gebhart/patrepeval huggingface dataset:
MDG-SAT: an automated methodology for efficient safety checking (2012)

Multiway decision graph (MDG) is a canonical representation of a subset of many-sorted first-order logic. It generalises the logic of equality with abstract types and uninterpreted function symbols. The area of satisfiability (SAT) has been the subject of intensive research in recent years, with significant theoretical and practical contributions. In this paper, we propose a new design verification tool integrating MDG and SAT, to check the safety of a design by invariant checking. Using MDG to encode the set of states provides a powerful mean of abstraction. We use a SAT solver to search for paths of reachable states violating the property under certain encoding constraints. In addition, we introduce an automated conversion-verification methodology to convert a directed formula (DF) into a conjunctive normal form (CNF) formula that can be fed to a SAT solver. The formal verification of this conversion is conducted within the HOL theorem prover. Finally, we present experimental results and a case study to show the correctness and the efficiency of our proposed methodology.
New Sections for JPC A/B/C (2018)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTNew Sections for JPCA/B/CAnne B. McCoyAnne B. McCoyMore by Anne B. McCoyhttp://orcid.org/0000-0001-6851-6634, Joan-Emma SheaJoan-Emma SheaMore by Joan-Emma Sheahttp://orcid.org/0000-0002-9801-9273, Catherine J. MurphyCatherine J. MurphyMore by Catherine J. Murphyhttp://orcid.org/0000-0001-7066-5575, and George C. SchatzGeorge C. SchatzMore by George C. Schatzhttp://orcid.org/0000-0001-5837-4740Cite this: J. Phys. Chem. B 2018, 122, 10, 2703Publication Date (Web):March 15, 2018Publication History Published online15 March 2018Published inissue 15 March 2018https://pubs.acs.org/doi/10.1021/acs.jpcb.8b01718https://doi.org/10.1021/acs.jpcb.8b01718editorialACS PublicationsCopyright © 2018 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views686Altmetric-Citations-LEARN 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 PDF (278 KB) Get e-AlertscloseSUBJECTS:Biomaterials,Biophysics,Hybrid materials,Interfaces,Spectroscopy Get e-Alerts
Cardiomyocyte-Specific Overexpression of Nitric Oxide Synthase 3 Improves Left Ventricular Performance and Reduces Compensatory Hypertrophy After Myocardial Infarction (2004)

Nitric oxide (NO) is an important modulator of cardiac performance and left ventricular (LV) remodeling after myocardial infarction (MI). We tested the effect of cardiomyocyte-restricted overexpression of one NO synthase isoform, NOS3, on LV remodeling after MI in mice. LV structure and function before and after permanent LAD coronary artery ligation were compared in transgenic mice with cardiomyocyte-restricted NOS3 overexpression (NOS3-TG) and their wild-type littermates (WT). Before MI, systemic hemodynamic measurements, echocardiographic assessment of LV fractional shortening (FS), heart weight, and myocyte width (as assessed histologically) did not differ in NOS3-TG and WT mice. The inotropic response to graded doses of isoproterenol was significantly reduced in NOS3-TG mice. One week after LAD ligation, the infarcted fraction of the LV did not differ in WT and NOS3-TG mice (34+/-4% versus 36+/-12%, respectively). Four weeks after MI, however, end-systolic LVID was greater, and fractional shortening and maximum and minimum rates of LV pressure development were less in WT than in NOS3-TG mice. LV weight/body weight ratio was greater in WT than in NOS3-TG mice (5.3+/-0.2 versus 4.6+/-0.5 mg/g; P<0.01). Myocyte width in noninfarcted myocardium was greater in WT than in NOS3-TG mice (18.8+/-2.0 versus 16.6+/-1.6 microm; P<0.05), whereas fibrosis in noninfarcted myocardium was similar in both genotypes. Cardiomyocyte-restricted overexpression of NOS3 limits LV dysfunction and remodeling after MI, in part by decreasing myocyte hypertrophy in noninfarcted myocardium.
Translation of the human papillomavirus type 16 E7 oncoprotein from bicistronic mRNA is independent of splicing events within the E6 open reading frame (1995)

In this study we investigated the translational capacities of bicistronic and spliced mRNAs originating from the E6 and E7 regions of the high-risk genital human papillomavirus type 16 (HPV-16) and the low-risk HPV-11. For HPV-16 it was found, unexpectedly, that E7 protein could be translated from full-length bicistronic E6-E7 mRNAs. E6*I and E6*II splicing events were not required for E7 synthesis, nor did splicing increase the efficiency of E7 translation significantly. In cells, E7 synthesis from all known naturally occurring mRNA structures was very inefficient compared with that from synthetic monocistronic controls, suggesting that HPV-16 employs translational mechanisms to restrict E7 protein levels. For HPV-11, only RNAs initiated at the P264 promoter, located within the E6 open reading frame, were capable of providing an efficient template for E7 synthesis. P264-initiated mRNAs were as efficient in vivo as monocistronic controls, suggesting that the low-risk HPV-11 does not limit E7 synthesis by translational mechanisms. A detailed analysis of HPV-16 templates by using site-directed mutagenesis showed that the majority of ribosomes which ultimately translate E7 have not reinitiated after translating some or all of the upstream open reading frames. The data support a model in which the failure of 40S ribosomal initiation complexes to recognize the E6 AUG renders them capable of proceeding efficiently to translate E7.
Creep crack initiation and growth characteristics in weldment for P92 based on C*, dδ/dt and Q* parameters (2010)

Most boiler component structures are mainly fabricated by welding which are likely to be regions of crack initiation and propagation. However, the technique of predicting the life of creep crack initiation and growth have not been clearly developed f
Combined proton–photon therapy for non‐small cell lung cancer (2022)

Optimally combined proton-photon plans improve treatment plan quality compared to IMRT only, potentially reducing the risk of toxicity while also allowing to potentially increase accessibility to proton therapy for NSCLC patients.
<title>Vector properties of Bessel light beams</title> (2001)

In the present paper the new strict solutions of Maxwell equations and vector wave equation for different modes of an electromagnetic field of nondiffraction beams of a light are obtained. It is shown, that the set of solutions is multiparameter and consequently there is an arbitrariness in choice of main types of modes. The expressions for the polarization characteristics of different Te and TM modes of Bessel beams are obtained. The principle of reciprocity permitting to realize transition from E-modes to M-modes and backward is justified. Their average density of energy and Poynting's vector have been calculated. The main legitimacies of TE and TM modes are established. The obtained results may be used in the description of the transformation of Bessel light beams of different types.
The influence of implanted sub-collector on CMOS latchup robustness (2005)

This paper discusses the integration of sub-collector implants into a dual-well CMOS for improvement in CMOS latchup robustness. Experimental work demonstrates CMOS latchup tradeoffs exist between the enhancement of the npn bipolar current gain, betanpn and reduction of the pnp bipolar current gain, betapnp. Additionally, the integration of sub-collectors, as well as trench isolation (TI) and deep trench (DT) isolation structures into CMOS dual-well structures will be highlighted.
Amino Terminal Recognition by a CCR6 Chemokine Receptor Antibody Blocks CCL20 Signaling and IL-17 Expression via β-arrestin (2021)

Abstract Background: CCR6 chemokine receptor is an important target in inflammatory diseases. Th17 cells express CCR6 and a number of inflammatory cytokines, including IL-17 and IL-22, which are involved in the propagation of inflammatory immune responses. CCR6 antagonist would be a potential treatment for inflammatory diseases such as psoriasis or rheumatoid arthritis. The aim of this study is to develop an antagonistic monoclonal antibody (mAb) against human CCR6 receptor (hCCR6). Results: We generate monoclonal antibodies against hCCR6 immunizing Balb/c mice with hCCR6 overexpressing cells. The antibodies were tested by flow cytometry for specific binding to hCCR6, cloned by limiting dilution and resulted in the isolation and purification monoclonal antibody 1C6. By ELISA and flow cytometry, was determined that the antibody obtained binds to hCCR6 N-terminal domain. The ability of 1C6 to neutralize hCCR6 signaling was tested and we determined that 1C6 antibody were able to block response in β-arrestin recruitment assay with IC 50 10.23 nM, but did not inhibit calcium mobilization. In addition, we found in a chemotaxis assay that 1C6 reduces the migration of hCCR6 cells to their ligand CCL20. Finally, we determined by RT-qPCR that the expression of IL-17A in Th17 cells treated with 1C6 was inhibited. Conclusions: In the present study, we applied whole cell immunization for successfully obtain an antibody that is capable to neutralize hCCR6 signaling and to reduce hCCR6 cells migration and IL-17 expression. These results provide an efficient approach to obtain therapeutic potential antibodies in the treatment of CCR6-mediated inflammatory diseases.
Antigen-Specific Immune Modulation Targets mTORC1 Function To Drive Chemokine Receptor–Mediated T Cell Tolerance (2016)

To contain autoimmunity, pathogenic T cells must be eliminated or diverted from reaching the target organ. Recently, we defined a novel form of T cell tolerance whereby treatment with Ag downregulates expression of the chemokine receptor CXCR3 and prevents diabetogenic Th1 cells from reaching the pancreas, leading to suppression of type 1 diabetes (T1D). This report defines the signaling events underlying Ag-induced chemokine receptor-mediated tolerance. Specifically, we show that the mammalian target of rapamycin complex 1 (mTORC1) is a major target for induction of CXCR3 downregulation and crippling of Th1 cells. Indeed, Ag administration induces upregulation of programmed death-ligand 1 on dendritic cells in a T cell-dependent manner. In return, programmed death-ligand 1 interacts with the constitutively expressed programmed death-1 on the target T cells and stimulates docking of Src homology 2 domain-containing tyrosine phosphatase 2 phosphatase to the cytoplasmic tail of programmed death-1. Active Src homology 2 domain-containing tyrosine phosphatase 2 impairs the signaling function of the PI3K/protein kinase B (AKT) pathway, leading to functional defect of mTORC1, downregulation of CXCR3 expression, and suppression of T1D. Thus, mTORC1 component of the metabolic pathway serves as a target for chemokine receptor-mediated T cell tolerance and suppression of T1D.
Microglia as neuroprotective, immunocompetent cells of the CNS (2002)

The role of glial cells is to support and sustain proper neuronal function and microglia are no exception to this. This viewpoint article emphasizes the fundamental interdependence of microglia and neurons and takes a look at the possibility of what could happen if microglial cells became dysfunctional as a result of aging, genetics, or epigenetics. Could microglial senescence be a factor in the pathogenesis of Alzheimer's and other neurodegenerative diseases? The cautious answer to that question is 'yes'. Future studies along these lines may provide novel insights into microglial involvement in neurodegenerative disease pathogenesis.
Combined modality treatment improves tumor control and overall survival in patients with early stage Hodgkin's lymphoma: a systematic review (2009)

Combined modality treatment (CMT) of chemotherapy followed by localized radiotherapy is standard treatment for patients with early stage Hodgkin's lymphoma. However, the role of radiotherapy has been questioned recently and some clinical study groups advocate chemotherapy only for this indication. We thus performed a systematic review with meta-analysis of randomized controlled trials comparing chemotherapy alone with CMT in patients with early stage Hodgkin's lymphoma with respect to response rate, tumor control and overall survival (OS). We searched Medline, EMBASE and the Cochrane Library as well as conference proceedings from January 1980 to February 2009 for randomized controlled trials comparing chemotherapy alone versus the same chemotherapy regimen plus radiotherapy. Progression free survival and similar outcomes were analyzed together as tumor control. Effect measures used were hazard ratios for OS and tumor control as well as relative risks for complete response (CR). Meta-analyses were performed using RevMan5. Five randomized controlled trials involving 1,245 patients were included. The hazard ratio (HR) was 0.41 (95% confidence interval (CI) 0.25 to 0.66) for tumor control and 0.40 (95% CI 0.27 to 0.59) for OS for patients receiving CMT compared to chemotherapy alone. CR rates were similar between treatment groups. In sensitivity analyses another 6 trials were included that did not fulfill the inclusion criteria of our protocol but were considered relevant to the topic. These trials underlined the results of the main analysis. In conclusion, adding radiotherapy to chemotherapy improves tumor control and OS in patients with early stage Hodgkin's lymphoma.
New Access Device for Hemodialysis (1998)

A new subcutaneous device (Dialock; Biolink Corp., Middleboro, MA) provides vascular access to patients who currently require hemodialysis (HD). The device consists of a port-like valve, implanted subcutaneously below the clavicle, which provides a linear flow passage to two catheters placed in the right atrium via the jugular vein. The valve is accessed percutaneously with needle-cannulas that functionally convert the device to twin catheters for connecting the patient to the HD lines. Interdialytic patency is maintained using a standard heparin lock. The device has been implanted in 10 outpatients under local anesthesia, with almost immediate use for HD (median, 3 days) and has functioned successfully for more than 6 months (mean +/- SD, 4.0 +/- 1.7; > 400 dialysis sessions). Blood flows over 300 ml/min were consistently achieved (average, 320 +/- 50) with venous and arterial pressures of 197 +/- 42 mmHg and -241 +/- 31 mmHg, respectively. After 40 patient-months, condition of the needle puncture sites remains satisfactory. Four systemic infections have occurred in three patients; all have resolved without the need for device removal. There have been no infections at the puncture sites. One patient whose heparin lock was not changed for 23 days (for reasons unrelated to the device) required fibrin sheath stripping of his catheters. Patient and nurse acceptance has been excellent. The device may offer substantial improvement over conventional devices for HD access.
Inhibitory Effect of Extracts of Platycodon grandiflorum (the Ballon Flower) on Oxidation and Nitric Oxide Production (2011)

본 연구에서는 도라지 분말을 유기용매로 추출한 후 도라지의 추출물과 분획물들에 의한 세포 내 활성산소종 및 glutathione (GSH)를 측정하여 항산화효과를 검토하였고 NO 생성 저해 효과를 알아보았다. 세포 내 활성산소종 생성억제 실험에서 건조 도라지의 A+M 및 MeOH 추출물과 추출물을 n-hexane, 85% aq. MeOH, n-BuOH, water로 다시 추출하여 얻어진 각각의 분획물들을 농도별로 HT1080 세포에 처리하였을 때 A+M과 MeOH 추출물 모두 측정시간 120분 동안 <TEX>$500\;{\mu}M$</TEX> <TEX>$H_2O_2$</TEX>만을 처리한 control군에 비해 세포 내 활성산소종을 크게 억제시켰으며, MeOH 추출물에 의한 항산화 효과가 더 높게 나타났다. 또한, 각 분획물들 중 n-BuOH 분획물이 다른 분획물들에 비해 우수한 항산화 활성을 보였다. GSH 농도 측정 실험에서 A+M 및 85% aq. MeOH 분획물를 처리했을 때 GSH 함량이 증가하였다. NO 생성 저해 실험에서는 A+M 및 MeOH 추출물이 0.01 및 0.05 mg/mL의 농도에서 NO 생성을 억제하는 것으로 나타났으며, A+M 추출물에 의한 저해 효과가 높았다. 각 분획물들은 모두 control보다 낮은 NO 생성량을 나타내었으며, 특히 85% aq. MeOH 및 n-BuOH 분획물은 0.05 mg/mL 농도에서 blank에 가까운 NO 생성 억제율을 나타냈다. 이상의 연구결과로부터 n-BuOH 분획물에 의한 세포 내 활성산소종 생성 억제 효과 및 NO 생성 저해 효과가 우수함을 알 수 있었으며, 향후 분획물의 분리 정제를 통한 새로운 기능성 물질의 개발이 필요할 것으로 사료된다. We explored the effect of extracts of dried Platycodon grandiflorum on production of reactive oxygen species (ROS), glutathione (GSH) and nitric oxide (NO). To determine antioxidant activity in the presence of <TEX>$H_2O_2$</TEX>-induced oxidative stress, DCFH-DA (dichlorodihydrofluorescin diacetate) assay was employed. Acetone/methylene chloride (A+M) and methanolic (MeOH) extracts of P. grandiflorum reduced intracellular ROS levels. Of the various tested fractions, n-BuOH fraction showed the highest protective effect in terms of lipid peroxide production. Total GSH levels were measured after treatment of HT1080 cells with the A+M and MeOH extracts, and other solvent fractions, at various concentration. The A+M extacts and 85% (v/v) aqueous MeOH fraction significantly increased GSH levels (p<0.05). When lipopolysaccharide (LPS)-induced NO production was evaluated, all tested crude extracts, and fractions thereof, significantly reduced NO production (p<0.05), and the n-BuOH and 85% (v/v) aqueous MeOH fractions (at 0.05 mg/mL) showed the strongest inhibitory effects. The results showed that the n-BuOH fraction inhibited both cellular oxidation and NO production, and this fraction may thus contain valuable active compounds.
Stick-slip based micropositioning stage for transmission electron microscope (2006)

This paper presents work that has been done on design of a micropositioning stage for a transmission electron microscope. Topics covered include mechanical design of the positioning stage, sawtooth-like high voltage generator, report on experimental identification of the system, some thoughts and experience with input command shaping, finite-element analysis and design of capacitive 2-axis position sensor and design of signal processing circuitry for this sensor
Spatiotemporal reconstruction of list-mode PET data (2002)

We describe a method for computing a continuous time estimate of tracer density using list-mode positron emission tomography data. The rate function in each voxel is modeled as an inhomogeneous Poisson process whose rate function can be represented using a cubic B-spline basis. The rate functions are estimated by maximizing the likelihood of the arrival times of detected photon pairs over the control vertices of the spline, modified by quadratic spatial and temporal smoothness penalties and a penalty term to enforce nonnegativity. Randoms rate functions are estimated by assuming independence between the spatial and temporal randoms distributions. Similarly, scatter rate functions are estimated by assuming spatiotemporal independence and that the temporal distribution of the scatter is proportional to the temporal distribution of the trues. A quantitative evaluation was performed using simulated data and the method is also demonstrated in a human study using 11C-raclopride.
Comparison of human and mouse orthologs (2011)

<b>Copyright information:</b>Taken from "Discovery of estrogen receptor α target genes and response elements in breast tumor cells"Genome Biology 2004;5(9):R66-R66.Published online 12 Aug 2004PMCID:PMC522873.Copyright © 2004 Lin et al.; licensee BioMed Central Ltd. Statistics from the comparative analysis of predicted EREs in human and mouse orthologous putative target gene pairs. Venn diagram showing that out of the 72 orthologous pairs extracted for analysis, only 22 pairs have ERE predictions made in both the human and mouse sequences.
Threat Modeling of Cyber-Physical Systems - A Case Study of a Microgrid System (2022)

Cyber threat modeling is an analytical process that is used for identifying the potential threats against a system and supporting the selection of security requirements in the early stages of the system development life cycle. Thus, threat modeling is a vital instrument for the realization of the secure-by-design principle. Despite being a well-known practice in software development projects, its adaptation to cyber-physical systems still requires systematic elaboration. The complex interactions between cyber and physical spaces and their reflection on the cyber threat landscape constitute a significant challenge for the system development teams. This study proposes a detailed methodology to apply STRIDE to cyber-physical systems and demonstrates its applicability in a case study of a microgrid system. Our methodology provides a systematic threat elicitation procedure based on an attack taxonomy that was created for this research. This paper also shows how assets could be identified, data flow diagrams formed, trust boundaries determined, and threats prioritized, in the case of a cyber-physical system.
Estimation of arrival directions using MUSIC algorithm with a planar array (2002)

As one of the technologies used to overcome multipath fading in land mobile communications, adaptive array antennas and adaptive equalizers have been investigated. To put adaptive array antennas to practical use, the multipath signal propagation characteristics, such as the time delay and arrival direction, must be clarified. This can be accomplished via the antenna design and by developing an adaptive algorithm. The author has already proposed methods for measuring complex delay profiles with a virtual planar array. This involved scanning a linear array antenna and estimating the time delays and arrival directions of multipath signals by a two-dimensional discrete Fourier transform. This time, the author applied MUSIC algorithm to the virtual planar array to precisely estimate the arrival directions of multipath signals. In this paper, the performance and features of the MUSIC algorithm in estimating the arrival directions of multipath signals via computer simulation are clarified.
Concurrent programming with revisions and isolation types (2010)

Building applications that are responsive and can exploit parallel hardware while remaining simple to write, understand, test, and maintain, poses an important challenge for developers. In particular, it is often desirable to enable various tasks to read or modify shared data concurrently without requiring complicated locking schemes that may throttle concurrency and introduce bugs.