gebhart/patrepeval huggingface dataset:
Efficient Flp-Int HK022 dual RMCE in mammalian cells (2013)

Recombinase-mediated cassette exchange, or RMCE, is a clean approach of gene delivery into a desired chromosomal location, as it is able to insert only the required sequences, leaving behind the unwanted ones. RMCE can be mediated by a single site-specific DNA recombinase or by two recombinases with different target specificities (dual RMCE). Recently, using the Flp-Cre recombinase pair, dual RMCE proved to be efficient, provided the relative ratio of the enzymes during the reaction is optimal. In the present report, we analyzed how the efficiency of dual RMCE mediated by the Flp-Int (HK022) pair depends on the variable input of the recombinases-the amount of the recombinase expression vectors added at transfection-and on the order of the addition of these vectors: sequential or simultaneous. We found that both in the sequential and the simultaneous modes, the efficiency of dual RMCE was critically dependent on the absolute and the relative concentrations of the Flp and Int expression vectors. Under optimal conditions, the efficiency of 'simultaneous' dual RMCE reached ∼12% of the transfected cells. Our results underline the importance of fine-tuning the reaction conditions for achieving the highest levels of dual RMCE.
Predictive block-matching motion estimation schemes for video compression. I. Inter-block prediction (2002)

A novel motion estimation/compensation scheme for full-motion interframe video compression is proposed. This scheme is based on prediction of interblock motion information by using minimum absolute difference block matching and hence substantially increases the searching and computation efficiency. A comparison is made with the 'optimal' full motion searching scheme for a standard test sequence. The experimental results show that the proposed scheme provides a computationally efficient algorithm in a real-time video communication environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Vaginal Microbiome and Epithelial Gene Array in Post-Menopausal Women with Moderate to Severe Dryness (2011)

After menopause, many women experience vaginal dryness and atrophy of tissue, often attributed to the loss of estrogen. An understudied aspect of vaginal health in women who experience dryness due to atrophy is the role of the resident microbes. It is known that the microbiota has an important role in healthy vaginal homeostasis, including maintaining the pH balance and excluding pathogens. The objectives of this study were twofold: first to identify the microbiome of post-menopausal women with and without vaginal dryness and symptoms of atrophy; and secondly to examine any differences in epithelial gene expression associated with atrophy. The vaginal microbiome of 32 post-menopausal women was profiled using Illumina sequencing of the V6 region of the 16S rRNA gene. Sixteen subjects were selected for follow-up sampling every two weeks for 10 weeks. In addition, 10 epithelial RNA samples (6 healthy and 4 experiencing vaginal dryness) were acquired for gene expression analysis by Affymetrix Human Gene array. The microbiota abundance profiles were relatively stable over 10 weeks compared to previously published data on premenopausal women. There was an inverse correlation between Lactobacillus ratio and dryness and an increased bacterial diversity in women experiencing moderate to severe vaginal dryness. In healthy participants, Lactobacillus iners and L. crispatus were generally the most abundant, countering the long-held view that lactobacilli are absent or depleted in menopause. Vaginal dryness and atrophy were associated with down-regulation of human genes involved in maintenance of epithelial structure and barrier function, while those associated with inflammation were up-regulated consistent with the adverse clinical presentation.
VOXALEADNEWS: A scalable content based video search engine (2012)

Video search is still largely based on text search human-supplied metadata, sometimes supplemented by extracted thumbnails. We have been developing a broadcast news search system based on recent progress in automatic speech recognition (ASR), natural language processing (NLP) and video and image processing to provide a rich content-based search to news. Our public online demonstrator of the Voxalead application, described here, currently indexes daily broadcast news content from 60 sources in English, French, Chinese, Arabic, Spanish, Dutch, Italian, German and Russian and make them searchable few time after they have been published.
Significantly Improved Method for the Pd‐Catalyzed Coupling of Phenols with Aryl Halides: Understanding Ligand Effects. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Near field enhancement in silver nanoantenna-superlens systems (2012)

We demonstrate near field enhancement generation in silver nanoantenna-superlens systems via numerical modeling. Using near-field interference and global optimization algorithms, we can design nanoantenna-superlens systems with mismatched permittivities, whose performance can match those with matched permittivities. The systems studied here may find broad applications in the fields of sensing, such as field-enhanced fluorescence and surface-enhanced Raman scattering, and the methodology used here can be applied to the designing and optimization of other devices, such as two-dimensional near field focusing lens.
STARLET: Multi-document Summarization of Service and Product Reviews with Balanced Rating Distributions (2011)

Reviews about products and services are abundantly available online. However, selecting information relevant to a potential buyer involves a significant amount of time reading user's reviews and weeding out comments unrelated to the important aspects of the reviewed entity. In this work, we present STARLET, a novel approach to multi-document summarization for evaluative text that considers the rating distribution as summarization feature to consistently preserve the overall opinion distribution expressed in the original reviews. We demonstrate how this method improves traditional summarization techniques and leads to more readable summaries.
Fusicoccin Ring System by [4 + 4] Cycloaddition. Control of Diastereoselectivity through Hydrogen Bonding (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTFusicoccin Ring System by [4 + 4] Cycloaddition. Control of Diastereoselectivity through Hydrogen BondingScott McN. Sieburth, Kevin F. McGee, and Taleb H. Al-TelView Author Information Department of Chemistry State University of New York Stony Brook, New York 11794-3400 Cite this: J. Am. Chem. Soc. 1998, 120, 3, 587–588Publication Date (Web):January 8, 1998Publication History Received1 October 1997Published online8 January 1998Published inissue 1 January 1998https://pubs.acs.org/doi/10.1021/ja973422qhttps://doi.org/10.1021/ja973422qrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views556Altmetric-Citations35LEARN 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:Conformation,Cyclization,Ethers,Noncovalent interactions,Solvents Get e-Alerts
Heterogeneity in tuberculosis pathology, microenvironments and therapeutic responses (2015)

Tuberculosis (TB) lesions are extremely complex and dynamic. Here, we review the multiple types and fates of pulmonary lesions that form following infection by Mycobacterium tuberculosis and the impact of this spatial and temporal heterogeneity on the bacteria they harbor. The diverse immunopathology of granulomas and cavities generates a plethora of microenvironments to which M. tuberculosis bacilli must adapt. This in turn affects the replication, metabolism, and relative density of bacterial subpopulations, and consequently their respective susceptibility to chemotherapy. We outline recent developments that support a paradigm shift in our understanding of lesion progression. The simple model according to which lesions within a single individual react similarly to the systemic immune response no longer prevails. Host-pathogen interactions within lesions are a dynamic process, driven by subtle and local differences in signaling pathways, resulting in diverging trajectories of lesions within a single host. The spectrum of TB lesions is a continuum with a large overlap in the lesion types found in latently infected and active TB patients. We hope this overview will guide TB researchers in the design, choice of read-outs, and interpretation of future studies in the search for predictive biomarkers and novel therapies.
Bivalent ligands promote endosomal trafficking of the dopamine D3 receptor-neurotensin receptor 1 heterodimer (2021)

Bivalent ligands are composed of two pharmacophores connected by a spacer of variable size. These ligands are able to simultaneously recognize two binding sites, for example in a G protein-coupled receptor heterodimer, resulting in enhanced binding affinity. Taking advantage of previously described heterobivalent dopamine-neurotensin receptor ligands, we demonstrate specific interactions between dopamine D3 (D<sub>3</sub>R) and neurotensin receptor 1 (NTSR1), two receptors with expression in overlapping brain areas that are associated with neuropsychiatric diseases and addiction. Bivalent ligand binding to D<sub>3</sub>R-NTSR1 dimers results in picomolar binding affinity and high selectivity compared to the binding to monomeric receptors. Specificity of the ligands for the D<sub>3</sub>R-NTSR1 receptor pair over D<sub>2</sub>R-NTSR1 dimers can be achieved by a careful choice of the linker length. Bivalent ligands enhance and stabilize the receptor-receptor interaction leading to NTSR1-controlled internalization of D<sub>3</sub>R into endosomes via recruitment of β-arrestin, highlighting a potential mechanism for dimer-specific receptor trafficking and signalling.
Nonlinear Distortion in a Silicon Microring-Based Electro-Optic Modulator for Analog Optical Links (2010)

We analyze silicon microring modulators for analog signal generation, in terms of harmonic and intermodulation distortions. Free carrier plasma dispersion effect in silicon, Lorentzian-shaped resonance profile, and cavity photon lifetime are identified as the sources of modulation nonlinearity. Simulations show that the silicon microring modulators exhibit good modulation index and carrier-to-distortion ratio (CDR). For the generation of 10-GHz suboctave analog signals, a high optical-modulation-index of up to 46%, a CDR of 57 dB, and a spurious free dynamic range of 96 dB can be obtained. In fiber transmission, the microring-generated signal CDR can be improved by 10 dB due to the interaction between frequency chirp and chromatic dispersion.
Abstract 1350: Novel ABI analogs target the colchicine site in tubulin and overcome multidrug resistance in metastatic melanoma (2011)

Abstract With rapidly rising incidences of metastatic melanoma and its high resistance to current therapeutic agents, developing more effective drugs is urgently needed. We recently discovered a novel class of 2-aryl-4-benzoyl-imidazoles (ABI) analogs. These compounds showed great antiproliferative activity on melanoma cells and the IC50 is as low as 8 nM. ABIs showed equal potency against multidrug resistant melanoma cells and the sensitive parent cells, suggesting that they can effectively overcome P-gp meditated multidrug resistance. ABIs inhibited capillary network formation which indicates high potential for anti-angiogenesis. Cell cycle analysis showed ABIs arrested cells in the G2/M phase and inhibited tubulin polymerization. ABIs bind to the colchicine binding site in the α/β-tubulin heterodimer as indicated by a number of evidences including competitive binding and molecular modeling studies. Immunofluorescence experiments revealed that microtubule modality was dramatically changed with ABIs treatment. In vivo studies using both B16-F1/C57BL model and A375/SHO model showed significant inhibition of melanoma tumor growth by ABIs. These novel analogs hold great promise as new selective agents for the improved treatment of malignant melanoma. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1350. doi:10.1158/1538-7445.AM2011-1350
Integrin αvβ3 Mediates Chemotactic and Haptotactic Motility in Human Melanoma Cells through Different Signaling Pathways (1996)

Distinctions between chemotaxis and haptotaxis of cells to extracellular matrix proteins have not been defined in terms of mechanisms or signaling pathways. Migration of A2058 human melanoma cells to soluble (chemotaxis) and substratum-bound (haptotaxis) vitronectin, mediated by v 3 , provided a system with which to address these questions. Both chemotaxis and haptotaxis were completely inhibited by treatment with RGDcontaining peptides. Chemotaxis was abolished by a blocking antibody to v 3 (LM609), whereas haptotaxis was inhibited only by approximately 50%, suggesting involvement of multiple receptors and/or signaling pathways. However, blocking antibodies to v 5 , also present on A2058 cells, did not inhibit. Pertussis toxin treatment of cells inhibited chemotaxis by >80%, but did not inhibit haptotaxis. Adhesion and spreading over vitronectin induced the phosphorylation of paxillin on tyrosine. In cells migrating over substratum-bound vitronectin, tyrosine phosphorylation of paxillin increased 5-fold between 45 min and 5 h. Dilutions of anti- v 3 that inhibited haptotaxis also inhibited phosphorylation of paxillin (by 50%) and modestly reduced cell spreading. In contrast, soluble vitronectin (50 -100 g/ ml) did not induce tyrosine phosphorylation of paxillin. The data suggest that soluble vitronectin stimulates chemotaxis predominantly through a G protein-mediated pathway that is functionally linked to v 3 . Haptotaxis is analogous to directional cell spreading and requires v 3 -mediated tyrosine phosphorylation of paxillin.
Dual Stack Hosts Using "Bump-in-the-API" (BIA) (2010)

This document describes the Bump-In-the-API (BIA) host based
protocol translation mechanism that allows applications supporting
only one IP address family to communicate with peers that are
reachable or supporting only the other address family. This
specification addresses scenarios where a host is provided dual stack,
IPv6 only or IPv4 only network connectivity. In the dual stack network
case, single address family applications in the host will communicate
directly with other hosts using the same address family. In the case
of IPv6 only network or IPv6 only destination, IPv4- originated
communications have to be be translated into IPv6. IPv6 communications
may have to translated similarly to IPv4. Technically, the BIS-enabled
host resolves both IPv4 and IPv6 addresses of the destination and
behaves according to received responses.
Angiopoietins bind thrombomodulin and inhibit its function as a thrombin cofactor (2018)

Angiopoietin-1 (Ang1) and Angiopoietin-2 (Ang2) are ligands for Tie2, an endothelial-specific receptor tyrosine kinase that is an essential regulator of angiogenesis. Here we report the identification, via expression cloning, of thrombomodulin (TM) as another receptor for Ang1 and Ang2. Thrombomodulin is an endothelial cell surface molecule that plays an essential role as a coagulation inhibitor via its function as a cofactor in the thrombin-mediated activation of protein C, an anticoagulant protein, as well as thrombin-activatable fibrinolysis inhibitor (TAFI). Ang1 and Ang2 inhibited the thrombin/TM-mediated generation of activated protein C and TAFI in cultured endothelial cells, and inhibited the binding of thrombin to TM in vitro. Ang2 appears to bind TM with higher affinity than Ang1 and is a more potent inhibitor of TM function. Consistent with a potential role for angiopoietins in coagulation, administration of thrombin to mice rapidly increased plasma Ang1 levels, presumably reflecting release from activated platelets (previously shown to contain high levels of Ang1). In addition, Ang1 levels were significantly elevated in plasma prepared from wound blood, suggesting that Ang1 is released from activated platelets at sites of vessel injury. Our results imply a previously undescribed role for angiopoietins in the regulation of hemostasis.
Chip-Based Tunable Direct Comb Spectroscopy (2017)

We demonstrate mode-hop-free tuning of a modelocked frequency comb over 60 GHz in a silicon microresonator. A gas-phase spectroscopy of acetylene is performed with a high-spectral-resolution (&lt; 80 MHz) over a bandwidth of 40 THz.
Power, Performance, and Thermal Management for High-Performance Systems (2007)

In future high-performance systems it will be essential to balance often-conflicting objectives of performance, power, energy, and temperature under variable workload and environmental conditions. In this work, we describe a goal-driven approach that conveys multiple expectations to managers that dynamically tune operating states to best meet those demands. We show the benefit of a concise goal specification for complex objectives and the feasibility of managing multiple constraints while maintaining high performance and safe operation. We evaluate key features of our approach with a prototype implementation on a Pentium M platform with Red Hat Enterprise 4 that controls voltage and frequency scaling to achieve the desired performance, power and temperature goals.
Open-Source Chromatographic Data Analysis for Reaction Optimization and Screening (2023)

Automation and digitalization solutions in the field of small molecule synthesis face new challenges for chemical reaction analysis, especially in the field of high-performance liquid chromatography (HPLC). Chromatographic data remains locked in vendors hardware and software components, limiting their potential in automated workflows and data science applications. In this work, we present an open-source Python project called MOCCA for the analysis of HPLC-DAD (photodiode array detector) raw data. MOCCA provides a comprehensive set of data analysis features, including an automated peak deconvolution routine of known signals, even if overlapped with signals of unexpected impurities or side products. We highlight the broad applicability of MOCCA in four studies: (i) a simulation study to validate MOCCAs data analysis features; (ii) a reaction kinetics study on a Knoevenagel condensation reaction demonstrating MOCCAs peak deconvolution feature; (iii) a closed-loop optimization study for the alkylation of 2-pyridone without human control during data analysis; (iv) a well plate screening of categorical reaction parameters for a novel palladium-catalyzed cyanation of aryl halides employing O-protected cyanohydrins. By publishing MOCCA as a Python package with this work, we envision an open-source community project for chromatographic data analysis with the potential of further advancing its scope and capabilities.
A Look Inside 5G Standards to Support Time Synchronization for Smart Manufacturing (2020)

Connectivity has a major role in the current transformation of smart manufacturing. 5G is foreseen as an integral part of an end-to-end networking infrastructure supporting smart manufacturing operation. The integration of 5G with time-sensitive networking (TSN)is seen as a holistic communication solution for smart factories. The next generation of industrialization consists of real-time processes, automation, fixed and cellular networks, and high diversity of devices. The integration of fixed and cellular devices in a single infrastructure to enable end-to-end deterministic communications requires high accuracy of time synchronization. The transport technologies in fixed networks have been evolving toward TSN and deterministic networking to fulfill the requirements for industrial communications. The latest cellular specifications for 5G are targeting ultra-reliable and low-latency communications that enable the Industrial Internet of Things. This article describes the state of the art for integrating TSN with 5G networks based on the support given in 3GPP TS 23.501 Release 16. The requirements for time synchronization in factory automation and integration with 5G networks are presented, together with the most recent advancements in the standardization process.
Graph Search and Beyond (2015)

Modern Web data is highly structured in terms of entities and relations from large knowledge resources, geo-temporal references and social network structure, resulting in a massive multidimensional graph. This graph essentially unifies both the searcher and the information resources that played a fundamentally different role in traditional IR, and "Graph Search" offers major new ways to access relevant information. Graph search affects both query formulation (complex queries about entities and relations building on the searcher's context) as well as result exploration and discovery (slicing and dicing the information using the graph structure) in a completely personalized way. This new graph based approach introduces great opportunities, but also great challenges, in terms of data quality and data integration, user interface design, and privacy. We view the notion of "graph search" as searching information from your personal point of view (you are the query) over a highly structured and curated information space. This goes beyond the traditional two-term queries and ten blue links results that users are familiar with, requiring a highly interactive session covering both query formulation and result exploration. The workshop attracted a range of researchers working on this and related topics, and made concrete progress working together on one of the greatest challenges in the years to come.
Perillyl alcohol mediated radiosensitization via augmentation of the Fas pathway in prostate cancer cells (2003)

The unique manner of radiosensitization in addition to its low toxicity profile makes POH a promising new agent for preclinical evaluation as a potential radiosensitizer in the treatment of prostate cancer.