gebhart/patrepeval huggingface dataset:
Achieving anonymity via clustering (2010)

Publishing data for analysis from a table containing personal records, while maintaining individual privacy, is a problem of increasing importance today. The traditional approach of deidentifying records is to remove identifying fields such as social security number, name, etc. However, recent research has shown that a large fraction of the U.S. population can be identified using nonkey attributes (called quasi-identifiers) such as date of birth, gender, and zip code. The k -anonymity model protects privacy via requiring that nonkey attributes that leak information are suppressed or generalized so that, for every record in the modified table, there are at least k −1 other records having exactly the same values for quasi-identifiers. We propose a new method for anonymizing data records, where quasi-identifiers of data records are first clustered and then cluster centers are published. To ensure privacy of the data records, we impose the constraint that each cluster must contain no fewer than a prespecified number of data records. This technique is more general since we have a much larger choice for cluster centers than k -anonymity. In many cases, it lets us release a lot more information without compromising privacy. We also provide constant factor approximation algorithms to come up with such a clustering. This is the first set of algorithms for the anonymization problem where the performance is independent of the anonymity parameter k . We further observe that a few outlier points can significantly increase the cost of anonymization. Hence, we extend our algorithms to allow an ϵ fraction of points to remain unclustered, that is, deleted from the anonymized publication. Thus, by not releasing a small fraction of the database records, we can ensure that the data published for analysis has less distortion and hence is more useful. Our approximation algorithms for new clustering objectives are of independent interest and could be applicable in other clustering scenarios as well.
P2D-1 High Contrast Ultrasound Imaging by Motion-Compensated Time-Averaging Method (2006)

Motion-compensated time-averaged imaging (MTI), a method of accumulating frames with a motion compensation technique using small subregions was conducted to improve power Doppler and B-mode imaging. In our previous study, MTI was shown to be able to clearly image vasculature with contrast agents without image blurring even if the target tissue was moving [Yoshikawa, H, 2006]. The purpose of this study is to investigate whether MTI is applicable to power Doppler and B-mode imaging. It was found that image qualities improved in each case. The motion artifact of a power Doppler image of rabbit kidney was reduced without blurring the image. Also, in the B-mode image of a human carotid artery, the inner membrane was clearly imaged, which is not possible with conventional imaging. The motion of carotid arteries in the slice direction leads to signal compounding at various angles in that direction and results in clear imaging without speckles. Although MTI is a powerful tool for improving ultrasound images, it incurs high computational costs because tissue motion must be compensated in every consecutive frame of an MTI image. As a feasibility test, we investigated whether we could carry out real-time MTI processing with a MAP processor (Equator Technologies, Inc.), which decreases computational cost. We estimated the cost of carrying out MTI with a MAP processor and found that it can be done at frame rates of up to 23 frames per second
Consistency Checking and Optimization of Macromodels (2009)

Circuit macromodeling has been in use for many years to improve the efficiency of simulation at the expense of some accuracy. While this approach has been found to be quite effective, the success or failure of the method depends critically on how closely the macromodels approximate the actual behavior of the functional blocks. This paper describes a systematic methodology for automatic consistency checking and optimization of parameterized macromodels. Initially, an overview of the entire macromodel verification system, iMAVERICK, is provided. An efficient stochastic algorithm to optimize the parameters of a given macromodel is then described and a number of characteristics of the algorithm are presented. Next, a waveform comparison technique for evaluating the performance of the proposed configuration in the optimization process is described. Finally, several examples of macromodel optimization using the iMAVERICK system are presented.
Effect of Source Decay in Bioluminescence Tomography: A Phantom Study (2009)

Recent studies in bioluminescence tomography have been mainly focusing on the ill-posedness and non-uniqueness nature of the problem. In this paper, we demonstrate the significance of the effect of bioluminescence source decay on the reconstruction results with both simulations and phantom studies. Time variation of the bioluminescence source can cause artifacts in the tomographic images. The results show that source dynamic information is pivotal for accurate reconstruction when the decay half-life is comparable to the duration of the data acquisition.
The effects of endomorphin‐1 and endomorphin‐2 in CHO cells expressing recombinant μ‐opioid receptors and SH‐SY5Y cells (1999)

1 Endomorphin-1 and -2 (E-1/E-2) have been proposed as endogenous ligands for the mu-opioid receptor. The aims of this study are to characterize the binding of E-1/E-2 and the subsequent effects on cyclic AMP formation and [Ca2+]i levels in SH-SY5Y and Chinese hamster ovary (CHO) cells expressing endogenous and recombinant mu-opioid receptors. 2 E-1 displaced [3H]-diprenorphine ([3H]-DPN) binding in CHO micro and SH-SY5Y membranes with pKi values of 8.02+/-0.09 and 8.54+/-0.13 respectively. E-2 displaced [3H]-DPN binding in CHOmu and SH-SY5Y cells with pKi values of 7.82+/-0.11 and 8.43+/-0.13 respectively. E-1/E-2 bound weakly to CHOdelta and CHOkappa membranes, with IC50 values of greater than 10 microM. 3 In CHOmu cells, E-1/E-2 inhibited forskolin (1 microM) stimulated cyclic AMP formation with pIC50 values of 8.03+/-0.16 (Imax = 53.0+/-9. 3%) and 8.15+/-0.24 (Imax = 56.3+/-3.8%) respectively. In SH-SY5Y cells E1/E2 inhibited forskolin stimulated cyclic AMP formation with pIC50 values of 7.72+/-0.13 (Imax=46.9+/-5.6%) and 8.11+/-0.31 (Imax = 40.2+/-2.8%) respectively. 4 E-1/E-2 (1 microM) increased [Ca2+]i in fura-2 loaded CHOmu cell suspensions in a thapsigargin sensitive and naloxone reversible manner. Mean increases observed were 106+/-28 and 69+/-6.7 nM respectively. In single adherent cells E-1/E-2 (1 microM) increased [Ca2+]i with a mean 340/380 ratio change of 0.81+/-0.09 and 0.40+/-0.08 ratio units respectively. E-1/E-2 failed to increase intracellular calcium in CHOdelta, CHOkappa and SH-SY5Y cells. 5 These data show that E-1/E-2 bind with high affinity and selectivity to mu-opioid receptors and modulate signal transduction pathways typical of opioids. This provides further evidence that these two peptides may be endogenous ligands at the mu-opioid receptor.
The Transcription Factor, α1ACT, Acts Through a MicroRNA Network to Regulate Neurogenesis and Cell Death During Neonatal Cerebellar Development (2022)

MicroRNAs, a class of small RNA regulators, function throughout neurodevelopment, from neural stem cell neurogenesis to neuronal maturation, synaptic formation, and plasticity. α1ACT, a transcription factor (TF), plays a critical role in neonatal cerebellar development by regulating an ensemble of genes. Of these, ChIP-seq analysis matched near 50% genes directly regulated by α1ACT. Yet, more than half the regulated transcripts lacked direct interaction with α1ACT. To investigate whether α1ACT acts through a microRNA network, we studied α1ACT-associated simultaneous miRNA:mRNA transcriptome profiles, using miRNA-seq paired with RNA-seq. Thirty-one differentially expressed miRNAs (DEMs) associated with α1ACT-regulated differentially expressed genes (DEGs) were profiled in α1ACT-overexpressing PC12 cells and were further validated in neonatal transgenic mouse cerebellum overexpressing α1ACT in a context-dependent manner. Here, we also demonstrated that α1ACT facilitates neurogenesis and development of dendritic synapses and is partially a result of the downregulation of the miR-99 cluster, miR-143, miR-23, miR-146, miR-363, and miR-484. On the other hand, the miR-181, miR-125, and miR-708 clusters were upregulated by α1ACT, which inhibit MAPK signaling and cell death pathways by targeting Ask1, Odc1, Atf4, and Nuf2 for decreased expression. MiR-181a-5p was verified as the most abundant DEM in neonatal cerebellum, which was further induced by α1ACT. Overall, under α1ACT modulation, up-/downregulated miRNA clusters with their paired target genes may form a regulatory network controlling the balance between the neuronal proliferation, differentiation, and cell death in the cerebellum to promote neonatal development. Our findings concerning the α1ACT-related miRNA/mRNA expression profiles in neonatal cerebellum may inform future investigations for cerebellar development.
Cyber-Physical Systems of Systems (2016)

We are called to be architects of the future, not its victims" Richard Buckminster-Fuller This book is about "systems-of-systems". If you search in Google for this term, you get 176,000,000 results in 0.60 seconds (20.9.2016). This clearly shows the importance and vibrancy of this field! However, it also shows the wide and diverging variety of viewpoints, concepts, and opinions related to systems-of-systems.
Analysis of Fibre Comminution Rates during High Intensity Thermo-mechanical Pulping of Spruce and Pine (2002)

A three-fraction comminution analysis was conducted on thermo-mechanical pulps produced from two predominant North American softwoods, black spruce (P. mariana) and loblolly pine (P. taeda). High intensity pulps were produced from both wood species at elevated temperature and refiner disk speeds, using a pilot scale two-stage pressurized refining configuration. The rates of Bauer McNett R14 and R28 comminution and P28 formation increased with refiner disk speed. Conversion of R14 into R28 was the most favoured breakdown process, requiring less energy than the breakdown of R14 to P28 or R28 to P28. The pine comminuted at a faster rate than the spruce, at all levels of refining intensity. With the pine furnish a critical level of wood breakdown was observed, beyond which pulp strength properties deteriorated rapidly. The morphological properties of a given wood species have a defining influence on the refining behaviour, and the study suggests that further increases in refining intensity might further reduce energy consumption during manufacture of high temperature thermo-mechanical pulps, particularly when using softwoods with more resilient fibres.
DEVELOPMENT OF A RAPID CO-PROTOTYPING ENVIRONMENT FOR INDUSTRIAL SERVICES (2018)

Service-oriented industrial companies need to manage the complexity of developing new services (NSD) besides products. Prototyping offers a way to increase the success of NSD. There are service prototyping environments, but they fall short in effectiveness. CoProtolab concept was developed for effective, comprehensive, immersive and collaborative prototyping of industrial services in a physical and virtual environments. The research follows an axiomatic design theory and results in a theoretical model for studying and developing virtual, physical and social service prototyping environments.
Survey of Performance Acceleration Techniques for Network Function Virtualization (2019)

The ongoing network softwarization trend holds the promise to revolutionize network infrastructures by making them more flexible, reconfigurable, portable, and more adaptive than ever. Still, the migration from hard-coded/hard-wired network functions toward their software-programmable counterparts comes along with the need for tailored optimizations and acceleration techniques so as to avoid or at least mitigate the throughput/latency performance degradation with respect to fixed function network elements. The contribution of this paper is twofold. First, we provide a comprehensive overview of the host-based network function virtualization (NFV) ecosystem, covering a broad range of techniques, from low-level hardware acceleration and bump-in-the-wire offloading approaches to high-level software acceleration solutions, including the virtualization technique itself. Second, we derive guidelines regarding the design, development, and operation of NFV-based deployments that meet the flexibility and scalability requirements of modern communication networks.
Hydroxymethylnitrofurazone Is Active in a Murine Model of Chagas' Disease (2010)

The addition of a hydroxymethyl group to the antimicrobial drug nitrofurazone generated hydroxymethylnitrofurazone (NFOH), which had reduced toxicity when its activity against Trypanosoma cruzi was tested in a murine model of Chagas' disease. Four groups of 12 Swiss female mice each received 150 mg of body weight/kg/day of NFOH, 150 mg/kg/day of nitrofurazone (parental compound), 60 mg/kg/day of benznidazole (BZL), or the solvent as a placebo. Treatments were administered orally once a day 6 days a week until the completion of 60 doses. NFOH was as effective as BZL in keeping direct parasitemia at undetectable levels, and PCR results were negative. No histopathological lesions were seen 180 days after completion of the treatments, a time when the levels of anti-T. cruzi antibodies were very low in mice treated with either NFOH or BZL. Nitrofurazone was highly toxic, which led to an overall rate of mortality of 75% and necessitated interruption of the treatment. In contrast, the group treated with its hydroxymethyl derivative, NFOH, displayed the lowest mortality (16%), followed by the BZL (33%) and placebo (66%) groups. The findings of histopathological studies were consistent with these results, with the placebo group showing the most severe parasite infiltrates in skeletal muscle and heart tissue and the NFOH group showing the lowest. The present evidence suggests that NFOH is a promising anti-T. cruzi agent.
Plasma after both SARS-CoV-2 boosted vaccination and COVID-19 potently neutralizes BQ.1.1 and XBB.1 (2023)

Recent 2022 SARS-CoV-2 Omicron variants, have acquired resistance to most neutralizing anti-Spike monoclonal antibodies authorized, and the BQ.1.* sublineages are notably resistant to all authorized monoclonal antibodies. Polyclonal antibodies from individuals both vaccinated and recently recovered from Omicron COVID-19 (VaxCCP) could retain new Omicron neutralizing activity. Here we reviewed BQ.1.* virus neutralization data from 920 individual patient samples from 43 separate cohorts defined by boosted vaccinations (Vax) with or without recent Omicron COVID-19, as well as infection without vaccination (CCP) to determine level of BQ.1.* neutralizing antibodies and percent of plasma samples with neutralizing activity. More than 90 % of the plasma samples from individuals in the recently (within 6 months) boosted VaxCCP study cohorts neutralized BQ.1.1, and BF.7 with 100 % neutralization of WA-1, BA.4/5, BA.4.6 and BA.2.75. The geometric mean of the geometric mean 50 % neutralizing titres (GM (GMT<sub>50</sub>) were 314, 78 and 204 for BQ.1.1, XBB.1 and BF.7, respectively. Compared to VaxCCP, plasma sampled from COVID-19 naïve subjects who also recently (within 6 months) received at least a third vaccine dose had about half of the GM (GMT<sub>50</sub>) for all viral variants. Boosted VaxCCP characterized by either recent vaccine dose or infection event within 6 months represents a robust, variant-resilient, neutralizing antibody source against the new Omicron BQ.1.1, XBB.1 and BF.7 variants.
High-speed silicon photonic electro-optic Kerr modulation (2023)

Silicon-based electro-optic modulators contribute to easing the integration of high-speed and low-power consumption circuits for classical optical communications and data computations. Beyond the plasma dispersion modulation, an alternative solution in silicon is to exploit the DC Kerr effect, which generates an equivalent linear electro-optical effect enabled by applying a large DC electric field. Although some theoretical and experimental studies have shown its existence in silicon, limited contributions relative to plasma dispersion have been achieved in high-speed modulation so far. This paper presents high-speed optical modulation based on the DC Kerr effect in silicon PIN waveguides. The contributions of both plasma dispersion and Kerr effects have been analyzed in different waveguide configurations, and we demonstrated that the Kerr induced modulation is dominant when a high external DC electric field is applied in PIN waveguides. High-speed optical modulation response is analyzed, and eye diagrams up to 80 Gbit/s in NRZ format are obtained under a d.c. voltage of 30 V. This work paves the way to exploit the Kerr effect to generate high-speed Pockels-like optical modulation.
Detection of Avian H7N9 Influenza A Viruses in the Yangtze Delta Region of China During Early H7N9 Outbreaks (2015)

Since the first H7N9 human case in Shanghai, February 19, 2013, the emerging avian-origin H7N9 influenza A virus has become an epizootic virus in China, posing a potential pandemic threat to public health. From April 2 to April 28, 2013, some 422 oral-pharyngeal and cloacal swabs were collected from birds and environmental surfaces at five live poultry markets (LPMs) and 13 backyard poultry farms (BPFs) across three cities, Wuxi, Suzhou, and Nanjing, in the Yangtze Delta region. In total 22 isolates were recovered, and six were subtyped as H7N9, nine as H9N2, four as H7N9/H9N2, and three unsubtyped influenza A viruses. Genomic sequences showed that the HA and NA genes of the H7N9 viruses were similar to those of the H7N9 human isolates, as well as other avian-origin H7N9 isolates in the region, but the PB1, PA, NP, and MP genes of the sequenced viruses were more diverse. Among the four H7N9/H9N2 mixed infections, three were from LPM, whereas the other one was from the ducks at one BPF, which were H7N9 negative in serologic analyses. A survey of the bird trading records of the LPMs and BPFs indicates that trading was a likely route for virus transmission across these regions. Our results suggested that better biosecurity and more effective vaccination should be implemented in backyard farms, in addition to biosecurity management in LPMs.
Visual performance-based image enhancement methodology: an investigation of contrast enhancement algorithms (2006)

While vast numbers of image enhancing algorithms have already been developed, the majority of these algorithms have not been assessed in terms of their visual performance-enhancing effects using militarily relevant scenarios. The goal of this research was to apply a visual performance-based assessment methodology to evaluate six algorithms that were specifically designed to enhance the contrast of digital images. The image enhancing algorithms used in this study included three different histogram equalization algorithms, the Autolevels function, the Recursive Rational Filter technique described in Marsi, Ramponi, and Carrato<sup>1</sup> and the multiscale Retinex algorithm described in Rahman, Jobson and Woodell<sup>2</sup>. The methodology used in the assessment has been developed to acquire objective human visual performance data as a means of evaluating the contrast enhancement algorithms. Objective performance metrics, response time and error rate, were used to compare algorithm enhanced images versus two baseline conditions, original non-enhanced images and contrast-degraded images. Observers completed a visual search task using a spatial-forcedchoice paradigm. Observers searched images for a target (a military vehicle) hidden among foliage and then indicated in which quadrant of the screen the target was located. Response time and percent correct were measured for each observer. Results of the study and future directions are discussed.
Filoviruses: Hemorrhagic Fevers (2012)

In the United States, all filoviruses are classified as Select Agents, Risk Group 4 Pathogens, NIAID Priority Pathogens, and CDC Bioterrorism Agents because there is currently no FDA-approved vaccine for the prevention or antiviral for the treatment of infection. Experiments with these viruses is limited to maximum-containment (BSL-4) facilities.
Timolol increased retrobulbar flow velocities in untreated glaucoma eyes but not in ocular hypertension (2001)

Peripheral resistance to blood flow was found to be increased in untreated glaucoma eyes as compared to a similar group of eyes with ocular hypertension. Timolol treatment diminished resistance significantly in the glaucoma group, but not in the ocular hypertension group. Thus the two groups responded differently to timolol treatment. The reaction to IOP lowering treatment could indicate defective autoregulation in the glaucoma group.
Abstract #3656: The BH3 alpha helical mimic BH3M-6 disrupts Bcl-xL/Bax and Mcl-1/Bax binding and induces apoptosis in human cancer cells in a Bcl-xL, Bcl2 and Mcl-1 dependent manner. (2009)

Evasion of apoptosis is a critical malignancy hallmark that is required for cancer cell survival. One mechanism by which tumor cells evade apoptosis is by overexpressing tumor survival proteins such as those of the Bcl family, which bind to the alpha helical BH3 domain of pro-apoptotic proteins such as Bax, Bim, and Bad. We designed a BH3 alpha helical mimic BH3M-6 which binds Bcl-xL and prevents its binding to Bax in vitro with an IC50 value of 750 nM using a fluorescence polarization assay. GST pulldown assays also demonstrated that BH3M-6 inhibits Bcl-xL/Bax and Mcl-1/Bax binding. Furthermore, using co-immunoprecipitation, cytosolic redistribution of mitochondrial GFP-Bad as well as Bimolecular Fluorescence Complementation assays we demonstrated that BH3M-6 inhibits in intact cells the binding of Bcl-xL to Bax, Bad and Bim. BH3M-6 induced cytochrome c release, capase 3 activation and PARP degradation. Finally, in human cancer cells that depend on the Bcl family members for survival, BH3M-6 induced apoptosis in a Bcl-Xl, Bcl-2 and Mcl-1-dependent manner. Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 3656.
Fluxomers: a new approach for 13 C metabolic flux (2011)

Background: The ability to perform quantitative studies using isotope tracers and metabolic flux analysis (MFA) is critical for detecting pathway bottlenecks and elucidating network regulation in biological systems, especially those that have been engineered to alter their native metabolic capacities. Mathematically, MFA models are traditionally formulated using separate state variables for reaction fluxes and isotopomer abundances. Analysis of isotope labeling experiments using this set of variables results in a non-convex optimization problem that suffers from both implementation complexity and convergence problems. Results: This article addresses the mathematical and computational formulation of 13 C MFA models using a new set of variables referred to as fluxomers. These composite variables combine both fluxes and isotopomer abundances, which results in a simply-posed formulation and an improved error model that is insensitive to isotopomer measurement normalization. A powerful fluxomer iterative algorithm (FIA) is developed and applied to solve the MFA optimization problem. For moderate-sized networks, the algorithm is shown to outperform the commonly used 13CFLUX cumomer-based algorithm and the more recently introduced OpenFLUX software that relies upon an elementary metabolite unit (EMU) network decomposition, both in terms of convergence time and output variability. Conclusions: Substantial improvements in convergence time and statistical quality of results can be achieved by applying fluxomer variables and the FIA algorithm to compute best-fit solutions to MFA models. We expect that the fluxomer formulation will provide a more suitable basis for future algorithms that analyze very large scale networks and design optimal isotope labeling experiments.