gebhart/patrepeval huggingface dataset:
Tracking Gene Expression after DNA Delivery Using Spatially Indexed Nanofiber Arrays (2004)

The penetration and residence of vertically aligned carbon nanofibers (VACNF) within live cell matrices is demonstrated upon substrates that incorporate spatially registered indices to facilitate temporal tracking of individual cells. Penetration of DNA-modified carbon nanofibers into live cells using this platform provides efficient delivery and expression of exogenous genes, similar to “microinjection”-styled methods, but on a massively parallel basis. Spatially registered indices on the substrate allow one to conveniently locate individual cells, facilitating temporal tracking of gene expression events. We describe fabrication and use of this gene delivery platform which consists of arrays of individual carbon nanofibers at 5-μm pitch within numerically indexed, 100-μm square grid patterns. Fabrication of these devices on silicon substrates enables mass production of 100 devices (5 mm2) per wafer, with each device providing over 800,000 nanofiber-based “needles” for cellular impalement and gene delivery applications.
Software Architecture Transformations (2000)

In order to understand and improve software, we commonly examine and manipulate its architecture. For example, we may want to examine the architecture at different levels of abstraction or zoom-in on one portion of the system. We may discover that the extracted architecture has deviated from our mental model of the software and hence we may want to repair it. This paper identifies the commonality between these architectural transformation actions -- that is, by manipulating the architecture in order to understand, analyze, and modify the software structure, we are in fact performing graph transformations. We categorize useful architectural transformations and describe them within the framework of graph transformations. By describing them in a unified way, we gain a better understanding of the transformations and thus, can work towards modeling, specifying and automating them. Keywords: software architecture, graph transformation, reverse engineering, program understanding 1. Introduc...
Low-Latency Real-Time Meeting Recognition and Understanding Using Distant Microphones and Omni-Directional Camera (2011)

This paper presents our real-time meeting analyzer for monitoring conversations in an ongoing group meeting. The goal of the system is to recognize automatically “who is speaking what” in an online manner for meeting assistance. Our system continuously captures the utterances and face poses of each speaker using a microphone array and an omni-directional camera positioned at the center of the meeting table. Through a series of advanced audio processing operations, an overlapping speech signal is enhanced and the components are separated into individual speaker's channels. Then the utterances are sequentially transcribed by our speech recognizer with low latency. In parallel with speech recognition, the activity of each participant (e.g., speaking, laughing, watching someone) and the circumstances of the meeting (e.g., topic, activeness, casualness) are detected and displayed on a browser together with the transcripts. In this paper, we describe our techniques and our attempt to achieve the low-latency monitoring of meetings, and we show our experimental results for real-time meeting transcription.
Cross-linked PMMA as a low-dimensional dielectric sacrificial layer (2003)

A surface nanomachining fabrication process using electron beam cross-linked poly(methyl) methacrylate (PMMA) has been developed and characterized. PMMA with different molecular weights (MW 100 K, MW 495 K, MW 950 K) in anisole casting solvent has been crosslinked with different electron beam irradiation levels ranging from 20 C/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> to 240 C/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . This is to investigate the quantifiable relationship between electron dose and its submicrometer remaining thickness after dissolving in acetone. This technique which uses electron beam lithography, offers a high resolution semi-three-dimensional (3-D) nanomachining of the sacrificial layer in a single run. Because of its low Young's modulus, it has been successfully integrated with nanoelectromechanical systems processing and has the advantage of producing low-stress submicrometer thick structures with lateral dimensions as low as, but not limited to 1 μm. A fast dry release time from 55 to 100 s using oxygen plasma ashing has been demonstrated for a sacrificial layer aspect ratio of 125. This corresponds to an etch rate of about 0.6 μm/s at an average temperature of 40°C. The success of using cross-linked PMMA as a gate dielectric is demonstrated by the fabrication of multilayered gated lateral quantum dot devices. Periodic and continuous conductance oscillations arising from Coulomb charging effects are clearly observed in the transport properties at 50 mK.
Dendritic Polyglycerols with Oligoamine Shells Show Low Toxicity and High siRNA Transfection Efficiency in Vitro (2010)

RNA interference provides great opportunities for treating diseases from genetic disorders, infection, and cancer. The successful application of small interference RNA (siRNA) in cells with high transfection efficiency and low cytotoxicity is, however, a major challenge in gene-mediated therapy. Several pH-responsive core shell architectures have been designed that contain a nitrogen shell motif and a polyglycerol core, which has been prepared by a two-step protocol involving the activation of primary and secondary hydroxyl groups by phenyl chloroformate and amine substitution. Each polymer was analyzed by particle size and ζ potential measurements, whereas the respective polyplex formation was determined by ethidium bromide displacement assay, atomic force microscopy (AFM), and surface charge analysis. The in vitro gene silencing properties of the different polymers were evaluated by using a human epithelial carcinoma cell (HeLaS3) line with different proteins (Lamin, CDC2, MAPK2). Polyplexes yielded similar knockdown efficiencies as HiPerFect controls, with comparably low cytotoxicity. Therefore, these efficient and highly biocompatible dendritic polyamines are promising candidates for siRNA delivery in vivo.
Synthetic agonists of Toll-like receptors 7, 8 and 9 (2007)

TLRs (Toll-like receptors) are a family of innate immune receptors that induce protective immune responses against infections. Single-stranded viral RNA and bacterial DNA containing unmethylated CpG motifs are the ligands for TLR7 and TLR8 and 9 respectively. We have carried out extensive structure-activity relationship studies of DNA- and RNA-based compounds to elucidate the impact of nucleotide motifs and structures on these TLR-mediated immune responses. These studies have led us to design novel DNA- and RNA-based compounds, which act as potent agonists of TLR9 and TLR7 and 8 respectively. These novel synthetic agonists produce different immune response profiles depending on the structures and nucleotide motifs present in them. The ability to modulate TLR-mediated immune responses with these novel DNA- and RNA-based agonists in a desired fashion may allow targeting a broad range of diseases, including cancers, asthma, allergies and infections, alone or in combination with other therapeutic agents, and their use as adjuvants with vaccines. IMO-2055, our first lead candidate, is a TLR9 agonist that is currently in clinical evaluation in oncology patients. A second candidate, IMO-2125, is also a TLR9 agonist that has been shown to induce high and sustained levels of IFN (interferon) in non-human primates and is being evaluated in HepC-infected human subjects.
Wavelets for computer graphics: a primer.1 (1995)

Wavelets are a mathematical tool for hierarchically decomposing functions. They allow a function to be described in terms of a coarse overall shape, plus details that range from broad to narrow. Regardless of whether the function of interest is an image, a curve, or a surface, wavelets offer an elegant technique for representing the levels of detail present. The article is intended to provide people working in computer graphics with some intuition for what wavelets are, as well as to present the mathematical foundations necessary for studying and using them. We discuss the simple case of Haar wavelets in one and two dimensions, and show how they can be used for image compression.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Chirp-managed laser and MLSE-RX enables transmission over 1200 km at 1550 nm in a DWDM environment in NZDSF at 10 gb/s without any optical dispersion compensation (2006)

The small form factor chirp-managed laser (CML) source at 1550 nm was used in conjunction with postdetection electronic signal processing to successfully achieve transmission over 1200 km of nonzero dispersion-shifted fiber in a dense wavelength-division-multiplexing environment, without using any optical dispersion compensation. In a comparative study, the dispersion tolerance and the transmission performance of the CML were found to be better than the duobinary format.
Mechanisms associated with the generation of biologically active human immunodeficiency virus type 1 particles from defective proviruses. (1991)

The human immunodeficiency virus (HIV) is the etiological agent of acquired immunodeficiency syndrome (AIDS). HIV exhibits extensive genetic diversity and it is apparent that an infected individual contains different populations of distinct viral strains, a large proportion of which has been found surprisingly to be defective for replication. A similar phenomenon has also been observed with some cell lines that are known to produce infectious viral particles but harbor defective proviral genomes. Here, we investigated the molecular basis of this phenomenon by cloning proviral genomes of HIV from a cell line that was capable of producing high titers of biologically active HIV particles that readily induced syncytia with CD4+ cell lines and peripheral blood lymphocytes. This cell line was found to contain five proviral genomes, all of which, when tested individually, failed to produce replication-competent viruses upon transfection into human cells. However, when a specific combination of two proviral genomes was used in such transfection studies, it was possible to obtain biologically active, replication-competent viral particles that infected and replicated in CD4+ cell lines and induced syncytia characteristic of HIV. Such a result may be due to homologous recombination between proviral DNAs occurring in cells after transfection and/or complementation of replication-defective proviral DNAs. The diploid nature of the viral RNA genome present in the viral particle may enable the persistence of defective HIV genomes.
Amiloride and vertebrate gustatory responses to NaCl (1998)

Amiloride at < or = 1 microM may block epithelial Na+ channels without affecting other cellular mechanisms, and attenuates gustatory responses to lingual NaCl from the chorda tympani nerves (CT) of gerbil, hamster, rhesus monkey, and several strains of laboratory rat and mouse, and from glossopharyngeally innervated frog taste-receptor cells; at 5 microM to 50 microM, also from Wistar rat and mongrel dog CT. Affected units responded more to NaCl than to KCl. Suppression of CT responses to KCl, HCl, NH4Cl, or saccharides also occurred in some mammals, but amiloride did not elicit responses. Taste-dependent behaviors towards NaCl or KCl were altered. DBA and 129/J laboratory mice, and mudpuppy, were unaffected by amiloride. In humans, 10 microM amiloride both produced taste reports and reduced total intensity of NaCl and LiCl by 15-20%. NaCl and LiCl sourness, and KCl and QHCl bitterness declined, but saltiness generally did not change. Effects on sweetness were inconsistent. Amiloride-sensitive gustatory mechanisms were prominent in some mammals, were not necessary for responses to NaCl, and were of minor importance for human taste.
Drill-in fluid reduces formation damage, increases production rates (1998)

A sodium formate drill-in fluid system reduced formation damage, resulting in better-than-expected production rates for an off-shore Dutch development well. Programmed to optimize production capacity and reservoir drainage from a Rotliegend sandstone gas discovery, the 5-7/8-in. subhorizontal production interval was drilled and completed barefoot with a unique, rheologically engineered sodium formate drill-in fluid system. The new system, consisting of a sodium formate (NaCOOH) brine as the base fluid and properly sized calcium carbonate as the formation-bridging agent, was selected on the basis of its well-documented record in reducing solids impairment and formation damage in similar sandstone structures in Germany. The system was engineered around the low-shear-rate viscosity (LSRV) concept, designed to provide exceptional rheological properties. After describing the drilling program, the paper gives results on the drilling and completion.
Central Role of Toll-Like Receptor 4 Signaling and Host Defense in Experimental Pneumonia Caused by Gram-Negative Bacteria (2004)

ABSTRACT Toll-like receptor 4 (TLR4) has been identified as a receptor for lipopolysaccharide. However, the precise role of TLR4 in regulating gene expression in response to an infection caused by gram-negative bacteria has not been fully elucidated. The role of TLR4 signaling in coordinating gene expression was assessed by gene expression profiling in lung tissue in a mouse model of experimental pneumonia with a low-dose infection of Klebsiella pneumoniae . We analyzed four mouse strains: C57BL/6 mice, which are resistant to bacterial dissemination; 129/SvJ mice, which are susceptible; C3H/HeJ mice, which are susceptible and have defective TLR4 signaling; and their respective control strain, C3H/HeN (intermediate resistance). At 4 h after infection, C57BL/6 and C3H/HeN mice demonstrated the greatest number of genes, with 67 shared induced genes which were TLR4 dependent and highly associated with the resistance phenotype. These genes included cytokine and chemokine genes required for neutrophil activation or recruitment, growth factor receptors, MyD88 (a critical adaptor protein for TLR signaling), and adhesion molecules. TLR4 signaling accounted for over 74% of the gene expression in the C3H background. These data suggest that early TLR4 signaling controls the vast majority of gene expression in the lung in response to an infection caused by gram-negative bacteria and that this subsequent gene expression determines survival of the host.
An adenoviral vector cancer vaccine that delivers a tumor-associated antigen/CD40-ligand fusion protein to dendritic cells (2003)

To develop a method to overcome the anergy that exists in tumor hosts to cancer, we have designed an adenoviral vector for the in vivo activation and tumor antigen loading of dendritic cells. This adenoviral vector encodes a fusion protein composed of an amino-terminal tumor-associated antigen fragment fused to the CD40 ligand (CD40L). Subcutaneous injection of an adenoviral vector encoding a fusion protein of the human papillomavirus E7 foreign antigen linked to the CD40L generates CD8+ T cell-dependent immunoresistance to the growth of the E7-positive syngeneic TC-1 cancer cells in C57BL/6 mice for up to 1 year. We also studied the s.c. injection of a vector carrying the gene for the human MUC-1 (hMUC-1) self-antigen fused to the CD40L. When this vector was injected into hMUC-1.Tg mice, which are transgenic for the hMUC-1 antigen, the growth of syngeneic hMUC-1-positive LL1/LL2hMUC-1 mouse cancer cells was suppressed in 100% of the injected animals. The hMUC-1.Tg mice are anergic to the hMUC-1 antigen before the injection of the vector. These experimental results show that it is possible to use vector injection to activate a long-lasting cellular immune response against self-antigens in anergic animals. The vector-mediated in vivo activation, and tumor-associated antigen loading of dendritic cells does not require additional cytokine boosting to induce the immune response against the tumor cells. This vector strategy may therefore be of use in the development of immunotherapy for the many carcinomas in which the hMUC-1 antigen is overexpressed.
Ruthenium(II) and Osmium(II) Bis(terpyridine) Complexes in Covalently-Linked Multicomponent Systems: Synthesis, Electrochemical Behavior, Absorption Spectra, and Photochemical and Photophysical Properties (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRuthenium(II) and Osmium(II) Bis(terpyridine) Complexes in Covalently-Linked Multicomponent Systems: Synthesis, Electrochemical Behavior, Absorption Spectra, and Photochemical and Photophysical PropertiesJean Pierre Sauvage, Jean Paul Collin, Jean Claude Chambron, Stephane Guillerez, Christophe Coudret, Vincenzo Balzani, Francesco Barigelletti, Luisa De Cola, and Lucia FlamigniCite this: Chem. Rev. 1994, 94, 4, 993–1019Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/cr00028a006https://doi.org/10.1021/cr00028a006research-articleACS PublicationsRequest reuse permissionsArticle Views9007Altmetric-Citations1380LEARN 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
Dynamic regulation of c‐Myc proto‐oncogene expression during lymphocyte development revealed by a GFP‐c‐Myc knock‐in mouse (2008)

c-Myc induces widely varying cellular effects, including cell proliferation and cell death. These different cellular effects are determined, in part, by c-Myc protein expression levels, which are regulated through several transcriptional and post-transcriptional pathways. c-Myc transcripts can be detected in cells at all stages of B and T lymphocyte development. However, little is known about c-Myc protein expression, and how it varies, in developing lymphocytes. Here mice have been generated in which the endogenous c-Myc locus has been modified (c-Myc(G)) so that it encodes a GFP-c-Myc fusion protein. c-Myc(G/G) mice are viable, appear normal and exhibit grossly normal lymphocyte development. Flow cytometric analyses revealed significant heterogeneity in c-Myc protein expression levels in developing c-Myc(G/G) B and T lymphocytes. GFP-c-Myc expression levels were highest in proliferating lymphocytes, suggesting that c-Myc up-regulation is important for promoting lymphocyte cell division, and demonstrating that GFP-c-Myc expression is a marker of proliferating lymphocytes in vivo.
Oxidative Processes in Soybean and Pea Seeds (1987)

Oxidative processes are probable determinants of longevity of seeds in storage. Measurements of actual oxygen uptake rates were made for soybean and pea seeds as a comparison of short and long lived seeds when light, temperature, and moisture contents were varied. In both peas and soybeans, the oxygen uptake was depressed at low temperatures (<16 degrees C) and low water contents (< 0.25 gram H2O per gram dry weight). Apparent activation energies under these conditions are very high, while apparent activation energies of seeds at higher water contents and at temperatures greater than 22 degrees C are much less. Light enhances the level of oxygen uptake in pea, but reduces the level of oxygen uptake in soybean. The complexities of the interactions of oxygen uptake with environmental conditions in soybean compared to pea suggest that oxidative processes occur in soybean at low water contents, but are essentially absent in pea. It is suggested that the additional oxidative processes in soybean with moisture contents between 0.10 and 0.24 gram per gram may contribute to the poorer longevity of soybean seed compared to pea seed.
Abnormal expression and mutation of p53 in cervical cancer--a study at protein, RNA and DNA levels. (1997)

p53 overexpression or mutation does not seem to play a significant role in cervical carcinomas.
New Drugs: Antisense Oligodeoxynucleotides as Clinical Therapeutic Agents (1996)

(1996). New Drugs: Antisense Oligodeoxynucleotides as Clinical Therapeutic Agents. Cancer Investigation: Vol. 14, No. 1, pp. 54-65.
Novel 1,4-dihydropyridine calcium antagonists. I. Synthesis and hypotensive activity of 4-(substituted pyridyl)-1,4-dihydropyridine derivatives. (1990)

A series of 4-(substituted pyridyl)-1,4-dihydropyridine derivatives were synthesized and their hypotensive effects examined. Several compounds, 2-(N-benzyl-N-methylamino)ethyl methyl 1,4-dihydro-2,6-dimethyl-4-(3-nitro-2-pyridyl)-3,5-pyridinedicarboxylate (2b), its 4-(4-nitro-2-pyridyl) analogue (2g), 4-(3-trifluoromethyl-2-pyridyl) analogue (2c), 4-(2-trifluoromethyl-3-pyridyl) analogue (3e), 4-(4-cyano-2-pyridyl) analogue (2e), 4-(2-cyano-3-pyridyl) analogue (3d), and 4-(6-bromo-2-pyridyl) analogue (2i), were found to have a hypotensive activity parallel to that of nicardipine; 2c and 3e, in particular, had approximately twice the duration of nicardipine, and 2e had the most potent hypotensive activity of all the derivatives synthesized.