gebhart/patrepeval huggingface dataset:
Characterisation of the novel apoptotic and therapeutic activities of the histone deacetylase inhibitor romidepsin (2008)

Histone deacetylase inhibitors (HDACi) are compounds that target the epigenome and cause tumor cell-selective apoptosis. A large number of these agents that have different chemical structures and can target multiple HDACs are being testing in clinical trials and vorinostat is now an approved drug for the treatment of cutaneous T-cell lymphoma. Although these agents are showing promise for the treatment of hematologic malignancies, it is possible that different drugs may have different mechanistic, biological, and therapeutic activities. When comparing an HDACi belonging to the hydroxamic acid class of compounds (vorinostat) with a cyclic tetrapeptide (romidepsin), we showed that these agents regulate the expression of a common set of cellular genes, but certain genes specifically responded to each agent. Using the Emu-myc mouse model of B-cell lymphoma, we showed previously that overexpression of the prosurvival proteins Bcl-2 and Bcl-XL inhibited the apoptotic and therapeutic activities of the vorinostat. Herein, we compared and contrasted the apoptotic-inducing activities of the hydroxamic acid oxamflatin with romidepsin. Like vorinostat, oxamflatin was unable to kill lymphomas overexpressing Bcl-2 and Bcl-XL, indicating that these proteins can generally protect cells against this class of HDACi. In contrast, romidepsin was able to induce apoptosis in lymphomas overexpressing Bcl-2 with delayed kinetics of cell death and could mediate therapeutic responses against these lymphomas. However, romidepsin was inactive when Bcl-XL was overexpressed. These data provide strong support that HDACi of different chemical classes may have subtle yet potentially important differences in their molecular and biological activities.
Synthesis of a Molybdenum-Containing Silsesquioxane Which Rapidly Catalyzes the Metathesis of Olefins (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of a Molybdenum-Containing Silsesquioxane Which Rapidly Catalyzes the Metathesis of OlefinsFrank J. Feher and Tracey L. TajimaCite this: J. Am. Chem. Soc. 1994, 116, 5, 2145–2146Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/ja00084a065https://doi.org/10.1021/ja00084a065research-articleACS PublicationsRequest reuse permissionsArticle Views424Altmetric-Citations103LEARN 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
Efficient equalization hardware architecture for SC-FDMA systems without cyclic prefix (2012)

Single carrier frequency domain multiple access (SC-FDMA) system achieves better spectral efficiency when cyclic prefix (CP) is not transmitted. However, the chained turbo equalization (CHATUE) algorithm, an equalizer required to both equalize the multipath fading effect and cancel the inter-block interference of SC-FDMA without CP, requires high computational complexity due to the non-circulant structure of the past and the future interference matrices. This paper proposes efficient hardware architecture based on systolic architecture for practical implementation. The main idea is to minimize the number of required processing elements by utilizing efficient resources sharing method while exploiting concurrency of the processing. A new computation method using masking matrices is introduced to obtain interference matrix from its corresponding circulant channel matrix. The results with fixed point computation show that the computational complexity can be significantly reduced up to 96% for practical implementation without significant degradation in bit-error-rate (BER) performances.
Rapid Tracheal Infusion of Surfactant versus Bolus Instillation in Rabbits: Effects on Oxygenation, Blood Pressure and Surfactant Distribution (1996)

Rapid tracheal infusion of surfactant results in poorer oxygenation, an inhomogeneous distribution and a similar decrease in blood pressure compared to the bolus instillation method. Blood pressure changes could not be prevented by a PAF receptor-specific antagonist.
L6 monoclonal antibody binds prostate cancer (1998)

BACKGROUND Radioimmunotherapy (RIT) is a promising new modality for targeted, systemic delivery of radionuclides specifically to sites of androgen-independent metastatic prostate cancer. To be effective, RIT requires an antibody with specificity for malignant cells and appropriate pharmacokinetics in the body. METHODS Specific binding of the L6 monoclonal antibody to prostate cancer cell lines or cell lysates was determined by enzyme-linked immunoabsorbent assay (ELISA), solid-phase radioimmunoassay, and immunofluorescent staining. Biodistribution, tumor uptake, and whole body and blood clearances of 125I-L6 were determined in nude mice bearing human prostate cancer xenografts. RESULTS The L6 monoclonal antibody showed strong binding to the lysates of PC3 and DU145 prostate cancer cell lines, and 66% binding to live PC3 cells. The L6 antibody specifically targeted prostate cancer in PC3 and DU145-tumored nude mice, where approximately 10% of the injected dose of 125I-L6 bound to prostate cancer. Low-normal organ uptake was found, and the blood clearances were similar in each group of tumored mice. CONCLUSIONS The L6 monoclonal antibody targets human prostate cancer xenografts in nude mice and has low-normal organ uptake. Therefore, further study of the radiolabeled L6 monoclonal antibody for RIT of prostate cancer is warranted. Prostate 37:91–97, 1998. © 1998 Wiley-Liss, Inc.
Comparison of Upper Gastrointestinal Toxicity of Rofecoxib and Naproxen in Patients with Rheumatoid Arthritis (2000)

In patients with rheumatoid arthritis, treatment with rofecoxib, a selective inhibitor of cyclooxygenase-2, is associated with significantly fewer clinically important upper gastrointestinal events than treatment with naproxen, a nonselective inhibitor.
Controversies in the Medical Management of Persistent and Recurrent Acute Otitis Media Recommendations of a Clinical Advisory Committee (2000)

Streptococcus pneumoniae is the predominant bacterial pathogen associated with acute otitis media (AOM), causing an estimated 7 million cases annually in the United States. Bacterial resistance should be considered when selecting an antimicrobial agent for otitis media. Significant increases in drug-resistant S pneumoniae are documented worldwide, and less than 50% of S pneumoniae strains are fully susceptible to penicillin in some regions of the United States. Although amoxicillin is recommended for uncomplicated AOM, treatment guidelines should be flexible and adaptable, taking into consideration local and regional susceptibility patterns, the age of the patient, the frequency of prior infections, and the response to prior therapy. Resistant organisms are more prevalent in children younger than 2 years of age and in those who have recurrent or persistent AOM. Overdiagnosing AOM, selecting inappropriate empiric therapy, or both, leads to overuse and misuse of antibiotics and causes increased drug resistance. This article reviews persistent and recurrent AOM and discusses the pitfalls of diagnosis and the practical limitations of current treatment recommendations.
Evidence for a Structural Requirement for the Aggregation of Platelets by Collagen (1974)

This study investigates whether soluble collagen can initiate platelet aggregation or whether a higher degree of polymerization is required. Purified rat skin collagen was prepared in four states. Soluble monomeric collagen, containing 2 muM calcium chloride, was maintained at 4 degrees C until use. A previously uncharacterized form of collagen, soluble microfibrillar collagen, was prepared from monomeric collagen containing calcium chloride by allowing it to polymerize at 23 degrees C. Viscometric and electron microscopic characterization of microfibrillar collagen indicated polymerization to ordered native filaments. Particulate native macrofibrillar collagen was prepared from monomeric collagen by allowing it to polymerize at 37 degrees C in the absence of calcium. Particulate collagen, in which the fibers were randomly associated, was prepared by salt precipitation of calcium-free monomeric collagen. Microfibrillar and native macrofibrillar collagen initiated platelet aggregation, with a lag phase of approximately 60 s. Monomeric collagen initiated aggregation with a lag phase of approximately 180 s. The duration of the lag phase for platelet aggregation initiated by monomeric collagen was independent of the dose. Salt-precipitated particulate collagen did not initiate platelet aggregation. Agents which prolong the transition from monomeric collagen to fibrillar collagen (urea, arginine) retarded or prevented the aggregation of platelets by monomeric collagen. Sodium borohydride, which stabilizes the intraand intermolecular cross-links of collagen did not affect platelet aggregation. Penicillamine, which displaces the intermolecular cross-links and binds the intramolecular cross-links of collagen, did not prevent platelet aggregation. The data suggest that an architectural requirement exists for the initiation of self-perpetuating platelet aggregation; that tropocollagen units do not fulfill this requirement; that a soluble collagen preparation, microfibrillar collagen, contains the minimal structural unit; and that cross-linkages within collagen do not play a critical role in platelet aggregation.
Virtual Private Networks Identifier (1999)

Virtual Private IP networks may span multiple Autonomous Systems or Service Providers. There is a requirement for the use of a globally unique VPN identifier in order to be able to refer to a particular VPN (see section 6.1.1 of [1]). This document proposes a format for a globally unique VPN identifier.
1,8‐Naphthyridines. Part I. Synthesis of some trifluoromethyl‐1,8‐naphthyridine derivatives (1976)

Abstract The synthesis of some 2‐amino‐1,8‐naphthyridine derivatives substituted in the 5‐ and/or 7‐positions with trifluoromethyl is described along with their conversions to the corresponding 1,8‐naphthyridin‐2(1 H )ones. A modified procedure for oxidizing electron‐deficient heterocyclic compounds to their N ‐oxides is presented.
MINIMUM REDUNDANCY FEATURE SELECTION FROM MICROARRAY GENE EXPRESSION DATA (2005)

How to selecting a small subset out of the thousands of genes in microarray data is important for accurate classification of phenotypes. Widely used methods typically rank genes according to their differential expressions among phenotypes and pick the top-ranked genes. We observe that feature sets so obtained have certain redundancy and study methods to minimize it. We propose a minimum redundancy - maximum relevance (MRMR) feature selection framework. Genes selected via MRMR provide a more balanced coverage of the space and capture broader characteristics of phenotypes. They lead to significantly improved class predictions in extensive experiments on 6 gene expression data sets: NCI, Lymphoma, Lung, Child Leukemia, Leukemia, and Colon. Improvements are observed consistently among 4 classification methods: Naive Bayes, Linear discriminant analysis, Logistic regression, and Support vector machines. SUPPLIMENTARY: The top 60 MRMR genes for each of the datasets are listed in http://crd.lbl.gov/~cding/MRMR/. More information related to MRMR methods can be found at http://www.hpeng.net/.
Purification and physiological evaluation of a guanylate cyclase activating protein from retinal rods. (1994)

In retinal rods light triggers a cascade of enzymatic reactions that increases cGMP hydrolysis and generates an electrical signal by causing closure of cGMP-gated ion channels in the photoreceptor outer segment. This leads to a decrease in internal Ca, which activates guanylate cyclase and promotes photoresponse recovery by stimulating the resynthesis of cGMP. We report here that the activation of guanylate cyclase by low Ca is mediated by an approximately 20-kDa protein purified from bovine rod outer segments by using DEAE-Sepharose, hydroxylapatite, and reverse-phase chromatographies. In a reconstituted system, this protein restores the Ca-sensitive regulation of guanylate cyclase and when dialyzed into functionally intact lizard rod outer segment decreases the sensitivity, time to peak, and recovery time of the flash response.
Effects of nucleotide sequence on the specificity of rne-dependent and RNase E-mediated cleavages of RNA I encoded by the pBR322 plasmid. (1994)

RNase E, an endoribonuclease encoded by the Escherichia coli ams/rne/hmp1 locus, cleaves RNA I, an antisense regulator of the replication of ColE1 type plasmids, in a single-stranded region near its 5' end. The rne-3071 mutation prolongs the RNA 1 half-life in cells cultured at an elevated temperature and imparts temperature sensitivity on RNase E isolated from the mutant strain. Here we report the effects of specific sequence changes introduced by site-directed mutagenesis on the location of ribonucleolytic cleavage near the 5' end of pBR322 RNA I in rne-3071 and congenic rne+ E. coli and on cleavage of RNA I by RNase E in vitro. Primer extension analyses showed that the occurrence and position of cleavages in vivo and in vitro are altered highly specifically by sequence changes but that the site of cleavage bears no simple relationship to a particular nucleotide order. Our results do not support either the notion that cleavage by RNase E is determined by a consensus sequence or the contrary view that RNase E is a virtually nonspecific single-stranded endonuclease with a preference for cutting 5' to an AU dinucleotide.
Old or Frail: What Tells Us More? (2004)

Using frailty as the criterion to select older persons at risk for interventions may be better than selecting persons based only on their chronological age.
Bismuth Subcitrate and Omeprazole Inhibit <i>Helicobacter pylori</i>F<sub>1</sub>-ATPase (1995)

The effects of various types of antiulcer agents against Helicobacter pylori F1-ATPase were studied. ATPase was released into the aqueous phase (i.e., solubilized) by sonication. The enzyme activity depended on Mg2+, but not Ca2+. The maximum activity occurred at an ATP/Mg2+ ratio of 1/5 and at pH 7.5. Mg(2+)-dependent ATPase activity was inhibited by sodium azide and the monovalent cations K+ and Na+, but not by oligomycin, dicyclohexylcarbodiimide, ouabain, or SCH 28080. The antiulcer agents ranitidine, pirenzepine, aluminum hydroxide, and sucralfate failed to influence H. pylori F1-ATPase. In contrast, bismuth subcitrate and the H+/K(+)-ATPase inhibitor omeprazole inhibited the enzyme. Inhibition was prevented and reversed by the mercaptan glutathione, indicating that both drugs interfere with sulfhydryl groups of the enzyme. The data suggest that bismuth subcitrate and omeprazole owe their antibacterial activity against H. pylori, at least in part, to inhibition of F1-ATPase, an enzyme involved in bacterial energy metabolism.
[New therapeutic possibilities for disseminated sclerosis?]. (1994)

Multiple sclerosis is a demyelinating disease of unknown origin. Immunological processes are thought to be of pathophysiological importance. Immunosuppressive treatment has been tried with various drugs in order to influence the immunological process. Steroid hormones are able to reduce the duration of an acute attack, but have no influence on the long-term progression. Cyclophosphamide can reduce disease activity a little, but has severe side effects. Azathioprine may reduce the frequency of acute attacks and disease progression a little. Cyclosporine A in the treatment of multiple sclerosis is only effective in doses so high that the side effects are unacceptable. Plasmapheresis in combination with immunosuppressive treatment is shown to stabilize the disease in some experiments. Intravenous polyclonal immunoglobulin has shown promising results in the treatment of other immunologically based diseases, and is a potentially beneficial treatment in multiple sclerosis. At Rigshospitalet, ongoing clinical trials will evaluate the efficacy of plasmapheresis and polyclonal immunoglobulin.
A promoting role of androgen receptor in androgen-sensitive and -insensitive prostate cancer cells (2007)

Although the vital role of the androgen receptor (AR) has been well demonstrated in primary prostate cancers, its role in the androgen-insensitive prostate cancers still remains unclear. Here, we used a small hairpin RNA approach to directly assess AR activity in prostate cancer cells. Reduction of AR expression in the two androgen-sensitive prostate cancer cell lines, LNCaP and LAPC4, significantly decreased AR-mediated transcription and cell growth. Intriguingly, in two androgen-insensitive prostate cell lines, LNCaP-C42B4 and CWR22Rv1, knockdown of AR expression showed a more pronounced effect on AR-induced transcription and cell growth than androgen depletion. Using cDNA microarrays, we also compared the transcriptional profiles induced by either androgen depletion or AR knockdown. Although a significant number of transcripts appear to be regulated by both androgen depletion and AR knockdown, we observed a subset of transcripts affected only by androgen depletion but not by AR knockdown, and vice versa. Finally, we demonstrated a direct role for AR in promoting tumor formation and growth in a xenograft model. Taken together, our results elucidate an important role for the AR in androgen-insensitive prostate cancer cells, and suggest that AR can be used as a therapeutic target for androgen-insensitive prostate cancers.
Ordered and Disordered Patterns in Two-Phase Flows in Microchannels (2003)

We show that wetting properties crucially control the patterns in two-phase flows of immiscible fluids in microchannels. Ordered patterns, continuously entrained by the flow, are obtained when one phase completely wets the walls, while disordered patterns, intermittently adhering to the channel walls, are unavoidably produced when wetting is partial. A lower limit for the channel sizes capable of generating well structured objects (drops, pears, pearl necklaces, ...) is presented.
Joint transcoding of multiple MPEG video bitstreams (2003)

This paper addresses the problem of bit-rate conversion of a previously compressed video. We provide an MPEG joint transcoder for transcoding several video bitstreams simultaneously. We show that joint transcoding reduces the quality variation between multiple video sequences, as compared to independently transcoding each sequence at a fixed bit rate. Hence, joint transcoding results in a better utilization of the channel capacity. The joint transcoder can be used in a congested communication network as an alternative to data/packet dropping, and in applications which require multiplexing video signals onto a fixed communication channel such as video servers providing video on demand (VOD) service.
Contact and delayed hypersensitivity in the mouse. I. Active sensitization and passive transfer. (1968)

Ear swelling in mice was measured with a micrometer and used to quantify 24-hour skin reactions. Specific contact sensitivity occurred in mice immunized with picryl chloride, 2-phenyl-4-ethoxymethylene oxazolone, dinitrofluorobenzene and tetramethyl-p-phenylenediamine as shown by ear swelling 24 hours after challenge. In some mice sensitized with oxazolone significant swelling occurred 4 hours after challenge. It was possible to induce tolerance in adult mice and contact sensitivity to dinitrochlorobenzene was diminished by prior treatment with dinitrobenzenesulphonic acid. There was some evidence of delayed hypersensitivity to protein antigens. Twenty-four-hour skin reactions to PPD (purified protein derivative of tuberculin) occurred in mice immunized with live BCG or dead tubercle bacilli in Freund's adjuvant. In most experiments the swelling at 24 hours was greater than at 4 hours. Similar reactions to egg albumin and bovine γ-globulin were seen in mice immunized with these antigens in Freund's complete adjuvant and one group of mice showed greater swelling at 24 hours after challenge than at 4 hours. Contact sensitivity was readily transferred in inbred mice by peritoneal exudate cells when the challenge was undertaken immediately after transfer. Variable and usually inferior passive transfer was obtained with lymph node cells. Attempts to transfer contact sensitivity in outbred mice were unsuccessful.
‘All‐or‐none’ mechanism of the molten globule unfolding (1992)

The Gdm-HCl-induced unfolding of bovine carbonic anhydrase B and S. aureus beta-lactamase was studied at 4 degrees C by a variety of methods. With the use of FPLC it has been shown that within the transition from the molten globule to the unfolded state the distribution function of molecular dimensions is bimodal. This means that equilibrium intermediates between the molten globule and the unfolded states are absent, i.e. the molten globule unfolding follows the 'all-or-none' mechanism.
Laser-Capture Microdissection: Refining Estimates of the Quantity and Distribution of Latent Herpes Simplex Virus 1 and Varicella-Zoster Virus DNA in Human Trigeminal Ganglia at the Single-Cell Level (2005)

There remains uncertainty and some controversy about the percentages and types of cells in human sensory nerve ganglia that harbor latent herpes simplex virus 1 (HSV-1) and varicella-zoster virus (VZV) DNA. We developed and validated laser-capture microdissection and real-time PCR (LCM/PCR) assays for the presence and copy numbers of HSV-1 gG and VZV gene 62 sequences in single cells recovered from sections of human trigeminal ganglia (TG) obtained at autopsy. Among 970 individual sensory neurons from five subjects, 2.0 to 10.5% were positive for HSV-1 DNA, with a median of 11.3 copies/positive cell, compared with 0.2 to 1.5% of neurons found to be positive by in situ hybridization (ISH) for HSV-1 latency-associated transcripts (LAT), the classical surrogate marker for HSV latency. This indicates a more pervasive latent HSV-1 infection of human TG neurons than originally thought. Combined ISH/LCM/PCR assays revealed that the majority of the latently infected neurons do not accumulate LAT to detectable levels. We detected VZV DNA in 1.0 to 6.9% of individual neurons from 10 subjects. Of the total 1,722 neurons tested, 4.1% were VZV DNA positive, with a median of 6.9 viral genomes/positive cell. After removal by LCM of all visible neurons on a slide, all surrounding nonneuronal cells were harvested and assayed: 21 copies of HSV-1 DNA were detected in approximately 5,200 nonneuronal cells, while nine VZV genomes were detected in approximately 14,200 nonneuronal cells. These data indicate that both HSV-1 and VZV DNAs persist in human TG primarily, if not exclusively, in a moderate percentage of neuronal cells.
The effects of miglitol on glucagon‐like peptide‐1 secretion and appetite sensations in obese type 2 diabetics (2002)

Miglitol induced an enhanced and prolonged GLP-1 release at high physiological concentrations after ingesting an ordinary meal in glycaemic-controlled diabetics. The excessive postprandial GLP-1 elevation after miglitol therapy modified feeding behaviour and food intake, and thereby has potential value in regulating appetite and stabilizing body weight in obese type-2-diabetic patients.