gebhart/patrepeval huggingface dataset:
Locality-Aware Content Distribution (2004)

We present the design and deployment of the Julia locality aware content distribution algorithm. Our novel contributions are locality aware node selection, forming a dynamically changing topology and division of the file into varying length chunks based on locality of the transfer. We present a large scale WAN deployment on over than 250 PlanetLab machines. We show that our technique can improve average download speed up by a factor of two compared with non locality aware solutions. Finally we compare our prototype’s performance with that of BitTorrent, presently one of the most stable and efficient deployed content dissemination tools. 1
A New Workflow to Study the Impact of Artificial Maturations on the Petrophysical Properties of Unconventional Shale Rocks (2022)

Abstract Multiple challenges are associated with the characterization and development of unconventional shale reservoirs. The petrophysical properties play significant roles in hydrocarbon production from unconventional reservoirs. Several techniques can be used to determine the petrophysical properties such as routine core analysis, nuclear magnetic resonance (NMR), and dielectric techniques. This study presents an effective workflow to characterize the petrophysical properties of unconventional shales at different maturation stages. In this study, the conducted measurements are X-ray diffraction (XRD) analysis, Rock-Eval pyrolysis, helium porosity, NMR, and dielectric experiments. The rock samples were prepared for the measurements by drying the samples under a vacuum. In addition, the samples were artificially maturated using a muffle furnace at different temperatures and heating times. The impact of shale maturation on the petrophysical properties was captured by evaluating the rock properties after each maturation stage. Results show that the shale samples have a TOC of 17.5 wt.% on average, and a hydrogen index (HI) of 809, indicating that the samples are belonging to kerogen type I. The mineralogical analysis indicates that the used shale samples have a calcite percentage of around 59.9%. Moreover, the artificial maturation led to reducing the total organic content, due to the conversion of organic matter into hydrocarbon fluids. NMR and dielectric measurements showed that the shale porosity system was altered due to artificial maturation. The real dielectric constant was reduced indicating a reduction in the kerogen percentages. The cumulative probability density was increased after the maturation, revealing the shale porosity was increased which could be attributed to the dissolution of kerogen during the maturation process. Ultimately, this study improves our understanding of characterizing unconventional shale formations. Also, a reliable workflow is proposed for a better characterization of the unconventional formations by integrating routine core analysis, Rock-Eval, NMR, and dielectric techniques. Such workflow can pave the way to introduce a downhole technique to characterize unconventional resources more effectively.
Metropolis Evaluation of the Hartree–Fock Exchange Energy (2014)

We examine the possibility of using a Metropolis algorithm for computing the exchange energy in a large molecular system. Following ideas set forth in a recent publication (Baer, Neuhauser, and Rabani, Phys. Rev. Lett. 111, 106402 (2013)) we focus on obtaining the exchange energy per particle (ExPE, as opposed to the total exchange energy) to a predefined statistical error and on determining the numerical scaling of the calculation achieving this. For this we assume that the occupied molecular orbitals (MOs) are known and given in terms of a standard Gaussian atomic basis set. The Metropolis random walk produces a sequence of pairs of three-dimensional points (x,x'), which are distributed in proportion to ρ(x,x')(2), where ρ(x,x') is the density matrix. The exchange energy per particle is then simply the average of the Coulomb repulsion energy υC(|x-x'|) over these pairs. To reduce the statistical error we separate the exchange energy into a short-range term that can be calculated deterministically in a linear scaling fashion and a long-range term that is treated by the Metropolis method. We demonstrate the method on water clusters and silicon nanocrystals showing the magnitude of the ExPE standard deviation is independent of system size. In the water clusters a longer random walk was necessary to obtain full ergodicity as Metropolis walkers tended to get stuck for a while in localized regions. We developed a diagnostic tool that can alert a user when such a situation occurs. The calculation effort scales linearly with system size if one uses an atom screening procedure that can be made numerically exact. In systems where the MOs can be localized efficiently the ExPE can even be computed with "sublinear scaling" as the MOs themselves can be screened.
Design and analysis of MIMO antennas for UWB communications (2010)

International audience
Epitaxy of SrTiO<sub>3</sub> on Silicon: The Knitting\nMachine Strategy (2016)

SrTiO&lt;sub&gt;3&lt;/sub&gt; (STO) crystalline layers grown on Si open unique\nperspectives for the monolithic integration of functional oxides in\nsilicon-based devices, but their fabrication by molecular beam epitaxy\n(MBE) is challenging due to unwanted interfacial reactions. Here we\nshow that the formation of single-crystal STO layers on Si by MBE\nat the moderate growth temperature imposed by these interface reactions\nresults from the crystallization of a partially separated amorphous\nmixture of SrO and TiO&lt;sub&gt;2&lt;/sub&gt; activated by an excess of Sr. We\nidentify the atomic pathway of this mechanism and show that it leads\nto an antiphase domain morphology. On the basis of these results,\nwe suggest and test alternative STO growth strategies to avoid antiphase\nboundary formation and significantly improve the STO structural quality.\nThe understanding provided by these results offers promising prospects\nto crystallize perovskite oxides on semiconductors at moderate temperature\nand circumvent the issue of parasitic interface reactions.
High-throughput screening of drug-binding dynamics to HERG improves early drug safety assessment (2012)

The use of computational models to predict drug-induced changes in the action potential (AP) is a promising approach to reduce drug safety attrition but requires a better representation of more complex drug-target interactions to improve the quantitative prediction. The blockade of the human ether-a-go-go-related gene (HERG) channel is a major concern for QT prolongation and Torsade de Pointes risk. We aim to develop quantitative in-silico AP predictions based on a new electrophysiological protocol (suitable for high-throughput HERG screening) and mathematical modeling of ionic currents. Electrophysiological recordings using the IonWorks device were made from HERG channels stably expressed in Chinese hamster ovary cells. A new protocol that delineates inhibition over time was applied to assess dofetilide, cisapride, and almokalant effects. Dynamic effects displayed distinct profiles for these drugs compared with concentration-effects curves. Binding kinetics to specific states were identified using a new HERG Markov model. The model was then modified to represent the canine rapid delayed rectifier K(+) current at 37°C and carry out AP predictions. Predictions were compared with a simpler model based on conductance reduction and were found to be much closer to experimental data. Improved sensitivity to concentration and pacing frequency variables was obtained when including binding kinetics. Our new electrophysiological protocol is suitable for high-throughput screening and is able to distinguish drug-binding kinetics. The association of this protocol with our modeling approach indicates that quantitative predictions of AP modulation can be obtained, which is a significant improvement compared with traditional conductance reduction methods.
Reactivity patterns and epitope specificities of anti-Cryptococcus neoformans monoclonal antibodies by enzyme-linked immunosorbent assay and dot enzyme assay (1997)

Cryptococcus neoformans glucuronoxylomannans (GXM) are capsular polysaccharides important for virulence in cryptococcosis. This study used dot enzyme assays (DEA) and enzyme-linked immunosorbent assays (ELISA) to determine the reactivity patterns of 21 murine monoclonal antibodies (MAbs) with structurally defined GXMs from five serotypes. The MAbs were categorized into eight groups on the basis of DEA and five groups on the basis of ELISA. MAbs 302, 339, and 439 were studied extensively for their binding to various native and chemically modified GXMs. Quantitative variation in the inhibitory effects of GXMs on the binding of MAbs 302, 339, and 439 were observed by competitive ELISA. O-Deacetylation of serotype A, B, and D GXM resulted in the complete loss of their inhibitory properties. Carboxyl group reduction of GXMs from serotypes A and D resulted in a significant decrease of inhibitory activity for MAb. Xylomannans and methyl glycosides exhibited no detectable inhibitory activity on MAb binding to GXM. The results indicate (i) the existence of five to eight MAb-defined distinct epitopes in C. neoformans GXM that can elicit antibody responses, (ii) MAb detection of antigenic variation within GXMs assigned to a particular serotype, (iii) good correspondence between the patterns of MAb reactivities and polyclonal rabbit factor sera, (iv) good agreement between MAb molecular structure and serotype reactivity, and (v) a dependence of the serotype reactivity profile for a given MAb on the technique used to measure binding.
Classification of human liposarcoma and lipoma using ex vivo proton NMR spectroscopy (1999)

Prognostication in patients with liposarcoma is a complex and controversial subject based on recognition of lipoblasts, adipocyte nuclear atypia, and qualitative estimations of cellularity and cell size. We show here that for 30 patients with liposarcoma and 5 patients with lipoma, spectral differences on high-resolution, magic angle spinning proton nuclear magnetic resonance (hr-MAS 1H-NMR) spectroscopy relate to known biochemical changes and correlate with adipocyte tissue differentiation, histologic cell type, and cellularity. The NMR-visible level of triglyceride is shown to correlate with liposarcoma differentiation, since the triglyceride level in well-differentiated liposarcoma is 33-fold higher on average than for myxoid/round cell liposarcoma, which in turn is 6-fold higher than the dedifferentiated and/or pleomorphic subtypes. The NMR-visible phosphatidylcholine level serves as an estimate of total tissue cell membrane phospholipid mass and was found to correlate with liposarcoma subtype. Pleomorphic liposarcoma, the most aggressive and metastatic subtype, was found to have a threefold increase in NMR-visible phosphatidylcholine level compared with dedifferentiated liposarcoma. The level of NMR-visible phosphatidylcholine was twofold greater in well-differentiated liposarcoma compared with lipoma and was threefold larger for the hypercellular myxoid/round cell subtype compared with the pure myxoid histology. Thus, NMR-derived parameters of tissue lipid may be used for objective distinction of liposarcoma histologic subtype/grade and lipoma from liposarcoma. These biochemical parameters may ultimately improve prognostication in patients with liposarcoma.
Room-temperature NIR phosphorescence of new iridium (III) complexes with ligands derived from benzoquinoxaline (2006)

A new series of new iridium (III) complexes (15) bearing ligands derived from benzoquinoxaline were designed and synthesized. X-ray structural analyses of 1 reveal a distorted octahedral geometry around the Ir atom in which the pyrazolate chelate is located opposite to the cis-oriented carbon donor atoms of benzoquinoxaline, while the benzoquinoxaline ligands adopt an eclipse configuration and their coordinated nitrogen atoms and carbon adopt trans- and cis-orientation, respectively. Complexes 15 exhibit moderate NIR phosphorescence with peak maxima located at around 910930 nm. As supported by the TDDFT approach, the transition mainly involves benzoquinoxaline 3 ππ* intraligand charge transfer (ILCT) and metal (Ir) to benzoquinoxaline charge transfer (MLCT) of which the spectroscopy and dynamics of relaxation have been thoroughly investigated. The relatively weak NIR emission can be tentatively rationalized by the low energy gap of which the radiationless deactivation may be governed by nearly temperature-independent, weak-bonding motions in combination with a minor channel incorporating small torsional motions associated with phenyl ring in the benzoquinoxaline sites.Key words: phosphorescence, NIR, iridium, benzoquinoxaline, isoquinoline, bipyridine, pyrazolate, acetylacetonate.
A statistical field prediction model for urban environment (2003)

A statistical approach to the study and the prediction of urban propagation is presented. The method is based on a "statistical ray tracing" approach where the statistical characteristics of the multipath are derived by analytical processing from the statistical characteristics of the environment. Thanks to the adopted approach, the model does not require a detailed, site-specific description of the environment, nor a high computation time as required by methods such as traditional ray tracing tools. Also, it is more complete and accurate than conventional models such as Hata-like models.
TCR-mimic bispecific antibodies to target the HIV-1 reservoir (2022)

HIV-1 infection is incurable due to the persistence of the virus in a latent reservoir of resting memory CD4+ T cells. “Shock-and-kill” approaches that seek to induce HIV-1 gene expression, protein production, and subsequent targeting by the host immune system have been unsuccessful due to a lack of effective latency-reversing agents (LRAs) and kill strategies. In an effort to develop reagents that could be used to promote killing of infected cells, we constructed T cell receptor (TCR)-mimic antibodies to HIV-1 peptide-major histocompatibility complexes (pMHC). Using phage display, we panned for phages expressing antibody-like variable sequences that bound HIV-1 pMHC generated using the common HLA-A*02:01 allele. We targeted three epitopes in Gag and reverse transcriptase identified and quantified via Poisson detection mass spectrometry from cells infected in vitro with a pseudotyped HIV-1 reporter virus (NL4.3 dEnv). Sequences isolated from phages that bound these pMHC were cloned into a single-chain diabody backbone (scDb) sequence, such that one fragment is specific for an HIV-1 pMHC and the other fragment binds to CD3ε, an essential signal transduction subunit of the TCR. Thus, these antibodies utilize the sensitivity of T cell signaling as readouts for antigen processing and as agents to promote killing of infected cells. Notably, these scDbs are exquisitely sensitive and specific for the peptide portion of the pMHC. Most importantly, one scDb caused killing of infected cells presenting a naturally processed target pMHC. This work lays the foundation for a novel therapeutic killing strategy toward elimination of the HIV-1 reservoir.
Identification of Novel Biomarkers in Seasonal Allergic Rhinitis by Combining Proteomic, Multivariate and Pathway Analysis (2011)

We identified several novel biomarkers for GC treatment response in SAR with combined proteomics, multivariate and pathway analysis. The analytical principles may be generally applicable to identify biomarkers in clinical studies of complex diseases.
Secreted venom allergen-like proteins of helminths: Conserved modulators of host responses in animals and plants (2018)

Despite causing considerable damage to host tissue at the onset of parasitism, invasive helminths establish remarkably persistent infections in both animals and plants. Secretions released by these obligate parasites during host invasion are thought to be crucial for their persistence in infection. Helminth secretions are complex mixtures of molecules, most of which have unknown molecular targets and functions in host cells or tissues. Although the habitats of animal- and plant-parasitic helminths are very distinct, their secretions share the presence of a structurally conserved group of proteins called venom allergen-like proteins (VALs). Helminths abundantly secrete VALs during several stages of parasitism while inflicting extensive damage to host tissue. The tight association between the secretion of VALs and the onset of parasitism has triggered a particular interest in this group of proteins, as improved knowledge on their biological functions may assist in designing novel protection strategies against parasites in humans, livestock, and important food crops.
Mixed Protonic-Electronic Conductivity of SrCe 1−x Pr x O 3− δ (2021)

Protonic conductors are gaining use in solid oxide fuel cells (SOFCs) and electrolysis cells (SOECs) as well as for H 2 separation membranes. However, for SOFC/SOEC electrode and membrane applications their performance is limited by low electronic conductivity. One of the most promising classes of ceramic proton conductors, perovskites, have highly-tunable compositions allowing for the optimization of both ionic and electronic conductivity. In this work Pr-doped SrCeO 3 was studied over a wide range of oxygen partial pressures ( p O 2 ’s) and temperatures to determine its defect properties and conductivity. Under reducing conditions Pr-doped SrCeO 3 was found to be chemically and structurally stable, with an optimal Pr doping level of 10%. This composition shows greater conductivity compared to previously reported Eu-doped SrCeO 3 . Under low p O 2 Pr-doped SrCeO 3 exhibited n -type behavior as conductivity increased with decreasing p O 2 , suggesting that the electronic conductivity of SrCeO 3 is significantly enhanced by Pr doping. Under high p O 2 conditions, Pr-doped SrCeO 3 exhibited p -type conductivity with higher conductivity in the presence of water affirming its protonic conductivity. This work validates the use of Pr as a means of enhancing electronic conductivity in proton conducting perovskites.
<title>Finding optimal convex gray-scale structuring elements for morphological multiscale representation</title> (1996)

Recent papers in multiscale morphological filtering, particularly, have renovated the interest in signal representation via multiscale openings. Although most of the analysis was done with flat structuring elements, extensions to grayscale structuring elements (GSE) are certainly possible. In fact, we have shown that opening a signal with convex and symmetric GSE does not introduce additional zero-crossings as the filter moves to a coarser scales. However, the issue of finding an optimal GSE is still an open problem. In this paper, we present a procedure to find an optimal GSE under the least mean square (LMS) algorithm subject to three constraints: The GSE must be convex, symmetric, and non-negative. The use of the basis functions simplifies the problem formulation. In fact, we show that the basis functions for convex and symmetric GSE are concave and symmetric, thus alternative constraints are developed. The results of this algorithm are compared with our previous work.
ChemInform Abstract: Heteroarylation of Azine N‐Oxides. (2012)

Abstract The process is highly efficient for the preparation of various heterobiaryl structures.
Computationally efficient blood vessels segmentation in fundus image on shared memory parallel machines (2018)

Blood vessels segmentation in fundus image is a requiring step in order to detect retinopathies. A higher performing segmentation was been proposed in [12]. It consists at three dependent stages: Provide two binary images to extract wide vessels, compute features of the remaining pixels on binary images in order to extract fine vessels, and then combine both wide and fine vessels. The segmentation execution time is about 3-12 seconds when it is performed with fundus image having resolutions between 768*584 and 999*960. These latest resolutions are quite smaller than ones provided by actual retinograph, which leads to a higher rise on execution time. In this paper, we propose a parallelism strategy of the segmentation approach for implementation in Shared Memory Parallel Machine (SMPM). First, both binary images are provided in parallel. Thereafter, features processing is split according to their computational complexities. At the later stage, wide vessels and fine vessels images are subdivided adequately in the objective of a parallel combination. The parallel strategy is implemented using OpenCV and then assessed on STARE public data sets. Experimental analyses of execution time and efficiency are presented and discussed.
Time-Frequency Modulation Diversity to Combat Periodic Impulsive Noise in Narrowband Powerline Communications (2015)

Non-Gaussian noise/interference severely limits communication performance of narrowband powerline communication (PLC) systems. Such noise/interference is dominated by periodic impulsive noise whose statistics varies with the AC cycle. The periodic impulsive noise statistics deviates significantly from that of additive white Gaussian noise, thereby causing dramatic performance degradation in conventional narrowband PLC systems. In this paper, we propose a robust transmission scheme and corresponding receiver methods to combat periodic impulsive noise in OFDM-based narrowband PLC. Towards that end, we propose (1) a time-frequency modulation diversity scheme at the transmitter and a diversity demodulator at the receiver to improve communication reliability without decreasing data rates; and (2) a semi-online algorithm that exploits the sparsity of the noise in the frequency domain to estimate the noise power spectrum for reliable decoding at the diversity demodulator. In the simulations, compared with a narrowband PLC system using Reed-Solomon and convolutional coding, whole-packet interleaving and DBPSK/BPSK modulation, our proposed transceiver methods achieve up to 8 dB gains in E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> with convolutional coding and a smaller-sized interleaver/deinterleaver.
Norepinephrine Transporter in Major Depressive Disorder: A PET Study (2016)

These findings revealed altered norepinephrine transmission in patients with major depressive disorder, suggesting that this alteration could be related to attention in this patient population.