bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting the wrinkling of elastic bilayers I: linear analysis
Authors: Alawiye Hamza , Kuhl Ellen , Goriely Alain 
Published: March 2019

Wrinkling is a universal instability occurring in a wide variety of engineering and biological materials. It has been studied extensively for many different systems but a full description is still lacking. Here, we provide a systematic analysis of the wrinkling of a thin hyperelastic film over a substrate in plane strain using stream functions. For comparison, we assume that wrinkling is generated either by the isotropic growth of the film or by the lateral compression of the entire system. We perform an exhaustive linear analysis of the wrinkling problem for all stiffness ratios and under a variety of additional boundary and material effects. Namely, we consider the effect of added pressure, surface tension, an upper substrate and fibres. We obtain analytical estimates of the instability in the two asymptotic regimes of long and short wavelengths.
This article is part of the theme issue ‘Rivlin's legacy in continuum mechanics and applied mathematics’.
Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning
Authors: Baar Ivo , Hübner Lukas , Oettig Peter , Zapletal Adrian , Schlag Sebastian , Stamatakis Alexandros , Morel Benoit 
Published: March 2019

AbstractThe so-called site repeats (SR) technique can be used to accelerate the widely-used phylogenetic likelihood function (PLF) by identifying identical patterns among multiple sequence alignment (MSA) sites, thereby omitting redundant calculations and saving memory. However, this complicates the optimal data distribution of MSA sites in parallel likelihood calculations, as the cost of computing the likelihood for individual sites strongly depends on the sites-to-cores assignment. We show that finding a ‘good’ sites-to-cores assignment can be modeled as a hypergraph partitioning problem, more specifically, a specific instance of the so-called judicious hypergraph partitioning problem. We initially develop, parallelize, and make available HyperPhylo, an efficient open-source implementation for this flavor of judicious partitioning where all vertices have the same degree. Using empirical MSA data, we then show that sites-to-core assignments computed via HyperPhylo are substantially better than those obtained via a previous na ï ve approach for phylogenetic data distribution under SRs.
The Fruit Fly Brain Observatory: From Structure to Function
Authors: Ukani Nikul H. , Yeh Chung-Heng , Tomkins Adam , Zhou Yiyin , Florescu Dorian , Ortiz Carlos Luna , Huang Yu-Chi , Wang Cheng-Te , Turkcan Mehmet K. , Liu Tingkai , Richmond Paul , Lo Chung-Chuan , Coca Daniel , Chiang Ann-Shyn , Lazar Aurel A. 
Published: March 2019

AbstractThe fruit fly is a key model organism for studying the activity of interconnected brain circuits. A large scattered global research community of neurobiologists and neurogeneticists, computational and theoretical neuroscientists, and computer scientists and engineers has been developing a vast trove of experimental and modeling data that has yet to be distilled into new knowledge and understanding of the functional logic of the brain. Developing open shared models, modelling tools and data repositories that can be accessed from anywhere in the world is the necessary engine for accelerating our understanding of how the brain works.To that end we developed the Fruit Fly Brain Observatory (FFBO), the next generation open-source platform to support open, collaborative Drosophila neuroscience research. FFBO provides a (i) hub for storing and integrating fruit fly brain research data from multiple data sources worldwide, (ii) unified repository of tools and methods to build, emulate and compare fruit fly brain models in health and disease, and (iii) an open framework for fruit fly brain data processing and model execution. FFBO provides access to application tools for visualizing, configuring, simulating and analyzing computational models of brain circuits of the (i) cell type map, (ii) connectome, (iii) synaptome, and (iv) activity map using intuitive queries in plain English. Tools are provided to extract the function inherent in these structural maps. All applications can be accessed with any modern browser.
A Sex-Specific Switch in Platelet Receptor Signaling Following Myocardial Infarction
Authors: Kim Beom Soo , Auerbach David A. , Sadhra Hamza , Ling Frederick S. , Toth Sandra , Mohan Amy , Tura Sara , Goldenberg Ilan , Rich David Q. , Cameron Scott J. 
Published: March 2019

ABSTRACTBACKGROUNDA Sex-specific, personalized approach to anti-platelet therapy may be important in patients with myocardial infarction (MI).OBJECTIVESOur goal was to determine whether platelets activate differently in healthy men and women compared to following MI.METHODSBlood was obtained from healthy subjects or patients presenting acutely with ST-segment Elevation Myocardial Infarction (STEMI) and non-ST Segment Elevation Myocardial Infarction (NSTEMI). Platelet function through surface receptor activation was examined in healthy subjects, in patients with MI, and in age- and strain-matched mice before and after MI. Multivariate regression analyses revealed clinical variables associated with platelet receptor sensitivity at the time of MI.RESULTSPlatelets from healthy women are dose-dependently more active compared to men, particularly through the platelet thromboxane signaling pathway (7.8-fold increase in women vs. 3.0-fold in men, P=0.02). At the time of MI, platelet activation through surface protease-activated receptor 1 (PAR1) was less in women than men (3.5-fold vs. 8.5-fold, respectively, P=0.0001). Multivariate regression analyses revealed male sex (P=0.04) and NSTEMI (P=0.003) as independent predictors of enhanced platelet PAR1 signaling at the time of MI. Similar to humans, healthy female mice showed preferential thrombin-mediated platelet activation compared to male mice (8.7-fold vs. 4.8-fold, respectively; P<0.001). In the immediate post-MI environment, male mice showed preferential thrombin-mediated platelet activation compared to female mice (12.4-fold vs. 5.5-fold, respectively; P<0.001).CONCLUSIONSThese results outline a previously unrecognized sex-dependent platelet phenotype where inhibition of thrombin signaling in the peri-MI environment—particularly in males—may be an important consideration.CONDENSED ABSTRACTPreclinical studies evaluating anti-platelet drugs are generally conducted in platelets isolated from healthy individuals. Growing evidence suggests changes in platelet signaling properties in certain disease conditions compared to healthy platelets may alter the response to anti-platelet medications. This investigation revealed that platelets from men and women who are healthy and following MI signal differently, particularly through thromboxane and PAR1 receptors. This effect was especially noted in patients with NSTEMI compared to STEMI. These observations raise the possibility of considering a sex-specific anti-platelet regimen for males and females in atheroembolic vascular diseases such as NSTEMI.
An investigation into serotonergic and environmental interventions against depression in a simulated delayed reward paradigm
Authors: Porr Bernd , Trew Alex , Miller Alice 
Published: March 2019

AbstractThe disruption of the serotonergic (5HT) system has been implicated in causing major depression and the standard view is that a lack of serotonin is to blame for the resulting symptoms. Consequently, pharmacological interventions aim to increase serotonin concentration in its target areas or stimulating excitatory 5HT receptors. A standard approach is to use serotonin reuptake inhibitors (SSRIs) which cause a higher accumulation of serotonin. Another approach is to stimulate excitatory serotonin receptors with psychedelic drugs. This paper compares these two approaches by first setting up a system level limbic system model of the relevant brain areas and then modelling a delayed reward paradigm which is known to be disrupted by a lack of 5HT. Central to our model is how serotonin changes the response characteristics of decision making neurons where low levels of 5HT allows small signals to pass through whereas high levels of 5HT create a barrier for smaller signals but amplifying larger ones. We show with both standard behavioural simulations and model checking that SSRIs perform significantly better against interventions with psychedelics. However, psychedelics might work better in other paradigms where a high level of exploration is beneficial to obtain rewards.
Synthesizing Disparate LiDAR and Satellite Datasets through Deep Learning to Generate Wall-to-Wall Regional Forest Inventories
Authors: Ayrey Elias , Hayes Daniel J. , Kilbride John B. , Fraver Shawn , Kershaw John A. , Cook Bruce D. , Weiskittel Aaron R. 
Published: March 2019

AbstractLight detection and ranging (LiDAR) has become a commonly-used tool for generating remotely-sensed forest inventories. However, LiDAR-derived forest inventories have remained uncommon at a regional scale due to varying parameters between LiDAR datasets, such as pulse density. Here we develop a regional model using a three-dimensional convolutional neural network (CNN), a form of deep learning capable of scanning a LiDAR point cloud as well as coincident satellite data, identifying features useful for predicting forest attributes, and then making a series of predictions. We compare this to the standard modeling approach for making forest predictions from LiDAR data, and find that the CNN outperformed the standard approach by a large margin in many cases. We then apply our model to publicly available data over New England, generating maps of fourteen forest attributes at a 10 m resolution over 85 % of the region. Our estimates of attributes that quantified tree size were most successful. In assessing aboveground biomass for example, we achieved a root mean square error of 36 Mg/ha (44 %). Our county-level mapped estimates of biomass were in good agreement with federal estimates. Estimates of attributes quantifying stem density and percent conifer were moderately successful, with a tendency to underestimate of extreme values and banding in low density LiDAR acquisitions. Estimate of attributes quantifying detailed species groupings were less successful. Ultimately we believe these maps will be useful to forest managers, wildlife ecologists, and climate modelers in the region.
The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3
Authors: Kuang Zheng , Wang Yuhao , Li Yun , Ye Cunqi , Ruhn Kelly A. , Behrendt Cassie L. , Olson Eric N. , Hooper Lora V. 
Published: March 2019

AbstractCircadian rhythmicity is a defining feature of mammalian metabolism that synchronizes metabolic processes to day-night light cycles. Here, we show that the intestinal microbiota programs diurnal metabolic rhythms in the mouse small intestine through histone deacetylase 3 (HDAC3). The microbiota induced expression of intestinal epithelial HDAC3, which was recruited rhythmically to chromatin and produced synchronized diurnal oscillations in histone acetylation, metabolic gene expression, and nutrient uptake. HDAC3 also functioned non-canonically to coactivate estrogen related receptor α (ERRα), inducing microbiota-dependent rhythmic transcription of the lipid transporter gene Cd36 and promoting lipid absorption and diet-and jet lag-induced obesity. Our findings reveal that HDAC3 integrates microbial and circadian cues to regulate diurnal metabolic rhythms, and pinpoint a key mechanism by which the microbiota controls host metabolism.One sentence summaryThe intestinal microbiota induces daily metabolic rhythms and controls lipid uptake through the enzyme histone deacetylase 3.
Static and Dynamic Functional Connectivity Analysis of Cerebrovascular Reactivity: An fMRI Study
Authors: Lewis N. , Lu H. , Liu P. , Hou X. , Damaraju E. , Iraji Armin , Calhoun V. 
Published: March 2019

ABSTRACTThe human brain, as a finely-tuned system, needs a constant flow of oxygen to function properly. To accomplish this, the cerebrovascular system ensures a steady stream of oxygenation to brain cells. One tool that the cerebrovascular system uses is cerebrovascular reactivity (CVR), which is the system’s ability to react to vasoactive stimuli. Understanding CVR can provide unique information about cerebrovascular diseases and general brain function. CVR can be evaluated by scanning subjects with blood-oxygenation-level-dependent (BOLD) functional magnetic resonance imaging (fMRI) while they periodically inhale room air and CO2-enriched gas, a powerful and widely-used vasodilator. Our goal is to understand the effect of vasodilation on individual intrinsic connectivity networks (ICNs), as well as how functional network connectivity (FNC) adapts to the same vasodilation. To achieve this goal, we first developed an innovative metric to measure the effect of CVR on ICNs, which contrasts to the commonly used voxel-wise CVR. Furthermore, for the first time, we studied static (sFNC) and dynamic (dFNC) FNC in the context of CVR. Our results show that network connectivity is generally weaker during vascular dilation, and these results are more pronounced in dFNC analysis. dFNC analysis reveals that participants did not return to the pre-CO2 inhalation state, suggesting that the one-minute period of room-air inhalation is not enough for the CO2 effect to fully dissipate in humans. Overall, we see new relationships between CVR and ICNs, as well as how FNC adapts to vascular system changes.
Multi-omics integration of the phenome, transcriptome and genome highlights genes and pathways relevant to essential tremor
Authors: Liao Calwing , Sarayloo Faezeh , Rochefort Daniel , Houle Gabrielle , Akçimen Fulya , He Qin , Laporte Alexandre D. , Spiegelman Dan , Rajput Alex , Dion Patrick A. , Rouleau Guy A. 
Published: March 2019

AbstractThe genetic factors predisposing to essential tremor (ET), of one of the most common movement disorders, remains largely unknown. While current studies have examined the contribution of both common and rare genetic variants, very few have investigated the ET transcriptome. To understand pathways and genes relevant to ET, we used an RNA sequencing approach to interrogate the transcriptome of two cerebellar regions, the dentate nucleus and cerebellar cortex, in 16 cases and 16 age- and sex-matched controls. Additionally, a phenome-wide association study (pheWAS) of the dysregulated genes was conducted, and a genome-wide gene association study (GWGAS) was done to identify pathways overlapping with the transcriptomic data. We identified several novel dysregulated genes includingCACNA1A, a calcium voltage-gated channel implicated in ataxia. Furthermore, several pathways including axon guidance, olfactory loss, and calcium channel activity were significantly enriched. A subsequent examination of the ET GWGAS data (N=7,154) also flagged genes involved in calcium ion-regulated exocytosis of neurotransmitters to be significantly enriched. Interestingly, the pheWAS identified that the dysregulated gene,SHF, is associated with a blood pressure medication (P=9.3E-08), which is commonly used to reduce tremor in ET patients. Lastly, it is also notable that the dentate nucleus and cerebellar cortex have different transcriptomes, suggesting that different regions of the cerebellum have spatially different transcriptomes.
Atypical developmental features of cortical thickness trajectories in Autism Spectrum Disorder
Authors: Nunes Adonay S , Vakorin Vasily A , Kozhemiako Nataliia , Peatfield Nicholas , Ribary Urs , Doesburg Sam M 
Published: March 2019

AbstractNeuroimaging studies have reported numerous region-specific atypicalities in the brains of individuals with Autism Spectrum Disorder (ASD), including alterations in cortical thickness (CT). However, there are many inconsistent findings, and this is probably due to atypical CT developmental trajectories in ASD. To this end, we investigated group differences in terms of shapes of developmental trajectories of CT between ASD and typically developing (TD) populations.Using the Autism Brain Imaging Data Exchange (ABIDE) repository (releases I and II combined), we investigated atypical shapes of developmental trajectories in ASD using a linear, quadratic and cubic models at various scales of spatial coarseness, and their association with symptomatology using the Autism Diagnostic Observation Schedule (ADOS) scores. These parameters were also used to predict ASD and TD CT development.While no overall group differences in CT was observed across the entire age range, ASD and TD populations were different in terms of age-related changes. Developmental trajectories of CT in ASD were mostly characterized by decreased cortical thinning during early adolescence and increased thinning at later stages, involving mostly frontal and parietal areas. Such changes were associated with ADOS scores. The curvature of the trajectories estimated from the quadratic model was the most accurate and sensitive measure for detecting ASD. Our findings suggest that under the context of longitudinal changes in brain morphology, robust detection of ASD would require three time points to estimate the curvature of age-related changes.
The parietal operculum preferentially encodes heat pain and not salience
Authors: Horing Björn , Sprenger Christian , Büchel Christian 
Published: March 2019

AbstractSubstantial controversy exists as to which part of brain activity is genuinely attributable to pain-related percepts, and which activity is due to general aspects of sensory stimulation, such as its salience, or the accompanying arousal. The challenge posed by this question rests largely in the fact that pain per se exhibits highly intense but unspecific characteristics. These therefore should be matched by potential control conditions. Here, we used a unique combination of functional magnetic resonance imaging, behavioral and autonomic measures to address this longstanding debate in pain research.Subjects rated perceived intensity in a sequence alternating between heat and sound stimuli. Neuronal activity was monitored using fMRI. Either modality was presented in six different intensities, three of which lay above the pain threshold (for heat) or the unpleasantness threshold (for sound). We performed our analysis on 26 volunteers in which psychophysiological responses (as per skin conductance responses) did not differ between the two stimulus modalities. Having thus ascertained a comparable amount of stimulation-related but unspecific activation, we analyzed stimulus response functions after painful stimulation, and contrasted them with those of the matched acoustic control condition. Furthermore, analysis of fMRI data was performed on the brain surface to circumvent blurring issues stemming from the close proximity of several regions of interest located in heavily folded cortical areas. We focused our analyses on insular and periinsular regions which are strongly involved in processing of painful stimuli. We employed an axiomatic approach to determine areas showing higher activation in painful compared to non-painful heat, and at the same time showing a steeper stimulus response function for painful heat as compared to unpleasant sound. Intriguingly, an area in the posterior parietal operculum emerged whose response showed a pain preference after satisfying all axiomatic constraints.This result has important implications for the interpretation of functional imaging findings in pain research, as it clearly demonstrates that there are areas whose activity following painful stimulation is not due to general attributes or results of sensory stimulation, such as salience or arousal. Conversely, several areas did not conform to the formulated axioms to rule out general factors as explanations.
Sensitivity studies and optimization of arrangements of optically pumped magnetometers in simulated magnetoencephalography
Authors: Eichardt Roland , Strohmeier Daniel , Hunold Alexander , Machts René , Haueisen Jens , Oelsner Gregor , Schmidt Christian B. , Schultze Volkmar , Stolz Ronny , Graichen Uwe 
Published: March 2019

Purpose
The purpose of this paper is to present a simulation study using a model of a new optically pumped magnetometer sensor for application in the field of magnetoencephalography. The effects of sensor distance and orientation on the measurement information and the sensitivity to neuronal sources are investigated. Further, this paper uses a combinatorial optimization approach for sensor placement to measure spontaneous activity in the region of the occipital cortex.

Design/methodology/approach
This paper studies the effects of sensor distance and orientation on sensitivity to cortical sources and measurement information. A three-compartment model of the head, using the boundary element method, is applied. For sensor setup optimization, a combinatorial optimization scheme is developed.

Findings
The sensor distance to sources considerably affects the sensitivity and the retrieved information. A specific arrangement of four sensors for measuring spontaneous activity over the occipital part of the head is optimized by effectively avoiding position conflicts.

Research limitations/implications
Individual head models, as well as more detailed noise and signal models, will increase the significance for specific-use cases in future studies.

Originality/value
Effects of sensor distance and orientation are specifically evaluated for a new optically pumped magnetometer. A discrete optimization scheme for sensor optimization is introduced. The presented methodology is applicable for other sensor characterization and optimization problems. The findings contribute significantly to the development of new sensors.
Marketing madness or financial folly?
Authors: Gamble Jordan Robert 
Published: March 2019

Purpose The purpose of this paper is to explore the implementation of equity crowdfunding (ECF) within the record industry in terms of challenges and opportunities, in addition to the marketing and financial implications for independent music artists and major record labels. Design/methodology/approach This study adopted a qualitative methodology consisting of two-stage interview-based research methods. A total of 44 semi-structured in-depth interviews were conducted with the CEOs of ECF platforms in the record industry, other related record industry informants, independent artist managers and senior executives from major record labels. Findings The loyalty aspect of ECF may have significant marketing potential in terms of inconspicuously using the equity platform as a “prosumer” identification mechanism. As this early career stage of artists is delicate in terms of establishing trust and patronage from their fans, these early marketing and ECF ventures should be implemented directly from the artist without external third-party involvement. Research limitations/implications The implications of this paper’s findings and theoretical model are not limited to the two studied stakeholder groups of the record industry. The insights in relation to the obstinate lack of understanding and clarity (particularly for independent artists) which surround ECF are likely to influence short-term strategic approaches by other players throughout the wider music industry. Practical implications The insights regarding negative approaches towards ECF by the labels may influence future “coopetition strategies” for independent labels, as they seek to navigate the changing industry dynamics. Originality/value This paper is the first study to empirically explore the predominantly under-researched area of ECF implementation in the record industry in terms of marketing and financial consequences for artists and labels.