gebhart/patrepeval huggingface dataset:
Interval Type-2 Fuzzy-Logic-Based Constant Switching Frequency Control of a Sliding-Mode-Controlled DC–DC Boost Converter (2023)

The inherent unlimited high switching frequency of the sliding mode controller (SMC) is limited by practical constraints of the hysteresis modulation (HM) technique. The inductor current and output voltage of a converter can be regulated using a combination of HM-SMC. However, HM-SMC results in a variable switching frequency operation, which is not preferred due to Electromagnetic Interference (EMI) issues. In this paper, an interval fuzzy controller is designed and developed as a solution to enable HM-SMC. In addition, a robust sliding surface is proposed, which provides an improved dynamic response. The two proposed controllers’ compatibility with one another has been tested via experiments such as a step change in input voltage, load resistance variation, and finally, a step change in output voltage reference value. The test results validate that while the interval type-2 fuzzy maintains a constant switching frequency with acceptable dynamic responses, it successfully regulates the state variables of the system. A comparison of the performance of the proposed control method with existing techniques in the literature is presented.
Biochemistry and molecular biology of CAM (1992)

Crassulacean Acid Metabolism (CAM) has been called a curiosity (Osmond, 1978), the importance of which has been long overlooked in the context of environmental adaptations of plants to cope with arid, hot environments. CAM has since been studied more intensely and our knowledge has been extended by focusing on physiological studies (Ting & Gibbs, 1982; Ting, 1985; Cockburn, 1985), on the biochemical characterisation of important enzymes (O'Leary, 1982; Nimmo et al., 1986), and on ecological aspects (Kluge & Ting, 1978; Lüttge, 1987).
LIGHT Expression by Mucosal T Cells May Regulate IFN-γ Expression in the Intestine (2004)

The TNF superfamily of cytokines play an important role in T cell activation and inflammation. Sustained expression of lymphotoxin-like inducible protein that competes with glycoprotein D for binding herpesvirus entry mediator on T cells (LIGHT) (TNFSF14) causes a pathological intestinal inflammation when constitutively expressed by mouse T cells. In this study, we characterized LIGHT expression on activated human T cell subsets in vitro and demonstrated a direct proinflammatory effect on regulation of IFN-gamma. LIGHT was induced in memory CD45RO CD4+ T cells and by IFN-gamma-producing CD4+ T cells. Kinetic analysis indicated rapid induction of LIGHT by human lamina propria T cells, reaching maximal levels by 2-6 h, whereas peripheral blood or lymph node-derived T cells required 24 h. Further analysis of intestinal specimens from a 41 patient cohort by flow cytometry indicated membrane LIGHT induction to higher peak levels in lamina propria T cells from the small bowel or rectum but not colon, when compared with lymph node or peripheral blood. Independent stimulation of the LIGHT receptor, herpesvirus entry mediator, induced IFN-gamma production in lamina propria T cells, while blocking LIGHT inhibited CD2-dependent induction of IFN-gamma synthesis, indicating a role for LIGHT in the regulation of IFN-gamma and as a putative mediator of proinflammatory T-T interactions in the intestinal mucosa. Taken together, these findings suggest LIGHT-herpesvirus entry mediator mediated signaling as an important immune regulatory mechanism in mucosal inflammatory responses.
Managing educational change in the ICT discipline at the tertiary education level (2009)

Professor Joe Chicharo, University of Wollongong Professor Fazel Naghdy, University of Wollongong Professor Ron Weber, Monash University Dr Judy Sheard, Monash University Professor Simon Kaplan, Queensland University of Technology Associate Professor Sylvia Edwards, Queensland University of Technology Associate Professor Tom Hintz, University of Technology Sydney Associate Professor David Wilson, University of Technology Sydney
Encapsulating Biopolymer for Control of Clay and Fines Generation in Unconventional Reservoirs (2018)

Abstract The current trends to re-evaluate the need for traditional clay control additives and the interest in increasing hydrocarbon production from secondary fracture networks are leading to the use of more appropriate fluid compositions. Additives historically used to dehydrate or exchange interlayer cations in water-reactive phyllosilicates introduce instability in the reservoir matrix and have been used in shale reservoirs without thorough assessments of potential formation damage. Framing the need for clay control in these reservoirs solely on the need to control water-reactive clays led naturally to the removal of clay control additives from fluids during the recent downturn. While justified from a cost perspective, these simplified fluids were introduced without assessments of the impact of near colloidal (10-40um diameter) fines generation. Completion experts who realize the formation damage risk of fines generation recognized these problems. This paper updates the industry on an approach to proportion clay control and shale stabilization with fluid design better aligned to reservoir mineralogy and the stress introduced on the reservoir during hydraulic fracturing. The paper reports swelling clay control and near colloidal fines evaluations from four world class unconventional oil &amp; gas reservoirs in North America. Reproducible fundamental trends in CST and near-colloidal fines generation data are correlated to clay control additive type and use of oxidative breaker. Additionally, this new test method has the potential to be easily and commercially viable for rapid field evaluation to assess formation damage due to fines generation.
Design of a 5' exonuclease-based real-time PCR assay for simultaneous detection of Bacillus licheniformis, members of the 'B. cereus group' and B. fumarioli in gelatine (2004)

Aims: The design of a fast, sensitive and specific detection method for Bacillus licheniformis, members of the ‘B. cereus group’ and B. fumarioli in gelatine. Methods and Results: Specific Taqman probes were designed and tested in a real‐time PCR setting. A specific fluorescent signal could be obtained for all gelatine isolates attributed to these species in one single real‐time PCR reaction. After sample preparation, a gelatine sample spiked with 1 CFU provided enough template DNA for a significant signal. Conclusion: The potential of a real‐time PCR assay for simultaneous detection of B. licheniformis, members of the ‘B. cereus group’ and B. fumarioli in gelatine is demonstrated. Significance and Impact of the Study: Implementation of the assay in gelatine producing plants may shorten delivery terms and inform on hazards to public health and suitable remediation procedures.
Complexation of Cd(SeCN)(2) with imidazolidine-2-thione and its derivatives: Solid state, solution NMR and anti-bacterial studies (2008)

Reactions of imidazolidine-2-thione (Imt), 1,3-diazinane-2-thione (Diaz) and 1,3-diazipane-2-thione (Diap) with Cd(SeCN)2 in acetonitrile resulted in the formation of 2:1 tetrahedral complexes. Both solid state and solution NMR, confirm the exocyclic thione atom to be the donor in all cases. 113Cd shielding tensors and anisotropies were calculated from the solid-state NMR spectra. Based on the solid NMR data, a distorted tetrahedral dispositions of ligands around cadmium is proposed for the Imt complex. However, when the Imt ligand is substituted with one or two R groups (where R=Me, Et or i-Pr) forming RImt or R2Imt, a five coordinate complex with polymeric structure [(RImt)Cd(SeCN)2]∞ or [(R2Imt)Cd(SeCN)2]∞ is observed. Antibacterial studies of some of the complexes were carried out.
Ras-GTP dimers activate the Mitogen-Activated Protein Kinase (MAPK) pathway (2015)

Rat sarcoma (Ras) GTPases regulate cell proliferation and survival through effector pathways including Raf-MAPK, and are the most frequently mutated genes in human cancer. Although it is well established that Ras activity requires binding to both GTP and the membrane, details of how Ras operates on the cell membrane to activate its effectors remain elusive. Efforts to target mutant Ras in human cancers to therapeutic benefit have also been largely unsuccessful. Here we show that Ras-GTP forms dimers to activate MAPK. We used quantitative photoactivated localization microscopy (PALM) to analyze the nanoscale spatial organization of PAmCherry1-tagged KRas 4B (hereafter referred to KRas) on the cell membrane under various signaling conditions. We found that at endogenous expression levels KRas forms dimers, and KRas(G12D), a mutant that constitutively binds GTP, activates MAPK. Overexpression of KRas leads to formation of higher order Ras nanoclusters. Conversely, at lower expression levels, KRas(G12D) is monomeric and activates MAPK only when artificially dimerized. Moreover, dimerization and signaling of KRas are both dependent on an intact CAAX (C, cysteine; A, aliphatic; X, any amino acid) motif that is also known to mediate membrane localization. These results reveal a new, dimerization-dependent signaling mechanism of Ras, and suggest Ras dimers as a potential therapeutic target in mutant Ras-driven tumors.
Calcein Binding to Assess Mineralization in Hydrogel Microspheres (2021)

We describe a method to assess mineralization by osteoblasts within microspheres using calcein. Fluorescence imaging of calcein bound to the calcium in hydroxyapatite permits assessment of the mineralized portion of the extracellular matrix. Colorimetric imaging of Alizarin Red S complexed with calcium also gives measures of mineralization, and in tissue cultures calcein and Alizarin Red S have been shown to bind to the same regions of mineral deposits. We show that when the mineralization takes place within hydrogel microspheres, Alizarin Red S does not stain mineral deposits as consistently as calcein. As tissue engineers increasingly encapsulate osteoprogenitors within hydrogel scaffolds, calcein staining may prove a more reliable method to assess this mineralization.
Transitioning rationally designed catalytic materials to real “working” catalysts produced at commercial scale: nanoparticle materials (2017)

Catalyst design, from idea to commercialization, requires multi-disciplinary scientific and engineering research and development over 10–20 year time periods. Historically, the identification of new or improved catalyst materials has largely been an empirical trial-and-error process. However, advances in computational capabilities (new tools and increased processing power) coupled with new synthetic techniques have started to yield rationally-designed catalysts with controlled nano-structures and tailored properties. This technological advancement represents an opportunity to accelerate the catalyst development timeline and to deliver new materials that outperform existing industrial catalysts or enable new applications, once a number of unique challenges associated with the scale-up of nano-structured materials are overcome.
Finite Element Analysis for Surface Acoustic Wave Device Characteristic Properties and Sensitivity (2019)

The most vital step in the development of novel and existing surface acoustic wave (SAW)-based sensors and transducers is their design and optimization. Demand for SAW devices has been steadily increasing due to their low cost, portability, and versatility in electronics, telecommunications, and biosensor applications. However, a full characterization of surface acoustic wave biosensors in a three-dimensional (3D) finite element model has not yet been developed. In this study, a novel approach is developed for analyzing shear horizontal Love wave resonator devices. The developed modeling methodology was verified using fabricated devices. A thorough analysis of the 3D model and the experimental device was performed in this study including scattering parameters (S-parameters), reflection coefficient parameters, transmission parameters, and phase velocity. The simulated results will be used as a design guideline for future device design and optimization, which has thus far resulted in close matching between prediction and experimental results. This manuscript is the first to demonstrate a 3D finite element model to correlate the sensitivity of the SAW device with the magnitude of the phase shift, the real and imaginary part of the response, insertion loss, and the frequency shift. The results show that the imaginary part of the response shift has a higher sensitivity compared to other parameters.
Interpreting the Mechanisms of Continuous Renal Replacement Therapy in Sepsis: The Peak Concentration Hypothesis (2003)

Severe sepsis and septic shock are the primary causes of multiple organ dysfunction syndrome (MODS), which is the most frequent cause of death in intensive care unit patients. Many water-soluble mediators with pro- and anti-inflammatory action such as TNF, IL-6, IL-8, and IL-10 play a strategic role in septic syndrome. In intensive care medicine, blocking any one mediator has not led to a measurable outcome improvement in patients with sepsis. CRRT is a continuously acting therapy, which removes in a nonselective way pro- and anti-inflammatory mediators; "the peak concentration hypothesis" is the concept of cutting peaks of soluble mediators through continuous hemofiltration. Furthermore, there is evidence of increased efficacy of high-volume hemofiltration compared to conventional CVVH, and other blood purification techniques that utilize large-pore membranes or sorbent plasmafiltration are conceptually interesting.
The Protein Interaction Networks of Catalytically-Active and Catalytically-Inactive PqsE in Pseudomonas aeruginosa (2022)

ABSTRACT Pseudomonas aeruginosa is a human pathogen that relies on quorum sensing to establish infections. The PqsE quorum-sensing protein is required for P. aeruginosa virulence factor production and infection. PqsE has a reported enzymatic function in the biosynthesis of the quorum-sensing autoinducer called PQS. However, this activity is redundant because, in the absence of PqsE, this role is fulfilled by alternative thioesterases. Rather, PqsE drives P. aeruginosa pathogenic traits via a protein-protein interaction with the quorum-sensing receptor/transcription factor, RhlR, an interaction that enhances affinity of RhlR for target DNA sequences. PqsE catalytic activity is dispensable for interaction with RhlR. Thus, PqsE virulence function can be decoupled from its catalytic function. Here, we present an immunoprecipitation-mass spectrometry method employing eGFP-PqsE fusions to define the protein interactomes of wildtype PqsE and the catalytically inactive PqsE(D73A) variant in P. aeruginosa and their dependence on RhlR. Several proteins were identified to have specific interactions with wildtype PqsE, while not forming associations with PqsE(D73A). In the Δ rhlR strain, an increased number of specific PqsE interactors were identified, including the partner autoinducer synthase to RhlR, called RhlI. Collectively, these results suggest that specific protein-protein interactions depend on PqsE catalytic activity and that RhlR may prevent proteins from interacting with PqsE, possibly due to competition between RhlR and other proteins for PqsE binding. Our results provide a foundation for the identification of the in vivo PqsE catalytic function and, potentially, new proteins involved in P. aeruginosa quorum sensing. IMPORTANCE Pseudomonas aeruginosa causes hospital-borne infections in vulnerable patients, including in immunocompromised individuals, burn victims, and cancer patients undergoing chemotherapy. There are no effective treatments for P. aeruginosa infections, which are usually broadly resistant to antibiotics. Animal models show that to establish infection and to cause illness, P. aeruginosa relies on an interaction between two proteins: PqsE and RhlR. There could be additional protein-protein interactions involving PqsE, which, if defined, could be exploited for the design of new therapeutic strategies to combat P. aeruginosa . Here, we reveal previously unknown protein interactions in which PqsE participates that will be investigated for potential roles in pathogenesis.
ACDT: Architected Composite Data Types trading-in unfettered data access for improved execution (2014)

With Exascale performance and its challenges in mind, one ubiquitous concern among architects is energy efficiency. Petascale systems projected to Exascale systems are unsustainable at current power consumption rates. One major contributor to system-wide power consumption is the number of memory operations leading to data movement and management techniques applied by the runtime system. To address this problem, we present the concept of the Architected Composite Data Types (ACDT) framework. The framework is made aware of data composites, assigning them a specific layout, transformations and operators. Data manipulation overhead is amortized over a larger number of elements and program performance and power efficiency can be significantly improved. We developed the fundamentals of an ACDT framework on a massively multithreaded adaptive runtime system geared towards Exascale clusters. Showcasing the capability of ACDT, we exercised the framework with two representative processing kernels - Matrix Vector Multiply and the Cholesky Decomposition - applied to sparse matrices. As transformation modules, we applied optimized compress/decompress engines and configured invariant operators for maximum energy/performance efficiency. Additionally, we explored two different approaches based on transformation opaqueness in relation to the application. Under the first approach, the application is agnostic to compression and decompression activity. Such approach entails minimal changes to the original application code, but leaves out potential application-specific optimizations. The second approach exposes the decompression process to the application, hereby exposing optimization opportunities that can only be exploited with application knowledge. The experimental results show that the two approaches have their strengths in HW and SW respectively, where the SW approach can yield performance and power improvements that are an order of magnitude better than ACDT-oblivious, hand-optimized implementations. We consider the ACDT runtime framework an important component of compute nodes that will lead towards power efficient Exascale clusters.
Precise Predictions of Linear B Cell Epitopes in Protean 3D (2012)

B cell epitopes–the part of an antigen recognized by an antibody–are conformational in nature; however, accurately predicting these epitopes is difficult for proteins without a known three-dimensional (3D) structure. DNASTAR presents the NeoClone method, a machine learning approach that improves the ability to predict linear B cell epitopes (a peptide segment) using only sequence-based information. This method provides better overall predictive accuracy than COBEpro and Epitopia, two leading epitope prediction methods. Free trial software is available at dnastar.com.
Effects of nitrogen and titanium on blow hole formation and microstructure in copper weld metal by Ar-N2 gas metal arc welding. (1984)

OFHC copper plates were welded with Cu and Cu-Ti electrode wires using Ar-N2 gas shielding. The effects of welding conditions, N2% in the shielding gas and titanium content of the electrode wire on the porosity and the microstructure of the weld metal were systematically examined. The results are as follows:(1) Using copper electrode wire, the weld metal shows better surface appearance, less porosity and deeper penetration with increase of the welding current.(2) As N2% in the shielding gas increases, the porosity of the weld metal increases. However, the tendency becomes very slight in the case of using Cu-Ti electrode wire.(3) The nitrogen content of the weld metal increases with N2% in the shielding gas. This tendency becomes more remarkable with increase of the titanium content of the electrode wire.(4) Using Cu-Ti electrode wire, a secondary phase is observed in the weld metal. The fractional area of the secondary phase in the weld metal increases with N2% in the shielding gas and titanium content of the electrode wire.(5) The electron diffraction patterns of the secondary phase are in good agreement with those of TiN.(6) The temperature of molten copper pool was measured and the formation of TiN was discussed by using thermodynamic data.
Fabrication of High-Aspect Metal Nanostructure Using Anodic Porous Alumina and Its Optical Property (2020)

High-aspect nanostructure, such as a nanohole and a coaxial nanocable, are considered as a powerful candidate for a light waveguide. Especially, a coaxial nanocable can efficiently propagate the incident light because the coaxial nanocable does not have cut-off wavelength as seen in a nanohole. In addition, by reducing the opening size of the coaxial nanocable, the coaxial nanocable can propagate the light to an area less than a wavelength of the incident light beyond the diffraction limit. Therefore, the coaxial nanocable is expected to be applied to fabricate various types of functional optical devices, such as nanoimaging device and high-density optical recording device. However, it is still difficult to fabricate the high-aspect nanostructure with complicated geometrical features such as the coaxial nanocable because of fabrication difficulties. Until now, our group had been reported fabrication process of the high-aspect metal nanostructures using an anodic porous alumina and its optical property [1-3]. Anodic porous alumina has an ordered array of straight nanoholes having high aspect ratio. Due to this unique geometrical character, anodic porous alumina is commonly used as a starting material to fabricate nanostructures having high aspect feature. In our previous work, we reported fabrication of the coaxial nanocables having high aspect ratio using anodic porous alumna [3]. In addition, it was observed that the coaxial nanocable could efficiently propagate the visible light. In the present work, with the aim of improving the performance of the functional devices based on the coaxial nanocable, reduction of opening size of the coaxial nanocable and evaluation of the optical property were demonstrated. This fabrication process is expected to be applied to fabricate various types of functional optical devices requiring the fine coaxial nanocable. K. Nishio, M. Nakao, A. Yokoo, H. Masuda, Jpn. J. Appl. Phys., 42 , L83 (2003). T. Kondo, N. Kitagishi, T. Yanagishita, H. Masuda, Appl. Phys. Express , 8 , 06200 (2015). T. Kondo, R. Ichinose, M. Kurosawa, T. Yanagishita, H. Masuda, The 87 th ECSJ Spring Meeting , 1C06 (2020).
Time-resolved multi-mass ion imaging: femtosecond UV-VUV pump-probe spectroscopy with the PImMS camera (2017)

_Publication history_ - Original document (Authorea), DOI: 10.22541/au.149030711.19068540. - arXiv 1702.00744 (Feb. 2017) - J. Chem. Phys. special issue “Developments and Applications of Velocity Mapped Imaging Techniques”, (March 2017), DOI: 10.1063/1.4978923 - Data and analysis scripts (OSF), DOI: 10.17605/OSF.IO/RRFK3. _See also_ - AIP Press Release: _The Inner Lives of Molecules_ (April 2017) - PImMS camera website - Vallance group website - Femtolab website