gebhart/patrepeval huggingface dataset:
STEM‐CL investigations on the influence of stacking faults on the optical emission of cubic GaN epilayers and cubic GaN/AlN multi‐quantum wells (2015)

Abstract We report the influence of {111} stacking faults on the cathodoluminescence (CL) emission characteristics of cubic GaN (c‐GaN) films and cubic GaN/AlN multi‐quantum wells. Transmission electron microscopy (TEM) measurements indicate that stacking faults (SFs) on the {111} planes are the predominant crystallographic defects in epitaxial films, which were grown on 3C‐SiC/Si (001) substrates by plasma‐assisted molecular beam epitaxy. The correlation of the SFs and the luminescence output is evidenced with a CL setup integrated in a scanning TEM (STEM). By comparing the STEM images and the simultaneously measured CL signals it is demonstrated that SFs in these films lead to a reduced CL emission intensity. Furthermore, the CL emission intensity is shown to increase with increasing film thickness and decreasing SF density. This correlation can be connected to the reduction of the full width at half maximum of X‐ray diffraction rocking curves with increasing film thickness of c‐GaN films. (© 2015 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
AvrPto-dependent Pto-interacting proteins and AvrPto-interacting proteins in tomato (2000)

The plant-intracellular interaction of the avirulence protein AvrPto of Pseudomonas syringae pathovar tomato, the agent of bacterial speck disease, and the corresponding tomato resistance protein Pto triggers responses leading to disease resistance. Pto, a serine/threonine protein kinase, also interacts with a putative downstream kinase, Pto-interactor 1, as well as with members of a family of transcription factors Pto-interactors 4, 5, and 6. These proteins are likely involved, respectively, in a phosphorylation cascade resulting in hypersensitive cell death, and in defense gene activation. The mechanism by which the interaction of AvrPto and Pto initiates defense response signaling is not known. To pursue the hypothesis that tertiary interactions are involved, we modified the yeast two-hybrid protein interaction trap and conducted a search for tomato proteins that interact with Pto only in the presence of AvrPto. Five classes of AvrPto-dependent Pto interactors were isolated, and their interaction specificity confirmed. Also, to shed light on a recently demonstrated virulence activity of AvrPto, we conducted a standard two-hybrid screen for tomato proteins in addition to Pto that interact with AvrPto: i.e., potential virulence targets or modifiers of AvrPto. By constructing an N-terminal rather than a C-terminal fusion of AvrPto to the LexA DNA binding domain, we were able to overcome autoactivation by AvrPto and identify four classes of specific AvrPto-interacting proteins.
Establishment and characterization of a multipotential neural cell line that can conditionally generate neurons, astrocytes, and oligodendrocytes in vitro (1995)

In the mammalian central nervous system (CNS), multipotential neural stem cells in the neuroepithelium generate the three major types of neural cells, namely, neurons, astrocytes, and oligodendrocytes. To explore the molecular mechanisms underlying proliferation and differentiation of these neural stem cells, we established a cell line named MNS-57 from the embryonic day 12 rat neuroepithelium by introducing the mycer fusion gene, in which c-myc can be conditionally activated by adding oestrogen to the culture medium. MNS-57 cells expressed nestin, vimentin, and the RC1 antigen, which are potential markers for neural stem cells. We show that under particular culture conditions, MNS-57 cells can conditionally generate neurons, astrocytes, and oligodendrocytes in vitro, indicating that they are likely to originate from multipotential neural stem cells. Incubating MNS-57 cells with either oestrogen, which activates mycer, or growth factors such as basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) stimulated their growth, and the combination of oestrogen and bFGF (or EGF) had a synergistically stronger mitogenic effect than the single factors. Furthermore, both c-myc activation and bFGF appeared to be necessary for the differentiation of MNS-57 cells, and only when stimulated by both signals simultaneously, the cells committed to generating multiple neural cell types. Thus, the property of the cell line is unique in that its differentiation into neurons and glia can be conditionally manipulated in vitro in an exogenous signal-dependent manner. We propose that the cell line described here will provide an useful in vitro model to understand genetic and environmental mechanisms that control the generation of neural cell diversity in the CNS.
Crystal Structures and Structure–Activity Relationships of Imidazothiazole Derivatives as IDO1 Inhibitors (2014)

Indoleamine 2,3-dioxygenase 1 (IDO1) is considered as a promising target for the treatment of several diseases, including neurological disorders and cancer. We report here the crystal structures of two IDO1/IDO1 inhibitor complexes, one of which shows that Amg-1 is directly bound to the heme iron of IDO1 with a clear induced fit. We also describe the identification and preliminary optimization of imidazothiazole derivatives as novel IDO1 inhibitors. Using our crystal structure information and structure-activity relationships (SAR) at the pocket-B of IDO1, we found a series of urea derivatives as potent IDO1 inhibitors and revealed that generation of an induced fit and the resulting interaction with Phe226 and Arg231 are essential for potent IDO1 inhibitory activity. The results of this study are very valuable for understanding the mechanism of IDO1 activation, which is very important for structure-based drug design (SBDD) to discover potent IDO1 inhibitors.
A sensitivity scale for targeting T cells with chimeric antigen receptors (CARs) and bispecific T-cell Engagers (BiTEs) (2012)

Although T cells can mediate potent antitumor responses, immune tolerance mechanisms often result in the deletion or inactivation of T cells that express T-cell receptors (TCRs) against potentially effective target epitopes. Various approaches have been devised to circumvent this problem. In one approach, the gene encoding an antibody against a cancer-associated antigen is linked, in the form of a single-chain variable fragment (scFv), to genes that encode transmembrane and signaling domains. This chimeric antigen receptor (CAR) is then introduced into T cells for adoptive T-cell therapy. In another approach, the anti-cancer scFv is fused to a scFv that binds to the CD3ε subunit of the TCR/CD3 complex. This fusion protein serves as a soluble, injectable product that has recently been termed bispecific T-cell engager (BiTE). Both strategies have now been tested in clinical trials with promising results, but the comparative efficacies are not known. Here, we performed a direct comparison of the in vitro sensitivity of each strategy, using the same anti-cancer scFv fragments, directed against a tumor-specific glycopeptide epitope on the sialomucin-like transmembrane glycoprotein OTS8, which results form a cancer-specific mutation of Cosmc. While both approaches showed specific responses to the epitope as revealed by T cell-mediated cytokine release and target cell lysis, CAR-targeted T cells were more sensitive than BiTE-targeted T cells to low numbers of antigens per cell. The sensitivity scale described here provides a guide to the potential use of these two different approaches.
Oxidation, cross-linking, and insolubilization of recombinant tropoelastin by purified lysyl oxidase (1993)

The use of recombinant human tropoelastin (rTE) and selected variants thereof as substrates for the assay of lysyl oxidase activity in vitro was explored. The possibility was also assessed that an insoluble elastin-like product could be generated from this elastin precursor in the absence of other macromolecules found associated with elastin in vivo. rTE was more efficiently oxidized by lysyl oxidase than the insoluble chick aorta elastin substrate conventionally used. Anionic amphiphilic elastin ligands strongly inhibited rTE oxidation consistent with the importance of electrostatic enzyme-substrate interactions previously noted with the insoluble elastin substrate. An rTE variant, rTE delta 26A, lacking the hydrophilic sequence coded by exon 26A, was a less effective substrate than rTE, largely due to an increase in Km, while the kinetic parameters for the oxidation of rTE delta 36, lacking the C-terminal polybasic sequence coded by exon 36, were quite similar to those for rTE. Incubation of rTE delta 26A with lysyl oxidase not only resulted in the generation of peptidyl alpha-aminoadipic-delta-semialdehyde and lysine-derived cross-linkages, but also yielded a product insoluble in hot 0.1 N NaOH, consistent with the properties of insoluble elastin. Thus, oxidation, cross-linking and insolubilization of elastin substrates by lysyl oxidase can occur in the absence of other macromolecules implicated as being involved in this process in vivo, although such macromolecules may be essential to obtain the proper alignment between tropoelastin units for specifically placed cross-linkages and optimally functional elastic fibers.
CRISPR adaptive immunity systems of prokaryotes (2012)

CRISPR (clustered regularly interspaced short palindromic repeats) systems were found in the genomes of many eubacteria and the vast majority of archaea. Their unique feature is that CRISPR-mediated immunity is adaptive and can be programmed to protect cells against mobile genetic elements. The review describes the general principles of CRISPR-mediated immunity and characterizes the CRISPR systems of various microorganisms.
Human myeloma cells stimulate the receptor activator of nuclear factor-κB ligand (RANKL) in T lymphocytes: a potential role in multiple myeloma bone disease (2002)

The biologic mechanisms involved in the pathogenesis of multiple myeloma (MM) bone disease are not completely understood. Recent evidence suggests that T cells may regulate bone resorption through the cross-talk between the critical osteoclastogenetic factor, receptor activator of nuclear factor-kappaB ligand (RANKL), and interferon gamma (IFN-gamma) that strongly suppresses osteoclastogenesis. Using a coculture transwell system we found that human myeloma cell lines (HMCLs) increased the expression and secretion of RANKL in activated T lymphocytes and similarly purified MM cells stimulated RANKL production in autologous T lymphocytes. In addition, either anti-interleukin 6 (anti-IL-6) or anti-IL-7 antibody inhibited HMCL-induced RANKL overexpression. Consistently, we demonstrated that HMCLs and fresh MM cells express IL-7 mRNA and secrete IL-7 in the presence of IL-6 and that bone marrow (BM) IL-7 levels were significantly higher in patients with MM. Moreover, we found that the release of IFN-gamma by T lymphocytes was reduced in presence of both HMCLs and purified MM cells. Furthermore, in a stromal cell-free system, osteoclastogenesis was stimulated by conditioned medium of T cells cocultured with HMCLs and inhibited by recombinant human osteoprotegerin (OPG; 100 ng/mL to 1 microg/mL). Finally, RANKL mRNA was up-regulated in BM T lymphocytes of MM patients with severe osteolytic lesions, suggesting that T cells could be involved at least in part in MM-induced osteolysis through the RANKL overexpression.
Detection of influenza, parainfluenza, adenovirus and respiratory syncytial virus during asthma attacks in children older than 2 years old (2003)

The rate of viral identification was higher in asthmatic children, whether symptomatic or not, suggesting a possible susceptibility to viral infections. Virus could also be a triggering factor in attacks, although it is not the most preponderant in older children.
Quantitative analysis of the factors which affect the interpatient organ‐at‐risk dose sparing variation in IMRT plans (2012)

Quantitative analysis of patient anatomical features and their correlation with OAR dose sparing has identified a number of important factors that explain significant amount of interpatient DVH variations in OARs. These factors can be incorporated into evidence-based learning models as effective features to provide patient-specific OAR dose sparing goals.
The risk of congestive heart failure in rheumatoid arthritis: A population‐based study over 46 years (2005)

Compared with persons without RA, patients with RA have twice the risk of developing CHF. This excess risk is not explained by traditional CV risk factors and/or clinical ischemic heart disease.
Computer viruses and methods of combatting them (1991)

This article examines the current virus situation for personal computers and time-sharing computers. Basic methods of combatting viruses are presented. Specific recommendations are given to eliminate the most widespread viruses. A short description is given of a universal antiviral system, PHENIX, which has been developed.
Protein kinase C activation and protooncogene expression in differentiation/retrodifferentiation of human U-937 leukemia cells. (1991)

Human U-937 leukemia cells differentiate along the monocytic lineage following 3-day exposures to 12-O-tetradecanoylphorbol-13-acetate (TPA). This induction of differentiation is accompanied by adherence and loss of proliferation, as well as expression/repression of differentiation-associated genes. Long term culture of TPA-differentiated U-937 cells in the absence of phorbol ester for 32-36 days resulted in a process of retrodifferentiation. The retrodifferentiated cells detached from the substrate and reinitiated proliferation. Other cellular parameters, such as glycosidase activities, cytokine release, and filament expression, returned to levels similar to that observed in uninduced cells. Treatment of U-937 cells with TPA resulted in a rapid translocation of protein kinase C (PKC) from the cytosol to cell membrane fractions within 2-8 min. Increased levels of membrane-associated PKC activity persisted until 17-29 days. However, longer periods of incubation were associated with a return to the distribution of PKC in control cells. Activation of PKC has been implicated in the regulation of certain immediate early response genes, and in the present studies, TPA rapidly induced c-fos and c-jun gene expression. Levels of c-fos and c-jun transcripts remained elevated during periods of PKC activation and also returned to levels observed in control cells by 30-36 days, when the cells entered retrodifferentiation. Staurosporine, a nonspecific inhibitor of PKC, partially blocked TPA-induced adherence and growth inhibition and concomitantly prevented TPA-induced c-fos and c-jun gene expression.(ABSTRACT TRUNCATED AT 250 WORDS)
Dengue-3 (16562) PGMK 33 vaccine: neurovirulence, viremia and immune responses in Macaca fascicularis. (1994)

Investigation of monkey neurovirulence of dengue-3 viruses (DEN-3, 16562) was undertaken to provide an evaluation of the relative safety of virus strain attenuated for potential use of live virus vaccine. Ten flavivirus-negative, cynomolgus monkeys (Macacafascicularis) were used in the test. The animals were inoculated intrathalamically, intraspinally and intramuscularly with DEN-3 PGMK 33 attenuated live virus vaccine (6 monkeys): parent virus (2) and control cell culture fluid (2). Blood samples were collected on days 0, 1, 2, 4, 6, 8, 10, 12 and 21 for virus isolation and days 0 and 21 or 22 for serologic testing. One monkey with DEN-3 (16562) PGMK 33 candidate vaccine had detectable viremia on day 10. By day 21, all recipients of PGMK 33 and both monkeys with DEN-3 parent virus developed serum neutralizing antibodies to DEN-3 titers ranged from 56-320. The monkeys showed no evidence of illness and none died of dengue infection. Histopathological examination of tissue collected on day 21 or 22 revealed only minimal neurovirulence lesions as scored by the routine grading system. No differences were observed between the DEN-3 parent and vaccine viruses and it is concluded that neither virus is neurovirulent for cynomolgus monkeys.
Differences in cerebrospinal fluid proteins between patients with schizophrenia and normal persons. (1985)

A survey of cerebrospinal fluid (CSF) proteins from normal persons and patients with schizophrenia reveals differences between the two populations. Computer-assisted densitometry of 68 proteins, resolved by two-dimensional electrophoresis and made visible by silver staining, shows six changes. Compared with their occurrence in the normal group, two proteins are increased in the schizophrenic patients by 22% and 27%, while four proteins are decreased by 29%, 46%, 20%, and 37% (p less than 0.005). Furthermore, two additional 40 000-Da proteins are found in CSF from 31.5% of the schizophrenic patients. Although these disease-associated proteins have not yet been found in 12 other neurological and psychiatric conditions, they have been found in patients with herpes simplex encephalitis (90%), Creutzfeldt-Jakob disease (67%), multiple sclerosis (13%), Parkinson's disease (12%), and a single case of Guillain-Barré syndrome. These two 40 000-Da proteins have never been found in CSF from any of 99 normal persons.
Double‐stranded RNA‐mediated gene silencing of cysteine proteases (falcipain‐1 and ‐2) of Plasmodium falciparum (2002)

Malaria remains a public health problem of enormous magnitude, affecting over 500 million people every year. Lack of success in the past in the development of new drug/vaccines has mainly been attributed to poor understanding of the functions of different parasite proteins. Recently, RNA interference (RNAi) has emerged as a simple and incisive technique to study gene functions in a variety of organisms. In this study, we report the results of RNAi by double-stranded RNA of cysteine protease genes (falcipain-1 and -2) in the malaria parasite, Plasmodium falciparum. Using RNAi directed towards falcipain genes, we demonstrate that blocking the expression of these genes results in severe morphological abnormalities in parasites, inhibition of parasite growth in vitro and substantial accumulation of haemoglobin in the parasite. The inhibitory effects produced by falcipain double-stranded (ds)RNAs are reminiscent of the effects observed upon administering E-64, a cysteine protease inhibitor. The parasites treated with falcipain's dsRNAs also show marked reduction in the levels of corresponding endogenous falcipain mRNAs. We also demonstrate that dsRNAs of falcipains are broken into short interference RNAs approximately 25 nucleotides in size, a characteristic of RNAi, which in turn activates sequence-specific nuclease activity in the malaria parasites. These results thus provide more evidence for the existence of RNAi in P. falciparum and also suggest possibilities for using RNAi as an effective tool to determine the functions of the genes identified from the P. falciparum genome sequencing project.
RNA‐dependent RNA polymerase activity encoded by GB virus‐B non‐structural protein 5B (2000)

Phylogenetic analysis and polyprotein organization comparison have shown that GB virus-B (GBV-B) is closely related to hepatitis C virus (HCV). In this study, the coding region for GBV-B non-structural protein 5B (NS5B) was isolated by reverse transcription-polymerase chain reaction (RT-PCR) from pooled serum of GBV-B-infected tamarins. Expression of soluble GBV-B NS5B protein in Escherichia coli was achieved by removal of a 19-amino acid hydrophobic domain at the C-terminus of the protein. The truncated GBV-B NS5B (NS5BDeltaCT19) was purified to homogeneity and shown to possess an RNA-dependent RNA polymerase (RdRp) activity in both gel-based and scintillation proximity assays. NS5BDeltaCT19 required the divalent cation Mn2+ for enzymatic activity, at an optimal concentration of 15 mM. Interestingly, Mg2+, at concentrations up to 20 mM, did not support the GBV-B NS5B activity. This differs from HCV NS5B where both Mn2+ and Mg2+ can support RdRp activity. Zn2+ was found to inhibit the activity of GBV-B NS5B, with a 50% inhibitory concentration (IC50) of 5-10 microM. Higher concentrations of monovalent salts (NaCl or KCl > 100 mM) and glycerol (> 3%) were also inhibitory. NS5BDeltaCT19 was able to bind to RNA homopolymers, but utilized most efficiently poly(C), the one with the lowest binding affinity for RNA synthesis. Mutational analysis of GBV-B NS5B demonstrated the importance of several conserved sequence motifs for enzymatic activity. Based on sequence homology ( approximately 37% identity and 52% similarity) between GBV-B and HCV NS5B proteins, the active GBV-B RdRp provides a good surrogate assay system for HCV polymerase studies.
Providing Written Feedback on Students' Oral Presentations: An Analysis (2001)

Recent reviews on assessment in higher education have emphasised the importance of written formative assessment as part of the process of assessing oral presentation skills, and have identified the need for case studies to investigate the content and character of feedback which students receive. The paper analyses the written feedback provided by teachers who acted as assessors for conference presentations made by engineering students enrolled in a fourth year subject at The University of New South Wales. The study employs content analysis to describe the extent, content, and character of these comments, and to identify which performance skills staff focus on in providing such feedback.
Voiding Dysfunction after Total Mesorectal Excision in Rectal Cancer (2011)

Voiding dysfunction is common after rectal cancer surgery but can be recovered in 6 months after surgery or earlier. Abdominoperineal resection was shown to be an unfavorable factor for postoperative voiding. Larger prospective study is needed to determine the long-term effect of rectal cancer surgery in relation to male and female baseline voiding condition.
Discovering Web access patterns and trends by applying OLAP and data mining technology on Web logs (2002)

As a confluence of data mining and World Wide Web technologies, it is now possible to perform data mining on Web log records collected from the Internet Web-page access history. The behaviour of Web page readers is imprinted in the Web server log files. Analyzing and exploring regularities in this behaviour can improve the system performance, enhance the quality and delivery of Internet information services to the end user, and identify populations of potential customers for electronic commerce. Thus, by observing people using collections of data, data mining can bring a considerable contribution to digital library designers. In a joint effort between the TeleLearning-NCE (Networks of Centres of Excellence) project on the Virtual University and the NCE-IRIS project on data mining, we have been developing a knowledge discovery tool, called WebLogMiner, for mining Web server log files. This paper presents the design of WebLogMiner, reports current progress and outlines future work in this direction.