gebhart/patrepeval huggingface dataset:
Resistant starch and arabinoxylan augment SCFA absorption, but affect postprandial glucose and insulin responses differently (2014)

The effects of increased colonic fermentation of dietary fibres (DF) on the net portal flux (NPF) of carbohydrate-derived metabolites (glucose, SCFA and, especially, butyrate), hormones (insulin, C-peptide, glucagon-like peptide 1 and glucose-dependent insulinotropic peptide) and NEFA were studied in a healthy catheterised pig model. A total of six pigs weighing 59 (SEM 1·6) kg were fitted with catheters in the mesenteric artery and in the portal and hepatic veins, and a flow probe around the portal vein, and included in a double 3 × 3 cross-over design with three daily feedings (at 09.00, 14.00 and 19.00 hours). Fasting and 5 h postprandial blood samples were collected after 7 d adaptation to each diet. The pigs were fed a low-DF Western-style control diet (WSD) and two high-DF diets (an arabinoxylan-enriched diet (AXD) and a resistant starch-enriched diet (RSD)). The NPF of insulin was lower (P= 0·04) in AXD-fed pigs (4·6 nmol/h) than in RSD-fed pigs (10·5 nmol/h), despite the lowest NPF of glucose being observed in RSD-fed pigs (203 mmol/h, P= 0·02). The NPF of total SCFA, acetate, propionate and butyrate were high, intermediate and low (P< 0·01) in AXD-, RSD- and WSD-fed pigs, respectively, with the largest relative increase being observed for butyrate in response to arabinoxylan supplementation. In conclusion, the RSD and AXD had different effects on the NPF of insulin and glucose, suggesting different impacts of arabinoxylan and resistant starch on human health.
Developmental expression of murine β-trace in embryos and adult animals suggests a function in maturation and maintenance of blood-tissue barriers (1996)

The complete cDNA for murine Beta-trace protein was isolated by RT-PCR using degenerate primers designed according to amino acid sequences derived from tryptic peptides. It encodes a protein of 165 amino acids (calculated molecular weight 18,472 Da) with a predicted 24-amino-acid leader peptide. In situ analyses during mouse embryonic development and in adult animals revealed a specific temporal expression pattern of Beta-trace. Beta-Trace mRNA was initially detected at 14.5 days postconception in mesenchymal cells destined to become leptomeninges and in the developing testis. Later in development, a lower level of expression was additionally observed in choroid plexus epithelium, in strictly confined regions of the eye (pigment and ciliary epithelium), in the ear (cochlear duct), and within single cells in the brain. Expression was also found in epithelia of the epididymis and the testis Leydig cells of postpubertal animals. The highly specific expression at blood-tissue barriers such as the blood-cerebrospinal fluid, blood-retina blood-aqueous humor, and blood-testis barriers indicates a potential role for this lipocalin in transport and/or in maturation and maintenance of these barriers.
Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers (2011)

Relaxation of a self-assembled structure of 144 peptide amphiphile (PA) molecules into cylindrical nanofibers is studied using atomistic molecular dynamics simulations including explicit water with physiological ion concentration. The PA for these studies includes a hydrophobic alkyl chain that is attached to the N-terminus of the sequence SLSLAAAEIKVAV. The self-assembly is initiated with PA molecules in a roughly cylindrical configuration, as suggested from previous experimental and theoretical investigations, and the cylindrical configuration that results is found to be stable during 40 ns simulations. In the converged structure of the resulting nanofiber, the cylinder radius is ∼44 Å, a result that is consistent with experimental results. Water and sodium ions can penetrate into the peptide portion of the fiber but not between the alkyl chains. Even though each PA has an identical sequence, a broad distribution of secondary structure is found in the converged structure of the nanofiber. The β-sheet population for the SLSL and IKV segments of the peptide is ∼25%, which is consistent with previous circular dichroism results. We also found that the epitope sequence IKVAV is located on the surface of the nanofiber, as designed for the promotion of the neurite growth. Our findings will be useful for designing new PA fibers that have improved bioactive properties.
Fingerprinting of Cyanobacteria Based on PCR with Primers Derived from Short and Long Tandemly Repeated Repetitive Sequences (1998)

The presence of repeated DNA (short tandemly repeated repetitive [STRR] and long tandemly repeated repetitive [LTRR]) sequences in the genome of cyanobacteria was used to generate a fingerprint method for symbiotic and free-living isolates. Primers corresponding to the STRR and LTRR sequences were used in the PCR, resulting in a method which generate specific fingerprints for individual isolates. The method was useful both with purified DNA and with intact cyanobacterial filaments or cells as templates for the PCR. Twenty-three Nostoc isolates from a total of 35 were symbiotic isolates from the angiosperm Gunnera species, including isolates from the same Gunnera species as well as from different species. The results show a genetic similarity among isolates from different Gunnera species as well as a genetic heterogeneity among isolates from the same Gunnera species. Isolates which have been postulated to be closely related or identical revealed similar results by the PCR method, indicating that the technique is useful for clustering of even closely related strains. The method was applied to nonheterocystus cyanobacteria from which a fingerprint pattern was obtained.
An Analysis of South Korea's Import Demand (2002)

This article, applying Johansen multivariate cointegration analysis and error correction modeling techniques, analyses the relationship between Korean imports and the components of final demand expenditure and relative prices. Firstly, the major determinants of import demand in the long run are found to be relative price, final consumption expenditure and export demand with elasticities -0.6, 1.04 and 0.49 respectively. Secondly, in the case of import demand specification with disaggregated income variable, final consumption expenditure, relative price and capacity utilization are found to Granger-cause import demand in the short run. Thirdly, the different estimation results between the components basis and aggregation basis imply the traditional estimation can cause an aggregation bias.
Managing professional and personal sensitive information (2010)

All organizations have to manage sensitive information related to their business operations. Unfortunately, universities have the added challenge of not only managing administrative and academic sensitive information, but often times the personal sensitive information of students and employees. This study reflects on the current best practices in managing sensitive information and discusses how Youngstown State University implements controls for sensitive information.
NF-&#954;B in Human Disease: Current Inhibitors and Prospects for De Novo Structure Based Design of Inhibitors (2005)

Nuclear-Factor kappa B (NF-kappaB) is an inducible transcription factor of the Rel family, sequestered in the cytoplasm by the IkappaB family of proteins. NF-kappaB exists in several dimeric forms, but the p50/p65 heterodimer is the predominant one. Activation of NF-kappaB by a range of physical, chemical, and biological stimuli leads to phosphorylation and proteasome dependent degradation of IkappaB, leading to the release of free NF-kappaB. This free NF-kappaB then binds to its target sites (kappaB sites in the DNA), to initiate transcription. This transcription has been known to be involved in a number of diseases including cancer, AIDS, and inflammatory disorders. The present article focuses on two important issues of current and future interest- firstly a review of the main human diseases which are initiated due to NF-kappaB mediated transcription is presented. Next, comprehensive information on the current inhibitors which are targeted to interfere with the NF-kappaB pathway is provided. This latter section presents a critical review on different types of latest inhibitors targeting the complex NF-kappaB pathway at several stages. The inhibitors developed till date and still under investigation, include mainly those which interfere with the activation of NF-kappaB. Based on the complexity of NF-kappaB activation, and the current knowledge of the structural biology of NF-kappaB-DNA binding, finally it is proposed that a better approach to inhibit NF-kappaB induced transcription exists. In this context, a perspective is presented in the end, proposing de novo design of inhibitors which directly interact with the DNA Binding region of the free NF-kappaB (p50 subunit), so as to generate more specific and selective leads of NF-kappaB-DNA binding.
Towards the design, analysis, and illustration of assemblies (1997)

This document presents an integrated approach for helping designers specify, revise, analyze, and illustrate assemblies of mechanical parts within the context of a common data structure and set of assembly features. An implementation to test the validity of these ideas has been integrated into an existing spline-based geometric modeling system.
There were several distinct facets to this research effort. Methodology for assembly planning was explored to allow a user to lay out the assembly in a diagrammatic form, before creating any geometry. A rough design, laid out initially, can gradually be refined, and the individual components can be designed and edited later using spline-based geometric modeling operations. Research into assembly specification examined how best to allow the user to describe the way parts are actually connected together to form subassemblies and eventually the final product. Also considered were questions of part interference and part removability in order to help the user evaluate the utility and manufacturability of the design. Finally, exploded view illustration was explored, with a view toward enabling the user to create clear and informative exploded views of the assembly with minimal intervention. Throughout, information obtained in earlier stages of design was useful in helping to automate later design steps.
During the course of this project, I developed a representation of an assembly convenient for handling multiple assembly-related tasks, addressed the special problems of interactive assembly design by introducing new constructs for specifying assembly information, explored the usefulness of interactive interference detection techniques, and considered artistic issues, such as good ways to arrange exploded parts in an illustration, as part of creating a practical application.
Cloning and expression of the H chain V region of antibody OVB3 that reacts with human ovarian cancer. (1988)

Hybridoma OVB3 produces an antibody (IgG2b kappa) that reacts with an Ag present on the surface of almost all human ovarian carcinomas. An EcoRI fragment of genomic DNA containing the rearranged H chain V region of monoclonal OVB3 was cloned from a lambda gtWES library and then sub-cloned into a pGEM4 vector. To show that the cloned DNA sequence did encode the V region of a functional antibody, the DNA fragment was inserted into plasmid pSV-VNP gamma SNase in place of VNp to produce pSV-VOVB3 gamma SNase. This plasmid was then transfected into variant OVB3 hybridoma cells, which no longer produced the H chain of antibody OVB3, and functional antibody was secreted by the recipient cells. The recombinant chimeric antibody bound to ovarian cancer cells and contained Staphylococcus aureus nuclease activity, proving that a functional V region gene had been cloned.
Phase I/II Study of the Mammalian Target of Rapamycin Inhibitor Everolimus (RAD001) in Patients with Relapsed or Refractory Hematologic Malignancies (2006)

Everolimus is well tolerated at a daily dose of 10 mg daily and may have activity in patients with myelodysplastic syndrome. Studies of everolimus in combination with therapeutic agents directed against other components of the phosphatidylinositol 3-kinase/Akt/mTOR pathway are warranted.
In-depth Proteomic Analysis of Nonsmall Cell Lung Cancer to Discover Molecular Targets and Candidate Biomarkers (2012)

Advances in proteomic analysis of human samples are driving critical aspects of biomarker discovery and the identification of molecular pathways involved in disease etiology. Toward that end, in this report we are the first to use a standardized shotgun proteomic analysis method for in-depth tissue protein profiling of the two major subtypes of nonsmall cell lung cancer and normal lung tissues. We identified 3621 proteins from the analysis of pooled human samples of squamous cell carcinoma, adenocarcinoma, and control specimens. In addition to proteins previously shown to be implicated in lung cancer, we have identified new pathways and multiple new differentially expressed proteins of potential interest as therapeutic targets or diagnostic biomarkers, including some that were not identified by transcriptome profiling. Up-regulation of these proteins was confirmed by multiple reaction monitoring mass spectrometry. A subset of these proteins was found to be detectable and differentially present in the peripheral blood of cases and matched controls. Label-free shotgun proteomic analysis allows definition of lung tumor proteomes, identification of biomarker candidates, and potential targets for therapy.
Histone 3 Lysine 9 Trimethylation Is Differentially Associated With Isocitrate Dehydrogenase Mutations in Oligodendrogliomas and High-Grade Astrocytomas (2013)

Trimethylation of histone 3 lysine 9 (H3K9me3) is a marker of repressed transcription. Cells transfected with mutant isocitrate dehydrogenase (IDH) show increased methylation of histone lysine residues, including H3K9me3, because of inhibition of histone demethylases by 2-hydroxyglutarate. Here, we evaluated H3K9me3 and its association with IDH mutations in 284 gliomas. Trimethylation of H3K9 was significantly associated with IDH mutations in oligodendrogliomas. Moreover, 72% of World Health Organization grade II and 65% of grade III oligodendrogliomas showed combined H3K9me3 positivity and 1p19q codeletion. In astrocytic tumors, H3K9me3 positivity was found in all grades of tumors; it showed a significant relationship with IDH mutational status in grade II astrocytomas but not in grade III astrocytomas or glioblastomas. Finally, H3K9me3-positive grade II oligodendrogliomas, but not other tumor subtypes, showed improved overall survival compared with H3K9me3-negative cases. These results suggest that repressive trimethylation of H3K9 in gliomas may occur in a context-dependent manner and is associated with IDH mutations in oligodendrogliomas but may be differently regulated in high-grade astrocytic tumors. Furthermore, H3K9me3 may define a subset of grade II oligodendrogliomas with better overall survival. Our results suggest variable roles for IDH mutations in the pathogenesis of oligodendrogliomas versus astrocytic tumors.
FlashTier (2012)

The availability of high-speed solid-state storage has introduced a new tier into the storage hierarchy. Low-latency and high-IOPS solid-state drives (SSDs) cache data in front of high-capacity disks. However, most existing SSDs are designed to be a drop-in disk replacement, and hence are mismatched for use as a cache.
Cochlear gene therapy with ancestral AAV in adult mice: complete transduction of inner hair cells without cochlear dysfunction (2017)

The use of viral vectors for inner ear gene therapy is receiving increased attention for treatment of genetic hearing disorders. Most animal studies to date have injected viral suspensions into neonatal ears, via the round window membrane. Achieving transduction of hair cells, or sensory neurons, throughout the cochlea has proven difficult, and no studies have been able to efficiently transduce sensory cells in adult ears while maintaining normal cochlear function. Here, we show, for the first time, successful transduction of all inner hair cells and the majority of outer hair cells in an adult cochlea via virus injection into the posterior semicircular canal. We used a "designer" AAV, AAV2/Anc80L65, in which the main capsid proteins approximate the ancestral sequence state of AAV1, 2, 8, and 9. Our injections also transduced ~10% of spiral ganglion cells and a much larger fraction of their satellite cells. In the vestibular sensory epithelia, the virus transduced large numbers of hair cells and virtually all the supporting cells, along with close to half of the vestibular ganglion cells. We conclude that this viral vector and this delivery route hold great promise for gene therapy applications in both cochlear and vestibular sense organs.
Clozapine treatment of psychosis in patients with tardive dystonia: Report of three cases (1994)

Among the tardive dyskinesia syndromes, dystonia can be the most difficult to treat. It may be severe to the point of being disabling, yet the patients may require antipsychotic medications for an even more disabling psychosis. Clozapine, an atypical neuroleptic drug that lacks extrapyramidal effects, may be the drug of choice for such patients. This report describes three patients with significant dystonia, previously disabled by their psychoses, who have been successfully managed with clozapine plus other agents for > 3 years.
[Can chronic hepatitis B patients overcome resistance to antiviral therapy due to production of antibodies to recombinant alpha-2-interferon?]. (1995)

Virologic screening helped single out a group of 25 patients with chronic hepatitis B not responding to antiviral therapy with recombinant interferon, with persistence of HBeAg and HBV DNA in the blood sera. Enzyme immunoassay revealed in 7 of them antibodies to alpha 2-interferon (anti-IF). To reduce anti-IF production, preliminary immunosuppressive therapy with azathioprine (100 mg) and prednisolone (40 mg daily) with gradual decrease of the dose and discontinuation of therapy by the end of the 4th week was carried out. Then a course of antiviral therapy with IF in dose 4 min U i.m. every other day was carried out, total dose per course being at least 100 min U. In 2 of the 4 patients administered a complete course of immunosuppressive and antiviral therapy anti-IF, HBeAg, anti-HBc IgM, receptor to polymerized human serum albumin, and HBV DNA were no longer detected. If anti-IF still persisted after a course of immunosuppressive therapy, subsequent antiviral treatment did not influence the level of virus replication. Patients responding to therapy by elimination of HBeAg and HBV DNA had much lower titers of HBeAg and lower concentration of HBV DNA. The initial level of anti-IF was not related to the pattern of response.
Inhibition of N-linked glycosylation down-regulates insulin-like growth factor-1 receptor at the cell surface and kills Ewing's sarcoma cells: therapeutic implications. (2000)

The insulin-like growth factor-1 receptor (IGF-1R) has been shown to be of critical importance for tumor development and tumor cell survival of various types of malignancies. We have previously demonstrated that an adequate N-linked glycosylation of IGF-1R is required for its translocation to the cell surface in melanoma cells. This raises the possibility of using glycosylation inhibitors as therapeutic agents against IGF-1R-dependent malignancies. In this study we show that inhibition of N-linked glycosylation using tunicamycin or the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitor lovastatin resulted in down-regulation of IGF-1R at the cell surface in Ewing's sarcoma cell lines (RD-ES and ES-1 cells). The down-regulation of plasma membrane-bound IGF-1R was correlated with a drastic decrease in IGF-1R autophosphorylation, suggesting biochemical inactivation of the receptor. Whereas RD-ES and ES-1 cells responded differently with regard to DNA synthesis, the decrease in IGF-1R expression was accompanied by a rapid and substantial decrease in survival of both cell lines. Our data suggest that relatively untoxic HMG-CoA reductase inhibitors (e.g. lovastatin) could have therapeutic significance in IGF-1R-dependent neoplasms like Ewing's sarcoma.
Length-dependent prediction of protein intrinsic disorder (2006)

The VSL2 predictors are applicable to disordered regions of any length and can accurately identify the short disordered regions that are often misclassified by our previous disorder predictors. The success of the VSL2 predictors further confirmed the previously observed differences in amino acid compositions and sequence properties between short and long disordered regions, and justified our approaches for modelling short and long disordered regions separately. The VSL2 predictors are freely accessible for non-commercial use at http://www.ist.temple.edu/disprot/predictorVSL2.php.
Colorectal polyps and diet: A case‐control study in Marseilles (1987)

This study investigates the differences in usual past diet between 252 subjects with newly diagnosed adenomatous or villous polyps of the colon and rectum and a group of 238 hospital controls. Cases and controls were interviewed in hospital by 3 nutritionists using a dietary history questionnaire focused on the diet during the preceding year. Nutrient intake was estimated by means of ad hoc food tables adapted from French and British tables. Out of 16 food groups considered in the analyses, the cases reported lower consumption of oil and potatoes and higher consumption of sugar added to food and drink. Among nutrients, we found that cases had a lower consumption of carbohydrates (not taking into account added sugar), potassium, magnesium and vitamin B6. We found a slightly lower intake of fibre and a slightly higher intake of saturated fat among cases, though neither was statistically significant. Intake values for fibre and for carbohydrates were highly intercorrelated and, due to measurement errors, the effect of one may be masked by the other and vice versa. The hypothesis that some components of carbohydrates (starches, fibre and natural sugars but not added sugar) play a protective role in relation to the biology of tumours of the intestinal tract is considered in further multivariate analyses and in the "Discussion".