gebhart/patrepeval huggingface dataset:
Thin-film Nitrate Sensor Performance Prediction Based on Preprocessed Sensor Images (2021)

Automating the assessment of sensor quality in the production of thin-film nitrate sensors can yield significant advantages. Currently, the inspection process is extremely time and labor intensive, requiring technicians to manually examine sensors from each batch to determine their performance. Not only is manually examining sensors costly, it also takes days to conclude the results. It is possible to utilize image based learning approach to entirely automate the quality assessment process by accurately predicting the performance of every sensor; this allows for instant performance analysis and rapid changes to the fabrication parameters. The fabrication parameters will directly control the thickness of the ion-selective membrane (ISM) of the nitrate sensor. The thickness of the ISM directly affects the texture on the sensor’s surface. Because of the reliable correlation between sensor performance and sensor surface texture, it allows us to use learning methods to predict sensor performance through images instead of direct measurements. We propose a method to predict sensor quality using noncontact sensor images through a series of image processing techniques followed by machine and deep learning.
Characterization of L1 retrotransposition with high-throughput dual-luciferase assays (2010)

Recent studies employing genome-wide approaches have provided an unprecedented view of the scope of L1 activities on structural variations in the human genome, and further reinforced the role of L1s as one of the major driving forces behind human genome evolution. The rapid identification of novel L1 elements by these high-throughput approaches demands improved L1 functional assays. However, the existing assays use antibiotic selection markers or fluorescent proteins as reporters; neither is amenable to miniaturization. To increase assay sensitivity and throughput, we have developed a third generation assay by using dual-luciferase reporters, in which firefly luciferase is used as the retrotransposition indicator and Renilla luciferase is encoded on the same or separate plasmid for normalization. This novel assay is highly sensitive and has a broad dynamic range. Quantitative data with high signal-to-noise ratios can be obtained from 24- up to 96-well plates in 2-4 days after transfection. Using the dual-luciferase assays, we have characterized profiles of retrotransposition by various human and mouse L1 elements, and detailed the kinetics of L1 retrotransposition in cultured cells. Its high-throughput and short assay timeframe make it well suited for routine tests as well as large-scale screening efforts.
Genotyping chip data lift-over to reference genome build GRCh38/hg38 v1 (2018)

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Topical Delivery of siRNA-Based Spherical Nucleic Acid Nanoparticle Conjugates for Gene Regulation* (2020)

Topical application of nucleic acids offers many potential therapeutic advantages for suppressing genes in the skin, and potentially for systemic gene delivery. The recent development of small molecule inhibitors and antibodies that target components of signaling pathways has revolutionized the treatment of cancers, inflammatory diseases, and genetic disorders, including those that largely manifest in skin. Given the importance of EGFR signaling in epidermal cell proliferation and its recognized overexpression in many malignancies, EGFR was chosen as an initial target for gene suppression. Because the SNA-NCs easily enter hKCs in in vitro experiments, we explored their ability to penetrate both mouse skin and human skin models. Historically, researchers have relied on physicochemical methods to facilitate epidermal penetration and cellular delivery of negatively charged nucleic acids.
A new biologic role for C3a and C3a desArg: regulation of TNF-α and IL-1 β synthesis (1996)

The complement activation products C3a and C3a desArg are generated in the course of trauma, infection, tissue injury, and ischemia. We have investigated the effects of C3a and C3a desArg on gene expression and protein synthesis of TNF-alpha and IL-1 beta in PBMC. Neither C3a nor C3a desArg alone induced detectable protein or mRNA levels for TNF-alpha and IL-1 beta. C3a modulated LPS-induced TNF-alpha and IL-1 beta synthesis. In nonadherent PBMC, C3a suppressed LPS-induced synthesis of TNF-alpha (20-71% decrease by 0.2-10 microgram/ml of C3a, p less than 0.01) and IL-1 beta (19-57% decrease by 0.5-10 microgram/ml of C3a, p less than 0.01), independently of endogenous production of PGE2. C3a also suppressed LPS-induced mRNA levels for TNF-alpha and IL-1 beta. In contrast, in adherent PBMC, C3a at 5 to 20 microgram/ml enhanced LPS-induced TNF-alpha (75-188% increase, p less than 0.001) and IL-1 beta (119-274% increase, p less than 0.001) synthesis. C3a enhanced TNF-alpha and IL-1 beta mRNA levels in LPS-stimulated adherent cells. Furthermore, C3a desArg shared with C3a the ability to modulate LPS-induced mRNA and protein synthesis for TNF-alpha and IL-1 beta. These results suggest that C3a, thought to be proinflammatory, and C3a desArg, thought to be biologically inactive, are modulators of inflammation. Both C3a and C3a desArg may enhance cytokine synthesis by adherent monocytes at local inflammatory sites, while inhibiting the systemic synthesis of proinflammatory cytokines by circulating cells.
The Electrocatalytic Conversion of CO2 to Fuels and Chemicals (2012)

Abstract not Available.
Fluid Structure Interaction Analysis of Blood Flow Through a Mechanical Heart Valve (2008)

Modeling pulsatile flow past heart valves remains a relatively unexplored but critical area. Due to the geometric complexity and the interaction between the flowing blood and the heart valve leaflets, existing numerical techniques that require domain discretization, such as finite element methods or finite difference techniques, cannot fully represent the moving and deforming boundaries present in an operating valve. Our aim is to develop a technique to model the flow through heart valves which includes the interaction between the blood flow and the valve leaflets using the radial functions method (RFM). The RFM is a meshless technique that fully accounts for moving and deforming surfaces and thus is well suited to model the blood flow and its interaction with leaflet motion. Here we present a 2D fluid structure interaction (FSI) model of the blood flow through a bileaflet mechanical heart valve (MHV).
Chemotherapy Alone or Chemotherapy with Chest Radiation Therapy in Limited Stage Small Cell Lung Cancer (1987)

A regimen of combined chemotherapy and chest radiation therapy given concurrently is superior to chemotherapy given alone in inducing remission and prolonging survival in patients with limited stage small cell lung cancer, and the benefit of combined therapy is reduced by its greater toxicity.
Nonlinear diffraction in orientation-patterned semiconductors (2015)

This work represents experimental demonstration of nonlinear diffraction in an orientation-patterned semiconducting material. By employing a new transverse geometry of interaction, three types of second-order nonlinear diffraction have been identified according to different configurations of quasi-phase matching conditions. Specifically, nonlinear Čerenkov diffraction is defined by the longitudinal quasi-phase matching condition, nonlinear Raman-Nath diffraction satisfies only the transverse quasi-phase matching condition, and nonlinear Bragg diffraction fulfils the full vectorial quasi-phase matching conditions. The study extends the concept of transverse nonlinear parametric interaction toward infrared frequency conversion in semiconductors. It also offers an effective nondestructive method to visualise and diagnose variations of second-order nonlinear coefficients inside semiconductors.
Evidence of a $J/\\psi \\varLambda$ structure and observation of excited $\\varXi^-$ states in the $\\varXi_b^-\\to J/\\psi \\varLambda K^-$ decay (2020)

First evidence of a structure in the $J/\\psi \\varLambda$ invariant mass distribution is obtained from an amplitude analysis of $\\varXi_b^- \\to J/\\psi \\varLambda K^-$ decays. The observed structure is consistent with being due to a charmonium pentaquark with strangeness. Its mass and width are determined to be $4458.8\\pm2.9\\,^{+4.7}_{-1.1}$MeV and $17.3\\pm6.5\\,^{+8.0}_{-5.7}$MeV, where the quoted uncertainties are statistical and systematic, respectively. The structure is also consistent with being due to two resonances. In addition, the narrow excited $\\varXi^-$ states, $\\varXi(1690)^-$ and $\\varXi(1820)^-$, are seen for the first time in a $\\varXi_b^-$ decay, and their masses and widths are measured with improved precision. The analysis is performed using $pp$ collision data corresponding to a total integrated luminosity of 9fb$^{-1}$, collected with the LHCb experiment at centre-of-mass energies of $7$, $8$ and $13$TeV.
Ultrafast energy and electron transfer in donor-acceptor molecules for photovoltaics (2001)

Summary form only given. The rapid advancement in fullerene chemistry allows the covalent functionalization of C/sub 60/ with electron donors. Various C/sub 60/-based donor-acceptor dyads have been synthesized and studied to gain insight in the intramolecular photophysical processes, like energy and electron transfer. Although these dyads can serve as a model compounds for the conjugated photovoltaic cells, only a few examples have been reported with these C/sub 60/-based dyads. Apart from being well-defined model systems for photophysical characterization, the covalent linkage between donor,and acceptor in these molecular arrays provides a simple method to achieve control over the phase segregation in donor-acceptor networks. We investigate an oligo(phenylene vinylene)fullerene dyad with 4 phenyl groups (C/sub 60/-OPV/sub 4/) in solvents of different polarity using femtosecond pump-probe spectroscopy. We find that photoexcitation of the oligomer leads first to an intramolecular energy transfer to the fullerene, while an electron transfer is a secondary process, only allowed in polar solvents.
Analysis of Food Waste Resources Available for Sustainable Energy Production in the Finger Lakes Region of New York State (2013)

Prior research conducted by our Institute has revealed the large quantities of food waste available in New York State, particularly in the Upstate corridor extending from Buffalo to Syracuse. The Finger Lakes region is heavily populated with agricultural operations, dairy farms and food processing plants, including those producing milk, yogurt, wine, and canned fruits and vegetables. The diverse supply of organic waste generated by these facilities offers the opportunity for sustainable energy production through one of three primary pathways: • Anaerobic digestion to produce methane • Fermentation to produce alcohols • Transesterification to produce biodiesel. Generally speaking, food wastes are better suited for biochemical conversion instead of thermo-chemical conversion (combustion, gasification, pyrolysis) due to their relatively high moisture content. The current paper provides an initial assessment of food wastes within the 9-County Finger Lakes region around Rochester, New York. Available databases were utilized to first identify all the relevant companies operating in one of four broad industry sectors: agriculture, food processing, food distribution and food services (including restaurants). Our analysis has demonstrated that anaerobic digestion can be a viable method for sustainable energy production from food waste in the Finger Lakes region, due to the dual economic benefits of effective disposal cost reduction and production of methane-rich biogas.
Positive Bradford Curves through Sharpening (1999)

The Bradford curves are used in the CIECAM97 colour appearance model, and are &#x2018;sharpened&#x2019; in the sense that they have narrower support than the cone fundamentals. Spectral sharpening is a method which finds the linear combination of a set of sensors that is most sensitive to a given interval of the visible spectrum. Here we investigate the relationship between the apparently sharp Bradford curves and the spectral sharpening method (since spectral sharpening was not used to derive the Bradford curves). We find that Bradford curves can be derived using spectral sharpening but the sharpening intervals are not the ones we would might have expected or wished for. The Bradford intervals are far from the &#x2018;prime wavelength&#x2019; intervals: those parts of the visible spectrum where there is maximal visual sensitivity. Also, independent of any sharpening argument, the Bradford curves are unexpected in the sense that they have some negative sensitivity. Here we address both these concerns and produce sharpened versions of the Bradford curves that are both all-positive and also sharpened within wavelength intervals around the prime wavelengths. In a sense, we are continuing the work of MacAdam, and Pearson and Yule, in forming positive combinations of the colour-matching functions. However, the advantage of the spectral sharpening approach is that not only can we produce positive curves, but the process is &#x2018;steerable&#x2019; in that we can produce positive curves with as good or better properties for sharpening within a given set of sharpening intervals. At base, however, it is positive colours in the transformed space that are the prime objective. Therefore we also carry out sharpening of sensor curves governed not by positivity of the curves themselves but of colours resulting from them. Curves that result have negative lobes, but generate positive colours. We find that this type of constrained sharpening generates the best results, almost as good as for unconstrained sharpening but without the penalty of negative colours.
ATPS-91GSK-3 INHIBITOR 9-ING-41 ENHANCES GENOTOXIC THERAPY OF GBM LEADING TO CURE FROM INTRACRANIAL BRAIN TUMOR (2015)

BACKGROUND: Glycogen Synthase Kinase-3 (GSK-3), a positive regulator of NF-kappaB-mediated survival of cancer cells, has been identified as a potential therapeutic target for the treatment of GBM. We hypothesized that the inhibition of GSK-3 may overcome NF-kappaB-associated chemo- and radioresistance in human GBM. METHODS: We used GBM6 and GBM12 patient-derived xenograft (PDX) orthotopic tumor models, enabled for bioluminescence imaging (BLI) through luciferase modification, for evaluating the novel GSK-3 inhibitor 9-ING-41, when used in combination with genotoxic chemotherapy or radiotherapy. In vivo imaging system (IVIS) was used to study the effect of mono- and combination treatments, along with determination of survival benefit from treatment after intracranial transplantation of GBM tumor. RESULTS: BLI of animal subjects revealed that NF-kappaB is constitutively active in orthotopic GBM tumor expressing an NF-kappa luciferase reporter. Intravenous injection of 9-ING-41 significantly reduced the bioluminescence of orthotopic GBM PDX, indicative of reduced NF-kappaB transcriptional activity. When used in combination with the DNA alkylator CCNU, 9-ING-41 significantly increased CCNU anti-tumor activity against orthotopic GBM12 (no response to CCNU monotherapy) or GBM6 (partial response to CCNU monotherapy) xenografts, as indicated by the absence of tumor bioluminescence signal in mouse brain and by significantly increased animal subject survival. The treatment with CCNU + 9-ING-41 resulted in apparent cure for all mice with intracranial GBM6 and GBM12 tumors, as supported by histological evaluation that revealed a complete absence of cancer cells in mouse brain. CONCLUSIONS: Our results suggest that GSK-3 inhibitor 9-ING-41, a novel clinical drug candidate, enhances the efficacy of genotoxic therapy for human GBM, and warrants consideration for clinical evaluation. The combination of 9-ING-41 and radiotherapy, for the treatment of GBM12 orthotopic PDX tumors, is ongoing and will be presented.
A novel assistive method for rigidity evaluation during deep brain stimulation surgery using acceleration sensors (2016)

OBJECTIVE Despite the widespread use of deep brain stimulation (DBS) for movement disorders such as Parkinson's disease (PD), the exact anatomical target responsible for the therapeutic effect is still a subject of research. Intraoperative stimulation tests by experts consist of performing passive movements of the patient's arm or wrist while the amplitude of the stimulation current is increased. At each position, the amplitude that best alleviates rigidity is identified. Intrarater and interrater variations due to the subjective and semiquantitative nature of such evaluations have been reported. The aim of the present study was to evaluate the use of an acceleration sensor attached to the evaluator's wrist to assess the change in rigidity, hypothesizing that such a change will alter the speed of the passive movements. Furthermore, the combined analysis of such quantitative results with anatomy would generate a more reproducible description of the most effective stimulation sites. METHODS To test the reliability of the method, it was applied during postoperative follow-up examinations of 3 patients. To study the feasibility of intraoperative use, it was used during 9 bilateral DBS operations in patients suffering from PD. Changes in rigidity were calculated by extracting relevant outcome measures from the accelerometer data. These values were used to identify rigidity-suppressing stimulation current amplitudes, which were statistically compared with the amplitudes identified by the neurologist. Positions for the chronic DBS lead implantation that would have been chosen based on the acceleration data were compared with clinical choices. The data were also analyzed with respect to the anatomical location of the stimulating electrode. RESULTS Outcome measures extracted from the accelerometer data were reproducible for the same evaluator, thus providing a reliable assessment of rigidity changes during intraoperative stimulation tests. Of the 188 stimulation sites analyzed, the number of sites where rigidity-suppressing amplitudes were found increased from 144 to 170 when the accelerometer evaluations were considered. In general, rigidity release could be observed at significantly lower amplitudes with accelerometer evaluation (mean 0.9 ± 0.6 mA) than with subjective evaluation (mean 1.4 ± 0.6 mA) (p < 0.001). Of 14 choices for the implant location of the DBS lead, only 2 were the same for acceleration-based and subjective evaluations. The comparison across anatomical locations showed that stimulation in the fields of Forel ameliorates rigidity at similar amplitudes as stimulation in the subthalamic nucleus, but with fewer side effects. CONCLUSIONS This article describes and validates a new assistive method for assessing rigidity with acceleration sensors during intraoperative stimulation tests in DBS procedures. The initial results indicate that the proposed method may be a clinically useful aid for optimal DBS lead placement as well as a new tool in the ongoing scientific search for the optimal DBS target for PD.
Otimização do Consumo de Energia em Redes de Rádio Heterogêneo via Cooperação (2016)

O crescimento exponencial da carga de tráfego e a necessidade de acesso ubı́quo provocaram uma expansão da infraestrutura de rede e uma demanda crescente de energia. Portanto, foi elaborado um modelo baseado em programação linear inteiro misto (PLIM) para otimizar a economia de energia nas redes sem fio.
Population Pharmacokinetics of Candesartan in Patients with Chronic Heart Failure (2020)

Heart failure (HF) causes pathological changes in multiple organs, thus affecting the pharmacokinetics (PK) of drugs. The aim of this study was to investigate the PK of candesartan in patients with HF while examining significant covariates and their related impact on estimated clearance using a population PK (Pop-PK) modeling approach. Data from a prospective, multicenter study were used. Modeling and simulations were conducted using Nonlinear Mixed-Effects Modeling (NONMEM) and R software. A total of 281 white patients were included to develop the Pop-PK model. The final model developed for apparent oral clearance (CL/F) included weight, estimated glomerular filtration rate (eGFR), and diabetes, which partly explained its interindividual variability. The mean CL/F value estimated was 7.6 L/h (1.7-22.6 L/h). Simulations revealed that an important decrease in CL/F (> 25%) is obtained with the combination of the factors retained in the final model. Considering these factors, a more individualized approach of candesartan dosing should be investigated in patients with HF.
Distributed Optimal Power Flow for Smart Microgrids (2013)

Optimal power flow (OPF) is considered for microgrids, with the objective of minimizing either the power distribution losses, or, the cost of power drawn from the substation and supplied by distributed generation (DG) units, while effecting voltage regulation. The microgrid is unbalanced, due to unequal loads in each phase and non-equilateral conductor spacings on the distribution lines. Similar to OPF formulations for balanced systems, the considered OPF problem is nonconvex. Nevertheless, a semidefinite programming (SDP) relaxation technique is advocated to obtain a convex problem solvable in polynomial-time complexity. Enticingly, numerical tests demonstrate the ability of the proposed method to attain the globally optimal solution of the original nonconvex OPF. To ensure scalability with respect to the number of nodes, robustness to isolated communication outages, and data privacy and integrity, the proposed SDP is solved in a distributed fashion by resorting to the alternating direction method of multipliers. The resulting algorithm entails iterative message-passing among groups of consumers and guarantees faster convergence compared to competing alternatives.
Value tensions in design (2007)

We report on the value sensitive design, development, and appropriation of a groupware system to support software engineering knowledge sharing. Usage data (5,965 visitors) and semi-structured interviews (18 individuals) suggest the methods employed were successful in addressing value tensions, particularly with respect to privacy, awareness, and reputation. Key contributions include: (1) "proof-of-concept" that established Value Sensitive Design principles and methods can be used to good effect for the design of groupware in an industry setting, (2) a new design method for addressing value tensions, Value Dams and Flows, and (3) demonstration of the co-evolution of technology and organizational policy.
Time-Frequency Analysis of Lamb Waves Caused by Partial Discharges and Free Particles in GIS (2002)

We investigated propagation properties of Lamb waves in GIS tank using time-frequency analysis to diagnose insulation performance of GIS. We measured the acoustic signals excited by a metallic particle colliding with the tank sheath, and those emitted by partial discharge in GIS as well. The Wavelet Transform was applied to decompose the wave data into its timefrequency components. As the result, it was confirmed that Lamb waves with the dispersive property of the velocity are excited and the waves propagate spirally along the tank wall due to the cylindrical structure of the tank. Taking these results into consideration, we proposed a new technique for identification of the defect location in GIS based on the time-frequency analysis of the acoustic waves using the Wavelet Transform.