gebhart/patrepeval huggingface dataset:
Manipulation of Types of Fats and Cholesterol Intake Can Successfully Improve the Lipid Profile While Maintaining the Efficacy of the Ketogenic Diet (2009)

The ketogenic diet (KD) is a dietary therapy that effectively treats intractable epilepsy in children. Hyperlipidemias are common side effects of KD and have been reported in approximately 30% to 50% of patients on this diet. Fats comprise 90% of the calories, and saturated fats are often used as 50% of the fat intake. The purpose of this study was to investigate whether alterations of the dietary fat sources can improve the lipid profiles while maintaining seizure control in the ketogenic diet. Using a retrospective chart review, the authors evaluated their practices of treating hyperlipidemias in 6 children on the KD who developed elevated lipid profiles. All had normal or mildly elevated lipid profiles before beginning the KD. The elevated lipid levels were detected after an average of 7 months of KD treatment. Changing the dietary fat types to mainly oils (polyunsaturated fats) and decreasing the use of protein foods high in saturated fats and cholesterol resulted in a normalized or baseline lipid profile in all 3 months later. Seizure control was unaffected. Hyperlipidemia is not a cause for discontinuing the KD and can be managed by changing the dietary fat sources.
miRNA deregulation by epigenetic silencing disrupts suppression of the oncogene PLAG1 in chronic lymphocytic leukemia (2009)

MicroRNAs (miRNA) play a key role in cellular regulation and, if deregulated, in the development of neoplastic disorders including chronic lymphocytic leukemia (CLL). RNAs from primary cells of 50 treatment-naive CLL patients and peripheral B cells of 14 healthy donors were applied to miRNA expression profiling using bead chip technology. In CLL cells, a set of 7 up- and 19 down-regulated miRNAs was identified. Among the miRNAs down-regulated in CLL cells, 6 of 10 miRNA promoters examined showed gain of methylation compared with normal B-cell controls. Subsequent target prediction of deregulated miRNAs revealed a highly significant binding prediction at the 3' untranslated region of the pleomorphic adenoma gene 1 (PLAG1) oncogene. Luciferase reporter assays including site-directed mutagenesis of binding sites revealed a significant regulation of PLAG1 by miR-181a, miR-181b, miR-107, and miR-424. Although expression of PLAG1 mRNA was not affected, PLAG1 protein expression was shown to be significantly elevated in CLL cells compared with the levels in healthy donor B cells. In summary, we could demonstrate disruption of miRNA-mediated translational control, partly due to epigenetic transcriptional silencing of miRNAs, with subsequent overexpression of the oncogenic transcription factor PLAG1 as a putative novel mechanism of CLL pathogenesis.
Secondary Malignancies Following Cancer Chemotherapy (1994)

Many agents used in cancer chemotherapy are known carcinogens. However, few secondary malignancies have been definitely linked to chemotherapy, since studies on this problem are complicated by methodological problems. A causal relationship has been established between alkylating agents and leukaemia and between cyclophosphamide and bladder cancer. The risk of leukaemia peaks at 5-10 years after beginning of chemotherapy and declines steadily after its end. The interaction between chemotherapy and radiotherapy has not been fully clarified, nor has the leukaemogenic potency of individual drugs, although combinations without nitrogen mustard seem to entail a lower risk. Other tumours reported at increased incidence, in particular among Hodgkin's disease patients, for whom a carcinogenic effect of chemotherapy seems plausible, are non-Hodgkin's lymphoma and lung cancer. Other secondary solid tumors have also been reported, but for none of them an independent effect of chemotherapy has been demonstrated.
p97: An Emerging Target for Cancer, Neurodegenerative Diseases, and Viral Infections (2019)

The AAA+ ATPase, p97, also referred to as VCP, plays an essential role in cellular homeostasis by regulating endoplasmic reticulum-associated degradation (ERAD), mitochondrial-associated degradation (MAD), chromatin-associated degradation, autophagy, and endosomal trafficking. Mutations in p97 have been linked to a number of neurodegenerative diseases, and overexpression of wild type p97 is observed in numerous cancers. Furthermore, p97 activity has been shown to be essential for the replication of certain viruses, including poliovirus, herpes simplex virus (HSV), cytomegalovirus (CMV), and influenza. Taken together, these observations highlight the potential for targeting p97 as a therapeutic approach in neurodegeneration, cancer, and certain infectious diseases. This Perspective reviews recent advances in the discovery of small molecule inhibitors of p97, their optimization and characterization, and therapeutic potential.
Automatic Optimization of In-Flight Memory Transactions for GPU Accelerators Based on a Domain-Specific Language for Medical Imaging (2012)

An efficient memory bandwidth utilization for GPU accelerators is crucial for memory bound applications. In medical imaging, the performance of many kernels is limited by the available memory bandwidth since only a few operations are performed per pixel. For such kernels only a fraction of the compute power provided by GPU accelerators can be exploited and performance is predetermined by memory bandwidth. As a remedy, this paper investigates the optimal utilization of available memory bandwidth by means of increasing in-flight memory transactions. Instead of doing this manually for different GPU accelerators, the required CUDA and OpenCL code is automatically generated from descriptions in a Domain-Specific Language (DSL) for the considered application domain. Moreover, the DSL is extended to also support global reduction operators. We show that the generated target-specific code improves bandwidth utilization for memory-bound kernels significantly. Moreover, competitive performance compared to the GPU back end of the widely used image processing library OpenCV can be achieved.
A Cholesterol Tag at the N Terminus of the Relatively Broad-Spectrum Fusion Inhibitory Peptide Targets an Earlier Stage of Fusion Glycoprotein Activation and Increases the Peptide's Antiviral Potency <i>In Vivo</i> (2013)

In previous work, we designed peptides that showed potent inhibition of Newcastle disease virus (NDV) and infectious bronchitis virus (IBV) infections in chicken embryos. In this study, we demonstrate that peptides modified with cholesterol or 3 U of polyethylene glycol (PEG3) conjugated to the peptides' N termini showed even more promising antiviral activities when tested in animal models. Both cholesterol- and cholesterol-PEG3-tagged peptides were able to protect chicken embryos from infection with different serotypes of NDV and IBV when administered 12 h prior to virus inoculation. In comparison, the untagged peptides required intervention closer to the time of viral inoculation to achieve a similar level of protection. Intramuscular injection of cholesterol-tagged peptide at 1.6 mg/kg 1 day before virus infection and then three times at 3-day intervals after viral inoculation protected 70% of the chickens from NDV infection. We further demonstrate that the cholesterol-tagged peptide has an in vivo half-life greater than that of untagged peptides. It also has the potential to cross the blood-brain barrier to enter the avian central nervous system (CNS). Finally, we show that the cholesterol-tagged peptide could play a role before the viral fusion peptide's insertion into the host cell and thereby target an earlier stage of fusion glycoprotein activation. Our findings are of importance for the further development of antivirals with broad-spectrum protective effects.
Performance of Feral and Cry1Ac-Selected Helicoverpa zea (Lepidoptera: Noctuidae) Strains on Transgenic Cottons Expressing One or Two Bacillus thuringiensis ssp. kurstaki Proteins Under Greenhouse Conditions (2004)

Efficacy of Bollgard (DP50B) and Bollgard II (DP50BX) cottons that express either one or two Bacillus thuringiensis Berliner proteins, respectively, along with the conventional sister genotype (DP50), was determined for a feral strain of bollworm, Helicoverpa zea (Boddie), and a Cry1Ac-selected bollworm strain in 1999. In 2000, a greenhouse study was designed to compare the efficacy of three transgenic cottons expressing either the Cry1Ac endotoxin alone (DP50B), the Cry2Ab endotoxin alone (DP50X), or both the CrylAc and Cry2Ab endotoxins (DP50BX) against a feral and a Cry1Ac-selected bollworm strain. Results from the 1999 greenhouse study evaluating both a feral and a Cry1Ac-selected bollworm strain demonstrated that when averaged across bollworm strains, the Bollgard II genotype significantly reduced larval survival and fruit penetration by bollworm compared to the Bollgard variety. Also, the Cry1Ac-selected bollworm strain displayed increased larval survival, superficial fruit damage, and fruit penetration compared to the feral strain when averaged across genotypes. In the 2000 study, the Bollgard II genotype significantly reduced fruit penetration by bollworm below that of the Bollgard variety when averaged across strains; however, the single Cry2Ab-producing genotype performed similarly to both Bollgard and Bollgard II with respect to fruit penetration. The Cry1Ac-selected bollworm strain exhibited significantly greater larval survival and superficial fruit damage on the Bollgard variety compared to the feral strain, but no differences among larval strains were evident for other genotypes. Also, when averaged across genotypes, the Cry1Ac-selected bollworm strain penetrated a higher proportion of cotton fruit compared to the feral strain. These results suggest that commercialization of Bollgard II cottons would significantly reduce bollworm survival and damage compared to that experienced by current Bollgard varieties. Bollgard II plantings also should have a positive impact on Bt resistance management of bollworm.
Purification and characterization of sheep platelet cyclo-oxygenase Acetylation by aspirin prevents haemin binding to the enzyme (1986)

Arachidonate cyclo-oxygenase (prostaglandin synthetase; prostaglandin endoperoxide synthetase; EC 1.14.99.1) was purified from sheep platelets. The purification procedure involved hydrophobic column chromatography using either Ibuprofen-Sepharose, phenyl-Sepharose or arachidic acid-Sepharose as the first step followed by metal-chelate Sepharose and haemin-Sepharose affinity chromatography. The purified enzyme (Mr approximately 65,000) was homogeneous as observed by SDS/polyacrylamide-gel electrophoresis and silver staining. The enzyme was a glycoprotein with mannose as the neutral sugar. Haemin or haemoglobin was essential for activity. The purified enzyme could bind haemin exhibiting a characteristic absorption maximum at 410 nm. The enzyme after metal-chelate column chromatography could undergo acetylation by [acetyl-3H]aspirin. The labelled acetylated enzyme could not bind to haemin-Sepharose, presumably due to acetylation of a serine residue involved in the binding to haemin. The acetylated enzyme also failed to show its characteristic absorption maximum at 410 nm when allowed to bind haemin.
Natural History of Chronic Hepatitis B Virus Infection in Taiwan: Studies of Hepatitis B Virus Dna in Serum (1985)

Hepatitis B virus DNA (HBV DNA) in serum was measured by a Spot hybridization technique in a consecutive series of 79 cases with chronic HBV infection from Taiwan. HBV DNA was found in 96.3% (52/54) of HBeAg-positive, 66% (2/3) with neither HBeAg or anti-HBe and in 63.6% (14/22) of anti-HBe positive patients. The levels of HBV DNA in the HBe-Ag-positive patients were significantly higher than in the anti-HBe positive patients (median, 944 vs. 58 pg per ml, p less than 0.001). The mean ages increased from 28.7 years for the cases with high levels of HBV DNA, to 34.7 years for those with low levels (p less than 0.01) and to 41.0 years in those without HBV DNA in serum (p less than 0.05 when compared with those with low level of HBV DNA). Ninety per cent of patients (27/30) with high levels of HBV DNA showed only minor hepatic inflammatory activity, as did 91% (10/11) of those without HBV DNA. In contrast, histologic signs of chronic active hepatitis or chronic lobular hepatitis were demonstrated in 76% of cases (29/38) with low levels of HBV DNA. These data are consistent with the hypothesis that liver damage occurs during the period of clearance of hepatocytes supporting HBV replication, and are inconsistent with the view that HBV may be directly cytopathic. Thus, the natural history of chronic HBV infection may be divided into three phases.(ABSTRACT TRUNCATED AT 250 WORDS)
A new gasoline injector with exhaust gas recirculation (2008)

A new injector is presented for improving the gasoline spray and combustion by utilizing the exhaust gases. This new gasoline injector has two magnetic coils attracting two armatures correspondingly, one controlling the pressurized exhaust gases, and another operating the gasoline. The exhaust gases mix with the gasoline at the tip of injector in order to promote the fuel atomization. Furthermore, these exhaust gases from the injector exist inside the fuel spray field basically so as to improve the gasoline combustion and lower its emissions. This new gasoline injector with exhaust gas recirculation is designed and simulated by computing the fuel injection velocity, nozzle pressure and fuel injection mass changing with time. The computational results show that the injection time and fuel mass can be controlled if the switching time of magnetic valves is set precisely. Finally, more researches must be accomplished to understand this new injector.
Molecular Structures and Dynamics of the Stepwise Activation Mechanism of a Matrix Metalloproteinase Zymogen:  Challenging the Cysteine Switch Dogma (2007)

Activation of matrix metalloproteinase zymogen (pro-MMP) is a vital homeostatic process, yet its molecular basis remains unresolved. Using stopped-flow X-ray spectroscopy of the active site zinc ion, we determined the temporal sequence of pro-MMP-9 activation catalyzed by tissue kallikrein protease in milliseconds to several minutes. The identity of three intermediates seen by X-ray spectroscopy was corroborated by molecular dynamics simulations and quantum mechanics/molecular mechanics calculations. The cysteine-zinc interaction that maintains enzyme latency is disrupted via active-site proton transfers that mediate transient metal-protein coordination events and eventual binding of water. Unexpectedly, these events ensue as a direct result of complexation of pro-MMP-9 and kallikrein and occur before proteolysis and eventual dissociation of the pro-peptide from the catalytic site. Here we demonstrate the synergism among long-range protein conformational transitions, local structural rearrangements, and fine atomic events in the process of zymogen activation.
Phase Behavior of EVAL Polymers in Water-2-Propanol Cosolvent (1998)

Isothermal phase diagrams for semicrystalline poly(ethylene-co-vinyl alcohol) (EVAL) using two nonsolvents (water and 2-propanol) serving as a cosolvent system have been determined. The locations of the liquid−liquid demixing and the crystallization-induced gelation in the phase diagrams at 60 °C were identified. Attempts were made to correlate the experimental findings with predictions on the basis of the modified Flory−Huggins theory for ternary solutions using three binary interaction parameters (χij) and one ternary interaction parameter (χT). No good agreement was found between the theoretical predictions and experimentally obtained data if the ternary interaction parameter was neglected. But an improvement can be obtained when a ternary interaction parameter is considered. The optimum value has been found to be approximately −1.7 + 0.5φ2 + 1.0φ3. Therefore, it is necessary to introduce the ternary interaction parameter when the binary parameters provide an inadequate description of phase behavior, but in most systems studied so far the ternary interaction parameter is ignored.
Identification and Characterization of a Retinoic Acid-regulated Human Homologue of the unc-33-like Phosphoprotein Gene (hUlip) from Neuroblastoma Cells (1997)

A cDNA, 7G1, was isolated from retinoic acid (RA) differentiated neuroblastoma cells whose expression was high in human fetal brain and spinal cord mRNA but undetectable in adult brain or non-neuronal tissues. Sequence analysis indicates that 7G1 is homologous to the Caenorhabditis elegans gene unc-33. A 5.5-kilobase pair full-length cDNA from a human fetal brain cDNA library contains an 1710-base pair open reading frame. Because the predicted 570 amino acid sequence of 7G1 shares 98% identity with the murine Ulip gene product, an unc-33-like-phosphoprotein, we refer to 7G1 as the human Ulip (hUlip). hUlip is also similar to the bacterial enzyme D-hydantoinase and the recently described vertebrate gene products CRMP62, TOAD-64, CRMP1, CRMP2, and mUNC. RA stimulates an increase in hUlip mRNA that is transcriptionally regulated. RA stimulates an increase in polypeptides of 58, 60, 65, and 70 kDa with the 58- and 65-kDa species being dephosphorylated forms of the 60- and 70-kDa species. This study presents a model in which to study the regulation and expression of the hUlip gene, a member of an emerging family of molecules that potentially mediates signals involved in axonal outgrowth.
Bacterial tyrosine kinases: evolution, biological function and structural insights (2012)

Reversible protein phosphorylation is a major mechanism in the regulation of fundamental signalling events in all living organisms. Bacteria have been shown to possess a versatile repertoire of protein kinases, including histidine and aspartic acid kinases, serine/threonine kinases, and more recently tyrosine and arginine kinases. Tyrosine phosphorylation is today recognized as a key regulatory device of bacterial physiology, linked to exopolysaccharide production, virulence, stress response and DNA metabolism. However, bacteria have evolved tyrosine kinases that share no resemblance with their eukaryotic counterparts and are unique in exploiting the ATP/GTP-binding Walker motif to catalyse autophosphorylation and substrate phosphorylation on tyrosine. These enzymes, named BY-kinases (for Bacterial tYrosine kinases), have been identified in a majority of sequenced bacterial genomes, and to date no orthologues have been found in Eukarya. The aim of this review was to present the most recent knowledge about BY-kinases by focusing primarily on their evolutionary origin, structural and functional aspects, and emerging regulatory potential based on recent bacterial phosphoproteomic studies.
NMR chemical shift of xenon-129 dissolved in polymers (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNMR chemical shift of xenon-129 dissolved in polymersJ. B. Miller, J. H. Walton, and C. M. RolandCite this: Macromolecules 1993, 26, 21, 5602–5610Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://doi.org/10.1021/ma00073a011RIGHTS & PERMISSIONSArticle Views185Altmetric-Citations35LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
Clonogen Content of Intestinal Crypts: Its Deduction Using a Microcolony Assay on Whole Mount Preparations and Its Dependence on Radiation Dose (1994)

A new method for detecting surviving intestinal microcolonies in whole mount preparations is presented. This approach is not subject to the sampling problems encountered with microcolony assay using data from tissue sections, associated with the size of the microcolonies and the random nature of the sections in relation to these colonies. This new method has been used to determine the crypt survival after one or two fractions of gamma-irradiation, and hence to estimate the crypt clonogen number. The survival levels are similar using the two techniques and similar estimates for the number of clonogens per crypt are obtained. The results using this novel approach thus confirm the validity of the traditional approaches using sections. The estimates of initial clonogen number per crypt show a dependence on the size of dose used to estimate the number, and the estimates range from about eight clonogens per crypt for doses between 7 and 8 Gy, to about 40 clonogens per crypt for doses between 9 and 10 Gy.
Sulfines (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSulfinesWilliam A. Sheppard and Jurgen. DiekmannCite this: J. Am. Chem. Soc. 1964, 86, 9, 1891–1892Publication Date (Print):May 5, 1964Publication History Published online1 May 2002Published inissue 5 May 1964https://pubs.acs.org/doi/10.1021/ja01063a075https://doi.org/10.1021/ja01063a075research-articleACS PublicationsRequest reuse permissionsArticle Views253Altmetric-Citations65LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Dynamic Modelling of Thermal Shock (2005)

When a spacecraft's orbit passes through the earth's shadow, known as an eclipse, temperature changes arise in the vehicle. These thermal gradients can cause components to deform from their nominal position. For satellites with appendages that are sensitive to thermal changes, the deformations can be very rapid. As a result, angular momentum is transferred between the spacecraft body and the moving appendages. Thus, pointing errors occur. Several spacecraft have experienced this while in orbit and, depending upon their requirements and geometry, the errors range from being tolerable to unacceptable. The phenomena is called thermal shock and an alternative dynamic modelling strategy for the physical disturbance is presented herein. The model varies in complexity and integrity from conventional modelling techniques. However, the alternative model yields similar results, despite the differences in fidelity, compared to the more complex models. The strengths and weaknesses of the models are discussed. In particular, those factors which influence the choice of a model for a specific analysis or design problem are discussed.