gebhart/patrepeval huggingface dataset:
Oriented Bacteriorhodopsin/Polycation Multilayers by Electrostatic Layer-by-Layer Assembly (1998)

The purple membrane (PM) containing bacteriorhodopsin (BR) is a promising biomaterial for many potential optical and optoelectronic device applications. Organized, heterogeneous assemblies using polycationic poly(dimethyldiallylammonium chloride) (PDAC) and PM fragments have been successfully constructed by the spontaneous alternating adsorption of PDAC and PM. The fabrication process of the multilayers was followed by UV−vis absorption spectroscopy and ellipsometry. The results indicate that the deposition process is linear and highly reproducible from layer to layer and that a monomolecular film of PM may be obtained in each PDAC/PM bilayer by controlling the adsorption time. Second harmonic generation measurements from the composite films gave a second-order susceptibility χ(2) of 8.1 × 10-9 esu and confirm that the PM fragments are arrayed with a high degree of orientation and acentric polar order in the films. Atomic force microscopy images provided the surface morphology of sequential layers of PDAC and PM fragments. Relative PDAC/PM bilayer thicknesses of 55 Å were observed, and the homogeneity of the layers was found to improve as the number of layers increased.
Neuropsychological outcome and quantitative image analysis of acute haemorrhage in traumatic brain injury: Preliminary findings (1994)

The effect on neuropsychological outcome of the number of acute haemorrhages, lesion volume, and lesion location in traumatic brain injury (TBI) was evaluated. Haemorrhagic lesion volume was associated with severity of injury. However, the number of petechial haemorrhages was not reliably associated with any of the clinical outcome measures. Likewise, despite the use of detailed morphometric methods to quantify volume, the acute lesion size did not significantly relate to neuropsychological sequelae. Furthermore, brain quadrant localization methods did not enhance outcome prediction. These results are discussed in the context of acute lesion analysis contrasted with chronic TBI-induced neuropathological changes associated with neuropsychological outcome.
Dual Equal VCT - A Variable Camshaft Timing Strategy for Improved Fuel Economy and Emissions (1995)

&lt;div class="htmlview paragraph"&gt;In the Dual Equal variable camshaft timing strategy, the intake and exhaust events are equally phase-shifted relative to the crankshaft as a function of engine operating conditions. The primary emphasis is on improved fuel economy and emissions at part load. The external EGR system is potentially eliminated, with consequent improvement in the transient control of residual dilution. Additional benefits with optimized phasing are moderate improvements in idle stability and full load performance.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;In this paper, the Dual Equal VCT strategy is described, and engine dynamometer test results are shown which illustrate the benefits at part load, idle, and WOT. Implications of the strategy on phase-shifter response requirements and on the engine control system are discussed.&lt;/div&gt;
CHOLINE SUPPRESSES INFLAMMATORY RESPONSES (2006)

Systemic inflammation caused by excessive production of TNF and other pro-inflammatory cytokines is a hallmark of sepsis. Recent studies demonstrate that electrical stimulation of the efferent vagus nerve inhibits TNF production and attenuates systemic inflammation (Nature, 2000, 420:853; Nature, 2003, 421:384). The α7 nicotinic acetylcholine receptor (α7nAChR) expressed on macrophages plays a key role in mediating the vagal anti-inflammatory effect (Nature, 2003, 421:384). These findings suggest the therapeutic potential of specifically targeting the α7nAChR to activate endogenous immunoregulatory mechanisms to temper excessive inflammatory responses. Here we examined the ability of the endogenous and selective α7nAChR agonist choline to attenuate TNF production in vitro and in vivo. Choline (0.01 - 50 mM) dose-dependently inhibited TNF release from endotoxin-stimulated RAW 264.7 mouse macrophages and primary human macrophages, which express α7nAchR (Nat. Med., 2004, 10(11): 1216; Nature, 2003, 421:384). Inhibition of TNF production from RAW 264.7 macrophages correlated with attenuation of NF-κB activity, suggesting that NF-κB represents a downstream target of cholinergic anti-inflammatory signaling. Choline treatment (5 and 50 mg/kg, i.p.), 30 min prior to endotoxin administration (6 mg/kg, i.p.) in mice, dose-dependently reduced serum TNF levels. These data demonstrate the anti-inflammatory activity of choline, an endogenous α7nAChR agonist, and indicate its therapeutic potential in restraining excessive inflammation. This study was funded in part by a FIMR research award to VAP.
Energy-Efficient Distributed Transmission Scheme for MTC in Dense Wireless Networks: A Mean-Field Approach (2019)

In this article, we address the problem of long-term resource allocation for a 5G and beyond dense wireless network. Of particular interest within the considered framework are machine-type communications (MTCs). To establish an optimal operation for an energy-efficient MTC system, the power allocation policy should be designed by taking into consideration both channel and queue states of the devices. This problem formulation belongs to the category of complex stochastic optimization that can be recast as a Markov decision process (MDP) over high-dimensional state space. We circumvent the hurdle inherent to state space of a huge dimension by resorting to mean-field approximation on the MDP. More specifically, we demonstrate that the formulated MDP converges to a deterministic control problem provided that the number of devices approaches infinity. We develop a low-complexity power allocation scheme to efficiently solve the original high-dimensional state space stochastic optimization problem. Our proposed power allocation policy is drawn from the solution of the Hamilton-Jacobi-Bellman equation. It can be understood as a threshold-based policy and can be implemented in a decentralized manner that makes it very appealing for high scale networks. Finally, the simulations analyses are provided to establish the effectiveness of our proposed framework.
Photonic Integration in State-of-the-Art Silicon Electronics Processes (2012)

Photonic integration within state-of-the-art CMOS and DRAM processes leverages the existing electronic manufacturing infrastructure to minimize cost. Suitable design techniques combined with in-foundry optimization or post-processing have enabled integration within several advanced technologies.
Evaluation of a remote webcam-based eye tracker (2011)

In this paper we assess the performance of an open-source gaze tracker in a remote (i.e. table-mounted) setup, and compare it with two other commercial eye trackers. An experiment with 5 subjects showed the open-source eye tracker to have a significantly higher level of accuracy than one of the commercial systems, Mirametrix S1, but also a higher error rate than the other commercial system, a Tobii T60. We conclude that the web-camera solution may be viable for people who need a substitute for the mouse input but cannot afford a commercial system.
Exploration of Activated Pathways for Improving Antifungal Agent FR901469 Productivity in Fungal Species No.11243 Using Comprehensive Pathway Model (2017)

Secondary metabolites are important for various industrial applications. The production of secondary metabolites is often improved by the activation of substrate supply pathways for biosynthesis. However, many important pathways have remained unclear. In this study, we explored possible pathways related to substrate supply for the biosynthesis of the antifungal agent FR901469 which is a nonribosomal peptide and a fungal secondary metabolite. To clarify the unknown activated pathways, we utilized the Comprehensive Pathway Model (CPM) which was developed in our previous study. We verified that the overexpression of the hypothetical beta-alanine-aminotransferase (BAL-AT), which was included in the explored pathways, improved the FR901469 productivity. The genes encoding the BAL metabolic enzymes are considered to be important for improving the FR901469 productivity.
Bioengineering heart valves using autologous endothelial progenitor cell‐seeded bioscaffolds (2010)

Current valve replacement procedures often require repeat operations. Presently, the options available for heart valve replacements have limited durability and slow integration and often require lifelong anticoagulation. We hypothesize that tissue engineered heart valves (TEHVs) using autologous endothelial progenitor cell (EPC)‐derived endothelial cells (ECs) to cover a bioscaffold will provide an implant that does not require anticoagulation, produces minimal host immune response, and has the potential to remodel as the patient grows. Autologous EPCs were isolated from the peripheral circulation by random blood sampling and affinity column separation using an arterial‐venous shunt containing a column of antibodies recognizing the CD‐133 surface marker. Decellularized pig pulmonary heart valves were seeded with EPC‐derived ECs under static conditions or under pulsatile flow using a bioreactor, which then enhances cell coverage while maintaining biomechanical properties. Re‐endothelialization of decellularized pulmonary heart valve scaffolds may enhance the functionality and longevity of TEHVs. It is postulated that these bioengineered valves will integrate into host tissue faster, remodel as the patient grows and respond to in vivo physiological signaling, producing a longer lasting valve implant.
Oxidative Catabolism of (+)-Pinoresinol Is Initiated by an Unusual Flavocytochrome Encoded by Translationally Coupled Genes within a Cluster of (+)-Pinoresinol-Coinduced Genes in Pseudomonas sp. Strain SG-MS2 (2020)

<i>Burkholderia</i> sp. strain SG-MS1 and <i>Pseudomonas</i> sp. strain SG-MS2 have previously been found to mineralize (+)-pinoresinol through a common catabolic pathway. Here, we used comparative genomics, proteomics, protein semipurification, and heterologous expression to identify a flavoprotein from the vanillyl alcohol oxidase/<i>p</i>-cresol methyl hydroxylase (VAO/PCMH) enzyme family in SG-MS2 that carries out the initial hydroxylation of (+)-pinoresinol at the benzylic carbon. The cognate gene is translationally coupled with a downstream cytochrome gene, and the cytochrome is required for activity. The flavoprotein has a unique combination of cofactor binding and cytochrome requirements for the VAO/PCMH family. The heterologously expressed enzyme has a <i>K<sub>m</sub></i> of 1.17 μM for (+)-pinoresinol. The enzyme is overexpressed in strain SG-MS2 upon exposure to (+)-pinoresinol, along with 45 other proteins, 22 of which were found to be encoded by genes in an approximately 35.1-kb cluster also containing the flavoprotein and cytochrome genes. Homologs of 18 of these 22 genes, plus the flavoprotein and cytochrome genes, were also found in a 38.7-kb cluster in SG-MS1. The amino acid identities of four of the other proteins within the SG-MS2 cluster suggest they catalyze conversion of hydroxylated pinoresinol to protocatechuate and 2-methoxyhydroquinone. Nine other proteins upregulated in SG-MS2 on exposure to (+)-pinoresinol appear to be homologs of proteins known to comprise the protocatechuate and 2-methoxyhydroquinone catabolic pathways, but only three of the cognate genes lie within the cluster containing the flavoprotein and cytochrome genes.<b>IMPORTANCE</b> (+)-Pinoresinol is an important plant defense compound, a major food lignan for humans and some other animals, and the model compound used to study degradation of the β-β' linkages in lignin. We report a gene cluster, in one strain each of <i>Pseudomonas</i> and <i>Burkholderia</i>, that is involved in the oxidative catabolism of (+)-pinoresinol. The flavoprotein component of the α-hydroxylase which heads the pathway belongs to the 4-phenol oxidizing (4PO) subgroup of the vanillyl alcohol oxidase/<i>p</i>-cresol methyl hydroxylase (VAO/PCMH) enzyme family but constitutes a novel combination of cofactor and electron acceptor properties for the family. It is translationally coupled with a cytochrome gene whose product is also required for activity. The work casts new light on the biology of (+)-pinoresinol and its transformation to other bioactive molecules. Potential applications of the findings include new options for deconstructing lignin into useful chemicals and the generation of new phytoestrogenic enterolactones from lignans.
Selective inhibition of neutrophil elastase by BAY 85-8501 improves exercise capacity and pulmonary hypertension in a porcine pancreatic elastase-induced emphysema model (2014)

Neutrophil elastase is a serine proteinase, that has the ability to degrade a wide range of matrix proteins, especially elastin, and plays an important role for the modulation of the inflammatory response. Uninhibited neutrophil elastase activity has been implicated in the development of emphysema and pulmonary vascular remodeling. We therefore investigated the novel selective neutrophil elastase inhibitor BAY 85-8501 in a porcine pancreatic elastase (pPE)-induced emphysema model in mice. After a single orotracheal administration of pPE (0.3 U), male C57Bl6J mice displayed a reduced exercise capacity (running distance, top speed) during the following three weeks. At day 21 hemodynamic and morphological investigations showed an elevated right ventricular systolic pressure and right ventricular hypertrophy. Treatment with BAY 85-8501 significantly reduced right ventricular pressure and right ventricular hypertrophy. This was associated with a significant larger running distance and higher top speed in comparison to the placebo group. RVPsys, mmHg RV/(LV+S) Control 21 ± 0.48* 0.29 ± 0.01* pPE + Vehicle 30.61 ± 2.53 0.40 ± 0.03 pPE + BAY 85-8501 25.74 ± 0.53* 0.31 ± 0.01* Mean ± SEM. N=8-12/group.*, p&lt;0.05 vs. vehicle, RVP=right ventricular systolic pressure Conclusion: The orotracheal application of porcine pancreatic elastase in mice induces tissue damage and inflammation, leading to pulmonary hypertension associated with emphysema. Selective inhibition of neutrophil elastase by BAY 85-8501 significantly increases exercise capacity and substantially improves hemodynamic and morphological parameters.
Small-Signal, High Frequency Performance of Vertical GaN FinFETs with fmax = 5.9 GHz (2021)

GaN vertical finFETs are capable of high breakdown voltages and large current density without the need for regrowth or p-type doping. These attributes make them a promising candidate for next-generation high-frequency power applications. Here, we demonstrate the first high frequency characterization of vertical GaN finFETs. These devices utilize a highly insulating sapphire substrate and a quasi-vertical design that avoids the expensive bulk-GaN substrates typically used in vertical power applications. Moreover, contacts remain on the top of the wafer, thereby enabling high-frequency characterization and potentially easing future system integration.
Measurement of deformation of paper subjected to tensile loads using electronic speckle pattern interferometry (2003)

This study deals with the measurement of the deformation of sheets of recycled paper subjected to tensile loads using an electronic speckle pattern interferometry (ESPI) technique. Specimens with fibers, which constitute a sheet of paper, parallel and perpendicular to the direction of paper making are used to investigate the effect of the arrangement of fibers on the tensile property. The deformation of recycled paper is compared with that of virgin pulp paper. Results reveal that a large two-dimensional deformation of recycled paper can be measured using the ESPI technique, and that the directions of fibers, which constitute a sheet of paper, have a significant effect on the two-dimensional deformation of recycled paper.
Architecting for innovation (2011)

We argue that the biggest problem with the current Internet architecture is not a particular functional deficiency, but its inability to accommodate innovation. To address this problem we propose a minimal architectural "framework" in which comprehensive architectures can reside. The proposed Framework for Internet Innovation (FII) --- which is derived from the simple observation that network interfaces should be extensible and abstract --- allows for a diversity of architectures to coexist, communicate, and evolve. We demonstrate FII's ability to accommodate diversity and evolution with a detailed examination of how information flows through the architecture and with a skeleton implementation of the relevant interfaces.
Output tracking for quadrotor-based aerial manipulators (2015)

For a class of aerial manipulators given by a quadrotor aerial vehicle endowed with a robotic arm, this work focuses on the design of a feedback control strategy to let the position and the orientation of the end-effector to track a desired trajectory. Different configurations of robotic arms are taken into account so as to link the number of actuated degrees of freedom to the achievable tracking performances. In particular, when a robotic arm characterized by the minimum number of actuated joints is considered, it is shown how the presence of an offset between the point in which the manipulator is attached and the center of gravity of the vehicle may introduce some unstable internal dynamics affecting the achievable asymptotic performances. Such a limitation can be removed by properly exploiting robotic manipulators characterized by a redundant number of actuated joints. The proposed feedback control strategy is then shown to be able to exploit the mechanical layout of the manipulator so as to achieve asymptotic or practical tracking of the desired references.
Effects of sulfurization temperature on Cu2ZnSnS4thin film deposited by single source thermal evaporation method (2015)

In this study, the effects of sulfurization temperature on the properties of thermally evaporated Cu2ZnSnS4 (CZTS) thin films were investigated. Molybdenum (Mo) coated soda lime glass (SLG) was used as substrates and stoichiometric CZTS powder (99.95%) was used as the source material. XRD patterns showed that CZTS were formed with preferential orientations of (112) > (220) > (312) for all the investigated films. The intensity of (112) peak is found increasing until a certain temperature indicating that the highest degree of crystallinity is achieved together with secondary phases such as ZnS and SnS. It was confirmed by raman shift at 338 cm−1 from Raman spectroscopy, scanning electron microscopy (SEM) and atomic force microscopy (AFM) results showed a trend for surface roughness as well as morphology. From Hall effect measurement, all deposited films exhibited p-type conductivity. From UV–vis spectroscopy measurement, the optical band gap of all the films are found in the range of potential absorbers for CZTS based thin film solar cells.
Domestication of Campylobacter jejuni NCTC 11168 (2019)

Abstract Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterised isolates among laboratories has parallelised research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C. jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates identified previously to have aberrant phenotypes varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37°C, invasion of chicken and human cell lines and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. Impact statement In this paper, we comment on the changing role of laboratory reference strains. While the model organism allows basic comparison within and among laboratories, it is important to remember the effect even small differences in isolate genomes can have on the validity and reproducibility of experimental work. We quantify differences in 23 reference Campylobacter genomes and compare them with observable differences in common laboratory phenotypes. Data summary Short read data are archived on the NCBI SRA associated with BioProject accession PRJNA517467 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467 ). All assembled genomes are also available on FigShare (doi: 10.6084/m9.figshare.7849268). Phylogeny visualised on microreact: https://microreact.org/project/NCTC11168 . Repositories Short read data are archived on the NCBI SRA repository, associated with BioProject accession PRJNA517467 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467 ; Table S1 ). The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Predator-secreted sulfolipids induce fear-like defense responses in C. elegans (2017)

Abstract Animals respond to predators by altering their behavior and physiological states, but the underlying signaling mechanisms are poorly understood. Using the interactions between Caenorhabditis elegans and its predator, Pristionchus pacificus , we show that neuronal perception by C. elegans of a predator-specific molecular signature induces instantaneous escape behavior and a prolonged reduction in oviposition. Chemical analysis revealed this predator-specific signature to consist of a class of sulfolipids, produced by a biochemical pathway required for developing predacious behavior and specifically induced by starvation. These sulfolipids are detected by four pairs of C. elegans amphid sensory neurons that act redundantly and recruit cyclic nucleotide-gated (CNG) or transient receptor potential (TRP) channels to drive both escape and reduced oviposition. Specific abolishment of predator-evoked C. elegans responses by the anti-anxiety drug sertraline as well as functional homology of the delineated signaling pathways suggests a conserved or convergent strategy for managing predator threats.
Stem Cells Rejuvenate Radiation-Impaired Vasculogenesis in Murine Distraction Osteogenesis (2014)

Bone marrow stromal cells used together with distraction osteogenesis can rejuvenate radiation-impaired vasculogenesis in the mandible, reversing radiation therapy-induced isotropy and creating a robust vascular network. Bone marrow stromal cells may offer clinicians an alternative reconstructive modality that could improve the lifestyle of patients with hypovascular bone.
Hydrothermal Oxidation of Olive Oil Mill Wastewater with Multi-Injection of Oxygen: Simulation and Experimental Data (2008)

Hydrothermal oxidation is an alternative process to conventional methods for wastewater treatment. In this study, a new reactor concept with oxygen multi-injection was used to carry out the oxidation of olive oil mill wastewater. Different experiments have been performed with feed temperatures of 200, 250, 280, and 300°C at the reactor inlet. The global reaction heat was found equal to −590 kJ/mol. The temperature profiles along the reactor have been registered and compared to the simulation of the process performed with PROSIM.