bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reporting Results of Molecular Tests: A Retrospective Examination of BRAF Mutation Reporting
Authors: Treece Amanda L. , Gulley Margaret L. , Vasalos Patricia , Paquette Cherie , Lindeman Neal I. , Jennings Lawrence J. , Bartley Angela N. 
Published: March 2017

Context.—With enormous growth in the field of molecular pathology, the reporting of results gleaned from this testing is essential to guide patient care.Objective.—To examine molecular reports from laboratories participating in proficiency testing for required elements to convey molecular laboratory test results to clinicians and patients.Design.—Molecular laboratories participating in the College of American Pathologists (CAP) proficiency testing program for BRAF mutation analysis were solicited to submit examples of final reports from 2 separate proficiency testing reporting cycles. Reports were reviewed for the presence or absence of relevant components.Results.—A total of 107 evaluable reports were received (57 demonstrating a positive result for the BRAF V600E mutation and 50 negative). Methods for BRAF testing varied, with 95% (102 of 107) of reports adequately describing their assay methods and 87% (93 of 107) of reports adequately describing the target(s) of their assays. Information on the analytic sensitivity of the assay was present in 74% (79 of 107) of reports and 83% (89 of 107) reported at least 1 assay limitation, though only 34% (36 of 107) reported on variants not detected by their assays. Analytic and clinical interpretive comments were included in 99% (106 of 107) and 90% (96 of 107) of reports, respectively. Of participants that perform a laboratory-developed test, 88% (88 of 100) included language addressing the development of the assay.Conclusions.—Laboratories participating in BRAF proficiency testing through the CAP are including most of the required reporting elements to unambiguously convey molecular results. Laboratories should continue to strive to report these results in a concise and comprehensive manner.
Basic Properties and Parameters of Superconductors
Authors: Kleiner Reinhold 
Published: March 2017

AbstractThis chapter shows that the main ingredient of the superconducting state is that electron pairs form a macroscopic matter wave. The well‐defined phase of the matter wave leads to the ideal diamagnetism at not too large fields and to the vortex state in type‐II superconductors. The chapter introduces important length scales like the London penetration depth λL, the Ginzburg–Landau coherence length ξGL, and the BCS coherence length ξ0. The rationale that the phenomenon of superconductivity in high‐temperature superconductors (HTS) can be conceptually reduced to the physics of the CuO2layers has evolved to more 2D view in terms of CuO2planes. In order to put the superconducting proximity phenomenon into a broader context, the chapter commences with a simplest version of the proximity effect (PE) by considering a relatively trivial case of a metal–insulator (MI) contact. Finally, tunneling, flux pinning, losses and numerical modeling of superconductors are discussed.
Bulk Superconducting Magnets for Bearings and Levitation
Authors: Hull John R. 
Published: March 2017

Abstract
In this chapter the main features of superconducting magnets used for particle accelerators are reviewed. Magnet design, mechanical structure, field quality and training behavior as well as stability and protection of the magnets used for present and past accelerators is discussed. An overview of more recent new lay‐outs of advanced magnets using Nb3Sn is given. The main focus is on dipoles for High Energy Physics colliders, however, magnets for fast synchrotrons are also discussed.
This section on NMR and medical diagnostic MRI magnets begins with introductory remarks on NMR and MRI, their unique field requirements, both spatial and temporal, and types of superconducting coils that constitute NMR and medical diagnostic MRI magnets. Discussed next are key design issues: stress analysis (electromagnetic, thermal, winding); stability of adiabatic magnet; magnet protection; cryogenics (liquid; liquid‐free; solid); field analysis (general and harmonic); field shimming (superconducting; copper; ferromagnetic); field shielding (passive vs. active); and safety. Discussion continues with the statuses (2014) of NMR (solid state and solution) and medical diagnostic MRI magnets. The section concludes with potential applications of the enabling technology of HTS to the next generation of NMR and MRI Magnets.

The need for superconducting magnets in large fusion devices was already recognized in the middle of the 1970s, associated with several development programs for the conductor and for the coils. Today five superconducting fusion systems are in operation and most prominently Tore Supra, which started operation 25 years ago, demonstrating the reliability of this technology for confining high temperature plasmas. The most emblematic project is now ITER, including about 700 tons of NbTi and Nb
3
Sn superconducting strands. The ITER magnet system, whose main component is the TF system, storing 40 GJ of magnetic energy, represents about 30 % of the ITER cost investment. The Cable in Conduit Conductor (CICC) is now the selected conductor of all the superconducting tokamaks, for its ability to carry high currents, sustain high voltages and its stability against magnetic field disturbances. The protection against quench of the magnet system is ensured by resistive voltage detection and external extraction of the magnetic energy. The quench detection has to be made as early as possible, which is made difficult due to the slow quench propagation in CICC and due to magnetic disturbances.

For DEMO, the next step after ITER, aiming at producing electricity, an extrapolation of the ITER magnet system is envisaged with the same order of magnitude for the magnetic field and the same technology mainly for the magnets. The increase of the fusion power will be essentially produced by the increase of the tokamak size.
Cavities for Accelerators
Authors: Belomestnykh Sergey A. , Padamsee Hasan S. 
Published: March 2017

The article contains sections titled:Introduction to Radio Frequency Superconductivity for AcceleratorsPhysics ofRFSuperconductivityFabrication and Surface PreparationEffects Limiting Performance of Superconducting CavitiesConcluding RemarksAcknowledgments
Automatic segmentation of coronary tree in CT angiography images
Authors: Gao Zhifan , Liu Xin , Qi Song , Wu Wanqing , Hau William Kongto , Zhang Heye 
Published: March 2017

SummaryIn this study, we proposed an automatic approach to segment the three‐dimensional coronary tree from computed tomography angiography (CTA) image data. Compared to the previous studies, our approach can efficiently locate the coronary root through extracting aorta by using circular Hough transform. Then, we extracted the two‐dimensional coronary borders in multiple projection directions by dynamic programming and used the border information to reconstruct the coronary surface by the spline fitting. The performance of our approach has been validated on the CTA dataset from 50 subjects, with the comparison to the manual segmentation by an experienced medical physician on the corresponding CTA data and X‐ray angiography data. Our experiments have shown that the average bias between our approach and the manual segmentation are 2.44 mm2 with confidence interval [‐2.20 mm2, 6.68 mm2] for cross‐sectional lumen area, 0.84 mm with confidence interval [‐2.76 mm, 4.44 mm] for maximum lumen diameter, and 0.32 mm with confidence interval [‐1.14 mm, 1.78 mm] for minimum lumen diameter. The results can demonstrate the potential effectiveness of our approach in CTA image processing.
Assessment of renal response with urinary exosomes in patients with AL amyloidosis: A proof of concept
Authors: Ramirez‐Alvarado Marina , Barnidge David R. , Murray David L. , Dispenzieri Angela , Marin‐Argany Marta , Dick Christopher J. , Cooper Shawna A. , Nasr Samih H , Ward Christopher J. , Dasari Surendra , Jiménez‐Zepeda Víctor H. , Leung Nelson 
Published: March 2017

AbstractImmunoglobulin light chain (AL) amyloidosis is a fatal complication of B‐cell proliferation secondary to deposition of amyloid fibrils in various organs. Urinary exosomes (UEX) are the smallest of the microvesicles excreted in the urine. Previously, we found UEX of patients with AL amyloidosis contained immunoglobulin light chain (LC) oligomers that patients with multiple myeloma did not have. To further explore the role of the LC oligomers, UEX was isolated from an AL amyloidosis patient with progressive renal disease despite achieving a complete response. LC oligomers were identified. Mass spectrometry (MS) of the UEX and serum identified two monoclonal lambda LCs. Proteomics of the trypsin digested amyloid fragments in the kidney by laser microdissection and MS analysis identified a λ6 LC. The cDNA from plasma cell clone was from the IGLV‐ 6‐57 family and it matched the amino acid sequences of the amyloid peptides. The predicted mass of the peptide product of the cDNA matched the mass of one of the two LCs identified in the UEX and serum. UEX combined with MS were able to identify 2 monoclonal lambda LCs that current clinical methods could not. It also identified the amyloidogenic LC which holds potential for response assessment in the future.
Germabenzenylpotassium: A Germanium Analogue of a Phenyl Anion
Authors: Mizuhata Yoshiyuki , Fujimori Shiori , Sasamori Takahiro , Tokitoh Norihiro 
Published: March 2017

AbstractReduction of the stable germabenzene, 1‐Tbt‐2‐tert‐butyl‐germabenzene (Tbt=2,4,6‐tris[bis(trimethylsilyl)methyl]phenyl), with KC8 resulted in the formation of 2‐tert‐butylgermabenzenylpotassium, that is, the germanium analogue of phenylpotassium, under concomitant elimination of the aryl group from the Ge atom. Under an inert atmosphere, this germabenzenylpotassium could be isolated in the form of stable yellow crystals. In the crystalline state, as well as in solution, the germabenzenyl moiety adopts a monomeric form, even though the X‐ray diffraction analysis suggests the presence of highly reactive Ge=C double bonds. The spectroscopic and X‐ray crystallographic analyses, in combination with theoretical calculations indicate an ambident character for this germabenzenyl anion, with contributions from aromatic and germylene resonance structures.
Iterative C−H Functionalization Leading to Multiple Amidations of Anilides
Authors: Park Juhyeon , Lee Jia , Chang Sukbok 
Published: March 2017

AbstractPolyaminobenzenes were synthesized by the ruthenium‐catalyzed iterative C−H amidation of anilides using dioxazolones as an amino source. This strategy could be implemented by the sequential activation of C−H bonds of formerly generated compounds by cascade chelation assistance of newly installed amide groups. Computational studies provided a rationale.
Regioselective Photoisomerization/C−C Bond Formation of Asymmetric B(ppy)(Mes)(Ar): The Role of the Aryl Groups on Boron
Authors: Mellerup Soren K. , Li Cally , Peng Tai , Wang Suning 
Published: March 2017

AbstractAsymmetric N,C‐chelate organoboron compounds bearing two different aryl groups at the boron center undergo photoisomerization reactions that involve exclusively the less bulky aryl group, generating various strongly colored “dark isomers”. These species thermally isomerize to 4bH‐azaborepin molecules by direct hydrogen atom transfer from a borirane cycle to the pyridyl moiety and ring expansion. Mechanistic insight into these highly regioselective transformations was obtained from kinetic data and through computational studies.
A novel assay to determine acetylcholinesterase activity: The application potential for screening of drugs against Alzheimer's disease
Authors: Peng Liang , Rong Zhengxing , Wang Hao , Shao Biyun , Kang Lei , Qi Hong , Chen Hongzhuan 
Published: March 2017

AbstractAcetycholinesterase (AChE) that regulates hydrolysis of acetylcholine (ACh) in the brain, is an important target for treatment of Alzheimer's disease (AD), a feature of which is ACh deficiency. However, the methods to precisely determine AChE activity are still under development. We developed a new method to exploit acetylcholine‐d4 as a surrogate substrate of ACh and measure product choline‐d4 via liquid chromatography–tandem mass spectrometry (LC–MS/MS). This assay detected activity of AChE present in the normal mouse brain, which is consistent with the standard Ellman assay that determines products spectrophotometrically. In AD mouse models, the result of LC–MS/MS assay showed significant higher AChE activity than that seen in control normal mice, while treatment of AD mice with an AChE inhibitor, huperzine A, led to partial decreases in AChE activity. Our results suggest that this surrogate‐based LC–MS/MS method is a new, sensitive and convenient assay for the determination of AChE activity, providing a useful means for screening active compounds that target AChE.
Halogen‐Bonding Interactions of Polybrominated Diphenyl Ethers and Thyroid Hormone Derivatives: A Potential Mechanism for the Inhibition of Iodothyronine Deiodinase
Authors: Marsan Eric S. , Bayse Craig A. 
Published: March 2017

AbstractPolybrominated diphenyl ethers (PBDEs) increase flame resistance in consumer goods, but these compounds and their hydroxylated derivatives (OH‐BDEs) impair normal thyroid function. Halogen bonding (XB) of PBDEs to an active site selenocysteine may prevent iodothyronine deiodinase(Dio)‐catalyzed activation/deactivation of thyroid hormone (TH) derivatives. In this study, we compare the strength of the XB interactions of TH derivatives, iodine‐based contrast agents and PBDEs/OH‐BDEs with a methylselenolate model of the Dio active site using density functional theory calculations. The strength of the XB interaction depends upon the acceptor halide, the position of the halide, the number of ring substituents, and the proximity of hydroxyl groups to the XB site. The weaker Se⋅⋅⋅Br interactions relative to Se⋅⋅⋅I interactions are consistent with a model of competitive inhibition that blocks binding of THs at elevated PBDE/OH‐BDE concentrations. XB interactions were generally more favorable at ortho and meta positions and in substrates with more electron‐withdrawing substituents. PBDEs/OH‐BDEs that mimic the binding behavior of THs, that is, containing ortho and meta bromides and adjacent hydroxyl groups, may be the most effective inhibitors. Highly‐brominated PBDEs/OH‐BDEs have comparable interaction energies to THs and may undergo debromination. These results may also suggest that XB strength must exceed a threshold value in order for PBDEs/OH‐BDEs to undergo nucleophilic attack by Dio.
Stereocontrolled Synthesis of Amino‐Substituted Carbocycles by Pd‐Catalyzed Alkene Carboamination Reactions
Authors: White Derick R. , Wolfe John P. 
Published: March 2017

AbstractAmino‐substituted alkylidenecyclopentanes were synthesized through a stereoselective intermolecular Pd‐catalyzed alkene carboamination reaction between alkenyl triflates bearing a pendant alkene and exogenous amine nucleophiles. The reactions are effective with a range of different substrate combinations, and proceed with generally high diastereoselectivity. Use of (S)‐tBuPhox as the ligand in reactions of achiral substrates provides enantioenriched products with up to 98.5:1.5 e.r.
Anterior and posterior parts of the rat ventral tegmental area and the rostromedial tegmental nucleus receive topographically distinct afferents from the lateral habenular complex
Authors: Petzel Anja , Bernard René , Poller Wolfram C. , Veh Rüdiger W. 
Published: March 2017

AbstractThat activation of the reward system involves increased activity of dopaminergic (DA) neurons in the ventral tegmental area (VTA) is widely accepted. In contrast, the lateral habenular complex (LHb), which is known as the center of the anti‐reward system, directly and indirectly inhibits DA neurons in the VTA. The VTA, however, is not a homogenous entity. Instead, it displays major functional differences between its anterior (aVTA) and posterior (pVTA) regions. It is not precisely known, whether habenular input to the aVTA, pVTA, and the newly recognized rostromedial tegmental nucleus (RMTg) are similarly or differently organized. Consequently, the present investigation addressed the connections between LHb and aVTA, pVTA, and RMTg using retrograde and anterograde tracing techniques in the rat. Our experiments disclosed strictly reciprocal and conspicuously focal interconnections between LHbM (LHbMPc/LHbMC) and PN, as well as between RLi and LHbLO. In addition, we found that LHb inputs to the aVTA are dorsoventrally ordered. Dorsal parts of the aVTA receive afferents from LHbL and LHbM, whereas ventral parts of the aVTA are preferentially targeted by the LHbM. LHb afferents to the pVTA are distinct from those to the RMTg, given that the RMTg is primarily innervated from the LHbL, whereas pVTA receives afferents from LHbM and LHbL. These data indicate the existence of two separate pathways from the LHb to the VTA, a direct and an indirect one, which may subserve distinct biological functions.
C 1s Peak of Adventitious Carbon Aligns to the Vacuum Level: Dire Consequences for Material's Bonding Assignment by Photoelectron Spectroscopy
Authors: Greczynski Grzegorz , Hultman Lars 
Published: March 2017

AbstractThe C 1s signal from ubiquitous carbon contamination on samples forming during air exposure, so called adventitious carbon (AdC) layers, is the most common binding energy (BE) reference in X‐ray photoelectron spectroscopy studies. We demonstrate here, by using a series of transition‐metal nitride films with different AdC coverage, that the BE of the C 1s peak
varies by as much as 1.44 eV. This is a factor of 10 more than the typical resolvable difference between two chemical states of the same element, which makes BE referencing against the C 1s peak highly unreliable. Surprisingly, we find that C 1s shifts correlate to changes in sample work function
, such that the sum
is constant at 289.50±0.15 eV, irrespective of materials system and air exposure time, indicating vacuum level alignment. This discovery allows for significantly better accuracy of chemical state determination than offered by the conventional methods. Our findings are not specific to nitrides and likely apply to all systems in which charge transfer at the AdC/substrate interface is negligible.
Assessment of oral cytological features in smokers and nonsmokers after application of toluidine blue
Authors: Sharbatdaran Majid , Abbaszadeh Hamid , Siadati Sepideh , Ranaee Mohammad , Hajian‐Tilaki Karimollah , Rajabi‐Moghaddam Mahdieh 
Published: March 2017

IntroductionSmoking is the most important etiologic factor of oral cancer. Exfoliative cytology is the best method for early detection of oral cancer. Toluidine blue staining is used for detection of oral premalignant and malignant lesions. The aim of this study was to enhance the accuracy of oral exfoliative cytology in evaluating dysplastic features using toluidine blue staining.Methods and MaterialsThis clinical trials study was performed on 60 male smokers and nonsmokers without clinically oral lesion. Oral exfoliative cytological smears were prepared before and after application of toluidine blue and stained with Papanicolaou and evaluated under light microscope. Cytological features such as cellular clumping nuclear‐to‐cytoplasmic ratio, cellular and nuclear pleomorphism, micronuclei, binucleation, presence of bacterial colonies, and keratin flakes were assessed and compared before and after application of toluidine blue.ResultsResults showed that cellular clumping and micronuclei were significantly decreased after application of toluidine blue and conversely cellular and nuclear pleomorphisms were significantly increased. Frequency of micronuclei and binucleation were greater in smokers than nonsmokers which were insignificant. Cellular and nuclear pleomorphisms were significantly higher in smokers than nonsmokers after application of toluidine blue.ConclusionToluidine blue improved cellular, nuclear, and structural features of oral cytological smears and filtered false‐positive or false‐negative results. Thus, application of toluidine blue in combination with oral exfoliative cytology for early detection of oral cancer is recommended. Diagn. Cytopathol. 2017;45:513–519. © 2017 Wiley Periodicals, Inc.
Design of hysteretic dampers with optimal ductility for the transverse seismic control of cable‐stayed bridges
Authors: Camara Alfredo , Cristantielli Roberto , Astiz Miguel A. , Málaga‐Chuquitaype Christian 
Published: March 2017

SummaryCable‐stayed bridges require a careful consideration of the lateral force exerted by the deck on the towers under strong earthquakes. This work explores the seismic response of cable‐stayed bridges with yielding metallic dampers composed of triangular plates that connect the deck with the supports in the transverse direction. A design method based on an equivalent single‐degree of freedom approximation is proposed. This is proved valid for conventional cable‐stayed bridges with 200‐ and 400‐m main spans, but not 600 m. The height of the plates is chosen to (1) achieve a yielding capacity that limits the maximum force transmitted from the deck to the towers, and to (2) control the hysteretic energy that the dampers dissipate by defining their design ductility. In order to select the optimal ductility and the damper configuration, a multi‐objective response factor that accounts for the energy dissipation, peak damper displacement and low‐cycle fatigue is introduced. The design method is applied to cable‐stayed bridges with different spans and deck–support connections. The results show that the dissipation by plastic deformation in the dampers prevents significant damage in the towers of the short‐to‐medium‐span bridges under the extreme seismic actions. However, the transverse response of the towers in the bridge with a 600‐m main span is less sensitive to the dampers. Copyright © 2017 John Wiley & Sons, Ltd.
Acetylcholinesterase inhibitors for electroconvulsive therapy‐induced cognitive side effects: a systematic review
Authors: Henstra Marieke J. , Jansma Elise P. , van der Velde Nathalie , Swart Eleonora L. , Stek Max L. , Rhebergen Didi 
Published: March 2017

ObjectiveElectroconvulsive therapy (ECT) is an effective treatment for severe late‐life depression; however, ECT‐induced cognitive side effects frequently occur. The cholinergic system is thought to play an important role in the pathogenesis. We systematically reviewed the evidence for acetylcholinesterase inhibitors (Ache‐I) to prevent or reduce ECT‐induced cognitive side effects.MethodsA systematic search was performed in Pubmed, EMBASE, PsychINFO, and the Cochrane database to identify clinical trials investigating the effect of Ache‐I on ECT‐induced cognitive side effects. Key search terms included all synonyms for ECT and Ache‐I. Risk of bias assessment was conducted by using the Cochrane Collaboration's tool.ResultsFive clinical trials were eligible for inclusion. All studies focused on cognitive functioning as primary endpoint, but assessment of cognitive functioning varied widely in time point of assessment and in cognitive tests that were used. There was also great variety in study medication, route and time of administration and dosages, duration of drug administration, and ECT techniques. Finally, only two out of five studies were considered at low risk of bias. Despite the aforementioned shortcomings, without exception, all studies demonstrated significantly better cognitive performance in individuals treated with Ache‐I.ConclusionsDespite large heterogeneity in studies, Ache‐I appear to have beneficial effects on ECT‐induced cognitive side effects, supporting an association with the cholinergic system in ECT‐induced cognitive impairment. Methodological sound studies controlling for putative confounders are warranted. Copyright © 2017 John Wiley & Sons, Ltd.