gebhart/patrepeval huggingface dataset:
Cerebral infarction in systemic lupus: association with anticardiolipin antibodies. (1984)

We report fifteen patients, thirteen with systemic lupus and two patients with a "lupus-like" illness who developed cerebral infarction. All fifteen patients were shown to have elevated anticardiolipin antibody levels using a newly devised solid phase radioimmunoassay. The lupus anticoagulant was detected in all eleven patients tested. It is proposed that anticardiolipin antibodies and the lupus anticoagulant make up a population of antiphospholipid antibodies capable of causing cerebral vascular injury and thrombosis resulting in cerebral infarction. These antibodies may also play a pathogenic role in autoimmune disorders other than lupus where cerebral thrombotic disease is a prominent feature.
Circular Permutation in Proteins (2012)

The authors have declared that no competing interests exist.



The RCSB PDB is managed by two members of the RCSB: Rutgers and UCSD, and is funded by National Science Foundation (NSF), National Institute of General Medical Sciences, Department of Energy (DOE), National Library of Medicine, National Cancer Institute, National Institute of Neurological Disorders and Stroke and National Institute of Diabetes and Digestive and Kidney Diseases. The RCSB PDB is a member of the wwPDB. This work was supported by the RCSB PDB grant NSF DBI 0829586. The funders had no role in the preparation of the manuscript.
The Greening of Synfuels (2008)

An old, dirty technology to make transportation fuels from coal could fight global warming, say proponents. The trick is using more biomass and burying the carbon dioxide thati?½s generated.
β-Galactoside-binding protein secreted by activated T cells inhibits antigen-induced proliferation of T cells (1998)

We have used mRNA differential display PCR to search for genes induced in activated T cells and have found the LGALS1 (lectin, galactoside-binding, soluble) gene to be strongly up-regulated in effector T cells. The protein coded by the LGALS1 gene is a beta-galactoside-binding protein (betaGBP), which is released by cells as a monomeric negative growth factor but which can also associate into homodimers (galectin-1) with lectin properties. Northern blot analysis revealed that ex vivo isolated CD8+ effector T cells induced by a viral infection expressed high amounts of LGALS1 mRNA, whereas LGALS1 expression was almost absent in resting CD8+ T cells. LGALS1 expression could be induced in CD4+ and CD8+ T cells upon activation with the cognate peptide antigen and high levels of LGALS1 expression were found in concanavalin A-activated T cells but not in lipopolysaccharide-activated B cells. Gel filtration and Western blot analysis revealed that only monomeric betaGBP was released by activated CD8+ T cells and in vitro experiments further showed that recombinant betaGBP was able to inhibit antigen-induced proliferation of naive and antigen-experienced CD8+ T cells. Thus, these data indicate a role of betaGBP as an autocrine negative growth factor for CD8+ T cells.
A probabilistic model of information and retrieval: development and status (2021)

The paper combines a comprehensive account of the probabilistic model of retrieval with new systematic experiments on TREC Programme material. It presents the model from its foundations through its logical development to cover more aspects of retrieval data and a wider range of system functions. Each step in the argument is matched by comparative retrieval tests, to provide a single coherent account of a major line of research. The experiments demonstrate, for a large test collection, that the probabilistic model is effective and robust, and that it responds appropriately, with major improvements in performance, to key features of retrieval situations.
The hybrid PAX3-FKHR fusion protein of alveolar rhabdomyosarcoma transforms fibroblasts in culture. (1996)

Pediatric alveolar rhabdomyosarcoma is characterized by a chromosomal translocation that fuses parts of the PAX3 and FKHR genes. PAX3 codes for a transcriptional regulator that controls developmental programs, and FKHR codes for a forkhead-winged helix protein, also a likely transcription factor. The PAX3-FKHR fusion product retains the DNA binding domains of the PAX3 protein and the putative activator domain of the FKHR protein. The PAX3-FKHR protein has been shown to function as a transcriptional activator. Using the RCAS retroviral vector, we have introduced the PAX3-FKHR gene into chicken embryo fibroblasts. Expression of the PAX3-FKHR protein in these cells leads to transformation: the cells become enlarged, grow tightly packed and in multiple layers, and acquire the ability for anchorage-independent growth. This cellular transformation in vitro will facilitate studies on the mechanism of PAX3-FKHR-induced oncogenesis.
Characterization of 911: A New Helper Cell Line for the Titration and Propagation of Early Region 1-Deleted Adenoviral Vectors (1996)

Currently, the preferred host for the production of early region-1 (E1)-deleted recombinant adenoviruses (rAdV) is cell line 293, which was generated by transformation of human embryonic kidney cells by sheared adenovirus 5 (Ad5) DNA. To develop alternative hosts for the production of rAdV, we generated adenovirus-transformed human cell lines by transformation of human embryonic retinoblasts (HER) with a plasmid containing base pairs 79-5789 of the Ad5 genome. One of the established HER cell lines, which we called 911, exhibited favorable growth characteristics and was chosen for further study. This cell line is demonstrated to have several characteristics in common with the well-known 293 cell line: The 911 cell line is highly transfectable, and exhibits similar frequencies of homologous recombination. However, it has additional characteristics that make it a useful alternative for 293. The 911 cells perform particularly well in plaque assays. Upon infection with E1-deleted adenoviruses, plaques become apparent in monolayers of 911 cells already after 3-4 days versus 4-10 days in monolayers of 293 cells, thereby reducing the time required for quantitative plaque assays. Furthermore, yields of E1-deleted adenovirus vectors up to three times as high as those achieved with 293 cells can be obtained with 911 cells. Finally, the Ad5-DNA content of the 911 cell line is completely known. These features make the 911 cell line a useful alternative for the construction, propagation, and titration of E1-deleted recombinant adenoviruses.
Long-term Evaluation of Bilateral Fetal Nigral Transplantation in Parkinson Disease (1999)

Fetal nigral tissue can be transplanted into the postcommissural putamen bilaterally in patients with advanced PD safely and with little morbidity. In this open-label pilot study we observed consistent long-term clinical benefit and increased fluorodopa uptake on positron emission tomography. Clinical improvement appears to be related to the survival and function of transplanted fetal tissue.
Whole-Genome Genotyping on Bead Arrays (2009)

In this review, we describe the laboratory implementation of Infinium whole genome genotyping (WGG) technology for whole genome association studies and copy number studies. Briefly, the Infinium WGG assay employs a single tube whole genome amplification reaction to amplify the entire genome; genomic loci of interest are captured on an array by specific hybridization of picomolar concentrations amplified gDNA. After target capture, single nucleotide polymorphisms (SNPs) are genotyped on the array by a primer extension reaction using hapten-labeled nucleotides. The resultant hapten signal is amplified by immunhistochemical sandwich staining and the array is read out on a high resolution confocal scanner. We have combined this Infinium assay with high-density BeadChips to create the first array platform capable of genotyping over 1 million SNPs per slide. Additionally, the complete Infinium assay is automated using Tecan GenePaint slide processing system. Hybridization, washing, array-based primer extension and staining are performed directly in the Tecan capillary gap Te-Flow Through chambers. This automation process greatly increases assay robustness and throughput while enabling Laboratory Information Management System (LIMS) control of sample tracking. Finally, we give several examples of how this advance in genotyping technology is being applied in whole genome association and copy number studies.
Insulin Resistance — Mechanisms, Syndromes, and Implications (1991)

The past 20 years have witnessed a remarkable increase in our knowledge of the cellular and molecular mechanisms that underlie the diverse actions of insulin, the central hormone of metabolic regulation. Interest in the molecular details of insulin action has been heightened by the prevalence of insulin resistance and by the fact that insulin resistance has a key role in the pathogenesis of many disorders, including obesity, diabetes mellitus, ovarian hyperan-drogenism, and possibly hypertension. In this review, we discuss current concepts of the mechanisms of insulin action and insulin resistance and the implications of insulin resistance for a variety of . . .
Autoantibodies against the High-Affinity IgE Receptor as a Cause of Histamine Release in Chronic Urticaria (1993)

Histamine-releasing IgG autoantibodies against the alpha subunit of the high-affinity IgE receptor are present in the circulation of some patients with chronic urticaria. Autoantibody-induced cross-linking of IgE receptors may be an important mechanism in the pathogenesis of chronic urticaria and other diseases mediated by mast cells.
Spontaneous Mutations Restore the Viability of Tick-Borne Encephalitis Virus Mutants with Large Deletions in Protein C (2002)

The capsid protein, C, of tick-borne encephalitis virus has recently been found to tolerate deletions up to a length of 16 amino acid residues that partially removed the central hydrophobic domain, a sequence element conserved among flaviviruses which may be crucial for virion assembly. In this study, mutants with deletion lengths of 19, 21, 27, or 30 residues, removing more or all of this hydrophobic domain, were found to yield viable virus progeny, but this was without exception accompanied by the emergence of additional mutations within protein C. These point mutations or sequence duplications were located downstream of the engineered deletion and generally increased the hydrophobicity, suggesting that they may compensate for the loss of the central hydrophobic domain. Two of the second-site mutations, together with the corresponding deletion, were introduced into a wild-type genetic backbone, and the analysis of these "double mutants" provided direct evidence that the viability of the deletion mutant indeed depended on the presence of the second-site mutation. Our results corroborate the notion that hydrophobic interactions of protein C are essential for the assembly of infectious flavivirus particles but rule out the possibility that individual residues of the central hydrophobic domain are absolutely required for infectivity. Furthermore, the double mutants were found to be highly attenuated and capable of inducing a protective immune response in mice at even lower inoculation doses than the previously characterized 16-amino-acid-residue deletion mutant, suggesting that the combination of large deletions and second-site mutations may be a superior way to generate safe, attenuated flavivirus vaccine strains.
Clinicopathological Aspects of 542 Cases of Pancreatic Cancer: a Special Emphasis on Small Pancreatic Cancer (2007)

Small pancreatic cancers (longest diameter </=2 cm) have been regarded as preliminary to early pancreatic cancer, which was thought to be highly curable. During our experience since 1989, we evaluated 542 cases of pancreatic cancer. Among them we found 74 cases of tumors </=2 cm in diameter, small pancreatic cancer (TS1 pancreatic cancer). Well-differentiated adenocarcinomas (18.9%) and absence of symptoms (8.1%) were more frequent in patients with TS1 than in those with larger pancreatic tumors. Only 16 of the 74 patients (21.6%) with small pancreatic cancers had T1 tumors. According to the International Union Against Cancer (UICC) staging, only 11 patients (14.9%) were stage IA: their 5-yr survival rate was 23.3% and their median survival was 30.0 months. Among these 11 patients, 3 had tumors <1cm; their median survival time was 30.0 months and their 5-yr survival rate was 50.0%. These findings may indicate that 'small' pancreatic cancer is not equivalent to 'early' pancreatic cancer.
Spreading of methylation within RUNX3 CpG island in gastric cancer (2005)

RUNX3 is a novel tumor suppressor gene that is frequently silenced by promoter hypermethylation in gastric cancer. The methylation status of multiple regions within the RUNX3 promoter CpG island (3,478 bp) was examined in gastric cancer cell lines, primary gastric cancers and non-neoplastic gastric mucosa to clarify how methylation spreads within the CpG island. The critical regions for RUNX3 silencing were evaluated by analysis of cell lines. The most 5' region of the CpG island was methylated in 90% (9/10) of gastric cancer cell lines, 96% (43/45) of primary gastric cancers and in 96% (43/45) of non-neoplastic gastric mucosa. The frequencies of methylation were less near the transcription start site and were 40% (4/10) in cell lines, 53% (24/45) in primary gastric cancers and 11% (5/45) in non-neoplastic gastric mucosa, where methylation was proven to be critical for gene silencing. Thus, hypermethylation initially occurs at the most 5' region of the RUNX3 CpG island and spreads to the transcription start site before ultimately shutting down RUNX3 mRNA expression. The detection of hypermethylation at multiple regions within the RUNX3 CpG island may be useful in the diagnosis and risk assessment of gastric cancer.
Anti‐ICAM‐1 antibody reduces ischemic cell damage after transient middle cerebral artery occlusion in the rat (1994)

Intercellular adhesion molecule-1 (ICAM-1) is a glycoprotein expressed on endothelial cells that facilitates leukocyte adhesion. To test the hypothesis that reduction of leukocytes in an ischemic lesion reduces ischemic brain damage, we measured the effect of administration of an anti-ICAM-1 monoclonal antibody on ischemic brain damage after transient middle cerebral artery occlusion in the rat. ICAM-1 expression increased in the ischemic lesion, and the lesion volume was significantly reduced by 41% in the anti-ICAM-1 antibody group compared with the control group (p < 0.05). Numbers of polymorphonuclear leukocytes (PMNs) were significantly reduced in the cortices of the anti-ICAM-1 antibody group compared with the control animals (p < 0.05). Our data indicate that administration of anti-ICAM-1 antibody results in a significant reduction of ischemic brain damage concomitant with a reduction of PMNs in the lesion after transient focal cerebral ischemia in the rat.
Drug interactions with cyclosporine: Focus on antimicrobial agents (1992)

Unique pharmacokinetics and a narrow therapeutic range predispose cyclosporine to interactions with antimicrobial agents. Such interactions may occur through increased or decreased cyclosporine blood levels, or through enhanced nephrotoxicity. Ketoconazole and erythromycin have consistently been associated with elevated cyclosporine levels. While both ketoconazole and erythromycin inhibit hepatic cytochrome P450 enzymes, increased oral absorption of cyclosporine also contributes to the erythromycin‐cyclosporine interaction. Other antimicrobial agents that have been suggested to increase cyclosporine levels include fluconazole, itraconazole, josamycin, posinomycin, pristinamycin, roxithromycin, troleandomycin, norfloxacin and imipenem/cilastatin. On the other hand, coadministration of rifampin consistently results in reduced cyclosporine levels, which have led to allograft rejection in some patients. Nafcillin, intravenous sulphadimidine and imipenem/cilastatin have also been postulated to decrease cyclosporine levels. When these antimicrobial agents are used in conjunction with cyclosporine, cyclosporine levels should be monitored frequently. Aminoglycosides and amphotericin B are known nephrotoxins and have been shown to potentiate cyclosporine‐induced nephrotoxicity. Coadministration of ciprofloxacin or trimethoprim‐sulfamethoxazole with cyclosporine has also been implicated, in several reports, in increased renal damage. These antimicrobial agents should be used with cyclosporine only when therapeutic benefit outweighs the risk of enhanced nephrotoxicity.
THIS ARTICLE HAS BEEN RETRACTED Chronic cardiac allograft rejection in mice is alleviated by inhibition of CCR5 in combination with cyclosporine A (2008)

The chemokine receptor CCR5 plays important roles in acute allograft rejection. In this study, we examined the inhibition of CCR5 in combination with the treatment with cyclosporine A (CsA) in chronic rejection in cardiac transplantation. Forty-five transplant recipients were randomized to three groups. Recipients in group A were treated with anti-CCR5 mAb and CsA, mice in group B were given anti-CCR5 mAb alone, and animals in group C were administered with only CsA. On day 45 after transplantation, the allografts were harvested and examined by immunohistologic technique and PT-PCR methods. Allografts treated with anti-CCR5 mAb and CsA showed significantly prolonged survival (44.73 ± 0.258 days, P < 0.01) as compared with CsA-treated group (37.00 ± 2.04 days). Treatment with anti-CCR5 mAb plus CsA significantly inhibited the progression of cardiac allograft vasculopathy. Our findings demonstrated that anti-CCR5 mAb in combination with CsA can prolong the survival of allograft through their cardio-protective and immunomodulative properties. Thus, combined administration of anti-CCR5 mAb and CsA may become a new therapeutic approach for the prevention of cardiac graft failure that has not been obviated by conventional immunosuppressive agents.
Effective surgical treatment of the carotid sinus sindrome. (2009)

Elderly patients frequently suffer from dizziness and syncope; however, an underlying disease may not always be identified. Three patients aged 69, 71 and 56, respectively, experienced spells of dizziness and syncope. Massage of the carotid sinus demonstrated the presence of a carotid sinus syndrome (CSS), an abnormal baroreflex response of the carotid sinus that leads to asystole and extreme hypotension. Conventional treatment is generally by insertion of a pacemaker. These patients, however, were referred to the vascular surgery department of our hospital for removal of adventitial layers of proximal portions of the internal carotid artery. Recovery was uneventful; all three are now free of symptoms. CSS should be considered in the differential diagnosis of dizziness and syncope. Surgical denervation of the carotid artery is a valid treatment option, especially in the vasodepressive or mixed type of CSS.
Ab Initio Studies of [1,5]-H Shifts:  Pentadiene and Beyond (2000)

Ab initio calculations of the [1,5]-H shift in (3Z)-penta-1,3-diene and other substituted pentadienes and heteroanalogues using the hybrid density functional Becke3LYP with the 6-31G basis set are presented. Electron-donating substituents, such as methoxy in (3Z)-3-methoxypenta-1,3-diene 1, or heteroatoms such as a nitrogen atom in (Z)-ethylidenevinylamine 2, (1Z)-buta-1,3-dienylamine 3, (2Z)-but-2-enylideneamine 4, (Z)-allylidenemethylamine 5, and methylene-(Z)-propenylamine 6 are introduced. The electron-withdrawing fluoride is substituted for the hydrogen atoms in (3Z)-3-fluoropenta-1,3-diene 7, (3Z)-2,4-difluoropenta-1,3-diene 8, (3Z)-1,1',2,3,4,5,5'-heptafluoropenta- 1,3-diene 10, (1E,3E)-1,3,5-trifluoropenta-1,3-diene 11, and (1Z,3E)-1,3,5- trifluoropenta-1,3-diene 13. A detailed analysis of the geometries, energies, and electronic characteristics of the sigmatropic transposition compared to those of the unsubstituted case provides insights into substituent effects of this prototype of pericyclic reaction. The inductive and mesomeric effects of heteroatoms or heterosubstituents are of a great importance and in a continuous balance in the energetics of the transformation. Sterics can also play an important role due to the geometrical constraints of the reaction. As a general trend, decreasing the electron density of the phi system destabilizes the aromatic transition structure and increases the activation energy, and vice versa.
Status of liposomes as MR contrast agents (1993)

Recent work on the development of liposomal magnetic resonance (MR) contrast agents has yielded structures with higher overall relaxivity than that of other nanoparticles of similar diameter. Liposomes incorporating membrane-bound complexes of manganase ("memsomes") produce greater hepatic enhancement per micromole of metal ion than either ferrite particles or paramagnetic chelates. Memsomes also hold promise for targeting of sites outside the liver. Work is in progress to take these agents into clinical trials.
A new role for bicarbonate in mucus formation (2010)

The impact of small anions on the physical properties of gel-forming mucin has been almost overlooked relative to that of cations. Recently, based on the coincident abnormalities in HCO(3)(-) secretion and abnormal mucus formed in the hereditary disease cystic fibrosis (CF), HCO(3)(-) was hypothesized to be critical in the formation of normal mucus by virtue of its ability to sequester Ca(2+) from condensed mucins being discharged from cells. However, direct evidence of the impact of HCO(3)(-) on mucus properties is lacking. Herein, we demonstrate for the first time that mucin diffusivity (∼1/viscosity) increases as a function of [HCO(3)(-)]. Direct measurements of exocytosed mucin-swelling kinetics from airway cells showed that mucin diffusivity increases by ∼300% with 20 mM extracellular HCO(3)(-) concentration. Supporting data indicate that HCO(3)(-) reduces free Ca(2+) concentration and decreases the amount of Ca(2+) that remains associated with mucins. The results demonstrate that HCO(3)(-) enhances mucin swelling and hydration by reducing Ca(2+) cross-linking in mucins, thereby decreasing its viscosity and likely increasing its transportability. In addition, HCO(3)(-) can function as a Ca(2+) chelator like EGTA to disperse mucin aggregates. This study indicates that poor HCO(3)(-) availability in CF may explain why secreted mucus remains aggregated and more viscous in affected organs. These insights bear on not only the fundamental pathogenesis in CF, but also on the process of gel mucus formation and release in general.
Comparison of the temporary diagnostic relief of transforaminal epidural steroid injection approaches: conventional versus posterolateral technique. (2007)

Our findings suggest that the posterolateral approach is an alternative method for TFESI in cases where needle tip positioning in the anterior epidural space is difficult.
Parallel Cache Model Based on Grid Memory (2007)

For supporting the concurrent access for the hot segments of large files during the peak access phase in Internet, a parallel cache model based on the grid memory (PCMGM) was proposed in this paper. By using of the free memories of the idle computers in dynamic network environment (DNE) composed of multi-clusters, the grid memory was constructed. Through the division technique for large files, basing the ability of idle computer, and adopting the multiagent, we discussed the load balance allotting approach for grid memory. The PCMGM access process is described. The experiment results show that PCMGM resolves effectively the problems of peak access for hot segments and it can improve the use rate of resources in DNE. It can be applied for grid computing and VOD for hot segment.