gebhart/patrepeval huggingface dataset:
Simultaneous production of interleukin 6, interferon‐β and colony‐stimulating activity by fibroblasts after viral and bacterial infection (1989)

Different viruses were compared with the double-stranded RNA poly(rI).poly(rC) and interleukin (IL) 1 for their IL 6-inducing potential in several human and animal cell types. The laboratory viruses Sendai, Mengo and Newcastle disease virus were found to dose dependently stimulate IL 6 production in diploid fibroblasts. A similar effect was obtained with the human pathogens, measles and rubella virus. Concomitantly with IL 6, two other cytokine activities, i.e., interferon-beta and colony-stimulating activity for granulocytes and monocytes, were induced. In addition, these three activities were also produced by fibroblasts in response to Escherichia coli, whereas lipopolysaccharide was only marginally active. The specificity of the induction phenomenon was confirmed by the lack of IL 6 induction with inactivated infectious agents and by the complete neutralization of produced IL 6 by specific antibodies. This study indicates that the coordinate production of hemopoietic growth factors and interferon, originating from cells that do not classically belong to the immune system, can influence the local and systemic reactions observed during host defence against various infectious agents.
Cell Migration--Movin' On (1999)

Cell migration is crucial for embryonic development, the inflammatory immune response, wound repair, and tumor formation and metastasis (1). It begins with an initial protrusion or extension of the plasma membrane at the front (leading edge) of the cell (see the figure). The protrusions are driven by the polymerization of a network of cytoskeletal actin filaments and are stabilized through the formation of adhesive complexes. These adhesive complexes are regions of the plasma membrane where integrin receptors, actin filaments, and associated proteins cluster together. As the cells migrate, the small nascent adhesive complexes (focal complexes) at the front of the cell grow and strengthen into larger, more organized adhesive complexes (focal adhesions) that serve as points of traction over which the body of the cell moves. Finally, release of adhesions at the rear results in a net displacement of the cell. The mechanisms that regulate the formation of focal complexes at the cell's leading edge and the release of focal adhesions at the cell's rear remain unclear. Now, on page 1172 of this issue, Smilenov et al. (2) demonstrate that focal adhesions are highly motile in stationary fibroblasts yet stationary in migrating fibroblasts, suggesting the existence of a molecular clutch that couples traction and contractile forces. Other recent findings highlight the importance of tension, the actin and myosin filament network, the Rho/Rac family of signaling molecules, and microtubules in cell migration. Coordinating all of these complex processes is the challenge facing cells that are on the move.
Rheumatoid arthritis synovial fluid fibroblasts express TRAIL‐R2 (DR5) that is functionally active (2004)

Fibroblasts grown from the synovial fluid and synovial membrane of RA patients express TRAIL-R2 that is functionally active. An agonistic anti-TRAIL-R2 antibody that does not induce hepatocyte toxicity may be an alternative strategy for treatment of RA.
Achieving single channel, full duplex wireless communication (2010)

This paper discusses the design of a single channel full-duplex wireless transceiver. The design uses a combination of RF and baseband techniques to achieve full-duplexing with minimal effect on link reliability. Experiments on real nodes show the full-duplex prototype achieves median performance that is within 8% of an ideal full-duplexing system.
Solution Structure of a Two-Base DNA Bulge Complexed with an Enediyne Cleaving Analog (1996)

Nucleic acid bulges have been implicated in a number of biological processes and are specific cleavage targets for the enediyne antitumor antibiotic neocarzinostatin chromophore in a base-catalyzed, radical-mediated reaction. The solution structure of the complex between an analog of the bulge-specific cleaving species and an oligodeoxynucleotide containing a two-base bulge was elucidated by nuclear magnetic resonance. An unusual binding mode involves major groove recognition by the drug carbohydrate unit and tight fitting of the wedge-shaped drug in the triangular prism pocket formed by the two looped-out bulge bases and the neighboring base pairs. The two drug rings mimic helical DNA bases, complementing the bent DNA structure. The putative abstracting drug radical is 2.2 +/- 0.1 angstroms from the pro-S H5' of the target bulge nucleotide. This structure clarifies the mechanism of bulge recognition and cleavage by a drug and provides insight into the design of bulge-specific nucleic acid binding molecules.
Sequence-dependent effects on DNA stability resulting from guanosine replacements by inosine (1994)

The effect of replacing a G.C base-pair with an I.C base-pair on DNA stability was investigated for a related set of 14-mers. DNA melting analysis of the 14-mers was used to determine delta Hzero, delta Szero and delta G(zero)37 of the double to single stranded transition. All 14mers were shown to have B-DNA character by circular dichroism analysis. 14mers substituted with a single inosine in place of guanosine at different positions showed that consequences on DNA stability are sequence-dependent. Large changes in delta Hzero and delta Szero result when inosine is substituted within the trinucleotide sequence d(TCG).d(CGA) while substitution within d(TCC).d(GGA) causes minor changes in enthalpy and entropy. Moreover, some 14-mers with two inosine substitutions five base-pairs apart showed non-additive free energy changes for the double to single stranded transition. These results clearly indicate that the structural consequences of replacing a single guanosine with an inosine are transmitted over a significant distance.
The optogenetic (r)evolution (2011)

Optogenetics is a rapidly evolving field of technology that allows optical control of genetically targeted biological systems at high temporal and spatial resolution. By heterologous expression of light-sensitive microbial membrane proteins, opsins, cell type-specific depolarization or silencing can be optically induced on a millisecond time scale. What started in a petri dish is applicable today to more complex systems, ranging from the dissection of brain circuitries in vitro to behavioral analyses in freely moving animals. Persistent technical improvement has focused on the identification of new opsins, suitable for optogenetic purposes and genetic engineering of existing ones. Optical stimulation can be combined with various readouts defined by the desired resolution of the experimental setup. Although recent developments in optogenetics have largely focused on neuroscience it has lately been extended to other targets, including stem cell research and regenerative medicine. Further development of optogenetic approaches will not only highly increase our insight into health and disease states but might also pave the way for a future use in therapeutic applications.
Role of laminin and basement membrane in the morphological differentiation of human endothelial cells into capillary-like structures. (1988)

We have defined a signal responsible for the morphological differentiation of human umbilical vein and human dermal microvascular endothelial cells in vitro. We find that human umbilical vein endothelial cells deprived of growth factors undergo morphological differentiation with tube formation after 6-12 wk, and that human dermal microvascular endothelial cells differentiate after 1 wk of growth factor deprivation. Here, we report that morphological differentiation of both types of endothelial cells is markedly accelerated by culture on a reconstituted gel composed of basement membrane proteins. Under these conditions, tube formation begins in 1-2 h and is complete by 24 h. The tubes are maintained for greater than 2 wk. Little or no proliferation occurs under these conditions, although the cells, when trypsinized and replated on fibronectin-coated tissue culture dishes, resume division. Ultrastructurally, the tubes possess a lumen surrounded by endothelial cells attached to one another by junctional complexes. The cells possess Weibel-Palade bodies and factor VIII-related antigens, and take up acetylated low density lipoproteins. Tubule formation does not occur on tissue culture plastic coated with laminin or collagen IV, either alone or in combination, or on an agarose or a collagen I gel. However, endothelial cells cultured on a collagen I gel supplemented with laminin form tubules, while supplementation with collagen IV induces a lesser degree of tubule formation. Preincubation of endothelial cells with antibodies to laminin prevented tubule formation while antibodies to collagen IV were less inhibitory. Preincubation of endothelial cells with synthetic peptides derived from the laminin B1 chain that bind to the laminin cell surface receptor or incorporation of these peptides into the gel matrix blocked tubule formation, whereas control peptides did not. These observations indicate that endothelial cells can rapidly differentiate on a basement membrane-like matrix and that laminin is the principal factor in inducing this change.
Activation of Retinoid X Receptor increases dopamine cell survival in models for Parkinson's disease (2009)

RXR ligands rescue DA neurons from degeneration caused by the PD simulating 6-OHDA as well as hypoxia. Thus, RXR is a novel promising target for PD research. mESC-derived DA cells provide a valid and accessible in vitro-platform for studying PD inducing toxins and potential trophic agents.
Sp1 Is Involved in Akt-mediated Induction of VEGF Expression through an HIF-1–independent Mechanism (2004)

Increased expression of vascular endothelial growth factor (VEGF) contributes to the growth of many tumors by increasing angiogenesis. Although hypoxia is a potent inducer of VEGF, we previously showed that epidermal growth factor receptor amplification and loss of PTEN, both of which can increase phosphatidylinositol-3-kinase (PI3K) activity, increase VEGF expression. Using both adenoviral vectors and a cell line permanently expressing constitutively active myristoylated Akt (myrAkt), we show that activation of Akt, which is downstream of PI3K, increases VEGF expression in vitro and increases angiogenesis in a Matrigel plug assay. Transient transfection experiments using reporter constructs containing the VEGF promoter showed that up-regulation of VEGF by Akt is mediated through Sp1 binding sites located in the proximal promoter. Small interfering RNA directed against Sp1 prevented the induction of VEGF mRNA in response to myrAkt but not to hypoxia. Expression of myrAkt is associated with increased phosphorylation of Sp1 and its increased binding to a probe corresponding to the -88/-66 promoter region. In conclusion, our results indicate that Sp1 is required for transactivation of the VEGF by Akt. Others have proposed that the PI3K/Akt pathway can increase VEGF expression via the hypoxia-inducible factor 1 (HIF-1); however, our results suggest an alternative mechanism can also operate.
A unique Mycobacterium ESX‐1 protein co‐secretes with CFP‐10/ESAT‐6 and is necessary for inhibiting phagosome maturation (2007)

The ESX-1 secretion system plays a critical role in the virulence of Mycobacterium tuberculosis and M. marinum. To date, three proteins are known to be secreted by ESX-1 and necessary for virulence, two of which are CFP-10 and ESAT-6. The ESX-1 secretion and the virulence mechanisms are not well understood. In this study, we have examined the M. marinum secretomes and identified four proteins specific to ESX-1. Two of those are CFP-10 and ESAT-6, and the other two are novel: MM1553 (homologous to Rv3483c) and Mh3881c (homologous to Rv3881c). We have shown that Mh3881c, CFP-10 and ESAT-6 are co-dependent for secretion. Mh3881c is being cleaved at close to the C-terminus during secretion, and the C-terminal portion is critical to the co-dependent secretion, the ESAT-6 cellular levels, and interaction with ESAT-6. The co-dependent secretion is required for M. marinum intracellular growth in macrophages, where the Mh3881c C-terminal portion plays a critical role. The role of the co-dependent secretion in intracellular growth correlates with its role in inhibiting phagosome maturation. Both the secretion and the virulence defects of the Mh3881c mutant are complemented by Mh3881c or its M. tuberculosis homologue Rv3881c, suggesting that in M. tuberculosis, Rv3881c has similar functions.
Synthesis and Properties of Low Molecular Weight Polyphosphazenes (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and Properties of Low Molecular Weight PolyphosphazenesYoun Soo Sohn, Yang Ha Cho, Hyounggee Baek, and Ok-Sang JungCite this: Macromolecules 1995, 28, 22, 7566–7568Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://doi.org/10.1021/ma00126a039RIGHTS & PERMISSIONSArticle Views712Altmetric-Citations102LEARN 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 InReddit PDF (297 KB) Get e-Alerts Get e-Alerts
A topological study of the human γ-glutamyl carboxylase (2000)

γ-Glutamyl carboxylase (GC), a polytopic membrane protein found in the endoplasmic reticulum (ER), catalyzes vitamin K–dependent posttranslational modification of glutamate to γ-carboxyl glutamate. In an attempt to delineate the structure of this important enzyme, in vitro translation and in vivo mapping were used to study its membrane topology. Using terminus-tagged full-length carboxylase, expressed in 293 cells, it was demonstrated that the amino-terminus of the GC is on the cytoplasmic side of the ER, while the carboxyl-terminus is on the lumenal side. In addition, a series of fusions were made to encode each predicted transmembrane domain (TMD) followed by a leader peptidase (Lep) reporter tag, as analyzed by the computer algorithm TOPPRED II. Following in vitro translation of each fusion in the presence of canine microsomes, the topological orientation of the Lep tag was determined by proteinase K digestion and endoglycosidase H (Endo H) cleavage. From the topological orientation of the Lep tag in each fusion, the GC spans the ER membrane at least 5 times, with its N-terminus in the cytoplasm and its C-terminus in the lumen.
Semantic Visual Localization (2018)

Robust visual localization under a wide range of viewing conditions is a fundamental problem in computer vision. Handling the difficult cases of this problem is not only very challenging but also of high practical relevance, e.g., in the context of life-long localization for augmented reality or autonomous robots. In this paper, we propose a novel approach based on a joint 3D geometric and semantic understanding of the world, enabling it to succeed under conditions where previous approaches failed. Our method leverages a novel generative model for descriptor learning, trained on semantic scene completion as an auxiliary task. The resulting 3D descriptors are robust to missing observations by encoding high-level 3D geometric and semantic information. Experiments on several challenging large-scale localization datasets demonstrate reliable localization under extreme viewpoint, illumination, and geometry changes.
Logic decomposition during technology mapping (1997)

A problem in technology mapping is that the quality of the final implementation depends significantly on the initially provided circuit structure. This problem is critical, especially for mapping with tight and complicated constraints. In this paper, we propose a procedure which takes into account a large number of circuit structures during technology mapping. A set of circuit structures is compactly encoded in a single graph, and the procedure dynamically modifies the set during technology mapping by applying simple local transformations to the graph. State-of-the-art technology mapping algorithms are naturally extended, so that the procedure finds an optimal tree implementation over all of the circuit structures examined. We show that the procedure effectively explores the entire solution space obtained by applying algebraic decomposition exhaustively. However, the run time is proportional to the size of the graph, which is typically logarithmic in the number of circuit structures encoded. The procedure has been implemented and used for commercial design projects, We present experimental results on benchmark examples to demonstrate its effectiveness.
Design decision in the implementation of a raw architecture workstation (1999)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1999.
First microprocessors with immersion lithography (2005)

Immersion lithography has emerged as the leading solution for semiconductor manufacturing for the 45nm node. With the emergence of the first full-field immersion lithography scanners, the technology is getting ready to be inserted in semiconductor manufacturing facilities throughout the world. In the initial implementation phase, the enhanced depth-of-focus provided by immersion will be utilized to mitigate the narrow process window in which leading-edge semiconductor manufacturing has been forced to operate, creating a new set of opportunities.<sup>1</sup> The area of defects, however, has remained of critical concern for this technology. It has become clear that the ultimate proof of the readiness of immersion, especially from a defect point of view, must be attained by integrating the immersion process in a production environment. In this paper, we demonstrate that fully functional 90nm PowerPC<sup>TM</sup> microprocessors have been fabricated using immersion lithography for one of the litho-critical via levels, achieving the goal of confirming that immersion lithography is a viable manufacturing solution. For this demonstration, we utilized the AT1150i (ASML), currently at Albany NanoTech (NY). The system is a 0.75 NA full-field 193nm projection (4x) scanner. We were able to achieve lithographic and overlay performance that exceeded product specifications while achieving a sufficiently low defect count so as to have yielding chips and modules. We have classified the leading types of defects that can be attributed to the immersion process and have assessed their processing impact. Electrical characterization of the integrated devices confirmed full functionality at both wafer final test (WFT) and module test (MT).
Clinical interventions to reduce secondhand smoke exposure among pregnant women: a systematic review (2014)

Clinical interventions delivered in prenatal care settings appear to reduce SHS exposure, but study weaknesses limit our ability to draw firm conclusions. More rigorous studies, using biochemical validation, are needed to identify strategies for reducing SHS exposure in pregnant women.
Al wire-grid polarizer using the s-polarization resonance effect at the 08-µm-wavelength band (1997)

An aluminum wire-grid polarizer whose period is 0.39 microm has been fabricated on a quartz substrate by electron-beam direct-writing lithography and the lift-off method. By using the s -polarization resonance effect and optimizing structural parameters, characteristics such as a loss of less than 20% and an extinction ratio larger than 1000 have been experimentally obtained at the 0.8- microm -wavelength band. Theoretical analysis is performed and found to be consistent with the experimental results.
The effects of social environment on adult neurogenesis in the female prairie vole (2002)

In the mammalian brain, adult neurogenesis has been found to occur primarily in the subventricular zone (SVZ) and dentate gyrus of the hippocampus (DG) and to be influenced by both exogenous and endogenous factors. In the present study, we examined the effects of male exposure or social isolation on neurogenesis in adult female prairie voles (Microtus ochrogaster). Newly proliferated cells labeled by a cell proliferation marker, 5-bromo-2'-deoxyuridine (BrdU), were found in the SVZ and DG, as well as in other brain areas, such as the amygdala, hypothalamus, neocortex, and caudate/putamen. Two days of male exposure significantly increased the number of BrdU-labeled cells in the amygdala and hypothalamus in comparison to social isolation. Three weeks later, group differences in BrdU labeling generally persisted in the amygdala, whereas in the hypothalamus, the male-exposed animals had more BrdU-labeled cells than did the female-exposed animals. In the SVZ, 2 days of social isolation increased the number of BrdU-labeled cells compared to female exposure, but this difference was no longer present 3 weeks later. We have also found that the vast majority of the BrdU-labeled cells contained a neuronal marker, indicating neuronal phenotypes. Finally, group differences in the number of cells undergoing apoptosis were subtle and did not seem to account for the observed differences in BrdU labeling. Together, our data indicate that social environment affects neuron proliferation in a stimulus- and site-specific manner in adult female prairie voles.
Synthesis of 2′-Deoxypyrimidine Nucleosides via Copper (I) Iodide Catalysis (1989)

Abstract The coupling of various 5-substituted-2,4- disilyl pyrimidines with ã–2-deoxy-3,5-di-p-toluyl ribofuransyl chloride in the presence of copper (I) iodide in chloroform yields predominantly β-nucleosides (>15/1 β/α selectivity in some cases) in >90% overall yields.