gebhart/patrepeval huggingface dataset:
The acquisition of resistance to TNFα in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray (2011)

While the autophagic process is mainly regulated at the post-translational level, a growing body of evidence suggests that autophagy might also be regulated at the transcriptional level. The identification of transcription factors involved in the regulation of autophagy genes has provided compelling evidence for such regulation. In this context, a powerful high throughput analysis tool to simultaneously monitor the expression level of autophagy genes is urgently needed. Here we describe setting up the first comprehensive human autophagy database (HADb, available at www.autophagy.lu) and the development of a companion Human Autophagy-dedicated cDNA Microarray which comprises 234 genes involved in or related to autophagy. The autophagy microarray tool used on breast adenocarcinoma MCF-7 cell line allowed the identification of 47 differentially expressed autophagy genes associated with the acquisition of resistance to the cytotoxic effect of TNFα. The autophagy-core machinery genes DRAM (Damage-Regulated Autophagy Modulator), BNIP3L (BCL2/adenovirus E1B 19 kDa interacting protein 3-like), BECN1 (Beclin 1), GABARAP (Gamma-AminoButyric Acid Receptor-Associated Protein) and UVRAG (UV radiation resistance associated gene) were found upregulated in TNF-resistant cells, suggesting a constitutive activation of the autophagy machinery in these cells. More interestingly, we identified NPC1 as the most upregulated genes in TNF-resistant compared to TNF-sensitive MCF-7 cells, suggesting a relation between the intracellular transport of cholesterol, the regulation of autophagy and NPC1 expression in TNF-resistant tumor cells. In conclusion, we describe here new tools that may help investigating autophagy gene regulation in various cellular models and diseases.
Defining response in systemic lupus erythematosus: a study by the Systemic Lupus International Collaborating Clinics group. (2004)

The physician VAS may be too blunt to assess response in SLE, because even among experienced lupus assessors, there were considerable differences in what influenced scoring decisions.
Initial Clinical Studies of CVD 112 Vibrio cholerae O139 Live Oral Vaccine: Safety and Efficacy against Experimental Challenge (1995)

Since October 1992, epidemics of cholera associated with Vibrio cholerae O group 139 have occurred in India, Bangladesh, and much of the rest of Asia. A volunteer model was used to determine the safety, immunogenicity, and efficacy of an attenuated delta ctxA delta zot delta ace delta cep V. cholerae O139 vaccine strain, designated CVD 112. Six volunteers received 10(6) cfu and 6 received 10(8) cfu of CVD 112. No subject who received the 10(6) dose had diarrhea or other severe symptoms after vaccination; 3 vaccinees developed mild diarrhea (mean stool volume, 648 mL) after receiving the higher dose. Five weeks after vaccination, 8 vaccinees and 15 unvaccinated control subjects underwent challenge with 10(6) cfu of wild type V. cholerae O139 AI1837. One vaccinee (13%) and 12 control subjects (80%) developed diarrhea after challenge (P = .003). The short-term protective efficacy conferred by vaccine strain CVD 112 was 84% and was remarkably similar to that conferred by primary wild type clinical infection (80%).
Modeling the effects of burst packet loss and recency on subjective voice quality (2001)

This paper describes VQmon, a non-intrusive monitoring technique for Voice over IP networks that is computationally efficient and suitable for integrating or embedding into VoIP gateways or IP Phones. This uses an extended version of the ITU G.107 E-Model incorporating the effects of time varying packet loss and “recency”. A 4 state Markov model is used to represent the time distribution of packet loss during a VoIP call. QoS, Voice over Packet, E model, subjective quality A.
Dialkylaminogermanes and Dialkylaminosilanes (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDialkylaminogermanes and DialkylaminosilanesHerbert H. AndersonCite this: J. Am. Chem. Soc. 1952, 74, 6, 1421–1423Publication Date (Print):March 1, 1952Publication History Published online1 May 2002Published inissue 1 March 1952https://pubs.acs.org/doi/10.1021/ja01126a017https://doi.org/10.1021/ja01126a017research-articleACS PublicationsRequest reuse permissionsArticle Views335Altmetric-Citations45LEARN 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
3-(Iodoacetamido)-benzoylurea: a novel cancericidal tubulin ligand that inhibits microtubule polymerization, phosphorylates bcl-2, and induces apoptosis in tumor cells. (1998)

3-(Iodoacetamido)-benzoylurea (3-IAABU) is a newly synthesized antitubulin compound with a molecular weight of 347. 3-IAABU exhibited anticancer activity in a variety of tumor cell lines with ID90 in the range of 0.015-0.29 microM for leukemic cells and 0.06-0.92 microM for solid tumors. Higher selectivity against malignant cells was observed with 3-IAABU than that with vinblastine and paclitaxel. It inhibits microtubule assembly in tubulin systems either with or without microtubule-associated proteins (ID50 was 0.1 microM and 1.2 microM, respectively) and microtubule depolymerization was not affected, indicating an inhibition of polymerization by binding of 3-IAABU to the heterodimeric subunit of tubulin. 3-IAABU was shown to inhibit the binding of colchicine, a subunit binding compound, but did not inhibit binding of vinblastine and guanosine 5'-triphosphate/guanosine 5'-diphosphate, indicating that colchicine site corresponds to the site that 3-IAABU locates. Tumor cells treated with 3-IAABU showed scattered chromosomes in metaphase. Normal microtubule architecture or spindle apparatus was absent in these cells; instead, punctuated aggregates of tubulin were found by an immunofluorescent staining. Cell cycle analyses showed an accumulation of tumor cells at M phase after a 4-h treatment with 3-IAABU. The phosphorylated bcl-2 representative of an inactivated form of the oncoprotein was found in the cells 12 h after treatment with 3-IAABU. These cells progressed to apoptosis within 16 h. As a new tubulin ligand, 3-IAABU could be a promising agent in cancer chemotherapy.
39.3: Material and Device Structure Design of Blue Phosphorescent OLEDs for High Efficiency and Enhanced Stability (2010)

Abstract We developed stable and efficient blue phosphorescent materials for OLEDs on the basis of the evaluation of their stability under UV irradiation. Structures of OLEDs with the above‐stated materials were improved with the aid of a method to estimate the site distribution of exciton formation in the emissive layer by doping a small amount of fluorophore in it with varied position. The improved blue phosphorescent OLED exhibited high external quantum efficiency (7.9%) with a half life of 10,000 h on a practical luminance (360 cd/m 2 ).
Comprehensive Genome Sequence Analysis of a Breast Cancer Amplicon (2001)

Gene amplification occurs in most solid tumors and is associated with poor prognosis. Amplification of 20q13.2 is common to several tumor types including breast cancer. The 1 Mb of sequence spanning the 20q13.2 breast cancer amplicon is one of the most exhaustively studied segments of the human genome. These studies have included amplicon mapping by comparative genomic hybridization (CGH), fluorescent in-situ hybridization (FISH), array-CGH, quantitative microsatellite analysis (QUMA), and functional genomic studies. Together these studies revealed a complex amplicon structure suggesting the presence of at least two driver genes in some tumors. One of these, ZNF217 , is capable of immortalizing human mammary epithelial cells (HMEC) when overexpressed. In addition, we now report the sequencing of this region in human and mouse, and on quantitative expression studies in tumors. Amplicon localization now is straightforward and the availability of human and mouse genomic sequence facilitates their functional analysis. However, comprehensive annotation of megabase-scale regions requires integration of vast amounts of information. We present a system for integrative analysis and demonstrate its utility on 1.2 Mb of sequence spanning the 20q13.2 breast cancer amplicon and 865 kb of syntenic murine sequence. We integrate tumor genome copy number measurements with exhaustive genome landscape mapping, showing that amplicon boundaries are associated with maxima in repetitive element density and a region of evolutionary instability. This integration of comprehensive sequence annotation, quantitative expression analysis, and tumor amplicon boundaries provide evidence for an additional driver gene prefoldin 4 ( PFDN4 ), coregulated genes, conserved noncoding regions, and associate repetitive elements with regions of genomic instability at this locus.
A ribosomal ambiguity mulation in the 530 loop ofE.coli16S rRNA (1992)

A series of base substitution and deletion mutations were constructed in the highly conserved 530 stem and loop region of E. coli 16S rRNA involved in binding of tRNA to the ribosomal A site. Base substitution and deletion of G517 produced significant effects on cell growth rate and translational fidelity, permitting readthrough of UGA, UAG and UAA stop codons as well as stimulating +1 and -1 frameshifting in vivo. By contrast, mutations at position 534 had little or no effect on growth rate or translational fidelity. The results demonstrate the importance of G517 in maintaining translational fidelity but do not support a base pairing interaction between G517 and U534.
Renal cell carcinoma in relation to cigarette smoking: Meta-analysis of 24 studies (2004)

Renal cell carcinoma (RCC) accounts for 3% of adult deaths from cancer. The risk factors for its development are still under intense investigation. Although tobacco smoke is a risk factor, the data are inconsistent and the extent of the increased risk is unclear. Estimates from 19 case-control and 5 cohort studies were used. The case-control reports included 8,032 cases and 13,800 controls; the cohort estimates were based on 1,457,754 participants with 1,326 cases of RCC. The relative risk (RR) for RCC for ever smokers as compared to lifetime never smokers was 1.38 (95% confidence interval [CI] = 1.27-1.50). The RR for male smokers was 1.54 (95% CI = 1.42-1.68) and for female smokers was 1.22 (95% CI = 1.09-1.36). For men and women there was a strong dose-dependent increase in risk. Ever smoker men who had smoked 1-9, 10-20 or 21 or more cigarettes/day had a RR of 1.60 (95% CI = 1.21-2.12), 1.83 (95% CI = 1.30-2.57), or 2.03 (95% CI = 1.51-2.74), respectively. For women, the relative risks were 0.98 (95% CI = 0.71-1.35), 1.38 (95% CI = 0.90-2.11), or 1.58 (95% CI = 1.14-2.20), respectively. The advantages of smoking cessation were confirmed by a reduction in RR for those who had quit smoking for >10 years as compared to those who had quit for 1-10 years. Inhaled tobacco smoke is clearly implicated in the etiology of RCC, with a strong dose-dependent increase in risk associated with numbers of cigarettes smoked per day and a substantial reduction in risk for long-term former smokers.
High‐Mobility Air‐Stable n‐Type Semiconductors with Processing Versatility: Dicyanoperylene‐3,4:9,10‐bis(dicarboximides) (2004)

Taking up the semiconducting baton: Organic field-effect transistors fabricated with a new class of extremely electron-deficient cyanated perylene diimides are air-stable and exhibit n-type mobilities as high as 0.64 cm2 V−1 s−1 (see scheme). Devices can be fabricated from vapor-deposited and solution-cast films as well as top- and bottom-contact electrode configurations. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z461324_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Prevention of orthotopic human lung cancer growth by intratracheal instillation of a retroviral antisense K-ras construct. (1993)

An orthotopic human lung cancer model in nu/nu mice was used to study the effect of an antisense K-ras (AS-K-ras) retroviral construct on tumor growth in vivo. A 2-kilobase genomic AS-K-ras DNA fragment linked to a beta-actin promoter was cloned into the LNSX retroviral vector. The recombinant construct was packaged into GP+envAm12 cells and titers greater than 10(6) colony-forming units/ml were obtained. Irradiated (350 cGy) nu/nu mice were first inoculated intratracheally with 10(5) H460a human large cell lung carcinoma cells which have a codon 61 mutation of the K-ras oncogene. Three days later they received intratracheal instillation of viral supernatant (5 x 10(6) colony-forming units/ml) from either LNSX, LNSX-AS-K-ras, LNSX-sense-K-ras producer cells, or medium daily for 3 days. At autopsy, 30 days after tumor cell inoculation, 90% of the control mice had tumors whereas 87% of mice treated with the LNSX-AS-K-ras viral supernatant were free of tumors. The efficacy of the viral supernatant was dose dependent. Intratracheal administration of retroviral LNSX-AS-K-ras supernatant prevents the growth of human lung cancer cells implanted orthotopically in nu/nu mice.
IscR, an Fe-S cluster-containing transcription factor, represses expression of Escherichia coli genes encoding Fe-S cluster assembly proteins (2001)

IscR (iron-sulfur cluster regulator) is encoded by an ORF located immediately upstream of genes coding for the Escherichia coli Fe-S cluster assembly proteins, IscS, IscU, and IscA. IscR shares amino acid similarity with MarA, a member of the MarA/SoxS/Rob family of transcription factors. In this study, we found that IscR functions as a repressor of the iscRSUA operon, because strains deleted for iscR have increased expression of this operon. In addition, in vitro transcription reactions established a direct role for IscR in repression of the iscR promoter. Analysis of IscR by electron paramagnetic resonance showed that the anaerobically isolated protein contains a [2Fe-2S](1+) cluster. The Fe-S cluster appears to be important for IscR function, because repression of iscR expression is significantly reduced in strains containing null mutations of the Fe-S cluster assembly genes iscS or hscA. The finding that IscR activity is decreased in strain backgrounds in which Fe-S cluster assembly is impaired suggests that this protein may be part of a novel autoregulatory mechanism that senses the Fe-S cluster assembly status of cells.
Memory buddies (2009)

Many data center virtualization solutions, such as VMware ESX, employ content-based page sharing to consolidate the resources of multiple servers. Page sharing identifies virtual machine memory pages with identical content and consolidates them into a single shared page. This technique, implemented at the host level, applies only between VMs placed on a given physical host. In a multiserver data center, opportunities for sharing may be lost because the VMs holding identical pages are resident on different hosts. In order to obtain the full benefit of content-based page sharing it is necessary to place virtual machines such that VMs with similar memory content are located on the same hosts. In this paper we present Memory Buddies, a memory sharingaware placement system for virtual machines. This system includes a memory fingerprinting system to efficiently determine the sharing potential among a set of VMs, and compute more efficient placements. In addition it makes use of live migration to optimize VM placement as workloads change.We have implemented a prototype Memory Buddies system with VMware ESX Server and present experimental results on our testbed, as well as an analysis of an extensive memory trace study. Evaluation of our prototype using a mix of enterprise and e-commerce applications demonstrates an increase of data center capacity (i.e. number of VMs supported) of 17%, while imposing low overhead and scaling to as many as a thousand servers.
Site-directed Mutagenesis of Escherichia Coli Succinyl-CoA Synthetase (1989)

Chemical modification experiments have shown that sulfhydryl groups play an important role in the mechanism of action of Escherichia coli succinyl-CoA synthetase. One of these sulfhydryl groups has been localized in the beta-subunit of the enzyme using the coenzyme A affinity analog, CoA disulfide-S,S-dioxide (Collier, G. E., and Nishimura, J. S. (1978) J. Biol. Chem. 253, 4938-4943). Recently, it has been shown that the reactive sulfhydryl group resides in Cys325 (Nishimura, J. S., Mitchell, T., Ybarra, J., and Matula, J. M., submitted to Eur. J. Biochem. for publication). In the present study, we have changed Cys325 to a glycine residue using the technique of site-directed mutagenesis and have purified the mutant enzyme to homogeneity. The resulting mutant enzyme is 83% as active as wild type enzyme. In contrast to wild type succinyl-CoA synthetase, the mutant is refractory to chemical modification by CoA disulfide-S,S-dioxide and methyl methanethiolsulfonate. It is also less reactive with N-ethylmaleimide. Thus, beta-Cys325 is a nonessential active site residue.
Endothelial cell injury due to copper-catalyzed hydrogen peroxide generation from homocysteine. (1986)

We have examined whether the toxic effects of homocysteine on cultured endothelial cells could result from the formation and action of hydrogen peroxide. In initial experiments with a cell-free system, micromolar amounts of copper were found to catalyze an oxygen-dependent oxidation of homocysteine. The molar ratio of homocysteine oxidized to oxygen consumed was approximately 4.0, which suggests that oxygen was reduced to water. The addition of catalase, however, decreased oxygen consumption by nearly one-half, which suggests that H2O2 was formed during the reaction. Confirming this hypothesis, H2O2 formation was detected using the horseradish peroxidase-dependent oxidation of fluorescent scopoletin. Ceruloplasmin was also found to catalyze oxidation of homocysteine and generation of H2O2 in molar amounts equivalent to copper sulfate. Finally, homocysteine oxidation was catalyzed by normal human serum in a concentration-dependent manner. Using cultured human and bovine endothelial cells, we found that homocysteine plus copper could lyse the cells in a dose-dependent manner, an effect that was completely prevented by catalase. Homocystine plus copper was not toxic to the cells. Specific injury to endothelial cells was seen only after 4 h of incubation with homocysteine plus copper. Confirming the biochemical studies, ceruloplasmin was also found to be equivalent to Cu++ in its ability to cause injury to endothelial cells in the presence of homocysteine. Since elevated levels of homocysteine have been implicated in premature development of atherosclerosis, these findings may be relevant to the mechanism of some types of chronic vascular injury.
An efficient approach to detect lack of synchronization in acyclic workflow graphs. (2010)

Control-flow analysis of business process models requires to check the absence of lack of synchronization. We use workflow graphs, which may contain inclusive OR gateways, to represent the control-flow of business process models. We structurally characterize lack of synchronization in an acyclic workflow graph. Based on this characterization, we show how to detect lack of synchronization in quadratic time.
Parity lost and parity regained (2008)

RAID storage systems protect data from storage errors, such as data corruption, using a set of one or more integrity techniques, such as checksums. The exact protection offered by certain techniques or a combination of techniques is sometimes unclear. We introduce and apply a formal method of analyzing the design of data protection strategies. Specifically, we use model checking to evaluate whether common protection techniques used in parity-based RAID systems are sufficient in light of the increasingly complex failure modes of modern disk drives. We evaluate the approaches taken by a number of real systems under single-error conditions, and find flaws in every scheme. In particular, we identify a parity pollution problem that spreads corrupt data (the result of a single error) across multiple disks, thus leading to data loss or corruption. We further identify which protection measures must be used to avoid such problems. Finally, we show how to combine real-world failure data with the results from the model checker to estimate the actual likelihood of data loss of different protection strategies. 1
Effect of oxidation on the properties of apolipoproteins A-I and A-II. (1988)

Purified apolipoprotein A-I has been separated by reversed-phase high performance liquid chromatography (HPLC) into multiple peaks and these peaks have been characterized. One peak, apoA-Ib had a relatively longer retention time on HPLC but its retention time could be shortened by treatment by hydrogen peroxide. CNBr cleavage studies indicated that the differences in apoA-Ib and in its oxidation product, apoA-Ia, were due to the different oxidation states of methionine. This phenomenon was also observed in apoA-II, where methionine oxidation produced two more forms of this apolipoprotein in addition to the native form. These isomers were found to have different secondary structures and affinities for lipid. Model peptide analogs of the amphipathic helix with the same sequence but with methionine and methionine sulfoxide at the nonpolar face of the amphipathic helix were synthesized and studied. It was found that the lipid affinities of these synthetic peptide isomers were very different. They also differed in their secondary structures as studied by circular dichroism (CD). We propose that methionine oxidation introduces hydrophilic residues at the nonpolar face of the amphipathic helical domains of these apolipoproteins and, therefore, alters their secondary structure and lipid affinity.