gebhart/patrepeval huggingface dataset:
Hurdles for a DRAM-based Match-Action Table (2020)

The P4 language has gained traction as a tool for programming packet processing pipelines. Current commercial use is focused on single-chip pipelines, but as network scales grow, the need to enable programmability of multi-chip pipelines grows as well. Combining a P4-capable ASIC with a DRAM scale match-action table is a useful exercise for studying the obstacles to delivering efficient tools for programming multi-chip pipeline systems. We have constructed a demonstration environment for investigating those obstacles and learning what compilation tuning mechanisms will be required in the p4 tools used by system designers.
Performance evaluation of canny edge detection on a tiled multicore architecture (2010)

In the last few years, a variety of multicore architectures have been used to parallelize image processing applications. In this paper, we focus on assessing the parallel speed-ups of different Canny edge detection parallelization strategies on the Tile64, a tiled multicore architecture developed by the Tilera Corporation. Included in these strategies are different ways Canny edge detection can be parallelized, as well as differences in data management. The two parallelization strategies examined were loop-level parallelism and domain decomposition. Loop-level parallelism is achieved through the use of OpenMP,1 and it is capable of parallelization across the range of values over which a loop iterates. Domain decomposition is the process of breaking down an image into subimages, where each subimage is processed independently, in parallel. The results of the two strategies show that for the same number of threads, programmer implemented, domain decomposition exhibits higher speed-ups than the compiler managed, loop-level parallelism implemented with OpenMP.
Measuring the Temporal Behavior of Real-World Person Re-Identification (2018)

Designing real-world person re-identification (re-id) systems requires attention to operational aspects not typically considered in academic research. Typically, the probe image or image sequence is matched to a gallery set with a fixed candidate list. On the other hand, in real-world applications of re-id, we would search for a person of interest in a gallery set that is continuously populated by new candidates over time. A key question of interest for the operator of such a system is: how long is a correct match to a probe likely to remain in a rank-k shortlist of candidates? In this paper, we propose to distill this information into what we call a Rank Persistence Curve (RPC), which unlike a conventional cumulative match characteristic (CMC) curve helps directly compare the temporal performance of different re-id algorithms. To carefully illustrate the concept, we collected a new multi-shot person re-id dataset called RPIfield. The RPIfield dataset is constructed using a network of 12 cameras with 112 explicitly time-stamped actor paths among about 4000 distractors. We then evaluate the temporal performance of different re-id algorithms using the proposed RPCs using single and pairwise camera videos from RPIfield, and discuss considerations for future research.
Additive Interactions Between Susceptibility Single-Nucleotide Polymorphisms Identified in Genome-Wide Association Studies and Breast Cancer Risk Factors in the Breast and Prostate Cancer Cohort Consortium (2014)

Additive interactions can have public health and etiological implications but are infrequently reported. We assessed departures from additivity on the absolute risk scale between 9 established breast cancer risk factors and 23 susceptibility single-nucleotide polymorphisms (SNPs) identified from genome-wide association studies among 10,146 non-Hispanic white breast cancer cases and 12,760 controls within the National Cancer Institute's Breast and Prostate Cancer Cohort Consortium. We estimated the relative excess risk due to interaction and its 95% confidence interval for each pairwise combination of SNPs and nongenetic risk factors using age- and cohort-adjusted logistic regression models. After correction for multiple comparisons, we identified a statistically significant relative excess risk due to interaction (uncorrected P = 4.51 × 10(-5)) between a SNP in the DNA repair protein RAD51 homolog 2 gene (RAD51L1; rs10483813) and body mass index (weight (kg)/height (m)(2)). We also compared additive and multiplicative polygenic risk prediction models using per-allele odds ratio estimates from previous studies for breast-cancer susceptibility SNPs and observed that the multiplicative model had a substantially better goodness of fit than the additive model.
Iron and dental caries. (1988)

Studies of human and animal caries, experiments in vitro and laboratory reports initiated the present study of a possible caries preventing effect of iron. The study comprises two sections. (I) Coatings on teeth of hamsters treated with iron salts and films formed on various solutions containing ferrous ions were examined with scanning electron microscopy and x-ray fluorescence analysis. (II) Enamel surface layers, remineralized caries lesions, fluorosed rat bone, coatings on teeth of hamsters treated with iron salts and films formed on solutions containing ferrous ions were examined with transmitting electron microscopy and electron diffraction. Based on the findings the following effects were visualized. When brought into the mouth, even in small amounts, iron ions will be precipitated on the enamel surface as thin acid resistant coatings containing gels and crystals of hydrous iron oxides. In addition, by adsorbing salivary calcium and phosphate ions these iron compounds seem to be able to nucleate the formation of apatites, thus mediating a replacement of minerals, which have been dissolved during the acid phases of the caries process.
Distinct host immune programs in lung macrophages elicit cell-type specific Mycobacterium tuberculosis transcriptional responses (2020)

Abstract During Mycobacterium tuberculosis (Mtb) infection, bacteria are inhaled into the lung where they first infect resident, alveolar macrophages (AM). The majority of the infection remains in AM until D14, when other cells, including recruited monocyte-derived macrophages (MDM) begin to become infected. By the peak of infection (D28) MDM represent the major infected cell type. However, even at this time point, a small population of infected AM remain. This led us to ask how these cell types control Mtb. Using microscopy, we observed that AM harbor more bacteria than MDM on a per cell basis at multiple time points, including after the initiation of the T cell response. Using RNA-seq, we identified multiple differentially expressed pathways between the two cell types. While infected MDM upregulate proinflammatory signaling pathways associated with Mtb control, infected AM are enriched for proliferation and fatty acid metabolism pathways. We performed validation studies using dyes to track cell division and mitochondrial metabolism and observed that AM were more proliferative and had sustained engagement of mitochondrial metabolism relative to MDM. In parallel, we analyzed the bacterial transcriptome and found that Mtb in MDM have a signature associated with late hypoxia. These bacterial responses also suggested that Mtb may differ in its drug tolerance in a cell type specific manner, which we are currently investigating. Together, this work is in agreement with other studies demonstrating differences in the response to Mtb by tissue resident and recruited macrophages and suggests that these differences may lead to distinct transcriptional changes in the bacteria, which could have important implications for therapeutic interventions.
Propagation Characteristics of Seven-core Fiber for Spatial and Wavelength Division Multiplexed 10-Gbit/s Channels (2011)

Propagation characteristics of seven-core fiber were investigated for multiplexed signals of spatial-division and wavelength-division. Effect of chromatic dispersion and inter-core crosstalk were evaluated for 5-km fiber by using 10-Gbit/s channels.
Front Cover: Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline (2018)

DOI: 10.1002/pmic.201700332 In the post-genomic era of drug discovery, combined multi-omics methods are widely applied in order to boost the discovery of novel natural products and the biosynthetic gene clusters that encode them. The basis is formed by collections of actinobacteria and other microorganisms. Advanced metabolomics-based screening combined with genome mining allows for narrowing down the number of candidate producer strains. Multi-omics methods, including genomics, proteomics and integrated data analysis, complete the modern discovery workflow. Further details are found in article number 1700332 by Chao Du and Gilles P. van Wezel.
Genetic Associations With 6MMP Preferential Metabolizers by Elevated 6MMP:6TGN Ratios Reveal Novel Pathways Involved in Purine Metabolism: Presidential Poster (2015)

Introduction: The thiopurine drugs, 6-mercaptopurine (6MP) and azathioprine (AZA), are the mainstay of immunomodulator treatment in inflammatory bowel disease (IBD). Thiopurine methyltransferase (TPMT) genotype and enzymatic activity play a role in determining 6-tioguanine (6TGN) and 6-methylmercaptopurine (6MMP) metabolite levels, which are associated with bone marrow suppression and hepatotoxicity, respectively. A portion of patients with normal TPMT demonstrate preferential metabolism towards 6-MMP and can be identified when the 6-MMP is noted to be >5700 pmol/8x108 RBC with a low 6TGN. Examination of the 6MMP:6TGN ratio in these patients when the 6MMP level is < 5700 can help identify patients at risk for preferential metabolism and help identify novel pathways in thiopurine metabolism. The aim of this study is to identify genetic factors associated with susceptibility to 6-MMP preferential metabolism. Methods: After quality control, there were 420 IBD subjects treated at Cedars-Sinai IBD Center with 6-MP or AZA from 1999-2012 in whom immunochip and thiopurine metabolite data were available. Known preferential metabolizers were defined as having 6MMP levels >5700 pmol/8x108 RBC. To identify an at-risk 6MMP:6TGN ratio, the highest 6-MMP level of these patients that was 19.00, regardless of absolute 6-MMP level, was identified as a suspected preferential metabolizer. Linear regression was performed on 133,530 post-QC Immunochip SNPs after correcting for population structure. Results: There were 189 suspected preferential metabolizers with a 6MMP:6TGN ratio>19.00 and 231 normal metabolizers. Three loci achieved a nominal level of significance: a SNP tagging LRIG1/KBTBD8 (rs1580143) showed strongest association (p=5.00E-05); rs3934809 tagging. ARL8A/GPR37L1/ LGR6/PTPN7 (p=2.06E-05); and rs58926232 (p=3.56E-05) that tags the known IBD locus at PRDM1/ATG5. The strongest associated SNP involved the gene LRIG1, which encodes proteins involved in granulocyte differentiation, neovascularization, metastasis, and TGFbeta signaling. Conclusion: The SNPs described may provide useful genetic markers for early identification of patients at greatest risk for preferential 6MMP metabolism. Pre-emptive use of allopurinol or split-dosing of thiopurines may reduce thiopurine toxicity in patients with these genetic markers.
Improving Polygenic Prediction in Ancestrally Diverse Populations (2021)

ABSTRACT Polygenic risk scores (PRS) have attenuated cross-population predictive performance. As existing genome-wide association studies (GWAS) were predominantly conducted in individuals of European descent, the limited transferability of PRS reduces its clinical value in non-European populations and may exacerbate healthcare disparities. Recent efforts to level ancestry imbalance in genomic research have expanded the scale of non-European GWAS, although most of them remain under-powered. Here we present a novel PRS construction method, PRS-CSx, which improves cross-population polygenic prediction by integrating GWAS summary statistics from multiple populations. PRS-CSx couples genetic effects across populations via a shared continuous shrinkage prior, enabling more accurate effect size estimation by sharing information between summary statistics and leveraging linkage disequilibrium (LD) diversity across discovery samples, while inheriting computational efficiency and robustness from PRS-CS. We show that PRS-CSx outperforms alternative methods across traits with a wide range of genetic architectures, cross-population genetic overlaps and discovery GWAS sample sizes in simulations, and improves the prediction of quantitative traits and schizophrenia risk in non-European populations.
Cytomorphologic Spectrum of Hurthle Cell Lesions of Thyroid: A Study of 54 Cases. (2018)

Out of the 9 parameters studied, the cytological features shown to be statistically significant in predicting HCN and distinguishing them from benign hurthle cell lesions(BHCLs) were increased cellularity, non-macro follicular architecture, >90% Hurthle cells, absence of background colloid and absence of chronic inflammation.
Influence of Extraction Parameters on the Yield, Phytochemical, TLC-Densitometric Quantification of Quercetin, and LC-MS Profile, and how to Standardize Different Batches for Long Term from Ageratum conyoides L. Leaves (2017)

Introduction: Ageratum conyzoides Linn is one of the Indonesian herbs are used as folk medicine. There are many studies to the therapeutic activity. However, the study of the influence in extraction parameters and how to standardize different batches of plant is still limited. Objective: The present study was designed to investigate the influence of extraction parameters on the variables matter, yield, phytochemical profile, and total quercetin from A. conyzoides L. leaves extract. The study also evaluates Liquid Chromatography-Mass Spectroscopy (LC-MS) and TLC fingerprint profiles of the extract to determine the proper quality of plant material of A. conyzoides L. leaves. Methods: Different temperatures (from 0C to 60C), solvent types (water and 70% ethanol (%v/v), and extraction time (192 h VS 2 h) were used to investigate the influence of extraction parameters. The profiles of extract were performed by TLC and LC-MS method. Results: The extract yield was influenced by temperature, solvent types, and time extraction. Our results suggest that the digestion technique at 60C with 70% ethanol for 2h was recommended for the extraction method to obtained high yield and quercetin content as bioactive compound in A. conyzoides L. leaves extract. The range of quercetin content (40-52 ppm) combined with TLC and LC-MS profile can be used to determine the proper quality of plant material. Conclusion: All parameter of extraction have an affect on the yield extract and total quercetin on the final extract. Thus, there is a need an optimized method to obtain the suitable method.
Effect of Backbone Regioregularity on the Structure and Orientation of a Donor–Acceptor Semiconducting Copolymer (2014)

A regioregular (RR) donor–acceptor conjugated copolymer based on cyclopenta[2,1-b:3,4-b′]dithiophene (CDT) and pyridal[2,1,3]thiadiazole (PT) structural units was prepared by using polymerization reactions involving reactants specifically designed to avoid random orientation of the asymmetric PT heterocycle along the copolymer backbone. Compared to its regioirregular (RI) counterpart, the RR polymer exhibits a 2 orders of magnitude increase in hole mobility from 0.005 to 0.6 cm2 V–1 s–1. To probe the reason for this difference in mobility, we examined the crystalline structure and its orientation in thin films of both copolymers as a function of depth via grazing incidence wide-angle X-ray scattering (GIWAXS). In the RI film, the π–π stacking direction of the crystallites is mainly perpendicular to the substrate normal (edge-on orientation) while in the RR film the crystallites adopt a mixed π–π stacking orientation in the center of the film as well as near the interface between the polymer and the dielectric layer. These results demonstrate that control of backbone regularity is another important design criterion to consider in the synthesis and optimization of new conjugated copolymers with asymmetric structural units.
Ureide metabolism in plant-associated bacteria: purine plant-bacteria interactive scenarios under nitrogen deficiency (2018)

Background The erratic alterations in climate being experienced in agriculture, such as extended periods of drought or heavy rainfalls, are bringing increasing concerns about nitrogen (N) management. Even in highinput farming systems, unpredictable weather patterns can cause N deficiencies and result in nutrient losses that contribute to major pollution issues in groundwater, lakes, and even the oceans. Our present understanding of the beneficial interactions between N-deficientchallenged plants and plant-associated bacteria (PAB), mainly of the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria, is largely based on
Comparison of posterior foraminotomy and anterior foraminotomy with fusion for treating spondylotic foraminal stenosis of the cervical spine: study protocol for a randomized controlled trial (ForaC) (2014)

Current Controlled Trials: ISRCTN82578069.
A portable switching bi-phasic stimulator with level-shifting inverter for functional electrical stimulation operating under a 6V supply voltage (2015)

This paper presents a compact architecture of portable functional electrical stimulator (FES) together with a level-shifting digital inverter. The presented architecture is composed of boost converter block with compact limiter circuit. The bi-phasic pulse generation is made from H-bridge switches with the boosted voltage from the boost converter block. The H-bridge switches are controlled by a level-shifting inverter which is composed of only four MOSFET devices with two capacitors. The clocking scheme for minimize power consumption is also a key point for reducing average power consumption in this work. The simulation results from LTSpice IV show that the presented stimulator can generate stimulating bi-phasic pulses with approximately +/-21V amplitude in voltage and constantly supply +/-19.2mA current to the load. The simulated bi-phasic pulse has pulse width of 326μs with frequency of 28.6Hz. The presented system can be operated under a single 6V supply voltage and the average power consumption is 117mW at stimulating frequency of 28.6Hz which can continuously operate under two CR2032 batteries for more than 11 hours. With this level of power consumption, the presented work is very suitable for using as a portable stimulator.
Compressing and focusing a short laser pulse by a thin plasma lens (2001)

We consider the possibility of using a thin plasma slab as an optical element to both focus and compress an intense laser pulse. By thin we mean that the focal length is larger than the lens thickness. We derive analytic formulas for the spot size and pulse length evolution of a short laser pulse propagating through a thin uniform plasma lens. The formulas are compared to simulation results from two types of particle-in-cell code. The simulations give a greater final spot size and a shorter focal length than the analytic formulas. The difference arises from spherical aberrations in the lens which lead to the generation of higher-order vacuum Gaussian modes. The simulations also show that Raman side scattering can develop. A thin lens experiment could provide unequivocal evidence of relativistic self-focusing.
Physics of cancer propagation: A game theory perspective (2012)

This is a theoretical paper which examines at a game theoretical perspective the dynamics of cooperators and cheater cells under metabolic stress conditions and high spatial heterogeneity. Although the ultimate aim of this work is to understand the dynamics of cancer tumor evolution under stress, we use a simple bacterial model to gain fundamental insights into the progression of resistance to drugs under high competition and stress conditions.
Polymorph Separation by Ordered Patterning (2022)

We herein address the problem of polymorph selection by introducing a general and straightforward concept based on their ordering. We demonstrated the concept by the ordered patterning of four compounds capable of forming different polymorphs when deposited on technologically relevant surfaces. Our approach exploits the fact that, when the growth of a crystalline material is confined within sufficiently small cavities, only one of the possible polymorphs is generated. We verify our method by utilizing several model compounds to fabricate micrometric "logic patterns" in which each of the printed pixels is easily identifiable as comprising only one polymorph and can be individually accessed for further operations.
Modeling of Quench Protection Concepts for Canted-Cosine-Theta Type High-Field Magnets (2020)

An innovative high-field superconducting magnet of Canted-Cosine-Theta (CCT) type has been proposed for Future Circular Collider 16 T dipole magnet design. The unique mechanical structure intercepts the accumulated forces lowering the stress on the windings, constituting intrinsic stress management in high-field Nb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> Sn accelerator magnets. However, this structure also constitutes a barrier for heat to quickly propagate in case of a quench. To succeed in the CCT-type magnet design and construction, quench protection is a challenging task that requires a detailed investigation of the electrothermal behavior of the magnet. In this paper, the protectability of a two-layer short model CD1 (Canted Dipole) built at PSI is studied using multiphysics simulations. Two protection methods are considered: energy extraction and coupling-loss induced quench. The 2D User-Defined Elements (UDEs) developed at Lawrence Berkeley National Laboratory in ANSYS Parametric Design Language, which support the multi-dependence material properties and include the effect of inter-filament coupling currents, are adapted and used in the coupled electrothermal, electrodynamic and electrical circuits calculations. A first-of-a-kind CCT-type magnet protection study using UDEs is presented. The generic model method will be validated through CD1 cold tests. Furthermore, these studies will prepare the ground for four-layer CCT protection concepts for FCC.
A tale of 10 European centres – 2010 APOSSM travelling fellowship review in ACL surgery (2012)

The purpose of ESSKA- APOSSM Travelling fellowship is to better understand the epidemiology, management and surgical techniques for sports across continents. There has been a progressive evolution in ACL reconstruction and there is variation in technique in ACL reconstruction amongst the most experienced surgeons in different continents. During this one month fellowship, we saw various ACL reconstruction techniques using different graft sources, with a variety of graft fixation methods, with the common aim of recreating an anatomical ACL reconstruction.
Report on Wines (1939)

Journal Article Report on Wines Get access B G Hartmann B G Hartmann Associate Referee U. S. Food and Drug Administration, Washington, D. C Search for other works by this author on: Oxford Academic Google Scholar Journal of Association of Official Agricultural Chemists, Volume 22, Issue 2, 1 May 1939, Page 210, https://doi.org/10.1093/jaoac/22.2.210 Published: 18 February 2020
New Approaches to Pore Size Engineering of Mesoporous Silicates (1998)

Pore size engineering of silicates has always been a critical issue in the field of mesoporous materials design. A new method for obtaining silicates with pore sizes up to 11 nm and narrow pore size distributions is described by the authors. Treating non-calcined MCM-41 silicate in aqueous emulsions of long-chain alkylamines, they generated these materials with large pores and exceptionally high pore volumes. Direct synthesis in the presence of long-chain alkylamines affords materials with up to 8 nm pores. These simple techniques are thought to be applicable to other molecular sieves.