gebhart/patrepeval huggingface dataset:
Computationally efficient mode selection in H.264/AVC video coding (2008)

In the H.264/AVC video coding standard, the mode selection part requires a considerable amount of computation and memory access. This paper presents a fast or computationally efficient mode prediction and selection approach which has the following attributes: (a) both the spatial and temporal information are used to achieve early termination using adaptive thresholds, (b) inclusion of a modulator capable of trading off computational efficiency and accuracy and (c) a homogenous region detection procedure for 8times8 blocks based on adaptive thresholds. It is shown that the above attributes lead to a computationally efficient video coding implementation as compared to the previous fast approaches. The results obtained on QCIF, CIF, and HD format video sequences based on two different implementation platforms JM12 and x264 are presented to show the computational efficiency of the developed approach at the expense of acceptably low losses in video quality. Improvement in memory access performance is also demonstrated using a DSP processor simulator.
Emergence in Cyber-Physical Systems-of-Systems (CPSoSs) (2016)

The essence of the concept emergence is aptly communicated by the following quote, attributed to Aristotle, who lived more than 2000 years ago: The Whole is Greater than the Sum of its Parts.
360 (2014)

Zhou, Jiachen1; Badawi, Omar1; Hassan, Erkan1; Breslow, Michael1; Rosenfeld, Brian1; Lilly, Craig2; Liu, Xinggang1 Author Information
Diffusion-Limited Retention of Porous Particles at Density Interfaces Proceedings of the National Academy of Sciences (2010)

Downward carbon flux in the ocean is largely governed by particle settling. Most marine particles settle at low Reynolds numbers and are highly porous, yet the fluid dynamics of this regime have remained unexplored. We present results of an experimental investigation of porous particles settling through a density interface at Reynolds numbers between 0.1 and 1. We tracked 100 to 500 μm hydrogel spheres with 95.5% porosity and negligible permeability. We found that a small negative initial excess density Δρp relative to the lower (denser) fluid layer, a common scenario in the ocean, results in long retention times of particles at the interface. We hypothesized that the retention time was determined by the diffusive exchange of the stratifying agent between interstitial and ambient fluid, which increases excess density of particles that have stalled at the interface, enabling their settling to resume. This hypothesis was confirmed by observations, which revealed a quadratic dependence of retention time on particle size, consistent with diffusive exchange. These results demonstrate that porosity can control retention times and therefore accumulation of particles at density interfaces, a mechanism that could underpin the formation of particle layers frequently observed at pycnoclines in the ocean. We estimate retention times of 3 min to 3.3 d for the characteristic size range of marine particles. This enhancement in retention time can affect carbon transformation through increased microbial colonization and utilization of particles and release of dissolved organics. The observed size dependence of the retention time could further contribute to improve quantifications of vertical carbon flux.
Rough and smooth variants of Mycobacterium abscessus are differentially controlled by host immunity during chronic infection of adult zebrafish (2022)

Prevalence of Mycobacterium abscessus infections is increasing in patients with respiratory comorbidities. After initial colonisation, M. abscessus smooth colony (S) variants can undergo an irreversible genetic switch into highly inflammatory, rough colony (R) variants, often associated with a decline in pulmonary function. Here, we use an adult zebrafish model of chronic infection with R and S variants to study M. abscessus pathogenesis in the context of fully functioning host immunity. We show that infection with an R variant causes an inflammatory immune response that drives necrotic granuloma formation through host TNF signalling, mediated by the tnfa, tnfr1 and tnfr2 gene products. T cell-dependent immunity is stronger against the R variant early in infection, and regulatory T cells associate with R variant granulomas and limit bacterial growth. In comparison, an S variant proliferates to high burdens but appears to be controlled by TNF-dependent innate immunity early during infection, resulting in delayed granuloma formation. Thus, our work demonstrates the applicability of adult zebrafish to model persistent M. abscessus infection, and illustrates differences in the immunopathogenesis induced by R and S variants during granulomatous infection.
Subcellular Distribution of Dietary Methyl-Mercury in Gammarus fossarum and Its Impact on the Amphipod Proteome (2021)

The transfer of methyl-Hg (MeHg) from food is central for its effects in aquatic animals, but we still lack knowledge concerning its impact on invertebrate primary consumers. In aquatic environments, cell walls of plants are particularly recalcitrant to degradation and as such remain available as a food source for long periods. Here, the impact at the proteomic level of dietary MeHg in <i>Gammarus fossarum</i> was established and linked to subcellular distribution of Hg. Individuals of <i>G. fossarum</i> were fed with MeHg in cell wall or intracellular compartments of <i>Elodea nuttallii</i>. Hg concentrations in subcellular fractions were 2 to 6 times higher in animals fed with cell wall than intracellular compartments. At the higher concentrations tested, the proportion of Hg in metal-sensitive fraction increased from 30.0 ± 6.1 to 41.0 ± 5.7% for individuals fed with intracellular compartment, while biologically detoxified metal fraction increased from 30.0 ± 6.1 to 50.0 ± 2.8% when fed with cell wall compartment. Data suggested that several thresholds of proteomic response are triggered by increased bioaccumulation in each subcellular fraction in correlation with Hg exclusively bound to the metal-sensitive fraction, while the increase of biologically detoxified metal likely had a cost for fitness. Proteomics analysis supported that the different binding sites and speciation in shoots subsequently resulted in different fate and cellular toxicity pathways to consumers. Our data confirmed that Hg bound in cell walls of plants can be assimilated by <i>G. fossarum</i>, which is consistent with its feeding strategy, hence pointing cell walls as a significant source for Hg transfers and toxicity in primary consumers. The high accumulation of Hg in macrophytes makes them a risk for food web transfer in shallow ecosystems. The present results allowed gaining new insights into the effects and uptake mechanisms of MeHg in aquatic primary consumers.
M2 Pseudomonas aeruginosa (Pa) biofilm-forming potential and metabolomic phenotypes differ between chronically infected patients with cystic fibrosis (CF) and non-CF bronchiectasis (Bx) (2019)

<h3></h3> Chronic Pa infection in CF is linked to biofilm formation in the airways and there is modest evidence for this process in Bx. Pa demonstrates numerous other phenotypes which may play a role in enabling persistence in these diseases. We have previously demonstrated that Pa metabolome and virulence-related metabolites, including rhamnolipids and quorum sensing molecules, can be characterized using direct-from-sample mass spectrometry.<sup>1</sup> We hypothesized that these techniques would demonstrate disease specific differences in Pa strain characteristics. <h3>Methods</h3> Pa strains from chronically infected patients (CF, n=70; Bx from all causes, including idiopathic Bx, but excluding CF, n=70) were cultured in rich media in a static crystal violet biofilm assay before measuring adherent biofilm biomass. Growth over the same time period was assessed for each strain. Separately Pa strains were cultured on agar before laser assisted mass spectrometry analysis. <h3>Results</h3> CF strains demonstrated 1.7 fold greater biofilm biomass than Bx strains (p=0.02). Biofilm biomass correlated with bacterial growth rate (Spearman r 0.64 (95% CI 0.53–0.73), p&lt;0.0001) though the increased biofilm biomass of CF strains persisted after growth correction. Mass spectrometry analysis was successful in 126 Pa strains. As observed before, there was considerable overlap in the principle component analysis of CF and Bx Pa metabolome. A supervised partial least squares-discriminant analysis (PLS-DA) demonstrated separation of the groups. Five component cross validation accuracy 0.89, R2=0.81, Q2=0.63. In future, we hope to identify the spectral features causing this separation. <h3>Conclusion</h3> We demonstrated differences in Pa biofilm biomass and metabolome from CF and Bx patients, which may relate to variation in Pa airway adaptation. Possible explanations include pathophysiological (eg. surface liquid composition, pH) or therapeutic differences (eg. drugs to aid airway clearance, short and long-term antibiotics). Understanding features of Pa adaptation in CF and Bx could lead to identification of biomarkers of disease severity and novel approaches to treat Pa airway infection. Supported by the British Lung Foundation. Affiliated to the UK CF Trust-funded Strategic Research Centre for Pseudomonas infection. <h3>Reference</h3> Bardin EE, <i>et al</i>. <i>Sci. Rep</i>. 2018;8(1):10952.
Pectin remodeling belongs to a homeostatic system and triggers transcriptomic and hormonal modulations (2021)

SUMMARY Here, we focused on the biological modifications arisen from a strong and transient variation of the pectin methylesterification status during the seed-to-seedling transition. A reverse genetic approach was used to trigger specific reduction of pectin de-methylesterification during the seed maturation stage and the related physiological effects were assessed using a combination of biochemical, transcriptomic and microscopic analyses. Arabidopsis PME36 is required to implement the characteristic pattern of de-methylesterified pectin in the mature seed. While this pattern is strongly impaired in pme36-1 and pme36-2 mature seed, no phenotypical effect is observed in the knockout mutant during seed germination. By analyzing hormone homeostasis and gene expression regulation, we show a strong and dynamic physiological disorder in the mutant, which reveals the existence of a complex compensatory mechanism overcoming the defect in pectin de-methylesterification. Our results reveal that pectin methylesterification status acts as upstream modulator involved in an undescribed homeostatic system in which pectin remodeling, hormone signaling and transcriptomic regulations interact to ensure the maintenance of a normal seed-to-seedling developmental program.
Association of Rare and Common Variation in the Lipoprotein Lipase Gene With Coronary Artery Disease (2017)

The presence of rare damaging mutations in LPL was significantly associated with higher triglyceride levels and presence of coronary artery disease. However, further research is needed to assess whether there are causal mechanisms by which heterozygous lipoprotein lipase deficiency could lead to coronary artery disease.
Dibutyryl‐Cyclic GMP Stimulation of Ca2+‐ATPase Activity in Rat Brain Synaptic Membranes (1985)

The effects of dibutyryl cyclic AMP (db-cAMP) and dibutyryl cyclic GMP (db-cGMP) were tested on Ca2+-ATPase, Mg2+-ATPase, and (Ca2+ + Mg2+)-ATPase activities in lysed synaptosomes prepared from whole rat brains (minus cerebellum). At concentrations from 0.1 to 2.0 mM, db-cGMP produced a selective, concentration-dependent increase in Ca2+-ATPase activity. Both db-cGMP and db-cAMP slightly reduced Mg2+-ATPase activity, whereas neither compound had concentration-dependent effects on (Ca2+ + Mg2+)-ATPase activity. These findings suggest that the Mg2+-independent, Ca2+-ATPase activity in rat brain is regulated by a cyclic GMP-dependent process. Further, the data provide evidence that the Ca2+-ATPase activity in lysed synaptosomal membranes represents an enzyme that is distinguishable from both the Mg2+ -and (Ca2+ + Mg2+)-ATPase.
The microstructural response of quartz and feldspar under shock loading at variable temperatures (1993)

Shock recovery experiments were carried out on Westerly granite and Hospital Hill quartzite targets in the peak pressure range 8 to 25 GPa, preshock temperatures of 25°, 450°, and 750°C and pulse durations of 2 to 7 μs using internally heated momentum traps and explosive plane wave generators. Optical and transmission electron microscopy analyses of quartz and feldspar shocked at 25°C revealed the previously documented progression, with increasing pressure: (1) fracturing; (2) planar fractures and shock mosaicism; (3) shock mosaicism and planar deformation features (PDFs); and (4) isotropization. This same sequence is observed for experiments at elevated preshock temperature but with specific microstructures occurring at lower pressures than those in previous experiments at room temperature. At 750°C, strong shock mosaicism, partially thermally recovered, is characteristic of feldspar shocked to 8 GPa, whereas 15 GPa is required for its development in quartz and for the generation of PDFs in both minerals. The results suggest that threshold pressures for formation of the various microstructures and phases are expected to vary systematically as a function of the preshock temperature of the target material. We suggest that PDFs are generated in the shock transition by progressive, heterogeneous, phase transformation of the crystal structure to form dense glass or high pressure polymorphs. The onset pressures for PDFs in specific crystallographic orientations is not influenced strongly by temperature, but the character of the PDFs does change as preshock temperature is increased at the same peak shock stress. The change from multiple sets of thin PDFs at low temperature to thicker single sets of PDFs at moderate temperature, and finally to complete isotropization at high temperatures, reflects a change in the phase transformation mechanism as a function of temperature. In contrast, development of shock mosaicism in quartz and feldspar occurs throughout the duration of shock loading and is better developed at elevated temperatures where the kinetics are enhanced by the additional thermal energy in the target.
Li6La3SnMO12(M = Sb, Nb, Ta), a Family of Lithium Garnets with High Li-Ion Conductivity (2012)

In order to investigate the influence of covalent bonding within the garnet framework on the conductivity of Li+ in the interstitial space, the Li+ conductivities in the family of Sn-based compounds Li6La3SnMO12 (M = Sb, Nb, Ta) have been obtained and are compared with those of Li6La3ZrMO12. Refinement of the neutron diffraction pattern of Li6La3SnNbO12 shows that the interstitial tetrahedral sites (24d) are about half-occupied and most of the Li in the interstitial bridging octahedral sites are displaced from the center position (48g). The Sb-based compound has the largest lattice parameter while the Ta-based compound has the highest Li+-ion conductivity of 0.42×10−4 S cm−1.
ChemInform Abstract: COMPETITION BETWEEN (1,7) HYDROGEN MIGRATION AND ELECTROCYCLIC RING CLOSURE IN 6‐METHYLHEPTA‐1,3,5‐TRIENE (1979)

Abstract Die Heptatriene (Z)‐(III) und (Z,Z)‐(VI) waren bei der bereits untersuchten Thermolye (300‐475°C) des Cyclohexadiens (IV) als Intermediäre postuliert worden.
A Simplified Computational Kernel for Trellis-Based Decoding (2004)

A simplified branch metric and add-compare-select (ACS) unit is presented for use in trellis-based decoding architectures. The simplification is based on a complementary property of best feedforward and some systematic feedback encoders. As a result, one adder is saved in every other ACS unit. Furthermore, only half the branch metrics have to be calculated. It is shown that this simplification becomes especially beneficial for rate 1/2 convolutional codes. Consequently, area and power consumption will be reduced in a hardware implementation.
Computed Tomography Coronary Angiography and Computational Fluid Dynamics Based Fractional Flow Reserve Before and After Percutaneous Coronary Intervention (2021)

Invasive fractional flow reserve (FFR) is recommended to guide stent deployment. We previously introduced a non-invasive FFR calculation (FFR<sub>B</sub>) based on computed tomography coronary angiography (CTCA) with reduced-order computational fluid dynamics (CFD) and resistance boundary conditions. Current study aimed to assess the feasibility and accuracy of FFR<sub>B</sub> for predicting coronary hemodynamics before and after stenting, with invasive FFR as the reference. Twenty-five patients who had undergone CTCA were prospectively enrolled before invasive coronary angiography (ICA) and FFR-guided percutaneous coronary intervention (PCI) on 30 coronary vessels. Using reduced-order CFD with novel boundary conditions on three-dimensional (3D) patient-specific anatomic models reconstructed from CTCA, we calculated FFR<sub>B</sub> before and after virtual stenting. The latter simulated PCI by clipping stenotic segments from the 3D coronary models and replacing them with segments to mimic the deployed coronary stents. Pre- and post-virtual stenting FFR<sub>B</sub> were compared with FFR measured pre- and post-PCI by investigators blinded to FFR<sub>B</sub> results. Among 30 coronary lesions, pre-stenting FFR<sub>B</sub> (mean 0.69 ± 0.12) and FFR (mean 0.67 ± 0.13) exhibited good correlation (<i>r</i> = 0.86, <i>p</i> < 0.001) and agreement [mean difference 0.024, 95% limits of agreement (LoA): -0.11, 0.15]. Similarly, post-stenting FFR<sub>B</sub> (mean 0.84 ± 0.10) and FFR (mean 0.86 ± 0.08) exhibited fair correlation (<i>r</i> = 0.50, <i>p</i> < 0.001) and good agreement (mean difference 0.024, 95% LoA: -0.20, 0.16). The accuracy of FFR<sub>B</sub> for identifying post-stenting ischemic lesions (FFR ≤ 0.8) (residual ischemia) was 87% (sensitivity 80%, specificity 88%). Our novel FFR<sub>B</sub>, based on CTCA with reduced-order CFD and resistance boundary conditions, accurately predicts the hemodynamic effects of stenting which may serve as a tool in PCI planning.
No signal of interactions between influenza vaccines and drugs used for chronic diseases: a case-by-case analysis of the vaccine adverse event reporting system and vigibase (2018)

The relative paucity of detected interactions does not impact on the benefit of the vaccination against influenza, which remains strongly recommended; this does not exclude that closer monitoring for selected patients exposed to concomitant chronic pharmacological therapies and affected by predisposing factors may be useful.
Improvement of SNR in MRgFUS with strategic design of bath medium and transducer ground plane (2020)

MR-guided Focused Ultrasound (MRgFUS) of the head at 3 Tesla suffers from low image Signal-to-Noise ration in exactly the region of interest in the brain due to severe dielectric effects from the water bolus surrounding the head to facilitate cooling of the scalp and transmission of ultrasonic energy. We show that by changing the medium of the bath and adding slots to the ground plane it is possible to go from low SNR to high SNR I the region of interest.
A Single Monooxygenase, Ese, Is Involved in the Metabolism of the Organochlorides Endosulfan and Endosulfate in an Arthrobacter sp (2006)

ABSTRACT In this paper we describe isolation of a bacterium capable of degrading both isomers of the organochloride insecticide endosulfan and its toxic metabolite, endosulfate. The bacterium was isolated from a soil microbial population that was enriched with continuous pressure to use endosulfate as the sole source of sulfur. Analysis of the 16S rRNA sequence of the bacterium indicated that it was an Arthrobacter species. The organochloride-degrading activity was not observed in the presence of sodium sulfite as an alternative sulfur source, suggesting that the activity was part of the sulfur starvation response of the strain. A gene, ese , encoding an enzyme capable of degrading both isomers of endosulfan and endosulfate was isolated from this bacterium. The enzyme belongs to the two-component flavin-dependent monooxygenase family whose members require reduced flavin for activity. Nuclear magnetic resonance analyses identified the metabolite of endosulfan as endosulfan monoalcohol and the metabolite of endosulfate as endosulfan hemisulfate. The ese gene was located in a cluster of 10 open reading frames encoding proteins with low levels of sulfur-containing amino acids. These open reading frames were organized into two apparent divergently orientated operons and a gene encoding a putative LysR-type transcriptional regulator. The operon not containing ese did contain a homologue whose product exhibited 62% amino acid identity to the ese -encoded protein.
AN MDL METHOD FOR FINDING HAPLOTYPE BLOCKS AND FOR ESTIMATING THE STRENGTH OF HAPLOTYPE BLOCK BOUNDARIES (2002)

We describe a new method for finding haplotype blocks based on the use of the minimum description length principle. We give a rigorous definition of the quality of a segmentation of a genomic region into blocks, and describe a dynamic programming algorithm for finding the optimal segmentation with respect to this measure. We also describe a method for finding the probability of a block boundary for each pair of adjacent markers: this gives a tool for evaluating the significance of each block boundary. We have applied the method to the published data of Daly et al. The results are in relatively good agreement with the published results, but also show clear differences in the predicted block boundaries and their strengths. We also give results on the block structure in population isolates.
Electronic Structure, Bandgap, and Thermal Quenching of Sr[Mg3SiN4]:Eu2+ in Comparison to Sr[LiAl3N4]:Eu2+ (2015)

In this study the band gap and electronic structure of the next‐generation, red phosphor Sr[Mg 3 SiN 4 ]:Eu 2+ (SMS) are explored through a combination of soft X‐ray spectroscopy, density functional theory calculations, and thermal quenching data for the Eu 2+ 5d→4f emissions. The results will be compared to those for the high‐efficiency phosphor Sr[LiAl 3 N 4 ]:Eu 2+ (SLA), which shows different, yet exceptional emission characteristics in the red‐spectral region. It is found that SMS has an indirect band gap of 3.28 ± 0.20 eV, strong uniformity in the density of states of its nonequivalent nitrogen sites, and an estimated energetic separation between the lowest Eu 2+ 5d state and the conduction band of ≈0.13 eV. The Eu 2+ 5d–conduction band separation in SLA is found to be ≈0.28 eV, which points to why the visible emissions of SLA, and not SMS, show outstanding thermal stability. A bonding scheme explaining the band gap difference of SMS and SLA is proposed based on the density of states of SMS. Modifications to each lattice are put forward for achieving optimized phosphor characteristics for use in pc‐LEDs.