gebhart/patrepeval huggingface dataset:
Whole Genome Sequencing of Avian Pathogenic Escherichia coli Causing Bacterial Chondronecrosis and Osteomyelitis in Australian Poultry (2023)

Bacterial chondronecrosis with osteomyelitis (BCO) impacts animal welfare and productivity in the poultry industry worldwide, yet it has an understudied pathogenesis. While Avian Pathogenic <i>Escherichia coli</i> (APEC) are known to be one of the main causes, there is a lack of whole genome sequence data, with only a few BCO-associated APEC (APEC<sub>BCO</sub>) genomes available in public databases. In this study, we conducted an analysis of 205 APEC<sub>BCO</sub> genome sequences to generate new baseline phylogenomic knowledge regarding the diversity of <i>E. coli</i> sequence types and the presence of virulence associated genes (VAGs). Our findings revealed the following: (i) APEC<sub>BCO</sub> are phylogenetically and genotypically similar to APEC that cause colibacillosis (APEC<sub>colibac</sub>), with globally disseminated APEC sequence types ST117, ST57, ST69, and ST95 being predominate; (ii) APEC<sub>BCO</sub> are frequent carriers of ColV-like plasmids that carry a similar set of VAGs as those found in APEC<sub>colibac</sub>. Additionally, we performed genomic comparisons, including a genome-wide association study, with a complementary collection of geotemporally-matched genomes of APEC from multiple cases of colibacillosis (APEC<sub>colibac</sub>). Our genome-wide association study found no evidence of novel virulence loci unique to APEC<sub>BCO</sub>. Overall, our data indicate that APEC<sub>BCO</sub> and APEC<sub>colibac</sub> are not distinct subpopulations of APEC. Our publication of these genomes substantially increases the available collection of APEC<sub>BCO</sub> genomes and provides insights for the management and treatment strategies of lameness in poultry.
Ignition dynamics and activation energies of metallic thermites: From nano- to micron-scale particulate composites (2005)

Ignition behaviors associated with nano- and micron-scale particulate composite thermites were studied experimentally and modeled theoretically. The experimental analysis utilized a CO2 laser ignition apparatus to ignite the front surface of compacted nickel (Ni) and aluminum (Al) pellets at varying heating rates. Ignition delay time and ignition temperature as a function of both Ni and Al particle size were measured using high-speed imaging and microthermocouples. The apparent activation energy was determined from this data using a Kissinger isoconversion method. This study shows that the activation energy is significantly lower for nano- compared with micron-scale particulate media (i.e., as low as 17.4 compared with 162.5kJ∕mol, respectively). Two separate Arrhenius-type mathematical models were developed that describe ignition in the nano- and the micron-composite thermites. The micron-composite model is based on a heat balance while the nanocomposite model incorporates the energy of phase transformation in the alumina shell theorized to be an initiating step in the solid-solid diffusion reaction and uniquely appreciable in nanoparticle media. These models were found to describe the ignition of the Ni∕Al alloy for a wide range of heating rates.
Butterflies and moths at home : sixty photographs from nature / by A. Forrester. (1905)

no.4 (1905)
Characterisation of discontinuity effects in triple ridge waveguides using 90° and 180° unit elements (2003)

The discontinuity effect at a step between any two waveguides is an important aspect in the design of impedance steps and filter structures. The purpose of this paper is to characterise the effect between a regular rectangular waveguide and a triple ridge waveguide propagating its dominant mode. One method of achieving this is to employ a 180° UE in conjunction with a calculation of the characteristic impedance and wavelength of the ridge waveguide. Another method is to have recourse to its odd-mode eigen-network. Both procedures are employed in order to obtain data on such a discontinuity. Results are in accord with separate calculations using a commercial finite element (FE) solver.
Conductance Change Induced by the Rashba Effect in the LaAlO<SUB>3</SUB>/SrTiO<SUB>3</SUB> Interface (2015)

The LaAlO3/SrTiO3 (LAO/STO) heterostructure has an inherent space inversion asymmetry causing an internal electric field near the interface. The Rashba spin-orbit coupling arising from this structural characteristic has a considerable influence on spin transport. With application of an external magnetic field, we observed conductance change in the LAO/STO interface which depends on the sign and magnitude of the field. Our systematic study revealed that these results come from spin dependent transport, by which we obtained quantitative strength of the Rashba effect. The Rashba strength in this system depends on the temperature: it varies from 2.6 x 10(-12) eVm to negligible value in the temperature range of 1.8 K-12 K. This method for detecting Rashba effect covers a wider temperature range in comparison with those obtained from Shubnikov-de Haas oscillation or weak antilocalization measurements.
Tiny Neural Networks for Environmental Predictions: An Integrated Approach with Miosix (2020)

Collecting vast amount of data and performing complex calculations to feed modern Numerical Weather Prediction (NWP) algorithms require to centralize intelligence into some of the most powerful energy and resource hungry supercomputers in the world. This is due to the chaotic complex nature of the atmosphere which interpretation require virtually unlimited computing and storage resources. With Machine Learning (ML) techniques, a statistical approach can be designed in order to perform weather forecasting activity. Moreover, the recently growing interest in Edge Computing Tiny Intelligent architectures is proposing a shift towards the deployment of ML algorithms on Tiny Embedded Systems (ES). This paper describes how Deep but Tiny Neural Networks (DTNN) can be designed to be parsimonious and can be automatically converted into a STM32 microcontroller-optimized C-library through X-CUBE-AI toolchain; we propose the integration of the obtained library with Miosix, a Real Time Operating System (RTOS) tailored for resource constrained and tiny processors, which is an enabling factor for system scalability and multi tasking. With our experiments we demonstrate that it is possible to deploy a DTNN, with a FLASH and RAM occupation of 45,5 KByte and 480 Byte respectively, for atmospheric pressure forecasting in an affordable cost effective system. We deployed the system in a real context, obtaining the same prediction quality as the same DNN model deployed on the cloud but with the advantage of processing all the necessary data to perform the prediction close to environmental sensors, avoiding raw data traffic to the cloud.
Remotely Activated Protein-Producing Nanoparticles (2012)

The development of responsive nanomaterials, nanoscale systems that actively respond to stimuli, is one general goal of nanotechnology. Here we develop nanoparticles that can be controllably triggered to synthesize proteins. The nanoparticles consist of lipid vesicles filled with the cellular machinery responsible for transcription and translation, including amino acids, ribosomes, and DNA caged with a photolabile protecting group. These particles served as nanofactories capable of producing proteins including green fluorescent protein (GFP) and enzymatically active luciferase. In vitro and in vivo, protein synthesis was spatially and temporally controllable, and could be initiated by irradiating micrometer-scale regions on the time scale of milliseconds. The ability to control protein synthesis inside nanomaterials may enable new strategies to facilitate the study of orthogonal proteins in a confined environment and for remotely activated drug delivery.
Remote Lasing in Humid Air from Atomic Hydrogen (2020)

Over the last few years, air lasing has emerged as an attractive topic in standoff detection research. However, existing approaches have relied on the major species of air as the gain medium. This work presents the first experimental demonstration of an air laser based on water vapor, a minor constituent of air. The approach relies on photodissociation of water vapor molecules followed by two-photon pumping of the constituent hydrogen atoms to produce lasing on the well-known Balmer-alpha line. This hydrogen laser is characterized in both the forward as well as return direction, and this paper discusses the effect of some parameters, including the presence and type of buffer gas, as well as the pump beam focusing. It is found that most of these results can be explained in terms of their influence on the gain of the stimulated emission process. This method can be potentially applied to other hydrogen-containing molecules and offers a promising approach for standoff detection of trace species.
The Spastic Paraplegia-Associated Phospholipase DDHD1 Is a Primary Brain Phosphatidylinositol Lipase (2018)

Deleterious mutations in the serine hydrolase DDHD domain containing 1 (DDHD1) cause the SPG28 subtype of the neurological disease hereditary spastic paraplegia (HSP), which is characterized by axonal neuropathy and gait impairments. DDHD1 has been shown to display PLA1-type phospholipase activity with a preference for phosphatidic acid. However, the endogenous lipid pathways regulated by DDHD1 in vivo remain poorly understood. Here we use a combination of untargeted and targeted metabolomics to compare the lipid content of brain tissue from DDHD1<sup>+/+</sup> and DDHD1<sup>-/-</sup> mice, revealing that DDHD1 inactivation causes a substantial decrease in the level of polyunsaturated lysophosphatidylinositol (LPI) lipids and a corresponding increase in the level of phosphatidylinositol (PI) lipids. Levels of other phospholipids were mostly unchanged, with the exception of decreases in the levels of select polyunsaturated lysophosphatidylserine (LPS) and lysophosphatidylcholine lipids and a striking remodeling of PI phosphates (e.g., PIP and PIP2) in DDHD1<sup>-/-</sup> brain tissue. Biochemical assays confirmed that DDHD1 hydrolyzes PI/PS to LPI/LPS with sn-1 selectivity and accounts for a substantial fraction of the PI/PS lipase activity in mouse brain tissue. These data indicate that DDHD1 is a principal regulator of bioactive LPI and other lysophospholipids, as well as PI phosphates, in the mammalian nervous system, pointing to a potential role for these lipid pathways in HSP.
Relaxation of coherency stresses by dislocation networks in lamellar γ-TiAl (2001)

Abstract Dislocation networks may relax the coherency stresses at the γ-γ interface of lamellar γ-TiAl. Generally, however, the information on these networks is incomplete. In this paper, we show, with a specific example, that a systematic theoretical analysis is necessary to remove at least part of the uncertainty and give all the possible solutions. The conclusions of this analysis are compared with available published results.
Quantitative immunohistochemical differences between catalase and thioredoxin in different anatomic compartments of the lung in severe COPD (2014)

Extensive evidence indicates that tobacco smoke-induced COPD is associated with an altered cellular redox state and an uncontrolled immune-inflammatory response in a genetically susceptible host. Catalase (CAT) is a primary-line antioxidant and the scavenging thioredoxin (TRX) system plays a decisive role in the maintenance of a reduced intracellular redox state. AIMS investigates the density of immunoreactivity to CAT/TRX and the interrelationship between inflammatory profiles, destructive(DI)/proliferative index (PI) in severe COPD. Immunocytochemistry was performed using paraffin-embedded sections from controls (non-smokers), and subjects with very severe COPD. Quantitative differences in the distribution of macrophages (MQ), neutrophils, CAT/TRX were analyzed in the same Region-of-Interset (ROI) in three different anatomical compartments: small airways, peripheral pulmonary artery, and alveolar parenchyma for each subject. A moderate CAT immunostaining in the luminal bronchiolar epithelium and stronger immunostaining in SMM was observed in the COPD group. The intensity of CAT-staining showed a positive correlation between histological neutrophils reactions/PI mostly in alveolar parenchyma. The percentage of TRX immunoreactivity was significantly higher in bronchiolar epithelium and moderate in bronchiolar adventitial compartments. In contrast, the TRX-immunostaing was weak in tunica intima but significantly greater in adventitia. In summary, the intensity of positive staining of adventitial compartments/SMM regions was significantly higher for both CAT and TRX; moreover CAT staining positively correlates with neutrophils.
A Comparison between Class-E DC-DC Design Methodologies for Wireless Power Transfer (2021)

We consider the design of Wireless Power Transfer (WPT) systems based on inductive links and focus on recent works where the whole WPT system (i.e. both energy transmitter and energy receiver) is designed as an isolated resonant class-E DC-DC converter characterized by a loosely-coupled transformer. The aim of this work is to compare the classic WPT design approach with a novel one, which allows achieving the same performance with a significant reduction in the number of reactive components of the circuit, with beneficial effects in terms of system complexity, size, and cost. We will also show that such a reduction in the number of reactive components leads to improved performance robustness to variations in the inductive link coupling factor.
Simultaneous biplane high speed 1000 fps x-ray angiography (HSAngio) (2022)

High-speed 1000-fps x-ray Angiography (HSAngio) images can be used to visualize blood-flow patterns and derive flow velocities during neurointerventional procedures. In this work, we present for the very first-time, orthogonal views of contrast injection in an aneurysm model acquired simultaneously using biplane HSAngio imaging. 3-D printed in-vitro models A and B of two different internal carotid-artery aneurysms were connected to a flow loop (circulation fluid: 60% water, 40% glycerol solution, circulation flow rate: 8 L/s). An automatic programmable injector (KD Scientific Legato 110) injected iodine contrast agent at a rate of 88 mL/min for a duration of 3 sec. With an RQA5 spectrum, 1000 fps HSAngio sequences of the contrast injection were acquired simultaneously on the frontal plane using the Actaeon detector (Direct Conversion, Stockholm) and on the lateral plane using the Aries (Direct Conversion, Stockholm) detector. The start of contrast injection and simultaneous biplane x-ray exposures and detector image acquisitions were manually synchronized to capture the initial inflow of contrast into the aneurysm region. For model A the frontal plane images gave a better visualization of the flow streamlines in the parent artery in the inflow (average velocity 28 cm/s) and outflow (average velocity 24 cm/s) region of the aneurysm. The vortices within the aneurysm region especially within the aneurysm dome were better visualized in the lateral plane images (average velocity 27 cm/s). Biplane HSAngio imaging techniques can give more accurate representations of 3-D blood flow within the complex vascular pathology of the human brain, compared to single-plane imaging.
On the use of low-cost PVA fiber to develop ECC material for pavement use (2016)

In this study, new ECC mixture designs have been developed using a type of low-cost PVA fiber without oil-coating. High fly ash content, fly ash cenosphere and crumb rubber were incorporated into the mixture design to compensate for the micromechanical change associated with using the low-cost PVA fiber. Compressive and tensile test were conducted to characterize the performance of the newly developed ECC mixtures. ECC with tensile strength of 5.6 MPa and tensile strain capacity of 1.9% has been successfully developed using such fiber. For applications requiring higher tensile ductility, by increasing fly ash content and incorporating FAC or crumb rubber, the tensile ductility of the new ECCs can be further enhanced with moderate decrease in compressive and tensile strength. By incorporating low-cost PVA fiber, the cost-effectiveness of ECC has been greatly improved, which is expected to greatly promote the application of ECC in pavement engineering field in China.
[Psychodynamic consequences of a family history with psychiatric disorders]. (2018)

A positive family history for psychiatric disorders is the most important risk indicator for developing psychopathology. Often, the psychological consequences of a positive family history are insufficiently acknowledged. <br/> AIM: To provide insight into the psychodynamics of children who grow up in a family with psychopathology, such as psychosis, to demonstrate how these effects can last a lifetime, and to suggest ways in which such effects might be prevented.<br/> METHOD: We review the relevant literature, discuss theoretical concepts, and make clinical recommendations.<br/> RESULTS: Parental psychopathology, including psychosis, can have a strong and lasting influence on the child's identity and sense of self.<br/> CONCLUSION: A positive family history for psychiatric disorders has the potential to seriously disrupt the normal development of identity and sense of self. Various types of psychosocial interventions might be able to reduce these harmful effects.
Optimization of mixture preparation in an S.I. engine (1994)

This thesis commences with a survey of literature relevant to the subject of toxic emissions from SI engines and the methods available for reduction. The survey pointed to a particular route for reducing emissions by the use of a device in the port to increase in-cylinder motion at low engine speed and load conditions, coupled with an improvement in mixture preparation. This was to be investigated on an ECP2 engine which had been designed and manufactured by Jaguar. Initial testing was performed on a steady flow test rig using ECP2 hardware to investigate air flow patterns within the port. An understanding of the air flow in the inlet port is a precursor to the understanding of subsequent fuel/air interactions. This was followed by a series of tests to evaluate an air-assisted atomiser fuel injector, carried out by applying laser diffraction particle sizing techniques. The main body of work is associated with the investigation of mixture preparation within the cylinder and this required the design of a purpose-built single-cylinder engine. The design and construction of the optically-accessed research engine is covered in some depth. The engine was fitted with a 70 mm diameter quartz window in the piston crown and with smaller windows in the inlet ports. The development of engine and instrumentation control systems is also described. These tasks included electronic circuit design, calibration, and computer software development. A test program was performed on the engine using a copper-vapour laser and high-speed cine equipment. Photographic procedures were refined to obtain high-speed cine films of in-cylinder fuel behaviour in the firing engine. Image digitisation equipment was developed and software techniques were established to process the cine-film results of engine tests. The results of the test program are presented along with discussions and conclusions drawn. The design of a novel fuel vaporisation/atomisation unit is also described.
Transmission ion microscopy and time-of-flight spectroscopy (2021)

A Transmission Ion Microscope (TIM), the Galileo prototype, has been built at the Luxembourg Institute of Science and Technology (LIST) This is part of a new interest in the imaging properties of transmitted helium ions [2] [3] [4]. This allows the combination of both helium ions and neutrals to be detected after passing through a sample, or, if post sample deflection is used, then only the signal from the neutrals (Figure The helium ions have an energy between 10 keV and 20 keV and are produced in a Duoplasmatron ion source.
Reconstructing anisotropic conductivities on two-dimensional Riemannian manifolds from power densities (2022)

We consider an electrically conductive compact two-dimensional Riemannian manifold with smooth boundary. This setting defines a natural conductive Laplacian on the manifold and hence also voltage potentials, current fields and corresponding power densities arising from suitable boundary conditions. Motivated by Acousto-Electric Tomography we show that if the manifold has genus zero and the metric is known, then the anisotropic conductivity can be recovered uniquely and constructively from knowledge of a few power densities. We illustrate the procedure numerically by reconstructing an anisotropic conductivity on the catenoid, i.e. the classical genus zero minimal surface in three-space.
PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae (1996)

A PCR-method for fast production of disruption cassettes is introduced, that allows the addition of long flanking homology regions of several hundred base pairs (LFH-PCR) to a marker module. Such a disruption cassette was made by linking two PCR fragments produced from genomic DNA to kanMX6, a modification of dominant resistance marker making S. cerevisiae resistant to geneticin (G418). In a first step, two several hundred base pairs long DNA fragments from the 5'- and 3'- region of a S. cerevisiae gene were amplified in such a way that 26 base pairs extensions homologous to the kanMX6 marker were added to one of their end. In a second step, one strand of each of these molecules then served as a long primer in a PCR using kanMX6 as template. When such a LFH-PCR-generated disruption cassette was used instead of a PCR-made disruption cassette flanked by short homology regions, transformation efficiencies were increased by at least a factor of thirty. This modification will therefore also help to apply PCR-mediated gene manipulations to strains with decreased transformability and/or unpredictable sequence deviations.
Analysis of a Urinary Biomarker Panel for Incident Kidney Disease and Clinical Outcomes (2013)

Whether novel biomarkers improve the assessment of incident kidney disease and related adverse outcomes remains to be tested in longitudinal observational studies. We tested 14 urinary biomarkers for association with incident kidney, cardiovascular, and mortality outcomes in 2948 Framingham Heart Study participants. Baseline examinations were performed between 1995 and 1998; mean follow-up was 10.1 years for renal outcomes and 11.2 years for survival analyses. Primary outcomes were incident CKD, incident albuminuria, incident cardiovascular disease, and all-cause mortality. Secondary analyses assessed incident congestive heart failure (CHF) and mortality with coexistent kidney disease. Biomarkers were tested for association with renal end points using logistic regression and incident cardiovascular and mortality outcomes in proportional hazards models; α1-microglobulin, Kim-1, and TFF-3 predicted all-cause mortality (hazard ratio per SD increase in log-transformed biomarker [HR] range, 1.15 to 1.21; 95% confidence interval [CI] range, 1.04 to 1.34; P values=0.007 to <0.001), whereas α1-microglobulin, β2-microglobulin, KIM-1, and TFF-3 associated with death with coexistent kidney disease (HR range, 1.72-2.25; 95% CI, 1.17 to 3.24; P values<0.01). KIM-1 also associated with the risk of incident CHF (HR, 1.32; 95% CI, 1.07 to 1.63; P=0.008). CTGF associated nominally with CKD (HR, 0.83; 95% CI, 0.71 to 0.98; P=0.03), but no other biomarkers associated with incident CKD or albuminuria. Addition of α1-microglobulin and TFF-3 resulted in a nonsignificant net reclassification index (NRI) of 3% for all-cause mortality beyond clinical risk factors. In conclusion, components of a panel of 14 subclinical biomarkers of kidney injury were associated with important clinical outcomes and merit additional investigation.