gebhart/patrepeval huggingface dataset:
Molecular Typing of ST239-MRSA-III From Diverse Geographic Locations and the Evolution of the SCCmec III Element During Its Intercontinental Spread (2018)

ST239-MRSA-III is probably the oldest truly pandemic MRSA strain, circulating in many countries since the 1970s. It is still frequently isolated in some parts of the world although it has been replaced by other MRSA strains in, e.g., most of Europe. Previous genotyping work (Harris et al., 2010; Castillo-Ramírez et al., 2012) suggested a split in geographically defined clades. In the present study, a collection of 184 ST239-MRSA-III isolates, mainly from countries not covered by the previous studies were characterised using two DNA microarrays (i) targeting an extensive range of typing markers, virulence and resistance genes and (ii) a SCCmec subtyping array. Thirty additional isolates underwent whole-genome sequencing (WGS) and, together with published WGS data for 215 ST239-MRSA-III isolates, were analysed using in-silico analysis for comparison with the microarray data and with special regard to variation within SCCmec elements. This permitted the assignment of isolates and sequences to 39 different SCCmec III subtypes, and to three major and several minor clades. One clade, characterised by the integration of a transposon into nsaB and by the loss of fnbB and splE was detected among isolates from Turkey, Romania and other Eastern European countries, Russia, Pakistan and (mainly Northern) China. Another clade, harbouring sasX/sesI is widespread in South-East Asia including China/Hong Kong, and surprisingly also in Trinidad & Tobago. A third, related, but sasX/sesI-negative clade occurs not only in Latin America but also in Russia and in the Middle East from where it apparently originated and from where it also was transferred to Ireland. Minor clades exist or existed in Western Europe and Greece, in Portugal, in Australia and New Zealand as well as in the Middle East. Isolates from countries where this strain is not epidemic (such as Germany) frequently are associated with foreign travel and/or hospitalisation abroad. The wide dissemination of this strain and the fact that it was able to cause a hospital-borne pandemic that lasted nearly 50 years emphasises the need for stringent infection prevention and control and admission screening.
An ITO–graphene heterojunction integrated absorption modulator on Si-photonics for neuromorphic nonlinear activation (2021)

The high demand for machine intelligence of doubling every three months is driving novel hardware solutions beyond charging of electrical wires, given a resurrection to application specific integrated circuit (ASIC)-based accelerators. These innovations include photonic-based ASICs (P-ASICs) due to prospects of performing optical linear (and also nonlinear) operations, such as multiply–accumulate for vector matrix multiplications or convolutions, without iterative architectures. Such photonic linear algebra enables picosecond delay when photonic integrated circuits are utilized via “on-the-fly” mathematics. However, the neuron’s full function includes providing a nonlinear activation function, known as thresholding, to enable decision making on inferred data. Many P-ASIC solutions perform this nonlinearity in the electronic domain, which brings challenges in terms of data throughput and delay, thus breaking the optical link and introducing increased system complexity via domain crossings. This work follows the notion of utilizing enhanced light–matter interactions to provide efficient, compact, and engineerable electro-optic neuron nonlinearity. Here, we introduce and demonstrate a novel electro-optic device to engineer the shape of this optical nonlinearity to resemble a leaky rectifying linear unit—the most commonly used nonlinear activation function in neural networks. We combine the counter-directional transfer functions from heterostructures made out of two electro-optic materials to design a diode-like nonlinear response of the device. Integrating this nonlinearity into a photonic neural network, we show how the electrostatics of this thresholder’s gating junction improves machine learning inference accuracy and the energy efficiency of the neural network.
On time-varying cyclic delay diversity (2006)

Abstract: Cyclic Delay Diversity (CDD) was introduced in 2001 to obtain spatial diversity in an Orthogonal Divi-sion Multiplexing (OFDM) based transmission system. In contrast to Space-Time Codes, CDD introduces no addi-tional effort at the receiver side, since CDD changes only the channel impulse response seen by the receiver by in-creasing the frequency selectivity. In this paper, we ana-lyze CDD for an Orthogonal Frequency Division Multiple Access (OFDMA) based transmission system. To increase not only the frequency selectivity but also the time selec-tivity, we introduce Time-Varying Cyclic Delay Diversity (TV-CDD), which changes the cyclic shift with each OFDM symbol. Especially in systems, where each user can only allocate a few subchannels for data transmission, TV-CDD improves the performance of the OFDMA based transmis-sion system significantly. 1.
A virtual product development strategy for minimally invasive medical devices (2010)

Virtual design tools are gaining more and more importance in the production process of medical devices.Biomedical devices and their surrounding boundary conditions are usually characterized by complex geometrical shapes, materials and interactions, and current Abaqus capabilities in dealing with highly nonlinear problems are highly needed to realistically capture these complexities.As an example, stents can be laser-cut or braided, driven by folded balloons to expand or be self-expanding and they interact with stenosed, tortuous, highly non-linear and anisotropic blood vessels.In order to investigate in detail some of the above mentioned aspects of stenting we have developed a dedicated pre-and postprocessing tool based on the open-source design software pyFormex.The enormous potential of combining this design environment with Abaqus is illustrated in this paper, focusing on balloon-and self-expanding stents, embolic protection filters and patient specific modeling.This paper aims at providing a survey of the latest developments carried out in our research unit in this area and detailed information with respect to the simulations can be found in the cited works.
Properties of thermoacoustic engines desirable for space applications (2005)

The advantages of a technology that are promoted at its inception are not always those that may eventually allow it to win out over its competition. A collaboration with Northrop Grumman Space Technology on a small thermoacoustic-Stirling electric generator has shed some light on certain advantages of thermoacoustic-Stirling engines beyond ‘‘no moving parts’’ or ‘‘less moving parts.’’ Some of these advantages will be discussed
Influence of Shot Peening on the Isothermal Fatigue Behavior of the Gamma Titanium Aluminide Ti-48Al-2Cr-2Nb at 750 °C (2021)

One possibility to improve the fatigue life and strength of metallic materials is shot peening. However, at elevated temperatures, the induced residual stresses may relax. To investigate the influence of shot peening on high-temperature fatigue behavior, isothermal fatigue tests were conducted on shot-peened and untreated samples of gamma TiAl 48-2-2 at 750 °C in air. The shot-peened material was characterized using EBSD, microhardness, and residual stress analyses. Shot peening leads to a significant increase in surface hardness and high compressive residual stresses near the surface. Both effects may have a positive influence on lifetime. However, it also leads to surface notches and tensile residual stresses in the bulk material with a negative impact on cyclic lifetime. During fully reversed uniaxial tension-compression fatigue tests (R = −1) at a stress amplitude of 260 MPa, the positive effects dominate, and the fatigue lifetime increases. At a lower stress amplitude of 230 MPa, the negative effect of internal tensile residual stresses dominates, and the lifetime decreases. Shot peening leads to a transition from surface to volume crack initiation if the surface is not damaged by the shots.
PROPRIEDADES MECÂNICAS A ALTAS TEMPERATURAS DE FERROS FUNDIDOS CINZENTOS APLICADOS A CABEÇOTES DE MOTOR A DIESEL (2014)

Os efeitos de elevadas temperaturas e do tempo de exposio sobre as propriedades mecnicas de um ferro fundido cinzento hipoeuttico foram avaliados em amostras de dois ferros fundidos da classe FC300, de mesma base, com diferentes percentuais de molibdnio. Ensaios de trao at ruptura a quente foram realizados em corpos de prova com dimetro de 10 mm, usinados de um pino bruto de 30 mm de dimetro. Os ensaios foram realizados a frio (temperatura ambiente) e a quente (200C, 300C, 350C, 400C, 450C, 500C e 550C). Os tempos de exposio a elevadas temperaturas, aps homogeneizao trmica do material, foram de 0, 60, 90 e 120 minutos. As amostras com maior percentual de molibdnio (0,27% em peso) apresentaram melhores propriedades mecnicas para todas as condies ensaiadas. De acordo com a literatura a reduo na resistncia mecnica com a elevao da temperatura atribuda ocorrncia de decomposio da perlita, como resultado da difuso do carbono vindo da cementita s lamelas de grafita, que o responsvel pelo aumento da quantidade de grafita no material. As anlises metalogrficas evidenciam a ocorrncia deste fenmeno. Aumentos no tempo de exposio a temperaturas elevadas tambm contriburam para a degenerao da perlita.
Estimation of delay times from a delayed optical feedback laser experiment (1998)

We estimate delay times from high-dimensional chaotic time series experimentally obtained from a fast optical time-delayed feedback system. The experiment consists of a semiconductor laser, where the instabilities are induced by an external T-shaped cavity introducing two delay times into the laser. The delay times are determined by a filling factor analysis and found to give a better estimate than those obtained by autocorrelation functions. Finally, the possibility of this method for the reconstruction of the system's differential equations is discussed.
Mild Rh(III)-Catalyzed C–H Activation and Annulation with Alkyne MIDA Boronates: Short, Efficient Synthesis of Heterocyclic Boronic Acid Derivatives (2012)

Taking advantage of Rh(III)-catalyzed C-H activation reactions, we have developed a mild, short, and efficient method for the synthesis of bench-stable 3-isoquinolone MIDA boronates. The reaction is practical and scalable. The product formed has been applied in the Suzuki-Miyaura reaction with high efficiency. This strategy has also been successfully expanded to the synthesis of MIDA boronate functionalized heterocycles such as isoquinoline, pyrrole, and indole.
Preliminary studies on the relationship among peel force, quantitative measures of skin damage and subjective discomfort (2008)

In this system, there was not a correspondence between adhesion as measured by peel force and skin damage or self-report of discomfort. Further investigations will be required to establish the predictive value of other biophysical measurements and discomfort.
A complete distortion correction for MR images: I. Gradient warp correction (2005)

MR images are known to be distorted because of both gradient nonlinearity and imperfections in the B0 field, the latter caused either by an imperfect shim or sample-induced distortions. This paper describes in detail a method for correcting the gradient warp distortion, based on a direct field mapping using a custom-built phantom with three orthogonal grids of fluid-filled rods. The key advance of the current work over previous contributions is the large volume of the mapping phantom and the large distortions (>25 mm) corrected, making the method suitable for use with large field of view, extra-cranial images. Experimental measurements on the Siemens AS25 gradient set, as installed on a Siemens Vision scanner, are compared with a theoretical description of the gradient set, based on the manufacturer's spherical harmonic coefficients. It was found that over a volume of 320x200x340 mm3 distortions can be successfully mapped to within the voxel resolution of the raw imaging data, whilst outside this volume, correction is still good but some systematic errors are present. The phenomenon of through-plane distortion (also known as 'slice warp') is examined in detail, and the perturbation it causes to the measurements is quantified and corrected. At the very edges of the region of support provided by the phantom, through-plane distortion is extreme and only partially corrected by the present method. Solutions to this problem are discussed. Both phantom and patient data demonstrate the efficacy of the gradient warp correction.
Microcavity engineering using plasma immersion ion implantation (2002)

Microcavities or bubbles formed by hydrogen and helium plasma immersion ion implantation (PIII) possess intriguing properties. For example, they emit light similar to porous silicon, but because they are buried, the optical properties are not affected by surface conditions such as those encountered by conventional porous silicon materials. These bubbles also form excellent internal gettering sites for metallic impurities and are stable even at high temperature. Last but not least, the ion-cut/bonding technology utilizing the mechanical stress created by these microcavities to achieve thin film transfer is used to fabricate silicon-on-insulator (SOI).
The apurinic/apyrimidinic endonuclease activity of Ape1/Ref-1 contributes to human glioma cell resistance to alkylating agents and is elevated by oxidative stress. (2002)

Alkylating agents are standard components of adjuvant chemotherapy for gliomas. We provide evidence here that Ape1/Ref-1, the major mammalian apurinic/apyrimidinic endonuclease (Ap endo), contributes to alkylating agent resistance in human glioma cells by incising DNA at abasic sites. We show that antisense oligonucleotides directed against Ape1/Ref-1 in SNB19, a human glioma cell line lacking O(6)-methylguanine-DNA-methyltransferase, mediate both reduction in Ape1/Ref-1 protein and Ap endo activity and concurrent reduction in resistance to methyl methanesulfonate and the clinical alkylators temozolomide and 1,3-(2-chloroethyl)-1-nitrosourea. An accompanying increase in the level of abasic sites indicates that the DNA repair activity of Ape1/Ref-1 contributes to resistance. Conversely, we also show that exposure of SNB19 cells to HOCl, a generator of reactive oxygen species (ROS), results in elevated Ape1/Ref-1 protein and Ap endo activity, enhanced alkylator resistance, and reduced levels of abasic sites. Given current evidence that heightened oxidative stress prevails within brain tumors, the finding that ROS increase resistance to clinical alkylators in glioma cells may have significance for the response of gliomas to alkylating agent-based chemotherapy. Our results may also be relevant to the design of therapeutic regimens using concurrent ionizing radiation (a generator of ROS) and alkylating agent-based chemotherapy.
Detecting Network Effects (2017)

Randomized experiments, or A/B tests, are the standard approach for evaluating the causal effects of new product features, i.e., treatments. The validity of these tests rests on the "stable unit treatment value assumption" (SUTVA), which implies that the treatment only affects the behavior of treated users, and does not affect the behavior of their connections. Violations of SUTVA, common in features that exhibit network effects, result in inaccurate estimates of the causal effect of treatment. In this paper, we leverage a new experimental design for testing whether SUTVA holds, without making any assumptions on how treatment effects may spill over between the treatment and the control group. To achieve this, we simultaneously run both a completely randomized and a cluster-based randomized experiment, and then we compare the difference of the resulting estimates. We present a statistical test for measuring the significance of this difference and offer theoretical bounds on the Type I error rate. We provide practical guidelines for implementing our methodology on large-scale experimentation platforms. Importantly, the proposed methodology can be applied to settings in which a network is not necessarily observed but, if available, can be used in the analysis. Finally, we deploy this design to LinkedIn's experimentation platform and apply it to two online experiments, highlighting the presence of network effects and bias in standard A/B testing approaches in a real-world setting.
Sand Fly Colony Crash Tentatively Attributed to Nematode Infestation (2020)

Maintenance of laboratory colonies of insects and other arthropod pests offers significant research advantages. The availability, age, sex, housing conditions, nutrition, and relative uniformity over time of biological material for research facilitate comparison of results between experiments that would otherwise be difficult or impossible. A laboratory research colony of Phlebotomus papatasi (Scopoli), old world sand flies, was maintained with high-colony productivity for a number of years, but within a relatively short (4-6 mo) time period, colony productivity declined from over 10,000 flies per week to less than 100 per week. Mites and nematodes were both visible in the larval medium; however, the mites had been present throughout high productivity periods; therefore, it seemed reasonable to investigate the nematodes. PCR amplification of 18S rRNA yielded a clean cDNA sequence identified by BLAST search as Procephalobus sp. 1 WB-2008 (Rhabditida: Panagrolaimidae) small subunit ribosomal RNA gene, GenBank EU543179.1, with 475/477 nucleotide identities. Nematode samples were collected and identified as Tricephalobus steineri, (Andrássy, 1952) Rühm, 1956 (Rhabditida: Panagrolaimidae) based on morphological characteristics of the esophagus and the male copulatory apparatus. Mites (Tyrophagus putrescentiae [Acariformes: Acaridae]) may have played an additional predatory role in the loss of sand fly colony productivity. We hypothesized that the origin of the nematode infestation was rabbit dung from a local rabbitry used in preparation of the larval medium. Colony productivity was fully restored within 3 mo (two sand fly generational periods) by replacement of the rabbit dung from a clean source for use to prepare sand fly larval medium.
Evidence From Men for Ovary-independent Effects of Genetic Risk Factors for Polycystic Ovary Syndrome (2021)

Genetic risk factors for PCOS have phenotypic consequences in men, indicating that they can act independently of ovarian function. Thus, PCOS in women may not always be a primary disorder of the ovaries.
CLARQ: A Dynamic ARQ Solution for Ultra-High Closed-Loop Reliability (2021)

Emerging wireless control applications demand for extremely high closed-loop reliability under strict latency constraints, which the conventional Automatic Repeat reQuest (ARQ) solutions with static schedules fail to provide. To overcome this issue and enable data-link layer error control for ultra reliable low-latency communication (URLLC) services, we propose a novel protocol: the Closed-Loop ARQ (CLARQ), which forces to accomplish an information exchange round within a fixed loop-back latency, and dynamically re-allocates the remaining resource between uplink and downlink slots upon the result of last uplink transmission. The proposed method guarantees to meet the latency requirement, while delivering high communication reliability and power efficiency. It can be efficiently offline optimized by means of dynamic programming techniques, and is capable of real-time deployment with a low-cost implementation based on look-up tables. Numerical evaluations have verified that CLARQ outperforms baselines with significantly improved closed-loop reliability and reduced energy consumption. Especially, over a Rayleigh channel with 0 dB mean SNR, it is able to provide a closed-loop error rate below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−7</sup> within 10 ms loop-back latency, which makes our proposal competitive for practical URLLC applications in future 5G-and-beyond networks.
Mass Spectrometry and Protein Analysis (2006)

Mass spectrometry is a central analytical technique for protein research and for the study of biomolecules in general. Driven by the need to identify, characterize, and quantify proteins at ever increasing sensitivity and in ever more complex samples, a wide range of new mass spectrometry-based analytical platforms and experimental strategies have emerged. Here we review recent advances in mass spectrometry instrumentation in the context of current and emerging research strategies in protein science.
Generalizable Embeddings with Cross-batch Metric Learning (2023)

Global average pooling (GAP) is a popular component in deep metric learning (DML) for aggregating features. Its effectiveness is often attributed to treating each feature vector as a distinct semantic entity and GAP as a combination of them. Albeit substantiated, such an explanation's algorithmic implications to learn generalizable entities to represent unseen classes, a crucial DML goal, remain unclear. To address this, we formulate GAP as a convex combination of learnable prototypes. We then show that the prototype learning can be expressed as a recursive process fitting a linear predictor to a batch of samples. Building on that perspective, we consider two batches of disjoint classes at each iteration and regularize the learning by expressing the samples of a batch with the prototypes that are fitted to the other batch. We validate our approach on 4 popular DML benchmarks.
Carcinoid heart disease. Clinical and echocardiographic spectrum in 74 patients. (1993)

The broad spectrum of carcinoid heart disease is detailed in this large series. This includes not only right-sided valvular lesions but also left-sided involvement, pericardial effusion, and myocardial metastases.
Study of Practical Use of Welding Consumables for Steel of Hot Dip Galvanizing Bath. (2000)

This study was carried out to select suitable welding methods and welding consumables used for constructing a galvanizing bath. In this report, these were selected in terms of the elevated temperature strength, the susceptibility of liquid metal embrittlement and corrosion resistance in liquid zinc.The base metal used was a carbon steel specialized for a galvanizing bath. The shielded metal arc (SMA) and gas shield arc weldings (GMA) were used with a covered electrode (E1) and solid and flux cored wires (F1, F2 and F3).The elevated temperature strength of all deposited metals were measured at the temperature range from room temperature to 600°C.Moreover, the notched bar tensile (NBT) test, where the bottom of notch was coated by liquid zinc, was performed at the temperature of 480°C to know the susceptibility of liquid metal embrittlement. Corrosion resistance was measured at the temperature of 450°C in molten zinc of practical bath.Strength at the elevated temperature of deposited metals by GMA welding was higher than that by SMA welding. The susceptibilities of liquid metal embrittlement of deposited metals became high in the order of E1, F3, F1 and F2. The susceptibilities of F1 and F3 were almost corresponded with that of the base metal. The susceptibility of liquid metal embrittlement at liquid zinc increased with an increase in the term of C+Si+Mn. Moreover, corrosion resistances of F1 and F2 in liquid zinc were higher than those of the base metal, E1 and F3. When the value of C+Si+Mn exceeds 1.7%, corrosion resistance of weld metal decreases.The solid wire, F3 was. selected as a candidate of welding consumable used for constructing a galvanizing bath from the present results.