gebhart/patrepeval huggingface dataset:
Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding (2022)

The introduction of phosphorothioate (PS) linkages to the backbone of therapeutic nucleic acids substantially increases their stability and potency. It also affects their interactions with cellular proteins, but the molecular mechanisms that underlie this effect are poorly understood. Here, we report structural and biochemical studies of interactions between annexin A2, a protein that does not possess any known canonical DNA binding domains, and phosphorothioate-modified antisense oligonucleotides. We show that a unique mode of hydrophobic interactions between a sulfur atom of the phosphorothioate group and lysine and arginine residues account for the enhanced affinity of modified nucleic acid for the protein. Our results demonstrate that this mechanism of interaction is observed not only for nucleic acid-binding proteins but can also account for the association of PS oligonucleotides with other proteins. Using the anomalous diffraction of sulfur, we showed that preference for phosphorothioate stereoisomers is determined by the hydrophobic environment around the PS linkage that comes not only from protein but also from additional structural features within the ASO such as 5-Me groups on cytosine nucleobases.
Soft Lithography-Based Hydrogel Particles and the Effect of Shape and Size on Biodistribution (2009)

Poor solubility and rapid elimination can make smallmolecule therapeutics difficult to deliver. In addition, many old therapies are in need of repackaging. In order to overcome these obstacles we have employed a top-down particle fabrication technique called Particle Replication In Non-wetting Templates (PRINT ® ) to fabricate unique biocompatible particles with distinct therapeutic properties based on their composition, size, shape and cargo. Particles were tagged with a variety of imaging beacons making them effective as contrast agents for magnetic resonance imaging and fluorescence imaging. After tail vein injection balb-c mice were imaged by magnetic resonance imaging and near infrared fluorescence imaging.
Identification of rat pancreatic carcinoma genes associated with lymphogenous metastasis. (2002)

In order to identify metastasis-associated and promoting genes of pancreatic carcinoma we investigated the transcriptional profile of rat pancreatic carcinoma cell lines BSp73-AS (non-metastatic) and BSp73-ASML (highly metastatic) with Affymetrix GeneChip Array technology. We analyzed the expression profile of 7000 genes. Two hundred and ten genes (3%) were up-regulated and 247 genes (3.5%) were down-regulated in the metastatic cell line based on a fold change of expression of at least 3 and a change factor quality of > or = 2. In order to classify the de-regulated genes we defined the following categories: proteases and protease-related genes, cytokines, receptor tyrosine kinases, other transmembrane proteins/receptors, transcription, cell cycle/apoptosis, signaling, adhesion/extracellular matrix, metabolism, detoxification, protein modification, trafficking, immune response and other genes. We identified de-regulated AP1, FRA-1 and c-myc-mediated transcription in cell line BSp73-ASML. Up-regulation of transmembrane tyrosine kinase receptors c-met, IGFR1, IGFR2 and EGFR family-related ligands such as HB-EGF, TGFa, amphiregulin and neuregulin as well as c-met ligand HGF point to a possible role of this system in metastasis. We identified 56 non-tyrosine kinase transmembrane receptors as new target candidates for inhibition of metastasis, four of them representing already validated targets. In addition, we identified MMP9, uPA, uPAR, cyclin D1 and S100A4 (mts1) as possible contributors of the metastatic phenotype.
Influence of Low-Solidity Cascade Diffuser on Spike Stall Inception in a Centrifugal Compressor (2012)

Stall inception patterns for three low-solidity cascade diffusers were experimentally investigated to extend the operating range of centrifugal compressor. Pressure fluctuations on the wall and flow distributions at the diffuser inlet were measured, and static pressure-rises across the diffuser vane were also measured to clarify the mechanism of rotating stall inception. In the case of the original diffuser (LSD_O), which had the radius ratio between the impeller outlet and the diffuser vane inlet of 1.10 and a flat plate wing section, a short length-scale stall cell known as a spike first appeared in the positive slope of the diffuser static pressure-raise (after the flat slope was maintained), and then a surge occurred as flow-rate decreased. The propagation speed of short length-scale stall cell was about 13% of the impeller rotation speed. The measured flow distribution at the inlet of the LSD_O suggested that the flow separation occurred in the vaneless space and this separation influenced the rotating stall. In the case of the LSD_A, which had the radius ratio of 1.10 and the NACA 63 wing section, a short length-scale stall cell that was smaller than that of LSD_O was appeared in the positive slope of the diffuser static pressure-raise (without the flat slope). A surge also occurred as further flow-rate decreased. The propagation speed of short length-scale stall cell was about 13% just prior to surge point. In contrast, in the case of LSD_B, which had the radius ratio of 1.05 and the NACA 63 wing section, a small disturbance appeared without spike just prior to surge point and rotating stall did not occur. The small disturbance did not propagate in the circumferential direction. Moreover, the flow separation did not occur in the semi-vaneless space. At the stall inception point of LSD_O and LSD_A, the averaged absolute flow angle at the diffuser inlet agreed with the onset flow angel of rotating stall in vaneless diffuser predicted by Senoo. Therefore, it was considered that the flow separation also occurred in the vaneless space and this separation influenced the rotating stall in the case of LSD_A. Moreover, it was considered that the difference of two stall cell patterns between LSD_O and LSD_A depended on the static pressure-rise characteristic of diffuser determined by the design specifications in case of that the rotating stall occurred in the vaneless space. In contrast, at the point of the small disturbance appeared of LSD_B, the averaged absolute flow angle at the diffuser inlet is smaller than that predicted by Senoo. Therefore, in case of small the radius ratio, the reverse flow in vaneless diffuser is suppressed, and the rotating stall is also suppressed.
Similarity Analysis and Knowledge Acquisition by Use of Evolving Neural Models and Fuzzy Decision (2010)

This chapter contains sections titled: Introduction Basics of Information Granulation The Fixed Unsupervised Learning Algorithm for Information Granulation Growing Learning Algorithms for Information Granulation Comparison of the Growing and the Fixed Learning Algorithms for Information Granulation Selection of Features for the Similarity Analysis Example of Similarity Analysis of Images Two-Parameter Fuzzy Rule-Based Similarity Analysis Unsupervised Classification for Knowledge Acquisition Conclusion References
Geiger-Mode Avalanche Photodiode Arrays Integrated to All-Digital CMOS Circuits (2016)

This article reviews MIT Lincoln Laboratory's work over the past 20 years to develop photon-sensitive image sensors based on arrays of silicon Geiger-mode avalanche photodiodes. Integration of these detectors to all-digital CMOS readout circuits enable exquisitely sensitive solid-state imagers for lidar, wavefront sensing, and passive imaging.
Asymmetric Arylation of Ketone Enolates (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAsymmetric Arylation of Ketone EnolatesJens Åhman, John P. Wolfe, Malisa V. Troutman, Michael Palucki, and Stephen L. BuchwaldView Author Information Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Cite this: J. Am. Chem. Soc. 1998, 120, 8, 1918–1919Publication Date (Web):February 12, 1998Publication History Received4 November 1997Published online12 February 1998Published inissue 1 March 1998https://pubs.acs.org/doi/10.1021/ja973794zhttps://doi.org/10.1021/ja973794zrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views5811Altmetric-Citations261LEARN 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:Anions,Arylation,Enolates,Ketones,Stereoselectivity Get e-Alerts
Modulation of the longevity proteins FOXO3a and SIRT1 by chorionic gonadotropin prevents hepatocellular injury during acute liver inflammation (2009)

During pregnancy, the clinical improvement of autoimmune hepatitis is frequently observed. The understanding of this phenomenon is incomplete both from the side of the immune system and the liver. Using a murine model of autoimmune hepatitis and adult human hepatocytes in primary culture, we could show that the pregnancy hormone, human chorionic gonadotropin (hCG) regulates the longevity proteins FOXO3a and SIRT1, which permit hepatocytes to tolerate destructive T cell attack and protects mice from T cell-dependent liver injury. hCG-signaling induced the nuclear exclusion of wild type, but not phosphorylation-resistant or DNA-binding defective forms of FOXO3a in hepatocytes, decreased its transcriptional activity and concomitantly reduced transcription of its target genes Bim and Puma. The cytoprotective effect of hCG was dependent on the NAD-dependent deacetylase SIRT1, that upon activation of the hCG signaling pathway translocates to the nucleus in its phosphorylated form. Our findings provide novel insights on liver protection during pregnancy. Given that humans tolerate hCG very well, the modulation of FOXO3a and SIRT1 by hCG opens new perspectives for therapeutic intervention in a wide range of liver diseases.
Differences in Tissue-Remodeling Potential of Aortic and Pulmonary Heart Valve Interstitial Cells (2007)

Heart valve interstitial cells (VICs) appear to have a dynamic and reversible phenotype, an attribute speculated to be necessary for valve tissue remodeling during times of development and repair. Therefore, we hypothesized that the cytoskeletal (CSK) remodeling capability of the aortic and pulmonary VICs (AVICs and PVICs, respectively), which are dominated by smooth muscle alpha-actin, would exhibit unique contractile behaviors when seeded on collagen gels. Using a porcine cell source, we observed that VIC populations did not contract the gels at early time points (2 and 4 hours) as dermal fibroblasts did, but formed a central cluster of cells prior to contraction. After clustering, VICs appeared to radiate out from the center of the gels, whereas fibroblasts did not migrate but contracted the gels locally. VIC gels treated with transforming growth factor beta1 contracted the gels rapidly, revealing similar sensitivity to the cytokine. Moreover, we evaluated the initial mechanical state of the underlying CSK by comparing AVIC and PVIC stiffness with atomic force microscopy. Not only were AVICs significantly stiffer (p < 0.001) than the PVICs, but they also contracted the gels significantly more at 24 and 48 hours (p < 0.001). Taken together, these findings suggest that the AVICs are capable of inducing greater extra cellular matrix contraction, possibly manifesting in a more pronounced ability to remodel valvular tissues. Moreover, significant mechanobiological differences between AVICs and PVICs exist, and may have implications for understanding native valvular tissue remodeling. Elucidating these differences will also define important functional endpoints in the development of tissue engineering approaches for heart valve repair and replacement.
Instrumentation for Determination of Guardrail-Soil Interaction (1996)

A series of steel posts (W150 × 12.6) and timber posts (15.2 × 20.3 cm) were instrumented with soil pressure transducers to assess the soil-post load response to a 1,388-kg bogie striking the post at 33 km/hr. Soil pressure measurements demonstrated the dramatic effects of soil shear strength and modulus on the responses of both timber and wood posts. The differences in the failure mechanisms between stiff and soft cohesive soils and noncohesive soils are demonstrated by both stress distributions and total stresses measured by the pressure transducers. The measurement system has potential applications for measurement of loads during impact testing of guardrail systems and as a tool for developing more appropriate models of soil behavior during impact loading.
Abundant and Diverse Fungal Microbiota in the Murine Intestine (2006)

Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4',6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.
Two-Photon Excitation Induced Fluorescence of a Tri-fluorophore Labeled DNA (2005)

Two-photon excitation of a trifluorophore (6-carboxyfluorescein, N,N,N',N'-tetramethyl-6-carboxyrhodamine and cyanine-5 monofunctional dye) labeled DNA, which has a scaffold of 26 nucleotides, was achieved using focused laser light of a Q-switched Nd-YAG laser (1064 nm). The observed fluorescence signature (emission ratio from the three fluorophores) of the labeled DNA after two-photon excitation is very different from the fluorescence signatures produced by one-photon excitation at different wavelength. The additional fluorescence signatures produced by two-photon excitation of the fluorescent oligonucleotides will facilitate their use as combinatorial fluorescence energy transfer tags for multiplex genetic analysis.
The locus of microRNA-10b (2013)

Contemporary microRNA research has led to significant advances in our understanding of the process of tumorigenesis. MicroRNAs participate in different events of a cancer cell's life, through their ability to target hundreds of putative transcripts involved in almost every cellular function, including cell cycle, apoptosis, and differentiation. The relevance of these small molecules is even more evident in light of the emerging linkage between their expression and both prognosis and clinical outcome of many types of human cancers. This identifies microRNAs as potential therapeutic modifiers of cancer phenotypes. From this perspective, we overview here the miR-10b locus and its involvement in cancer, focusing on its role in the establishment (miR-10b*) and spreading (miR-10b) of breast cancer. We conclude that targeting the locus of microRNA 10b holds great potential for cancer treatment.
Abstract 1890: Curcumin inhibits tumor angiogenesis by suppressing protooncogene RBM3 expression (2010)

Abstract RBM3 is the first RNA binding protein to be identified as a protooncogene. In previous studies, we have shown that RBM3 overexpression results in increased stability and translation of vascular endothelial growth factor (VEGF) mRNA. Furthermore, knockdown of RBM3 in HCT-116 colon cancer xenografts resulted in reduction in VEGF expression and in tumor vasculature. Similarly, curcumin the active ingredient in the spice turmeric reduced the growth of HCT-116 tumor xenografts and inhibited VEGF expression. We have now extended these observations and show that RBM3 is a critical player in tumor angiogenesis, and that curcumin inhibits tumor angiogenesis in part by suppressing RBM3 expression. Methods. RBM3 was stably transfected into NIH-3T3 mouse fibroblast cells to generate 3T3R cells. These cells were implanted on chorioallantoic membranes (CAM) in chicken embryos to determine their effect on angiogenesis. For in vitro studies, human vascular endothelial cells (HUVEC) were treated with VEGF and expression of RBM3 was determined. HUVEC-mediated capillary network formation was performed in polymerized ECMatrix. Cells were also treated with 30 µM curcumin and effects on gene expression determined by western blot analyses. Results. HUVEC cells treated with VEGF (50 ng/ml) resulted in a significant increase RBM3 expression, and high levels of capillary formation in the in vitro angiogenesis assay. SiRNA-mediated downregulation of RBM3 expression in the cells resulted in significant reduction in capillaries, which was overcome when RBM3 was ectopically expressed suggesting that RBM3 is essential for VEGF-mediated angiogenesis. HUVEC cells treated with curcumin (30 µM) treatment also demonstrated in a reduction in RBM3 expression and capillary formation, which was rescued when RBM3 was overexpressed. To determine whether RBM3 plays role in angiogenesis in vivo, 3T3 and 3T3R cells were implanted in Matrigel subcutaneously into chorioallantoic membrane of chicken embryos. 3T3R significantly increased the number of blood vessels when compared to wild type 3T3 cells. Treatment with curcumin also inhibited blood vessel formation. To further confirm these results, we determined gene expression patterns and microvessel density in HCT-116 tumor xenografts following intraperitonial administration of curcumin (200 μg/Kg/d for 21 d). Curcumin suppressed the expression of RBM3 and VEGF in the xenografts. Furthermore, there was a significant reduction in tumor microvasculature based on CD31 immunohistochemistry. Conclusion. Curcumin suppresses tumor angiogenesis in part by inhibiting the expression of RNA binding protooncogene RBM3. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1890.
Processing Time and Traffic Capacity Analysis for RFID System Using LBT-Random Searching Scheme (2005)

In this paper, a processing time and traffic capacity analysis algorithm for RFID system using LBT-serial searching scheme is proposed. Service time, carrier sensing time, additional delay time required for contiguous frequency channel occupancy, and additional delay time required for the contiguous using the same frequency channel are considered and the processing delay and frequency channel capacity are analyzed for the steady state operation of the system. The simulation results showing maximum capacity of the system and explaining the accuracy of the algorithm are provided.
Cluster Approach for Quasicrystals (1994)

We consider a "cluster picture" to explain the structure and formation of quasicrystals. Quasicrystal ordering is attributed to a small set of low-energy atomic clusters which determine the state of minimum free energy. The nature of the ground state as $T\ensuremath{\rightarrow}0$, depending upon the clusters and cluster energies, ranges from energetically stable and unique (as in Penrose tilings), to entropically stable and degenerate (as in random tilings).
Nanoscale surface self-patterning of FeAl single crystals by vacancy absorption process (2006)

The surface morphology of B2-structured FeAl single crystals is modified on a nanoscale by the absorption process of supersaturated thermal vacancies. A high density of nano to mesoscale surface pores is successfully produced by the vacancy absorption process through water quenching, surface treatments, and aging heat treatment. Their shape, size, and density can be controlled by varying the surface orientation of single crystals, quenching temperature, aging temperature, and aging time. These results suggest that surface self-patterning by the vacancy absorption process is a useful bottom-up technique for obtaining nanoscale surface patterns in metallic materials.
Table S6 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma (2023)

&lt;p&gt;Table S6 contains results from the analysis of DNA methylation in SETD2 mutated and BAP1 inactivated samples.&lt;/p&gt;
Dispersion flat compensation fiber for dispersion shifted fiber (1996)

New type of dispersion flat compensation fiber (DFCF) to compensate dispersion slope of DSFs was designed with W-shaped profile. Fabricated DFCF could compensate the dispersion of non-zero DSF from -5 to 0 (ps/nm/km), and flatten the slope from 0.07 to 0.05 (ps/nm/sup 2//km).
Total Synthesis of Archazolid A (2007)

The archazolids are complex polyketides isolated from the myxobacterium Archangium gephyra and are potent inhibitors of vacuolar type ATPases. Herein, we report the first total synthesis of archazolid A, which establishes unequivocally the relative and absolute configuration of this macrolide antibiotic. Key features of our synthesis include an aldol condensation for construction of the delicate (Z,Z,E)-triene-system, an E-selective Heck reaction on a highly elaborate substrate, and a HWE macrocyclization to close the 24-membered macrolactone.