histone H2A and three peptides were investigated: acetyl-LLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK (H2A(34)), modeling the entire "C-tail" of H2A; SHHKAKGK (H2A(8)), modeling the cutoff product of hydrolysis; and acetyl-KTESHKAKGK (H2A(10)), modeling a putative Ni(II) binding site in a minor variant H2A.4 of human histone H2A. The Ni(II)-assisted hydrolysis of H2A and H2A(34) was found to proceed approximately 7-fold faster than that of the Ni(II)-acetyl-TESHHK-amide complex under comparable conditions. In both cases, the Ni(II) complex with H2A(8) was the smaller product of the hydrolysis, indicating a high site specificity of the reaction. Of three other metals tested with H2A(34), only Cu(II) cleaved the E-S bond, although much less efficiently than Ni(II); Co(II) and Zn(II) had no effect whatsoever. The H2A(10) peptide appeared to be fully resistant to hydrolytic cleavage and did not exhibit any redox activity versus H(2)O(2) in the presence of Ni(II) at pH 7.4. Likewise, redox-inactive was the Ni(II)-H2A(34) complex. In contrast, the Ni(II)-H2A(8) complex promoted oxidative damage of pUC19 DNA by H(2)O(2), evidenced by a significant increase in the number of single strand breaks and nucleobase modifications typical for a hydroxyl radical-like species attack on DNA. Interestingly, instead of 8-oxopurines, the corresponding formamidopyrimidines were the major products of the damage. The difference in redox activity between the Ni(II)-H2A(34) and Ni(II)-H2A(8) complexes is most likely associated with their different geometries: octahedral and square planar, respectively. Incubation of the Ni(II)-H2A(8) complex with H(2)O(2) also resulted in degradation of the peptide ligand, especially at its Ser and His residues. Thus, binding of Ni(II) to the ESHHK motif of the histone H2A C-tail is damaging to the histone C-terminal tail and to histone-associated DNA. The results support a dual mechanism of Ni(II)-induced carcinogenesis, including both genotoxic and epigenetic effects.
Mechanisms of tissue–iron relaxivity: Nuclear magnetic resonance studies of human liver biopsy specimens (2005)

MRI is becoming an increasingly important tool to assess iron overload disorders, but the complex nature of proton-iron interactions has troubled noninvasive iron quantification. Intersite and intersequence variability as well as methodological inaccuracies have been limiting factors to its widespread clinical use. It is important to understand the underlying proton relaxation mechanisms within the (human) tissue environment to address these differences. In this respect, NMR relaxometry was performed on 10 fresh human liver biopsy specimens taken from patients with transfusion-dependent anemia. T1 (1/R1) inversion recovery, T2 (1/R2) single echo, and multiecho T2 CPMG measurements were performed on a 60-MHz Bruker Minispectrometer. NMR parameters were compared to quantitative iron levels and tissue histology. Relaxivities R1 and R2 both increased linearly with hepatic iron content, with R2 being more sensitive to iron. CPMG data were well described by a chemical-exchange model and predicted effective iron center dimensions consistent with hemosiderin-filled lysosomes. Nonexponential relaxation was evident at short refocusing intervals with R2 and amplitude behavior suggestive of magnetic susceptibility-based compartmentalization rather than anatomic subdivisions. NMR relaxometry of human liver biopsy specimens yields unique insights into the mechanisms of tissue-iron relaxivity.
Recruitment of dorsal column fibers in spinal cord stimulation: influence of collateral branching (1992)

An electrical network model of myelinated dorsal column nerve fibers is presented. The effect of electrical stimulation was investigated using both a homogeneous volume conductor and a more realistic model of the spinal cord. An important feature of dorsal column nerve fibers is the presence of myelinated collaterals perpendicular to the rostro-caudal fibers. It was found that transmembrane potentials, due to external monopolar stimulation, at the node at which a collateral is attached, is significantly influenced by the presence of the collateral. It is concluded that both excitation threshold and blocking threshold of dorsal column fibers are decreased up to 50% compared to unbranched fibers.
A Novel Thermal Response Factor Method for the Dynamic Load Calculation of Buildings (2002)

The traditional thermal response factor method for load calculation employs invariable time-step. To ensure accuracy with the less possible computing quantity, the method with variable time steps is expected to deal with the complicated dynamic thermal loads of buildings. In this paper, the traditional method of excitation disintegration is analyzed first because the time step is initially fixed here. Two new functions for excitation disintegration are presented, namely the step function and the ramp-step function. Based on the new excitation method, a novel thermal response factor method with variable time steps is developed. In an example, the thermal response to a sine-wave input is evaluated by the traditional and present methods. It illustrates that about 36% computing quantity is decreased with the new method at the same precision.
Alginate Lyase: Review of Major Sources and Enzyme Characteristics, Structure-Function Analysis, Biological Roles, and Applications (2000)

Alginate lyases, characterized as either mannuronate (EC 4.2.2.3) or guluronate lyases (EC 4.2.2.11), catalyze the degradation of alginate, a complex copolymer of alpha-L-guluronate and its C5 epimer beta-D-mannuronate. Lyases have been isolated from a wide range of organisms, including algae, marine invertebrates, and marine and terrestrial microorganisms. This review catalogs the major characteristics of these lyases, the methods for analyzing these enzymes, as well as their biological roles. Analysis of primary sequence data identifies some markedly conserved motifs that should help elucidate functional domains. Information about the three-dimensional structure of a mannuronate lyase from Sphingomonas sp., combined with various mutagenesis studies, has identified residues that are important for catalytic activity in several lyases. Characterization of alginate lyases will enhance and expand the use of these enzymes to engineer novel alginate polymers for applications in various industrial, agricultural, and medical fields. In this review, we explore both past and present applications of this important enzyme and discuss its future prospects.
Visualization of DNA Replication in the Vertebrate Model System DT40 using the DNA Fiber Technique (2011)

Maintenance of replication fork stability is of utmost importance for dividing cells to preserve viability and prevent disease. The processes involved not only ensure faithful genome duplication in the face of endogenous and exogenous DNA damage but also prevent genomic instability, a recognized causative factor in tumor development. Here, we describe a simple and cost-effective fluorescence microscopy-based method to visualize DNA replication in the avian B-cell line DT40. This cell line provides a powerful tool to investigate protein function in vivo by reverse genetics in vertebrate cells(1). DNA fiber fluorography in DT40 cells lacking a specific gene allows one to elucidate the function of this gene product in DNA replication and genome stability. Traditional methods to analyze replication fork dynamics in vertebrate cells rely on measuring the overall rate of DNA synthesis in a population of pulse-labeled cells. This is a quantitative approach and does not allow for qualitative analysis of parameters that influence DNA synthesis. In contrast, the rate of movement of active forks can be followed directly when using the DNA fiber technique(2-4). In this approach, nascent DNA is labeled in vivo by incorporation of halogenated nucleotides (Fig 1A). Subsequently, individual fibers are stretched onto a microscope slide, and the labeled DNA replication tracts are stained with specific antibodies and visualized by fluorescence microscopy (Fig 1B). Initiation of replication as well as fork directionality is determined by the consecutive use of two differently modified analogues. Furthermore, the dual-labeling approach allows for quantitative analysis of parameters that influence DNA synthesis during the S-phase, i.e. replication structures such as ongoing and stalled forks, replication origin density as well as fork terminations. Finally, the experimental procedure can be accomplished within a day, and requires only general laboratory equipment and a fluorescence microscope.
Transparencia y credibilidad: el caso de los partidos políticos en España (2010)

La inexistencia de un plan contable especifico para partidos politicos se traduce en la elaboracion por parte de todas las formaciones de un registro de informacion economica y financiera heterogeneo y pleno de debilidades. Una normalizacion contable, ademas de incrementar la credibilidad de los partidos, permitiria ejercer un mayor control sobre sus finanzas.
Comparison of intravenous gamma globulin and a monoclonal anti-Fc receptor antibody as inhibitors of immune clearance in vivo in mice. (1986)

Fc-receptor-mediated clearance and nonspecific phagocytic clearance were assessed after the infusion of monomeric human IgG, heat-aggregated human IgG, and a monoclonal anti-mouse macrophage FcII receptor antibody (2.4G2) into normal mice. Each agent blocked Fc-receptor function in vivo, but 2.4G2 was much more potent per microgram than the other agents. Monomeric IgG in blocking doses did not affect other aspects of immune function. In contrast, aggregated IgG, and to a lesser extent, 2.4G2 reduced serum complement levels. In addition, these agents also caused moderate reductions in nonspecific phagocytic function. Monoclonal anti-mouse macrophage C3bi receptor antibody (Mac-1), another monoclonal antibody which binds to macrophage CR3 receptors without interfering with Fc-receptor function, also reduced serum complement and inhibited nonspecific phagocytic function. Complement depletion alone (produced by infusion of cobra venom factor) could not account for the observed changes in Fc receptor or nonspecific phagocytic function. We conclude that both monomeric IgG and anti-Fc-receptor antibodies can markedly inhibit Fc-receptor function in vivo; however, the pattern of physiologic changes produced by these agents differs.
Electrical Transport and Thermoelectric Properties of PbTe Prepared by HPHT (2004)

In this paper, n-type lead telluride (PbTe) compounds without doping were sucessfully prepared at high pressure and high temperature (HPHT). The carrier type was induced by the effect of pressure. The results of the electrical conductivity, Seebeck coefficient, thermal conductivity for n-type PbTe, which were measured at room temperature, show that the PbTe samples prepared by HPHT exhibit the same characteristics as heavily doped semiconductors. The figure-of-merit, Z, of 5.46 × 10−4 K−1 was obtained, which is higher than the heavily doped samples of PbTe at room temperature. These results indicate that this method has potential application in obtaining good quality thermoelectric materials with improved properties.
Scalable trapped ion quantum computation with a probabilistic ion-photon mapping (2004)

We propose a method fur scaling trapped ions fur large-scale quantum computation and communication based on a probabilistic ion photon mapping. Deterministic quantum gates between remotely located trapped ions can be achieved through detection of spontaneously-emitted photons, accompanied by the local Coulomb interaction between neighboring ions. We discuss gate speeds and tolerance to experimental noise for different probabilistic entanglement schemes.
Anti-CD37 antibodies for chronic lymphocytic leukemia (2014)

CD37 may offer advantages over CD20 as a target for CLL cells. It is selectively expressed on normal mature B cells and by most B-cell malignancies. Anti-CD37 antibodies may be useful for patients resistant or refractory to anti-CD20 mAb therapy or relapsing after such treatment. The development of these agents into a clinically useful therapy for CLL is probably many years away and will be followed with great interest by laboratory investigators and clinicians.
Illustrated Dictionary of Immunology (2002)

From the beginning, immunologists have maintained a unique nomenclature that has often mystified and even baffled their colleagues in other fields, causing them to liken immunology to a &quot;black box.&quot; With more than 1,200 illustrations that depict every concept of importance, the Illustrated Dictionary of Immunology, Second Edition p
Monomeric Calgranulins Measured by SELDI-TOF Mass Spectrometry and Calprotectin Measured by ELISA as Biomarkers in Arthritis (2008)

The SELDI-TOF MS technology is a powerful approach for analyzing the status of monomeric, truncated, or posttranslationally modified forms of arthritis biomarkers, such as the S100A8, S100A9, S100A12, and SAA proteins. The fact that the SELDI-TOF MS data were correlated with results obtained with the classic calprotectin ELISA test supports the reliability of this new proteomic technique.
A thorough assessment of benign genetic variability inGRNandMAPT (2009)

Mutations in APP, PSEN1, MAPTand GRNare the most common genetic causes of dementia. The previous miss-assignment of pathogenicity to benign variants in these genes stresses the importance of discerning between disease causing mutations and benign variants with no pathogenic effect on the function of the respective protein. In this study we sequenced GRNand MAPTin 282 samples from the Centre d'Etude du Polymorphisme Humain - Human Genome Diversity Cell Line Panel, in order to identify benign variants that could otherwise be mistaken for pathogenic mutations. We found sixteen different non-synonymous changes, eleven of which are novel variants.
SPARC, a secreted protein associated with morphogenesis and tissue remodeling, induces expression of metalloproteinases in fibroblasts through a novel extracellular matrix-dependent pathway. (1993)

SPARC (osteonectin/BM40) is a secreted protein that modifies the interaction of cells with extracellular matrix (ECM). When we added SPARC to cultured rabbit synovial fibroblasts and analyzed the secreted proteins, we observed an increase in the expression of three metalloproteinases--collagenase, stromelysin, and the 92-kD gelatinase--that together can degrade both interstitial and basement membrane matrices. We further characterized the regulation of one of these metalloproteinases, collagenase, and showed that both collagenase mRNA and protein are upregulated in fibroblasts treated with SPARC. Experiments with synthetic SPARC peptides indicated that a region in the neutral alpha-helical domain III of the SPARC molecule, which previously had no described function, was involved in the regulation of collagenase expression by SPARC. A sequence in the carboxyl-terminal Ca(2+)-binding domain IV exhibited similar activity, but to a lesser extent. SPARC induced collagenase expression in cells plated on collagen types I, II, III, and V, and vitronectin, but not on collagen type IV. SPARC also increased collagenase expression in fibroblasts plated on ECM produced by smooth muscle cells, but not in fibroblasts plated on a basement membrane-like ECM from Engelbreth-Holm-Swarm sarcoma. Collagenase was induced within 4 h in cells treated with phorbol diesters or plated on fibronectin fragments, but was induced after 8 h in cells treated with SPARC. A number of proteins were transiently secreted by SPARC-treated cells within 6 h of treatment. Conditioned medium that was harvested from cultures 7 h after the addition of SPARC, and depleted of residual SPARC, induced collagenase expression in untreated fibroblasts; thus, part of the regulation of collagenase expression by SPARC appears to be indirect and proceeds through a secreted intermediate. Because the interactions of cells with ECM play an important role in regulation of cell behavior and tissue morphogenesis, these results suggest that molecules like SPARC are important in modulating tissue remodeling and cell-ECM interactions.
[Spiral volumetric scanning and its applications in thoracic pathology]. (1994)

Spiral scanning (BSV) is a newly acquired scanning technique for all or part of the thoracic volume in a single breath-hold. It offers many advantages when compared to conventional CT scanning. The study of the lungs with a single breath-hold avoids the inconvenience of an anatomical discontinuity while acquiring the information. In a population of patients presenting with multiple, or solitary pulmonary nodules, or the absence of nodule, BSV shows 30 to 40% of supplementary nodules when compared to conventional scanning techniques. BSV enables the optimal use of contrast products in which the iodine is poorly concentrated to study the pulmonary vessels. Certainly this technique will not replace pulmonary angiography for the diagnosis of pulmonary emboli. However, it may be used first in certain situations, dispensing with invasive angiography in patients with an increased risk, or in the initial assessment of patients with pulmonary arterial hypertension of unknown aetiology, or to follow a previously documented pulmonary emboli. The correlation between spiral scanning and conventional angiography for the diagnosis of pulmonary emboli is excellent, to the level of segmental arteries. Finally the continuity, both anatomically and for the lesions obtained by BSV is such that it is now possible to apply to thoracic pathology techniques of multiplanar and three dimensional reconstruction. If all the information is contained in conventional transversal imaging slice by slice, not everything is perceived by the observer because the information is inconveniently presented because the anatomical and lesional picture is deconstructed. The reconstruction of the volume inspected in coronal, sagittal, oblique or three-dimensional viewing, furnishes supplementary information and announces the arrival of trachea-bronchography, and non-invasive angiography three-dimensionally. In parallel to the expected progress in IRM angiography, three-dimensional angio-CT of the thoracic vessels after appropriate evaluation is going to be substituted for more invasive techniques which are currently used.
A Model of Low‐Temperature Wafer Bonding And Its Applications (1996)

Si‒OH groups can polymerize to form strong covalent Si‒O‒Si bonds at low temperatures. Based on this behavior a model for hydrophilic Si wafer bonding is suggested which allows significant increase of bonding strength by low‐temperature annealing. A possible extension of this model to materials other than Si is discussed. Methods to prevent generation of interface bubbles during the low‐temperature annealing are presented. The low‐temperature bonding approach has been employed in layer transfer applications such as an ultrathin silicon‐on‐insulator layers by an implanted carbon etch stop, single‐crystal Si layer on quartz, glass, or sapphire. Analysis of thermal peeling stresses in bonded pairs of dissimilar materials led to the development of bonding and heating‐cooling schedules as well as a low vacuum bonding method to avoid peeling during annealing and subsequent thinning (etching).
Cryptococcus neoformans Galactoxylomannan Contains an Epitope(s) That Is Cross-Reactive with Aspergillus Galactomannan (2005)

We report a case of cryptococcosis in which a serum enzyme-linked immunosorbent assay (ELISA) for Aspergillus galactomannan was positive, with no evidence of aspergillosis. Soluble antigens from 19 Cryptococcus neoformans strains and purified carbohydrates of C. neoformans capsule were thus assayed in the Aspergillus galactomannan ELISA. Antigens from all C. neoformans strains, and purified galactoxylomannan, gave a positive reaction, suggesting that C. neoformans galactoxylomannan contains an epitope(s) that is cross-reactive with Aspergillus galactomannan.
Malignant Obstruction of Gastric Outlet and Duodenum: Palliation with Flexible Covered Metallic Stents (2001)

Flexible covered metallic stent placement can be useful for palliation in patients with malignant obstruction of the gastric outlet or duodenum.
Effect of Oxygen on Isolated Pancreatic Tissue (1989)

One approach to insulin replacement therapy is transplantation of islets of Langerhans immunoisolated from host tissue by a semipermeable membrane. In this state, islets depend on diffusion of nutrients and wastes to and from the 0-cell to provide a suitable environment for survival and secretion. A perifusion system was constructed to test glucose-stimulated (100–300 mg/100 ml) insulin secretion from whole islets, or small (5–10 cell) aggregates, under controlled pO2. First phase insulin secretion from adult rat islets was unaffected by hypoxic levels of pO2, but second phase secretion was rapidly reduced at pO2 levels below 60 mmHg in the bulk media. Secretion from single-cell aggregates was unaffected until pO2 levels dropped to 12 mmHg, at which point secretion progressively decreased with falling pO2. A theoretical reaction/diffusion model was developed to correlate intraislet pO2 with reduced insulin secretion. Oxygen limited secretion was reversible, and not a result of decreased cell viability, as ascertained by both long-term static culture and trypan blue staining. Insulin secretion is more sensitive to hypoxia than is cell viability, in part because O2 uptake increases with glucose stimulation. These results indicate that O2 may be the limiting factor in the ability of immunoisolated islets to respond to blood glucose changes. We conclude that maintenance of a sufficiently high islet pO2 for maximal insulin secretion may be an important issue for graft design and implant site selection.