gebhart/patrepeval huggingface dataset:
Welcome to Mobile DNA (2010)

We are pleased to launch a new journal, Mobile DNA, at a time rich with opportunity for the study of mobile genetic elements. For more than a decade, our discipline has been well fed by data from the various genome sequencing efforts - data that continues to be generated at accelerating rates. Genome sequences have revealed novel element lineages that move by yet unknown mechanisms, providing subject matter for study by molecular biologists, biochemists and structural biologists. In species throughout the tree of life, genome sequences make evident the significant impact mobile elements have on genome organization, by creating genome rearrangements, mobilizing gene fragments, and reshaping the epigenetic landscape. At a mechanistic level, we continue to gain an appreciation for the intimate relationship between mobile elements and their hosts, and how mobile elements have adapted and responded to their hosts' cellular environment and regulatory pathways. Our research also has impact beyond our community, due to the many uses mobile elements provide as vectors for gene delivery and as mutagens that enable gene discovery.
Molecular Epidemiology of Human Immunodeficiency Virus Type 1 Transmission in a Heterosexual Cohort of Discordant Couples in Zambia (2002)

Most human immunodeficiency virus type 1 (HIV-1) transmissions in sub-Saharan Africa are believed to occur between married adults who are discordant for their HIV-1 infection status; however, no studies to date have investigated the molecular epidemiology of such transmission events. Here we report the genetic characterization of HIV-1 strains from 149 transmission pairs that were identified prospectively in a cohort of discordant couples in Lusaka, Zambia. Subgenomic gag, gp120, gp41, and/or long terminal repeat regions were amplified by PCR analysis of uncultured blood samples from both partners and sequenced without interim cloning. Pairwise genetic distances were calculated for the regions analyzed and compared to those of subtype-specific reference sequences as well as local controls. Sequence relationships were also examined by phylogenetic tree analysis. By these approaches, epidemiological linkage was established for the majority of transmission pairs. Viruses from 129 of the 149 couples (87%) were very closely related and clustered together in phylogenetic trees in a statistically highly significant manner. In contrast, viruses from 20 of the 149 couples (13%) were only distantly related in two independent genomic regions, thus ruling out transmission between the two partners. The great majority (95%) of transmitted viruses were of subtype C origin, although representatives of subtypes A, D, G, and J were also identified. There was no evidence for extensive transmission networks within the cohort, although two phylogenetic subclusters of viruses infecting two couples each were identified. Taken together, these data indicate that molecular epidemiological analyses of presumed transmission pairs are both feasible and required to determine behavioral, virological, and immunological correlates of heterosexual transmission in sub-Saharan Africa with a high level of accuracy.
Orthogonal proteomics methods to unravel the HOTAIR interactome (2022)

Accumulating evidence highlights the role of long non-coding RNAs (lncRNAs) in cellular homeostasis, and their dysregulation in disease settings. Most lncRNAs function by interacting with proteins or protein complexes. While several orthogonal methods have been developed to identify these proteins, each method has its inherent strengths and limitations. Here, we combine two RNA-centric methods ChIRP-MS and RNA-BioID to obtain a comprehensive list of proteins that interact with the well-known lncRNA HOTAIR. Overexpression of HOTAIR has been associated with a metastasis-promoting phenotype in various cancers. Although HOTAIR is known to bind with PRC2 and LSD1 protein complexes, only very limited unbiased comprehensive approaches to map its interactome have been performed. Both ChIRP-MS and RNA-BioID data sets show an association of HOTAIR with mitoribosomes, suggesting that HOTAIR has functions independent of its (post-)transcriptional mode-of-action.
Abstract 1363: Inhibition of Neuropilin-1 by anti-Nrp1 results in reduced angiogenesis and inhibition of tumor growth (2010)

Abstract Neuropilin-1 (NRP1) guides the development of the nervous and vascular systems and has been implicated in modulating various aspects of tumor cell function. We have previously shown that an antibody directed against NRP1 inhibits tumor growth and reduces tumor angiogenesis, as a single agent and more potently in combination with anti-VEGF. However, as NRP1 was also expressed in the tumor cells tested, the impact from inhibiting tumor cell NRP1 in these experiments was unclear. The objective of this study was to determine if inhibition of tumor cell NRP1 was necessary for the observed anti-tumor effects previously described for anti-NRP1. We tested the effects of anti-NRP1 in tumor lines that do not express NRP1, and where expression of NRP1 is restricted to the vasculature. Inhibition of tumor growth as a single agent, and in combination with anti-VEGF in these xenografted tumor lines, confirm that tumor expression of NRP1 is not necessary for the anti-tumor effects of anti-NRP1. We furthermore demonstrate that anti-NRP1 treatment of endothelial cells in in vitro sprouting assays results in potent inhibition of vascular sprout formation, confirming its anti-angiogenic activity. In vivo, in developmental models of angiogenesis, treatment results in reduced angiogenesis that is augmented by anti-VEGF. Finally, we demonstrate that treatment of primates with anti-NRP1 results in up-regulation of cytokines, such as PlGF, that are commonly increased with anti-angiogenic agent treatment. In total, these data confirm that anti-NRP1 mechanistically acts to inhibit tumor angiogenesis, thus resulting in reduced tumor growth and this tumor inhibition is most effective in combination with VEGF inhibition. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1363.
Arachidonic Acid Drives Postnatal Neurogenesis and Elicits a Beneficial Effect on Prepulse Inhibition, a Biological Trait of Psychiatric Illnesses (2009)

Prepulse inhibition (PPI) is a compelling endophenotype (biological markers) for mental disorders including schizophrenia. In a previous study, we identified Fabp7, a fatty acid binding protein 7 as one of the genes controlling PPI in mice and showed that this gene was associated with schizophrenia. We also demonstrated that disrupting Fabp7 dampened hippocampal neurogenesis. In this study, we examined a link between neurogenesis and PPI using different animal models and exploring the possibility of postnatal manipulation of neurogenesis affecting PPI, since gene-deficient mice show biological disturbances from prenatal stages. In parallel, we tested the potential for dietary polyunsaturated fatty acids (PUFAs), arachidonic acid (ARA) and/or docosahexaenoic acid (DHA), to promote neurogenesis and improve PPI. PUFAs are ligands for Fabp members and are abundantly expressed in neural stem/progenitor cells in the hippocampus. Our results are: (1) an independent model animal, Pax6 (+/-) rats, exhibited PPI deficits along with impaired postnatal neurogenesis; (2) methylazoxymethanol acetate (an anti-proliferative drug) elicited decreased neurogenesis even in postnatal period, and PPI defects in young adult rats (10 weeks) when the drug was given at the juvenile stage (4-5 weeks); (3) administering ARA for 4 weeks after birth promoted neurogenesis in wild type rats; (4) raising Pax6 (+/-) pups on an ARA-containing diet enhanced neurogenesis and partially improved PPI in adult animals. These results suggest the potential benefit of ARA in ameliorating PPI deficits relevant to psychiatric disorders and suggest that the effect may be correlated with augmented postnatal neurogenesis.
Final results of the Sunbelt Melanoma Trial (2008)

9003 Background: The Sunbelt Melanoma Trial is a multicenter prospective randomized prospective trial to evaluate the role of high-dose interferon alfa-2b (IFN) or completion lymph node dissection (CLND) in patients with melanoma staged by sentinel lymph node (SLN) biopsy. Methods: Eligible patients aged 18 to 70 years with primary melanoma ≥1.0 mm Breslow thickness underwent SLN biopsy. In Protocol A, patients with a single tumor-positive lymph node after SLN biopsy and CLND were randomized to observation vs. high dose IFN (20 MU/m2/d i.v. x 4 wks followed by 10 MU/m2 s.q. TIW x 48 wks). In Protocol B, patients with tumor-negative SLN by standard histopathology and immunohistochemistry underwent molecular staging of the SLN by reverse transcriptase polymerase chain reaction (RT-PCR) to detect melanoma- specific mRNA (tyrosinase, MART 1, MAGE 3, gp100); patients with RT-PCR-positive SLN were randomized to observation vs. CLND vs. CLND + IFN (20 MU/m2/d i.v. x 4 wks only). Randomization was stratified for Breslow thickness and ulceration. Disease-free survival (DFS) and overall survival (OS) were the primary endpoints. Intention-to-treat and efficacy analyses were performed by Kaplan-Meier analyses and Cox Proportional Hazards Models. The final analysis was approved by the Data Safety and Monitoring Committee. Results: Patients were enrolled between 6/24/1997 and 10/31/2003. Median follow-up was 64 months. In the Protocol A intention-to-treat analysis, there were no significant differences in DFS (HR 0.82, 95% CI: 0.47–1.40, p=0.46) or OS (HR 1.07, CI: 0.65–1.78, p=0.79) for patients randomized to IFN (N=112) vs. observation (N=106). In Protocol B there were no significant differences in DFS or OS among patients randomized to CLND (N=192, DFS: HR 0.72, CI 0.42–1.23, p=0.23; OS: HR 0.94, CI 0.55–1.59, p=0.81) or CLND + IFN (N=184; DFS: HR 0.90, CI 0.54–1.50, p=0.69; OS: HR 0.96, CI 0.56–1.63, p=0.88) vs. observation (N=180). Similarly, efficacy analysis (excluding patients who did not receive the assigned treatment) did not demonstrate significant differences in DFS or OS. Conclusions: This study failed to demonstrate a benefit for adjuvant high-dose IFN for patients with a single positive SLN. Among patients with melanoma cells detected in the SLN by RT-PCR analysis, there was no significant benefit to CLND or CLND + IFN. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Schering Oncology Biotech Schering Oncology Biotech
Practical aspects of liquid‐state NMR with inductively coupled solenoid coils (2010)

Sensitivity enhancement by the use of inductively coupled milli- and microcoils has been demonstrated in solid-state as well as liquid-state NMR. In this work, we discuss the practical aspects of using inductively coupled solenoid coils of different sizes in a liquid-state NMR spectrometer. The sensitivity and resolution enhancements from these resonant coils, with sizes ranging between 3.0 and 0.75 mm i.d., are measured for (23)Na single-pulse and multidimensional imaging experiments and compared to the results obtained with the conventional liquids NMR 5.0-mm saddle coil. Enhancements in voxel-based sensitivity (SNR per √scans) were measured in multidimensional MR images and were found to be as large as 20.4 with the 0.75-mm coil.
Matrix-Induced Intensity Fluctuations in the Fluorescence from Single Oligo(phenylenevinylene) Molecules (2005)

Single molecule spectroscopy on oligo(phenylenevinylene) (OPV) chromophores shows that the fluorescence intermittency strongly correlates to the rigidity of the environment surrounding the molecules. For OPV single molecules, environmental rigidity inhibits twisting about the vinyl linkages, the molecular motion associated with the observed "off" (nonabsorbing) state. By increasing the rigidity of a single molecule's environment, we can tune its room temperature fluorescence from rapid, sub-millisecond "blinking" fluctuations (fluid polymer environment) to completely "on" with no blinking observed (molecules adsorbed to a rigid bare glass substrate). The difference in fluorescence intermittency from environment to environment is immediately apparent and explicit in single molecule intensity trajectories under cw (continuous wave) excitation, demonstrating the sensitivity of these chromophores to their surroundings and emphasizing the importance of morphological control in real-world applications involving phenylenevinylene-based materials.
Expression of EGFR isoform D is regulated by HER receptor activators in breast cancer cells (2022)

Human epidermal growth factor receptor isoform D (EGFR; isoform D) is a soluble protein from a 3 kb alternate mRNA transcript that arises from the human EGFR gene. Several studies have identified this circulating isoform of EGFR as a potential diagnostic biomarker for the detection of early stage of cancers. While the expression of the full-length EGFR (isoform A) is regulated by its cognate ligand, EGF, as well as by phorbol myristate acetate (PMA), no studies have examined the factors regulating the expression of EGFR isoform D. In this study, using breast cancer cell lines, we show that the HER receptor ligands, EGF and neuregulin (NRG-1β), as well as the phorbol ester, PMA, can increase the expression of EGFR isoform D, as well as isoform A. Our results, based on measurement of mRNA levels, suggest that EGF induced expression of both isoform A and isoform D occur through a mitogen activated protein kinase (MAPK)-dependent mechanism, and also suggest that protein kinase C is involved in PMA-induced regulation of both isoforms. We also demonstrate that NRG-1β increases isoform A and isoform D expression via the MAPK-dependent pathway, but this regulation occurs independently of phosphatidylinositol 3-kinase/Akt activation. These results suggest that regulation of EGFR isoform A and isoform D expression occur using similar mechanisms. Despite commonalities in the transcriptional regulation of these two EGFR isoforms, the half-lives of these two transcripts is quite different. Moreover, EGFR isoform D, unlike isoform A, is not post-transcriptionally modulated by EGFR activators in the breast cancer cell line MDA-MB-468.
Macrocyclic Tetraazatetraenato Ligands and their Metal Complexes (1978)

This chapter contains sections titled: 3-(Ethoxymethylene)-2,4-pentanedione 3,3′-[Ethylenebis(iminomethylidyne)]di-2,4-pentanedione {[3,3′-[Ethylenebis(iminomethylidyne)]di-2,4-pentanedionato](2-)}nickel(II) [6,13-Diacetyl-5,14-dimethyl-1,4,8,11-tetraazacyclotetradeca 4,6,11,13-tetraenato(2-)nickel(II)[6,13-Ac2-5,14-me2[14]-4,6,11,13-tetraenato(2-)-1,4,8,11-N4]Ni(II)] 5,14-Dimethyl-1,4,8,11-tetraazacyclotetradeca-4,6,11,13-tetraene Bis(hexafluorophosphate)(1-)](ligand abbreviation is 5,14-Me4[14]-4,6,11,13-tetraene-1,4,8,11-N4) [5,14-Dimethyl-1,4,8,11-tetraazacyclotetradeca-4,6,11,13-tetraenato(2-)]nickel(II)
Synthesis of Block Copolymers Containing Perfluoroalkane and Tetrafluoroethylene-Perfluoro(propyl vinyl ether) Block Copolymer with Sulfide Bonds (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Block Copolymers Containing Perfluoroalkane and Tetrafluoroethylene-Perfluoro(propyl vinyl ether) Block Copolymer with Sulfide BondsE. Tsuchida, K. Yamamoto, E. Shouji, J. Katoh, M. Matsuo, and H. KamiyaCite this: Macromolecules 1994, 27, 26, 7504–7510Publication Date (Print):December 1, 1994Publication History Published online1 May 2002Published inissue 1 December 1994https://pubs.acs.org/doi/10.1021/ma00104a002https://doi.org/10.1021/ma00104a002research-articleACS PublicationsRequest reuse permissionsArticle Views273Altmetric-Citations7LEARN 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
Methylation Patterns of the E-cadherin 5′ CpG Island Are Unstable and Reflect the Dynamic, Heterogeneous Loss of E-cadherin Expression during Metastatic Progression (2000)

Metastatic progression of most common epithelial tumors involves a heterogeneous, transient loss of expression of the homotypic cell adhesion protein, E-cadherin, rather than the uniform loss of a functional protein resulting from coding region mutation. Indeed, whereas E-cadherin loss may promote invasion, reexpression may facilitate cell survival within metastatic deposits. The mechanisms underlying such plasticity are unclear. We now show that the heterogeneous loss of E-cadherin expression in primary human breast cancers reflects a heterogeneous pattern of promoter region methylation, which begins early prior to invasion. In cultured human tumor cells, such heterogeneous methylation is dynamic, varying from allele to allele and shifting in relation to the tumor microenvironment. Following invasion in vitro, which favors diminished E-cadherin expression, the density of promoter methylation markedly increased. When these cells were cultured as spheroids, which requires homotypic cell adhesion, promoter methylation decreased dramatically, and E-cadherin was reexpressed. These data show that the methylation associated with E-cadherin loss in human breast cancer is heterogeneous and unstable and suggest that such epigenetic plasticity may contribute to the dynamic, phenotypic heterogeneity that drives metastatic progression.
Current-forced neutral injection ina three-phase rectifier/converter (1999)

A new three-phase rectifier/converter with low harmonic input currents and minimal DC voltage ripple is described. The device achieves continuous input line currents by injecting a triangular third harmonic current, derived from the DC link current, into the neutral point of a delta–star transformer at the supply. It uses a conventional six-pulse phase controlled converter, with an additional bridge of four devices in the DC link. The additional bridge also cancels much of the DC voltage ripple, allowing a much smaller DC link inductance to be used. A prototype 10 kW system, suitable for such applications as DC motor drives, load-commutated inverters, exciters for AC generators, and low-power DC links is described. Experimental results obtained from this system are compared with ideal theoretical predictions.
InGaAs/InP negative feedback avalanche diodes (NFADs) (2011)

In recent years substantial effort has been made in material growth, device design and fabrication, and driving circuitry to improve the performance of InGaAs/InP single photon avalanche diodes (SPADs) operated in Geiger mode. Despite these efforts, InGaAs/InP SPADs are constrained by certain performance limitations due to the inherent positive feedback involved in the avalanche process. With the goal of overcoming some of these performance limitations, we have successfully designed and implemented thin film resistors monolithically integrated with InGaAs/InP SPADs to provide a negative feedback mechanism to regulate the avalanche sizes. The monolithic integration scheme ensures very small parasitic effects, results in fast quenching of avalanches, and allows for wafer-level integration which facilitates the fabrication of array structures. We will discuss the design and operation of NFAD devices and performance characterization of these devices. Basic characteristics of NFADs such as pulse response, quenching and recovery dynamics will be described. We will also present device performance parameters such as photon detection efficiency (PDE), dark count rate (DCR) and afterpulsing probability (P<sub>ap</sub>). InGaAs/InP negative feedback avalanche diodes with different device sizes and quenching resistances have been designed and fabricated. Devices with ~10% PDE and acceptable P<sub>ap</sub> has been realized, which provides a simple, practical solution for certain photon-counting applications.
A new procedure, free from human assessment, that automatically grades some facial skin signs in men from selfie pictures. Application to changes induced by a severe aerial chronic urban pollution (2020)

Apart from some minor limitations, this A.I-based automatic grading system, free from human intervention, performed as well as the one previously developed in women, in close agreement with expert's assessments. In epidemiological studies, this system offers an easy, fast, affordable and confidential approach in the detection and quantification of male facial signs.
Exclusive mutation in epidermal growth factor receptor gene, HER‐2, and KRAS, and synchronous methylation of nonsmall cell lung cancer (2006)

The findings of the current study suggest that adenocarcinoma cases with CIMP have a poorer prognosis than adenocarcinoma cases without CIMP, and the EGFR mutation was shown to have an inverse correlation with methylation of SPARC and the p16INK4A gene in NSCLC.
Research and development activities on polymer for the 21st century in korea (1995)

Abstract The polymer industries have been expanded steadily from the beginning of 1970's. Accordingly, the production capacity of commodity plastics reached 5.37 million tons in 1993, which ranked fourth in the world. The market for the engineering plastics is not fully matured yet, but the recent annual increasing rate was higher than 20% for demand and 40% for production. A state of the art for research and development activities on polymer for 21st century in Korea will be briefly reviewed in terms of technology evolution, polymers for electronic industry, for environment, and for energy saving.
Estimating Scene Properties from Color Histograms (1992)

One of the key tools in applying physics-based models to machine vision has been the analysis of color histograms. In the mid-1980s it was recognized that the color histogram for a single inhomogeneous surface with highlights will have a planar distribution in color space. It has since been shown that the colors do not fall randomly in a plane, but form clusters at specific points. The shape of the histogram is related not only to the illumination color and object color, but also to such non-color properties as surface roughness and imaging geometry. We present here an algorithm for analyzing color histograms that yields estimates of surface roughness, phase angle between the camera and light source, and illumination intensity. These three scene parameters are related to three histogram measurements. However the relationship is complex and cannot be solved analytically. Therefore we have developed a method for estimating these properties by interpolating between histograms that come f...