bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomics Analysis for Verification of Rheumatoid Arthritis Biomarker Candidates Using Multiple Reaction Monitoring
Authors: Lee Jiyeong , Mun Sora , Kim Doojin , Lee You‐Rim , Sheen Dong‐Hyuk , Ihm Chunhwa , Lee Seung Hoon , Kang Hee‐Gyoo 
Published: September 2018

PurposeRheumatoid arthritis (RA) is an autoimmune disease in which autoantibodies attack the synovial membrane, causing joint inflammation. Blood tests would offer a powerful, minimally invasive method for early diagnosis of RA. However, no reliable biomarkers for RA are presently available. The aim is to develop biomarkers for RA by multiple reaction monitoring (MRM)‐based quantification of candidate biomarkers.Experimental designProteomics approaches are commonly used to identify and verify disease biomarkers. For discovery of biomarkers for RA, SWATH acquisition is performed and selected candidate biomarkers are validated by MRM. Target serum proteins are compared between patients with RA and healthy controls divided into three groups based on rheumatoid factor level.ResultsA total of 45 differentially expressed proteins are identified, as determined by SWATH acquisition. Of these, 13 proteins are selected as novel candidate biomarkers. A total of five proteins (transthyretin, gelsolin, angiotensinogen, lipopolysaccharide‐binding protein, and protein S100‐A9) are shown to have the potential to distinguish patients with RA from healthy controls.Conclusions and clinical relevanceThese five proteins may improve the efficiency of diagnosis of RA. MRM can be used to easily diagnose RA by detecting five proteins simultaneously in a single sample with high sensitivity.
Predicting X‐ray solution scattering from flexible macromolecules
Authors: Zhou Hao , Guterres Hugo , Mattos Carla , Makowski Lee 
Published: September 2018

AbstractWide‐angle X‐ray solution scattering (WAXS) patterns contain substantial information about the structure and dynamics of a protein. Solution scattering from a rigid protein can be predicted from atomic coordinate sets to within experimental error. However, structural fluctuations of proteins in solution can lead to significant changes in the observed intensities. The magnitude and form of these changes contain information about the nature and spatial extent of structural fluctuations in the protein. Molecular dynamics (MD) simulations based on a crystal structure and selected force field generate models for protein internal motions, and here we demonstrate that they can be used to predict the impact of structural fluctuations on solution scattering data. In cases where the observed and calculated intensities correspond, we can conclude that the X‐ray scattering provides direct experimental validation of the structural and MD results. In cases where calculated and observed intensities are at odds, the inconsistencies can be used to determine the origins of these discrepancies. They may be because of overestimates or underestimates of structural fluctuations in MD simulations, under‐sampling of the structural ensemble in the simulations, errors in the structural model, or a mismatch between the experimental conditions and the parameters used in carrying out the MD simulation.
Memory‐type multivariate control charts with auxiliary information for process mean
Authors: Haq Abdul , Khoo Michael B. C. 
Published: September 2018

AbstractIn statistical process control, it is a common practice to increase the sensitivity of a control chart with the help of an efficient estimator of the underlying process parameter. In this paper, we consider an efficient estimator that requires information on several study variables along with one or more auxiliary variables when estimating the mean of a multivariate normally distributed process. Using this auxiliary‐information‐based (AIB) process mean estimator, we propose new multivariate EWMA (MEWMA), double MEWMA (DMEWMA), and multivariate CUSUM (MCUSUM) charts for monitoring the process mean, denoted by the AIB‐MEWMA, AIB‐DMEWMA, and AIB‐MCUSUM charts, respectively. The run length characteristics of the proposed multivariate charts are computed using Monte Carlo simulations. The proposed charts are compared with their existing counterparts in terms of the run length characteristics. It turns out that the AIB‐MEWMA, AIB‐DMEWMA, and AIB‐MCUSUM charts are uniformly and substantially better than the MEWMA, DMEWMA, and MCUSUM charts, respectively, when detecting different shifts in the process mean. A real dataset is considered to explain the implementation of the proposed and existing multivariate control charts.
The matrix‐assisted laser desorption/ionisation in‐source decay of peptides using ion mobility enabled quadrupole‐time‐of‐flight mass spectrometry
Authors: Vrkoslav Vladimír , Muck Alexander , Brown Jeffery M. , Hubálek Martin , Cvačka Josef 
Published: September 2018

RationaleIn‐source decay (ISD) matrix‐assisted laser desorption/ionisation (MALDI) mass spectrometry with a 1,5‐diaminonaphthalene (1,5‐DAN) matrix is used for the structural characterisation of peptides. However, MALDI spectra are intrinsically complicated by the presence of matrix ions, which interfere with the peptide fragments. This may cause false‐positive results or reduced sequence coverage. This paper reports investigations of ISD processes in an intermediate pressure MALDI ion source and a protocol for the removal of interfering ions using ion mobility separation (IMS).MethodsAn intermediate pressure MALDI source of a Q‐IMS‐Q‐TOF instrument (Synapt G2) has been employed for the ISD of selected peptides using a 1,5‐DAN matrix.ResultsSuccessful coupling of the MALDI source tuned for ISD experiments using IMS is demonstrated. The IMS made it possible to remove interfering matrix ions effectively from the spectra and thus to increase the confidence of spectral interpretation. Extensive fragment series corresponding to N–Cα bond cleavages were observed under optimised conditions; on the other hand, weaker series of ions caused by peptide bond cleavages were prevalent for default conditions and/or the α‐hydroxycinnamic acid matrix.ConclusionsIon mobility has been used for the elimination of matrix ions. The technique has been applied to top‐down sequencing of non‐tryptic peptides, such as the human palmitoylated analogue of prolactin‐releasing peptide used in recent obesity studies, and human and insect antimicrobial peptides.
Impulsive stabilization for linear neutral‐type time‐delay systems
Authors: Chen Wu‐Hua , Lu Xiaomei , Zong Guangdeng 
Published: September 2018

SummaryThe problem of impulsive stabilization of linear neutral delay systems is investigated by using the impulse‐time‐dependent Lyapunov functions. The construction of impulse‐time‐dependent Lyapunov functions is based on the singular system representation of the impulsively controlled neutral delay system. In order to overcome the difficulty arising from time‐varying state delays, a Razumikhin‐type analysis method is developed and the key technique is to establish the relation between the slow and fast state variables by using a difference inequality. The derived stability criterion weakens the restriction condition on the impulse operators found in the previous result. For constant delay case, an improved stability criterion is derived by applying an impulse‐time‐dependent Lyapunov functional. Next, based on the newly established stability criteria, novel sufficient conditions on the existence of impulsive controllers with range dwell‐time constraint are presented. Finally, two numerical examples are given to demonstrate the effectiveness of the proposed results.
Roles and drivers of agribusiness shaping Climate‐Smart Landscapes: A review
Authors: Salvini Giulia , Dentoni Domenico , Ligtenberg Arend , Herold Martin , Bregt Arnold K. 
Published: September 2018

AbstractThe Climate‐Smart Landscape (CSL) approach has recently emerged as an integrated management strategy to address the increasing pressures on agricultural production, ecosystem conservation, rural livelihoods, and climate change mitigation/adaptation. Agribusiness companies play a controversial role in achieving CSL goals. On one hand, their operations cause land and natural resource degradation. On the other hand, they have technical, managerial, and financial resources to invest in more sustainable landscapes. Despite the controversy, empirical evidence on which practices agribusiness companies plan to undertake for sustainable landscape management and their intentions to contribute achieving CSL objectives is scarce and fragmented in the academic literature. To fill in this knowledge gap, this paper describes and reviews agribusiness companies' planned practices for integrated landscape management worldwide. Additionally, this paper evaluates to what extent companies plan to engage in two crucial factors to achieving CSL: stakeholder involvement and activities' monitoring. Results show that despite many agribusiness‐led initiatives have potential in contributing to more sustainable practices, major steps should still be taken to involve stakeholders and monitoring their process and outcomes to actually achieve CSL goals.
Toward Linux kernel memory safety
Authors: Reshetova Elena , Liljestrand Hans , Paverd Andrew , Asokan N. 
Published: September 2018

SummaryThe security of billions of devices worldwide depends on the security and robustness of the mainline Linux kernel. However, the increasing number of kernel‐specific vulnerabilities, especially memory safety vulnerabilities, shows that the kernel is a popular and practically exploitable target. Two major causes of memory safety vulnerabilities are reference counter overflows (temporal memory errors) and lack of pointer bounds checking (spatial memory errors). To succeed in practice, security mechanisms for critical systems like the Linux kernel must also consider performance and deployability as critical design objectives. We present and systematically analyze two such mechanisms for improving memory safety in the Linux kernel, ie, (1) an overflow‐resistant reference counter data structure designed to securely accommodate typical reference counter usage in kernel source code and (2) runtime pointer bounds checking using Intel memory protection extension in the kernel. We have implemented both mechanisms and we analyze their security, performance, and deployability. We also reflect on our experience of engaging with Linux kernel developers and successfully integrating the new reference counter data structure into the mainline Linux kernel.
Quantification of changeability level for engineering systems
Authors: Rehn Carl F. , Pettersen Sigurd S. , Garcia Jose J. , Brett Per O. , Erikstad Stein O. , Asbjørnslett Bjørn E. , Ross Adam M. , Rhodes Donna H. 
Published: September 2018

AbstractThis paper outlines a generic method for quantifying changeability level, to support better decision making in the early stages of design of engineering systems. Changeability represents the ability of a system to change form, function, or operation, and is a collective term for characteristics such as flexibility, adaptability, and agility. Quantification of changeability level must not be confused with valuation of changeability. The level of changeability in a design is essentially under the control of the designer. Two aspects of changeability are discussed, the first being how to structure changeable design alternatives using the Design for Changeability (DFC) variable. The DFC variable represents combinations of path enablers built into a design. Path enablers are characteristics of systems enabling them to change more easily. The second aspect is to quantify the level of changeability for a given design alternative, based on change cost and time. For the latter, we propose two measures for quantification: (1) bottom‐up, measuring the reduction of cost and time enabled for each relevant change, and (2) top‐down, measuring the span of change opportunities at given cost and time thresholds. A case study of a ship is presented to demonstrate the proposed generic method.
Mechanisms and Inhibitors of Histone Arginine Methylation
Authors: Fulton Melody D. , Brown Tyler , Zheng Y. George 
Published: September 2018

AbstractHistone methylation plays an important regulatory role in chromatin restructuring and RNA transcription. Arginine methylation that is enzymatically catalyzed by the family of protein arginine methyltransferases (PRMTs) can either activate or repress gene expression depending on cellular contexts. Given the strong correlation of PRMTs with pathophysiology, great interest is seen in understanding molecular mechanisms of PRMTs in diseases and in developing potent PRMT inhibitors. Herein, we reviewed key research advances in the study of biochemical mechanisms of PRMT catalysis and their relevance to cell biology. We highlighted how a random binary, ordered ternary kinetic model for PRMT1 catalysis reconciles the literature reports and endorses a distributive mechanism that the enzyme active site utilizes for multiple turnovers of arginine methylation. We discussed the impacts of histone arginine methylation and its biochemical interplays with other key epigenetic marks. Challenges in developing small‐molecule PRMT inhibitors were also discussed.
Reading and the Development of Social Understanding: Implications for the Literacy Classroom
Authors: Kozak Stephanie , Recchia Holly 
Published: September 2018

AbstractResearch has underscored the cognitive benefits of reading, but scholars have also begun to explore its implications in the socioemotional domain. The authors review research exploring the links between reading and social understanding skills such as empathy and perspective taking, examine the qualities of literature that are posited to foster social understanding, and propose explanations of why reading may confer these benefits. Building on this review, the authors include ideas on how to incorporate this research into literacy classrooms by providing specific book suggestions and accompanying activities that may leverage the potential sociocognitive benefits of reading within a classroom context.
Towards predictive computer simulations in cardiology: Finite element analysis of personalized heart models
Authors: Cansız Barış , Sveric Krunoslav , Ibrahim Karim , Strasser Ruth H. , Linke Axel , Kaliske Michael 
Published: September 2018

AbstractThe goal of this manuscript is to demonstrate the feasibility of our recent numerical developments towards predictive computer simulations in cardiology. In contrast to existing weakly coupled and strongly coupled monolithic approaches in the literature, we utilize a fully implicit staggered solution scheme that enables to study the strong excitation‐contraction coupling of the heart tissue in the monodomain and the bidomain setting through finite element simulations. On the constitutive level, we employ the recently proposed modified Hill model (CMAME 315; 434‐466, 2017) that treats the myocardium as an electro‐visco‐active material. All the time integrations are evaluated via an implicit backward Euler scheme that ensures unconditional stability. The performance of the framework is demonstrated by means of two clinically relevant and interesting examples. Firstly, basic deformation characteristics of a personalized left ventricle model such as rotation, twist and longitudinal shortening are simulated along with a physiological pressure‐volume relation. In addition, the results of the viscoelastic and elastic solutions are compared. In the second example, we simulate a continuously beating virtual biventricle model having dyssynchrony and imitate two different cardiac resynchronization therapy attempts in order to improve the cardiac output. The corresponding electrocardiograms and left ventricle volume‐time relations are recorded during the simulation and compared to the healthy case.
Three-dimensional mode selection of the flow past a rotating and inline oscillating cylinder
Authors: Lo Jacono David , Bourguet Rémi , Thompson Mark C. , Leontini Justin S. 
Published: September 2018

This paper studies the transition to three-dimensional flow in the wake of a cylinder immersed in a free stream, where the cylinder is externally forced to continuously rotate about its axis and to linearly oscillate in the streamwise direction. Floquet stability analysis is used to assess the stability of the nominal two-dimensional flows at a Reynolds number

$Re=100$

and rotation rate

$\unicode[STIX]{x1D6FC}=\unicode[STIX]{x1D714}D/U=3$

to three-dimensional perturbations, as a function of the amplitude and frequency of the linear oscillations. Two modes of instability are found, distinguished by their spatial structure, temporal behaviour and apparent mechanism. The first mode has a shorter wavelength in the spanwise direction and appears to be linked to a centrifugal instability in the layer of fluid near the rotating body. The second mode has a longer wavelength and is linked to an instability of the vortex cores in the wake that is subharmonic, leading to a period doubling. Either mode can be stable while the other is unstable, depending primarily on the frequency of the oscillation of the cylinder. This indicates that either mode can control the transition to a three-dimensional flow. The results are compared to the fully three-dimensional simulation results of a rotating cylinder elastically mounted and free to oscillate in the streamwise direction from Bourguet & Lo Jacono (J. Fluid Mech., vol. 781, 2015, pp. 127–165), and appear to be able to explain the surprising switching of the observed spanwise wavelength in that flow as a change in the dominant mode, and therefore mechanism, of instability.
Remasculinizing the Shirker: The JewishFrontkämpferunder Hitler
Authors: Geheran Michael J. 
Published: September 2018

AbstractThis article examines the impact of Nazi persecution on the gender identity of German-Jewish veterans of World War I. National Socialism threatened to erase everything these Jewish men had achieved and sacrificed. It sought to destroy the identity they had constructed as soldiers in the service of the Fatherland, as well as the high status they had earned asFrontkämpfer(front-line fighters) in the Great War, upon which their sense of masculinity identity rested. Although diminished and disempowered by Nazi terror, Jewish veterans were able to orient themselves toward hegemonic ideals of martial masculinity, which elevated military values as the highest expression of manhood, giving them a space to assert themselves and defy the Nazi classificationJew. For the Jewish men who fought in World War I, the Nazi years became a battle to reclaim their status and masculine honor. They believed that the manner in which they handled themselves under the Nazis was a reflection of their character: as men who had been tried and tested in the trenches, their responses to persecution communicated their identity as soldiers, as Jews, and as Germans.
Beyond not bad or just okay: social predictors of young adults’ wellbeing and functioning (a TRAILS study)
Authors: Richards J. S. , Hartman C. A. , Jeronimus B. F. , Ormel J. , Reijneveld S. A. , Veenstra R. , Verhulst F. C. , Vollebergh W. A. M. , Oldehinkel A. J. 
Published: September 2018

AbstractBackgroundVarious childhood social experiences have been reported to predict adult outcomes. However, it is unclear how different social contexts may influence each other's effects in the long run. This study examined the joint contribution of adolescent family and peer experiences to young adult wellbeing and functioning.MethodsParticipants came from the TRacking Adolescents’ Individual Lives Survey (TRAILS) study (n= 2230). We measured family and peer relations at ages 11 and 16 (i.e. family functioning, perceived parenting, peer status, peer relationship quality), and functioning as the combination of subjective wellbeing, physical and mental health, and socio-academic functioning at age 22. Using structural equation modelling, overall functioning was indicated by two latent variables for positive and negative functioning. Positive, negative and overall functioning at young adulthood were regressed on adolescent family experiences, peer experiences and interactions between the two.ResultsFamily experiences during early and mid-adolescence were most predictive for later functioning; peer experiences did not independently predict functioning. Interactions between family and peer experiences showed that both protective and risk factors can have context-dependent effects, being exacerbated or overshadowed by negative experiences or buffered by positive experiences in other contexts. Overall the effect sizes were modest at best.ConclusionsAdolescent family relations as well as the interplay with peer experiences predict young adult functioning. This emphasizes the importance of considering the relative effects of one context in relation to the other.
Hippocampal-subregion functional alterations associated with antidepressant effects and cognitive impairments of electroconvulsive therapy
Authors: Bai Tongjian , Wei Qiang , Xie Wen , Wang Anzhen , Wang Jiaojian , JI Gong-Jun , Wang Kai , Tian Yanghua 
Published: September 2018

AbstractBackgroundElectroconvulsive therapy (ECT), an effective antidepressive treatment, is frequently accompanied by cognitive impairment (predominantly memory), usually transient and self-limited. The hippocampus is a key region involved in memory and emotion processing, and in particular, the anterior-posterior hippocampal subregions has been shown to be associated with emotion and memory. However, less is known about the relationship between hippocampal-subregion alterations following ECT and antidepressant effects or cognitive impairments.MethodsResting-state functional connectivity (RSFC) based on the seeds of hippocampal subregions were investigated in 45 pre- and post-ECT depressed patients. Structural connectivity between hippocampal subregions and corresponding functionally abnormal regions was also conducted using probabilistic tractography. Antidepressant effects and cognitive impairments were measured by the Hamilton Depressive Rating Scale (HDRS) and the Category Verbal Fluency Test (CVFT), respectively. Their relationships with hippocampal-subregions alterations were examined.ResultsAfter ECT, patients showed increased RSFC in the hippocampal emotional subregion (HIPe) with the left middle occipital gyrus (LMOG) and right medial temporal gyrus (RMTG). Decreased HDRS was associated with increased HIPe-RMTG RSFC (r = −0.316, p = 0.035) significantly and increased HIPe-LMOG RSFC at trend level (r = −0.283, p = 0.060). In contrast, the hippocampal cognitive subregion showed decreased RSFC with the bilateral angular gyrus, and was correlated with decreased CVFT (r = 0.418, p = 0.015 for left; r = 0.356, p = 0.042 for right). No significant changes were found in structural connectivity.ConclusionThe hippocampal-subregions functional alterations may be specially associated with the antidepressant and cognitive effects of ECT.