gebhart/patrepeval huggingface dataset:
Binding of the DNA primase of bacteriophage T7 to its recognition sequence in DNA is modulated by the zinc‐binding domain (2010)

The zinc‐binding domains (ZBD) of prokaryotic DNA primases are critical for recognition of specific sequence in ssDNA at which primers are synthesized. ZBDs are structurally conserved in primases but they direct recognition of distinct trinucleotide sequences. In order to determine regions of the ZBD responsible for sequence‐specific recognition, we carried out homolog‐scanning mutagenesis on T7 DNA primase using a bacterial homolog from Bacillus stearothermophilus . Substitution of a five amino acid residue segment in the ZBD eliminates the ability of the primase to synthesize primers from a specific template sequence. The role of residues neighboring two cysteins (Cys17 and Cys20) in the primase was investigated by generating a library comprised of multiple amino acid substitutions at positions of Pro16, Asp18, and Asn19 followed by genetic screening for functional gene 4 protein. Examinations of the altered proteins reveal that substitutions at the three sites do not change the specific sequence recognized. However, the more positively charged residues in the region facilitates the better binding to a recognition site in a short template, leading to more efficient primer synthesis. Results from this study suggest that sophisticated architecture of ZBD determines recognition of specific sequence by DNA primase. This work was supported by Public Health Service Grant GM 54397.
Design and Synthesis of Novel Spiro Derivatives as Potent and Reversible Monoacylglycerol Lipase (MAGL) Inhibitors: Bioisosteric Transformation from 3-Oxo-3,4-dihydro-2H-benzo[b][1,4]oxazin-6-yl Moiety (2021)

The therapeutic potential of monoacylglycerol lipase (MAGL) inhibitors in central nervous system-related diseases has attracted attention worldwide. However, the availability of reversible-type inhibitor is still limited to clarify the pharmacological effect. Herein, we report the discovery of novel spiro chemical series as potent and reversible MAGL inhibitors with a different binding mode to MAGL using Arg57 and His121. Starting from hit compound <b>1</b> and its co-crystal structure with MAGL, structure-based drug discovery (SBDD) approach enabled us to generate various spiro scaffolds like <b>2a</b> (azetidine-lactam), <b>2b</b> (cyclobutane-lactam), and <b>2d</b> (cyclobutane-carbamate) as novel bioisosteres of 3-oxo-3,4-dihydro-2<i>H</i>-benzo[<i>b</i>][1,4]oxazin-6-yl moiety in <b>1</b> with higher lipophilic ligand efficiency (LLE). Optimization of the left hand side afforded <b>4f</b> as a promising reversible MAGL inhibitor, which showed potent in vitro MAGL inhibitory activity (IC<sub>50</sub> 6.2 nM), good oral absorption, blood-brain barrier penetration, and significant pharmacodynamic changes (2-arachidonoylglycerol increase and arachidonic acid decrease) at 0.3-10 mg/kg, po. in mice.
Supplementary Tables S1-S2 from M-CSF and GM-CSF Receptor Signaling Differentially Regulate Monocyte Maturation and Macrophage Polarization in the Tumor Microenvironment (2023)

&lt;p&gt;Antibodies for flow cytometry (S1); List of gene specific primer sequences for qRT-PCR (S2).&lt;/p&gt;
Efficient, Sparse Representation of Manifold Distance Matrices for Classical Scaling (2018)

Geodesic distance matrices can reveal shape properties that are largely invariant to non-rigid deformations, and thus are often used to analyze and represent 3-D shapes. However, these matrices grow quadratically with the number of points. Thus for large point sets it is common to use a low-rank approximation to the distance matrix, which fits in memory and can be efficiently analyzed using methods such as multidimensional scaling (MDS). In this paper we present a novel sparse method for efficiently representing geodesic distance matrices using biharmonic interpolation. This method exploits knowledge of the data manifold to learn a sparse interpolation operator that approximates distances using a subset of points. We show that our method is 2x faster and uses 20x less memory than current leading methods for solving MDS on large point sets, with similar quality. This enables analyses of large point sets that were previously infeasible.
Development of ambulatory ischemia detection devices (2010)

This paper presents the preliminary results of ambulatory electrocardiogram (ECG) devices for the automated detection of myocardial ischemia. We focus on the reduction of interfering artifacts such as baseline wander and motion artifacts that corrupt ambulatory ECG signals and affect accuracy of ST analysis. Several digital signal processing techniques are developed for testing recorded ECG signals. Computer simulation results are presented to show feasibility of these life-saving devices.
Modeling of polymer erosion (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModeling of polymer erosionAchim Gopferich and Robert LangerCite this: Macromolecules 1993, 26, 16, 4105–4112Publication Date (Print):August 1, 1993Publication History Published online1 May 2002Published inissue 1 August 1993https://pubs.acs.org/doi/10.1021/ma00068a006https://doi.org/10.1021/ma00068a006research-articleACS PublicationsRequest reuse permissionsArticle Views1012Altmetric-Citations151LEARN 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
Study of sudden death in Chagas disease: a proposed methodology (2002)

A methodology based on heart rate variability (HRV) analysis, is proposed to study ambulatory sudden death in Chagas patients who died while wearing a Holter monitor. The HRV evolution over time before death is carefully reviewed and a compressed spectral array graphic is obtained. The procedure is divided in three main parts whose technical aspects are considered here: ECG acquisition, heart rate signal generation and preprocessing, and HRV spectral analysis.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Solutions of random-phase approximation equation for positive-semidefinite stability matrix (2016)

It is mathematically proven that, if the stability matrix $\mathsf{S}$ is positive-semidefinite, solutions of the random-phase approximation (RPA) equation are all physical or belong to Nambu-Goldstone (NG) modes, and the NG-mode solutions may form Jordan blocks of $\mathsf{N\,S}$ ($\mathsf{N}$ is the norm matrix) but their dimension is not more than two. This guarantees that the NG modes in the RPA can be separated out via canonically conjugate variables.
First observation of SiO2/Si(100) interfaces by spherical aberration-corrected high-resolution transmission electron microscopy (2003)

SiO2/Si(100) interfaces were for the first time observed by a spherical aberration-corrected high-resolution transmission electron microscope in a cross-sectional mode. As the Fresnel fringes were not contrasted at the interfaces, the interfacial structures were clearly observed without the need for artificial image contrast. Atomic steps and defects on the Si(100) surfaces were accurately identified. Also, image simulations with the target imaging performance revealed oxygen atomic columns between silicon-silicon bonds. The present instrument is of potential use for semiconductor science and technology, even for the analysis of oxygen atoms at interfaces.
Rule Construction and its Execution for Root Cause Analysis (2012)

We have developed a root cause analysis system for enterprise IT system environment. In this paper, we propose a rule construction method which builds the analysis rule data object from the general analysis rules and the topology information of the actual target IT environment. By this method, IT administrator can use RCA system without any manual rule modifications. Regarding execution of analysis, we introduce the certainty factor to realize a robust analysis when the ordinarily and reachability of fault event can not be guaranteed.
Interference Cartography for Hierarchical Dynamic Spectrum Access (2008)

This paper describes a simple but effective concept in cognitive networks that provides awareness on the radio environment through geo-localized interference measurements: the interference cartography. The purpose of this novel concept is to combine location information with radio measurements carried out over the heterogeneous radio environment, and to provide a complete view of the environment to be used in autonomous decision making in a cognitive context. This is achieved by aggregating the already existing radio measurements that circulate in wireless networks forming the heterogeneous network panorama, combining this aggregated information with geo-localization information, performing advanced signal processing techniques to render the information complete and reliable, and updating the information to provide a viable picture of the environment for efficient detection, analysis and decision. Our focus is on hierarchical access models where licensed spectrum can be accessed by secondary users without creating harmful interference on the primaries. A complete description of a possible network implementation in a hierarchical access scheme is given, with a centralized architecture and a protocol structure that complies with the utilization of interference cartography. A case study of the proposed scheme is also given, demonstrating the utility of the notion of interference cartography.
Endothelial Cells Create a Stem Cell Niche in Glioblastoma by Providing NOTCH Ligands That Nurture Self-Renewal of Cancer Stem-Like Cells (2011)

One important function of endothelial cells in glioblastoma multiforme (GBM) is to create a niche that helps promote self-renewal of cancer stem-like cells (CSLC). However, the underlying molecular mechanism for this endothelial function is not known. Since activation of NOTCH signaling has been found to be required for propagation of GBM CSLCs, we hypothesized that the GBM endothelium may provide the source of NOTCH ligands. Here, we report a corroboration of this concept with a demonstration that NOTCH ligands are expressed in endothelial cells adjacent to NESTIN and NOTCH receptor-positive cancer cells in primary GBMs. Coculturing human brain microvascular endothelial cells (hBMEC) or NOTCH ligand with GBM neurospheres promoted GBM cell growth and increased CSLC self-renewal. Notably, RNAi-mediated knockdown of NOTCH ligands in hBMECs abrogated their ability to induce CSLC self-renewal and GBM tumor growth, both in vitro and in vivo. Thus, our findings establish that NOTCH activation in GBM CSLCs is driven by juxtacrine signaling between tumor cells and their surrounding endothelial cells in the tumor microenvironment, suggesting that targeting both CSLCs and their niche may provide a novel strategy to deplete CSLCs and improve GBM treatment.
Detection of precancerous gastric lesions and gastric cancer through exhaled breath (2015)

Clinical Trials.gov number, NCT01420588 (3/11/2013).
Antitumor activity of a folate-cleaving enzyme, carboxypeptidase G 1 . (1972)

Summary We have studied the antitumor activity of a folate-cleaving bacterial enzyme, carboxypeptidase G 1 (CPD G 1 ), which hydrolyzes the C-terminal glutamate residue from folic acid analogs. CPD G 1 completely inhibited the growth of all murine leukemic cell lines tested in tissue culture at enzyme levels of 0.02 to 0.025 unit/ml. A decrease in cell number was apparent after 12 hr of exposure to the enzyme, while a decrease in cell viability, as determined by soft-agar cloning, was evident after 6 hr. The biochemical effect of CPD G 1 in blocking incorporation of labeled deoxynucleosides into DNA was detected after 1 hr of incubation with the agent. Inhibition of DNA synthesis by CPD G 1 was characterized by a fall in the incorporation of both thymidine- 3 H and deoxyuridine- 3 H into DNA, rather than the selective depression of deoxyuridine- 3 H incorporation into DNA caused by methotrexate. The folate-depleting and antitumor activity of CPD G 1 was studied in mice. CPD G 1 , 800 units/kg, produced a prolonged (24-hr) fall in plasma folate to 20% of control levels and a gradual decline in hepatic folate stores. Daily doses of 800 units/kg, given for 5 to 7 days, produced a 19 to 27% prolongation of survival in mice inoculated with 10 5 L1210 cells, while daily doses of 20 to 100 units/kg produced a 43 to 89% increase in lifespan in rats with Walker 256 carcinosarcoma.
Bacterial Toxins: Potential Weapons Against HIV Infection (2005)

Natural toxins are the product of a long-term evolution, and have captured crucial events in the most essential and vital processes of living organisms. They can attack components of the protein synthesis machinery (as in the case of Diphteria and Shiga toxins, and Ribosome inactivating proteins), actin polymerization (Clostridium botulinum type C, C2, toxins and Enterotoxin A), signal transduction pathways (Cholera toxin, Heat-labile enterotoxins, Pertussis and Adenylate cyclase toxins), intracellular trafficking of vesicules (for Tetanus and Botulinum neurotoxin type C) as well as immune and/or inflammatory responses (Pyrogenic exotoxins, Cholera and Pertussis toxins). Of interest is the fact that several bacterial and vegetal toxins can either kill selectively cells infected with the human immunodeficiency virus (HIV) or exert inhibitory effects on its life cycle. In particular both pertussis toxin (PTX) and its nontoxic B-oligomeric component (PTX-B) can block the infectious process in vitro at multiple levels, by preventing the entry of CCR5-dependent (R5) HIV strains and by inhibiting both R5 and CXCR4-dependent HIVs at post-entry level(s). In addition, some toxins possess immunostimulating properties that have been exploited in terms of adjuvancy and induction of specific cytotoxic T lymphocytes responses to different vaccine preparations, including some experimental vaccine against HIV infection. Thus, toxins may represent a relatively unexplored exhibition of powerful biological agents that could either prevent infection or attack HIV-infected cells.
Generalized Grounding Graphs: A Probabilistic Framework for Understanding Grounded Commands (2017)

Many task domains require robots to interpret and act upon natural language commands which are given by people and which refer to the robot's physical surroundings. Such interpretation is known variously as the symbol grounding problem, grounded semantics and grounded language acquisition. This problem is challenging because people employ diverse vocabulary and grammar, and because robots have substantial uncertainty about the nature and contents of their surroundings, making it difficult to associate the constitutive language elements (principally noun phrases and spatial relations) of the command text to elements of those surroundings. Symbolic models capture linguistic structure but have not scaled successfully to handle the diverse language produced by untrained users. Existing statistical approaches can better handle diversity, but have not to date modeled complex linguistic structure, limiting achievable accuracy. Recent hybrid approaches have addressed limitations in scaling and complexity, but have not effectively associated linguistic and perceptual features. Our framework, called Generalized Grounding Graphs (G^3), addresses these issues by defining a probabilistic graphical model dynamically according to the linguistic parse structure of a natural language command. This approach scales effectively, handles linguistic diversity, and enables the system to associate parts of a command with the specific objects, places, and events in the external world to which they refer. We show that robots can learn word meanings and use those learned meanings to robustly follow natural language commands produced by untrained users. We demonstrate our approach for both mobility commands and mobile manipulation commands involving a variety of semi-autonomous robotic platforms, including a wheelchair, a micro-air vehicle, a forklift, and the Willow Garage PR2.
TU-AB-BRA-08: Radiomics in the Analysis of Breast Cancer Heterogeneity On DCE-MRI (2015)

Purpose: To investigate the heterogeneity of breast tumors in terms of variation in contrast enhancement as observed in computer-extracted MRI-based tumor phenotypes. Methods: Analysis was conducted on a retrospective dataset of 84 de-identified, multi-institutional breast magnetic-resonance images (MRIs) from the National Cancer Institute repository, The Cancer Imaging Archive, along with clinical, histopathological, and genomic data from The Cancer Genome Atlas and gene assay data. The 84 cases were classified into Normal-like, Luminal A, Luminal B, HER2-enriched, and Basal-like molecular subtypes based on gene expression classifications. For each case, analysis of the dynamic-contrast enhanced MRIs included computerized 3D lesion segmentation and phenotype extraction, which characterized tumor size, shape, morphology, enhancement texture, kinetic curve assessment, and enhancement variance kinetics of the breast tumors. Enhancement texture over the imaging sequence was calculated at the first, second and third post-contrast time frames. Associations between computer-extracted tumor phenotypes and molecular subtypes were assessed through inferences on the Kendall τ rank correlation coefficient. Results: By examining the relationship between image-based phenotype and the molecular subtypes, there is a positive trend for enhancement texture for the various molecular subtypes. The Kendall τ rank correlation coefficient of 0.2342 with a p-value of 0.0055 was obtained between enhancement texture of entropy which was calculated at the first post-contrast time frame of DCE-MR image and the molecular subtypes. This enhancement texture quantitatively characterizes the heterogeneous nature of contrast uptake within the breast tumor. Conclusion: Computer-extracted image-based phenotypes show promise as a means for high-throughput discrimination of breast cancer molecular subtypes. Funding: University of Chicago Dean Bridge Fund, NCI U24-CA143848-05, and Breast Cancer Research Foundation. COI: MLG is a stockholder in R2 technology/Hologic and receives royalties from Hologic, GE Medical Systems, MEDIAN Technologies, Riverain Medical, Mitsubishi, and Toshiba. MLG is a co-founder and stockholder in Quantitative Insights.
DSP Quant: design, validation, and applications of DSP hard real-time benchmark (2002)

Although the undeniable importance of high quality, efficient and effective DSP synthesis benchmark has been firmly and widely established, until now the emphasis of benchmarking has been restricted on assembling individual examples. In this paper we introduce the "ideal candidate benchmark methodology" which poses the development of the benchmark as well as defines a statistical and optimization problem. We first outline the goals and requirements relevant for the benchmark development. After discussing the computational complexity of the benchmark selection problem, we present a simulated annealing-based algorithm for solving this computationally intractable optimization task. Using this approach from 150 examples we select 12 examples for the new DSP Quant benchmark for DSP hard Real-Time applications. The DSP benchmark is statistically validated, and its application to the analysis and development of system-level synthesis algorithms is demonstrated,.
Hydrogenative Kinetic Resolution of Vinyl Sulfoxides (2015)

Enantiopure sulfoxides are valuable precursors of organosulfur compounds with broad application in organic and pharmaceutical chemistry. An unprecedented strategy for obtaining highly enantioenriched sulfoxides based on a hydrogenative kinetic resolution using Rh-complexes of phosphine-phosphite ligands as catalysts is reported. After optimization, highly efficient conditions for the kinetic resolution of racemic sulfoxides have been identified. This methodology has been applied to a set of racemic aralkyl or aryl vinyl sulfoxides and allowed the isolation of both recovered and reduced products in excellent yields and enantioselectivities (up to 99% and 97% ee, respectively; 16 examples).
Virus Nanoblocks for Molecular Electronics (2002)

Journal Article Virus Nanoblocks for Molecular Electronics Get access MJ Kim, MJ Kim Department of Materials Science, University of North Texas, Denton, TX 76205 Search for other works by this author on: Oxford Academic Google Scholar AS Blum, AS Blum Center for Bio/Molecular Science and Engineering, Naval Research Lab., Washington DC Search for other works by this author on: Oxford Academic Google Scholar B Gnade, B Gnade Department of Materials Science, University of North Texas, Denton, TX 76205 Search for other works by this author on: Oxford Academic Google Scholar BR Ratna BR Ratna Center for Bio/Molecular Science and Engineering, Naval Research Lab., Washington DC Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 8, Issue S02, 1 August 2002, Pages 1116–1117, https://doi.org/10.1017/S1431927602103655 Published: 01 November 2002
CaO을 첨가한 Mg 및 Mg-Al 합금의 산화거동 (2007)

【Oxidation behavior of CaO added Mg and Mg-5Al alloys was investigated. At $500^{\circ}C$ , oxidation rate of pure Mg was abruptly increased, while that of CaO added Mg was remarkably reduced with increasing CaO content. As a result of surface analysis by AES, there was the thin oxide layer mixed with MgO and CaO in CaO added Mg. Oxidation behavior of CaO added Mg was similar to that of Ca added Mg. Oxidation rate of 0.6CaO added Mg-5Al alloy was much lower than that of Mg-5Al alloy at $500^{\circ}C$ and both alloys showed the linear weight change at $400^{\circ}C$ .】
<title>External-cavity actively mode-locked GCSEL (grating coupled surface emitting laser) and amplification characteristics of GCSOA (grating coupled surface emitting semiconductor optical amplifier)</title> (2004)

We demonstrate an external cavity, active mode-locked GCSEL. The optical pulse duration from the actively mode-locked oscillator is 22.6ps and a 3 dB optical spectrum bandwidth is 0.07nm at 976nm. The average power from the oscillator is 0.72mW and its peak power is 108mW. The amplification characteristics of a GCSOA, optically injected with a continuously operated external cavity GCSEL, are also demonstrated. Despite the observation of lasing from the device, injection locking can be performed using an external source. At 4A peak current injection, 375mW output is achieved with 12mW injection.