gebhart/patrepeval huggingface dataset:
Structural implications for K5/K12‐di‐acetylated histone H4 recognition by the second bromodomain of BRD2 (2010)

The BET family proteins recognize acetylated chromatin through their two bromodomains, acting as transcriptional activators or tethering viral genomes to the mitotic chromosomes of their host. The structural mechanism for how the N-terminal bromodomain of human BRD2 (BRD2-BD1) deciphers the mono-acetylated status of histone H4 tail was recently reported. Here we show the crystal structure of the second bromodomain of BRD2 (BRD2-BD2) in complex with the di-acetylated histone H4 tail (H4K5ac/K12ac). To our surprise, a single K5ac/K12ac peptide interacts with two BRD2-BD2 molecules simultaneously: the K5ac residue binds to one BRD2-BD2 molecule while the K12ac residue binds to another. These results provide a structural basis for the recognition of two different patterns of the histone acetylation status by a single bromodomain.
Abstract A25: PPP2R1A mutations affect PP2A complex formation, and novel protein interactions in gynecological carcinoma cell lines (2013)

Abstract Gynecological malignancies (ovarian clear cell and endometrioid carcinomas, endometrial serous, endometrioid and clear cell carcinomas) harbor somatic mutations in the gene PPP2R1A, the scaffolding subunit of the serine/threonine protein phosphatase 2A (PP2A) complex. The PP2A complex is composed of an A (scaffold), C (catalytic) subunit, and different B (regulatory) subunits. The PPP2R1A mutations are proposed to play a role in PP2A B-subunit binding, and thus formation of a functional PP2A phosphatase complex. The aim of this study is to determine how PPP2R1A mutations affect the binding of B-subunits and other novel interactions within the context of ovarian and endometrial carcinomas. The ovarian clear cell line RMG2 and endometrial carcinoma cell lines Hec-1-A and Hec50 all harbor PPP2R1A mutations. The mismatch repair deficient cell line Hec-1-A express a PPP2R1A W257L heterozygous mutation; therefore somatic cell knockout technology was used to generate isogenic PPP2R1A clones that express only mutant PPP2R1A, and clones that express more wild-type than mutant. These Hec-1-A isogenic cell lines were used for PPP2R1A co-immunoprecipiation (Co-IP) followed by MS/MS-SWATHTM analysis to identify PP2A B-subunits and other novel protein interactions. Our preliminary results using Hec-1-A isogenic cell lines suggest that some PP2A B-subunits (PPP2R5D and PPP2R2A) are found to be decreased in abundance in the mutant cell lines. We were able to identify the catalytic subunit (PPP2CA) in PPP2R1A Co-IPs in all cell lines. We also show that PPP2R1A interacts with novel proteins such as histones (Histone 1, Histone H2B type 1-N), ubiquitin ligases (TRIM21) and proteins involved in mitotic control (ANKLE2). Of particular interest we have identified the cancer gene nucleophosmin (NPM1) as a potential novel interactor of PP2A. We have established the isogenic Hec-1-A cell lines as a model system to determine the functional effects of a somatic PPP2R1A mutation. These cell lines have shown that the PPP2R1A mutation affects the ability of some B-subunits to interact and form the PP2A complex. We have also shown that PP2A may interact with novel proteins such as NPM1 and histones. Ongoing work will be completed to determine how these interactions function in the context of ovarian and endometrial carcinomas. Citation Format: Melissa K. McConechy, Vincent Chen, Gregg Morin, James Brenton, David G. Huntsman. PPP2R1A mutations affect PP2A complex formation, and novel protein interactions in gynecological carcinoma cell lines. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A25.
ChemInform Abstract: Indium Trifluoromethanesulfonate (In(OTf)3). A New Catalyst for Beckmann Rearrangement of Ketoximes and Facile Dehydration of Aldoximes. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Cancer Immunotherapy: The Role Regulatory T Cells Play and What Can be Done to Overcome their Inhibitory Effects (2009)

Since multiple lines of experimental and clinical data clearly identified regulatory T cells as an integral part of the immune response, these cells have become a major focus of investigation in tumor immunology. Regulatory T cells are in place to dampen ongoing immune responses and to prevent autoimmunity, but they also have profound effects in blocking therapeutic anti-tumor activity. Therefore regulatory T cells are seen as a major hurdle that must be overcome in order for cancer immunotherapy to reach its therapeutic potential. Regulatory T cells are heterogeneous with sub-populations that exhibit distinct functional features. Here we will review the individual sub-populations in regards to their mode of action and their potential impact on blocking anti-tumor immunity. Approaches to measure function and frequency of regulatory T cells in model systems and clinical trails will be discussed. Finally, we will describe possible ways to interfere with regulatory T cell-mediated immune suppression with the focus on recent pre-clinical and clinical findings.
Handset-dependent background models for robust text-independent speaker recognition (2002)

This paper studies the effects of handset distortion on telephone-based speaker recognition performance, resulting in the following observations: (1) the major factor in speaker recognition errors is whether the handset type (e.g., electret, carbon) is different across training and testing, not whether the telephone lines are mismatched, (2) the distribution of speaker recognition scores for true speakers is bimodal, with one mode dominated by matched handset tests and the other by mismatched handsets, (3) cohort-based normalization methods derive much of their performance gains from implicitly selecting cohorts trained with the same handset type as the claimant, and (4) utilizing a handset-dependent background model which is matched to the handset type of the claimant's training data sharpens and separates the true and false speaker score distributions. Results on the 1996 NIST Speaker Recognition Evaluation corpus show that using handset-matched background models reduces false acceptances (at a 10% miss rate) by more than 60% over previously reported (handset-independent) approaches.
Inhibition of transport processes of intestinal segments following augmentation enterocystoplasty in rats. (1996)

Pathophysiologic derangements in intestinal segments interposed in the urinary tract include inhibition of sodium and chloride transport processes and mucosal hyperplasia. The use of the Ussing chamber/voltage clamp technique described herein offers a new approach for additional studies of the metabolic consequences following urinary diversion.
Wissenslogistik - Die "Link-Kultur" als neues Paradigma der betrieblichen Organisationsentwicklung (2010)

Die betriebliche Organisation der Zukunft wird vor allem daran gemessen werden, in welchem Maße sie es schafft neues Wissen aufzunehmen, bestehendes Wissen zu entwickeln und in die internen Prozesse einzubringen. Abhängig ist dies von den intraorganisationalen Kommunikations- und Beziehungsstrukturen des Unternehmens. Die unter dem Schlagwort „Web 2.0“ zusammengefassten interaktiven, Community-orientierten Services, z.B. Wikis, soziale Netzwerke oder Twitter, eröffnen Unternehmen vollkommen neue Möglichkeiten der Kommunikation, der Unterstützung und Abbildung sozialer Beziehungen sowie des Wissensaustausches. Mit dem zunehmenden Einzug junger, internet-affiner Menschen in die Arbeitswelt verschärft sich diese Entwicklung. Unternehmen stehen vor der Herausforderung, diese neuen Kommunikationsangebote im betrieblichen Umfeld nutzbar zu machen und zielführend einzusetzen. Die neuen Medien eignen sich in hohem Maße für den Transport und Austausch von Informationen und Wissen, die als Produktionsfaktoren weiter an Bedeutung gewinnen werden. Dabei gilt zu beachten, dass sich Kommunikations- und Wissensprozesse externen Steuerungs- und Planungsansätzen einer übergeordneten Managementfunktion weitgehend entziehen. Im Hinblick auf das noch junge Konzept der Wissenslogistik ist zu beachten, dass eine direkte Gestaltungsmöglichkeit nur über die kommunikative Infrastruktur des Unternehmens möglich scheint. Unter Wissenslogistik ist die Planung, Gestaltung, Steuerung und Kontrolle der betrieblichen Kommunikationsmedien vor dem Hintergrund logistischer Prinzipien und Prinzipien der Selbstorganisation zu verstehen. Sie stellt kommunikative Transport-, Umschlags- und Lagerungstechniken bereit, ohne den Anspruch einer direkten Steuer- und Planbarkeit von Kommunikations- und Wissensprozessen zu haben. Ziel der Dissertation ist es einen Gestaltungsansatz der betrieblichen Kommunikationswege zum Aufbau und Erhalt nachhaltiger Kommunikations- und Beziehungsstrukturen zu entwickeln. Die drei Forschungsfragen der Arbeit betreffen Themenbereiche an der Schnittstelle zwischen Wirtschaftsinformatik, betriebswirtschaftlicher Organisationslehre und Logistik. Erstens, welche Möglichkeiten bieten sich für die Gestaltung der betrieblichen Kommunikationswege im Unternehmen? Zweitens, welchen Beitrag kann das Konzept der Wissenslogistik im Hinblick auf das Management von Wissens- und Kommunikationsprozessen leisten? Und drittens, wie können Strukturen und Instrumente des WWW für die Gestaltung der kommunikativen Infrastruktur von Unternehmen adaptiert und eingesetzt werden? Die Arbeit basiert auf einer anwendungsorientierten, qualitativen Forschungsmethodik, deren Kern eine umfangreiche Literaturanalyse und sieben Experteninterviews bilden.
Asymmetric Reactions of Axially Chiral Amides: Use of Removable ortho‐Substituents in Radical Cyclizations of o‐Iodoacrylanilides and N‐Allyl‐N‐o‐iodoacrylamides. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
On minimal coverings and pairwise generation of some primitive groups of wreath product type (2023)

The covering number of a finite group $G$, denoted $σ(G)$, is the smallest positive integer $k$ such that $G$ is a union of $k$ proper subgroups. We calculate $σ(G)$ for a family of primitive groups $G$ with a unique minimal normal subgroup $N$, isomorphic to $A_n^m$ with $n$ divisible by $6$ and $G/N$ cyclic. This is a generalization of a result of E. Swartz concerning the symmetric groups. We also prove an asymptotic result concerning pairwise generation.
Reactivity of Zinc(II) 5-Oxoniaprotoporphyrin-IX: Synthesis of the First 5-Oxonia-15-phlorin (1999)

The reactivity of zinc(II) 5-oxoniaprotoporphyrin-IX with selected carbon nucleophiles is demonstrated to be highest at the 15-C(meso) position, enabling the first synthesis of a 5-oxonia-15-phlorin which has been isolated and studied by X-Ray crystallography.
Performance Versus Complexity Study of Neural Network Equalizers in Coherent Optical Systems (2021)

We present the results of the comparative performance-versus-complexity analysis for the several types of artificial neural networks (NNs) used for nonlinear channel equalization in coherent optical communication systems. The comparison is carried out using an experimental set-up with the transmission dominated by the Kerr nonlinearity and component imperfections. For the first time, we investigate the application to the channel equalization of the convolution layer (CNN) in combination with a bidirectional long short-term memory (biLSTM) layer and the design combining CNN with a multi-layer perceptron. Their performance is compared with the one delivered by the previously proposed NN-based equalizers: one biLSTM layer, three-dense-layer perceptron, and the echo state network. Importantly, all architectures have been initially optimized by a Bayesian optimizer. First, we present the general expressions for the computational complexity associated with each NN type; these are given in terms of real multiplications per symbol. We demonstrate that in the experimental system considered, the convolutional layer coupled with the biLSTM (CNN+biLSTM) provides the largest Q-factor improvement compared to the reference linear chromatic dispersion compensation (2.9 dB improvement). Then, we examine the trade-off between the computational complexity and performance of all equalizers and demonstrate that the CNN+biLSTM is the best option when the computational complexity is not constrained, while when we restrict the complexity to some lower levels, the three-layer perceptron provides the best performance.
CMOS image sensor for recording of intrinsic-optical-signal of the brain (2009)

Intrinsic optical signal (IOS) indicates activities of cerebral cortical neurons in the optical imaging method, which is one of the in vivo recording methods of activities of cerebral cortical neurons. We propose the IOS imaging method for craniotomy procedure such as diagnostic use of epilepsy surgery. We designed a prototype CMOS image sensor device using 0.35-¿m CMOS standard process for in vivo IOS imaging. The sensor device enables multi-functional recording of brain activities such as IOS, EEG, area image, electrical stimulation in order to improve reliability of diagnosis and allows simple measurement setup. Preliminary experiments using the fabricated device are demonstrated to detect hemoglobin filled in a blood vessel phantom.
Improved color rendering and luminous efficacy in phosphor-converted white light-emitting diodes by use of dual-blue emitting active regions (2009)

Conventional white-light sources suffer from a fundamental trade-off between color rendering index and the luminous efficacy; increasing one generally comes at the expense of the other. We demonstrate through simulation that dual-wavelength blue-emitting active regions in phosphor-converted white light sources maximize the output luminous flux while significantly increasing the color rendering ability. Our results indicate that such improvements can be achieved over a broad range of correlated color temperatures.
Aspirin reduced the incidence of colorectal cancer during 23-year follow-up in healthy men or patients with recent TIA (2007)

TherapeuticsNovember 1, 2007Aspirin reduced the incidence of colorectal cancer during 23-year follow-up in healthy men or patients with recent TIAVincent W.S. Wong, MD, Francis K.L. Chan, MDVincent W.S. Wong, MDChinese University of Hong Kong, Hong Kong SAR, China (V.W.W., F.K.C.)Search for more papers by this author, Francis K.L. Chan, MDChinese University of Hong Kong, Hong Kong SAR, China (V.W.W., F.K.C.)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/ACPJC-2007-147-3-072 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareFacebookTwitterLinkedInRedditEmail Source CitationFlossmann E, Rothwell PM. Effect of aspirin on long-term risk of colorectal cancer: consistent evidence from randomised and observational studies. Lancet. 2007;369:1603-13. https://pubmed.ncbi.nlm.nih.gov/17499602Clinical Impact RatingsGIM/FP/GP: Gastroenterology: Oncology: References1 Weitz J, Koch M, Debus J, et al. Colorectal cancer. Lancet. 2005;365:153-65. [PMID: 15639298] Google Scholar2 Arber N, Eagle CJ, Spicak J, et al. Celecoxib for the prevention of colorectal adenomatous polyps. N Engl J Med. 2006;355:885-95. [PMID: 16943401] Google Scholar3 Stürmer T, Glynn RJ, Lee IM, et al. Aspirin use and colorectal cancer: post-trial follow-up data from the Physicians' Health Study. Ann Intern Med. 1998;128:713-20. [PMID: 9556464] Google Scholar4 Cook NR, Lee IM, Gaziano JM, et al. Low-dose aspirin in the primary prevention of cancer: the Women's Health Study: a randomized controlled trial. JAMA. 2005;294:47-55. [PMID: 15998890] Google Scholar5 Dube C, Rostom A, Lewin G, et al. The use of aspirin for primary prevention of colorectal cancer: a systematic review prepared for the U.S. Preventive Services Task Force. Ann Intern Med. 2007;146:365-75. [PMID: 17339622] Google Scholar Author, Article, and Disclosure InformationAffiliations: Chinese University of Hong Kong, Hong Kong SAR, China (V.W.W., F.K.C.) PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails November 1, 2007Volume 147, Issue 3Page: 72KeywordsAlcoholismCancer treatmentColonoscopyColorectal cancerDrugsHemorrhageHemorrhagic strokeIschemic strokeMyocardial infarctionObstetrics and gynecologyPeptic ulcersPhysiciansRenal failureStrokeToxicityTransient ischemic attacksUlcers ePublished: 9 March 2020 Issue Published: November 1, 2007 Copyright & PermissionsCopyright © 2007 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Identification of Relaxin-3/INSL7 as an Endogenous Ligand for the Orphan G-protein-coupled Receptor GPCR135 (2003)

GPCR135, publicly known as somatostatin- and angiotensin-like peptide receptor, is expressed in the central nervous system and its cognate ligand(s) has not been identified. We have found that both rat and porcine brain extracts stimulated 35S-labeled guanosine 5'-O-(3-thiotriphosphate) (GTPgammaS) incorporation in cells over-expressing GPCR135. Multiple rounds of extraction, purification, followed by N-terminal sequence analysis of the ligand from porcine brain revealed that the ligand is a product of the recently identified gene, relaxin-3 (aka insulin-7 or INSL7). Recombinant human relaxin-3 potently stimulates GTPgammaS binding and inhibits cAMP accumulation in GPCR135 overexpressing cells with EC50 values of 0.25 and 0.35 nM, respectively. 125I-Relaxin-3 binds GPCR135 at high affinity with a Kd value of 0.31 nM. Relaxin-3 is the only member of the insulin/relaxin superfamily that can activate GPCR135. In situ hybridization showed that relaxin-3 mRNA is predominantly expressed in the dorsomedial ventral tegmental nucleus of the brainstem (aka nucleus incertus), as well as in discrete cells in the lateral periaqueductal gray and in the central gray nucleus. GPCR135 is expressed abundantly in the hypothalamus with discrete expression in the paraventricular nucleus of the hypothalamus and supraoptic nucleus, as well as in the cortex, septal nucleus, and preoptical area. Relaxin-3 has previously been shown to bind and activate the LGR7 relaxin receptor. However, we believe that neuroanatomical colocalization of GPCR135 and relaxin-3, coupled with a clear high affinity interaction, suggest that GPCR135 is the receptor for relaxin-3. The identification of relaxin-3 as the ligand for GPCR135 provides the framework for the discovery of a new brainstem/hypothalamus circuitry.
In Vitro Transcription of the Gal Operon Requires Cyclic Adenosine Monophosphate and Cyclic Adenosine Monophosphate Receptor Protein (1971)

In a transcription system containing Xpgal8 DNA as template and Escherichia coli RNA polymerase, the addition of cyclic adenosine monophosphate receptor protein (CRP) and 3',5'-cyclic AMP causes a 15-fold increase in gal mRNA synthesis.Gal mRNA was measured by hybridizing the 13H]RNA product to the separated strands of Xpgal8 DNA after removal of X mRNA by preliminary hybridization to X DNA.Competition experiments indicate that a large fraction of this RNA is identical with in vivo gQl mRNA.With Xpgal8 DNA as template but not with X DNA, 3',5'-cyclic AMP and CRP cause a 2-fold increase in X mRNA.Since the increment in h mRNA hybridizes to the left-hand half of the 1 strand of X DNA and is abolished by the addition of p, it is interpreted as read through from the 3',5'-cyclic AMP-CRP sensitive site in the gQl region of Xpgal8 DNA.The concentrations of CRP and 3',5'-cyclic AMP necessary for half-maximal stimulation of gal mRNA synthesis are 5 X 10e8 and 5 X 10e6 M, respectively.2',3'-Cyclic AMP and 5'-AMP do not stimulate gal mRNA synthesis; 3',5'cyclic GMP is an inhibitor.When 3',5' cyclic AMP, CRP, DNA, and RNA polymerase are incubated together for 10 min, a rifampicin-resistant preinitiation complex is formed, and, upon the addition of nucleoside triphosphates, gal mRNA synthesis occurs.3',5'-Cyclic GMP prevents the formation of this complex and can dissociate it after it has been formed.These results suggest that 3',5'-cyclic AMP and CRP stimulate gal transcription at a step prior to chain elongation.Cyclic AMP' is required for the synthesis of galactokinase and a number of other inducible enzymes in Escherichiu coli (1).
Effects of Insulin and Insulin-like Agents on the Glucose Transport System of Cultured Human Fibroblasts (1981)

We have studied the effects of insulin and insulin-like agents on glucose transport by cultured human fibro-blast monolayers. Initial rates of glucose transport were determined by measurement of 2-deoxy-D-glu-cose uptake. At physiologic concentrations, insulin stimulates 2-deoxy-D-glucose transport (average of 50% over basal) with a half-maximally effective insulin concentration of 3.3 ± 0.9 ng/ml. This effect of insulin is rapid and is half-maximal at 10 min and becomes maximal by about 30 min. Kinetic analyses showed that insulin increased the transport Vmax from 7.4 ± 0.9 nmol/min/106 cells to 11.0 ± 1.5 nmol/min/106 cells and had no effect on the Km value (2.5 ± 0.3 mM). While glucose starvation led to a higher overall rate of 2-deoxy-D-glucose transport, the relative stimulation by insulin was the same as in non-glucose-starved cells. Insulin mimickers [insulin-like growth factor (IGF), anti-insulin receptor antibody, and concanavalin A] also stimulate 2-deoxy-D-glucose transport by human fibroblast monolayers in a dose-dependent manner and the maximal effects of IGF and anti-insulin receptor antibody were the same as that of insulin, while the maximal effect of concanavalin A was only 78% of that of insulin. The maximal effects of either insulin and IGF or insulin and anti-insulin receptor antibody were not additive, suggesting that these agents all act via the same glucose transport effector system in human fibroblasts. In conclusion, human fibroblasts possess an insulin-sensitive glucose transport system that displays many of the characteristics common to other more well studied transport systems. Thus, cultured human fibroblasts can serve as an important model for physiologic studies of insulin action and glucose transport, and for studies of pathophysiologic abnormalities of these processes in cells obtained from patients with various disease states.
Oleylamine Assisted Synthesis of Ultralong Copper Nanowires (2015)

This paper reports the hydrothermal synthesis of smooth and ultralong copper nanowires (Cu NW) prepared using oleylamine (OM), oleic acid (OA), and Cl- ion as coordinating and etching agents respectively. Cu nanowires with mean diameters around 82.3 nm and lengths exceeding 300 μm were synthesized using 2 % vol. OM and 1.8 mM OA at 120ºC after 12 h. The Cu NWs exhibit five-fold twinning and growth along the [110] direction. The morphological evolution of the products were also observed and discussed. Without Cl-, octahedral crystals instead of nanowires were formed. The addition of oleic acid as coordinating agent resulted to fewer particles and smoother nanowires which exhibit excellent mechanical stability. This method provides a simple, low-cost and high yield synthesis of Cu NWs for applications such as gas sensors and transparent conducting electrodes.