gebhart/patrepeval huggingface dataset:
A phylogeny of the temperate seabasses (Moronidae) characterized by a translocation of the mt‐<i>nd</i>6 gene (2011)

The entire mitochondrial genome of the striped bass Morone saxatilis was sequenced together with the mitochondrial (mt) control regions of the white bass Morone chrysops, white perch Morone americana, yellow bass Morone mississippiensis, spotted seabass Dicentrarchus punctatus, European seabass Dicentrarchus labrax and the Japanese seabass Lateolabrax japonicus. The resultant 17 580 base pair circular genome of M. saxatilis contains 38 genes (13 proteins, 23 transfer RNAs and two ribosomal RNAs) and a control region bordered by the proline and phenylalanine mitochondrial tRNAs. Gene arrangement was similar to other vertebrates, except that the mt-nd6 gene was found within the control region rather than the canonical position between the mt-nd5 and mt-cyb genes. This translocation was found in all the Morone and Dicentrarchus species studied without functional copies or pseudogenes in the ancestral position. In L. japonicus, the mt-nd6 gene was found in the canonical position without evidence of an mt-nd6 gene in the control region. A Bayesian analysis of these and published mt-nd6 sequences from 45 other Perciformes grouped the Morone and Dicentrarchus species monophyletically with a probability of 1·00 with respect to L. japonicus and all other perciforms, and placed the Dicentrarchus species in the basal position. These data reinforce current placement of L. japonicus outside the Moronidae and provide a clear evolutionary character to define this family. The phylogeny of the Moronidae presented here also supports the hypothesis of an anadromous common ancestor to this family that gave rise to the North American estuarine and freshwater species. A series of tandem repeats previously reported in M. saxatilis was found in the control region of all Morone species between the mt-nd6 and mt-rnr1 genes, but not in either Dicentrarchus species, which reinforces the continued use of these two separate genera.
Fabrication and performance characteristics of 1.55-μm InGaAsP multiquantum well ridge guide lasers (1985)

We report the fabrication and performance characteristics of InGaAsP ridge waveguide lasers with multiquantum well (MQW) active layers emitting near 1.55 μm. The active region has four active wells (1.55 μm InGaAsP) and three barriers (1.3 μm InGaAsP). The thicknesses of the active wells and the barrier layers are ∼250 Å. The 360-μm-long lasers have threshold currents in the range 60–80 mA at 30 °C, external differential quantum efficiency ∼25% at 30 °C, and T0∼70 K. The modulation bandwidths of the lasers are ∼1.5 GHz and they exhibit less frequency chirping than similar lasers with conventional double heterostructure (DH) active layer. Since frequency chirp limits the performance of high bit rate long haul fiber communication system at 1.55 μm, we believe MQW lasers offer an advantage over conventional DH lasers.
A virtual instrument for automatic anemometer calibration with ANN based supervision (2003)

A fully automatic anemometer calibrator intended for performing fast and accurate calibrations has been developed to fulfill the increasing demand and strict requirements of the wind energy industry. Different sensors are connected to a computer where a virtual environment acquires and processes the incoming signals and controls a wind tunnel, allowing the calibration of the anemometer at the pre-selected air speed values. An important part of the resulting complex virtual environment is a supervising system, based on artificial neural networks and able to check and handle the possible malfunctions and deviations within the calibration process.
A computer simulation of the hypothalamic-pituitary-adrenal axis. (1994)

This paper describes the construction of a computer model that simulates the hypothalamic-pituitary-adrenal axis (HPA axis) regulation of cortisol production. It is presented to illustrate the process of physiological modeling using standard "off the shelf" technologies. The model simulates components of the HPA axis involved in the continuous secretion and elimination of cortisol, adrenocorticotropin (ACTH), and corticotropin releasing hormone (CRH). The physiological relations of these component pieces were modeled based on the current knowledge of their functioning. Rate constants, half lives, and receptor affinities were assigned values derived from the experimental literature. At its current level of development the model is able to accurately simulate the timing, magnitude and decay of the ACTH and cortisol concentration peaks resulting from the ovine-CRH stimulation test in normal and hypercortisolemic patients. The model will be used to predict the effects of lesions in different components of the HPA axis on the time course of cortisol and ACTH levels. We plan to use the model to explore the experimental conditions required to distinguish mechanisms underlying various disorders of the HPA axis, particularly depression. Efforts are currently underway to validate the model for a large variety of normal and pathological perturbations of the HPA axis.
Blood compatible microfluidic system for pharmacokinetic studies in small animals (2012)

New radiotracer developments for nuclear medicine imaging require the analysis of blood as a function of time in small animal models. A microfluidic device was developed to monitor the radioactivity concentration in the blood of rats and mice in real time. The microfluidic technology enables a large capture solid angle and a reduction in the separation distance between the sample and detector, thus increasing the detection efficiency. This in turn allows a reduction of the required detection volume without compromising sensitivity, an important advantage with rodent models having a small total blood volume (a few ml). A robust fabrication process was developed to manufacture the microchannels on top of unpackaged p-i-n photodiodes without altering detector performance. The microchannels were fabricated with KMPR, an epoxy-based photoresist similar to SU-8 but with improved resistance to stress-induced fissuring. Surface passivation of the KMPR enables non-diluted whole blood to flow through the channel for up to 20 min at low speed without clotting. The microfluidic device was embedded in a portable blood counter with dedicated electronics, pumping unit and computer control software for utilisation next to a small animal nuclear imaging scanner. Experimental measurements confirmed model predictions and showed a 4- to 19-fold improvement in detection efficiency over existing catheter-based devices, enabling a commensurate reduction in sampled blood volume. A linear dose-response relationship was demonstrated for radioactivity concentrations typical of experiments with rodents. The system was successfully used to measure the blood input function of rats in real time after radiotracer injection.
Potential for adhesive wear in friction couples of UHMWPE running against oxidized zirconium, titanium nitride coatings, and cobalt‐chromium alloys (2010)

The classical wear mechanisms abrasion, fatigue, and adhesion are the most frequent causes of surface changes of ultra high molecular weight polyethylene (UHMWPE) in artificial joints. The counterpart material has a strong influence on the wear and friction behavior of artificial joints due to its abrasive properties and adhesive interaction with UHMWPE. The formation of a transfer layer on the counterpart in UHMWPE bearing systems is often described as being a clear indication of strong adhesive forces. The influence of using a cobalt-chromium-molybdenum (CoCrMo) alloy, a titanium nitride plasma coating or an oxidized zirconium alloy on adhesive wear was studied. The surface free energy and the bonding forces of these counterpart materials to UHMWPE were investigated. Catalytic effects on the degradation behavior of polyethylene, the micro friction behavior, and the build-up and constitution of a transfer layer deposited under loads, and relative velocities that are relevant in knee joints were analyzed.
ChemInform Abstract: Homolytic Reactions of Diorganotellurium and Diorganoditellurium Compounds in Solution: An EPR Study (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Photodecarboxylative Benzylation of<i>N</i>-Alkylphthalimides: A Concise Route to the Aristolactam Skeleton (2004)

The photoinitiated metal-free benzylation of N-alkyl ­phthalimides with arylacetates in aqueous solution followed by acid-catalyzed dehydration serves as a convenient route to methoxy-substituted precursors to phenanthrene lactam alkaloids.
New Silicon Bonding Method (1996)

A new kind of inorganic adhesive for Si bonding has been developed by mixing polypermethylcyclosilazane (PMSZ), polycarbosilane, and silicon powders with xylene. Chemically and thermally stable bonded materials with more than 100 MPa of bonding strength are formed after heating at 1200°C in Ar. Plasticizer effect of PMSZ and the formation of porous structures after firing may cause the crack‐free bonding. Metal ion impurities in the adhesives can be reduced to render the materials suitable for semiconductor processing tools.
Adherence to Statin Therapy Under Drug Cost Sharing in Patients With and Without Acute Myocardial Infarction (2007)

Fixed patient copayment and coinsurance policies have negative effects on adherence to statin lipid-lowering drug therapy but not on their initiation after myocardial infarction.
Image-based patient-specific simulation: a computational modelling of the human left heart haemodynamics (2012)

International audience
Digitoxin-Induced Cytotoxicity in Cancer Cells Is Mediated through Distinct Kinase and Interferon Signaling Networks (2011)

Cardiac glycosides (e.g., digoxin, digitoxin) constitute a diverse family of plant-derived sodium pump inhibitors that have been in clinical use for the treatment of heart-related diseases (congestive heart failure, atrial arrhythmia) for many years. Recently though, accumulating in vitro and in vivo evidence highlight potential anticancer properties of these compounds. Despite the fact that members of this family have advanced to clinical trial testing in cancer therapeutics, their cytotoxic mechanism is not yet elucidated. In this study, we investigated the cytotoxic properties of cardiac glycosides against a panel of pancreatic cancer cell lines, explored their apoptotic mechanism, and characterized the kinetics of cell death induced by these drugs. Furthermore, we deployed a high-throughput kinome screening approach and identified several kinases of the Na-K-ATPase-mediated signal transduction circuitry (epidermal growth factor receptor, Src, pkC, and mitogen-activated protein kinases) as important mediators downstream of cardiac glycoside cytotoxic action. To further extend our knowledge on their mode of action, we used mass-spectrometry-based quantitative proteomics (stable isotope labeling of amino acids in cell culture) coupled with bioinformatics to capture large-scale protein perturbations induced by a physiological dose of digitoxin in BxPC-3 pancreatic cancer cells and identified members of the interferon family as key regulators of the main protein/protein interactions downstream of digitoxin action. Hence, our findings provide more in-depth information regarding the molecular mechanisms underlying cardiac glycoside-induced cytotoxicity.
Performance Evaluation of a PEM Scanner Using the NEMA NU 4—2008 Small Animal PET Standards (2010)

The recently published NEMA NU 4-2008 Standards has been specially designed for evaluating the performance of small animal PET scanners used in preclinical applications. In this paper, we report on the NU 4 performance of a clinical positron emission mammography (PEM) system. Since there are no PEM specific performance test protocols available, and the NU 2 protocol (intended for whole-body PET scanners) cannot be applied without modification due to the compact design of the PEM scanner, we decided to evaluate the NU 4 Standards as an alternative. We obtained the following results: Trans-axial spatial resolution 1.8 mm FWHM for high resolution reconstruction mode and 2.4 mm FWHM for standard resolution reconstruction mode with no significant variation within the field of view. The total system sensitivity was 0.16 cps/Bq. In image quality testing, the uniformity was found to be 3.9% STD at the standard resolution mode and 5.6% at the high resolution mode when measured with a 34 mm paddle separation. The NEMA NU 4-2008 Standards were found to be a practicable tool to evaluate the performance of the PEM scanner after some modifications to address the specifics of its detector configuration. Furthermore, the PEM scanner's in-plane spatial resolution was comparable to other small animal PET scanners with good image quality.
Role of Lattice Strain and Defect Chemistry on the Oxygen Vacancy Migration at the (8.3% Y<sub>2</sub>O<sub>3</sub>-ZrO<sub>2</sub>) / SrTiO<sub>3</sub> Hetero-Interface: A First Principles Study (2009)

We report on the mechanism and the upper limits in the increase of oxygen ion conductivity at oxide hetero-interfaces, particularly the 8.3%Y 2 O 3 -ZrO 2 /SrTiO 3 (YSZ/STO) as a model interface. We consider two factors contributing to the increase in ionic conductivity at or near the interface: 1) a favorable strain state to shift and/or change the symmetry of electron energy levels to provide improved charge transfer and mobility. 2) the alteration of the defect chemistry to enhance the density and distribution of oxygen vacancies. First principles and Kinetic Monte-Carlo simulations were performed to identify the atomic-scale nature of the hetero-interface and the oxygen vacancy migration barriers and diffusivity. Our results suggest that the modulation in both the lattice strain and the defect chemistry due to the YSZ/STO interface can enhance the ionic conductivity in YSZ up to six orders of magnitude by reducing the migration barrier and increasing the oxygen vacancy concentration, respectively.
Performance analysis of Impulse Radio Ultra-Wideband differential detection schemes for Body Area Networks (2010)

In this work differentially coherent communication schemes for Impulse Radio Ultra-Wideband (IR-UWB) that transmit single uninterrupted package of energy per symbol, expected to be included in the IR-UWB IEEE 802.15.6 wireless Body Area Networks (BAN) standard are considered. Models for two receiver architectures, suitable for such communication schemes and feasible to implement in current CMOS technology - duty-cycled sampling receiver and chirp receiver are derived. After that, two differential detection techniques for employed receiver architectures - ordinary DPSK and Sample-wise DPSK (S-DPSK) are described. Theoretical analysis of probability of error for S-DPSK is also provided. Performances of the sampling and the chirp receiver architectures with DPSK and S-DPSK detection methods employed are analyzed under narrowband and Frequency-Modulated UWB (FM-UWB) types of interference.
Osteosarcoma follow-up: chest X-ray or computed tomography? (2017)

A follow-up strategy with chest CT leads to a higher rate of CR-2 and significantly improves PRS and OS in osteosarcoma, compared to chest X-ray.
Additional property of interferometer symmetry (1978)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Joseph L. Horner, "Additional property of interferometer symmetry," Appl. Opt. 17, 505-505 (1978) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Cerebellar Functional Neuroanatomy: Recent Developments, Outstanding Questions, and Future Directions. (S34.008) (2018)

To review recent studies of cerebellar functional neuroanatomy by our group, discuss fundamental outstanding questions, and outline future approaches.
Passive tuning in lateral-mode thin-film piezoelectric oscillators (2011)

In this paper, for the first time frequency tuning in lateral-mode thin-film piezoelectric resonators is demonstrated through varying the termination load connected to an isolated tuning port. The dependency of frequency tuning on the design features of the resonator is studied as well. More than 4300ppm tuning range in a thin-film piezoelectric-on-silicon (TPoS) resonator and more than 9000ppm tuning range in a pure piezoelectric resonator is achieved at ∼29.5MHz and ∼31.5MHz respectively. Also, an oscillator tuning range of more than 2700ppm is reported which shows a great potential for temperature compensated oscillators.
Phase Formation and Magnetic Properties of Co-Rare Earth Magnetic Films (1998)

Co–Sm and Co–Pr films were deposited by dc magnetron sputtering. Transmission electron microscopy and magnetic measurement were used to study the microstructure and magnetic property relationship. The nanostructure of the as-deposited Co 19 at. % Sm films consists of two phases: the amorphous phase and the crystallite phase. Upon annealing at 600 °C, the Co5Sm phase with the Cu5Ca structure, having grain size of about 20 nm, is obtained along with high coercivity (45 kOe). The as-deposited Co 22 at. % Sm films also have nanostructure similar to the Co 19 at. % films except the volume fraction of the crystallite is reduced. This is related to the concentration of Sm which promotes the formation of the amorphous phase. A new metastable phase Co3Sm is formed upon annealing of the Co 22 at. % Sm film at 500 °C. This phase has the DO19 structure in which the Sm atoms take ordered positions of a triangular pattern in the close-packed planes. A relatively high coercivity value of 29 kOe was obtained from this ph...
Ultrasonography of ocular trauma patients (1990)

Ultrasound B--scan examination of traumatized eye is a safe , cheap & easy diagnostic method for visualization of the posterior pole of the eye.Ophthalmoscopic visualization of the fundus of traumatized eye can be obscured by corneal opacity, anterior chamber hyphema, cataractous change of the lens , or hemorrhage of the vitreous.Ultrasound B--scan examination of the posterior pole is imperative in such cases to detect any intraocular damage and the presence of a foreign body.So we performed ultrasound B-scan examination of traumatized eye in seventy eight patients & analyzed those findings.All cases were confirmed by follow up examination of ophthalmoscopy & ultrasound, or surgery.The results were as follows :1.The most common cause of the ocular injury was traffic accidents (19 patients , 24.4 %l, male was more commonly injured (63 patients, 80.8 %l, and the most common age group
Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics (2021)

Proteogenomics approaches often struggle with the distinction between true and false peptide-to-spectrum matches as the database size enlarges. However, features extracted from tandem mass spectrometry intensity predictors can enhance the peptide identification rate and can provide extra confidence for peptide-to-spectrum matching in a proteogenomics context. To that end, features from the spectral intensity pattern predictors MS<sup>2</sup>PIP and Prosit were combined with the canonical scores from MaxQuant in the Percolator postprocessing tool for protein sequence databases constructed out of ribosome profiling and nanopore RNA-Seq analyses. The presented results provide evidence that this approach enhances both the identification rate as well as the validation stringency in a proteogenomic setting.
Warhead verification as inverse problem: Applications of neutron spectrum unfolding from organic-scintillator measurements (2016)

Verification of future warhead-dismantlement treaties will require detection of certain warhead attributes without the disclosure of sensitive design information, and this presents an unusual measurement challenge. Neutron spectroscopy—commonly eschewed as an ill-posed inverse problem—may hold special advantages for warhead verification by virtue of its insensitivity to certain neutron-source parameters like plutonium isotopics. In this article, we investigate the usefulness of unfolded neutron spectra obtained from organic-scintillator data for verifying a particular treaty-relevant warhead attribute: the presence of high-explosive and neutron-reflecting materials. Toward this end, several improvements on current unfolding capabilities are demonstrated: deuterated detectors are shown to have superior response-matrix condition to that of standard hydrogen-base scintintillators; a novel data-discretization scheme is proposed which removes important detector nonlinearities; and a technique is described for re-parameterizing the unfolding problem in order to constrain the parameter space of solutions sought, sidestepping the inverse problem altogether. These improvements are demonstrated with trial measurements and verified using accelerator-based time-of-flight calculation of reference spectra. Then, a demonstration is presented in which the elemental compositions of low-Z neutron-attenuating materials are estimated to within 10%. These techniques could have direct application in verifying the presence of high-explosive materials in a neutron-emitting test item, as well as other for treaty verification challenges.
Kinetic Model of Stage Transformation and Intercalation in Graphite (1984)

We derive a set of diffusion equations based on time-dependent Landau-Ginzburg theory, which is capable of describing the role of domains in stage transformations and intercalation in layered materials. As illustrations of the formalism we study stage decomposition in a quenched sample and the intercalation of a dilute sample. Staggered domains of intermediate stages are shown to arise naturally as a consequence of the interactions and the kinetic constraints even for a sample without dislocations. Further, we show that intercalation proceeds through the formation and migration of islands of intermediate stages.