bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fragmentation of organic ions bearing fixed multiple charges observed in MALDI MS
Authors: Lou Xianwen , Li Bao , de Waal Bas F.M. , Schill Jurgen , Baker Matthew B. , Bovee Ralf A.A. , van Dongen Joost L.J. , Milroy Lech‐Gustav , Meijer E.W. 
Published: September 2017

AbstractMatrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI TOF MS) was used to analyze a series of synthetic organic ions bearing fixed multiple charges. Despite the multiple intrinsic charges, only singly charged ions were recorded in each case. In addition to the pseudo‐molecular ions formed by counterion adduction, deprotonation and electron capture, a number of fragment ions were also observed. Charge splitting by fragmentation was found to be a viable route for charge reduction leading to the formation of the observed singly charged fragment ions. Unlike multivalent metal ions, organic ions can rearrange and/or fragment during charge reduction. This fragmentation process will evidently complicate the interpretation of the MALDI MS spectrum. Because MALDI MS is usually considered as a soft ionization technique, the fragment ion peaks can easily be erroneously interpreted as impurities. Therefore, the awareness and understanding of the underlying MALDI‐induced fragmentation pathways is essential for a proper interpretation of the corresponding mass spectra. Due to the fragment ions generated during charge reduction, special care should be taken in the MALDI MS analysis of multiply charged ions. In this work, the possible mechanisms by which the organic ions bearing fixed multiple charges fragment are investigated. With an improved understanding of the fragmentation mechanisms, MALDI TOF MS should still be a useful technique for the characterization of organic ions with fixed multiple charges.
A numerical‐analytical methodology for acquiring the electrical force of carbon nanotube–based nanoactuator assuming an out‐of‐plane electrodes arrangement
Authors: Ouakad Hassen M. 
Published: October 2017

AbstractIn this paper, we develop a simple expression to evaluate the electric force acting on a carbon nanotube–(CNT) based nanoactuator assuming a nonparallel actuating plates (out‐of‐plane) arrangement. The actuating force is initiated by the asymmetry of the resultant electric fringing fields caused mainly due to the nonparallel electrodes arrangement. The nanoactuator is designed based on a CNT flexible electrode (nonstationary) and 2 symmetrically located actuating stationary rectangular shaped out‐of‐plane plates. The resultant electric force is mathematically approximated from the outcomes of a planar (2‐D) numerical solution of the electric problem via a finite element–based numerical analysis. The influence of the design geometrical parameters on the resultant electric force are examined. Several key design parameters were inspected: the width and thickness of the stationary actuating electrodes, the radius of the flexible electrode (the CNT), and the lateral and vertical separation distances between the movable and grounded electrodes. Through several simulations, we show the effect of the lateral and vertical offsets as well as the electrodes thickness in the optimization of the performance of the nanoactuator assuming such nonparallel plates actuating configuration. We also simulate the effect on the resultant actuating force level with the electrode thickness as well as the electrodes lateral separation distance.
High oxygen facilitates wound induction of suberin polyphenolics in kiwifruit
Authors: Wei Xiaopeng , Mao Linchun , Han Xueyuan , Lu Wenjing , Xie Dandan , Ren Xingchen , Zhao Yuying 
Published: September 2017

AbstractBACKGROUNDRapid wound healing would be critical for successful long‐term storage of fruits and vegetables. However, there was no direct evidence for the requirement and efficiency of oxygen in the fruit wound‐healing process. This study was conducted to investigate the role of oxygen in wound‐induced suberization by analyzing melanin, suberin polyphenolics (SPPs) and related enzymes in half‐cut kiwifruits exposed to 100%, 50%, 21% and 0% oxygen.RESULTSBy 3 days after wounding, the wound surface of kiwifruit in high (50 and 100%) oxygen appeared as a continuous layer of melanin and SPPs underneath, which effectively prevent excessive water vapor loss from the fruit halves. In contrast, melanin and SPPs deposition in the wound surface in 0% oxygen was significantly reduced, with high water vapor loss. Rapid decrease of soluble phenolic acids (caffeic, p‐coumaric, ferulic acids) was coupled with the increase of bound ferulic acid (coniferyl diacetate) especially in high oxygen by 9 days after wounding. Meanwhile, high oxygen enhanced peroxidase, catalase, phenylalanine ammonia‐lyase, and polyphenol oxidase activities.CONCLUSIONOxygen is required for wound‐induced melanin and SPPs formation, and high oxygen is effective in promoting wound suberization in postharvest kiwifruit. © 2017 Society of Chemical Industry
MRI to predict nipple‐areola complex (NAC) involvement: An automatic method to compute the 3D distance between the NAC and tumor
Authors: Giannini Valentina , Bianchi Veronica , Carabalona Silvia , Mazzetti Simone , Maggiorotto Furio , Kubatzki Franziska , Regge Daniele , Ponzone Riccardo , Martincich Laura 
Published: October 2017

ObjectivesTo assess the role in predicting nipple‐areola complex (NAC) involvement of a newly developed automatic method which computes the 3D tumor‐NAC distance.Patients and MethodsNinety‐nine patients scheduled to nipple sparing mastectomy (NSM) underwent magnetic resonance (MR) examination at 1.5 T, including sagittal T2w and dynamic contrast enhanced (DCE)‐MR imaging. An automatic method was developed to segment the NAC and the tumor and to compute the 3D distance between them. The automatic measurement was compared with manual axial and sagittal 2D measurements. NAC involvement was defined by the presence of invasive ductal or lobular carcinoma and/or ductal carcinoma in situ or ductal intraepithelial neoplasia (DIN1c − DIN3).ResultsTumor‐NAC distance was computed on 95/99 patients (25 NAC+), as three tumors were not correctly segmented (sensitivity = 97%), and 1 NAC was not detected (sensitivity = 99%). The automatic 3D distance reached the highest area under the receiver operating characteristic (ROC) curve (0.830) with respect to the manual axial (0.676), sagittal (0.664), and minimum distances (0.664). At the best cut‐off point of 21 mm, the 3D distance obtained sensitivity = 72%, specificity = 80%, positive predictive value = 56%, and negative predictive value = 89%.ConclusionsThis method could provide a reproducible biomarker to preoperatively select breast cancer patients candidates to NSM, thus helping surgical planning and intraoperative management of patients.
Estimation of Ophidiomyces prevalence to evaluate snake fungal disease risk
Authors: Hileman Eric T. , Allender Matthew C. , Bradke Danielle R. , Faust Lisa J. , Moore Jennifer A. , Ravesi Michael J. , Tetzlaff Sasha J. 
Published: October 2017

ABSTRACTPathogenic fungi have become a global concern to wildlife populations over the last 2 decades. However, the threat of snake fungal disease (SFD; caused by Ophidiomyces ophiodiicola) to snake populations is still largely unknown. From 2014–2016, we monitored 3 disjunct populations of the federally threated eastern massasauga (Sistrurus catenatus) in Michigan, USA. We used clinical signs of SFD, quantitative TaqMan polymerase chain reaction (qPCR), repeated sampling of individuals and sites, and single‐season occupancy models to estimate site‐specific prevalence of Ophidiomyces. Point estimates of Ophidiomyces prevalence in 2016 were larger at the northernmost study site (0.17, 95% CI = 0.04–0.50), where 17 of 34 snakes were implanted with radio‐transmitters, and smaller at southern sites (0.03, 95% CI = 0.00–0.19). However, Ophidiomyces prevalence was not different between snakes with transmitters and snakes without transmitters. Swabbing snakes with 1 applicator resulted in a high probability of failure in detecting Ophidiomyces DNA for individuals with clinical signs of SFD and the probability was even higher for individuals without clinical signs of SFD. Repeated sampling of individuals reduced the probability of obtaining a false‐negative qPCR result by 72% for snakes with clinical signs and 12% for snakes without clinical signs when we swabbed individuals with 5 applicators. We recommend resampling individuals and sites as a sampling design for estimating fine‐scale, site‐specific Ophidiomyces prevalence and population‐level responses to SFD. If clinical signs are used as a surrogate for SFD, we recommend researchers standardize diagnosis of clinical signs of SFD by providing technicians adequate field training and educational materials, and minimize the number of observers recording clinical signs. We discourage the use of radio‐telemetry methods where SFD occurs unless sterile surgical, handling, and equipment protocols can be ensured and the benefits to the population from such activities outweigh the increased health risks to individuals. © 2017 The Wildlife Society.
Turkish Standardization of Movement Disorders Society Unified Parkinson's Disease Rating Scale and Unified Dyskinesia Rating Scale
Authors: Akbostanci Muhittin C. , Bayram Ece , Yilmaz Volkan , Rzayev Sefer , Özkan Serhat , Tokcaer Ayse Bora , Saka Esen , Durmaz Celik Fatma N. , Barut Banu Özen , Tüfekcioglu Zeynep , Acarer Ahmet , Balaban Hatice , Erer Sevda , Dogu Okan , Kibaroglu Seda , Aydin Nursel , Hanagasi Hasmet , Elibol Bülent , Emre Murat , Stebbins Glenn T. , Goetz Christopher G. 
Published: September 2017

AbstractBackgroundMovement Disorders Society Unified Parkinson's Disease Rating Scale (MDS‐UPDRS) and Unified Dyskinesia Rating Scale (UDysRS) were developed as standard tools to rate Parkinson's disease (PD) and drug‐induced dyskinesias of PD. As these scales have become widely used, there is a need for translation to non‐English languages. Here we present the standardization for the Turkish translations.MethodsThe scales were translated into Turkish and then back‐translated to English. These back‐translations were reviewed by the MDS team. After cognitive pretesting, movement disorder specialists from nine centers tested 352 patients for MDS‐UPDRS, and 250 patients for UDysRS. Confirmatory factor analyses (CFAs) were used to determine if the factor structures for the reference standards could be confirmed in the Turkish data. The comparative fit indexes (CFIs) for the scales were required to be 0.90 or higher. Exploratory factor analyses (EFAs) were conducted to explore the underlying factor structure without the constraint of a pre‐specified factor structure.ResultsFor both scales, the CFIs were 0.94 or greater as compared to the reference standard factor structures. The factor structures were consistent with that of reference standards, although there were some differences in some areas as compared to the EFA of the reference standard dataset. This may be due to the inclusion of patients with different stages of PD and different cultural properties of raters and patients.ConclusionsThese results demonstrate that the Turkish translations of MDS‐UPDRS and UDysRS have adequate clinimetric properties. They are established as the official translations and can be reliably used in Turkish speaking populations.
Development and validation of prognostic survival models in newly diagnosed Parkinson's disease
Authors: Macleod Angus D. , Dalen Ingvild , Tysnes Ole‐Bjørn , Larsen Jan Petter , Counsell Carl E. 
Published: October 2017

ABSTRACTObjectiveThe objective of this study was to develop valid prognostic models to predict mortality, dependency, and “death or dependency” for use in newly diagnosed Parkinson's disease (PD).MethodsThe models were developed in the Parkinsonism Incidence in North‐East Scotland study (UK, 198 patients) and validated in the ParkWest study (Norway, 192 patients), cohorts that attempted to identify and follow‐up all new PD cases in the study area. Dependency was defined using the Schwab & England scale. We selected variables measured at time of diagnosis to include in the models. Internal validation and external validation were performed by calculating C‐statistics (discrimination) and plotting observed versus predicted risk in quantiles of predicted risk (calibration).ResultsOlder age, male sex, increased severity of axial features, and Charlson comorbidity index were independent prognostic factors in the mortality model. Increasing age, higher smoking history, increased severity of axial features, and lower MMSE score were independent predictors in the models of dependency and “death or dependency.” Each model had very good internal calibration and very good or good discrimination (internal and external C‐statistics for the models were 0.73–0.75 and 0.68–0.78, respectively). Although each model clearly separated patients into groups according to risk, they tended to overestimate risk in ParkWest. The models were recalibrated to the baseline risk in the ParkWest study and then calibrated well in this cohort.ConclusionsWe have developed prognostic models for predicting medium‐term risk of important clinical outcomes in newly diagnosed PD. These models have validity for use for stratification of randomization, confounder adjustment, and case‐mix correction, but they are inadequate for individualized prognostication. © 2017. The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
Automatic segmentation of the clinical target volume and organs at risk in the planning CT for rectal cancer using deep dilated convolutional neural networks
Authors: Men Kuo , Dai Jianrong , Li Yexiong 
Published: September 2017

PurposeDelineation of the clinical target volume (CTV) and organs at risk (OARs) is very important for radiotherapy but is time‐consuming and prone to inter‐observer variation. Here, we proposed a novel deep dilated convolutional neural network (DDCNN)‐based method for fast and consistent auto‐segmentation of these structures.MethodsOur DDCNN method was an end‐to‐end architecture enabling fast training and testing. Specifically, it employed a novel multiple‐scale convolutional architecture to extract multiple‐scale context features in the early layers, which contain the original information on fine texture and boundaries and which are very useful for accurate auto‐segmentation. In addition, it enlarged the receptive fields of dilated convolutions at the end of networks to capture complementary context features. Then, it replaced the fully connected layers with fully convolutional layers to achieve pixel‐wise segmentation. We used data from 278 patients with rectal cancer for evaluation. The CTV and OARs were delineated and validated by senior radiation oncologists in the planning computed tomography (CT) images. A total of 218 patients chosen randomly were used for training, and the remaining 60 for validation. The Dice similarity coefficient (DSC) was used to measure segmentation accuracy.ResultsPerformance was evaluated on segmentation of the CTV and OARs. In addition, the performance of DDCNN was compared with that of U‐Net. The proposed DDCNN method outperformed the U‐Net for all segmentations, and the average DSC value of DDCNN was 3.8% higher than that of U‐Net. Mean DSC values of DDCNN were 87.7% for the CTV, 93.4% for the bladder, 92.1% for the left femoral head, 92.3% for the right femoral head, 65.3% for the intestine, and 61.8% for the colon. The test time was 45 s per patient for segmentation of all the CTV, bladder, left and right femoral heads, colon, and intestine. We also assessed our approaches and results with those in the literature: our system showed superior performance and faster speed.ConclusionsThese data suggest that DDCNN can be used to segment the CTV and OARs accurately and efficiently. It was invariant to the body size, body shape, and age of the patients. DDCNN could improve the consistency of contouring and streamline radiotherapy workflows.
Toward optimization of in vivo super‐resolution ultrasound imaging using size‐selected microbubble contrast agents
Authors: Ghosh Debabrata , Xiong Fangyuan , Sirsi Shashank R. , Shaul Philip W. , Mattrey Robert F. , Hoyt Kenneth 
Published: October 2017

PurposeMicrovascular processes play key roles in many diseases including diabetes. Improved understanding of the microvascular changes involved in disease development could offer crucial insight into the relationship of these changes to disease pathogenesis. Super‐resolution ultrasound (SR‐US) imaging has showed the potential to visualize microvascular detail down to the capillary level (i.e., subwavelength resolution), but optimization is still necessary. The purpose of this study was to investigate in vivo SR‐US imaging of skeletal muscle microvascularity using microbubble (MB) contrast agents of various size and concentration while evaluating different ultrasound (US) system level parameters such as imaging frame rate and image acquisition length.MethodsAn US system equipped with a linear array transducer was used in a harmonic imaging mode at low transmit power. C57BL/6J mice fed a normal diet were used in this study. An assortment of size‐selected MB contrast agents (1–2 μm, 3–4 μm, and 5–8 μm in diameter) were slowly infused in the tail vein at various doses (1.25 × 107, 2.5 × 107, or 5 × 107 MBs). US image data were collected before MB injection and thereafter for 10 min at 30 frames per s (fps). The US transducer was fixed throughout and between each imaging period to help capture microvascular patterns along the same image plane. An adaptive SR‐US image processing technique was implemented using custom Matlab software.ResultsExperimental findings illustrate the use of larger MB results in better SR‐US images in terms of skeletal muscle microvascular detail. A dose of 2.5 × 107 MBs resulted in SR‐US images with optimal spatial resolution. An US imaging rate of at least 20 fps and image acquisition length of at least 8 min also resulted in SR‐US images with pronounced microvascular detail.ConclusionsThis study indicates that MB size and dose and US system imaging rate and data acquisition length have significant impact on the quality of in vivo SR‐US images of skeletal muscle microvascularity.
Comparison of Targeted Mass Spectrometry Techniques with an Immunoassay: A Case Study for HSP90α
Authors: Güzel Coşkun , Govorukhina Natalia I. , Stingl Christoph , Dekker Lennard J. M. , Boichenko Alexander , van der Zee Ate G. J. , Bischoff Rainer P.H. , Luider Theo M. 
Published: October 2017

PurposeThe objective of this study is to better understand factors governing the variability and sensitivity in SRM and PRM, compared to immunoassay.Experimental designA 2D‐LC–MS/MS‐based SRM and PRM assay is developed for quantitative measurements of HSP90α in serum. Forty‐three control sera are compared by SRM, PRM, and ELISA following the manufacturer's instructions. Serum samples are trypsin‐digested and fractionated by strong cation exchange chromatography prior to SRM and PRM measurements. Analytical parameters such as linearity, LOD, LOQ, repeatability, and reproducibility of the SRM, PRM, and ELISA are determined.ResultsPRM data obtained by high‐resolution MS correlate better with ELISA measurements than SRM data measured on a triple quadrupole mass spectrometer. While all three methods (SRM, PRM, and ELISA) are able to quantify HSP90α in serum at the ng mL–1 level, the use of PRM on a high‐resolution mass spectrometer reduces variation and shows comparable sensitivity to immunoassay.Conclusions and clinical relevanceUsing fractionation, it is possible to measure ng mL–1 levels of HSP90α in a reproducible, selective, and sensitive way using PRM in serum. This opens up the possibility to use PRM in a multiplexed way as an attractive alternative for immunoassays without the use of antibodies or comparable binders.
Two‐domain analysis of JmjN‐JmjC and PHD‐JmjC lysine demethylases: Detecting an inter‐domain evolutionary stress
Authors: Slama Patrick 
Published: October 2017

AbstractResidues at different positions of a multiple sequence alignment sometimes evolve together, due to a correlated structural or functional stress at these positions. Co‐evolution has thus been evidenced computationally in multiple proteins or protein domains. Here, we wish to study whether an evolutionary stress is exerted on a sequence alignment across protein domains, i.e., on longer sequence separations than within a single protein domain. JmjC‐containing lysine demethylases were chosen for analysis, as a follow‐up to previous studies; these proteins are important multidomain epigenetic regulators. In these proteins, the JmjC domain is responsible for the demethylase activity, and surrounding domains interact with histones, DNA or partner proteins. This family of enzymes was analyzed at the sequence level, in order to determine whether the sequence of JmjC‐domains was affected by the presence of a neighboring JmjN domain or PHD finger in the protein. Multiple positions within JmjC sequences were shown to have their residue distributions significantly altered by the presence of the second domain. Structural considerations confirmed the relevance of the analysis for JmjN‐JmjC proteins, while among PHD‐JmjC proteins, the length of the linker region could be correlated to the residues observed at the most affected positions. The correlation of domain architecture with residue types at certain positions, as well as that of overall architecture with protein function, is discussed. The present results thus evidence the existence of an across‐domain evolutionary stress in JmjC‐containing demethylases, and provide further insights into the overall domain architecture of JmjC domain‐containing proteins.
Global output‐feedback stabilization for nonlinear systems with unknown relative degree
Authors: Wang Meiqiao , Liu Yungang , Man Yongchao 
Published: October 2017

SummaryThis paper is devoted to the global stabilization via output feedback for a class of nonlinear systems with unknown relative degree, dynamics uncertainties, unknown control direction, and nonparametric uncertain nonlinearities. In particular, the unknown relative degree is without known upper bound, which renders us to research for a filter with varying dimension rather than the ones with over dimensions in the existing literature. In comparison with more popular but a bit stronger input‐to‐state stable or input‐to‐state practically stable requirement, only bounded‐input bounded‐state stable requirement is imposed on the dynamics uncertainties, which affect the systems in a persistent intensity rather than in a decaying one. In this paper, to compensate multiple serious system uncertainties and realize global output‐feedback stabilization, a design scheme via switching logic together with varying dimensional filter is developed. In this scheme, 2 switching sequences, which separately generate the gains of the controller and act as the varying dimensions of the filter, are designed to overcome unknown control direction, dynamics uncertainties and nonparametric uncertain nonlinearities, and unknown relative degree, respectively. A 2‐mass lumped‐parameter structure is provided to show the effectiveness of the proposed method in this paper.