bluuebunny/crossref_metadata_2025_split huggingface dataset:
One‐step nucleic acid amplification vs ultrastaging in the detection of sentinel lymph node metastasis in endometrial cancer patients
Authors: Kosťun Jan , Pešta Martin , Sláma Jiří , Slunéčko Robert , Vlasák Pavel , Bouda Jiří , Novotný Zdeněk , Topolčan Ondřej , Kučera Radek , Kulda Vlastimil , Houfková Kateřina , Berezovskiy Denis , Bartáková Alena , Presl Jiří 
Published: December 2018

Background and ObjectivesUtilisation of the one‐step nucleic acid amplification (OSNA) molecular biology method for the detection of the metastatic involvement of sentinel lymph nodes (SLNs) in endometrial cancer (EC) patients. A comparison with histopathological ultrastaging and a description of the clinical consequences.MethodsSurgically treated EC patients underwent detection of SLNs. Nodes greater than 5 mm were cut into sections 2‐mm thick parallel to the short axis of the node. Odd sections were examined according to the OSNA method, while even ones according to an appropriate ultrastaging protocol. Nodes less than or equal to 5 mm were cut into halves along the longitudinal axis with one half examined according to the OSNA method and the other half by ultrastaging.ResultsFifty‐eight patients were included and 135 SLNs were acquired. Both ultrastaging and OSNA agreed on 116 results. According to the OSNA method, 20.69% more patients were classified into International Federation of Gynecology and Obstetrics (FIGO) stage III. When comparing the results of the OSNA method to the conclusions of ultrastaging as a reference method, sensitivity of 90.9%, specificity of 85.5% and concordance of 85.9% were attained.ConclusionsThe results of the OSNA method showed a higher frequency of detection of micrometastases and included 20.69% more patients into FIGO stage III.
The Global academic research organization network: Data sharing to cure diseases and enable learning health systems
Authors: Fukushima Masanori , Austin Christopher , Sato Norihiro , Maruyama Tatsuya , Navarro Eileen , Rocca Mitra , Demotes Jacques , Haendel Melissa , Volchenboum Samuel L. , Cowperthwaite Matthew , Silverstein Jonathan C. , Webb Chris , Sim Ida , Chase Marianne , Speakman John , Augustine Erika , Ford Daniel E. , Kush Rebecca 
Published: December 2018

AbstractIntroductionGlobal data sharing is essential. This is the premise of the Academic Research Organization (ARO) Council, which was initiated in Japan in 2013 and has since been expanding throughout Asia and into Europe and the United States. The volume of data is growing exponentially, providing not only challenges but also the clear opportunity to understand and treat diseases in ways not previously considered. Harnessing the knowledge within the data in a successful way can provide researchers and clinicians with new ideas for therapies while avoiding repeats of failed experiments. This knowledge transfer from research into clinical care is at the heart of a learning health system.MethodsThe ARO Council wishes to form a worldwide complementary system for the benefit of all patients and investigators, catalyzing more efficient and innovative medical research processes. Thus, they have organized Global ARO Network Workshops to bring interested parties together, focusing on the aspects necessary to make such a global effort successful. One such workshop was held in Austin, Texas, in November 2017. Representatives from Japan, Taiwan, Singapore, Europe, and the United States reported on their efforts to encourage data sharing and to use research to inform care through learning health systems.ResultsThis experience report summarizes presentations and discussions at the Global ARO Network Workshop held in November 2017 in Austin, TX, with representatives from Japan, Korea, Singapore, Taiwan, Europe, and the United States. Themes and recommendations to progress their efforts are explored. Standardization and harmonization are at the heart of these discussions to enable data sharing. In addition, the transformation of clinical research processes through disruptive innovation, while ensuring integrity and ethics, will be key to achieving the ARO Council goal to overcome diseases such that people not only live longer but also are healthier and happier as they age.ConclusionsThe achievement of global learning health systems will require further exploration, consensus‐building, funding aligned with incentives for data sharing, standardization, harmonization, and actions that support global interests for the benefit of patients.
Feasibility of pedicled vascularized inguinal lymph node transfer in a mouse model: A preliminary study
Authors: Ishikawa Kosuke , Maeda Taku , Funayama Emi , Hayashi Toshihiko , Murao Naoki , Osawa Masayuki , Furukawa Hiroshi , Oyama Akihiko , Yamamoto Yuhei 
Published: December 2018

PurposeVascularized lymph node transfer is becoming more common in the treatment of lymphedema, but suitable small animal models for research are lacking. Here, we evaluated the feasibility of pedicled vascularized inguinal lymph node transfer in mice.MethodsTwenty‐five mice were used in the study. An inguinal lymph node‐bearing flap with a vascular pedicle containing the superficial caudal epigastric vessels was transferred into the ipsilateral popliteal fossa after excision of the popliteal lymph node. Indocyanine green (ICG) angiography was used to confirm vascularity of the flap. ICG lymphography was performed to evaluate lymphatic flow at 3 and 4 weeks postoperatively. Patent blue dye was injected into the ipsilateral hind paw to observe staining of the transferred lymph node at 4 weeks postoperatively. All transferred lymph nodes were then harvested and histologically evaluated by hematoxylin and eosin staining.ResultsIn 16 of the 25 mice, ICG lymphography showed reconnection between the transferred lymph node and the afferent lymphatic vessels, as confirmed by patent blue staining. Histologically, these transferred lymph nodes with afferent lymphatic reconnection significantly regressed in size (0.37 ± 0.24 mm2) and showed clear follicle formation, whereas those without afferent lymphatic reconnection showed less size regression (1.31 ± 1.17 mm2); the cell population was too dense to allow identification of follicles.ConclusionsWe established a mouse model of vascularized lymph node transfer with predictable afferent lymphatic reconnection. Both the vascularization and reconnection might be necessary for functional regeneration of the transferred lymph node.
Compact high gain UWB antenna using fractal geometry and UWB‐AMC
Authors: Dwivedi Ravi Prakash , Kommuri Usha Kiran 
Published: December 2018

AbstractA miniaturized fractal antenna using Coplanar Wave Guide (CPW) fed and ultrawideband (UWB)‐artificial magnetic conductor (AMC) for ultra wideband and Active integrated application is designed and presented. This antenna covers frequency range from 2.5 to 10 GHz with ultrabandwidth of 7.5GHz and return loss well below −10 dB over the entire band of application. The antenna has an average gain of 3.35 dB without AMC and 7.7 dBi with UWB‐AMC. Physical dimension of the proposed antenna is (27 × 28 mm × 1.6) mm3 and for UWB‐AMC is (40 × 40 × 1.6) mm3. Complet set of UWB‐antenna and A.MC‐ is fabricated using FR.‐4 substrate with εr = 4.4, d = 0.0001and thickness (h) = 1.6 mm. Ansys HFSS Tool is used to analyze and optimize the parameters of antenna and UWB‐AMC. Vector Network Analyzer is used to validate the experimental result with simulation parameter of proposedantenna.
Stacked microstrip patch antenna design for ISM band applications with 3D‐printing technology
Authors: Belen Mehmet A. 
Published: December 2018

AbstractWith the advances in the 3Dprinting technology these technologies are being used in many fields for fast and low‐cost prototyping procceses. One of the commonoly used applications is manufacturing of microwave circuits. Herein, design and realization of stacked microstrip patch array (SMPA) antenna for ISM band application with 3D‐printing technology is presented. Firstly design of a SMPA antenna consist of a patch fed by a microstrip line and a staced patch array 2×2 rectangular patch is studied for ISM band applications. Next, the antenna is fabricated by using a 3D printer. From the experiment results it can be concluded that 3D‐printed antenna has good performance, within the operation band with a good return loss performance of <–10 dB and a moderate gain of 11 dBi. Thus, in this work an efficient prototyping method had been proposed for low‐cost, high‐accuracy, and fast prototyping of microwave antennas by using 3D‐printer.
Delay‐compensation block for first‐order low‐pass delta‐sigma modulators
Authors: Ben Arfi Anis , Helaoui Mohamed , Ghannouchi Fadhel M. 
Published: December 2018

AbstractImplementing the Delta Sigma Modulator (DSM) processing blocks on hardware is challenging due to the additional tap delays required by the digital processing blocks to process and output the result. The tap‐delays, known as latency, are necessary for the Field Programmable Gate Array (FPGA) operation to allow the logic gates to process the data at a given clock rate. These latencies alter the transfer function of the first‐order DSM as they present additional tap‐delays to the inherent delays within the DSM loop. A compensation block for the first‐order DSM is proposed to cancel‐out the effect of these latencies. By studying the transfer function, a combination of delays able to reconstruct the correct transfer function is determined. The solution was implemented on FPGA and tested using a 2.5 MHz signal. The post‐compensated DSM achieved a Signal‐to‐Noise‐and‐Distortion Ratio (SNDR) = 42 dB and an Adjacent Channel Leakage Ratio (ACLR) = 39 dB.
Method of mode decomposition based on virtual ports for circularly polarized micro‐strip antenna
Authors: Wang Yi , Su Yan , Xie Ze‐Ming , Gao Kun 
Published: December 2018

AbstractA design method of circularly polarized (CP) micro‐strip antenna is proposed. The coefficients of eigen‐mode and the axial ratio (AR) are derived based on the cavity theory. The radiation feature can be estimated from port impedance. The optimal feeding position is found by means of virtual port method. During the derivation, corner truncated patch antenna is used to verify the method. A cross‐slotted CP micro‐strip antenna is designed, which is working at GPS band. Then the fabrication and measurement of the antenna are conducted. Its measured impedance, AR, radiation pattern agreed well with the simulation results, which verify high efficiency of this method for CP micro‐strip antenna design.
Radio‐morphology: Parametric shape‐based features in radiotherapy
Authors: Lakshminarayanan Pranav , Jiang Wei , Robertson Scott P. , Cheng Zhi , Han Peijin , Bowers Michael , Moore Joseph A. , Shpitser Ilya , Siddiqui Sauleh A. , Quon Harry , Taylor Russell H. , McNutt Todd 
Published: December 2018

PurposeIn radiotherapy, it is necessary to characterize dose over the patient anatomy to target areas and organs at risk. Current tools provide methods to describe dose in terms of percentage of volume and magnitude of dose, but are limited by assumptions of anatomical homogeneity within a region of interest (ROI) and provide a non‐spatially aware description of dose. A practice termed radio‐morphology is proposed as a method to apply anatomical knowledge to parametrically derive new shapes and substructures from a normalized set of anatomy, ensuring consistently identifiable spatially aware features of the dose across a patient set.MethodsRadio‐morphologic (RM) features are derived from a three‐step procedure: anatomy normalization, shape transformation, and dose calculation. Predefined ROI's are mapped to a common anatomy, a series of geometric transformations are applied to create new structures, and dose is overlaid to the new images to extract dosimetric features; this feature computation pipeline characterizes patient treatment with greater anatomic specificity than current methods.ResultsExamples of applications of this framework to derive structures include concentric shells based around expansions and contractions of the parotid glands, separation of the esophagus into slices along the z‐axis, and creating radial sectors to approximate neurovascular bundles surrounding the prostate. Compared to organ‐level dose‐volume histograms (DVHs), using derived RM structures permits a greater level of control over the shapes and anatomical regions that are studied and ensures that all new structures are consistently identified. Using machine learning methods, these derived dose features can help uncover dose dependencies of inter‐ and intra‐organ regions. Voxel‐based and shape‐based analysis of the parotid and submandibular glands identified regions that were predictive of the development of high‐grade xerostomia (CTCAE grade 2 or greater) at 3–6 months post treatment.ConclusionsRadio‐morphology is a valuable data mining tool that approaches radiotherapy data in a new way, improving the study of radiotherapy to potentially improve prognostic and predictive accuracy. Further applications of this methodology include the use of parametrically derived sub‐volumes to drive radiotherapy treatment planning.
Report of a National Cancer Institute special panel: Characterization of the physical parameters of particle beams for biological research
Authors: Durante Marco , Paganetti Harald , Pompos Arnold , Kry Stephen F. , Wu Xiaodong , Grosshans David R. 
Published: December 2018

PurposeTo define the physical parameters needed to characterize a particle beam in order to allow intercomparison of different experiments performed using different ions at the same facility and using the same ion at different facilities.MethodsAt the request of the National Cancer Institute (NCI), a special panel was convened to review the current status of the field and to provide suggested metrics for reporting the physical parameters of particle beams to be used for biological research. A set of physical parameters and measurements that should be performed by facilities and understood and reported by researchers supported by NCI to perform pre‐clinical radiobiology and medical physics of heavy ions were generated.ResultsStandard measures such as radiation delivery technique, beam modifiers used, nominal energy, field size, physical dose and dose rate should all be reported. However, more advanced physical measurements, including detailed characterization of beam quality by microdosimetric spectrum and fragmentation spectra, should also be established and reported. Details regarding how such data should be incorporated into Monte Carlo simulations and the proper reporting of simulation details are also discussed.ConclusionsIn order to allow for a clear relation of physical parameters to biological effects, facilities and researchers should establish and report detailed physical characteristics of the irradiation beams utilized including both standard and advanced measures. Biological researchers are encouraged to actively engage facility staff and physicists in the design and conduct of experiments. Modeling individual experimental setups will allow for the reporting of the uncertainties in the measurement or calculation of physical parameters which should be routinely reported.
Real‐time simultaneous shim and motion measurement and correction in glycoCEST MRI using double volumetric navigators (DvNavs)
Authors: Simegn Gizeaddis L. , Van der Kouwe Andre J.W. , Robertson Frances C. , Meintjes Ernesta M. , Alhamud Ali 
Published: December 2018

PurposeCEST MRI allows for indirect detection of molecules with exchangeable protons, measured as a reduction in water signal because of continuous transfer of saturated protons. CEST requires saturation pulses on the order of a second, as well as repeated acquisitions at different offset frequencies. The resulting extended scan time makes CEST susceptible to subject motion, which introduces field inhomogeneity, shifting offset frequencies and causing distortions in CEST spectra that resemble true CEST effects. This is a particular problem for molecules that resonate close to water, such as hydroxyl group in glycogen. To address this, a technique for real‐time measurement and correction of motion and field inhomogeneity is proposed.MethodsA CEST sequence was modified to include double volumetric navigators (DvNavs) for real‐time simultaneous motion and shim correction. Phantom tests were conducted to investigate the effects of motion and shim changes on CEST quantification and to validate the accuracy of DvNav motion and shim estimates. To evaluate DvNav shim and motion correction in vivo, acquisitions including 5 experimental conditions were performed in the calf muscle of 2 volunteers.ResultsPhantom data show that DvNav‐CEST accurately estimates frequency and linear gradient changes because of motion and corrects resulting image distortions. In addition, DvNav‐CEST improves CEST quantification in vivo in the presence of motion.ConclusionThe proposed technique allows for real‐time simultaneous motion and shim correction with no additional scanning time, enabling accurate CEST quantification even in the presence of motion and field inhomogeneity.
Simple and broadly applicable automatic quality control for 3D 1H MR spectroscopic imaging data of the prostate
Authors: Tayari Nassim , Obels Jiri , Kobus Thiele , Scheenen Tom W.J. , Heerschap Arend 
Published: December 2018

PurposeQuality control (QC) is a prerequisite for clinical MR spectroscopic imaging (MRSI) to avoid that bad spectra hamper data interpretation. The aim of this work was to present a simple automatic QC for prostate 1H MRSI that can handle data obtained with different commonly used pulse sequences, echo times, field strengths, and MR platforms.MethodsA QC method was developed with a ratio (Qratio) where the numerator and the denominator are functions of several signal heights, logically combined for their positive or negative contribution to spectral quality. This Qratio was tested on 4 data sets obtained at 1.5, 3, and 7T, with and without endorectal coil and different localization sequences and echo times. Spectra of 25,248 voxels in 26 prostates were labeled as acceptable or unacceptable by MRS experts as gold standard. A threshold value was determined for Qratio from a subset of voxels, labeled in consensus by 4 experts, for an optimal accuracy to separate spectra.ResultsApplying this Qratio threshold to the remaining test voxels, an automatic separation of good and bad spectra was possible with an accuracy of 0.88, similar to manual separation between the 2 classes. Qratio values were used to generate maps representing spectral quality on a binary or continuous scale.ConclusionAutomated QC of prostate 1H MRSI by Qratio is fast, simple, easily transferable and more practical than supervised feature extraction methods and therefore easy to integrate into different clinical MR systems. Moreover, quality maps can be generated to read the reliability of spectra in each voxel.
Lung development and emerging roles for type 2 immunity
Authors: Loering Svenja , Cameron Guy J. M. , Starkey Malcolm R , Hansbro Philip M 
Published: December 2018

AbstractLung development is a complex process mediated through the interaction of multiple cell types, factors and mediators. In mice, it starts as early as embryonic day 9 and continues into early adulthood. The process can be separated into five different developmental stages: embryonic, pseudoglandular, canalicular, saccular, and alveolar. Whilst lung bud formation and branching morphogenesis have been studied extensively, the mechanisms of alveolarisation are incompletely understood. Aberrant lung development can lead to deleterious consequences for respiratory health such as bronchopulmonary dysplasia (BPD), a disease primarily affecting preterm neonates, which is characterised by increased pulmonary inflammation and disturbed alveolarisation. While the deleterious effects of type 1‐mediated inflammatory responses on lung development have been well established, the role of type 2 responses in postnatal lung development remains poorly understood. Recent studies indicate that type 2‐associated immune cells, such as group 2 innate lymphoid cells and alveolar macrophages, are increased in number during postnatal alveolarisation. Here, we present the current state of understanding of the postnatal stages of lung development and the key cell types and mediators known to be involved. We also provide an overview of how stem cells are involved in lung development and regeneration, and the negative influences of respiratory infections. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Characterizations of HSP90‐Interacting Complex in Renal Cells Using Tandem Affinity Purification and Its Potential Role in Kidney Stone Formation
Authors: Manissorn Juthatip , Singhto Nilubon , Thongboonkerd Visith 
Published: December 2018

AbstractHeat shock protein 90 (HSP90) is a highly abundant molecular chaperone that interacts with many other intracellular proteins to regulate various cellular processes. However, compositions of the HSP90‐interacting complex remain underinvestigated. This study thus aims to characterize such complex in human embryonic kidney (HEK293T) cells under normal physiologic state using tandem affinity purification (TAP) followed by protein identification using an ultrahigh‐resolution tandem mass spectrometer (Qq‐TOF MS/MS). A total of 32 proteins, including four forms of HSP90 and 16 novel HSP90‐interacting partners, are successfully identified from this complex using TAP control to subtract nonspecific binders. Co‐immunoprecipitation followed by immunoblotting and immunofluorescence co‐staining confirms the association of HSP90 with known (HSP70, α‐tubulin, and β‐actin) and novel (vimentin, calpain‐1, and importin‐β1) partners. Knockdown of HSP90 by small‐interfering RNA (siHSP90) causes significant changes in levels of HSP70, α‐tubulin, β‐actin, vimentin, and calpain‐1, all of which are calcium oxalate (CaOx) crystal‐binding proteins that play significant roles in kidney stone formation. Moreover, crystal‐binding capability is significantly decreased in siHSP90‐transfected cells as compared to non‐transfected control and siControl‐transfected cells. In summary, herein, a number of novel HSP90‐interacting proteins in renal cells is reported and the potential role of HSP90‐interacting complex in kidney stone formation is demonstrated.
A Comment on Effective Field Theories of Flux Vacua
Authors: Kachru Shamit , Trivedi Sandip P. 
Published: December 2018

AbstractWe discuss some basic aspects of effective field theory applied to supergravity theories which arise in the low‐energy limit of string theory. Our discussion is particularly relevant to the effective field theories of no‐scale supergravities that break supersymmetry, including those that appear in constructing de Sitter solutions of string theory.