gebhart/patrepeval huggingface dataset:
Addressing difficulties in using XRD intensity for structural study of thin films (2008)

Abstract The problem of structure investigation of thin films using laboratory XRD diffraction intensities was discussed as a matter of debate. Is the variation in relative intensities of the diffraction patterns due to crystallographic preferred orientation, lattice defects or both? The answer to this question shows a discrepancy in the literatures. The present work is an attempt to propose a possible approach to judge the most probable answer. Thin films of SnO 2 were prepared by spray pyrolysis technique using solution of different SnCl 2 concentrations (molarity); at fixed substrate temperature and deposition time. The theoretically calculated integrated intensities together with the experimentally obtained and calculated XRD data (relative intensities, texture coefficients and profile analysis) were considered together in order to get the proper picture of the structure characteristics of the prepared films. The complete picture can be assembled by integration and correlation of all the crystallographic information that are extracted from the diffraction pattern including not only the observed intensities but also the size/strain analysis and lattice parameters. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
All-optical packet-switched metropolitan-area network proposal (1993)

A proposal for developing a precompetitive, commercially viable all-optical network architecture using dense optical wavelength division is described. The objective was to demonstrate a packet-switched high-capacity all-optical LAN/MAN network based on wavelength-division multiplexing (WDM) and capable of supporting several hundred to a thousand nodes, each requiring gigabit-per-second throughputs. The discussion covers the rationale and objectives of the program; tunable components, optical amplifiers, network protocol, and application development; network interconnection studies; and testbed construction.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Stem cell antigen-1 expression in the pulmonary vascular endothelium (2003)

Although the function of the cell surface protein stem cell antigen-1 (Sca-1) has not been identified, expression of this molecule is a characteristic of bone marrow-derived hematopoietic stem cell populations. Expression of Sca-1, however, is not restricted to hematopoietic tissue. By RT-PCR and Western analysis, we found that Sca-1 is expressed in the adult mouse lung. Sca-1 immunohistochemistry revealed a linear staining pattern on the endothelial surface of large and small pulmonary arteries and veins and alveolar capillaries. Expression of Sca-1 in the pulmonary endothelium was confirmed by dual fluorescent microscopy on lung sections and by fluorescence-activated cell sorting analysis of digested lung tissue; each of these methods showed colocalization with the endothelial marker platelet/endothelial cell adhesion molecule-1. In the kidney, Sca-1 expression was also noted in large vessels, but, in contrast to the lung, was not observed in capillaries. Overall, our data indicate that Sca-1 expression helps define the surface phenotype of endothelial cells throughout the pulmonary vasculature.
Amplification of surface-enhanced Raman scattering due to substrate-mediated localized surface plasmons in gold nanodimers (2017)

Surface-enhanced Raman scattering (SERS) is significantly enhanced by placing plasmonic nanoantennas on a plasmonic substrate.
Analysis of the electrocardiogram signal by the lifting scheme (2004)

We present in this communication an analysis of the cardiac signals by the lifting scheme wavelet transform (LS.W.T). The principal goal of this study is to make the diagnosis of the signals electrocardiogram ECG respect the fidelity criterion of reconstruction i.e. good a value of P.R.D (percent root square difference) which evaluates the quality of equivalence between the original and the reconstructed signals of ECG. The diagnosis of the electrocardiograms ECG is based on a multiresolution wavelet analysis. The method starts with the decomposition and approximation of ECG signals into the details. We give some examples of the application of this method on electrocardiography signals and we also treat it in two cases - ECG with normal rhythm and the other disturbs the rhythm. Thus we locate the frequencies components of the ECGs.
Trametinib as a promising therapeutic option in alleviating vascular defects in an endothelial KRAS-induced mouse model (2022)

Somatic activating Kirsten rat sarcoma viral oncogene homologue (KRAS) mutations have been reported in patients with arteriovenous malformations. By producing LSL-Kras (G12D); Cdh5 (PAC)-CreERT2 [iEC-Kras (G12D*)] mice, we hoped to activate KRAS within vascular endothelial cells (ECs) to generate an arteriovenous malformation mouse model. Neonatal mice were treated daily with tamoxifen from postnatal (PN) days 1-3. Mortality and phenotypes varied amongst iEC-Kras (G12D*) pups, with only 31.5% surviving at PN14. Phenotypes (focal lesions, vessel dilations) developed in a consistent manner, although with unpredictable severity within multiple soft tissues (such as the brain, liver, heart and brain). Overall, iEC-Kras (G12D*) pups developed significantly larger vascular lumen areas compared with control littermates, beginning at PN8. We subsequently tested whether the MEK inhibitor trametinib could effectively alleviate lesion progression. At PN16, iEC-Kras (G12D*) pup survival improved to 76.9%, and average vessel sizes were closer to controls than in untreated and vehicle-treated mutants. In addition, trametinib treatment helped normalize iEC-Kras (G12D*) vessel morphology in PN14 brains. Thus, trametinib could act as an effective therapy for KRAS-induced vascular malformations in patients.
Optical Coherence Tomography Angiography of the Peripapillary Retina in Glaucoma (2015)

Using OCT angiography, reduced peripapillary retinal perfusion in glaucomatous eyes can be visualized as focal defects and quantified as peripapillary flow index and peripapillary vessel density, with high repeatability and reproducibility. Quantitative OCT angiography may have value in future studies to determine its potential usefulness in glaucoma evaluation.
Extended sequencing of vaccine and wild‐type capripoxvirus isolates provides insights into genes modulating virulence and host range (2019)

The genus Capripoxvirus in the subfamily Chordopoxvirinae, family Poxviridae, comprises sheeppox virus (SPPV), goatpox virus (GTPV) and lumpy skin disease virus (LSDV), which cause the eponymous diseases across parts of Africa, the Middle East and Asia. These diseases cause significant economic losses and can have a devastating impact on the livelihoods and food security of small farm holders. So far, only live classically attenuated SPPV, GTPV and LSDV vaccines are commercially available and the history, safety and efficacy of many have not been well established. Here, we report 13 new capripoxvirus genome sequences, including the hairpin telomeres, from both pathogenic field isolates and vaccine strains. We have also updated the genome annotations to incorporate recent advances in our understanding of poxvirus biology. These new genomes and genes grouped phenetically with other previously sequenced capripoxvirus strains, and these new alignments collectively identified several recurring alterations in genes thought to modulate virulence and host range. In particular, some of the many large capripoxvirus ankyrin and kelch-like proteins are commonly mutated in vaccine strains, while the variola virus B22R-like gene homolog has also been disrupted in many vaccine isolates. Among these vaccine isolates, frameshift mutations are especially common and clearly present a risk of reversion to wild type in vaccines bearing these mutations. A consistent pattern of gene inactivation from LSDV to GTPV and then SPPV is also observed, much like the pattern of gene loss in orthopoxviruses, but, rather surprisingly, the overall genome size of ~150 kbp remains relatively constant. These data provide new insights into the evolution of capripoxviruses and the determinants of pathogenicity and host range. They will find application in the development of new vaccines with better safety, efficacy and trade profiles.
Performance degradation due to coupling between high-speed traces and on-board antennas (2013)

Self-interference between digital interfaces and on-board wireless modules and antennas is rapidly becoming a major problem for Printed Circuit Board engineers. In this paper, the severity of on-board self-interference is quantified. Two working conditions are considered. First, the situation is considered in which the antenna is in receive mode. As the incoming (signal) fields are most often rather low, only small (signal) voltages are induced at the antenna port. It is shown with a simple example that the level of the noise voltage induced at the antenna port due to the switching of digital interfaces can be significant compared to the signal voltage, thereby leading to a low Signal-to-Noise Ratio. Second, the situation is considered in which the antenna is in transmit mode. As the power radiated by the on-board antenna can be quite large (e.g. typically 2 Watt for GSM), the signal voltages at the antenna port can be quite large. With the same simple example, it is shown that this leads to a significant noise signal at the digital interfaces, thereby increasing the Bit Error Rate.
3-D velocity registration from optically processed stereoscopic particle image velocimetry records (1990)

Particle image velocimetry (PIV) is extended to 30 velocity measurements by stereoscopic imaging. Optical processing yields all velocity components in a single output.
Doping integrity diagnostics of planar transistor channel structures by scanning nonlinear dielectric microscopy (2006)

The integrity of doping in transistor structures was diagnosed using scanning nonlinear dielectric microscopy (SNDM). Nonlinear capacitance profiling and pinpoint capacitance-voltage analysis were done through SNDM, and the results clearly discriminated between a depletion layer and a tailing of carrier distribution due to outdiffusion of dopants in an n+∕p junction. This analysis was applied to n+∕p∕n+ and p+∕n∕p+ transistor channel structures formed with different process parameters. An increase in the n+ activation temperature from 800to950°C caused a narrowing of the p-type region in the n+∕p∕n+ structure. A decrease in the substrate doping concentration from 2×1018to2×1017cm−3 caused a depletion of the entire channel when the gate length was less than 200nm. The influence of channel depletion was proven to be more severe in p+∕n∕p+ transistor channel structures because boron had higher diffusivity than arsenic.
Hybridization of G-Quadruplex-Forming Peptide Nucleic Acids to Guanine-Rich DNA Templates Inhibits DNA Polymerase η Extension (2014)

The guanine quadruplex (G-quadruplex) is a highly stable secondary structure that forms in G-rich repeats of DNA, which can interfere with DNA processes, including DNA replication and transcription. We showed previously that short guanine-rich peptide nucleic acids (PNAs) can form highly stable hybrid quadruplexes with DNA. We hypothesized that such structures would provide a stronger block to polymerase extension on G-rich templates than a native DNA homoquadruplex because of the greater thermodynamic stability of the PNA-DNA hybrid structures. To test this, we analyzed the DNA primer extension activity of polymerase η, a translesion polymerase implicated in synthesis past G-quadruplex blocks, on DNA templates containing guanine repeats. We observed a PNA concentration-dependent decrease in the level of polymerase η extension to the end of the template and an increase in the level of polymerase η inhibition at the sequence prior to the G-rich repeats. In contrast, the addition of a complementary C-rich PNA that hybridizes to the G-rich repeats by Watson-Crick base pairing led to a decrease in the level of polymerase inhibition and an increase in the level of full-length extension products. The G-quadruplex-forming PNA exhibited inhibition (IC50=16.2±3.3 nM) of polymerase η DNA synthesis on the G-rich templates stronger than that of the established G-quadruplex-stabilizing ligand BRACO-19 (IC50=42.5±4.8 nM). Our results indicate that homologous PNA targeting of G-rich sequences creates stable PNA-DNA heteroquadruplexes that inhibit polymerase η extension more effectively than a DNA homoquadruplex. The implications of these results for the potential development of homologous PNAs as therapeutics for halting proliferating cancer cells are discussed.
OCIA domain containing 2 is highly expressed in adenocarcinoma mixed subtype with bronchioloalveolar carcinoma component and is associated with better prognosis (2006)

Although lung adenocarcinoma is a major cause of cancer death worldwide, details of its molecular carcinogenesis and stepwise progression are still unclear. To characterize the sequential progression from bronchioloalveolar adenocarcinoma of the lung (BAC, in situ carcinoma) to adenocarcinoma mixed subtype with BAC component polymerase chain reaction-based cDNA suppression subtractive hybridization (SSH) was carried out using two representative cases of BAC (non-invasive tumors) and adenocarcinoma mixed subtype with BAC (invasive tumors). Through differential screening, virtual reverse northern hybridization and quantitative real-time reverse-transcription-polymerase chain reaction (qRT-PCR) we selected five genes (TncRNA, OCIAD2, ANXA2, TMED4 and LGALS4) that were expressed at significantly higher levels in invasive adenocarcinoma mixed subtype with BAC than in BAC. After in situ hybridization and qRT-PCR analyses, we confirmed that only the OCIAD2 gene showed significantly higher expression in the tumor cells of invasive adenocarcinoma mixed subtype with BAC than in BAC (P = 0.026). We then carried out in situ hybridization of OCIAD2 in 56 adenocarcinoma mixed subtype with BAC component and assessed the correlation between OCIAD2 expression and clinicopathological features. In contrast to our expectation, the patients with OCIAD2 expression showed a better clinical outcome than those without OCIAD2 expression, and OCIAD2 expression showed an inverse correlation with lymphatic invasion, blood vessel invasion and lymph node metastasis. These results suggest that OCIAD2 begins to express at the progression from in situ to invasive carcinoma, and is associated with the favorable prognosis of adenocarcinoma mixed subtype with BAC component.
Somatic von Hippel–Lindau disease gene mutation in clear‐cell renal carcinomas associated with end‐stage renal disease/acquired cystic disease of the kidney (2002)

It has been documented that renal cell carcinomas (RCCs) occur frequently in patients treated with long-term dialysis, especially in cases of end-stage renal disease (ESRD)/acquired cystic disease of the kidney (ACDK). To address the molecular pathogenesis of ESRD/ACDK-associated RCCs, we examined 14 RCCs (7 clear-cell and 7 papillary carcinomas) in patients receiving dialysis for somatic mutations of the von Hippel-Lindau disease (VHL) gene as well as of the tyrosine kinase domain of the MET oncogene. Direct sequencing analyses revealed that three tumors exhibited VHL frameshifts (618delA, 386-395del10-bp, and 723-724insTC). One of the VHL mutated tumors showed additional loss of heterozygosity at the VHL gene locus. Histopathologic and clinical data demonstrated that the three tumors having VHL mutations were clear-cell RCCs occurring in ESRD with 55, 106, and 156 months of dialysis history, respectively. We did not find any tumors with mutations in the tyrosine kinase domain of the MET. These results demonstrated that the VHL tumor-suppressor gene is also involved in a subset of clear-cell RCCs occurring in ESRD/ACDK, as in the case of sporadic clear-cell RCCs. However, mutations of the MET oncogene could not be found in the seven ESRD/ACDK-associated papillary RCCs examined.
Efficient Waveguide Mode Conversions by Spoof Surface Plasmon Polaritons at Terahertz Frequencies (2017)

In this paper, waveguide mode conversions in a parallel plate waveguide, rectangular waveguide, and circular waveguide are all demonstrated at terahertz frequencies. Different from the traditional ways to realize mode conversions, an ultracompact design method based on the inner-embedded subwavelength metallic gratings is provided. The principle of the method relies on modulating the phase velocities of spoof surface plasmon polaritons (SSPPs) supported on the gratings to generate π phase difference. Owing to the gradient matching the phase velocities of the waveguide modes and SSPPs, the efficiencies of the mode conversions are considerable. The output mode purities of the both demonstrations are very good. Besides, waveguide bend is also achieved by this method. The work in this paper hopes to establish a universal technique for compact waveguide mode control, especially in the terahertz frequency range.
Surface Enhanced Raman Scattering Of Gold Nanostructures: Role Of Dipolar And Multipolar Localized Surface Plasmons (2010)

We have studied the Surface‐Enhanced Raman Scattering (SERS) of shape controlled metallic nanoparticles: nanocylinders and nanowires, designed through electron beam lithography and lift off techniques. We have notably studied the influence of Localized Surface Plasmon Resonance (LSPR) on the efficiency of SERS. We will demonstrate that the nanowires have specific enhancement behavior and can actually act as nano‐antenna.
A Concurrency Modeling Technique for Performance Evaluation of Multiprocessor and Multicore Systems (2012)

The analytical techniques are either highly inaccurate or often require unaffordable computational costs to evaluate the concurrency in complex multiprocessor and multicore systems. Recent studies show that simulation techniques are being used in engineering and scientific researches more than ever. Simulation technique can be a promising alternative to analytical techniques as the real-world complex and expensive systems can be modeled as simplified representations including only relevant aspects of the problem. As billions of transistors are available on a single chip, the total number of CPUs in a multiprocessor system and the total number of cores in a multicore architecture are expected to grow significantly. As the number of processing cores increases, currently available simulators will become inadequate to simulate the concurrency of future computation extensive systems. Therefore, we propose a simulation technique to effectively model the concurrency in multiprocessor and multicore systems. Proposed VisualSim accelerated concurrency modeling approach is able to evaluate system performance. We model concurrency in a multi-processor shared-memory system and measure two performance metrics, average response time and task completion time. We find the proposed concurrency modeling technique easy, flexible, and capable of determining deadlock and starvation, balancing loads, and scheduling tasks.
Bio-SiC ceramics coated with hydroxyapatite using gas-detonation deposition: An alternative to titanium-based medical implants (2013)

Silicon-carbide (SiC) ceramics synthesized using forced infiltration and coated with bioactive hydroxyapatite (HA), represents a great potential for replacement of traditional titanium medical implants. In this paper the surface morphology, structural properties and phase content of HA coatings deposited onto nano-porous bio-SiC ceramics with pore orientation being parallel or perpendicular to the plain of subsequently deposited HA film have been studied. The HA coatings produced at 5 s of deposition contained cracks, while the uniform hydroxyapatite coating has been produced at 10 s of deposition. X-ray diffraction analysis revealed that the HA coatings preserve crystal structure of the initial hydroxyapatite powder during deposition. From the intensity ratio of Raman scattering peaks, corresponding to crystalline (967 cm⁻¹) and amorphous (951 cm⁻¹) HA, the least and most crystalline structures were found. The structural perfection of the HA coating was higher for SiC substrates with parallel pore orientation (with respect to the plane of HA growth), indicating that structural properties of SiC ceramics affect the morphological and structural perfection of deposited HA coating.
Perceiving head, shoulders, eyes and toes in augmented virtuality interfaces for mobile robots (2006)

Occupancy grid maps derived from laser range finder readings can be used to create virtual worlds for planar environments. These virtual worlds can be augmented with video to create augmented virtuality displays. Such displays, suitably adapted to represent local terrain and pan-tilt-zoom cameras, can make it easier for operators to simultaneously perceive the pose of the robot and its relation to information in the world. We motivate this claim using two abstractions from a model of cognitive information processing: working memory and mental models. We then describe visualization techniques that try to minimize cognitive workload by displaying information about the "head", "shoulders", "eyes", and "toes" of a teleoperated robot.
Process-oriented abstraction of the complex evolvable systems (2008)

Architectural design and lifecycle management of complex Evolvable Systems encounter contexts and environments in which ambiguity and volatility are of essence. Ambiguity relates to the content of the information the architect has available at the time of the design and maps to the aspects, dimensions and boundaries of the system. Volatility represents constant changes of vision, knowledge and information due to the advances in science or techniques of handling and demands the architect to redesign the system to match the new realities of the time. As a result, the nature of the complex Evolvable Systems introduces serious challenges to the conventional Software Architecture and Software Engineering. This paper presents a new method called Nuclear-Process Oriented Analysis and Modeling (NPOAM), for the design of complex Open Evolvable Systems [1], and focuses on its implementation within the scope of the Problem Model construction [2] for a Cardiac Arrhythmia Management model. Our Problem Model construction develops its conceptualization on the premises of the complexities and requirements of scientific domains. Yet its applicability is not exclusive to scientific domains but since it is designed for more complex scientific environments, it is perfectly applicable to business domains as well. One of the critical contributions of NPOAM is providing the capability of random process modeling and design. The paper concludes with addressing the model analysis and verification issues.