gebhart/patrepeval huggingface dataset:
A Novel Approach to Unsupervised Automated Extraction of Standard Cell Library for Reverse Engineering and Hardware Assurance (2019)

Abstract Reverse engineering today is supported by several tools, such as ICWorks, that assist in the processing and extraction of logic elements from high definition layer by layer images of integrated circuits. To the best of our knowledge, they all work under the assumption that the standard cell library used in the design process of the integrated circuit is available. However, in situations where reverse engineering is done on commercial off-the-shelf components, this information is not available thereby, rendering the assumption invalid. Until now, this problem has not been addressed. In this paper, we introduce a novel approach for the extraction of standard cell library using the contact layer from these images. The approach is completely automated and does not require any prior knowledge on the construction or layout of the target semiconductor integrated circuit. The performance of the approach is evaluated on two AES designs with 10,000 cells compiled from standard libraries with 32nm and 90nm node technologies having 350 and 340 standard cells respectively. We were able to successfully extract 94% and 60% of the standard cells from the 32nm and 90nm AES designs using the proposed approach. We also perform a case study using a realworld sample extracted from a smartcard. Finally, we also investigate the various challenges involved in the extraction of standard cells from images and the steps involved in resolving them.
Prime hAd5 Spike + Nucleocapsid Vaccination Induces Ten-Fold Increases in Mean T-Cell Responses in Phase 1 Subjects that are Sustained Against Spike Variants (2021)

ABSTRACT In response to the need for a safe, efficacious vaccine that elicits vigorous T cell as well as humoral protection against SARS-CoV-2 infection, we have developed a dual-antigen COVID-19 vaccine comprising both the viral spike (S) protein modified to increase cell-surface expression (S-Fusion) and nucleocapsid (N) protein with an Enhanced T-cell Stimulation Domain (N-ETSD) to enhance MHC class I and II presentation and T-cell responses. The antigens are delivered using a human adenovirus serotype 5 (hAd5) platform with E1, E2b, and E3 regions deleted that has been shown previously in cancer vaccine studies to be safe and effective in the presence of pre-existing hAd5 immunity. The findings reported here are focused on human T-cell responses due to the likelihood that such responses will sustain efficacy against emerging variants, a hypothesis supported by our in silico prediction of T-cell epitope HLA binding for both the first-wave SARS-CoV-2 ‘A’ strain and the B.1.351 strain K417N, E484K, and N501Y spike and T201I N variants. We demonstrate the hAd5 S-Fusion + N-ETSD vaccine antigens expressed by previously SARS-CoV-2-infected patient dendritic cells elicit Th1 dominant activation of autologous patient T cells, indicating the vaccine antigens have the potential to elicit immune responses in previously infected patients. For participants in our open-label Phase 1b study of the vaccine ( NCT04591717 ; https://clinicaltrials.gov/ct2/show/NCT04591717 ), the magnitude of Th-1 dominant S- and N-specific T-cell responses after a single prime subcutaneous injection were comparable to T-cell responses from previously infected patients. Furthermore, vaccinated participant T-cell responses to S were similar for A strain S and a series of spike variant peptides, including S variants in the B.1.1.7 and B.1.351 strains. The findings that this dual-antigen vaccine elicits SARS-CoV-2-relevant T-cell responses and that such cell-mediated protection is likely to be sustained against emerging variants supports the testing of this vaccine as a universal booster that would enhance and broaden existing immune protection conferred by currently approved S-based vaccines.
Mid infrared MEMS FTIR spectrometer (2016)

In this work we report, for the first time to the best of our knowledge, a bulk-micromachined wideband MEMS-based spectrometer covering both the NIR and the MIR ranges and working from 1200 nm to 4800 nm. The core engine of the spectrometer is a scanning Michelson interferometer micro-fabricated using deep reactive ion etching (DRIE) technology. The spectrum is obtained using the Fourier Transform techniques that allows covering a very wide spectral range limited by the detector responsivity. The moving mirror of the interferometer is driven by a relatively large stroke electrostatic comb-drive actuator. Zirconium fluoride (ZrF<sub>4</sub>) multimode optical fibers are used to connect light between the white light source and the interferometer input, as well as the interferometer output to a PbSe photoconductive detector. The recorded signal-to-noise ratio is 25 dB at the wavelength of 3350 nm. The spectrometer is successfully used in measuring the absorption spectra of methylene chloride, quartz glass and polystyrene film. The presented solution provides a low cost method for producing miniaturized spectrometers in the near-/mid-infrared.
Extrusion of broad‐molecular‐weight‐distribution polyethylenes (2004)

Abstract The extrusion (single‐screw) characteristics of four high‐molecular‐weight, broad‐molecular‐weight‐distribution (MWD) polyethylene resins are discussed with an emphasis on the output rate. Despite the high molecular weights of the subject polyethylenes, their broad MWD ( M w / M n range: 10 to 50) does not limit the pressure and torque developed during extrusion. However, the specific output of the four polymers was quite varied. First, the dynamics of the solids conveying section were examined with the highest‐molecular‐weight polyethylene exhibiting lower solids‐conveying rate than the other three. Further, a simple and quick method to evaluate the relative solids‐conveying efficiencies for various polyethylenes is presented. Finally, the dependence of the specific output on the melt rheology of the polymers is also addressed; specifically, the shear‐thinning extent of the melt in the metering section was found to influence output rate. The unique and counterintuitive temperature‐dependence of the shear‐thinning character for one of the four polymers will also be addressed in relation to its extrusion characteristics. Polym. Eng. Sci. 44:2266–2273, 2004. © 2004 Society of Plastics Engineers.
244. Development, Qualification, and Clinical Validation of an Immunodiagnostic assay for the Detection of 11 Additional S. pneumoniae Serotype-Specific Polysaccharides in Human Urine (2019)

Abstract Background Identifying Streptococcus pneumoniae (Sp) serotypes by urinary antigen detection assay (UAD) is the most sensitive and specific way to evaluate the changing epidemiology of non-bacteremic community-acquired pneumonia (CAP) and efficacy of pneumococcal vaccines. We first described an UAD to detect the Sp serotypes 1,-3,-4,-5,-6A,-6B,-7F,-9V,-14,-18C,-19A,-19F,-23F covered by the 13-valent Sp conjugate vaccine PCV13. To assess the pneumococcal disease burden of additional serotypes, a UAD-2 assay was developed to diagnose 11 additional Sp serotypes (-2,-8,-9N,-10A,-11A,-12F,-15B,-17F,-20,-22F,-33F). Methods UAD-2 specificity was achieved by capturing highly purified pneumococcal polysaccharides with serotype-specific monoclonal antibodies using Luminex technology. Assay qualification assessed accuracy, precision, and sample linearity. Serotype positivity was based on cutoffs determined by non-parametric statistical evaluation of urine samples from individuals without pneumococcal disease. Clinical sensitivity and specificity of the positivity cutoffs were assessed in a clinical validation. Results The UAD-2 was shown to be specific and reproducible. Clinical validation using urine samples from invasive disease patients demonstrated assay sensitivity and specificity of 92.2% and 95.9%, respectively compared with a gold standard of isolating and typing (by Quellung) Sp bacteria from patient samples. Analysis of 11,087 CAP patients showed a UAD-2 and UAD-1 serotype prevalence of 4.33% and 4.60%, respectively (bacteremic and non-bacteremic CAP combined). Conclusion The qualified/clinically validated UAD-2 method has applicability in understanding the epidemiology of nonbacteremic Sp CAP as well as assessing vaccine efficacy of future pneumococcal conjugate vaccines. Disclosures All authors: No reported disclosures.
Major problems and control measures of water ecological environment in Inner Mongolia-Xinjiang Plateau (2011)

实施西部大开发战略的重大决策, 对于平衡中国各区域间的发展位差以及提高整个国家的经济实力具有重要的战略意义.而西部脆弱的生态环境决定了西部大开发中要以生态保护优先的环境保护政策为切入点和立足点, 坚持经济大开发与可持续发展有机结合.本文系统地阐述了中国蒙新湖区在气候变化和人类活动的影响下水环境的主要问题及控制对策, 并以典型湖泊乌梁素海、呼伦湖、博斯腾湖、柴窝堡湖及艾比湖等为例, 综合分析了近几十年来水环境指标的变化情况, 证实了水生态环境的退化趋势, 旨在宏观上把握蒙新湖区湖泊现状特征, 为制定蒙新湖区湖泊资源的合理开发及水环境保护的策略提供理论依据.属干旱半干旱气候特征的蒙新湖区, 目前存在湖泊萎缩、湖泊咸化、水质恶化、水生生物种群结构变化等众多问题, 而中国关于蒙新高原湖区的研究, 虽然有一定研究基础和资料, 但与东部湖区相比明显滞后, 缺乏系统认识.研究气候变化条件下蒙新湖区湖泊水环境质量演变规律和发展趋势;水利工程调配对区域水动力条件、污染物输移过程的影响及评估水利调度对重要环境因子的影响作用;选定该湖区特征水环境理化因子, 如矿化度, 研究其对水生生物的影响作用, 以及探索发展适合于干旱半干旱地区特征气候条件影响下的水生态恢复技术应是今后该湖区主要的研究领域和方向。;The policy'The development campaign of the western regions'has great significance for balancing the developing disparities between different regions and improving the economic strength of China.The fragile ecological environment of the western regions determines that ecological protection should be set as the basic point, and that economic development should be combined with sustainable development in those regions.This paper systematically formulates major problems and control measures of aquatic ecosystems in Inner Mongolia-Xinjiang Plateau, where is under the influence of climate change and human activities.We choose Lake Wuliangsuhai, Lake Hulun, Lake Bosten, Lake Chaiwopu and Lake Ebinur as typical examples and analyze the changes in water ecological status in the recent decades.It is confirmed that the degradation of water ecological environment occurs.This paper aims at understanding the current characteristics of lakes in Inner Mongolia-Xinjiang Plateau and providing theoretical support for reasonable development of lake resources and protection of water ecological environment.At present, lakes in Inner Mongolia-Xinjiang Plateau is arid and semi-arid and there exists many problems, such as lake size shrinking, salinization, sediment, deterioration of water quality and structural changes of aquatic ecosystem.Compared with lakes in east China, the research on the Inner Mongolia-Xinjiang Plateau in our country lacks of systematic knowledge and lagging relatively, although some basic research and information have been developed.In the future, the following fields will be focused on:(1) the evolution and trend of water environ-mental quality in the Inner Mongolia-Xinjiang Plateau under the influence of climate change;(2) the effect of water allocation on regional hydrodynamic conditions, pollutant transport process and the influence of water scheduling to important environmental factors;(3) selecting characteristic physical and chemical factors of water environmental in the Plateau, such as mineralization degree, to examine their influence on the aquatic biological communities;(4) exploring aquatic ecological restoration technology which is suitable for arid and semi-arid regions.
Gabapentin and Gabapentinoids (2002)

This chapter contains sections titled: Introduction Gabapenti Pregabalin
Susceptibility of ascites tumor cells to ex-vivo killing by the oncolytic virus JX-963 in epithelial ovarian cancer (2009)

e16537 Background: Epithelial ovarian cancer (EOC) has a poor prognosis, and novel therapies are urgently needed. One-third of patients with EOC will develop clinical ascites, an adverse prognostic factor. The ascitic fluid is rich in tumor cells which can be purified and used as a valuable source of patient material for in vitro analysis. In this study, we describe a method to evaluate the efficacy of ascitic tumor cell killing by the oncolytic virus, JX-963 (vaccinia strain) currently approved for use in a NCIC-CTG phase I trial. Methods: Research ethics approval and patient consent was obtained for this study. 15 samples were collected prospectively with relevant clinicopathologic information. Infection with JX-963 was performed using viral doses ranging from a multiplicity of infection (MOI) of 0.5 to 8. Following a seven-day infection period, viability was assessed using the Alamar Blue metabolic assay and tracked by virally encoded green fluorescent protein (eGFP) expression, immunohistochemistry (IHC) and flow cytometry. Results: A standardized protocol was developed for the collection and purification of EOC cells from patient ascites for subsequent infection and quantification of viral killing. Qualitative analysis using phase contrast imaging of the total cell content showed greater opaque dead cell aggregates with increasing MOI over time. Although variable between individual samples, there was a strong correlation between escalating MOI and enhanced cell death in all patient ascites samples, when quantified by Alamar Blue assay and confirmed by flow cytometry and IHC. Similar cell killing profiles by JX-963 were observed for ascites tumor cells derived from both chemotherapy-naïve patients and chemotherapy-exposed (&gt;1 prior line of chemotherapy) patients. Conclusions: EOC cells from patient ascites show effective but differential susceptibility to viral oncolysis by the JX-963 virus that appears to be independent of prior exposure to chemotherapy. The relevance of this work is that in an individual patient, this assay will allow the testing of panels of oncolytic viruses to identify candidate viral therapeutics which may predict response to treatment. No significant financial relationships to disclose.
Using User Models In Music Information Retrieval Systems. (2000)

[TODO] Add abstract here.
2- to 20-GHz Switch Using III-Nitride Capacitively Coupled Contact Varactors (2013)

We report on the low-loss microwave switch monolithic microwave integrated circuit (MMIC) built using voltage-controlled capacitors formed by the two Schottky contacts deposited over an AlGaN/GaN heterostructure. A symmetrical structure of the varactor allows for either positive or negative control voltage. A small electrode and a spacing size of 2 μm ensure low on-impedance. The fabricated series-shunt switch MMIC shows 0.8-dB insertion loss and 28-dB isolation at 18 GHz and the maximum linear power of 34 dBm at 10 GHz and 38 dBm at 18 GHz (extrapolated from 2- to 10-GHz data). The device does not require contact alignment or annealing; it is robust, simple to fabricate, and well suited for MMICs.
An Efficient Reference-Based Approach to Outlier Detection in Large Datasets (2006)

A bottleneck to detecting distance and density based outliers is that a nearest-neighbor search is required for each of the data points, resulting in a quadratic number of pairwise distance evaluations. In this paper, we propose a new method that uses the relative degree of density with respect to a fixed set of reference points to approximate the degree of density defined in terms of nearest neighbors of a data point. The running time of our algorithm based on this approximation is 0(Rn log n) where n is the size of dataset and R is the number of reference points. Candidate outliers are ranked based on the outlier score assigned to each data point. Theoretical analysis and empirical studies show that our method is effective, efficient, and highly scalable to very large datasets.
Estimation of tumor heterogeneity using CGH array data (2009)

We demonstrate a new method for CGH array analysis that allows a tumor sample to be classified according to its heterogeneity. The method gives an interpretable series of copy number profiles, one for each major subpopulation in a tumor. The profiles facilitate identification of copy number alterations in cancer development.
N,O-Selectivity in the Synthesis of 3-Me-CycloSal-ddAMP (1999)

Abstract The factors influencing the N,O-regioselectivity during preparation of 3-Me-cycloSal-ddAMP were studied.
Advantages of Extended Bottom-Up Proteomics Using Sap9 for Analysis of Monoclonal Antibodies (2014)

Despite the recent advances in structural analysis of monoclonal antibodies with bottom-up, middle-down, and top-down mass spectrometry (MS), further improvements in analysis accuracy, depth, and speed are needed. The remaining challenges include quantitatively accurate assignment of post-translational modifications, reduction of artifacts introduced during sample preparation, increased sequence coverage per liquid chromatography (LC) MS experiment, and ability to extend the detailed characterization to simple antibody cocktails and more complex antibody mixtures. Here, we evaluate the recently introduced extended bottom-up proteomics (eBUP) approach based on proteolysis with secreted aspartic protease 9, Sap9, for analysis of monoclonal antibodies. Key findings of the Sap9-based proteomics analysis of a single antibody include: (i) extensive antibody sequence coverage with up to 100% for the light chain and up to 99-100% for the heavy chain in a single LC-MS run; (ii) connectivity of complementarity-determining regions (CDRs) via Sap9-produced large proteolytic peptides (3.4 kDa on average) containing up to two CDRs per peptide; (iii) reduced artifact introduction (e. g., deamidation) during proteolysis with Sap9 compared to conventional bottom-up proteomics workflows. The analysis of a mixture of six antibodies via Sap9-based eBUP produced comparable results. Due to the reasons specified above, Sap9-produced proteolytic peptides improve the identification confidence of antibodies from the mixtures compared to conventional bottom-up proteomics dealing with shorter proteolytic peptides.
Local Measurement of Loss Using Heated Thin Film Sensors (1998)

A calibration equation is derived linking the non-dimensional entropy generation rate per unit area with the non-dimensional aerodynamic wall shear stress and free stream pressure gradient. It is proposed that the latter quantities, which can be measured from surface gauges, be used to measure the profile entropy generation rate. It is shown that the equation is accurate for a wide range of well-defined laminar profiles. To measure the dimensional entropy generation rate per unit area requires measurement of the thickness of the boundary layer. A general profile equation is given and used to show the range of accuracy of a further simplification to the calibration. For flows with low free stream pressure gradients, the entropy generation rate is very simply related to the wall shear stress, if both are expressed without units. An array of heated thin film sensors is calibrated for the measurement of wall shear stress, thus demonstrating the feasibility of using them to measure profile entropy generation rate.
Altered cellular response to adsorbed matrix protein by chemoselective ligation of small molecules (2005)

In the field of tissue engineering, there is a constant drive to develop materials that enable control over cell adhesion, growth and differentiation for optimal tissue development. In many cases, these materials incorporate or are coated with extracellular matrix proteins to increase cell adhesion and spreading. Here we show that chemoselective modification of an adsorbed matrix protein can be used to selectively alter the response of cultured cells. Using the glycoprotein laminin-1, it was shown that oxidation of terminal sialic acid moieties resulted in the generation of aldehyde groups which could be employed to chemoselectively ligate hydrazide-bearing biomolecules. The hydrazide derivative of the tripeptide Leu–Arg–Glu, a “stop” signal for motoneuron outgrowth, was ligated to periodate-treated laminin and shown to inhibit the mean neurite length of primary spinal cord motoneurons by 39% in comparison to controls. These results demonstrate that adsorbed glycoproteins can be readily modified in order to alter the cell response and could enable matrices to be tailored to different cell types.
EPR Studies Associated with the Electrochemical Reduction of C60 and Supramolecular Complexes of C60 in Toluene−Acetonitrile Solvent Mixtures (1998)

Electron paramagnetic resonance (EPR) studies at 295 K of the radical anion of buckminsterfullerene (C60•-) generated electrochemically by bulk-controlled potential electrolysis of neutral C60 in mixed toluene−acetonitrile solvents (5−20% v/v acetonitrile with 0.1−0.2 M n-Hex4NPF6 or n-Bu4NPF6 as the supporting electrolyte) have shown that at least three different forms of C60•- exist in solution. The radical anions have different g values and can thus be detected by EPR spectroscopy in the form of single line signals with different line widths. The familiar species with the broad line width signal (ΔHpp = 6 mT) was present in a high percentage (ca. >95%) along with two species with narrow line width (ΔHpp = 0.16 and 0.07 mT) signals that were present between 1 and 5% of the total concentration of C60•-. The concentrations of the species with narrow line width EPR signals increased with increasing time so that over a 20-h period their EPR signal intensity approximately doubled. The purity of the toluene was found to be very important in determining the number of species detected with sharp EPR signals. Although two species were always detected with sharp EPR signals, when lower purity toluene (<99%) was used, the number of species with narrow line width signals increased to >2. The increase in the sharp EPR signals with increasing time is not inconsistent with a slow reaction between C60•- and low levels of impurities in the solvent to form lower symmetry paramagnetic species, the narrow line width signals being very similar to those reported for substituted fullerene radicals. EPR and cyclic voltammetry experiments were conducted on C60 in the presence of several complexing agents, cyclotriveratrylene (CTV), the symmetrical tris-allyl substituted analogue of CTV [CTV(allyl)3], and p-benzyl-calix[5]arene. The intensity of the narrow and broad line width EPR signals decreased when C60•- was electrochemically generated in the presence of the complexing agents, indicating that the host−guest π−π interactions were sufficiently strong to alter the EPR signals of C60•-. Cyclic voltammetry experiments performed on C60 in the presence of the complexing agents showed that the first four reduction processes of C60 split into two new processes upon complexation, with the time allowed for the host−guest reaction being critical in determining the voltammetric behavior.
Supplementary Table 2 from Natural Human Plasmacytoid Dendritic Cells Induce Antigen-Specific T-Cell Responses in Melanoma Patients (2023)

&lt;p&gt;Supplementary Table 2 PDF file - 30K, Patient characteristics and historical controls&lt;/p&gt;
An Electrochemistry Study of Cryoelectrolysis in Frozen Physiological Saline (2016)

Cryoelectrolysis is a new minimally invasive tissue ablation surgical technique that combines the processes of electrolysis and solid/liquid phase transformation (freezing). This study investigated this new technique by measuring the pH front propagation and the changes in resistance in a tissue simulant made of physiological saline gel with a pH dye as a function of the sample temperature in the high subzero range above the eutectic. Results demonstrated that effective electrolysis can occur in a high subzero freezing milieu and that the propagation of the pH front is only weakly dependent on temperature. These observations are consistent with a mechanism involving ionic movement through the concentrated saline solution channels between ice crystals at subfreezing temperatures above the eutectic. Moreover, results suggest that Joule heating in these microchannels may cause local microscopic melting, the observed weak dependence of pH front propagation on temperature, and the large changes in resistance with time. A final insight provided by the results is that the pH front propagation from the anode is more rapid than from the cathode, a feature indicative of the electro-osmotic flow from the cathode to the anode. The findings in this paper may be critical for designing future cryoelectrolytic ablation surgery protocols.