gebhart/patrepeval huggingface dataset:
Knockdown of survivin (BIRC5) causes apoptosis in neuroblastoma via mitotic catastrophe (2011)

BIRC5 (survivin) is one of the genes located on chromosome arm 17q in the region that is often gained in neuroblastoma. BIRC5 is a protein in the intrinsic apoptotic pathway that interacts with XIAP and DIABLO leading to caspase-3 and caspase-9 inactivation. BIRC5 is also involved in stabilizing the microtubule-kinetochore dynamics. Based on the Affymetrix mRNA expression data, we here show that BIRC5 expression is strongly upregulated in neuroblastoma compared with normal tissues, adult malignancies, and non-malignant fetal adrenal neuroblasts. The over-expression of BIRC5 correlates with an unfavorable prognosis independent of the presence of 17q gain. Silencing of BIRC5 in neuroblastoma cell lines by various antisense molecules resulted in massive apoptosis as measured by PARP cleavage and FACS analysis. As both the intrinsic apoptotic pathway and the chromosomal passenger complex can be therapeutically targeted, we investigated in which of them BIRC5 exerted its essential anti-apoptotic role. Immunofluorescence analysis of neuroblastoma cells after BIRC5 silencing showed formation of multinucleated cells indicating mitotic catastrophe, which leads to apoptosis via P53 and CASP2. We show that BIRC5 silencing indeed resulted in activation of P53 and we could rescue apoptosis by CASP2 inhibition. We conclude that BIRC5 stabilizes the microtubules in the chromosomal passenger complex in neuroblastoma and that the apoptotic response results from mitotic catastrophe, which makes BIRC5 an interesting target for therapy.
Electroosmotic Pumping and Valveless Control of Fluid Flow within a Manifold of Capillaries on a Glass Chip (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectroosmotic Pumping and Valveless Control of Fluid Flow within a Manifold of Capillaries on a Glass ChipKurt. Seiler, Zhonghui H. Fan, Karl. Fluri, and D. Jed. HarrisonCite this: Anal. Chem. 1994, 66, 20, 3485–3491Publication Date (Print):October 15, 1994Publication History Published online1 May 2002Published inissue 15 October 1994https://pubs.acs.org/doi/10.1021/ac00092a029https://doi.org/10.1021/ac00092a029research-articleACS PublicationsRequest reuse permissionsArticle Views792Altmetric-Citations186LEARN 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
Pseudomonas aeruginosa folliculitis after shower/bath exposure (2000)

Based on our experience, we suggest that shower/bath exposure should be definitively included amongst the possible pathogenic events causing PF. Pseudomonas aeruginosa is responsible for a number of clinical pictures, e.g. otitis externa, conjunctivitis, toe web intertrigo, green nail syndrome, infection of burns and wounds, and folliculitis. Pseudomonas aeruginosa folliculitis (PF) has been reported to develop as a consequence of exposure to contaminated water in heated swimming pools, whirlpools, and hot-tubes, or related to diving suits and leg waxing.1-4 We observed 14 cases of PF after shower/bath exposure. This is probably an underestimated pathogenic event; to our knowledge, only one case has been reported to date.5 In our patients, the clinical expression of dermatitis was constant, PF being a clinically well recognizable skin condition.
Photocyclization strategy for the synthesis of antitumor agent CC-1065: synthesis of dideoxy PDE-I and PDE-II. Synthesis of thiophene and furan analogs of dideoxy PDE-I and PDE-II (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotocyclization strategy for the synthesis of antitumor agent CC-1065: synthesis of dideoxy PDE-I and PDE-II. Synthesis of thiophene and furan analogs of dideoxy PDE-I and PDE-IIViresh H. Rawal, Robert J. Jones, and Michael P. CavaCite this: J. Org. Chem. 1987, 52, 1, 19–28Publication Date (Print):January 1, 1987Publication History Published online1 May 2002Published inissue 1 January 1987https://doi.org/10.1021/jo00377a004RIGHTS & PERMISSIONSArticle Views4168Altmetric-Citations108LEARN 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 (2 MB) Get e-Alertsclose Get e-Alerts
Supporting Context-Aware Media Recommendations for Smart Phones (2006)

A context-aware media recommendation platform uses an NtimesM-dimensional model and a hybrid processing approach to support media recommendation, adaptation, and delivery for smart phones. To provide media recommendations for smart phones based on all three context categories, we present a generic and flexible NtimesM-dimensional (N2M) recommendation model. The model considers context information ranging from user preference and situation to device and network capability as input for both content and presentation recommendations. We propose a hybrid recommendation approach to synergize content-based, Bayesian-classifier, and rule-based methods. Based on the recommendation model and hybrid-processing approach, we built a context-aware media recommendation platform called CoMeR to support media recommendation, adaptation, and delivery for smart phones
Down-regulation of cell growth and cell cycle regulated genes during chick osteoblast differentiation with the reciprocal expression of histone gene variants (1989)

Expression of cell cycle (core and H1 histone) and cell growth (c-myc and c-fos) regulated genes was examined in primary cultures of chick calvarial osteoblasts during a developmental sequence associated with the progressive maturation of the osteoblast in a bonelike mineralized extracellular matrix. We have identified a transition point early in the developmental sequence which occurs when proliferation ceases and expression of genes related to the differentiated phenotype of osteoblasts is initiated. During this transition period, cellular levels of RNA transcripts from core and H1 histone genes and the c-myc and c-fos protooncogenes decrease in a parallel and coordinate manner. The decline in histone gene transcription that accompanies the loss of accumulated histone mRNA indicates that the downregulation of histone gene expression is at least, in part, transcriptionally mediated. In contrast, persistence of c-myc and c-fos transcription following completion of the proliferation period, when the mRNAs are no longer present at detectable levels, suggests that the initial downregulation of protooncogene expression is controlled at the level of messenger RNA stability. Thus, two types of signaling mechanisms are operative in the down-regulation of cell proliferation genes during osteoblast differentiation--one that impinges on regulatory sequences that influence the interactions of transcription factors with cis-acting promoter elements and a second that modulates messenger RNA turnover. Of significance, downregulation of the cell cycle regulated histone genes is accompanied by a reciprocal increase in the expression of a structurally distinct subset of the histone genes that are not coupled with DNA replication during the period of expression of osteoblast phenotype markers.(ABSTRACT TRUNCATED AT 250 WORDS)
Antibodies to Cell Membrane Antigens Associated with Human T-Cell Leukemia Virus in Patients with AIDS (1983)

The acquired immune deficiency syndrome (AIDS), which has recently occurred at increasing rates in homosexual men, intravenous drug users, and others, is characterized by the development of Kaposi's sarcoma and several opportunistic infections including pneumonia caused by Pneumocystis carinii. Serum samples from patients with AIDS and from matched and unmatched control subjects were examined for the presence of antibodies to cell membrane antigens associated with human T-cell leukemia virus. Nineteen of 75 of the AIDS patients had antibodies directed to surface antigens of Hut 102, a reference T lymphoid cell line infected with leukemia virus, as did two of the 336 control subjects.
Towards Nucleotide Prodrugs Derived from 2,2-Bis(hydroxymethyl)malonate and Its Congeners: Hydrolytic Cleavage of 2-Cyano-2-(hydroxymethyl)-3-methoxy-3-oxopropyl and 3-(Alkylamino)-2-cyano-2-(hydroxymethyl)-3-oxopropyl Protections from the Internucleosidic Phosphodiester and Phosphorothioate Linkages (2002)

Thymidylyl-(3′→5′)-thymidine (TpT) and its stereoisomeric phosphoromonothioate analogs [P(R)]- and [P(S)]-Tp(s)T having the phosphate or thiophosphate linkage protected with a 2-cyano-2-{[(4,4′-dimethoxytrityl)oxy]methyl}-3-methoxy-3-oxopropyl group (see 5a,b), as well as [P(R)]-Tp(s)T bearing a S-(2-cyano-2-{[(4,4′-dimethoxytrityl)oxy]methyl}-3-oxo-3-[(2-phenylethyl)amino]propyl) protection (see 5c), were prepared. The kinetics of the cleavage of the protecting group from the corresponding detritylated compounds 6a–c was studied over a pH range from 2 to 7. All compounds undergo a hydroxide-ion-catalyzed reaction that releases the unprotected TpT (7a) or Tp(s)T (7b), in all likelihood by departure of the hydroxymethyl group as formaldehyde and concomitant elimination of the phosphodiester or phosphorothioate from the resulting carbanion. The half-life for the deprotection of 6a and 6b is ca. 6 s at pH 7 and 25°, and that of 6c ca. 600 s. The reasonably fast release of Tp(s)T from 6c offers a novel method for temporary intrachain attachment of peptides to oligonucleotides to enhance the cellular uptake.
Analysis of the rnc locus of Coxiella burnetii (1994)

A 3.2 kb EcoRI genomic DNA fragment of Coxiella burnetii was isolated by virtue of its ability to suppress mucoidy in Escherichia coli. Nucleotide sequence analysis revealed the presence of the genes homologous to rnc, era and recO of E. coli. Suppression of capsule synthesis, measured by beta-galactosidase expression in lon- cps-lac fusion strains of E. coli, is caused by gene-dosage effects of the plasmid-borne rnc genes of either C. burnetii or E. coli. The rnc gene of C. burnetii complemented rnc- E. coli hosts for lambda plaque morphology and stimulation of lambda N gene expression. We also demonstrated heterologous complementation of an E. coli strain defective for the expression of Era, an essential protein in E. coli, using the plasmid-borne C. burnetii era. Under the control of the bacteriophage lambda PL promoter, this 3.2 kb EcoRI DNA fragment directed the synthesis in E. coli of three proteins with approximate molecular masses of 35, 27 and 25 kDa. Antibodies against purified E. coli Era protein cross-reacted with the 35 kDa protein of C. burnetii on Western blots.
Development and Characterization of a Glucagon-Like Peptide 1-Albumin Conjugate (2003)

The rapid degradation of native glucagon-like peptide 1 (GLP-1) by dipeptidyl peptidase-IV (DPP-IV) has fostered new approaches for generation of degradation-resistant GLP-1 analogues. We examined the biological activity of CJC-1131, a DPP-IV-resistant drug affinity complex (DAC) GLP-1 compound that conjugates to albumin in vivo. The CJC-1131 albumin conjugate bound to the GLP-1 receptor (GLP-1R) and activated cAMP formation in heterologous fibroblasts expressing a GLP-1R. CJC-1131 lowered glucose in wild-type mice, but not in GLP-1R-/- mice. Basal glucose and glycemic excursion following glucose challenge remained significantly reduced 10-12 h following a single injection of CJC-1131. Twice daily administration of CJC-1131 to db/db mice significantly reduced glycemic excursion following oral and IP glucose challenge (P < 0.01 to 0.05) but did not significantly lower body weight during the 4-week study period. Levels of random fed glucose were significantly lower in CJC-1131-treated +/+ and db/db mice and remained significantly lower even 1 week following discontinuation of CJC-1131 administration. CJC-1131 increased levels of pancreatic proinsulin mRNA transcripts, percent islet area, and the number of bromodeoxyuridine-positive islet cells. These findings demonstrate that an albumin-conjugated DAC:GLP-1 mimics the action of native GLP-1 and represents a new approach for prolonged activation of GLP-1R signaling.
FreeDigiter: A Contact-Free Device for Gesture Control (2004)

We present FreeDigiter, an interface for mobile devices which enables rapid entry of digits using finger gestures. FreeDigiter is an infrared proximity sensor with a dual axis accelerometer and requires little signal processing. Initial laboratory experiments attain accuracy rates of 99.0%; and the system is tolerant to highly varying lighting conditions. The FreeDigiter system requires little power and could be implemented in a very small form factor appropriate for controlling in ear hearing aids, small MP3 players, and hands-free mobile phone headsets.
Exosome nanotechnology: An emerging paradigm shift in drug delivery (2011)

The demonstration that dendritic cell (DC)-derived exosomes can be exploited for targeted RNAi delivery to the brain after systemic injection provides the first proof-of-concept for the potential of these naturally occurring vesicles as vehicles of drug delivery. As well as being amenable to existing in vivo targeting strategies already in use for viruses and liposomes, this novel approach offers the added advantages of in vivo safety and low immunogenicity. Fulfilment of the potential of exosome delivery methods warrants a better understanding of their biology, as well as the development of novel production, characterisation, targeting and cargo-loading nanotechnologies. Ultimately, exosome-mediated drug delivery promises to overcome important challenges in the field of therapeutics, such as delivery of drugs across otherwise impermeable biological barriers, such as the blood brain barrier, and using patient-derived tissue as a source of individualised and biocompatible therapeutic drug delivery vehicles.
Papain catalysed peptide synthesis: control of amidase activity and the introduction of unusual amino acids (1987)

C. F. Barbas and C. Wong, J. Chem. Soc., Chem. Commun., 1987, 533 DOI: 10.1039/C39870000533
Simulation Study on Phase-Shifting Masks for Isolated Patterns (1991)

Optimization for various phase-shifting masks to fabricate 0.25-µm isolated resist patterns was carried out, and their performances were compared among themselves by simulation. They were evaluated under the assumptions that isolated patterns were located on the same layer with 0.25-µm lines and spaces with the Levenson-type phase-shifters and that the exposure dose was adjusted to the dense patterns. It was found that isolated patterns need to be designed with regard to unavoidable errors in the feature size. None of the isolated line masks studied is effective in improving resolution, except in the case where the Levenson-type phase shifter (shifter edge) can be located. All isolated space masks with optimized dimensions, in contrast, are effective in improving depth of focus for the 0.25-µm isolated pattern.
Lateral Scaling in Carbon-Nanotube Field-Effect Transistors (2003)

We have fabricated carbon-nanotube (CN) field-effect transistors with multiple, individually addressable gate segments. The devices exhibit markedly different transistor characteristics when switched using gate segments controlling the device interior versus those near the source and drain. We ascribe this difference to a change from Schottky-barrier modulation at the contacts to bulk switching. We also find that the current through the bulk portion is independent of gate length for any gate voltage, offering direct evidence for ballistic transport in semiconducting carbon nanotubes over at least a few hundred nanometers, even for relatively small carrier velocities.
Advantages of transanal hemorrhoidal dearterialization as compared to other surgical techniques for the treatment of hemorrhoidal disease. (2013)

When comparing transanal hemorrhoidal dearterialization with other methods, we found that it has an excellent aesthetic effect, requires shorter hospital stay and less analgesics, and causes less discomfort in the postoperative period.
BENEFIT OF MULTIPLE OVER SINGLE DOSES OF 3M KCL-EXTRACTED HISTOCOMPATIBILITY ANTIGEN IN THE POTENTIATING CYCLOSPORINE-INDUCED PROLONGATION OF RAT CARDIAC ALLOGRAFT SURVIVAL (1992)

Division of Immunology and Organ Transplantation, Department of Surgery, The University of Texas Medical School at Houston, Houston, Texas 77030
Activation of CDCA1-KNTC2, Members of Centromere Protein Complex, Involved in Pulmonary Carcinogenesis (2006)

We found cotransactivation of cell division associated 1 (CDCA1) and kinetochore associated 2 (KNTC2), members of the evolutionarily conserved centromere protein complex, in non-small cell lung carcinomas (NSCLC). Immunohistochemical analysis using lung cancer tissue microarray confirmed high levels of CDCA1 and KNTC2 proteins in the great majority of lung cancers of various histologic types. Their elevated expressions were associated with poorer prognosis of NSCLC patients. Knockdown of either CDCA1 or KNTC2 expression with small interfering RNA significantly suppressed growth of NSCLC cells. Furthermore, inhibition of their binding by a cell-permeable peptide carrying the CDCA1-derived 19-amino-acid peptide (11R-CDCA1(398-416)) that correspond to the binding domain to KNTC2 effectively suppressed growth of NSCLC cells. As our data imply that human CDCA1 and KNTC2 seem to fall in the category of cancer-testis antigens, and that their simultaneous up-regulation is a frequent and important feature of cell growth/survival of lung cancer, selective suppression of CDCA1 or KNTC2 activity and/or inhibition of the CDCA1-KNTC2 complex formation could be a promising therapeutic target for treatment of lung cancers.
Prediction of Survival in Follicular Lymphoma Based on Molecular Features of Tumor-Infiltrating Immune Cells (2004)

The length of survival among patients with follicular lymphoma correlates with the molecular features of nonmalignant immune cells present in the tumor at diagnosis.
Endogenous and Synthetic MicroRNAs Stimulate Simultaneous, Efficient, and Localized Regulation of Multiple Targets in Diverse Species (2006)

Recent studies demonstrated that pattern formation in plants involves regulation of transcription factor families by microRNAs (miRNAs). To explore the potency, autonomy, target range, and functional conservation of miRNA genes, a systematic comparison between plants ectopically expressing pre-miRNAs and plants with corresponding multiple mutant combinations of target genes was performed. We show that regulated expression of several Arabidopsis thaliana pre-miRNA genes induced a range of phenotypic alterations, the most extreme ones being a phenocopy of combined loss of their predicted target genes. This result indicates quantitative regulation by miRNA as a potential source for diversity in developmental outcomes. Remarkably, custom-made, synthetic miRNAs vectored by endogenous pre-miRNA backbones also produced phenocopies of multiple mutant combinations of genes that are not naturally regulated by miRNA. Arabidopsis-based endogenous and synthetic pre-miRNAs were also processed effectively in tomato (Solanum lycopersicum) and tobacco (Nicotiana tabacum). Synthetic miR-ARF targeting Auxin Response Factors 2, 3, and 4 induced dramatic transformations of abaxial tissues into adaxial ones in all three species, which could not cross graft joints. Likewise, organ-specific expression of miR165b that coregulates the PHABULOSA-like adaxial identity genes induced localized abaxial transformations. Thus, miRNAs provide a flexible, quantitative, and autonomous platform that can be employed for regulated expression of multiple related genes in diverse species.
Genetic and biochemical characterization of a mutation (fatA) that allows trans unsaturated fatty acids to replace the essential cis unsaturated fatty acids of Escherichia coli (1989)

Unsaturated fatty acid auxotrophs of Escherichia coli are able to use only unsaturated fatty acids of the cis configuration as the required growth supplement. A mutation in the fatA gene allows such auxotrophs to utilize unsaturated fatty acids with a trans double bond as well as fatty acids having a cis double bond. The fatA gene was mapped to min 69 near argG, and the allele studied (fatA1) was found to be dominant over the wild-type gene. fatA1 mutant strains grew at similar rates when supplemented with elaidate (trans-9-octadecenoate) or oleate (cis-9-octadecenoate). The fat+ strain, however, lysed when supplemented with the trans fatty acid. Physiological characterization of the fatA mutant strain was undertaken. The mutation appeared not to be involved with long-chain fatty acid transport. Introduction of lesions in known fatty acid transport genes abolished trans fatty acid utilization in the fatA mutant strain. Also, growth characteristics of the fat+ and the fatA1 mutant strains on elaidate as the sole carbon source were identical, which indicated comparables rate of fatty acid accumulation. The mutation appeared to be involved with recognition of the trans configuration after uptake into the cell. The levels of trans fatty acid incorporation into the phospholipids of the fat+ and the fatA strains differed considerably, with the mutant incorporating much higher levels. No significant accumulation of elaidate into nonphospholipid cellular components was observed. The fatA mutation did not appear to be involved with the cellular metabolic state, as cyclic AMP had no effect on the ability of the strains to utilize trans fatty acids.
RNAs with Dual Specificity and Dual RNAs with Similar Specificity (1994)

The biological role of RNA is delimited by its possible reactions, which can be explored by selection. A comparison of selected RNAs that bind one ligand with those that bind two related ligands suggests that a single nucleotide substitution can expand binding specificity. An RNA site with dual (joint) specificity has adenine and cytosine bases whose pKa's appear shifted upward, thereby mimicking an efficient general acid-base catalyst. The joint site also contains two conserved, looped arginine-coding triplets implicated in arginine site formation. Two selected joint RNAs are identical in some regions and distinct in others. The distinct regions, like some peptides, seem to function similarly without being similar in primary structure.