bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive approach for correcting voxel‐wise b‐value errors in diffusion MRI
Authors: Lee Yoojin , Kettinger Adam O. , Wilm Bertram Jakob , Deichmann Ralf , Weiskopf Nikolaus , Lambert Christian , Pruessmann Klaas Paul , Nagy Zoltan 
Published: December 2019

PurposeIn diffusion MRI, the actual b‐value played out on the scanner may deviate from the nominal value due to magnetic field imperfections. A simple image‐based correction method for this problem is presented.MethodsThe apparent diffusion constant (ADC) of a water phantom was measured voxel‐wise along 64 diffusion directions at b = 1000 s/mm2. The true diffusion constant of water was estimated, considering the phantom temperature. A voxel‐wise correction factor, providing an effective b‐value including any magnetic field deviations, was determined for each diffusion direction by relating the measured ADC to the true diffusion constant. To test the method, the measured b‐value map was used to calculate the corrected voxel‐wise ADC for additionally acquired diffusion data sets on the same water phantom and data sets acquired on a small water phantom at three different positions. Diffusion tensor was estimated by applying the measured b‐value map to phantom and in vivo data sets.ResultsThe b‐value‐corrected ADC maps of the phantom showed the expected spatial uniformity as well as a marked improvement in consistency across diffusion directions. The b‐value correction for the brain data resulted in a 5.8% and 5.5% decrease in mean diffusivity and angular differences of the primary diffusion direction of 2.71° and 0.73° inside gray and white matter, respectively.ConclusionThe actual b‐value deviates significantly from its nominal setting, leading to a spatially variable error in the common diffusion outcome measures. The suggested method measures and corrects these artifacts.
Accelerated spin‐echo functional MRI using multisection excitation by simultaneous spin‐echo interleaving (MESSI) with complex‐encoded generalized slice dithered enhanced resolution (cgSlider) simultaneous multislice echo‐planar imaging
Authors: Han SoHyun , Liao Congyu , Manhard Mary Kate , Park Daniel Joseph , Bilgic Berkin , Fair Merlin J. , Wang Fuyixue , Blazejewska Anna I. , Grissom William A. , Polimeni Jonathan R. , Setsompop Kawin 
Published: December 2019

PurposeSpin‐echo functional MRI (SE‐fMRI) has the potential to improve spatial specificity when compared with gradient‐echo fMRI. However, high spatiotemporal resolution SE‐fMRI with large slice‐coverage is challenging as SE‐fMRI requires a long echo time to generate blood oxygenation level‐dependent (BOLD) contrast, leading to long repetition times. The aim of this work is to develop an acquisition method that enhances the slice‐coverage of SE‐fMRI at high spatiotemporal resolution.Theory and MethodsAn acquisition scheme was developed entitled multisection excitation by simultaneous spin‐echo interleaving (MESSI) with complex‐encoded generalized slice dithered enhanced resolution (cgSlider). MESSI uses the dead‐time during the long echo time by interleaving the excitation and readout of 2 slices to enable 2× slice‐acceleration, while cgSlider uses the stable temporal background phase in SE‐fMRI to encode/decode 2 adjacent slices simultaneously with a “phase‐constrained” reconstruction method. The proposed cgSlider‐MESSI was also combined with simultaneous multislice (SMS) to achieve further slice‐acceleration. This combined approach was used to achieve 1.5‐mm isotropic whole‐brain SE‐fMRI with a temporal resolution of 1.5 s and was evaluated using sensory stimulation and breath‐hold tasks at 3T.ResultsCompared with conventional SE‐SMS, cgSlider‐MESSI‐SMS provides 4‐fold increase in slice‐coverage for the same repetition time, with comparable temporal signal‐to‐noise ratio. Corresponding fMRI activation from cgSlider‐MESSI‐SMS for both fMRI tasks were consistent with those from conventional SE‐SMS. Overall, cgSlider‐MESSI‐SMS achieved a 32× encoding‐acceleration by combining Rinplane × MB × cgSlider × MESSI = 4 × 2 × 2 × 2.ConclusionHigh‐quality, high‐resolution whole‐brain SE‐fMRI was acquired at a short repetition time using cgSlider‐MESSI‐SMS. This method should be beneficial for high spatiotemporal resolution SE‐fMRI studies requiring whole‐brain coverage.
Modeling cyclic shearing of sands in the semifluidized state
Authors: Barrero Andres R. , Taiebat Mahdi , Dafalias Yannis F. 
Published: December 2019

SummaryLiquefaction is associated with the loss of mean effective stress and increase of the pore water pressure in saturated granular materials due to their contractive tendency under cyclic shear loading. The loss of mean effective stress is linked to loss of grain contacts, bringing the granular material to a “semifluidized state” and leading to development and accumulation of large cyclic shear strains. Constitutive modeling of the cyclic stress‐strain response in earthquake‐induced liquefaction and post‐liquefaction is complex and yet very important for stress‐deformation and performance‐based analysis of sand deposits. A new state internal variable named strain liquefaction factor is introduced that evolves at low mean effective stresses, and its constitutive role is to reduce the plastic shear stiffness and dilatancy while maintaining the same plastic volumetric strain rate in the semifluidized state. This new constitutive ingredient is added to an existing critical state compatible, bounding surface plasticity reference model, that is well established for constitutive modeling of cyclic response of sands in the pre‐liquefaction state. The roles of the key components of the proposed formulation are examined in a series of sensitivity analyses. Their combined effects in improving the performance of the reference model are examined by simulating undrained cyclic simple shear tests on Ottawa sand, with focus on reproducing the increasing shear strain amplitude as well as its saturation in the post‐liquefaction response.
Combining deep learning and 3D contrast source inversion in MR‐based electrical properties tomography
Authors: Leijsen Reijer , van den Berg Cornelis , Webb Andrew , Remis Rob , Mandija Stefano 
Published: December 2019

Magnetic resonance electrical properties tomography (MR‐EPT) is a technique used to estimate the conductivity and permittivity of tissues from MR measurements of the transmit magnetic field. Different reconstruction methods are available; however, all these methods present several limitations, which hamper the clinical applicability. Standard Helmholtz‐based MR‐EPT methods are severely affected by noise. Iterative reconstruction methods such as contrast source inversion electrical properties tomography (CSI‐EPT) are typically time‐consuming and are dependent on their initialization. Deep learning (DL) based methods require a large amount of training data before sufficient generalization can be achieved. Here, we investigate the benefits achievable using a hybrid approach, that is, using MR‐EPT or DL‐EPT as initialization guesses for standard 3D CSI‐EPT. Using realistic electromagnetic simulations at 3 and 7 T, the accuracy and precision of hybrid CSI reconstructions are compared with those of standard 3D CSI‐EPT reconstructions. Our results indicate that a hybrid method consisting of an initial DL‐EPT reconstruction followed by a 3D CSI‐EPT reconstruction would be beneficial. DL‐EPT combined with standard 3D CSI‐EPT exploits the power of data‐driven DL‐based EPT reconstructions, while the subsequent CSI‐EPT facilitates a better generalization by providing data consistency.
Inpatient Rehabilitation Delirium Screening: Impact on Acute Care Transfers and Functional Outcomes
Authors: Bushi Sharon , Barrett A. M. , Oh‐Park Mooyeon 
Published: December 2019

BackgroundDelirium is well studied in the acute care setting, but there is limited understanding of its impact in the postacute care setting, particularly in the inpatient rehabilitation facility (IRF).ObjectiveTo investigate the prevalence and related outcomes of delirium in the IRF setting, particularly patients' transfers to acute care hospitals.DesignRetrospective cohort study.SettingA freestanding IRF.ParticipantsPatients discharged from an IRF between January 2016 and December 2016 (12 months).InterventionsNot applicable.Main Outcome MeasuresTransfer to acute care hospitals, motor and cognitive Functional Independence Measures (FIM), length of stay, discharge disposition.ResultsA total of 1567 patients (53.9% female, mean age 72.9 ± 13.9) were included in the analysis. Positive scores were found among 142 (9.1%) patients on a 3‐Minute Diagnostic Interview for Confusion Assessment Method (3D‐CAM), indicating delirium on admission. Fifty‐nine (3.8%) were unscorable on 3D‐CAM. Twice as many delirium patients were transferred to acute care hospitals compared to non‐delirium patients (22.5% vs. 10.8%, P < .001). Multivariate logistic regression showed that, for patients with 3D‐CAM positive scores, there was an increased risk of transfers to acute care hospitals at an odds ratio of 1.61 (1.03‐2.53, P = .04) after adjusting for age, gender, neurological diagnosis, and motor FIM score. The delirium group also showed lower gains in motor function, increased lengths of stay, and reduced discharges to home when compared to the non‐delirium group (P < .001).ConclusionsThis study finds that delirium on admission to an IRF is associated with worsened outcomes related to function, length of stay, discharge status, and transfer to acute care hospitals. Positive delirium screening is an independent predictor for transfer to acute care hospitals from an IRF. Early identification of delirium is recommended in order to mitigate preventable transfers.
Label‐Free Quantitative Proteomics versus Antibody‐Based Assays to Measure Neutrophil‐Derived Enzymes in Saliva
Authors: Silbereisen Angelika , Alassiri Saeed , Bao Kai , Grossmann Jonas , Nanni Paolo , Fernandez Claudia , Tervahartiala Taina , Nascimento Gustavo G. , Belibasakis Georgios N. , Heikkinen Anna‐Maria , Lopez Rodrigo , Sorsa Timo , Bostanci Nagihan 
Published: December 2019

PurposeThis study aims to validate label‐free quantitative proteomics (LFQ) against antibody‐based methods for quantifying established periodontal disease biomarkers in saliva.Experimental DesignIn an experimental gingivitis model, healthy volunteers (n = 10) provide saliva at baseline (d0), during the induction (d7, d14, d21) and resolution (d35) of gingival inflammation (total n = 50). Biomarker levels are analyzed by LFQ and time‐resolved immunofluorometric assay (IFMA) or enzyme‐linked immunosorbent assay (ELISA). Molecular matrix metalloproteinase (MMP)‐8 forms are assessed by Western blot (WB) analysis.ResultsLFQ detects significantly (p < 0.05) elevated MMP‐8 (d21vsd7, d35vsd7) and tissue inhibitor of matrix metalloproteinases (TIMP)‐1 (d35vsd7). Latent MMP‐8 (70–80 kDa) is present (d0–d35), but not active MMP‐8 (50–60 kDa). LFQ and immunoassay data significantly correlate for MMP‐8 (r = 0.36), myeloperoxidase (r = 0.39), polymorphonuclear leukocyte elastase (r = 0.33), and TIMP‐1 (r = −0.24).Conclusion and Clinical RelevanceLFQ can quantify enzyme levels in saliva, however lacks the ability to measure enzymatic activity. WB analysis reveals that MMP‐8 may not be activated during induction of gingival inflammation. Significant but weak correlations between IFMA or ELISA and LFQ suggest a limited capacity of available antibodies to reliably quantify salivary biomarkers for periodontal diseases. Novel “anti‐peptide” antibodies designed by newer targeted mass spectrometry‐based approaches can help to overcome these drawbacks.
Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering
Authors: Cannon Kevin A. , Park Rachel U. , Boyken Scott E. , Nattermann Una , Yi Sue , Baker David , King Neil P. , Yeates Todd O. 
Published: December 2019

AbstractIn recent years, new protein engineering methods have produced more than a dozen symmetric, self‐assembling protein cages whose structures have been validated to match their design models with near‐atomic accuracy. However, many protein cage designs that are tested in the lab do not form the desired assembly, and improving the success rate of design has been a point of recent emphasis. Here we present two protein structures solved by X‐ray crystallography of designed protein oligomers that form two‐component cages with tetrahedral symmetry. To improve on the past tendency toward poorly soluble protein, we used a computational protocol that favors the formation of hydrogen‐bonding networks over exclusively hydrophobic interactions to stabilize the designed protein–protein interfaces. Preliminary characterization showed highly soluble expression, and solution studies indicated successful cage formation by both designed proteins. For one of the designs, a crystal structure confirmed at high resolution that the intended tetrahedral cage was formed, though several flipped amino acid side chain rotamers resulted in an interface that deviates from the precise hydrogen‐bonding pattern that was intended. A structure of the other designed cage showed that, under the conditions where crystals were obtained, a noncage structure was formed wherein a porous 3D protein network in space group I213 is generated by an off‐target twofold homomeric interface. These results illustrate some of the ongoing challenges of developing computational methods for polar interface design, and add two potentially valuable new entries to the growing list of engineered protein materials for downstream applications.
Crystal structure of a Vip3B family insecticidal protein reveals a new fold and a unique tetrameric assembly
Authors: Zheng Meiying , Evdokimov Artem G. , Moshiri Farhad , Lowder Casey , Haas Jeff 
Published: December 2019

AbstractVegetatively expressed insecticidal proteins (VIPs) produced byBacillus thuringiensisfall into several classes of which the third, VIP3, is known for their activity against several key Lepidopteran pests of commercial broad acre crops and because their mode of action does not overlap with that of crystalline insecticidal proteins. The details of the VIP3 structure and mode of action have remained obscure for the quarter century that has passed since their discovery. In the present article, we report the first crystal structure of a full‐length VIP3 protein. Crystallization of this target required multiple rounds of construct optimization and screening—over 200 individual sequences were expressed and tested. This protein adopts a novel global fold that combines domains with hitherto unreported topology and containing elements seemingly borrowed from carbohydrate‐binding domains, lectins, or from other insecticidal proteins.
Lewis Fry Richardson: A Personal Narrative
Authors: Zinnes Dina A. 
Published: December 2019

AbstractThis chapter is the personal story of how the author, just out of graduate school, encountered Richardson’s two posthumous volumes, Arms and Insecurity and Statistics of Deadly Quarrels, and how these volumes helped her resolve key issues that had troubled her. What is theory and how does it differ from a model? The first volume pushed her to learn mathematics and, through various twists and turns, eventually to an understanding of the power of a mathematically written story. The second volume provided insights into data collection and measurement as well as a deeper understanding of the mechanics of mathematical modeling. Thus, the two volumes together gave her the basis for finally answering the questions from her graduate school days.
The Influence of the Richardson Arms Race Model
Authors: Smith Ron P. 
Published: December 2019

AbstractThis chapter reviews the Richardson arms race model: a pair of differential equations which capture an action reaction process. Whereas many of Richardson’s equations were quite specific about what they referred to, the arms race model was not. This lack of specificity was both a strength and a weakness. Its strength was that with different interpretations it could be applied as an organising structure in a wide variety of contexts. Its weakness was that the model could not be estimated or tested without some auxiliary interpretation. The chapter considers the impact of these issues in interpretation and empirical application on the influence of the Richardson arms race model.
What Richardson Got Right (and Wrong) About Arms Races and War
Authors: Diehl Paul F. 
Published: December 2019

AbstractThis chapter considers Richardson’s classic arms race model and his book Arms and Insecurity in relation to the association between arms races and war. The analysis begins with a short review of the academic debates and empirical research about arms races and war. This is a prelude to an examination of the dynamics of arms races as they are specified by Richardson in his book and in his arms race model. Following is an evaluation of the specific claims about arms races and war derived from the model as well as Richardson’s own empirical analyses about the connection between the two phenomena. Although in light of subsequent research, a number of Richardson’s arguments seem misguided or inaccurate, other insights were validated by later studies or remain understudied but worthy of future research.
Back to the Future: Richardson’s Multilateral Arms Race Model
Authors: Ward Michael D. 
Published: December 2019

AbstractLewis Fry Richardson was a groundbreaking scholar, not only in modern meteorology but also in world affairs. His two major books, both published posthumously in 1960, were harbingers for what was to follow in scholarly international relations. In one, he collected wide-ranging, detailed quantitative information on disaggregated conflict processes in a variety of historical contexts. In the other, he showed two basic innovations for the social sciences: (a) the power of mathematics for understanding complex social systems and (b) the importance of understanding the interdependence of things that are typically studied separately. That latter insight is the focus of this chapter wherein I show that the Richardsonian insight on coupled behaviors leads to a network perspective on social interactions at the global scale. We call these coupled interactionsnetworks. I trace the development of Richardson’s thinking about coupled phenomena to the development of network thinking in the social sciences. I conclude with some recommendations for the arms race research program as applied to the current era.
Initial conditions for electron and photon structure and fragmentation functions
Authors: Frixione S. 
Published: December 2019

Abstract
In the computation of short-distance cross sections initiated by electrons and photons one can adopt the so-called structure-function approach, in which these particles play formally the same roles as hadrons do in QCD factorisation theorems, and must thus be associated with PDFs (equivalently known as structure functions in this context). At variance with their QCD counterparts, such PDFs are entirely calculable in QED. In this paper we present the results, at the next-to-leading order in the QED coupling constant α, for the initial conditions of the unpolarised electron and photon PDFs, which are a nec- essary ingredient for their eventual collinear evolution at the next-to-leading logarithmic accuracy. We also compute the analogous final-state quantities, namely the initial condi- tions for fragmentation functions into electrons and photons.
Forbidden frozen-in dark matter
Authors: Darmé L. , Hryczuk A. , Karamitros D. , Roszkowski L. 
Published: December 2019

Abstract
We examine and point out the importance of a regime of dark matter pro- duction through the freeze-in mechanism that results from a large thermal correction to a decaying mediator particle mass from hot plasma in the early Universe. We show that mediator decays to dark matter that are kinematically forbidden at the usually considered ranges of low temperatures can be generically present at higher temperatures and actually dominate the overall dark matter production, thus leading to very distinct solutions from the standard case. We illustrate these features by considering a dark Higgs portal model where dark matter is produced via decays of a scalar field with a large thermal mass. We identify the resulting ranges of parameters that are consistent with the correct dark matter relic abundance and further apply current and expected future collider, cosmological, and astrophysical limits.
The integrated stress response promotes B7H6 expression
Authors: Obiedat Akram , Charpak-Amikam Yoav , Tai-Schmiedel Julie , Seidel Einat , Mahameed Mohamed , Avril Tony , Stern-Ginossar Noam , Springuel Lorraine , Bolsée Jennifer , Gilham David E. , Dipta Priya , Shmuel Miriam , Chevet Eric , Mandelboim Ofer , Tirosh Boaz 
Published: December 2019

Abstract
The B7 family member, B7H6, is a ligand for the natural killer cell receptor NKp30. B7H6 is hardly expressed on normal tissues, but undergoes upregulation on different types of tumors, implicating it as an attractive target for cancer immunotherapy. The molecular mechanisms that control B7H6 expression are poorly understood. We report that in contrast to other NK cell ligands, endoplasmic reticulum (ER) stress upregulates B7H6 mRNA levels and surface expression. B7H6 induction by ER stress requires protein kinase R-like ER kinase (PERK), one of the three canonical sensors of the unfolded protein response. PERK phosphorylates eIF2α, which regulates protein synthesis and gene expression. Because eIF2α is phosphorylated by several kinases following different stress conditions, the program downstream to eIF2α phosphorylation is called the integrated stress response (ISR). Several drugs were reported to promote the ISR. Nelfinavir and lopinavir, two clinically approved HIV protease inhibitors, promote eIF2α phosphorylation by different mechanisms. We show that nelfinavir and lopinavir sustainably instigate B7H6 expression at their pharmacologically relevant concentrations. As such, ER stress and ISR conditions sensitize melanoma targets to CAR-T cells directed against B7H6. Our study highlights a novel mechanism to induce B7H6 expression and suggests a pharmacological approach to improve B7H6-directed immunotherapy.

Key messages

B7H6 is induced by ER stress in a PERK-dependent mechanism.

Induction of B7H6 is obtained pharmacologically by HIV protease inhibitors.

Exposure of tumor cells to the HIV protease inhibitor nelfinavir improves the recognition by B7H6-directed CAR-T.