gebhart/patrepeval huggingface dataset:
Morphing voxels: the hype around structural imaging of headache patients (2009)

Neuroimaging analysis using structural data has begun to provide insights into the pathophysiology of headache syndromes. Several independent studies have suggested a decrease in grey matter in pain-transmitting areas in migraine patients. Most of these data are discussed as damage or loss of brain grey matter, reinforcing the idea of migraine as a progressive disease. However, given what we know about the nature of morphometric changes detectable by the methods we have to date, this interpretation is highly speculative and not supported by the data. It is likely that these changes are the consequence and not the cause of the respective headache syndromes, as they are probably not irreversible and only mirror the proportion or duration of pain suffered. Moreover, structural changes are not headache specific and have to be seen in the light of a wealth of pain studies using these methods. The studies in cluster headache patients prompted the use of stereotactic stimulation of the hypothalamic target point identified by functional and structural neuroimaging. Due to the nature of the methods used and due to a high anatomical variance it is more than questionable to use this point as a definite answer to the source of the headache in clusters and even more so when it is uncritically used in individuals. We need a way to study each patient individually using the functional imaging method with the highest spatial and temporal resolution available to enable us to target the seed point for deep brain stimulation on this individual basis. One of the major future challenges is to understand the behavioural consequences and cellular mechanisms underlying neuroanatomic changes in pain and headache.
4D‐ready marine seismic data (2000)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 20004D‐ready marine seismic dataAuthors: Stephen MoricePhilip ChristieAli ÖzbekTony CurtisJames MartinLeendert CombeeMorten SvendsenPeter VermeerStephen MoriceSchlumberger, Philip ChristieSchlumberger, Ali ÖzbekSchlumberger, Tony CurtisSchlumberger, James MartinSchlumberger, Leendert CombeeSchlumberger, Morten SvendsenSchlumberger, and Peter VermeerSchlumbergerhttps://doi.org/10.1190/1.1815721 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1815721FiguresReferencesRelatedDetailsCited byReferences14 March 2018References21 March 2012 SEG Technical Program Expanded Abstracts 2000ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2000 Pages: 2484 publication data© 2000 Copyright © 2000 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 04 Jan 2005 CITATION INFORMATION Stephen Morice, Philip Christie, Ali Özbek, Tony Curtis, James Martin, Leendert Combee, Morten Svendsen, and Peter Vermeer, (2000), "4D‐ready marine seismic data," SEG Technical Program Expanded Abstracts : 1607-1610. https://doi.org/10.1190/1.1815721 Plain-Language Summary PDF DownloadLoading ...
The inducible form of nitric oxide synthase (iNOS) in insulin-producing cells. (1995)

The enzyme nitric oxide synthase catalyzes the conversion of L-arginine to citrulline and the radical nitric oxide, a short-lived mediator which can be produced in a variety of cell types. Overproduction of nitric oxide is probably implicated in the pathogenesis of several immunologically mediated diseases, including insulin-dependent diabetes mellitus (Type 1). Insulin-producing cells exposed to cytokines, especially interleukin-1, express an inducible form of nitric oxide synthase which is similar to that observed in activated macrophages. Induction of this enzyme mRNA in these cells depends on protein synthesis, and it is probably modulated by protein products of early response genes, such as C-fos. Cytokines seem to activate beta-cell inducible-nitric oxide synthase mostly by stimulating mRNA transcription, but drugs such as nicotinamide and dexamethasone inhibit interleukin 1 induced nitric oxide production by posttranscriptional mechanisms. Considering the potential role for nitric oxide in beta-cell damage during the early stages of Type 1 diabetes, it is of high relevance to further characterize the regulation of this enzyme in insulin-producing cells.
Elitism-based compact genetic algorithms (2003)

This paper describes two elitism-based compact genetic algorithms (cGAs)-persistent elitist compact genetic algorithm (pe-cGA), and nonpersistent elitist compact genetic algorithm (ne-cGA). The aim is to design efficient cGAs by treating them as estimation of distribution algorithms (EDAs) for solving difficult optimization problems without compromising on memory and computation costs. The idea is to deal with issues connected with lack of memory by allowing a selection pressure that is high enough to offset the disruptive effect of uniform crossover. The pe-cGA finds a near optimal solution (i.e., a winner) that is maintained as long as other solutions generated from probability vectors are no better. The ne-cGA further improves the performance of the pe-cGA by avoiding strong elitism that may lead to premature convergence. It also maintains genetic diversity. This paper also proposes an analytic model for investigating convergence enhancement.
HLA immunogenetic heterogeneity in black American patients with Graves' disease (1987)

• Seventy-three American black patients with Graves' disease were typed for HLA-A, HLA-B, and HLA-DR antigens. There was a slight increase in HLA-DRw6 antigen frequency compared with 238 normal American black controls, but this was not significant after correction for the number of antigens tested. A significant increase in HLA-DR4 and HLA-DRw6 frequency was found in a subgroup of patients with exophthalmos (22.9% and 29.2% compared with 7.6% and 10.1% of normal black controls). There was a significant increase in HLA-DRw6 in a subgroup of patients who were thyroid antibody-positive (26.0%). The increment in HLA-DRw6 was higher in 32 patients who had both exophthalmos and who were antibody positive (37.5%). A significant increase in HLA-DR5 was found in a subgroup of patients who did not have exophthalmos and who were antibody-negative (83.3%). Our findings support previous evidence for immunogenetic heterogeneity in patients with toxic Graves' disease. In American blacks HLA-DRw6 is in some way associated with the disease in contrast to the wellrecognized HLA-DR3 association in whites. (<i>Arch Intern Med</i>1987;147:229-231)
Analysis of T cell receptor-gamma gene rearrangements by denaturing gradient gel electrophoresis of GC-clamped polymerase chain reaction products. Correlation with tumor-specific sequences. (1995)

We describe a modified denaturing gradient gel electrophoresis (DGGE) procedure with a 40-nucleotide GC clamp in the polymerase chain reaction to improve resolution in amplifying T cell receptor-gamma (TCR-gamma) rearrangements. DNA from 46 cases of lymphoblastic leukemia/lymphoma, 5T cell lines, 2 B cell lines, 7 normal lymphocytes, and 3 cases of Hodgkin's disease was amplified by polymerase chain reaction. In addition, 20 cases of paraffin-embedded T cell lymphomas and 5 cases of reactive hyperplasia were also studied. Clonal TCR-gamma rearrangements were identified on DGGE by the presence of a predominant band. Results obtained from 5 T cell lines and 12 lymphoblastic leukemia/lymphomas containing known TCR-gamma gene rearrangements revealed 100% concordance in detecting clonal rearrangements between DGGE and traditional Southern blot analysis. Of the remaining 34 lymphoblastic leukemia/lymphoma cases studied by DGGE alone, 30 were positive. DGGE analysis of 10 lymphoblastic leukemia/lymphoma cases with known group IV gamma to J gamma 1 or J gamma 2 rearrangement sequences confirmed that the electrophoretic migration was dependent on the tumor-specific rearranged TCR-gamma sequence. In addition, 17 of 20 cases of paraffin-embedded T cell lymphomas were positive by DGGE, 6 of which had the clonal population also identified in fresh tissue DNA. DGGE analysis of GC-clamped polymerase chain reaction products can provide a way to more accurately detect TCR-gamma clonality of lymphoid tumors and can be applied to archival tissues.
The RAR-RXR as well as the RXR-RXR pathway is involved in signaling growth inhibition of human CD34+ erythroid progenitor cells (1996)

Abstract Previous studies have shown that retinoic acid (RA), similar to tumor necrosis factor-alpha (TNF-alpha), can act as a bifunctional regulator of the growth of bone marrow progenitors, in that it can stimulate granulocyte-macrophage colony-stimulating factor (GM-CSF)- or interleukin-3 (IL-3)-induced GM colony formation, but potently inhibit G-CSF-induced growth. The present study, using highly enriched human CD34+ as well as Lin- murine bone marrow progenitor cells, demonstrates a potent inhibitory effect of 9-cis-RA on burst-forming unit-erythroid (BFU-E) colony formation regardless of the cytokine stimulating growth. Specifically, 9-cis-RA potently inhibited the growth of BFU-E response to erythropoietin (Epo) (100%), stem cell factor (SCF) + Epo (92%), IL- 3 + Epo (97%), IL-4 + Epo (88%), and IL-9 + Epo (100%). Erythroid colony growth was also inhibited when CD34+ progenitors were seeded at one cell per well, suggesting a direct action of RA. Using synthetic ligands to retinoic acid receptors (RARs) and retinoid X receptors (RXRs) that selectively bind and activate RAR-RXR or RXR-RXR dimers, respectively, we dissected the involvement of the two retinoid response pathways in the regulation of normal myeloid and erythroid progenitor cell growth. Transactivation studies showed that both the RAR (Ro 13– 7410) and RXR (Ro 25–6603 and Ro 25–7386) ligands were highly selective at 100 nmol/L. At this concentration, Ro 13–7410 potently inhibited G- CSF-stimulated myeloid as well as SCF + Epo-induced erythroid colony growth. At the same concentration, Ro 25–6603 and Ro 25–7386 had little or no effect on G-CSF-induced colony formation, whereas they inhibited 75% and 53%, respectively, of SCF + Epo-stimulated BFU-E colony growth. Thus, the RAR-RXR response pathway can signal growth inhibition of normal bone marrow myeloid and erythroid progenitor cells. In addition, we demonstrate a unique involvement of the RXR-RXR pathway in mediating growth inhibition of erythroid but not myeloid progenitor cells.
Expression of Semliki Forest virus proteins from cloned complementary DNA. I. The fusion activity of the spike glycoprotein. (1983)

A complementary (cDNA) molecule encoding the structural proteins of Semliki Forest virus (SFV) has been inserted into a Simian virus 40-derived eucaryotic expression vector lacking introns. Introduction of the recombinant DNA into nuclei of baby hamster kidney cells results in the synthesis of authentic SFV membrane glycoproteins E1 and E2. The glycoproteins are both transported to the cell surface and induce cell-cell fusion after a brief treatment of the cells with low pH medium. The pH dependence of the fusion reaction was the same as that induced by virus particles (White, J., J. Kartenbeck, and A. Helenius, 1980, J. Cell Biol., 89:674-679). Transfection of cells with another recombinant DNA molecule in which the SFV cDNA is engineered into the same expression vector including an intron has been shown before to result in the expression of only the E2 protein on the cell surface, whereas the E1 protein is trapped in the rough endoplasmic reticulum (Kondor-Koch, C., H. Riedel, K. Söderberg, and H. Garoff, 1982, Proc. Natl. Acad. Sci. USA, 79:4525-4529). Such cells do not exhibit pH-dependent polykaryon formation, suggesting that the E1 protein is necessary for fusion activity. Immunoblotting experiments show that the RER-trapped E1 protein expressed from the DNA construction with an intron has a smaller apparent molecular weight than authentic E1, and that is has lost its amphipathic characteristics.
Database for mobile group II introns (2003)

Group II introns are self-splicing RNAs and retroelements found in bacteria and lower eukaryotic organelles. During the past several years, they have been uncovered in surprising numbers in bacteria due to the genome sequencing projects; however, most of the newly sequenced introns are not correctly identified. We have initiated an ongoing web site database for mobile group II introns in order to provide correct information on the introns, particularly in bacteria. Information in the web site includes: (1) introductory information on group II introns; (2) detailed information on subfamilies of intron RNA structures and intron-encoded proteins; (3) a listing of identified introns with correct boundaries, RNA secondary structures and other detailed information; and (4) phylogenetic and evolutionary information. The comparative data should facilitate study of the function, spread and evolution of group II introns. The database can be accessed at http://www.fp.ucalgary.ca/group2introns/.
Risk factors for surgical site infection after elective resection for rectal cancer. A multivariate analysis on 2131 patients (2011)

Rectal surgery for malignant disease is associated with a considerable rate of SSI. Wound infection and organ space infection are related to different factors and therefore should be evaluated separately.
Cold Induction of Arabidopsis CBF Genes Involves Multiple ICE (Inducer of CBF Expression) Promoter Elements and a Cold-Regulatory Circuit That Is Desensitized by Low Temperature (2003)

The Arabidopsis CBF1, 2, and 3 genes (also known as DREB1b, c, and a, respectively) encode transcriptional activators that have a central role in cold tolerance. CBF1-3 are rapidly induced upon exposing plants to low temperature, followed by expression of CBF-targeted genes, the CBF regulon, resulting in an increase in plant freezing tolerance. At present, little is known about the cold-sensing mechanism that controls CBF expression. Results presented here indicate that this mechanism does not require a cold shock to bring about the accumulation of CBF transcripts, but instead, absolute temperature is monitored with a greater degree of input, i.e. lower temperature, resulting in a greater output, i.e. higher levels of CBF transcripts. Temperature-shift experiments also indicate that the cold-sensing mechanism becomes desensitized to a given low temperature, such as 4 degrees C, and that resensitization to that temperature requires between 8 and 24 h at warm temperature. Gene fusion experiments identified a 125-bp section of the CBF2 promoter that is sufficient to impart cold-responsive gene expression. Mutational analysis of this cold-responsive region identified two promoter segments that work in concert to impart robust cold-regulated gene expression. These sequences, designated ICEr1 and ICEr2 (induction of CBF expression region 1 or 2), were also shown to stimulate transcription in response to mechanical agitation and the protein synthesis inhibitor, cycloheximide.
Characteristics of ovarian cancer cells transduced by the bicistronic retroviral vector containing GM-CSF and HSV-TK genes. (2001)

The IRES sequence can be used to construct retroviral vectors to facilitate co-transfection of two genes. SKOV3/TK-GM cells can simultaneously express the HSV-TK and GM-CSF genes with biological activities which could be useful for enhancing the function of immune cells on the basis of suicide gene therapy.
Genome Scale Comparison ofMycobacterium aviumsubsp.paratuberculosiswithMycobacterium aviumsubsp.aviumReveals Potential Diagnostic Sequences (2002)

The genetic similarity between Mycobacterium avium subsp. paratuberculosis and other mycobacterial species has confounded the development of M. avium subsp. paratuberculosis-specific diagnostic reagents. Random shotgun sequencing of the M. avium subsp. paratuberculosis genome in our laboratories has shown >98% sequence identity with Mycobacterium avium subsp. avium in some regions. However, an in silico comparison of the largest annotated M. avium subsp. paratuberculosis contigs, totaling 2,658,271 bp, with the unfinished M. avium subsp. avium genome has revealed 27 predicted M. avium subsp. paratuberculosis coding sequences that do not align with M. avium subsp. avium sequences. BLASTP analysis of the 27 predicted coding sequences (genes) shows that 24 do not match sequences in public sequence databases, such as GenBank. These novel sequences were examined by PCR amplification with genomic DNA from eight mycobacterial species and ten independent isolates of M. avium subsp. paratuberculosis. From these analyses, 21 genes were found to be present in all M. avium subsp. paratuberculosis isolates and absent from all other mycobacterial species tested. One region of the M. avium subsp. paratuberculosis genome contains a cluster of eight genes, arranged in tandem, that is absent in other mycobacterial species. This region spans 4.4 kb and is separated from other predicted coding regions by 1,408 bp upstream and 1,092 bp downstream. The gene upstream of this eight-gene cluster has strong similarity to mycobacteriophage integrase sequences. The GC content of this 4.4-kb region is 66%, which is similar to the rest of the genome, indicating that this region was not horizontally acquired recently. Southern hybridization analysis confirmed that this gene cluster is present only in M. avium subsp. paratuberculosis. Collectively, these studies suggest that a genomics approach will help in identifying novel M. avium subsp. paratuberculosis genes as candidate diagnostic sequences.
Photoreceptor Layer Topography in Children with Leber Congenital Amaurosis Caused byRPE65Mutations (2008)

Photoreceptor loss in the foveal and extrafoveal retina was prominent, even in the youngest patients studied. Differences in the topography of residual photoreceptors in children with RPE65-LCA suggest that it may be advisable to use individualized ONL mapping to guide the location of subretinal injections for gene therapy and thereby maximize the potential for efficacy.
Selective Hydrolysis of 2,4-Diaminopyrimidine Systems:  A Theoretical and Experimental Insight into an Old Rule (2000)

Hydrolysis of the amino groups in condensed 2,4-diaminopyrimidine systems (1) has been used as a common method for the synthesis of oxo-substituted pyrimidines. In particular, the treatment with 6 M HCl usually yields exclusively the 2-amino-4-oxopyrimidine isomer (2). During our work, we found that the hydrolysis of the amino groups present in some condensed 2,4-diaminopyrimidine systems unexpectedly afforded exclusively the 4-amino-2-oxopyrimidine isomer (3). In this paper, we present the experimental work and ab initio calculations carried out to understand this discrepancy. As a part of such study, eight compounds containing a 2,4-diaminopyrimidine moiety were calculated in gas phase and in aqueous solution, and some acid hydrolyses were reexamined. Results showed that the presence of an electron-donating nitrogen linked to C6 of the 2,4-diaminopyrimidine ring changes the preferred hydrolysis site to yield the 4-amino-2-oxopyrimidine isomer.
The polymerase L528M mutation cooperates with nucleotide binding-site mutations, increasing hepatitis B virus replication and drug resistance (2001)

After receiving lamivudine for 3 years to treat chronic hepatitis B, 67-75% of patients develop B-domain L528M, C-domain M552I, or M552V mutations in the HBV polymerase that render hepatitis B virus (HBV) drug-resistant. The aim of this study was to evaluate the influence of these mutations on viral replication and resistance to antiviral agents. We investigated the replication fitness and susceptibility of the wild-type and five mutant HBVs (L528M, M552I, M552V, L528M/M552I, and L528M/M552V) to 11 compounds [lamivudine, adefovir, entecavir (BMS-200475) (+)-BCH-189 (+/-)-FTC (racivir) (-)-FTC (emtricitabine) (+)-FTC, L-D4FC, L-FMAU (clevudine), D-DAPD, and (-)-carbovir] by transfecting HBV DNA into hepatoma cells and monitoring viral products by Southern blotting. The replication competency of the single C-domain mutants M552I and M552V was markedly decreased compared with that of wild-type HBV. However, addition of the B-domain mutation L528M restored replication competence. Only adefovir and entecavir were effective against all five HBV mutants, and higher doses of these compounds were necessary to inhibit the double mutants compared with the single mutants. The B-domain mutation (L528M) of HBV polymerase not only restores the replication competence of C-domain mutants, but also increases resistance to nucleoside analogues.
Effects of pH on Bacterial Inactivation in Aqueous Solutions due to Low‐Temperature Atmospheric Pressure Plasma Application (2009)

Abstract Low‐temperature atmospheric pressure plasmas applied to the surface of an aqueous solution have been shown to be efficient bactericides for bacteria suspended in the solution, if the solution is sufficiently acidic. Especially of interest is the finding that there is a critical pH value of about 4.7 for the bactericidal effects, below which the bacteria are efficiently inactivated and above which the bacteria are hardly affected by the plasma application. It has been also found that the presence of superoxide anion radicals O • in the solution is essential for bacterial inactivation by the plasma application. Therefore, the critical pH value may arise from the p K a of the equilibrium reaction between O • and hydroperoxy radicals HOO•, which is known to be approximately 4.8. The present experiments, where plasmas are not directly applied to bacterium surfaces and it has been confirmed that neither UV light nor heat from the plasma is the cause of bacterial inactivation, suggest the importance of highly reactive species generated in the solution via plasma–liquid interaction for the bactericidal effects. magnified image
First trimester concentrations of pregnancy associated plasma protein A and placental protein 14 in Down's syndrome. (1992)

study more than a third of the abused women had been admitted five times or more. The greater differences in admissions in the ages over 30 might be related to ongoing domestic violence. Several studies indicate that the risk ofbeing the victim of wife beating is most pronounced in the fourth decade of life.' 24 The abused woman, in her exposed and desolate situation, does not always seek medical care for specific somatic diseases.3 The battered wife syndrome consists of somatic, psychosomatic, and psychiatric symptoms, and psychosocial support is an important reason for seeking hospital care.5 Any physician should consider the possibility of ongoing domestic violence when confronted with a female patient lacking other obvious reasons for frequent hospital admissions.