gebhart/patrepeval huggingface dataset:
Timing Prediction for Service-Based Applications Mapped on Linux-Based Multi-core Platforms (2018)

We develop a model-based approach to predict timing of service-based software applications on Linux-based multi-core platforms for alternative mappings (affinity and priority settings). Service-based applications consist of communicating sequential (Linux) processes. These processes execute functions (also called services), but can only execute them one at a time. Models are inferred automatically from execution traces to enable timing optimization of existing (legacy) systems. Our approach relies on a linear progress approximation of functions. We compute the expected share of each function based on the mapping (affinity and priority) parameters and the functions that are currently active. We validate our models by carrying out a controlled lab experiment consisting of a multi-process pipelined application mapped in different ways on a quadcore Intel i7 processor. A broad class of affinity and priority settings is fundamentally unpredictable due to Linux binding policies. We show that predictability can be achieved if the platform is partitioned in disjoint clusters of cores such that i) each process is bound to such a cluster, ii) processes with non real-time priorities are bound to singleton clusters, and iii) all processes bound to a non-singleton cluster have different real-time priorities. For mappings using singleton clusters with niceness priorities only, our model predicts execution latencies (for each pipeline iteration) with errors less than 5% relative to the measured execution times. For mappings using a non-singleton cluster (with different real-time priorities) relative errors of less than 2% are obtained. When real-time and niceness priorities are mixed, we predict with errors of 7%.
Selective Electrocatalytic H<sub>2</sub>O<sub>2</sub> Generation by Cobalt@N‐Doped Graphitic Carbon Core–Shell Nanohybrids (2019)

Electrocatalytic oxygen reduction (ORR) is an emerging synthetic strategy to prepare H<sub>2</sub> O<sub>2</sub> in a sustainable fashion. N-doped graphitic carbon with embedded cobalt nanoparticles was selected as an advanced material able to selectively trigger the ORR to form H<sub>2</sub> O<sub>2</sub> with a faradaic efficiency of almost 100 % at very positive applied potentials. The production of H<sub>2</sub> O<sub>2</sub> proceeded with high rates as calculated by bulk electrolysis (49 mmol g<sup>-1</sup> h<sup>-1</sup> ) and excellent current densities (≈-0.8 mA cm<sup>-2</sup> at 0.5 V vs. reversible hydrogen electrode). The totally selective behavior depended on the combination of concomitant material features, such as the textural properties, the nature of the metal, the distribution of N moieties, the acidic environment, and the applied potential.
Laboratory Findings Associated With Severe Illness and Mortality Among Hospitalized Individuals With Coronavirus Disease 2019 in Eastern Massachusetts (2020)

In this cohort, specific admission laboratory studies in concert with sociodemographic features and prior diagnosis facilitated risk stratification among individuals hospitalized for COVID-19.
Tumour cell characteristics and microenvironment composition correspond to clinical presentation in newly diagnosed nodular lymphocyte‐predominant Hodgkin lymphoma (2022)

Different studies have characterized the microenvironment and its prognostic impact in classic Hodgkin lymphoma whereas such analyses are pending for nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL). We thus investigated characteristics of tumour cells and microenvironment in NLPHL and evaluated possible correlations with the clinical presentation. Lymph node samples from 152 NLPHL patients who had first-line treatment within the randomized German Hodgkin Study Group HD16-HD18 trials were available and analysed with regard to IgD status and nuclear size of the tumour cells as well as presence of PD1-positive follicular T helper cells and CD163-positive macrophages in the microenvironment. While large tumour cell nuclei and high numbers of PD1-positive follicular T helper cells in the microenvironment were more common in patients presenting with early/intermediate stages than in patients with advanced-stage disease (p < 0.0001, unpaired t-test; p = 0.0022, Mann-Whitney test), no differences between risk groups were observed in terms of the IgD status of the tumour cells and the content of CD163-positive macrophages in the microenvironment. PD1-positive follicular T helper cells were present in both cases with typical and variant growth patterns and rosetting around the tumour cells was observed in 96% of patients, indicating an important role of PD1-positive follicular T helper cells in NLPHL.
Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding (2012)

Oncidium is an important ornamental plant but the study of its functional genomics is difficult. Erycina pusilla is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period, and its ability to complete its life cycle in vitro make E. pusilla a good model candidate and parent for hybridization for orchids. Although genetic information remains limited, systematic molecular analysis of its chloroplast genome might provide useful genetic information. By combining bacterial artificial chromosome (BAC) clones and next-generation sequencing (NGS), the chloroplast (cp) genome of E. pusilla was sequenced accurately, efficiently and economically. The cp genome of E. pusilla shares 89 and 84% similarity with Oncidium Gower Ramsey and Phalanopsis aphrodite, respectively. Comparing these 3 cp genomes, 5 regions have been identified as showing diversity. Using PCR analysis of 19 species belonging to the Epidendroideae subfamily, a conserved deletion was found in the rps15-trnN region of the Cymbidieae tribe. Because commercial Oncidium varieties in Taiwan are limited, identification of potential parents using molecular breeding method has become very important. To demonstrate the relationship between taxonomic position and hybrid compatibility of E. pusilla, 4 DNA regions of 36 tropically adapted Oncidiinae varieties have been analyzed. The results indicated that trnF-ndhJ and trnH-psbA were suitable for phylogenetic analysis. E. pusilla proved to be phylogenetically closer to Rodriguezia and Tolumnia than Oncidium, despite its similar floral appearance to Oncidium. These results indicate the hybrid compatibility of E. pusilla, its cp genome providing important information for Oncidium breeding.
Probable capacity of 3.5-inch magneto-optical disk using trilayer double-mask magnetically induced super-resolution media (1999)

This paper discusses the probable capacity of 3.5-in magneto-optical (MO) disks using trilayer double-mask magnetically induced super resolution (MSR) media and a conventional optical system. We measured the bit error rate of the double-mask MSR media on a land/groove substrate with a track pitch of 0.6 /spl mu/m. We obtained bit error rates as low as 1e-7 for a minimum bit length of 0.24 /spl mu/m. The recording power margin was /spl plusmn/11.3% and the tilt margin was /spl plusmn/0.7/spl deg/. These results indicate that a capacity of over 2.4 GB is possible for a 3.5-in MO disk using an optical head with a 685-nm laser diode having a lens numerical aperture of 0.55. The capacity corresponds to an areal density of 4.48 Gbit/in/sup 2/.
Femtosecond 3D IR spectroscopy (2006)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text F. Ding, E. C. Fulmer, and M. T. Zanni, "Femtosecond 3D IR spectroscopy," in 15th International Conference on Ultrafast Phenomena, OSA Technical Digest Series (CD) (Optica Publishing Group, 2006), paper ThE14. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Double-Pass PBS-Integrated Coherent Mixer Using Silica-based PLC (2010)

A coherent mixer with double-pass polarization-beam splitters integrated in silica-based PLC is newly developed. It is experimentally confirmed that the developed PLC-chip successfully works in the receiver for 40-Gbit/s dual-polarization quadrature phase-shift keying signal.
On the potential of ultrasound elastography for pressure ulcer early detection (2011)

Experiments demonstrated that ultrasound elastography is a promising technique for pressure ulcer detection, especially at an early stage of the pathology, when the disease is still visually undetectable. In the absence of any gold standard method, this is also a first step toward the development of a quantitative technique.
High-Power Digital Transmitters for Wireless Infrastructure Applications (A Feasibility Study) (2022)

Fully digital transmitters (DTXs) have the potential of replacing analog-intensive transmitter (TX) line-ups in future massive multiple-input and multiple-output (mMIMO) systems since they hold the promise of higher system integration level and energy efficiency. DTX operation so far has been limited to low RF output powers. This article introduces a concept that enables high-power DTX operation. A DTX demonstrator targeting both high output power and high efficiency is realized as a proof of concept. It is based on a custom <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${V_{T}}$ </tex-math></inline-formula> -shifted laterally-diffused MOS (LDMOS) technology, which is utilized to implement a segmented high-power output stage operated in class-BE. A low-voltage high-speed 40-nm CMOS controller drives the individual output stage segments at gigahertz rates. Measurements show the promising results for the proposed high-power DTX concept and provide valuable lessons for future DTX implementations.
Tandem Gold-Catalyzed Dehydrative Cyclization/Diels–Alder Reactions: Facile Access to Indolocarbazole Alkaloids (2015)

A gold-catalyzed synthesis of cyclic 2-oxodienes from readily prepared propargyl alcohols and the subsequent Diels-Alder reaction are reported. The dehydrative cyclization reactions proceeded smoothly, and the dienes formed in situ were demonstrated to undergo cycloaddition with a variety of dienophiles. This method offers a new strategy for the synthesis of indolocarbazole alkaloids, whereby the convergent synthetic design allows for differentiation between the indole nitrogens.
Performance evaluation of an optical hybrid switch with circuit queued reservations and circuit priority preemption (2006)

We provide here a new loss model for an optical hybrid switch that can function as an optical burst switch and/or optical circuit switch. Our model is general as it considers an implementation whereby some of the circuits have preemptive priority over bursts and others are allowed to queue their reservations. We first present an analysis based on a 3-dimension state-space Markov chain that provides exact results for the blocking probabilities of bursts and circuits, the proportion of circuits that are delayed and the mean delay of the circuits that are delayed. Because it is difficult to exactly compute the blocking probability in realistic scenarios with a large number of wavelengths, we derive computationally a scalable and accurate approximations based on reducing the 3-dimension state space into a single dimension. These scalable approximations that can produce performance results in a fraction of a second can readily enable switch dimensioning. Extensive numerical results are presented to demonstrate the accuracy and the use of the new approximations.
Nonlocal Constitutive Model for Simulating Localized Damage and Fracture of Viscoplastic Solids under High Energy Impacts (2011)

Developing and applying theoretical and computational models that guide the development of design criteria and fabrication processes of high impact/ballistic-resistant material are essential. However, as soon as material failure dominates a deformation process, the material increasingly displays strain softening (localization) and the finite element computations are considerably affected by the mesh size and alignment and gives non-physical descriptions of the damaged regions and failure of solids. This study is concerned with the development of a novel coupled thermo-hypoelasto, thermo-viscoplastic, and thermo-viscodamage constitutive model within the laws of thermodynamics in which implicit and explicit intrinsic material length scale parameters are incorporated through the nonlocal gradient-dependent viscoplasticity and viscodamage constitutive equations. In this current model, the Laplacian of the effective viscoplastic strain rate and its coefficient, which introduces a missing length scale parameter, enter the constitutive equations besides the local effective viscoplastic strain. It is shown through simulating plugging fracture in ballistic penetration of high-strength steel circular plates by hardened blunt-nose cylindrical steel projectiles that the Laplacian coefficient parameter plays the role of a localization limiter during the penetration and perforation processes allowing one to obtain meaningful values for the ballistic limit velocity (or perforation resistance) independent of the finite element mesh density. For the corresponding local model, on the other hand, the ballistic limit continuously decreases as the mesh density increases and does not converge even for the finest mesh.
Cyclic Thiosulfinates and Cyclic Disulfides Selectively Cross-Link Thiols While Avoiding Modification of Lone Thiols (2018)

This work addresses the need for chemical tools that can selectively form cross-links. Contemporary thiol-selective cross-linkers, for example, modify all accessible thiols, but only form cross-links between a subset. The resulting terminal "dead-end" modifications of lone thiols are toxic, confound cross-linking-based studies of macromolecular structure, and are an undesired, and currently unavoidable, byproduct in polymer synthesis. Using the thiol pair of Cu/Zn-superoxide dismutase (SOD1), we demonstrated that cyclic disulfides, including the drug/nutritional supplement lipoic acid, efficiently cross-linked thiol pairs but avoided dead-end modifications. Thiolate-directed nucleophilic attack upon the cyclic disulfide resulted in thiol-disulfide exchange and ring cleavage. The resulting disulfide-tethered terminal thiolate moiety either directed the reverse reaction, releasing the cyclic disulfide, or participated in oxidative disulfide (cross-link) formation. We hypothesized, and confirmed with density functional theory (DFT) calculations, that mono- S-oxo derivatives of cyclic disulfides formed a terminal sulfenic acid upon ring cleavage that obviated the previously rate-limiting step, thiol oxidation, and accelerated the new rate-determining step, ring cleavage. Our calculations suggest that the origin of accelerated ring cleavage is improved frontier molecular orbital overlap in the thiolate-disulfide interchange transition. Five- to seven-membered cyclic thiosulfinates were synthesized and efficiently cross-linked up to 10<sup>4</sup>-fold faster than their cyclic disulfide precursors; functioned in the presence of biological concentrations of glutathione; and acted as cell-permeable, potent, tolerable, intracellular cross-linkers. This new class of thiol cross-linkers exhibited click-like attributes including, high yields driven by the enthalpies of disulfide and water formation, orthogonality with common functional groups, water-compatibility, and ring strain-dependence.
First‐in‐Human Studies of MW01‐6‐189WH, a Brain‐Penetrant, Antineuroinflammatory Small‐Molecule Drug Candidate: Phase 1 Safety, Tolerability, Pharmacokinetic, and Pharmacodynamic Studies in Healthy Adult Volunteers (2020)

MW01-6-189WH (MW189) is a novel central nervous system-penetrant small-molecule drug candidate that selectively attenuates stressor-induced proinflammatory cytokine overproduction and is efficacious in intracerebral hemorrhage and traumatic brain injury animal models. We report first-in-human, randomized, double-blind, placebo-controlled phase 1 studies to evaluate the safety, tolerability, and pharmacokinetics (PK) of single and multiple ascending intravenous doses of MW189 in healthy adult volunteers. MW189 was safe and well tolerated in single and multiple doses up to 0.25 mg/kg, with no clinically significant concerns. The most common drug-related treatment-emergent adverse event was infusion-site reactions, likely related to drug solution acidity. No clinically concerning changes were seen in vital signs, electrocardiograms, physical or neurological examinations, or safety laboratory results. PK analysis showed dose-proportional increases in plasma concentrations of MW189 after single or multiple doses, with approximately linear kinetics and no significant drug accumulation. Steady state was achieved by dose 3 for all dosing cohorts. A pilot pharmacodynamic study administering low-dose endotoxin to induce a systemic inflammatory response was done to evaluate the effects of a single intravenous dose of MW189 on plasma cytokine levels. MW189 treatment resulted in lower levels of the proinflammatory cytokine TNF-α and higher levels of the anti-inflammatory cytokine IL-10 compared with placebo treatment. The outcomes are consistent with the pharmacological mechanism of MW189. Overall, the safety profile, PK properties, and pharmacodynamic effect support further development of MW189 for patients with acute brain injury.
CD25 (IL2RA) Is a Direct Transcriptional Target of PRDM1 in Activated Human Natural Killer Cells (2018)

Abstract Background: PRDM1 is a transcription factor that regulates differentiation and/or homeostasis of B and T lymphocytes. It may also play a role in natural killer (NK) cell homeostasis, and it is frequently inactivated in NK cell-derived lymphomas. Many target genes of PRDM1 have been reported; however, there is little insight into genes directly targeted by PRDM1 in NK cells. IL2 receptor signaling is crucial for many features of NK cell activation including sustained proliferation and survival. Here we evaluated whether CD25 (IL2Rα), a critical gene involved in NK cell activation, is transcriptionally repressed by PRDM1 in activated human NK cells. Methods: ChIP-Seq was applied on normal primary NK cells activated using a special co-culture system that involved genetically engineered NK cell target cells (i.e. K562-Cl9-mb21) to determine genomic locations occupied with PRDM1. PRDM1 binding site screen in CD25 was computationally performed using two different ChIP-Seq peak callers. Two malignant NK cell lines (NK92 and KHYG1) were transduced with a retroviral construct that co-expresses PRDM1α and GFP. CD25 transcription expression was evaluated with DNA microarray, RNA-Seq and RT-qPCR on GFP-sorted NK cells 48h post-transduction. CD25 expression was stably knocked-down with two different shRNAs in NK92 and KHYG1 cell lines. CD25 was ectopically expressed in primary human NK cells activated through coculturing with K562-Cl9-mb21. GFP competition assays were performed on CD25 shRNA-transduced NK cell lines or primary NK cells with ectopic CD25 expression in limiting IL2 concentrations, respectively. Results: PRDM1 occupancy on the 1st intron of CD25 was detected with CisGenome and MACS softwares in activated primary NK cells. Direct binding of PRDM1 on CD25 was further validated by ChIP-qPCR in normal activated NK cells. Two PRDM1α-transduced PRDM1-nonexpressing NK cell lines showed significant transcriptional repression of CD25 by DNA microarray and RNA-Seq, the repression of which was cross-validated with RT-qPCR. Stable knock-down of CD25 inhibited growth of two NK cell lines cultured in limiting IL2 concentrations. By contrast, ectopic expression of CD25 resulted in positive selection of ex vivo cultured primary NK cells. Conclusions: Altogether these results establish CD25 as a direct transcriptional target of PRDM1 in human NK cells. These observations provide additional support for the role of PRDM1 in termination of NK cell activation and growth, with implications on neoplastic transformation or NK cell function when it is deregulated. Disclosures No relevant conflicts of interest to declare.
TOWARDS COMPUTING BRAIN DEFORMATIONS FOR DIAGNOSIS, PROGNOSIS AND NEUROSURGICAL SIMULATION (2005)

The objective of our research is to create a system computing brain deformations. We have in view both clinical and training applications, such as "brain shift" calculation, prognosis and diagnosis of development of brain diseases as well as surgical simulators for planning and education. In this paper, we specifically address issues related to creating geometrically and mechanically precise representations of the brain. The method comprises of the following steps: (1) development of a 3D anatomical brain atlas, (2) construction of a finite element mesh of the atlas, (3) creation of a mathematical model, and (4) development of an efficient computational model. We discuss two types of approaches to model deformation behavior of the brain: single-phase brain tissue model, suitable for analysis of relatively short events such as surgical actions; and bi-phasic brain tissue model, well suited for calculations leading to prognosis of the development of diseases. As an illustration of the presented concepts we provide examples of 3D meshing, calculation of reaction force acting on a surgical tool using a single-phase mathematical model, and calculations of the development of hydrocephalus and the effects of tumor growth using the bi-phasic modeling approach.