gebhart/patrepeval huggingface dataset:
URI Regulates KAP1 Phosphorylation and Transcriptional Repression via PP2A Phosphatase in Prostate Cancer Cells (2016)

URI (unconventional prefoldin RPB5 interactor protein) is an unconventional prefoldin, RNA polymerase II interactor that functions as a transcriptional repressor and is part of a larger nuclear protein complex. The components of this complex and the mechanism of transcriptional repression have not been characterized. Here we show that KAP1 (KRAB-associated protein 1) and the protein phosphatase PP2A interact with URI. Mechanistically, we show that KAP1 phosphorylation is decreased following recruitment of PP2A by URI. We functionally characterize the novel URI-KAP1-PP2A complex, demonstrating a role of URI in retrotransposon repression, a key function previously demonstrated for the KAP1-SETDB1 complex. Microarray analysis of annotated transposons revealed a selective increase in the transcription of LINE-1 and L1PA2 retroelements upon knockdown of URI. These data unveil a new nuclear function of URI and identify a novel post-transcriptional regulation of KAP1 protein that may have important implications in reactivation of transposable elements in prostate cancer cells.
Imaging CXCR4 expression in breast cancer metastasis models using [64Cu]AMD3465 (2012)

519 Objectives The chemokine receptor 4 (CXCR4) is highly expressed in breast cancer and is critical for metastasis. To evaluate the potential of CXCR4-based imaging agents to detect metastases, MDA-MB-231 cell line derived bone and spontaneous metastasis models were investigated in SCID mice with [64Cu]AMD3465-PET. These studies were further validated in a syngeneic 4T1 tumor model in immunocompetent mice. Methods AMD3465 was radiolabeled with [64Cu]Cu(OAc)2 at pH 5.5. The MDA-MB-231 cell line expressing luciferase (231-Luc) was used as a metastasis model (n = 7/group). Bone metastases were generated by left cardiac ventricular injection of 231-Luc cells. Spontaneous metastases were generated by resection of primary tumor (~ 400 mm3) and metastatic spread was imaged at 30 days post-resection by [18F]FDG-PET, [64Cu]AMD3465-PET and bioluminescence (BLI) imaging. Whole body PET images were acquired at 60 and 90 min after the injection of [18F]FDG and [64Cu]AMD3465, respectively. Based on BLI data, regions of interest were drawn over metastatic sites on the PET images. Radioactivity uptake was calculated as %ID/cc and tumor-to-muscle (T/M) ratios were obtained. Similarly, spontaneous metastases developed using 4T1-Luc tumors were also imaged in immunocompetent mice. CXCR4 expression of metastatic tissue was confirmed with immunohistochemistry and qRT-PCR. Results Bone metastases were clearly detectable on the PET images and exhibited mean T/M ratio of 12.8 (range: 6.6 - 21.7) while that of control bone was 7.6 (4.0 - 11.4). MDA-MB-231 primary tumors exhibited mean T/M ratio of 8.5 (4.0 - 14.3) while that of the metastases was 17.4 (3.7 - 44.5). Similarly, 4T1 tumors showed a mean T/M ratio of 4.6 (3.3 - 7.0) with metastases showing a mean value of 9.0 (4.9 - 21.7). Conclusions Metastases that originated from the same tumor have variable levels of CXCR4 expression, which could be detected by CXCR4-based imaging agents. Research Support Elsa U. Pardee Foundatio
ARID1A gene mutation in ovarian and endometrial cancers (Review) (2015)

The AT-rich interacting domain‑containing protein 1A gene (ARID1A) encodes ARID1A, a member of the SWI/SNF chromatin remodeling complex. Mutation of ARID1A induces changes in expression of multiple genes (CDKN1A, SMAD3, MLH1 and PIK3IP1) via chromatin remodeling dysfunction, contributes to carcinogenesis, and has been shown to cause transformation of cells in association with the PI3K/AKT pathway. Information on ARID1A has emerged from comprehensive genome‑wide analyses with next‑generation sequencers. ARID1A mutations have been found in various types of cancer and occur at high frequency in endometriosis‑associated ovarian cancer, including clear cell adenocarcinoma and endometrioid adenocarcinoma, and also occur at endometrial cancer especially in endometrioid adenocarcinoma. It has also been suggested that ARID1A mutation occurs at the early stage of canceration from endometriosis to endometriosis‑associated carcinoma in ovarian cancer and also from atypical endometrial hyperplasia to endometrioid adenocarcinoma in endometrial cancer. Therefore, development of a screening method that can detect mutations of ARID1A and activation of the PI3K/AKT pathway might enable early diagnosis of endometriosis‑associated ovarian cancers and endometrial cancers. Important results may also emerge from a current clinical trial examining a multidrug regimen of temsirolimus, a small molecule inhibitor of the PI3K/AKT pathway, for treatment of advanced ovarian clear cell adenocarcinoma with ARID1A mutation and PI3K/AKT pathway activation. Also administration of sorafenib, a multikinase inhibitor, can inhibit cancer proliferation with PIK3CA mutation and resistance to mTOR inhibitors and GSK126, a molecular‑targeted drug can inhibit proliferation of ARID1A‑mutated ovarian clear cell adenocarcinoma cells by targeting and inhibiting EZH2. Further studies are needed to determine the mechanism of chromatin remodeling dysregulation initiated by ARID1A mutation, to develop methods for early diagnosis, to investigate new cancer therapy targeting ARID1A, and to examine the involvement of ARID1A mutations in development, survival and progression of cancer cells.
Unusual solvatochromism of the 4,4′-bis(dimethylamino)benzophenone (Michler's ketone)-tetracyanoethene electron donor-acceptor complex (1999)

The transition energy of the charge-transfer UV/Vis absorption maxima (νmax, CT) and the structure of the Michler's ketone (MK)–tetracyanoethene (TCNE) electron donor–acceptor (EDA) complex are remarkably solvent dependent. The UV/Vis spectra of the MK–TCNE complex were measured in 20 non-protic and seven protic solvents. In non-protic solvents, νmax, CT of the EDA complex is quantitatively described by a multiple LSE relationship using the Kamlet–Taft dipolarity/polarizability (π*) and basicity (β) parameters of the solvents. The influence of the two terms β and π* on νmax, CT is opposite, indicating a qualitatively different solvent-induced stabilization of the electronic ground and excited states of the complex. As expected, increasing dipolarity/dipolarizability of the solvent causes a bathochromic band shift (positive solvatochromism), whereas the basicity of solvents is responsible for a hypsochromic band shift due to specific solvation of the TCNE site. In protic solvents, the complex formation is associated with the formation of an ionic species (νmax = 19 800 cm−1) derived from Michler's ketone due to coordination of TCNE at the carbonyl oxygen of MK (called an n-complex). The solvent-induced switching of the π-complex into the n-complex is demonstrated for mixtures of DCE with protic solvents and for silica surfaces. Copyright © 1999 John Wiley & Sons, Ltd.
Transcriptome network analysis identifies protective role of the LXR/SREBP-1c axis in murine pulmonary fibrosis (2019)

Pulmonary fibrosis (PF) is an intractable disorder with a poor prognosis. Although lung fibroblasts play a central role in PF, the key regulatory molecules involved in this process remain unknown. To address this issue, we performed a time-course transcriptome analysis on lung fibroblasts of bleomycin- and silica-treated murine lungs. We found gene modules whose expression kinetics were associated with the progression of PF and human idiopathic PF (IPF). Upstream analysis of a transcriptome network helped in identifying 55 hub transcription factors that were highly connected with PF-associated gene modules. Of these hubs, the expression of Srebf1 decreased in line with progression of PF and human IPF, suggesting its suppressive role in fibroblast activation. Consistently, adoptive transfer and genetic modification studies revealed that the hub transcription factor SREBP-1c suppressed PF-associated gene expression changes in lung fibroblasts and PF pathology in vivo. Moreover, therapeutic pharmacological activation of LXR, an SREBP-1c activator, suppressed the Srebf1-dependent activation of fibroblasts and progression of PF. Thus, SREBP-1c acts as a protective hub of lung fibroblast activation in PF. Collectively, the findings of the current study may prove to be valuable in the development of effective therapeutic strategies for PF.
The Localized Sound Power Method (1985)

&lt;div class="htmlview paragraph"&gt;Single point microphone measurements in enclosed spaces lack sufficient stability to be useful for sound system equalization (above the Schroetter frequency). A new measurement technique for use in automobiles was developed to circumvent this problem. This paper will describe the problems encountered with single point measurements and the results obtained with the new system.&lt;/div&gt;
Finite-difference modelling of 2-D wave propagation in the vicinity of dipping interfaces: a comparison of anti-aliasing and equivalent medium approaches (2021)

SUMMARY Finite-difference (FD) modelling of seismic waves in the vicinity of dipping interfaces gives rise to artefacts. Examples are phase and amplitude errors, as well as staircase diffractions. Such errors can be reduced in two general ways. In the first approach, the interface can be anti-aliased (i.e. with an anti-aliased step-function, or a lowpass filter). Alternatively, the interface may be replaced with an equivalent medium (i.e. using Schoenberg &amp; Muir (SM) calculus or orthorhombic averaging). We test these strategies in acoustic, elastic isotropic, and elastic anisotropic settings. Computed FD solutions are compared to analytical solutions. We find that in acoustic media, anti-aliasing methods lead to the smallest errors. Conversely, in elastic media, the SM calculus provides the best accuracy. The downside of the SM calculus is that it requires an anisotropic FD solver even to model an interface between two isotropic materials. As a result, the computational cost increases compared to when using isotropic FD solvers. However, since coarser grid spacings can be used to represent the dipping interfaces, the two effects (an expensive FD solver on a coarser FD grid) equal out. Hence, the SM calculus can provide an efficient means to reduce errors, also in elastic isotropic media.
First clinical experience with DRD2/3 antagonist ONC201 in H3 K27M–mutant pediatric diffuse intrinsic pontine glioma: a case report (2019)

Diffuse intrinsic pontine gliomas (DIPGs) frequently harbor the histone H3 K27M mutation. Gliomas with this mutation commonly overexpress dopamine receptor (DR) D2 and suppress DRD5, leading to enhanced sensitivity to DRD2 antagonism. This study reports the first clinical experience with the DRD2/3 antagonist ONC201 as a potential targeted therapy for H3 K27M-mutant DIPG. One pediatric patient (a 10-year-old girl) with H3 K27M-mutant DIPG was enrolled in an investigator-initiated, IRB-approved compassionate-use study and began single-agent ONC201 treatment 1 month after completing radiotherapy. The study endpoints were clinical and radiographic response (primary) and toxicities (secondary).The patient presented with House-Brackmann grade IV facial palsy and unilateral hearing loss. MRI demonstrated a 2.3 × 2.1 × 2.8-cm pontomedullary tumor. Stereotactic biopsy confirmed H3 K27M-mutated DIPG. The tumor was treated with radiotherapy, but 1 month after completion of that treatment, the tumor and neurological symptoms showed only minimal change, and ONC201 treatment was initiated as described above. The tumor volume sequentially decreased by 26%, 40%, and 44% over the next 6 months, and remained stable at 18 months. Ipsilateral hearing normalized and the facial palsy improved to House-Brackmann grade I by 4 months. After 1 year of ONC201 treatment, 2 new lesions were identified outside of the prior high-dose radiotherapy volume. The patient was treated with dexamethasone, bevacizumab, and additional focal radiotherapy to these new tumors. These tumors remained stable in size over the subsequent 6 months on MRI. To date, no adverse events have been observed or reported due to ONC201. The patient remains clinically improved as of the latest follow-up visit, 19 months after starting ONC201 and 22 months from diagnosis. This case supports further investigation of this novel agent targeting H3 K27M-mutated DIPG.
Towards second-harmonic generation micropatterning of glass surface (2010)

Thermal poling of sodium borophosphate niobium glasses, previously coated with a thin silver layer micropatterned by femtosecond laser irradiation, is demonstrated. The field-assisted ion-exchange process for fabricating planar surface in this glass substrate is analyzed. Inside the silver ablated lines obtained by femtosecond laser irradiation, we clearly observe a change in the distribution of the frozen electrostatic field that is modulated by the Ag+/Na+ ion-exchange process during the thermal poling.
Effects of Chemical Compounds on the Activity of the N-acetyl-β-D-Glucosaminidase of the Marine Prawn, Palaemon serratus: Screening In Vitro (2023)

Abstract N-acetyl-β-D-glucosaminidase (NAGase) is important for crustaceans because the enzyme activity is necessary for the molting process. The present study aimed to assess the sensitivity of Palaemon serratus NAGase activity to a set of compounds of diverse chemical families in the context of in vitro exposures. Compounds representing different chemical families were selected according to their abundance, impact in the environment, and relevance as disruptors of the molting process. In a first step, four solvents (dimethylsulfoxide [DMSO], methanol, acetone, and ethanol) were tested to determine their suitability to dissolve hydrophobic compounds without affecting NAGase activity. Exclusively, ethanol had no effect on enzyme activity and on the integrity of the proteins present in the enzyme extract. The 18 other compounds were tested and four of these compounds, pentoxifylline, fenoxycarb, dithiocarbamate, and RH5849, showed a specific alteration on the activity of NAGase, without affecting the protein content. However, cadmium, zinc, and glyphosate showed a nonspecific alteration, affecting both the enzyme activity and the proteins, whereas ibuprofen exclusively altered the protein content. Finally, 10 of the 22 tested compounds (including DMSO, acetone, and methanol) showed a direct alteration of NAGase activity. Environ Toxicol Chem 2023;42:846–858. © 2023 SETAC
Translation on this Article from Fine Mapping of Chromosome 6q23-25 Region in Familial Lung Cancer Families Reveals <i>RGS17</i> as a Likely Candidate Gene (2023)

Translation on this Article from Fine Mapping of Chromosome 6q23-25 Region in Familial Lung Cancer Families Reveals &lt;i&gt;RGS17&lt;/i&gt; as a Likely Candidate Gene
Sequence and proposed secondary structure of theTetrahymena thermophilaU3-snRNA (1993)

Journal Article Sequence and proposed secondary structure of the Tetrahymena thermophila U3-snRNA Get access Henrik Ørum, Henrik Ørum The Royal Danish School of Pharmacy, Department of Biology, 2 UniversitetsparkenDK-2100 Copenhagen Search for other works by this author on: Oxford Academic PubMed Google Scholar Henrik Nielsen, Henrik Nielsen 1Department of Biochemistry B, The Panum institute, University of Copenhagen3 Blegdamsvej, DK-2200 Copenhagen, Denmark Search for other works by this author on: Oxford Academic PubMed Google Scholar Jan Engberg Jan Engberg The Royal Danish School of Pharmacy, Department of Biology, 2 UniversitetsparkenDK-2100 Copenhagen Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 21, Issue 10, 25 May 1993, Page 2511, https://doi.org/10.1093/nar/21.10.2511 Published: 25 May 1993 Article history Received: 14 April 1993 Accepted: 17 April 1993 Published: 25 May 1993
RNA splicing regulated by RBFOX1 is essential for cardiac function in zebrafish (2015)

Alternative splicing is one of the major mechanisms through which the proteomic and functional diversity of eukaryotes is achieved. However, the complex nature of the splicing machinery, its associated splicing regulators and the functional implications of alternatively spliced transcripts are only poorly understood. Here, we investigated the functional role of the splicing regulator rbfox1 in vivo using the zebrafish as a model system. We found that loss of rbfox1 led to progressive cardiac contractile dysfunction and heart failure. By using deep-transcriptome sequencing and quantitative real-time PCR, we show that depletion of rbfox1 in zebrafish results in an altered isoform expression of several crucial target genes, such as actn3a and hug. This study underlines that tightly regulated splicing is necessary for unconstrained cardiac function and renders the splicing regulator rbfox1 an interesting target for investigation in human heart failure and cardiomyopathy.
Nanotechnology Enabled Hybrid Power System Suitable for Portable Telecommunications and Sensor Applications (2010)

A prototype nanotechnology-enabled hybrid power system has been developed and tested in the laboratory.The system, which consists of a nanotechnology-based battery and supercapacitor plus a dynamic power management circuit, has been designed to meet the power needs of high power, low duty cycle applications, such as telecommunications equipment or unattended ground sensors.The hybrid system has almost 17 times the specific energy of the supercapacitor alone and 3 times the specific power of the battery alone.Under load conditions similar to those found in a telecommunications system, the nanotechnology-enabled hybrid power system has 34 per cent more capacity than the battery alone and 30 per cent more capacity than the combined capacities of the battery and supercapacitor taken together.15.
MMXTM mesalamine for the maintenance of remission in mild-to-moderate ulcerative colitis (2008)

To evaluate the efficacy of MMX mesalamine (LialdaTM [MezavantTM XL in the UK and Ireland; MezavantTM elsewhere]) a novel, high-strength (1.2g/tablet), oncedaily formulation of 5-ASA for the maintenance of remission of mild-to-moderate ulcerative colitis (UC). Patients with active, mild-to-moderate UC who had achieved clinical and endoscopic remission (defined as a modified UC Disease Activity Index score of ≤1, calculated as: scores of 0 for both rectal bleeding and stool frequency; a combined Physician's Global Assessment and sigmoidoscopy score of ≤1; no mucosal friability; and a sigmoidoscopy score reduction of ≥1 point from baseline) during studies evaluating MMX mesalamine for the induction of remission could subsequently enter an open-label extension study (SPD476-303) for the maintenance of remission, where they were randomized to MMX mesalamine 2.4g/day once daily (QD) or 1.2g twice daily (BID) for 12 months. Remission rates and relapse rates (defined as withdrawal from the study due to a requirement for alternative treatment for a UC exacerbation, including a dose increase or surgery) at 12 months are presented. In total, 362 patients in clinical and endoscopic remission entered the maintenance phase of whom 171 and 191 patients received MMX mesalamine 2.4g/day administered QD or BID, respectively. At month 12, 67.8 and 72.3% of patients in the QD and BID groups were in strictly defined clinical and endoscopic remission, respectively. At month 12, 88.7 and 92.5% of patients in the QD and BID groups, respectively, had not relapsed. During 12 months' MMX mesalamine therapy, less than 10% of patients experienced clinical relapse. Using stringent clinical and endoscopic criteria, more than two-thirds of patients remained in remission. These results indicate that MMX mesalamine is an effective maintenance therapy in UC.
Regio- and Stereocontrolled 6-Endo-Trig Radical Cyclization of Vinyl Radicals:  A Novel Entry to Carbasugars from Carbohydrates (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTADDITION / CORRECTIONThis article has been corrected. View the notice.Regio- and Stereocontrolled 6-Endo-Trig Radical Cyclization of Vinyl Radicals: A Novel Entry to Carbasugars from CarbohydratesAna M. Gómez, Gerardo O. Danelón, Serafín Valverde, and J. Cristóbal LópezView Author Information Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain Cite this: J. Org. Chem. 1998, 63, 26, 9626–9627Publication Date (Web):November 26, 1998Publication History Received1 October 1998Published online26 November 1998Published inissue 1 December 1998https://pubs.acs.org/doi/10.1021/jo981989zhttps://doi.org/10.1021/jo981989zrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views742Altmetric-Citations32LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Carbohydrates,Group 14 compounds,Hydrocarbons,Organic reactions,Vinyl Get e-Alerts
Challenges and Opportunities in Video Coding for 3D TV (2006)

This paper explores the challenges opportunities in developing and deploying 3D TV services. The 3D TV services can be seen as a general case of the multi-view video that has been receiving significant attention lately. The keys to a successful 3D TV experience are the availability of content, the ease of use, the quality of experience, and the cost of deployment. Recent technological advances have made possible experimental systems that can be used to evaluate the 3D TV services. We have developed a 3D TV prototype and have currently conducting our first user study to evaluate the quality and experience. These experiences have allowed us to identify challenges and opportunities in developing 3D TV services
Leakage-aware compilation for VLIW architectures (2005)

Power consumption has been widely recognised as the most important design limiter for continued increase in the number of transistors integrated into a chip. Specifically, static power consumption has emerged as a significant concern in newer technologies with smaller threshold voltages and feature sizes. Addressing this important challenge requires solutions at different levels of a chip design, ranging from improvements in fabrication process to energy-aware software design. The paper shows how a compiler can play an important role in reducing the leakage power consumption. The strategy is built upon a data-flow analysis that identifies basic blocks that do not use a given functional unit. Collecting this information from all basic blocks in the code, it then inserts activate/deactivate instructions in the code to set/reset a sleep signal which controls leakage current of functional units. To evaluate the effectiveness of their strategy, the authors implemented different versions of it using an experimental compiler and simulation environment and conducted experiments using a VLIW (very long instruction word) architecture and several media applications as well as array-intensive codes. Their experimental results show that the proposed compiler-based strategy is very effective in reducing leakage energy of functional units.