bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparative Study of Two Numerical Techniques To Analyze Double Screen Frequency Selective Surface
Authors: Silva Tercio L. , Campos Antonio L. P. S. , d'Assunção Adaildo G. , Maniçoba Robson H. C. 
Published: June 2013

ABSTRACTA comparative study of two techniques to analyze double screen frequency selective surface (FSS) is presented. The FSS are composed with perfectly conducting rectangular patch elements. Numerical and experimental results are presented. The two techniques are the scattering matrix (SM) and the spectral domain analysis. The study allowed us to set up main advantages and constraints of these techniques and define which one should be used for particular FSS geometries and conditions. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2206–2209, 2013
Experimental Verification of Passive Optical Network With Ring Topology
Authors: Lafata Pavel , Vodrážka Jiří 
Published: June 2013

ABSTRACTToday, tree or hybrid tree‐star topologies are mostly used for passive optical networks in practice. However, these topologies are significantly vulnerable against the failures of a central optical line termination (OLT) unit. Recently, an innovative idea about forming a simple ring topology by using asymmetric passive splitters together with secondary OLT unit has been presented and an elementary mathematical model for calculations of optimum splitting ratios of all splitters in a ring infrastructure has been described. The major advantage of presented ring topology is that both primary and secondary OLT units can be placed on the opposite sides of the ring, which could greatly increase the overall resistance of the whole network against critical failures, malfunctions, or sophisticated attacks. Next, this ring topology was successfully realized in practice by using real OLT and optical network units and the whole idea verified. The results of real measurements as well as theoretical calculations are presented in this article. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2201–2205, 2013
Adaptive Optics Integrated Surface Roughness Measurement of Sputtered PT Film on Silicon Substrate
Authors: Fuh Yiin Kuen , Wang Chia He 
Published: June 2013

ABSTRACTA new optical inspection system for in situ surface roughness measurement of sputtered Pt film on silicon is developed. In this study, we present an in‐process measurement of surface roughness by combining an optical probe of laser‐scattering phenomena and adaptive optics (AO) for aberration correction. The aim of this study was to demonstrate the necessity for AO compensation in regions containing turbulences. Measurement results of eight Pt film on top of P‐type silicon wafer samples with a roughness ranging from 58 to 83 nm demonstrate excellent correlation between the peak power and average roughness with a correlation coefficient (R2) of 0.9963. The proposed AO‐assisted system is in good agreement with stylus method and less than 0.70% error values are obtained for the aforementioned average sample roughness. The proposed system can be used as a rapid in‐process roughness monitor to further improve the stability of thin film–sputtering processes in situ. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2055–2059, 2013
A Dual‐Mode Split Microstrip Resonator and Its Applications in Frequency Selective Devices
Authors: Belyaev Boris A. , Serzhantov Aleksey M. , Tyurnev Vladimir V. 
Published: June 2013

ABSTRACTA dual‐mode microstrip resonator whose strip conductor is partially split from its one end by a longitudinal slot has been studied. The resonator has two fundamental modes, even and odd ones. The difference of their frequencies is controlled by varying the slot length. Based on such resonators, original structures of a diplexer and passband filters including dual‐band have been designed. Measured performances of their fabricated prototypes prove applicability of designed devices in microwave engineering. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2186–2190, 2013
Design of Compact Bandpass Filter with Controllable Multiple Transmission Zeros using The Second‐Order Inductive‐Coupled Resonator
Authors: Huang Hui‐Hsiang , Horng Tzyy‐Sheng 
Published: June 2013

ABSTRACTThis article proposes new synthetic design approach for a compact LTCC bandpass filter (BPF) with three transmission zeros over a wide stopband operating in the 2.4–2.5 GHz WLAN band. The BPFs have two feedback paths, one for a grounding inductor and one for a coupling capacitor, to provide controllable multiple transmission zeros at 1.07 and 5.05 GHz stopband, which suppresses the 0.82–0.96 GHz GSM850/GSM900 band and 4.8–5.0 GHz second harmonic band of the operating frequency. The presented design derives compact formulas for synthesizing a filter to meet the specification requirement. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2155–2157, 2013
Validation of the rotterdam MOVE2PC questionnaire for assessment of nurses' knowledge and opinions on palliative care
Authors: Witkamp Frederika E. , van Zuylen Lia , van der Rijt Carin C.D. , van der Heide Agnes 
Published: June 2013

AbstractThe purpose of this study was the psychometric testing of a questionnaire to assess nurses' opinions, subjective norms, perceived difficulties, and knowledge related to palliative care. The 63‐item MOVE2PC Questionnaire was tested among 219 nurses in groups differing in education and experience. The intra‐rater agreement was moderate to good (к > .5κmax), and internal consistency was good (alpha = .77). Construct validity was demonstrated by between‐groups differences in knowledge, opinions, and perceived difficulties. Responsiveness was shown by improved scores after an education program. Time of completion was 20 minutes, and 99% skipped at most five items, demonstrating feasibility. Findings support the usefulness of the instrument for assessing nurses' knowledge and views on palliative care. © 2013 Wiley Periodicals, Inc. Res Nurs Health 36: 512–523, 2013.
Random walks which prefer unvisited edges: Exploring high girth even degree expanders in linear time
Authors: Berenbrink Petra , Cooper Colin , Friedetzky Tom 
Published: June 2013

AbstractLet be a connected graph with vertices. A simple random walk on the vertex set of G is a process, which at each step moves from its current vertex position to a neighbouring vertex chosen uniformly at random.We consider a modified walk which, whenever possible, chooses an unvisited edge for the next transition; and makes a simple random walk otherwise. We call such a walk an edge‐process (or E‐process). The rule used to choose among unvisited edges at any step has no effect on our analysis. One possible method is to choose an unvisited edge uniformly at random, but we impose no such restriction.For the class of connected even degree graphs of constant maximum degree, we bound the vertex cover time of the E‐process in terms of the edge expansion rate of the graph G, as measured by eigenvalue gap of the transition matrix of a simple random walk on G.A vertex v is ℓ‐good, if any even degree subgraph containing all edges incident with v contains at least ℓ vertices. A graph G is ℓ‐good, if every vertex has the ℓ‐good property. Let G be an even degree ℓ‐good expander of bounded maximum degree. Any E‐process on G has vertex cover time

urn:x-wiley:10429832:media:rsa20504:rsa20504-math-0004

This is to be compared with the lower bound on the cover time of any connected graph by a weighted random walk. Our result is independent of the rule used to select the order of the unvisited edges, which could, for example, be chosen on‐line by an adversary.As no walk based process can cover an n vertex graph in less than n – 1 steps, the cover time of the E‐process is of optimal order when . With high probability random r‐regular graphs, even, have . Thus the vertex cover time of the E‐process on such graphs is . © 2013 Wiley Periodicals, Inc. Random Struct. Alg., 46, 36–54, 2015
Primary gastric synovial sarcoma: molecular diagnosis and prediction of prognosis
Authors: Kamata Kohsuke , Wada Ryuichi , Yajima Nobuhisa , Sawada Mitsuhiro , Wakasa Haruki , Yagihashi Soroku 
Published: June 2013

Abstract
A 42-year-old Japanese woman complained of upper abdominal pain. Endoscopic examination demonstrated an elevated lesion in the body of the stomach, and a biopsy specimen demonstrated proliferation of atypical spindle cells. She underwent partial gastrectomy; the resected tumor measured 3.5 × 2.8 × 1.2 cm in size. Histological examination disclosed the haphazard proliferation of spindle cells in the mucosa mixed with less prominent epithelioglandular component. The spindle cells were positive for cytokeratin, vimentin, EMA and CD99, but not for KIT, DOG1, desmin or S100. Reverse transcription-polymerase chain reaction using paraffin sections amplified a SYT-SSX1 chimera transcript. A diagnosis of synovial sarcoma was made. There has been no sign of recurrence or metastasis for 6 years after the operation. Synovial sarcoma in the stomach is very rare. Since differential diagnosis of synovial sarcoma from carcinosarcoma and mesenchymal tumors is critical for the treatment and prediction of prognosis, accurate diagnosis with molecular analysis is essential.
Calcium binding by the PKD1 domain regulates interdomain flexibility in Vibrio cholerae metalloprotease PrtV
Authors: Edwin Aaron , Rompikuntal Pramod , Björn Erik , Stier Gunter , Wai Sun N. , Sauer-Eriksson A. Elisabeth 
Published: June 2013

Vibrio cholerae, the causative agent of cholera, releases several virulence factors including secreted proteases when it infects its host. These factors attack host cell proteins and break down tissue barriers and cellular matrix components such as collagen, laminin, fibronectin, keratin, elastin, and they induce necrotic tissue damage. The secreted protease PrtV constitutes one virulence factors of V. cholerae. It is a metalloprotease belonging to the M6 peptidase family. The protein is expressed as an inactive, multidomain, 102 kDa pre‐pro‐protein that undergoes several N‐ and C‐terminal modifications after which it is secreted as an intermediate variant of 81 kDa. After secretion from the bacteria, additional proteolytic steps occur to produce the 55 kDa active M6 metalloprotease. The domain arrangement of PrtV is likely to play an important role in these maturation steps, which are known to be regulated by calcium. However, the molecular mechanism by which calcium controls proteolysis is unknown. In this study, we report the atomic resolution crystal structure of the PKD1 domain from V. cholera PrtV (residues 755–838) determined at 1.1 Å. The structure reveals a previously uncharacterized Ca2+‐binding site located near linker regions between domains. Conformational changes in the Ca2+‐free and Ca2+‐bound forms suggest that Ca2+‐binding at the PKD1 domain controls domain linker flexibility, and plays an important structural role, providing stability to the PrtV protein.
Signal-dependent fra-2 regulation in skeletal muscle reserve and satellite cells
Authors: Alli N S , Yang E C , Miyake T , Aziz A , Collins-Hooper H , Patel K , McDermott J C 
Published: June 2013

AbstractActivator protein-1 (AP-1) is a ubiquitous transcription factor that paradoxically also has some tissue-specific functions. In skeletal muscle cells, we document that the AP-1 subunit, Fra-2, is expressed in the resident stem cells (Pax7-positive satellite cells) and also in the analogous undifferentiated ‘reserve’ cell population in myogenic cultures, but not in differentiated myofiber nuclei. Silencing of Fra-2 expression enhances the expression of differentiation markers such as muscle creatine kinase and myosin heavy chain, indicating a possible role of Fra-2 in undifferentiated myogenic progenitor cells. We observed that Fra-2 is a target of cytokine-mediated extracellular signal-regulated kinase-1/2 signaling in cultured muscle cells, and extensive mass spectrometry and mutational analysis identified S320 and T322 as regulators of Fra-2 protein stability. Interestingly, Fra-2 S320 phosphorylation occurs transiently in activated satellite cells and is extinguished in myogenin-positive differentiating cells. Thus, cytokine-mediated Fra-2 expression and stabilization is linked to regulation of myogenic progenitor cells having implications for the molecular regulation of adult muscle stem cells and skeletal muscle regeneration.
Mineralocorticoid receptors and the heart, multiple cell types and multiple mechanisms: a focus on the cardiomyocyte
Authors: Bienvenu Laura A. , Reichelt Melissa E. , Delbridge Lea M. D. , Young Morag J. 
Published: June 2013

MR (mineralocorticoid receptor) activation in the heart plays a central role in the development of cardiovascular disease, including heart failure. The MR is present in many cell types within the myocardium, including cardiomyocytes, macrophages and the coronary vasculature. The specific role of the MR in each of these cell types in the initiation and progression of cardiac pathophysiology is not fully understood. Cardiomyocyte MRs are increasingly recognized to play a role in regulating cardiac function, electrical conduction and fibrosis, through direct signal mediation and through paracrine MR-dependent activity. Although MR blockade in the heart is an attractive therapeutic option for the treatment of heart failure and other forms of heart disease, current antagonists are limited by side effects owing to MR inactivation in other tissues (including renal targets). This has led to increased efforts to develop therapeutics that are more selective for cardiac MRs and which may have reduced the occurrence of side effects in non-cardiac tissues. A major clinical consideration in the treatment of cardiovascular disease is of the differences between males and females in the incidence and outcomes of cardiac events. There is clinical evidence that female sensitivity to endogenous MRs is more pronounced, and experimentally that MR-targeted interventions may be more efficacious in females. Given that sex differences have been described in MR signalling in a range of experimental settings and that the MR and oestrogen receptor pathways share some common signalling intermediates, it is becoming increasingly apparent that the mechanisms of MRs need to be evaluated in a sex-selective manner. Further research targeted to identify sex differences in cardiomyocyte MR activation and signalling processes has the potential to provide the basis for the development of cardiac-specific MR therapies that may also be sex-specific.
High-resolution laser spectroscopy between 0.9 and 14.3 THz in a supersonic beam: Rydberg-Rydberg transitions of atomic Xe at intermediate n values
Authors: Haase Christa , Agner Josef A. , Merkt Frédéric 
Published: June 2013

A laser-based, pulsed, narrow-band source of submillimeter-wave radiation has been developed that is continuously tunable from 0.1 THz to 14.3 THz. The source is based on difference-frequency mixing in the nonlinear crystal trans-4′-(dimethylamino)-N-methyl-4-stilbazolium tosylate. By varying the pulse length, the bandwidth of the submillimeter-wave radiation can be adjusted between 85 MHz and 2.8 MHz. This new radiation source has been integrated in a vacuum-ultraviolet–submillimeter-ware double-resonance spectrometer, with which low-frequency transitions of atoms and molecules in supersonic beams can be detected mass-selectively by photoionization and time-of-flight mass spectrometry. The properties of the radiation source and spectrometer are demonstrated in a study of 33f ← nd Rydberg-Rydberg transitions in Xe with n in the range 16–31. The frequency calibration of the submillimeter-wave radiation was performed with an accuracy of 2.8 MHz. The narrowest lines observed experimentally have a full-width at half-maximum of ∼3 MHz, which is sufficient to fully resolve the hyperfine structure of the Rydberg-Rydberg transitions of 129Xe and 131Xe. A total of 72 transitions were measured in the range between 0.937 THz and 14.245 THz and their frequencies are compared with frequencies calculated by multichannel quantum defect theory.
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato
Authors: Koenig Daniel , Jiménez-Gómez José M. , Kimura Seisuke , Fulop Daniel , Chitwood Daniel H. , Headland Lauren R. , Kumar Ravi , Covington Michael F. , Devisetty Upendra Kumar , Tat An V. , Tohge Takayuki , Bolger Anthony , Schneeberger Korbinian , Ossowski Stephan , Lanz Christa , Xiong Guangyan , Taylor-Teeples Mallorie , Brady Siobhan M. , Pauly Markus , Weigel Detlef , Usadel Björn , Fernie Alisdair R. , Peng Jie , Sinha Neelima R. , Maloof Julin N. 
Published: June 2013

Significance
One of the most important technological advances by humans is the domestication of plant species for the production of food. We have used high-throughput sequencing to identify changes in DNA sequence and gene expression that differentiate cultivated tomato and its wild relatives. We also identify hundreds of candidate genes that have evolved new protein sequences or have changed expression levels in response to natural selection in wild tomato relatives. Taken together, our analyses provide a snapshot of genome evolution under artificial and natural conditions.
Predicting protein contact map using evolutionary and physical constraints by integer programming
Authors: Wang Zhiyong , Xu Jinbo 
Published: June 2013

Abstract
Motivation: Protein contact map describes the pairwise spatial and functional relationship of residues in a protein and contains key information for protein 3D structure prediction. Although studied extensively, it remains challenging to predict contact map using only sequence information. Most existing methods predict the contact map matrix element-by-element, ignoring correlation among contacts and physical feasibility of the whole-contact map. A couple of recent methods predict contact map by using mutual information, taking into consideration contact correlation and enforcing a sparsity restraint, but these methods demand for a very large number of sequence homologs for the protein under consideration and the resultant contact map may be still physically infeasible.
Results: This article presents a novel method PhyCMAP for contact map prediction, integrating both evolutionary and physical restraints by machine learning and integer linear programming. The evolutionary restraints are much more informative than mutual information, and the physical restraints specify more concrete relationship among contacts than the sparsity restraint. As such, our method greatly reduces the solution space of the contact map matrix and, thus, significantly improves prediction accuracy. Experimental results confirm that PhyCMAP outperforms currently popular methods no matter how many sequence homologs are available for the protein under consideration.
Availability: http://raptorx.uchicago.edu.
Contact: jinboxu@gmail.com
A high-throughput framework to detect synapses in electron microscopy images
Authors: Navlakha Saket , Suhan Joseph , Barth Alison L. , Bar-Joseph Ziv 
Published: June 2013

Abstract
Motivation: Synaptic connections underlie learning and memory in the brain and are dynamically formed and eliminated during development and in response to stimuli. Quantifying changes in overall density and strength of synapses is an important pre-requisite for studying connectivity and plasticity in these cases or in diseased conditions. Unfortunately, most techniques to detect such changes are either low-throughput (e.g. electrophysiology), prone to error and difficult to automate (e.g. standard electron microscopy) or too coarse (e.g. magnetic resonance imaging) to provide accurate and large-scale measurements.
Results: To facilitate high-throughput analyses, we used a 50-year-old experimental technique to selectively stain for synapses in electron microscopy images, and we developed a machine-learning framework to automatically detect synapses in these images. To validate our method, we experimentally imaged brain tissue of the somatosensory cortex in six mice. We detected thousands of synapses in these images and demonstrate the accuracy of our approach using cross-validation with manually labeled data and by comparing against existing algorithms and against tools that process standard electron microscopy images. We also used a semi-supervised algorithm that leverages unlabeled data to overcome sample heterogeneity and improve performance. Our algorithms are highly efficient and scalable and are freely available for others to use.
Availability: Code is available at http://www.cs.cmu.edu/∼saketn/detect_synapses/
Contact: zivbj@cs.cmu.edu
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation
Authors: Le Hai-Son , Bar-Joseph Ziv 
Published: June 2013

Abstract
Motivation: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally. MiRNAs were shown to play an important role in development and disease, and accurately determining the networks regulated by these miRNAs in a specific condition is of great interest. Early work on miRNA target prediction has focused on using static sequence information. More recently, researchers have combined sequence and expression data to identify such targets in various conditions.
Results: We developed the Protein Interaction-based MicroRNA Modules (PIMiM), a regression-based probabilistic method that integrates sequence, expression and interaction data to identify modules of mRNAs controlled by small sets of miRNAs. We formulate an optimization problem and develop a learning framework to determine the module regulation and membership. Applying PIMiM to cancer data, we show that by adding protein interaction data and modeling cooperative regulation of mRNAs by a small number of miRNAs, PIMiM can accurately identify both miRNA and their targets improving on previous methods. We next used PIMiM to jointly analyze a number of different types of cancers and identified both common and cancer-type-specific miRNA regulators.
Contact: zivbj@cs.cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A framework for scalable parameter estimation of gene circuit models using structural information
Authors: Kuwahara Hiroyuki , Fan Ming , Wang Suojin , Gao Xin 
Published: June 2013

Abstract
Motivation: Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation.
Results: Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems.
Availability: http://sfb.kaust.edu.sa/Pages/Software.aspx
Contact: xin.gao@kaust.edu.sa
Supplementary information: Supplementary data are available at Bioinformatics online.