gebhart/patrepeval huggingface dataset:
Practical Privacy-Preserving K-means Clustering (2020)

Abstract Clustering is a common technique for data analysis, which aims to partition data into similar groups. When the data comes from different sources, it is highly desirable to maintain the privacy of each database. In this work, we study a popular clustering algorithm (K-means) and adapt it to the privacypreserving context. Specifically, to construct our privacy-preserving clustering algorithm, we first propose an efficient batched Euclidean squared distance computation protocol in the amortizing setting, when one needs to compute the distance from the same point to other points. Furthermore, we construct a customized garbled circuit for computing the minimum value among shared values.We believe these new constructions may be of independent interest. We implement and evaluate our protocols to demonstrate their practicality and show that they are able to train datasets that are much larger and faster than in the previous work. The numerical results also show that the proposed protocol achieve almost the same accuracy compared to a K-means plain-text clustering algorithm.
Measurement of Q degradation due to polarisation mode dispersion using multiple importance sampling (2003)

Multiple importance-sampling (IS) is used to measure the Q degradation due to the polarisation mode dispersion generated by three programmable DGD elements with uniform polarisation coupling between sections. The measured Q-penalty probability distribution extends to &lt;10−17 with only 1800 experimental samples.
Power electronics education: courses and laboratory (2002)

This paper presents a detailed description of the undergraduate and graduate education in the field of power electronics. Suggested power electronics undergraduate and graduate curriculum along with key course contents are presented. An outline for the simulation and hardware laboratory as a supporting facility for effective power electronics education is also addressed.
Ground-state selection as a four-wave-mixing process (2006)

We study nonlinear relaxation of the excited state in a system with two levels and a continuum. The process is first simulated in a one-dimensional waveguide array described by the discrete nonlinear Schr\"odinger equation. The results are interpreted in terms of degenerate four-wave mixing between the eigenmodes and diffraction properties of the array. We also show analytically that the role of the continuum can be played by a third bound state, with linear loss that replaces the diffraction in the continuum. This model enables derivation of the energy transfer rate and other parameters of the process.
Precursor Ion (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
ChemInform Abstract: 8‐Aminocyclazocine Analogues: Synthesis and Structure—Activity Relationships. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Epitaxial graphene-encapsulated surface reconstruction of Ge(110) (2018)

Understanding and engineering the properties of crystalline surfaces has been critical in achieving functional electronics at the nanoscale. Employing scanning tunneling microscopy, surface x-ray diffraction, and high-resolution x-ray reflectivity experiments, we present a thorough study of epitaxial graphene (EG)/Ge(110) and report a Ge(110) ``6 \ifmmode\times\else\texttimes\fi{} 2'' reconstruction stabilized by the presence of epitaxial graphene unseen in group-IV semiconductor surfaces. X-ray studies reveal that graphene resides atop the surface reconstruction with a 0.34 nm van der Waals (vdW) gap and provides protection from ambient degradation.
Proximity Effects of the Selective Atomic Layer Deposition of Cobalt on the Nanoscale: Implications for Interconnects (2021)

The continued scaling of transistor sizes has motivated the need to replace Cu with alternate metals to minimize resistivity, with cobalt being of interest for both interconnect via metallization as well as emerging die-bonding processes. The atomic layer deposition of cobalt using Co(tBu2DAD)2 and tertiary-butyl amine has nearly infinite selectivity (>1000 cycles) on metallic vs insulating (SiO2 or low-k SiCOH dielectric) planar samples. However, on patterned samples, selectivity under identical atomic layer deposition (ALD) conditions is limited, due to the diffusion of molecularly adsorbed metal precursors from reactive to non-reactive surfaces. X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM) were employed to investigate the effects of process parameters on surface precursor diffusion to determine the mechanism of selectivity loss on the nanoscale. Top-down SEM and XPS spectra of a striped test pattern of Cu and SiO2 indicated that selective vapor-phase passivation of SiO2 improved the selectivity for deposition on Cu versus SiO2 by reducing the number of insulator defects that facilitated trapping of precursor molecules and subsequent Co nucleus growth. The remaining nuclei were present due to incomplete defect passivation. Conversely, near-perfect selectivity during Co ALD was obtained with the periodic annealing of the substrate, consistent with a low temperature reflow process, allowing for Co nuclei on SiO2 defects to merge with the metallic growth surface.
Spontaneous development of anti-hepatitis B virus envelope (anti-idiotypic) antibodies in animals immunized with human liver endonexin II or with the F(ab')2 fragment of anti-human liver endonexin II immunoglobulin G: evidence for a receptor-ligand-like relationship between small hepatitis B surface antigen and endonexin II (1994)

In a previous study, we have identified endonexin II (E-II) on human liver plasma membranes as a specific, Ca(2+)-dependent, small hepatitis B surface antigen (HBsAg)-binding protein. In this article, we describe the spontaneous development of anti-HBs antibodies in rabbits immunized with native or recombinant human liver E-II and in chickens immunized with the F(ab')2 fragment of rabbit anti-human liver E-II immunoglobulin G. Anti-HBs activity was not observed in rabbits immunized with rat liver E-II. Cross-reactivity of anti-E-II antibodies to HBsAg epitopes was excluded, since anti-HBs and anti-E-II activities can be separated by E-II affinity chromatography. The existence of an anti-idiotypic antibody is further demonstrated by competitive binding of human liver E-II and this antibody (Ab2) to small HBsAg, suggesting that Ab2 mimics a specific E-II epitope that interacts with small HBsAg. In addition, it was demonstrated that anti-HBs antibodies developed in rabbits after immunization with intact human liver E-II or in chickens after immunization with F(ab')2 fragments of rabbit anti-human liver E-II immunoglobulin G recognize the same epitopes on small HBsAg. These findings strongly indicate that human liver E-II is a very specific small HBsAg-binding protein and support the assumption that human liver E-II is the hepatitis B virus receptor protein.
3-D imaging and illustration of mouse intestinal neurovascular complex (2012)

Because of the dispersed nature of nerves and blood vessels, standard histology cannot provide a global and associated observation of the enteric nervous system (ENS) and vascular network. We prepared transparent mouse intestine and combined vessel painting and three-dimensional (3-D) neurohistology for joint visualization of the ENS and vasculature. Cardiac perfusion of the fluorescent wheat germ agglutinin (vessel painting) was used to label the ileal blood vessels. The pan-neuronal marker PGP9.5, sympathetic neuronal marker tyrosine hydroxylase (TH), serotonin, and glial markers S100B and GFAP were used as the immunostaining targets of neural tissues. The fluorescently labeled specimens were immersed in the optical clearing solution to improve photon penetration for 3-D confocal microscopy. Notably, we simultaneously revealed the ileal microstructure, vasculature, and innervation with micrometer-level resolution. Four examples are given: 1) the morphology of the TH-labeled sympathetic nerves: sparse in epithelium, perivascular at the submucosa, and intraganglionic at myenteric plexus; 2) distinct patterns of the extrinsic perivascular and intrinsic pericryptic innervation at the submucosal-mucosal interface; 3) different associations of serotonin cells with the mucosal neurovascular elements in the villi and crypts; and 4) the periganglionic capillary network at the myenteric plexus and its contact with glial fibers. Our 3-D imaging approach provides a useful tool to simultaneously reveal the nerves and blood vessels in a space continuum for panoramic illustration and analysis of the neurovascular complex to better understand the intestinal physiology and diseases.
R5 Human Immunodeficiency Virus Type 1 (HIV-1) Replicates More Efficiently in Primary CD4+T-Cell Cultures Than X4 HIV-1 (2004)

In this report, we present evidence that R5 human immunodeficiency virus type 1 (HIV-1) replicates more efficiently in primary CD4+ T cells than X4 HIV-1. By comparing CD3/CD28-costimulated CD4+ T-cell cultures infected by several X4 and R5 HIV-1 strains, we determined that R5-infected CD4+ T cells produce more virus over time than X4-infected CD4+ T cells. In the first comparison, we found that more cells were infected by the X4-tropic strain LAI than by the R5-tropic strain JR-CSF and yet that higher levels of viral production were detected in the R5-infected cultures. The differential viral production was partially due to the severe cytopathic effects of the X4 virus. We also compared cultures infected with the isogenic HIV-1 strains NL4-3 (X4) and 49.5 (R5). We found that fewer cells were infected by the R5 strain, and yet similar levels of viral production were detected in both infected cultures. Cell death played less of a role in the differential viral production of these strains, as the cell viability remained comparable in both X4- and R5-infected cultures over time. The final comparison involved the primary R5-tropic isolate KP1 and the primary dual-tropic isolate KP2. Although both strains infected similar numbers of cells and induced comparable levels of cytopathicity, viral production was considerably higher in the R5-infected culture. In summary, these data demonstrate that R5 HIV-1 has an increased capacity to replicate in costimulated CD4+ T cells compared to X4 HIV-1.
Physiological changes before dialysis treatments can potentially mediate the effects of extreme heat events on hospital admission risk (2020)

Typical thermoregulatory response to elevated temperatures among healthy individuals include reduced blood pressure and perspiration. However, individuals living with end-stage renal disease (ESRD) are susceptible to physiological fluctuations that may increase their risk of mortality. As such, the underlying mechanism for extreme heat-related hospital admissions among individuals with ESRD undergoing hemodialysis (HD) is relatively unclear. Traditional mediation analysis was used to decompose the total effect between extreme heat and hospital admissions. We hypothesize that the exposure-outcome pathway is mediated by systolic blood pressure before HD treatment (preSBP) and inter-dialytic weight gain (IDWG). This study used records from ESRD patients treated at Fresenius Kidney Care clinics from 2003 to 2012 (n= 7962). Calendar day- and location-specific temperature thresholds were calculated to identify extreme heat events (EHEs) during the study period. We fitted Cox proportional hazards models with time-dependent covariates to estimate the association between EHEs and hospitalization using varying lag structures (lag0, lag1, and lag2). We examined preSBP and IDWG as mediators using VanderWeele’s difference method for each lag structure. Extreme heat exposure for each lag structure increased the hazard risk (HR) of hospital admission after model adjustments (lag2: adjusted HR= 1.09, 95% confidence interval, 1.01- 1.19; lag1: 1.08, 0.99- 1.17; and lag0: 1.16, 1.07- 1.26). In lag1 models, preSBP and IDWG significantly (p&lt;0.05) mediated 22.54% and 1.81% of its adjusted association, respectively, and 42.16% when both are included. In lag0 models, IDWG significantly mediated -19.10% of its adjusted association, suggesting a potential protective pathway against same-day EHE effects. This work has provided a step forward to understanding potential physiological linkages between extreme heat and hospitalization. Concomitant changes in blood pressure and IDWG may have possible antagonistic effects on extreme heat-related admission. Such findings could be critical in discerning potential interventions to minimize the impact of extreme heat among ESRD patients.
Phosphanyl-Amino Complexes of Nickel(II): Synthesis and Structure (1998)

New neutral pentacoordinate nickel(II) complexes of the type [NiCl2(PR3)(P∩N)] [PR3 = PMe3, PMe2Ph, PMePh2; P∩N = 2-(diphenylphosphanyl)aniline (P∩NH2), N-methyl-2-(diphenylphosphanyl)aniline (P∩NHMe), N,N-dimethyl-2-(diphenylphosphanyl)aniline (P∩NMe2)], as well as cationic tetracoordinate nickel(II) complexes of the type [NiCl(PR3)(P∩N)]+ have been synthesized and characterized both in the solid state and in solution. Interesting X-ray structural data have been collected for each class of compounds, which show, inter alia, that the pentacoordinate neutral complexes can be isolated in two different molecular forms, namely square-pyramidal or bipyramidal-trigonal.
Adalimumab safety and mortality rates from global clinical trials of six immune-mediated inflammatory diseases (2009)

Based on 10 years of clinical trial experience across six diseases, this safety report and the established efficacy of adalimumab in these diseases provide the foundation for a better understanding of its benefit-risk profile.
A data-analysis pipeline for large-scale gene expression analysis (2000)

In this article we describe a method for characterization of large cDNA clone libraries based on oligonucleotide fingerprints (OFPs). The main advantage of this technique lies in that, without sequencing, each clone is tagged in an almost unique way, which has a couple of interesting applications, e.g. clustering of clones that belong to the same gene or gene family followed by sequencing of representative clones for each cluster. Moreover, small clusters are likely to represent rarely expressed genes, which are difficult to find by common approaches. We will demonstrate that in the EST projects carried out in our lab the global redundancy is very low compared to similar projects described in the literature, and simultaneously the number of unknown (novel) genes detected using this method is very high. In addition OFPs can be used directly for data base mining, since the sequences of the oligos matching a specific clone is known Recent results are presented, which underline the potential of our method in finding novel genes or genes homologous to known data. We will also address future applications in gene expression profiling, and give an outline of the various bioinformatics tools, which have been developed so far and which are used for automated data processing and analysis.
CuH-Catalyzed Regio- and Enantioselective Hydrocarboxylation of Allenes: Towards Carboxylic Acids with Acyclic Quaternary Centers (2021)

We report a method to prepare &lt;i&gt;α&lt;/i&gt;-chiral carboxylic acid derivatives, including those bearing all-carbon quaternary centers, through an enantioselective CuH-catalyzed hydrocarboxylation of allenes with a commercially available fluoroformate. A broad range of heterocycles and functional groups on the allenes were tolerated in this protocol, giving enantioenriched &lt;i&gt;α&lt;/i&gt;-quaternary and tertiary carboxylic acid derivatives in good yields with exclusive branched regioselectivity. The synthetic utility of this approach was further demonstrated by derivatization of the products to afford biologically important compounds, including the antiplatelet drug indobufen.
Engrailed‐1 induces long‐lasting behavior benefit in an experimental Parkinson primate model (2019)

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Combined Magnesia, Ceria and Nickel catalyst supported over γ-Alumina Doped with Titania for Dry Reforming of Methane (2019)

This study investigated dry reforming of methane (DRM) over combined catalysts supported on γ-Al2O3 support doped with 3.0 wt. % TiO2. Physicochemical properties of all catalysts were determined by inductively coupled plasma/mass spectrometry (ICP-MS), nitrogen physisorption, X-ray diffraction, temperature programmed reduction/oxidation/desorption/pulse hydrogen chemisorption, thermogravimetric analysis, and scanning electron microscopy. Addition of CeO2 and MgO to Ni strengthened the interaction between the Ni and the support. The catalytic activity results indicate that the addition of CeO2 and MgO to Ni did not reduce carbon deposition, but improved the activity of the catalysts. Temperature programmed oxidation (TPO) revealed the formation of carbon that is mainly amorphous and small amount of graphite. The highest CH4 and CO2 conversion was found for the catalyst composed of 5.0 wt. % NiO-10.0 wt. % CeO2/3.0 wt. %TiO2-γ-Al2O3 (Ti-CAT-II), resulting in H2/CO mole ratio close to unity. The optimum reaction conditions in terms of reactant conversion and H2/CO mole ratio were achieved by varying space velocity and CO2/CH4 mole ratio.
Smart Nanosensors for In-Situ Temperature Measurement in Fractured Geothermal Reservoirs (2011)

Temperature measurements are important for the optimum development and energy extraction of enhanced and conventional geothermal resources. Currently, temperature is only measured in the wellbore, as no technology exists to provide information far into the formation. The development of temperature-sensitive nanotracers could allow for such measurements virtually anywhere in the formation. This paper describes the synthesis and characterization of two types of temperature-sensitive particles: tin-bismuth alloy nanoparticles and silica nanoparticles with covalently linked dye. Three experiments were performed with the tin-bismuth nanoparticles: a heating test, a slim-tube injection, and a Berea sandstone core injection. Both the heated sample and the effluent samples were characterized using Scanning Electron Microscopy (SEM) and Dynamic Light Scattering (DLS). A heating experiment was also performed with the dye-linked silica particles, and the heated sample was characterized using SEM imaging and fluorimetry. The feasibility of using nanomaterials as tracers to infer reservoir properties in-situ is addressed.
Transfer Learning and Meta Learning Based Fast Downlink Beamforming Adaptation (2020)

This paper studies fast adaptive beamforming optimization for the signal-to-interference-plus-noise ratio balancing problem in a multiuser multiple-input single-output downlink system. Existing deep learning based approaches to predict beamforming rely on the assumption that the training and testing channels follow the same distribution which may not hold in practice. As a result, a trained model may lead to performance deterioration when the testing network environment changes. To deal with this task mismatch issue, we propose two offline adaptive algorithms based on deep transfer learning and meta-learning, which are able to achieve fast adaptation with the limited new labelled data when the testing wireless environment changes. Furthermore, we propose an online algorithm to enhance the adaptation capability of the offline meta algorithm in realistic non-stationary environments. Simulation results demonstrate that the proposed adaptive algorithms achieve much better performance than the direct deep learning algorithm without adaptation in new environments. The meta-learning algorithm outperforms the deep transfer learning algorithm and achieves near optimal performance. In addition, compared to the offline meta-learning algorithm, the proposed online meta-learning algorithm shows superior adaption performance in changing environments.
Low signal strength enhances the antitumor activity of human CAR Th17 cells (2016)

Abstract We reported the antitumor activity of human Th17 cells (engineered to express a chimeric antigen receptor (CAR) that recognizes mesothelin) regresses large human mesothelioma tumors when infused into mice, but it remains unknown what type and what level of co-signal strength impacts their functional fate and antitumor activity. To address this question, human Th17 cells were activated with a high (3 beads: 1 T cell), medium (1:10) or low (1:100) signal via CD3-beads coated with either CD28 or ICOS agonists. We discovered Th17 cells activated with low ICOS signal were highly multifunctional (IL-17A, IFN-γ, IL-2 and IL-22) and possessed a less differentiated phenotype (high CD62L and CD45RA expression) than cells activated with a high ICOS signal. In comparison to low ICOS signal strength, Th17 cells activated with low CD28 signal strength were poorly functional and terminally differentiated. Of clinical significance, in two distinct tumor models (human mesothelioma and murine melanoma), we found that Th17 cells regressed large tumors to a better extent when primed with a low or medium ICOS signal strength compared to if they were activated with a high ICOS signal strength, or with any level of CD28 signal strength. Our data is compelling given that most ACT clinical trials use high CD3/CD28 activation to expand patients’ cells. Specifically, our work suggests the use of a low bead to T cell ratio will result in a more simple and clinically feasible method to expand highly therapeutic T cells for the clinic.