gebhart/patrepeval huggingface dataset:
HPP1‐mediated tumor suppression requires activation of STAT1 pathways (2007)

HPP1 is a recently discovered gene that is epigenetically silenced in a number of tumor types, suggesting a potential role as a tumor suppressor. However, whether HPP1 has tumor suppressor activity is not clearly known. We have sought to investigate the effects of HPP1 on tumor growth and survival and to identify signaling pathways that mediate HPP1's mechanism of action. Forced expression of HPP1 into HCT116 colon cancer cell lines blocked the ability of HCT116 tumors to grown in vivo in nude mice. In cell culture, ectopic expression of HPP1 induces apoptosis and potently inhibits soft agar colony formation. HPP1 overexpression was also associated with a moderate reduction in in vitro proliferation characterized by an accumulation of cells in the G0/G1 phase of the cell cycle. Microarray analysis revealed that ectopic expression of HPP1 resulted in a dramatic upregulation of STAT1 as well as a large number of associated interferon-inducible genes. RNA interference-mediated abrogation of STAT1 reversed HPP1's antiproliferative effects. We conclude that HPP1 demonstrates tumor suppressive and pro-apoptotic activity, both in vitro and in vivo. Coupled with its inactivation in a number of tumor types, our data provides evidence to support the role of HPP1 as a tumor suppressor gene. Moreover, activation of the STAT1 pathway likely represents the principal mediator of HPP1's tumor suppressive properties.
Automatic Tagging and Geotagging in Video Collections and Communities (2011)

Automatically generated tags and geotags hold great promise&#13;\nto improve access to video collections and online communi-&#13;\nties. We overview three tasks offered in the MediaEval 2010&#13;\nbenchmarking initiative, for each, describing its use scenario, definition and the data set released. For each task, a reference algorithm is presented that was used within MediaEval 2010 and comments are included on lessons learned. The Tagging Task, Professional involves automatically matching episodes in a collection of Dutch television with subject labels drawn from the keyword thesaurus used by the archive staff. The Tagging Task, Wild Wild Web involves automatically predicting the tags that are assigned by users to their online videos. Finally, the Placing Task requires automatically assigning geo-coordinates to videos. The specification of each task admits the use of the full range of available information including user-generated metadata, speech recognition transcripts, audio, and visual features.
TSM-A FEDERAL VIEWPOINT (1977)

The concept of Transportation Systems Management (TSM) is essentially that all elements of the urban transportation scene will be treated as members of a single transportation system and that emphasis will be put on maximizing the efficiency of existing transportation facilities and resources. The institutional framework for TSM is essentially coordinating traffic engineers, planners and transit operators. Traditionally, little thought had been given to broadening the scope of this mutal assistance to take in a large area or to attack a problem on a systems basis. The author believes that the Metropolitan Planning Organization (MPO) can play a critical role as conveyor and coordinator. Hopefully within the forum of the MPO, the various groups will sit down together and discuss their problems. Developing a constituency for TSM is essential for certain TSM strategies are likely to be controversial. Bringing these diverse groups together in the early phases of TSM planning can help identify and build rapport for further TSM actions. More cooperation must also be developed in the way projects are actually implemented. The author identifies two major areas of concern. The first is the relatively large unobligated balance of urban funds that is rapidly being built up. The second area of concern is the apparent lack of activity in exercising the funding flexibility that exists in the urban system program. The author concludes the paper with a discussion of the activities at the Federal level related to the urban system program. These include clarifying for State and local officials the options and flexibility available with respect to Federal-aid programs. Streamlining the planning and project development processes. Lastly, FHWA has developed in cooperation with the states an extensive and effective procedures for dealing with project development.
Extrinsic Signatures Embedding and Detection in Electrophotographic Halftone Images through Laser Intensity Modulation (2006)

In this paper, we demonstrated the feasibility of embedding unperceivable code sequence by modulating dot gains through laser intensity modulation for halftone images. From a communication systems point of view, a printer and a document scanner form the physical layer of a communication channel, where information can be hidden in halftone images and reliably transmitted and extracted. In the proposed approach, we will leverage our previous results in embedding unperceivable banding signals to halftone images and develop an integrated embedding and detection algorithm to embed and extract information with high payload capacity. Specifically, we will characterize the embedding capacity and detection rate associated with the proposed algorithm. Preliminary experimental results will be presented.
A high-sensitivity 40-Gbit/s optical receiver using packaged GaAs HBT-ICs (2002)

Summary form only given. In this paper, we report the development of 40-Gbit/s optical receiver that employs three packaged AlGaAs-InGaAs HBT ICs: a preamplifier, a distributed amplifier, and a D-type flip-flop circuit. Approaches have been applied in packaged IC design for high-speed operation, which resulted in a very high receiver sensitivity at 40 Gbit/s.
Abstract PR002: Durable complete response in a patient with metastatic melanoma following adoptive transfer of autologous T cells recognizing 10 mutated tumor antigens (2016)

Abstract Durable complete response rates of 20% have been observed in clinical trials of patients with metastatic melanoma employing adoptive cell transfer (ACT) of patient derived tumor infiltrating lymphocytes (TIL). Here we provide a detailed analysis of the response of TIL administered to a patient with metastatic melanoma who exhibited a complete response ongoing greater than 3 years. Using whole-exome and RNA-Seq sequencing and bioinformatic analysis of the patient's matched tumor and normal gDNA we identified over 4,000 non-synonymous somatic mutation variants. We screened 745 somatically mutated genes using tandem minigene constructs expressing transcripts expressed in autologous tumor cells whose expression levels were greater than 0.1% of the levels of beta actin. These tandem minigenes were then transfected into autologous B cells and then analyzed for their ability to stimulate the administered T cells. Our results indicated that the autologous TIL distinctly recognized 10 somatically mutated gene products, each of which was recognized in the context of three different HLA class I restriction elements expressed by the patient's tumor. Detailed T cell clonal analysis revealed that 9 of the top 20 most prevalent clones present in the infused TIL, comprised over ¼ of total infused cells and recognized mutated antigens. These results further supported our efforts to identify and enrich mutation-reactive T cells for the treatment of patients with metastatic cancer. Citation Format: Todd D. Prickett, Jessica Crystal, Jared Gartner, Xin Yao, Anna Pasetto, Alena Gros, Yong-Chen Lu, Yong F. Li, Mona El-Gamil, Steven A. Rosenberg, Paul Robbins. Durable complete response in a patient with metastatic melanoma following adoptive transfer of autologous T cells recognizing 10 mutated tumor antigens. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr PR002.
Circulating cell-free messenger RNA secretome characterization of primary sclerosing cholangitis (2023)

Blood-based whole-transcriptome cf-mRNA profiling revealed high abundance of liver-specific genes in sera of subjects with PSC, which may be used to diagnose patients with PSC. We identified several unique cf-mRNA profiles of subjects with PSC. These findings may also have utility for noninvasive molecular stratification of subjects with PSC for pharmacotherapy safety and response studies.
Mitochondrial mutation m.1555A>G as a risk factor for failed newborn hearing screening in a large cohort of preterm infants (2014)

Antenatal screening for the m.1555A>G mutation by maternal genotyping of pregnant women with preterm labour might be a reasonable approach to identify infants who are at increased risk for permanent hearing loss. Additional studies are needed to estimate the relevance of cofactors like aminoglycoside plasma levels and birth weight and the amount of preterm m.1555A>G-carriers with permanent hearing loss.
A figure of merit for mobile device thermal management (2016)

With mobile devices available in various sizes and shapes, it is challenging to think in a consistent and comparative manner about the effectiveness of the thermal management solutions that they employ. Here we define a universal thermal figure of merit - a dimensionless Coefficient of Thermal Spreading (CTS) - calculated using either numerical simulations or IR surface temperature imaging and can be used to compare the thermal design effectiveness of many mobile devices and power levels. Heat spreading at the mobile device surface becomes an important factor that impacts the overall device performance. In order to meet the various performance specifications (skin and junction limit temperatures), the processors have to be throttled to reduce the amount of power and avoid exceeding the temperature limits, which in turn reduces the device overall performance. The proposed CTS Figure of Merit quantifies the effectiveness of heat spreading within the device by means of the uniformity of the surface temperature, and addresses a long-time need to quantify the thermal design effectiveness of various mobile devices which are skin temperature limited. The CTS indicates how much a phone or other mobile device can be improved for the given shape and size/form factor. This paper includes details on the CTS Figure of Merit definition and governing equations, will quantify the design targets and how the CTS can be tested and improved.
D4 Expression of Human Endogenous Retrovirus Type-K (HML-2) is Activated by the Tat Protein of HIV-1 (2012)

Human Endogenous Retroviruses (HERVs) make up 8% of the human genome. Expression of HERV-K (HML-2), our most recent genome entrant, is tightly regulated but becomes markedly increased following infection with HIV-1. To better understand the mechanisms involved in this activation, we explored the role of the HIV-1 proteins in inducing expression of these retroviral genes. Transfection experiments showed that, out of all HIV-1 proteins, Tat and Vif where the only ones inducing significant activation of HERV-K (HML-2) gene expression. Out of these two proteins, Tat alone was sufficient to cause significant HERV-K (HML-2) expression. Administration of recombinant HIV-1 Tat protein caused a 13-fold increase in HERV-K (HML-2) gag transcripts in Jurkat T cells and a 10-fold increase in primary lymphocytes, and expression of the HERV-K (HML-2) rec and np9 oncogenes was also markedly increased. Additionally, transfection of a plasmid encoding Tat caused a strong increase in HERV-K (HML-2) gag protein expression. Luciferase reporter gene assays demonstrated that the effect of Tat on HERV-K (HML-2) expression occurred at the level of the transcriptional promoter. The transcription factors NF-kB and NF-AT contribute to the Tat-induced activation of the promoter, as shown by mutational analysis of the HERV-K (HML-2) LTR, ChIP assays, and treatments with agents that inhibit NF-AT or NF-kB activation. These studies show that HIV-1 Tat plays an important role in activating expression of HERV-K (HML-2) in the setting of HIV-1 infection. By increasing expression of HERV-K oncogenes, Tat might potentiate HIV-related disease, but increased expression of HERV-K antigens might also contribute to immunological control of HIV infection.
Video Coding Using 3D Dual-Tree Wavelet Transform (2007)

<p/> This work investigates the use of the 3D dual-tree discrete wavelet transform (DDWT) for video coding. The 3D DDWT is an attractive video representation because it isolates image patterns with different spatial orientations and motion directions and speeds in separate subbands. However, it is an overcomplete transform with 4: 1 redundancy when only real parts are used. We apply the noise-shaping algorithm proposed by Kingsbury to reduce the number of coefficients. To code the remaining significant coefficients, we propose two video codecs. The first one applies separate 3D set partitioning in hierarchical trees (SPIHT) on each subset of the DDWT coefficients (each forming a standard isotropic tree). The second codec exploits the correlation between redundant subbands, and codes the subbands jointly. Both codecs do not require motion compensation and provide better performance than the 3D SPIHT codec using the standard DWT, both objectively and subjectively. Furthermore, both codecs provide full scalability in spatial, temporal, and quality dimensions. Besides the standard isotropic decomposition, we propose an anisotropic DDWT, which extends the superiority of the normal DDWT with more directional subbands without adding to the redundancy. This anisotropic structure requires significantly fewer coefficients to represent a video after noise shaping. Finally, we also explore the benefits of combining the 3D DDWT with the standard DWT to capture a wider set of orientations.
Abemaciclib is a potent inhibitor of DYRK1A and HIP kinases involved in transcriptional regulation (2021)

Homeodomain-interacting protein kinases (HIPKs) belong to the CMGC kinase family and are closely related to dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs). HIPKs are regulators of various signaling pathways and involved in the pathology of cancer, chronic fibrosis, diabetes, and multiple neurodegenerative diseases. Here, we report the crystal structure of HIPK3 in its apo form at 2.5 Å resolution. Recombinant HIPKs and DYRK1A are auto-activated and phosphorylate the negative elongation factor SPT5, the transcription factor c-Myc, and the C-terminal domain of RNA polymerase II, suggesting a direct function in transcriptional regulation. Based on a database search, we identified abemaciclib, an FDA-approved Cdk4/Cdk6 inhibitor used for the treatment of metastatic breast cancer, as potent inhibitor of HIPK2, HIPK3, and DYRK1A. We determined the crystal structures of HIPK3 and DYRK1A bound to abemaciclib, showing a similar binding mode to the hinge region of the kinase as observed for Cdk6. Remarkably, DYRK1A is inhibited by abemaciclib to the same extent as Cdk4/Cdk6 in vitro, raising the question of whether targeting of DYRK1A contributes to the transcriptional inhibition and therapeutic activity of abemaciclib.
PCL2 modulates gene regulatory networks controlling self-renewal and commitment in embryonic stem cells (2011)

Recent reports have better elucidated the components of the Polycomb Repressive Complex 2 (PRC2) and its functional role in embryonic stem cells (ESCs) and their differentiated derivatives. The depletion of a newly described mammalian PRC2 associated protein, PCL2, leads to an increase in ESC self-renewal and a delay in differentiation, a phenotype similar to knockouts of the core PRC2 members. Genomic and cell biology data suggest that PCL2 is important in cell fate decisions and may play a role in recruitment of PRC2 to target genes and histone methylation. Importantly, depletion of PCL2 in ESCs leads to a decrease in 3meH3K27 at the proximal promoter regions of pluripotency transcription factors Tbx3, Klf4, Foxd3 and a concomitant increase in gene expression. These proteins subsequently activate expression of Oct4, Nanog and Sox2 through a feed-forward gene regulatory circuit, altering the core pluripotency network and driving cell fate decisions towards self-renewal. We propose a model whereby alteration of the epigenetic state of Tbx3, Klf4, and Foxd3 results in the enforced expression of the pluripotency network, preventing differentiation.
Multiscale Computations of Parameters of Power Transformer Windings at High Frequencies. Part II: Large-Scale Level (2007)

In this part of the paper, we focus on implementation of a hierarchical multiscale approach for modeling high-frequency electromagnetic processes in power transformers. We present a large-scale 3D computer model for calculating magnetic fields in a transformer and evaluating effective parameters (inductance and resistance) of its windings and losses. The model accounts for complex, anisotropic, and frequency-dependent effective diamagnetic properties of the windings, which are obtained by solving small-scale 2D field problems as described in Part I of the paper. Results of the computations performed for a test transformer are analyzed in the frequency range 10 Hz-10 MHz. We discuss effects of windings conditions (open and short-circuited) and their location on the transformer core.
Viscosity studies of poly(DL‐lactic acid) in supercritical CO2 (2012)

Abstract The effect of supercritical CO 2 on the viscosity and activation energy to viscous flow of P DL LA is investigated, using a high pressure parallel plate rheometer, over a range of temperatures (50–140 °C) and pressures (5–12 MPa). The Cross model is fitted to the data to enable calculation of the zero shear viscosity and critical shear rate. A significant decrease in the viscosity is observed on increasing both variables; however, at high temperatures, the pressure effect becomes negligible. An increase in the critical shear rate is also observed on raising the pressure, indicative of a reduction in the relaxation time of the polymer. Manipulation of the Arrhenius equation shows a reduction in the activation energy to viscous flow as the pressure is increased. Together, these results show that the melt processing temperature of P DL LA can be reduced in the presence of supercritical and high pressure CO 2 . © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012
Design method of stable force control system using new resonance ratio control and instantaneous state observer (2015)

This paper proposes a stable force control system to achieve the force control of industrial robots. The proposed stable force control system is designed by using an I-P force control system and a resonance ratio control system considering the required interaction with the environment. To design the resonance ratio control system considering the contact with the environment, this paper analyzes the stability of the proposed resonance ratio control and the bandwidth of a disturbance observer. This paper designs the resonance ratio control system using an instantaneous state observer considering the results of the stability analysis. In addition, a stable force control system is designed based on the resonance ratio control system using an instantaneous state observer. In this paper, the effectiveness of the proposed force control system is confirmed by performing numerical simulations and experiments using an industrial robot arm.
Fundamentals of developer-resist interactions for line-edge roughness and critical dimension control in model 248-nm and 157-nm photoresists (2004)

Organic polar solvent (1-butanol) versus aqueous base (tetramethylammonium hydroxide, (TMAH)) development quality are distinguished by neutral versus charged polymer (polyelectrolyte) dissolution behavior of photoresist bilayers on silicon substrates comprising poly(4-hydroxystyrene) and poly(4-<i>tert</i>-butoxycarbonyloxystyrene), PHOSt and PBOCSt, respectively. This model line-edge was broadened by photoacid catalyzed deprotection to a final interfacial width of 35.7 &angst; and subjected to different developers. 1-butanol develops with an increased penetration depth than aqueous base development consistent with an increased solubility of the protected containing component in the organic solvent. This enhanced dissolution with the polar solvent results in an increased surface roughness of 73 &angst;, whereas the development with TMAH at concentrations between (0.1 to 1.1) M<sup>1</sup> leads to surface roughness between (4.5 to 14.4) &angst;, as measured by atomic force microscopy. These measurements suggest that the elimination of resist swelling, in the presence of a protection gradient, is a viable strategy to reduce roughness and control critical dimensions. The influence of added salt to developer solutions was also examined by developing the model bilayer. A decrease in surface roughness from (10 to 6.5) &angst; was observed between (0 to 0.70) M KCl in 0.26 M TMAH.
Scaling Theory of Polyelectrolyte Solutions (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTScaling Theory of Polyelectrolyte SolutionsAndrey V. Dobrynin, Ralph H. Colby, and Michael RubinsteinCite this: Macromolecules 1995, 28, 6, 1859–1871Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/ma00110a021https://doi.org/10.1021/ma00110a021research-articleACS PublicationsRequest reuse permissionsArticle Views5800Altmetric-Citations815LEARN 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
Dense Segmentation-Aware Descriptors (2013)

In this work we exploit segmentation to construct appearance descriptors that can robustly deal with occlusion and background changes. For this, we downplay measurements coming from areas that are unlikely to belong to the same region as the descriptor's center, as suggested by soft segmentation masks. Our treatment is applicable to any image point, i.e. dense, and its computational overhead is in the order of a few seconds. We integrate this idea with Dense SIFT, and also with Dense Scale and Rotation Invariant Descriptors (SID), delivering descriptors that are densely computable, invariant to scaling and rotation, and robust to background changes. We apply our approach to standard benchmarks on large displacement motion estimation using SIFT-flow and wide-baseline stereo, systematically demonstrating that the introduction of segmentation yields clear improvements.