gebhart/patrepeval huggingface dataset:
277 Serum Soluble Trail Levels in Patients With Severe Persistent Allergic Asthma (2012)

BACKGROUND: The pathogenesis of allergic asthma and other allergic conditions are believed to be closely interrelated because of the similar dynamics of allergy-inducing cells and molecules, and the independent evidence for their clinical overlap. In this study we compare the diseases and the effect of Omalizumab treatment on the dynamics of cell apoptosis regulating molecules. METHODS: In the first group, 6 males and 8 females (a total of 14 patients) were selected with severe persistent asthma with a mean age of 42.4 years (Table I). All patients received omalizumab therapy for 4 months, with treatment administered every 2 weeks. Symptoms and severity of allergic reactions were recorded before and after treatment with omalizumab. Clinical changes and adverse effects were assessed and recorded at each patient visit. The second group consisted of 14 newly diagnosed allergic asthma patients with mean age was 43.8 years. All of these patients were followed up in the Immunology Allergy Clinic of the Antalya Education and Training Hospital, and were evaluated by clinical status. The third group consisted of 14 healthy volunteers, with no difference in age and sex (mean age was 43,3 years. Serum sTRAIL levels in all individuals (patients and healthy controls) were measured by a sandwich enzyme-linked immunosorbent assay (Diaclone, France). RESULTS: There were no differences between the healthy controls, newly diagnosed allergic asthma patients and non-treated severe persistent allergic asthma patients during the active phase (P < 0.05). Interestingly, the variance levels in patients who received omalizumab treatment were significantly lower than the healthy controls. CONCLUSIONS: In summary, we speculate that the physiological functions of sTRAIL in allergic conditions, and the elucidation of the molecular mechanisms by which sTRAIL: TRAIL receptor signals cells, will be of significant interest to the scientific allergy community in the coming years. Our study provides a novel perspective on severe persistent allergic asthma and the effect of omalizumab treatment on cell apoptosis, using serum sTRAIL measurements.
N-Terminal Acetylation by NatB Is Required for the Shutoff Activity of Influenza A Virus PA-X (2018)

N-terminal acetylation is a major posttranslational modification in eukaryotes catalyzed by N-terminal acetyltransferases (NATs), NatA through NatF. Although N-terminal acetylation modulates diverse protein functions, little is known about its roles in virus replication. We found that NatB, which comprises NAA20 and NAA25, is involved in the shutoff activity of influenza virus PA-X. The shutoff activity of PA-X was suppressed in NatB-deficient cells, and PA-X mutants that are not acetylated by NatB showed reduced shutoff activities. We also evaluated the importance of N-terminal acetylation of PA, because PA-X shares its N-terminal sequence with PA. Viral polymerase activity was reduced in NatB-deficient cells. Moreover, mutant PAs that are not acetylated by NatB lost their function in the viral polymerase complex. Taken together, our findings demonstrate that N-terminal acetylation is required for the shutoff activity of PA-X and for viral polymerase activity.
Linear tSNE optimization for the Web. (2018)

The t-distributed Stochastic Neighbor Embedding (tSNE) algorithm has become in recent years one of the most used and insightful techniques for the exploratory data analysis of high-dimensional data. tSNE reveals clusters of high-dimensional data points at different scales while it requires only minimal tuning of its parameters. Despite these advantages, the computational complexity of the algorithm limits its application to relatively small datasets. To address this problem, several evolutions of tSNE have been developed in recent years, mainly focusing on the scalability of the similarity computations between data points. However, these contributions are insufficient to achieve interactive rates when visualizing the evolution of the tSNE embedding for large datasets. In this work, we present a novel approach to the minimization of the tSNE objective function that heavily relies on modern graphics hardware and has linear computational complexity. Our technique does not only beat the state of the art, but can even be executed on the client side in a browser. We propose to approximate the repulsion forces between data points using adaptive-resolution textures that are drawn at every iteration with WebGL. This approximation allows us to reformulate the tSNE minimization problem as a series of tensor operation that are computed with TensorFlow.js, a JavaScript library for scalable tensor computations.
Fiber Surface Structure and Fiber Liberation in Soda-anthraquinone Kraft and Soda Pulps as Determined by Conventional Electron Microscopy (2007)

Comparative studies on the surface structure of defibrated fibers and fiber liberation in nondefibrated chips from three different pulping processes, soda-anthraquinone (soda/AQ), kraft and soda pulping, were performed via conventional electron microscopy. By comparing the exposed fiber surface structure with the degree of fiber liberation, delignification processes in middle lamella regions were elucidated for these pulping systems. Soda/AQ pulping resulted in fiber liberation with less lignin removal than for either kraft or soda pulping process.
Experimental Complex Modal Analysis of Machine Tool Structures (1989)

Despite the well-established theories and considerable experimental research, the identification of the complex mode shapes of a real machine tool structure with general damping still remains a formidable task. Moreover, the existence of closely coupled modes with heavy damping introduces additional difficulties. This paper presents a detailed procedure for experimental complex modal analysis of a machine tool structure by the Dynamic Data System method. The accuracy and efficiency are first illustrated by numerical examples through simulation studies. It has been shown that closely coupled modes and modes with heavy damping can be successfully identified from both simulated and actual experimental data from a machine tool. Complex mode shapes were also obtained without adding any complexity or losing accuracy as compared to normal mode analysis. The experimental results obtained by the proposed method were compared with those based on the FFT algorithm.
Effect of Incubation of CO2 and Lewis Acid on the Generation of Toluic Acid from Toluene and CO2 (2008)

p-Toluic acid is produced by reacting Lewis acid (1), CO2 (2), and toluene (3) at milder conditions. The order of addition of reactants is found to be able to change the course of the reaction toward the desired product and therefore must be 1, 2, and 3. Reaction occurs through in situ formation of a Lewis acid:CO2 adduct created by incubating CO2 and Lewis acid for 1 h prior to the addition of toluene. The order of addition led the reaction to occur with anhydrous Al2Cl6 and a few other Lewis acids than only anhydrous Al2Cl6 in the usual way of addition 2, 3, and 1. Spectacularly CuBr2 produces p-toluic acid as major product when incubated with CO2 at 57 bar and 80 °C prior to addition of toluene whereas bromotoluene is a major product when added with toluene and then pressurized with CO2 at the same temperature and pressure.
Abstract 2503: Distinct radiosensitivities of human FancG-/- and FancD2-/- cell lines (2011)

Abstract Background: Fanconi Anemia is an autosomal recessive disorder marked by a dysfunction of DNA repair, an increased sensitivity to DNA crosslinking agents, and some patients poorly tolerating ionizing irradiation. We determined the radiosensitivity of two Fanconi patient cell lines and we determined if the nitroxide radioprotector Tempo or a novel mitochondrial targeted nitroxide JP4-039 could alter their radiosensitivity. Materials and Methods: Fanconi patient derived fibroblastic cell lines, PD326 and PD20F, and their respective transgene restored cell lines FancG and FancD2 were irradiated to doses ranging from 0 to 8 Gy in the presence or absence of Tempo or JP4-039 (10 µm), plated, and colonies greater than 50 cells were counted eight days later. Results: The PD20F cell line was more radiosensitive compared to the restored FancD2 cell line (n = 1.6 + 0.2 and 10.7 + 3.1, respectively, p = 0.0423). In contrast the PD326 cell line was more radioresistant than its restored FancG cell line as seen by an increased shoulder on the survival curve (n = 8.1 + 1.4 and 2.2 + 0.3, respectively, p = 0.0174). JP4-039 but not Tempo increased radioresistance in the PD326 (n = 15.7 + 2.5, p = 0.0373), and FancG cell lines (10.2 + 2.1, p = 0.0151). Conclusions: The human Fanconi Anemia cell line PD326 is radioresistant when compared to its transgene restored FancG cell line, and this radioresistance is increased by treatment with the mitochondrial targeted nitroxide JP4-039. In contrast, PD20F is more radiosensitive when compared to its transgene restored FancD2 cell line. Testing the efficacy of JP4-039 and Tempo on mitigating the effects of mitomycin C treatment is being evaluated. Supported by 2U19A1068021-06 Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2503. doi:10.1158/1538-7445.AM2011-2503
A Shear Stress Sensing for Robot Hands -Orthogonal arrayed Piezoresistive Cantilevers standing in Elastic Material- (2006)

We propose a shear stress sensor that uses standing cantilevers embedded in an elastic material. Each cantilever independently measures one directional component of the shear stress applied to the sensor surface. We orthogonally arrayed these standing cantilevers, so that the directions and the magnitudes of applied shear stresses are detected. The efficiency of this sensor was experimentally confirmed in the range of – 5.0 to 5.0 kPa. By using this sensor, the directions and magnitudes of 2.45 kPa shear stresses, applied from 12 different directions, were detected.
Biological Evaluation of Potent Triclosan‐Derived Inhibitors of the Enoyl–Acyl Carrier Protein Reductase InhA in Drug‐Sensitive and Drug‐Resistant Strains of Mycobacterium tuberculosis (2014)

New triclosan (TRC) analogues were evaluated for their activity against the enoyl-acyl carrier protein reductase InhA in Mycobacterium tuberculosis (Mtb). TRC is a well-known inhibitor of InhA, and specific modifications to its positions 5 and 4' afforded 27 derivatives; of these compounds, seven derivatives showed improved potency over that of TRC. These analogues were active against both drug-susceptible and drug-resistant Mtb strains. The most active compound in this series, 4-(n-butyl)-1,2,3-triazolyl TRC derivative 3, had an MIC value of 0.6 μg mL(-1) (1.5 μM) against wild-type Mtb. At a concentration equal to its MIC, this compound inhibited purified InhA by 98 %, and showed an IC50 value of 90 nM. Compound 3 and the 5-methylisoxazole-modified TRC 14 were able to inhibit the biosynthesis of mycolic acids. Furthermore, mc(2) 4914, an Mtb strain overexpressing inhA, was found to be less susceptible to compounds 3 and 14, supporting the notion that InhA is the likely molecular target of the TRC derivatives presented herein.
Syntheses of Two Potential Ligands for Tc‐99m Labeling as Diagnosis Agents of Alzheimer's Disease (2003)

Abstract Two types of ligands‐biphenyl and stilbene derivatives, which can be labeled with Tc‐99m for the diagnosis of Alzheimer's disease (AD) have been synthesized successfully. The key steps in these two syntheses involved Suzuki reaction and Wittig reaction respectively. The new discovered debromination reaction may be expanded to the compounds with double or triple bond adjacent to the carbon atom bearing the bromine atoms. These types of syntheses provide a route to a series of biphenyl and stilbene derivatives that will benefit the search of new imaging agents for AD.
Recombination of Photogenerated Lophyl Radicals in Imidazolium‐Based Ionic Liquids (2009)

Laser flash photolysis is applied to study the recombination reaction of lophyl radicals in ionic liquids in comparison with dimethylsulfoxide as an example of a traditional organic solvent. The latter exhibits a similar micropolarity as the ionic liquids. The ionic liquids investigated are 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (1), 1-hexyl-3-methylimidazolium hexafluorophosphate (2), and 1-butyl-3-methylimidazolium tetafluoroborate (3). The recombination of the photolytic generated lophyl radicals occur significantly faster in the ionic liquids than expected from their macroscopic viscosities and is a specific effect of these ionic liquids. On the other hand, this reaction can be compared with the macroscopic viscosity in the case of dimethylsulfoxide. Activation parameters obtained for lophyl radical recombination suggest different, anion-dependent mechanistic effects. Quantum chemical calculations based on density functional theory provide a deeper insight of the molecular properties of the lophyl radical and its precursor. Thus, excitation energies, spin densities, molar volumes, and partial charges are calculated. Calculations show a spread of spin density over the three carbon atoms of the imidazolyl moiety, while only low spin density is calculated for the nitrogens.
Matrix‐assisted laser desorption/ionization mass spectrometry of collected bioaerosol particles (2005)

A method was developed for collection and analysis of bioaerosols by matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry using a modified Andersen N6 bioaerosol collector. The overall goal of the study was to develop methods for obtaining mass spectra with minimal reagents and treatment steps for potential use in remote collection and analysis systems. Test bioaerosol particles were generated from a nebulized E. coli bacterial suspension and collected on MALDI targets placed in an Andersen N6 single-stage aerosol impactor. The bioaerosols were mixed with matrix either by deposition on a bare target with the matrix solution added later, or by deposition on a target pre-coated with matrix. The matrix compounds alpha-cyano-4-hydroxycinnamic acid (CHCA) and sinapic acid (SA) were tested and the SA matrix was found to give the best results in number of peaks, resolution, and signal-to-noise ratio. Deposition of bioaerosol particles onto the matrix pre-coated target did not produce signal in the m/z region above 1000, but the signal could be recovered with the addition of a 1:1 (v/v) acetonitrile/water solvent. Addition of solvent by pipette to the pre-coated targets after particle deposition recovered signal comparable to the dried-droplet sample preparations, whereas solvent sprayed into the impactor recovered fewer peaks. Deposition on pre-coated targets with post-collection solvent addition was superior to deposition on bare target followed by post-collection addition of matrix solution.
On privacy-preserving data publishing and analysis (2012)

Data have exploded in recent years. The availability of data at ever finer granularity presents immense potential for uncovering knowledge and producing economic value in a variety of domains. However, much of these interesting data are private. Owners of such data have legal and ethical responsibilities to protect the privacy of individuals represented by the data. Perhaps for the fear of inadvertently breaching privacy, most private data are locked-up by data owners, hampering the data from being fully utilized. Developing privacy-preserving techniques to analyze data without compromising privacy is thus an important direction of research in the field of data management. 
This dissertation explores privacy-preserving data anonymization techniques in three different data models. It first studies the problem of anonymizing relational data. We observe that current state-of-the-art approach still leaks sensitive information when relational data are updated. We propose techniques to address this without significantly sacrificing utility. Set-valued data is another important data model, examples of which include market basket data and query logs. In the second part of this dissertation we propose a new top-down algorithm to anonymize set-valued data that achieves better utility than previous algorithms. Lastly, we focus on the popular streaming data model, which has attracted little attention for privacy research so far. We identify potential privacy concerns of a special form of stream processing called Complex Event Processing, and study the corresponding optimization problem of maximizing utility under privacy constraints in the last part of this dissertation.
20505 Magnetic field control of mode bifurcation on magnetic fluid Taylor-Couette vortex flow (2005)

A successful application of the ultrasonic velocity profile (UVP) measuring technique to investigations on the flow of magnetic fluids is described. The flow structure of a magnetic fluid in a concentric annular geometry with a small aspect ratio of 3 and a radius ratio of 0.6 was investigated for an inner cylinder rotation. Axial velocity distributions were measured using the UVP measuring technique. A non-uniform magnetic field was applied to the flow field using a permanent magnet located on the outside of the vessel. The UVP monitor is model X-3 PSi in basic ultrasound frequency of 8MHz. The UVP method was demonstrated to provide useful information on the structure of Taylor-Couette vortex flow in a magnetic fluid. The influence of the magnetic field to this flow is also discussed in the presentation.
Regulation of CTP:phosphocholine cytidylyltransferase activity and subcellular location by phosphorylation in Chinese hamster ovary cells. The effect of phospholipase C treatment. (1991)

The phosphorylation state of cytidylyltransferase in Chinese hamster ovary (CHO) cells was correlated with its subcellular distribution and activity in vivo. Western blot analysis of soluble and particulate fractions from control and phospholipase C-treated cells revealed slower migrating forms of cytidylyltransferase present only in the soluble fraction of control cells. These were abolished by incubating the soluble fraction at 37 degrees C in the presence of 5 mM Mg2+ but persisted if 135 mM NaF was present in the incubation. CHO cells were labeled with 32Pi, and cytidylyltransferase was immunoprecipitated from soluble and particulate fractions from control and phospholipase C-treated cells. The slower migrating forms of cytidylyltransferase, present in the soluble fraction of control cells, were phosphorylated at multiple sites. Although an equivalent amount of cytidylyltransferase was immunoprecipitated from the particulate fraction of phospholipase C-treated cells, it contained little 32P. Pretreatment of the CHO cells with okadaic acid, an inhibitor of type 1 and 2A phosphatases, prevented the stimulation of cytidylyltransferase in vivo by phospholipase C. These results demonstrate that dephosphorylation of soluble cytidylyltransferase is required for the phospholipase C-mediated translocation of cytidylyltransferase in CHO cells.
Actively-induced, Prompt Radiation Utilization in Nonproliferation Applications (2006)

The Pulsed Photonuclear Assessment (PPA) technique, which has demonstrated the ability to detect shielded nuclear material, is currently based on utilizing delayed neutrons and photons between accelerator pulses. While most active interrogation systems have focused on delayed neutron and gamma-ray signatures, the current requirements of various Homeland Security issues necessitate bringing faster detection and acquisition capabilities to field inspection applications. This push for decreased interrogation times, increased sensitivity and mitigation of false positives requires that detection systems take advantage of all available information. Collaborative research between Idaho National Lab (INL), Idaho State University's Idaho Accelerator Center (IAC), Los Alamos National Laboratory (LANL), and Oak Ridge National Laboratory (ORNL), has focused on exploiting actively-induced, prompt radiation signatures from nuclear material within a pulsed photonuclear environment. To date, these prompt emissions have not been effectively exploited due to difficulties in detection and signal processing inherent in the prompt regime as well as an overall poor understanding of the magnitude and yields of these emissions. Exploitation of prompt radiation (defined as during an accelerator pulse/(photo)fission event and/or immediately after (les 1 mus)) has the potential to dramatically reduce interrogation times since the prompt neutron yields are more than two orders of magnitude greater than delayed emissions. Successful exploitation of prompt emissions is critical for the development of an improved robust, high-throughput, low target dose inspection system for detection of shielded nuclear materials.
Multi-Agent Deep Reinforcement Learning For Distributed Handover Management In Dense MmWave Networks (2020)

The dense deployment of millimeter wave small cells combined with directional beamforming is a promising solution to enhance the network capacity of the current generation of wireless communications. However, the reliability of millimeter wave communication links can be affected by severe pathloss, blockage, and deafness. As a result, mobile users are subject to frequent handoffs, which deteriorate the user throughput and the battery lifetime of mobile terminals. To tackle this problem, our paper proposes a deep multi-agent reinforcement learning framework for distributed handover management called RHando (Reinforced Handover). We model users as agents that learn how to perform handover to optimize the network throughput while taking into account the associated cost. The proposed solution is fully distributed, thus limiting signaling and computation overhead. Numerical results show that the proposed solution can provide higher throughput compared to conventional schemes while considerably limiting the frequency of the handovers.
Analysis of Piezoelectric Materials for Energy Harvesting Devices under High-g Vibrations (2007)

We analyzed the miniaturized energy harvesting devices (each volume within 0.3 cm3) fabricated by using three types of piezoelectric materials such as lead zirconium titanate (PZT) ceramic, macro fiber composite (MFC) and poly(vinylidene fluoride) (PVDF) polymer to investigate the capability of converting mechanical vibration into electricity under larger vibration amplitudes or accelerations conditions (≥1g, gravitational acceleration). All prototypes based on a bimorph cantilever structure with a proof mass were aimed to operate at a vibration frequency of 100 Hz. PZT-based device was optimized and fabricated by considering the resonant frequency, the output power density, and the maximum operating acceleration or safety factor. PVDF- and MFC-prototypes were designed to have same resonant frequency as well as same volume of the piezoelectric materials as the PZT prototype. All three devices were measured to determine if they could generate enough power density to provide electric energy to power a wireless sensor or a microelectromechanical systems (MEMS) device without device failure.