gebhart/patrepeval huggingface dataset:
Self-Healing of Surfactant Surface Micelles on Millisecond Time Scales (2006)

We study the dynamics of surfactant micelles at the solid-liquid interface using a new atomic force-microscopic imaging mode to visualize the nanometer-level structural features of the micelles and the picometer-level lattice of the substrate simultaneously. We find that defects created in a crystalline micellar array by the scanning probe tip self-heal flawlessly in less than 6 ms.
Yersinia enterocolitica Type III Secretion: yscM1 and yscM2 Regulate yop Gene Expression by a Posttranscriptional Mechanism That Targets the 5′ Untranslated Region of yop mRNA (2002)

Pathogenic Yersinia spp. secrete Yops (Yersinia outer proteins) via the type III pathway. The expression of yop genes is regulated in response to environmental cues, which results in a cascade of type III secretion reactions. yscM1 and yscM2 negatively regulate the expression of Yersinia enterocolitica yop genes. It is demonstrated that yopD and lcrH are required for yscM1 and yscM2 function and that all four genes act synergistically at the same regulatory step. Further, SycH binding to the protein products of yscM1 and yscM2 can activate yop gene expression even without promoting type III transport of YscM1 and YscM2. Reverse transcription-PCR analysis of yopQ mRNA as well as yopQ and yopE gene fusion experiments with the npt (neomycin phosphotransferase) reporter suggest that yscM1 and yscM2 regulate expression at a posttranscriptional step. The 178-nucleotide 5' untranslated region (UTR) of yopQ mRNA was sufficient to confer yscM1 and yscM2-mediated regulation on the fused reporter, as was the 28-nucleotide UTR of yopE. The sequence 5'-AUAAA-3' is located in the 5' yop UTRs, and mutations that alter the sequence motif either reduced or abolished yscM1- and yscM2-mediated regulation. A model is proposed whereby YopD, LcrH, YscM1, YscM2, and SycH regulate yop expression in response to specific environmental cues and by a mechanism that may involve binding of some of these factors to a specific target sequence within the UTR of yop mRNAs.
Simian Immunodeficiency Virus Promoter Exchange Results in a Highly Attenuated Strain That Protects against Uncloned Challenge Virus (2004)

Among the many simian immunodeficiency virus (SIV) immunogens, only live attenuated viral vaccines have afforded strong protection to a natural pathogenic isolate. Since the promoter is crucial to the tempo of viral replication in general, it was reasoned that promoter exchange might confer a novel means of attenuating SIV. The core enhancer and promoter sequences of the SIV macaque 239nefstop strain (NF-kappaB/Sp1 region from -114 bp to mRNA start) have been exchanged for those of the human cytomegalovirus immediate-early promoter (CMV-IE; from -525 bp to mRNA start). During culture of the resulting virus, referred to as SIVmegalo, on CEMx174 or rhesus macaque peripheral blood mononuclear cells, deletions arose in distal regions of the CMV-IE sequences that stabilized after 1 or 2 months of culture. However, when the undeleted form of SIVmegalo was inoculated into rhesus macaques, animals showed highly controlled viremia during primary and persistent infection. Compared to parental virus infection in macaques, primary viremia was reduced by >1,000-fold to undetectable levels, with little sign of an increase of cycling cells in lymph nodes, CD4(+) depletion, or altered T-cell activation markers in peripheral blood. Moreover, in contrast to wild-type infection in most infected animals, the nef stop mutation did not revert to the wild-type codon, indicating yet again that replication was dramatically curtailed. Despite such drastic attenuation, antibody titers and enzyme-linked immunospot reactivity to SIV peptides, although slower to appear, were comparable to those seen in a parental virus infection. When animals were challenged intravenously at 4 or 6 months with the uncloned pathogenic SIVmac251 strain, viremia was curtailed by approximately 1,000-fold at peak height without any sign of hyperactivation in CD4(+)- or CD8(+)-T-cell compartment or increase in lymph node cell cycling. To date, there has been a general inverse correlation between attenuation and protection; however, these findings show that promoter exchange constitutes a novel means to highly attenuate SIV while retaining the capacity to protect against challenge virus.
Task-Oriented Near-Lossless Burst Compression (2022)

Unlike single images, capturing bursts enables many possible downstream tasks (e.g. superresolution, HDR enhancement) due to the rich information preserved in the consecutive frames. Efficient compression of these bursts is therefore essential given the additional frames to store. In this paper, we propose a novel near-lossless compression method that can preserve the most relevant information in the burst to enable multiple downstream image enhancement tasks, while at the same time reducing the file size. Specifically, we propose a two-bitstream near-lossless compression pipeline that controls the image-space distortion at frame level, and introduce the Lipschitz condition to bound the task-space distortion at burst level. Experiments conducted on a real-world burst dataset confirm the benefit of the proposed solution in terms of rate-distortion both in the burst frame space and the superresolution task space, a popular downstream task in burst processing.
A Self‐Assembled Tetracopper Triple‐Stranded Helicate: Towards the Controlled Synthesis of Finite One‐Dimensional Magnetic Chains (2003)

Spiraling into control: A finite linear arrangement of four magnetically coupled copper(II) centers has been generated within a triple-stranded helical motif that was formed through a strict self-assembly process between a single octadentate ligand and CuII ions (see picture). This approach opens the way to constructing finite one-dimensional magnetic chains in a controlled manner. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z51634_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Front Matter: Volume 9014 (2014)

This PDF file contains the front matter associated with SPIE Proceedings Volume 9014, including the Title Page, Copyright information, Table of Contents, Invited Panel Discussion, and Conference Committee listing.
Supplementary Figure Legends 1-16 from Danger Signaling Protein HMGB1 Induces a Distinct Form of Cell Death Accompanied by Formation of Giant Mitochondria (2023)

Supplementary Figure Legends 1-16 from Danger Signaling Protein HMGB1 Induces a Distinct Form of Cell Death Accompanied by Formation of Giant Mitochondria
Morphological operators on graph based on geodesic distance map (2015)

In this article, we are interested in the graph-based mathematical morphology operators (dilations, erosions, openings, closings, alternated filters) defined in [1] [2]. These operators depend on a size parameter and, as often in mathematical morphology; they are obtained by iterative successions of elementary dilations/erosions. The number of iterations of the elementary operators depends directly of the parameter size. Thus, this leads to running times that increase with respect to the parameter size. In order to optimize this computation time, we propose another algorithmic variant that is based on the computation of geodesic distance maps in graphs. The computed distance map allows us to determine (by thresholding), for any value of the parameter size, dilations and erosions that map a set of vertices to a set of edges and a set of edges to a set of vertices. The proposed algorithm allows the operators to be computed with a single (linear-time) iteration. Therefore, the processing time is improved compared to the time of the multi-iterations original method and does not depend of the parameter size anymore.
Hierarchical self-supported ZnAlEu LDH nanotubes hosting luminescent CdTe quantum dots (2017)

Self-supported oligo-layered ZnAlEu LDH nanotubes (∅ 20 nm) self-assemble upon controlled hydrolysis of the metal ions (Zn<sup>2+</sup>, Al<sup>3+</sup>, Eu<sup>3+</sup>) in the presence of 1,3,5-benzenetricarboxylate anions and non-ionic worm-like micelles. Their high surface area and easily accessible cylindrical mesopores (175 m<sup>2</sup> g<sup>-1</sup>; 0.75 cm<sup>3</sup> g<sup>-1</sup>) facilitate interaction with 5 nm CdTe quantum dots, enhancing the overall luminescence behavior.
Immunoluminometric Assay for Measurement of the C-Terminal Endothelin-1 Precursor Fragment in Human Plasma (2006)

CT-proET-1 measurement is a rapid and easy method for indirectly assessing the release of ET-1 in critically ill patients.
Novel Action of Botulinum Toxin on the Stromal and Epithelial Components of the Prostate Gland (2006)

BTX-A injection into the prostate alters cellular dynamics by inducing apoptosis, inhibiting proliferation and down-regulating alpha(1A) adrenergic receptors. BTX-A may potentially be the drug that has dual actions on the static and dynamic components of benign prostatic hyperplasia.
Results of a Nationwide Screening for Anderson-Fabry Disease among Dialysis Patients (2004)

Anderson-Fabry disease is possibly underdiagnosed in patients with end-stage renal disease. Nationwide screening was therefore undertaken for Anderson-Fabry disease among dialysis patients in Austria. Screening for alpha-galactosidase A (AGAL) deficiency was performed by a blood spot test. In patients with a positive screening test, AGAL activity in leukocytes was determined. Individuals with decreased leukocyte AGAL activity were subjected to mutation testing in the GLA gene. Fifty (90.9%) of 55 Austrian hemodialysis centers participated in this study; 2480 dialysis patients (80.1% of the Austrian dialysis population) were screened. In 85 patients, the screening test was positive (85 of 2480, 3.42%; women, 3.32%; men, 3.50%). Among these 85 patients, 4 men (in 3 of whom Anderson-Fabry disease was already known before screening) had a severely decreased and 11 subjects had a borderline low AGAL activity. Genetic testing revealed mutations associated with Fabry disease in all four men with severely decreased AGAL activity resulting in a prevalence of 0.161% for the entire study population. A nationwide screening of dialysis patients permitted detection of a hitherto unknown man with Anderson-Fabry disease. The overall prevalence among dialysis patients was at least ten times higher as compared with recent registry data. Screening programs among patients with end-stage renal disease, especially men, should be put in place to identify families with Anderson-Fabry disease who probably may benefit from specific clinical care, and perhaps from enzyme replacement therapy. In dialysis patients, however, there is no evidence to support enzyme replacement therapy at present.
Shear and Young's Moduli of MoS2 Nanotube Ropes (2003)

The interaction between individual nanotubes in MoS 2 bundles is investigated here using an atomic force microscope (AFM). Upon elastically deforming the ropes with the AFM, the value of the bending modulus of the MoS 2 tube ensemble could be evaluated. This is turn could be used to obtain a lower estimate of the shear and Young's moduli of the nanotubes. The results indicate that the MoS 2 ropes are highly anisotropic and that the interaction between the individual tubes comprising the rope is very weak.
Generation of Aeroservoelastic Reduced Order Models Using Time Scaling (2010)

Design of modern control laws motivates the creation of state-space models from aeroservoelastic models. Balanced truncation is often used to create reduced-order models. In the present work, a reduced order model that employs time scaling in computing the balancing transformation is developed. The transformation matrix necessary to transform the original (unscaled) aeroservoelastic model is found from that corresponding to the time scaled model. Results from an aeroservoelastic wing and a supersonic transport model are shown and it is demonstrated that with an appropriate choice of time scaling, the methodology results in greatly improved conditioning for the Lyapunov equations used to find the Gramians employed in the balancing transformation.
Implantable Glucose BioFuel Cells for Medical Devices (2013)

An Implantable BioFuel Cell (IBFC) is a device that produces power only from the chemicals that are naturally occurring inside the body. We have been working on two approaches to creating an IBFC. The first approach is to use chemicals such as glucose and oxygen to provide the fuel for an enzymatic IBFC. The second approach is to use electrolytes such as sodium to provide the fuel for a biomimetic IBFC.
Intravenous Allopurinol Decreases Myocardial Oxygen Consumption and Increases Mechanical Efficiency in Dogs With Pacing-Induced Heart Failure (1999)

Allopurinol, an inhibitor of xanthine oxidase, increases myofilament calcium responsiveness and blunts calcium cycling in isolated cardiac muscle. We sought to extend these observations to conscious dogs with and without pacing-induced heart failure and tested the prediction that allopurinol would have a positive inotropic effect without increasing energy expenditure, thereby increasing mechanical efficiency. In control dogs (n=10), allopurinol (200 mg IV) caused a small positive inotropic effect; (dP/dt)(max) increased from 3103+/-162 to 3373+/-225 mm Hg/s (+8.3+/-3.2%; P=0.01), but preload-recruitable stroke work and ventricular elastance did not change. In heart failure (n=5), this effect was larger; (dP/dt)(max) rose from 1602+/-190 to 1988+/-251 mm Hg/s (+24.4+/-8.7%; P=0.03), preload-recruitable stroke work increased from 55.8+/-9.1 to 84. 9+/-12.2 mm Hg (+28.1+/-5.3%; P=0.02), and ventricular elastance rose from 6.0+/-1.6 to 10.5+/-2.2 mm Hg/mm (P=0.03). Allopurinol did not affect myocardial lusitropic properties either in control or heart failure dogs. In heart failure dogs, but not controls, allopurinol decreased myocardial oxygen consumption (-49+/-4.6%; P=0. 002) and substantially increased mechanical efficiency (stroke work/myocardial oxygen consumption; +122+/-42%; P=0.04). Moreover, xanthine oxidase activity was approximately 4-fold increased in failing versus control dog hearts (387+/-125 versus 78+/-72 pmol/min. mg(-1); P=0.04) but was not detectable in plasma. These data indicate that allopurinol possesses unique inotropic properties, increasing myocardial contractility while simultaneously reducing cardiac energy requirements. The resultant boost in myocardial contractile efficiency may prove beneficial in the treatment of congestive heart failure.
Supplementary Figure Legends 1-9 from ALK Mutations Conferring Differential Resistance to Structurally Diverse ALK Inhibitors (2023)

&lt;p&gt;PDF file - 82K&lt;/p&gt;
NMR spectroscopic investigation of inclusion complexes between cyclodextrins and the neurotoxin tetramethylenedisulfotetramine (2012)

The binding stoichiometry, strength and structure of inclusion complexes formed between the neurotoxin tetramethylenedisulfotetramine (TETS) and both native and modified cyclodextrins (CyDs) were investigated using nuclear magnetic resonance (NMR) spectroscopy. Of all six examined cases, native β-cyclodextrin (β-CyD) and its chemically modified counterpart heptakis-(2,3,6-tris-(2-hydroxypropyl))-β-cyclodextrin (2HP-β-CyD) were found to associate most strongly with TETS as reflected in the magnitude of their binding constants (K = 537 ± 26 M(-1) for β-CyD and K = 514 ± 49 M(-1) for 2HP-β-CyD). Two-dimensional rotating-frame Overhauser effect spectroscopy NMR experiments confirm close proximity of the TETS molecule to both β-CyD and 2HP-β-CyD as intermolecular, through-space interactions between the H3 and H5 protons located in the interior of the CyD cavity and the methylene protons of TETS were identified.
Sinefungin and Derivatives : Synthesis, Biosynthesis and Molecular Target Studies in Leishmania (1986)

Sinefungin 1 is a natural nucleoside in which an ornithine residue is linked to the 5′ end of adenosine by a carbon-carbon bond. Its structure is similar to that of S-adenosyl-homocysteine (SAH) 2 and that of S-adenosyl-methionine 3 (Scheme I). It was isolated from cultures of Streptomyces griseolus at Lilly Research Laboratories (Hamill & Hoehn, 1973) and from cultures of S.incarnatus at Rhône-Poulenc Industries in France (Patent 761114 : Rhône Poulenc Industries France, 15th April, 1976).
Mist-CVD-derived Hf0.55Zr0.45O2 ferroelectric thin films post-annealed by rapid thermal annealing (2023)

We have newly applied Rapid Thermal Annealing (RTA) for the post-annealing of mist chemical-vapor-deposition (CVD)-derived Hf1−xZrxO2 (HZO) thin films. A ferroelectric polarization-electric field (P–E) curve was confirmed typically with noticeable polarization reversal currents. These ferroelectric properties of the HZO thin films provided quantitative estimation for Pr and Ec of ∼20 µC/cm2 and 1–1.5 MV/cm, respectively, compared to those reported from other growth methods, such as atomic-layer-deposition (ALD). It was revealed that the background leakage should be further reduced in a mist-CVD HZO film compared to those by ALD recently reported. The origin of the leakage was strongly related to the oxygen vacancy (Vo) generated in the film and near the HZO/bottom electrode interface. Nonetheless, it was found effective to use atmospheric pressure in air or oxygen in the post-RTA process for reducing leakage. In general, endurance behaviors for the mist-CVD HZO film revealed similar to those for samples prepared by other methods for both “wake-up” and “fatigue” phenomena, showing that the mist-CVD HZO film endured up to 2 × 109 counts. Finally, we expect that the mist-CVD HZO thin film would become a candidate for fabricating large-scale integration-oriented ferroelectric devices due to the intrinsic merits of the method.
Global regulation of gene expression by OxyR in an important human opportunistic pathogen (2012)

Most bacteria control oxidative stress through the H(2)O(2)-responsive transactivator OxyR, a member of the LTTR family (LysR Type Transcriptional Regulators), which activates the expression of defensive genes such as those encoding catalases, alkyl hydroperoxide reductases and superoxide dismutases. In the human opportunistic pathogen Pseudomonas aeruginosa, OxyR positively regulates expression of the oxidative stress response genes katA, katB, ahpB and ahpCF. To identify additional targets of OxyR in P. aeruginosa PAO1, we performed chromatin immunoprecipitation in combination with whole genome tiling array analyses (ChIP-chip). We detected 56 genes including all the previously identified defensive genes and a battery of novel direct targets of OxyR. Electrophoretic mobility shift assays (EMSAs) for selected newly identified targets indicated that ∼70% of those were bound by purified oxidized OxyR and their regulation was confirmed by quantitative real-time polymerase chain reaction. Furthermore, a thioredoxin system was identified to enzymatically reduce OxyR under oxidative stress. Functional classification analysis showed that OxyR controls a core regulon of oxidative stress defensive genes, and other genes involved in regulation of iron homeostasis (pvdS), quorum-sensing (rsaL), protein synthesis (rpsL) and oxidative phosphorylation (cyoA and snr1). Collectively, our results indicate that OxyR is involved in oxidative stress defense and regulates other aspects of cellular metabolism as well.
The effect of ultrasound irradiation on polycrystalline MoO3 (2001)

The effect of ultrasound irradiation on polycrystalline molybdenum trioxide suspended in n-decane has been investigated. The changes in the physicochemical properties of MoO3 have been investigated using techniques such as powder X-ray diffraction, UV–VIS and IR spectroscopies, BET surface area measurements, scanning electron microscopy, and EPR. Evidence for the formation of Mo(V) sites and shear defects has been presented. The physicochemical changes of MoO3 due to ultrasound irradiation have been attributed to the formation of radicals and also the mechanical effects that can be created by ultrasound, such as shear forces, micro-jets, and shock-waves. The mechanical effects are the results of the sonochemical cavity collapse onto molybdenum trioxide particles.
Enhanced radiation-loss-based radial-waveguide-coupled electrically pumped microresonator lasers with single-directional output (2010)

A novel enhanced radiation-loss (ERL)-based radial waveguide coupling mechanism for microresonator lasers is experimentally demonstrated for the first time, to the best of our knowledge, resulting in single-directional output from the lasers. A 20 microm diameter InGaAsP/InP electrically pumped microresonator laser in the form of a microcylinder resonator integrated with a transparent ERL radial output coupler is designed and fabricated. Measurement shows a low 1.5 mA lasing threshold and a relatively high output power of >0.4 mW.
Integrating bulk piezoelectric materials into MEMS for high authority actuators (2007)

This paper has been retracted by the authors following discussions with IOP Publishing. Whilst the work is scientifically correct, there are some unresolved issues relating to the authorship of a section of the paper as currently presented. The named authors intend to further review certain elements with a view to re-publishing the work at a later date. The authors and publisher therefore advise that the paper should not be referenced or used as a basis for future work.
Acoustic field of a spherically curved wedge transducer (2003)

High-intensity focused ultrasound (HIFU) applications typically utilize spherically curved transducers, often with modifications to the surface electrode. These modifications, such as rectangular cut-outs, can normally be modeled as a collection of annular rings and wedges. The acoustic field of an annular ring has been well characterized, but a wedge shape has not. We present a model of the acoustic field of a wedge transducer based on the spatial impulse response (SIR) method. A wedge transducer is created by making a cut normal to a spherical cap and keeping the section with the smaller surface area. Analytic expressions for the SIR are derived for an arbitrary point P in space. To find the time domain pressure at P, the SIR is convolved with the time derivative of the wedge surface velocity. Numerical examples of SIRs and the acoustic pressure field are given for a wedge formed from a spherical cap with a geometric focus of 9 cm and an outer diameter of 8 cm. For a single frequency drive of 4.7 MHz, calculations of pressure are compared to hydrophone measurements of a HIFU transducer with equivalent geometry. The results show an excellent agreement between theory and experiment.
Online Job Seekers in Canada: What Can We Learn from Bing Job Queries? (2021)

Labour markets in Canada and around the world are evolving rapidly with the digital economy. Traditional data are adapting gradually but are not yet able to provide timely information on this evolution.