gebhart/patrepeval huggingface dataset:
Recent Progress in In Vivo ESR Spectroscopy (2004)

The generation of free radicals and redox status is related to various diseases and injuries that are related to radiation, aging, ischemia-reperfusion, and other oxidative factors. In vivo electron spin resonance (ESR) spectroscopy is noninvasive and detects durable free radicals in live animals. ESR spectrometers for in vivo measurements operate at a lower frequency (approximately 3.5 GHz, approximately 1 GHz, 700 MHz, and approximately 300 MHz) than usual (9-10 GHz). Several types of resonators have been designed to minimize the dielectric loss of electromagnetic waves caused by water in animal bodies. In vivo ESR spectroscopy and its imaging have been used to analyze radical generation, redox status, partial pressure of oxygen and other conditions in various disease and injury models related to oxidative stress with probes, such as nitroxyl radicals. Through these applications, the clarification of the mechanisms related to oxidative diseases (injuries) and the accumulation of basic data for radiological cancer therapy are now ongoing. In vivo ESR measurement is performed in about 10 laboratories worldwide, including ours. To introduce in vivo ESR spectroscopy to life scientists, this article reviews the recent progress of in vivo ESR spectroscopy in instrumentation and its application to the life sciences.
2D implementation of quantum annealing algorisms for fourth order binary optimization problems (2016)

Quantum annealing may provide advantages over simulated annealing on solving some problems such as Kth order binary optimization problem. No feasible architecture exists to implement the high-order optimization problem (K > 2) on current quantum annealing hardware. We propose a two-dimensional quantum annealing architecture to solve the 4th order binary optimization problem by encoding four-qubit interactions within the coupled local fields acting on a set of physical qubits. All possible four-body coupling terms for an N-qubit system can be implemented through this architecture and are readily realizable with the existing superconducting circuit technologies. The overhead of the physical qubits is O(N4), which is the same as previously proposed architectures in four-dimensional space. The equivalence between the optimization problem Hamiltonian and the executable Hamiltonian is ensured by a gauge invariant subspace of the experimental system. A scheme to realize local gauge constraint by single ancillary qubit is proposed.
Recurrent Neural Networks vs. Joint Inference for Clinical Temporal Information Extraction (2016)

We submitted two systems to the SemEval2016 Task 12: Clinical TempEval challenge, participating in Phase 1, where we identified text spans of time and event expressions in clinical notes and Phase 2, where we predicted a relation between an event and its parent document creation time. For temporal entity extraction, we find that a joint inference-based approach using structured prediction outperforms a vanilla recurrent neural network that incorporates word embeddings trained on a variety of large clinical document sets. For document creation time relations, we find that a combination of date canonicalization and distant supervision rules for predicting relations on both events and time expressions improves classification, though gains are limited, likely due to the small scale of training data.
Earthquake early warning (2007)

緊急地震速報は，震源の近くの観測点のデータを用いて，震源とマグニチュードを高速で決定し，強震動の分布を推定し，その情報を利用者へ即座に伝える。震源からある程度はなれたところにいる人には，強い揺れが来る前にある程度の時間的余裕（数秒から数十秒）をもって警報することが可能である。震源の即時決定のためには，利用できる観測点の数によってB-Δ法，テリトリー法（1～2点），グリッドサーチ法（3～5点）などの方法を使う一方で，防災科学研究所が開発した着未着法も活用している。地震のマグニチュードは，P波段階でマグニチュードが推定できるようにP波マグニチュードの式を使い，時間とともに全ての波を使ったマグニチュードの式に切り替える方式になっている。各地の最大震度の推定には，震源とマグニチュードから基準基盤の最大速度振幅を求める経験式を使い，それから，地表面の最大速度振幅と最大震度を推定する経験式を使用する。 緊急地震速報の一部の地域で試験的な運用が始まった平成16年2月25日から平成19年4月30日までに，1449例の緊急地震速報が提供された。このうち，雷や人工ノイズなどによる誤報は29例あったが，2観測点以上を使った緊急地震速報では誤報はなかった。緊急地震速報で最大予測震度5弱以上を報じた地震（28例）について，最大震度5弱以上を観測したものが15例，その他の9例については最大震度4 ，4例については最大震度3を観測している。
<title>Support system for lung cancer screening by CT</title> (2000)

This paper presents a system for CAD of lung cancer screening by CT. The system consists of tow parts, automatic processing part and image based diagnosis part. The automatic processing part is to automatically detect the candidate regions of lung cancer based on the methods we proposed, and the image based diagnosis part is mainly used for doctor to make the mass screening. The result obtained by automatic processing part are provided to image based diagnosis pat as support information for increasing the performance of doctor screening.
Bio-inspired strategies for designing antifouling biomaterials (2016)

Contamination of biomedical devices in a biological medium, biofouling, is a major cause of infection and is entirely avoidable. This mini-review will coherently present the broad range of antifouling strategies, germicidal, preventive and cleaning using one or more of biological, chemical and physical techniques. These techniques will be discussed from the point of view of their ability to inhibit protein adsorption, usually the first step that eventually leads to fouling. Many of these approaches draw their inspiration from nature, such as emulating the nitric oxide production in endothelium, use of peptoids that mimic protein repellant peptides, zwitterionic functionalities found in membrane structures, and catechol functionalities used by mussel to immobilize poly(ethylene glycol) (PEG). More intriguing are the physical modifications, creation of micropatterns on the surface to control the hydration layer, making them either superhydrophobic or superhydrophilic. This has led to technologies that emulate the texture of shark skin, and the superhyprophobicity of self-cleaning textures found in lotus leaves. The mechanism of antifouling in each of these methods is described, and implementation of these ideas is illustrated with examples in a way that could be adapted to prevent infection in medical devices.
Non-Digestible Food Ingredients, Colonic Microbiota and the Impact on Gut Health and Immunity: A Role for Metabolomics (2009)

Increasing health issues related to immune and gut function such as inflammatory disorders, resistance to infections and metabolic syndrome demand modern analytical approaches to accelerate nutritional research aimed at health promotion and disease prevention. Gut microbial-human mutualism endows the host 'superorganism' with a fitness advantage including nutritional, immune and intestinal health aspects. The gut microbiome enlarges our genome and enhances our metabolic potential. Dietary modulation can significantly alter the microbiota community and metabolic activity, and consequently impacts on nutrient bioavailability and host metabolism. Although in an early stage, microbial metabolites generated during colonic fermentation of food stuffs may have beneficial or deleterious effects on intestinal health and immunity, as summarized in this review. However, current evidence is largely based on in vitro and animal studies while substantiation in humans is lacking. The challenge to establish coherent links between the bioconversion of non-digestible food ingredients, their bioavailability and their downstream effects on the host metabolism may be achieved by metabolomics. In this review, metabolomics studies focusing on microbe-host mutualism have demonstrated that metabolomics is capable of detecting and tracking diverse microbial metabolites from different non-digestible food ingredients, of discriminating between phenotypes with different inherent microbiota and of potentially diagnosing infection and gastrointestinal diseases. Integrative approaches such as the combined analysis of the metabolome in different biofluids together with other -omics technologies will cover exogenous and endogenous effects and hence show promise to generate novel hypotheses for innovative functional foods impacting gut health and immunity.
Kinetik der aeroben Abwasserreinigung durch Abbau von organischen Verbindungen und durch Nitrifikation (1986)

Abstract Kinetics of aerobic waste water treatment by degrading organic compounds and by nitrification . Both aerobic degradation of organic substances and nitrification can be described by the double substrate kinetics of Monod ; dissolved organic material and ammonium or nitrite are the first substrate and oxygen the second one. The determination of the different kinetic coefficients by evaluation of measurements on a laboratory scale is explained first, and known results are then presented and discussed. Finally, it is demonstrated by two examples, viz. the simultaneous oxidation of carbon and nitrogen compounds and oxygen‐limited substrate removal, how reaction kinetic models can be used to obtain important information about the characteristics of the bioreactions.
Stability and magnetism of strongly correlated single-layer<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>VS</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:math> (2016)

Single-layer transition metal dichalcogenides exhibit a variety of atomic structures and associated exotic electronic and magnetic properties. Density-functional calculations using the LDA+$U$ approximation show that single-layer ${\mathrm{VS}}_{2}$ is a strongly correlated material, where the stability, phonon spectra, and magnetic moments of the octahedral ($1T$) and the trigonal prismatic ($2H$) structures significantly depend on the effective Hubbard $U$ parameter, ${U}_{\mathrm{eff}}$. Comparison with the HSE06 hybrid density functional used as a benchmark indicates that ${U}_{\mathrm{eff}}=2.5$ eV, which consistently shows that the $2H$ structure is more stable than the $1T$ structure and a ferromagnetic semiconductor. The magnetic moments are localized on the V atoms and coupled ferromagnetically due to the superexchange interactions mediated by the S atoms. Calculations of the magnetic anisotropy show an easy plane for the magnetic moment. Assuming a classical $\mathit{XY}$ model with nearest neighbor coupling, we determine the critical temperature, ${T}_{\mathrm{c}}$, for the Berezinsky-Kosterlitz-Thouless transition of $2H$ single-layer ${\mathrm{VS}}_{2}$ to be about 90 K. Applying biaxial tensile strains can increase ${T}_{\mathrm{c}}$. Using Wannier interpolation, we evaluate the Berry curvature and anomalous Hall conductivity of $2H$ single-layer ${\mathrm{VS}}_{2}$. The coexistence of quasi-long-range ferromagnetic ordering and semiconducting behavior enables $2H$ single-layer ${\mathrm{VS}}_{2}$ to be a promising candidate for spintronics applications.
Analysis of WWW traffic in Cambodia and Ghana (2006)

In this paper we present an analysis of HTTP traffic captured from Internet cafés and kiosks from two different developing countries -- Cambodia and Ghana. This paper has two main contributions. The first contribution is a analysis of the characteristics of the web trace, including the distribution and classification of the web objects requested by the users. We outline notable features of the data set which effect the performance of the web for users in developing regions. Using the trace data, we also perform several simulation analyses of cache performance, including both traditional caching and more novel off-line caching proposals. The second contribution is a set of suggestions on mechanisms to improve the user experience of the web in these regions. These mechanisms include both applications of well-known research techniques as well as offering some less well-studied suggestions based on intermittent connectivity.
SILVER-POLYMER COMPOSITE MATERIALS WITH ANTIBACTERIAL PROPERTIES (2011)

A series of new polyurethane acrylates were prepared by in situ free-radical polymerization of acrylic acid or 2,2bis[5(methacryloyloxyethylcarbonylaminomethyl-1carbamoyloxymethyl)-3,3-trimethyl-ciclohexyl] propionic acid (UMA-1) into a polyurethane matrix, accompanied by the total/partial ionization of the carboxyl groups from the acrylic component with the amino groups from the macromolecular chain. For a set of samples, silver nitrate was added so that through an in situ electron transfer reaction, atomic silver was formed in the metal particles/polymer composites. The characterization of the polyurethane acrylates and hybrid composites was achieved through thermal methods (TGA) and surface analysis (contact angle), whereas the presence of silver nanoparticles was confirmed by energy-dispersive X-ray (EDX) and UV-vis spectroscopy. The mechanical parameters of the polymeric materials were investigated comparatively to the precursors as well as to the silver/polymer composites by tensile stress. Antibacterial properties of such hybrid composites were determined by using an agar diffusion test against both Gram positive (Staphylococcus aureus) and Gram negative (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae) cultures, the results showing a significant effect of these materials to inhibit the growth of bacteria on surface by silver nanoparticles.
Robust topic inference for latent semantic language model adaptation (2007)

We perform topic-based, unsupervised language model adaptation under an N-best rescoring framework by using previous-pass system hypotheses to infer a topic mixture which is used to select topic-dependent LMs for interpolation with a topici-ndependent LM. Our primary focus is on techniques for improving the robustness of topic inference for a given utterance with respect to recognition errors, including the use of ASR confidence and contextual information from surrounding utterances. We describe a novel application of metadata-based pseudo-story segmentation to language model adaptation, and present good improvements to character error rate on multigenre GALE Project data in Mandarin Chinese.
CAD-Integrated Cost Estimation and Build Orientation Optimization to Support Design for Metal Additive Manufacturing (2017)

Cost estimation techniques for Additive Manufacturing (AM) have limited synchronization with the metadata of 3D CAD models. This paper proposes a method for estimating AM build costs through a commercial 3D solid modeling program. Using an application programming interface (API), part volume and surface data is queried from the CAD model and used to generate internal and external support structures as solid-body features. The queried data along with manipulation of the part’s build orientation allows users to estimate build time, feedstock requirements, and optimize parts for AM production while they are being designed in a CAD program. A case study is presented with a macro programmed using the SolidWorks API with costing for a metal 3D-printed automotive component. Results reveal that an imprecise support angle can under-predict support volume by 34% and build time by 20%. Orientation and insufficient build volume packing can increase powder depreciation costs by nearly twice the material costs.
Low-temperature plasma enhanced chemical vapor deposition of SiO2 (1994)

Silicon dioxide (SiO2) films, with qualities approaching to those of thermal oxide, were deposited at 40 °C in a helical resonator plasma reactor from tetraethylorthosilicate (TEOS) and oxygen discharge. The films were characterized using transmission infrared spectroscopy, variable angle spectroscopic ellisometry, and wet etch rate measurements. It was found that the TEOS/O2 ratio, ℜ, in plasma enhanced chemical vapor deposition of SiO2 is as important a parameter as the substrate temperature. Using low TEOS/O2 ratio (ℜ&lt;1:20), high quality SiO2 films could be deposited by PECVD at room temperature. At high TEOS/O2 ratio, particularly at low temperature, ethoxy ligands of the TEOS molecule are incorporated into the film disrupting the connectedness of the SiO4 tetrahedra resulting in porous, low density films with high OH content.
Accelerator-Driven Subcritical Target Concept for Transmutation of Nuclear Wastes (1993)

A means of transmuting key long-lived nuclear wastes, primarily the minor actinides (neptunium, americium, and curium) and iodine, using a hybrid proton accelerator and subcritical lattice, is proposed. By partitioning the components of the light water reactor (LWR) spent fuel and by transmuting key elements, such as the plutonium, the minor actinides, and a few of the long-lived fission products, some of the most significant challenges in building a waste repository can be substantially reduced. The proposed machine, based on the described PHOENIX Concept, would transmute the minor actinides and the iodine produced by 75 LWRs and would generate usable electricity (beyond that required to run the large accelerator) of 850 MW(electric).
Omnicon:a mobile ip-based vertical handoff system for wireless LAN and GPRS links (2005)

Wi-Fi based hotspots offer mobile users broadband wireless Internet connectivity in public work spaces and corporate/ university campuses. Despite aggressive deployment of these hotspots in recent years, high-speed wireless Internet access remains restricted to a small number of geographical areas because of limited physical coverage of wireless LANs. On the other hand, despite their lower throughput, cellular networks have a significantly wider coverage and are thus much more available. Recognizing that 2.5G or 3G cellular networks can effectively complement wireless LANs, we set out to develop a vertical handoff system that allows mobile users to seamlessly fall back to such cellular networks as GPRS or 3G whenever wireless LAN connectivity is not available. The resulting handoff mechanism allows a network connection on a mobile node to operate over multiple wireless access networks in a way that is completely transparent to end user applications. In this paper, we present the design, implementation, and evaluation of a fully operational vertical handoff system, called OmniCon, which enables mobile nodes to automatically switch between wireless LAN and GPRS, based on wireless LAN availability, by introducing a simple extension to existing Mobile IP implementation. We discuss the design issues in the proposed vertical handoff system for heterogeneous networks, including connection setup problems due to network address translation, and the disparity in link characteristics between wireless LANs and GPRS. A detailed performance evaluation study of the OmniCon prototype demonstrates its ability to migrate active network connections between these two wireless technologies with low handoff latency and close to zero packet loss.
Modulation of survival pathways in ovarian carcinoma cell lines resistant to platinum compounds (2008)

Because cytotoxic stress elicits various signaling pathways that may be implicated in cell survival or cell death, their alterations may have relevance in the development of platinum-resistant phenotype. Thus, in the present study, we investigated cell response to the epidermal growth factor receptor (EGFR) inhibitor gefitinib of ovarian carcinoma cell lines, including cells selected for resistance to cisplatin (IGROV-1/Pt1) and oxaliplatin (IGROV-1/OHP). Resistant sublines exhibited a marked decrease in sensitivity to gefitinib and resistance to apoptosis. Gefitinib was capable of inhibiting the phosphorylation of EGFR in all the studied cell lines. The Akt and extracellular signal-regulated kinase 1/2 (ERK1/2) kinases, which act downstream of EGFR, were constitutively active in the three cell lines, but phospho-ERK1/2 levels were increased in the two resistant sublines. This feature was associated with reduced sensitivity to the MEK1/2 inhibitor U0126. Pretreatment of resistant cells with U0126 resulted in restoration of sensitivity to gefitinib. Gefitinib was more effective in inhibiting ERK1/2 and Akt phosphorylation in IGROV-1 cells than in IGROV-1/OHP and IGROV-1/Pt1 cells. Phospho-p38 was up-regulated in the resistant sublines, indicating the concomitant activation of distinct mitogen-activated protein kinases. The up-regulation of phospho-p38 was associated with a peculiar localization of EGFR, which, in resistant sublines, was mainly internalized. In conclusion, our results indicate that the development of resistance to platinum drugs is associated with multiple alterations including deregulation of survival pathways activated by EGFR resulting in a reduced cellular response to gefitinib.
Preoperative Glutamine Administration Induces Heat-Shock Protein 70 Expression and Attenuates Cardiopulmonary Bypass–Induced Inflammatory Response by Regulating Nitric Oxide Synthase Activity (2002)

These results suggest that preoperative glutamine administration induces HSP70 expression before CPB and attenuates CPB-induced inflammation by regulating NOS activity, which may be a prospective management for conferring tolerance to CPB-induced inflammatory response through a self-protective mechanism.
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell‐lines (2015)

Protein quantification at proteome-wide scale is an important aim, enabling insights into fundamental cellular biology and serving to constrain experiments and theoretical models. While proteome-wide quantification is not yet fully routine, many datasets approaching proteome-wide coverage are becoming available through biophysical and MS techniques. Data of this type can be accessed via a variety of sources, including publication supplements and online data repositories. However, access to the data is still fragmentary, and comparisons across experiments and organisms are not straightforward. Here, we describe recent updates to our database resource "PaxDb" (Protein Abundances Across Organisms). PaxDb focuses on protein abundance information at proteome-wide scope, irrespective of the underlying measurement technique. Quantification data is reprocessed, unified, and quality-scored, and then integrated to build a meta-resource. PaxDb also allows evolutionary comparisons through precomputed gene orthology relations. Recently, we have expanded the scope of the database to include cell-line samples, and more systematically scan the literature for suitable datasets. We report that a significant fraction of published experiments cannot readily be accessed and/or parsed for quantitative information, requiring additional steps and efforts. The current update brings PaxDb to 414 datasets in 53 organisms, with (semi-) quantitative abundance information covering more than 300,000 proteins.
A Masked Cuprous Hydride as a Catalyst for Carbonyl Hydrosilylation in Aqueous Solutions (2018)

Redox-unstable cuprous hydridotriphenylborate was isolated as an N-heterocyclic carbene adduct [(IPr)Cu(HBPh<sub>3</sub> )] (IPr=1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) with good thermal stability. Although this compound displays a contact ion-pair structure, Cu<sup>I</sup> H-like catalytic activity was envisaged in carbonyl hydrosilylation. Sufficient moisture stability allowed the catalysis in aqueous/organic media. Mechanistic study further showed that a phenyl group on the borate anion is abstracted by [(IPr)Cu]<sup>+</sup> to give the cationic organocopper complex [(IPr)<sub>2</sub> Cu<sub>2</sub> (μ-Ph)][BPh<sub>4</sub> ].
Inhibition of human immunodeficiency virus 1 (HIV-1) and herpes simplex virus 1 (HSV-1) infectivity with a broad range of lectins (1991)

Five lectins with specificity for N- and O-linked oligosaccharides were examined for inhibition of HIV-1 and HSV-1 infectivity in vitro. HIV-1 isolate HTLVIIIB was preincubated with lectin and subsequently inoculated onto MT-4 cells. Lectins specific for N-linked oligosaccharides blocked HIV infection in nanomolar-micromolar concentrations, but no anti-HIV effect was found with the lectin HPA, mainly reacting with O-linked oligosaccharides. HSV-1 infectivity was measured in a plaque reduction assay using Vero cells, and while both N- and O-linked oligosaccharide -specific lectins inhibited HSV-1 infection, the most potent inhibition was found with the lectin HPA. These results indicate that lectins may have a broad antiviral effect on enveloped viruses only limited by types of oligosaccharides present on individual viruses.