bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment and development of the gas kinetic boundary condition for the Boltzmann equation
Authors: Wu Lei , Struchtrup Henning 
Published: June 2017

Gas–surface interactions play important roles in internal rarefied gas flows, especially in micro-electro-mechanical systems with large surface area to volume ratios. Although great progress has been made to solve the Boltzmann equation, the gas kinetic boundary condition (BC) has not been well studied. Here we assess the accuracy of the Maxwell, Epstein and Cercignani–Lampis BCs, by comparing numerical results of the Boltzmann equation for the Lennard–Jones potential to experimental data on Poiseuille and thermal transpiration flows. The four experiments considered are: Ewartet al.(J. Fluid Mech., vol. 584, 2007, pp. 337–356), Rojas-Cárdenaset al.(Phys. Fluids, vol. 25, 2013, 072002) and Yamaguchiet al.(J. Fluid Mech., vol. 744, 2014, pp. 169–182; vol. 795, 2016, pp. 690–707), where the mass flow rates in Poiseuille and thermal transpiration flows are measured. This requires that the BC has the ability to tune the effective viscous and thermal slip coefficients to match the experimental data. Among the three BCs, the Epstein BC has more flexibility to adjust the two slip coefficients, and hence for most of the time it gives good agreement with the experimental measurements. However, like the Maxwell BC, the viscous slip coefficient in the Epstein BC cannot be smaller than unity but the Cercignani–Lampis BC can. Therefore, we propose to combine the Epstein and Cercignani–Lampis BCs to describe gas–surface interaction. Although the new BC contains six free parameters, our approximate analytical expressions for the viscous and thermal slip coefficients provide useful guidance to choose these parameters.
Relaxation drag history of shock accelerated microparticles
Authors: Bordoloi Ankur D. , Martinez Adam A. , Prestridge Katherine 
Published: June 2017

Experimental measurements of the displacements of shock accelerated microparticles from shortly after shock interaction to the particle relaxation time show time-dependent drag coefficients ($C_{D}$) that are much higher than those predicted by quasi-steady and unsteady drag models. Nylon particles with mean diameter of $4~\unicode[STIX]{x03BC}\text{m}$, accelerated by one-dimensional normal shocks (Mach number $M_{s}=1.2$, 1.3 and 1.4), have measured $C_{D}$ values that follow a power-law behaviour. The drag is a function of the time-dependent Knudsen number, $Kn^{\ast }=M_{s}/Re_{p}$, where the particle Reynolds number ($Re_{p}$) is calculated using the time-dependent slip velocity. Some portion of the drag can be attributed to quasi-steady forces, but the total drag cannot be predicted by current unsteady force models that are based on the Basset–Boussinesq–Oseen equation and pressure drag. The largest contribution to the total drag is the unsteady component ($C_{D,us}$) until the particle attains $Kn^{\ast }\approx 0.5{-}1.0$, then the unsteady contribution decays. The quasi-steady component ($C_{D,qs}$) increases almost linearly with $Kn^{\ast }$, intersects the $C_{D,us}$ at $Kn^{\ast }\approx 2$ and becomes the primary contributor to the drag towards the end of the relaxation zone as $Re_{p}\rightarrow 0$. There are currently no analytical models that are able to predict the nonlinear behaviour of the shock accelerated particles during the relaxation phase of the flow.
Regional and environmental variation in escalatory ecological trends during the Jurassic: a western Tethys hotspot for escalation?
Authors: Monarrez Pedro M. , Aberhan Martin , Holland Steven M. 
Published: June 2017

AbstractUnderstanding the drivers of macroevolutionary trends through the Phanerozoic has been a central question in paleobiology. Increasingly important is understanding the regional and environmental variation of macroevolutionary patterns and how they are reflected at the global scale. Here we test the role of biotic interactions on regional ecological patterns during the Mesozoic marine revolution. We test for escalatory trends in Jurassic marine benthic macroinvertebrate ecosystems using occurrence data from the Paleobiology Database parsed by region and environment. The escalation hypothesis posits that taxonomic groups that could adapt to intense predation and bioturbation proliferated, whereas groups unable to adapt were reduced in diversity and abundance or driven to extinction. We tested this hypothesis in five regions during Jurassic stages and among four depositional environments in Europe. Few escalatory trends were detected, although at least one escalatory trend was observed in every region, with the greatest number and strongest trends observed in Europe. These trends include increases in shallow infauna and cementing epifauna and occurrences of facultatively mobile invertebrates and decreases in pedunculate, free-lying, and sessile epifauna. Within Europe, escalatory trends occur in shallow-water environments but also in deeper-water environments, where they are predicted not to occur. When regional trends are aggregated, trends in Europe drive the global signal. The results of this study suggest that while evidence of escalation is rare globally, it is plausible that escalation drove macroevolutionary patterns in Europe. Furthermore, these results underline the need to dissect global fossil data at the regional scale to understand global macroevolutionary dynamics.
Polymorphisms of the TNF-α gene interact with plasma fatty acids on inflammatory biomarker profile: a population-based, cross-sectional study in São Paulo, Brazil
Authors: Oki Erica , Norde Marina N. , Carioca Antônio A. F. , Souza José M. P. , Castro Inar A. , Marchioni Dirce M. L. , Fisberg Regina M. , Rogero Marcelo M. 
Published: June 2017

AbstractThe aim of the present study was to investigate the relationship of four TNF-α SNP with inflammatory biomarkers and plasma fatty acids (FA), and the interaction among them in a population-based, cross-sectional study in São Paulo, Brazil. A total of 281 subjects, aged >19 and <60 years, participated in a cross-sectional, population-based study performed in Brazil. The following SNP spanning the TNF-α gene were genotyped: -238G/A (rs361525), -308G/A (rs1800629), -857C/T (rs1799724) and -1031T/C (rs1799964). In all, eleven plasma inflammatory biomarkers and plasma FA profile were determined. To analyse the interaction between TNF-α SNP and plasma FA, a cluster analysis was performed to stratify individuals based on eleven inflammatory biomarkers into two groups used as outcome: inflammatory (INF) and non-inflammatory clusters. The -238A allele carriers had higher TNF-α (P=0·033), IL-6 (P=0·013), IL-1β (P=0·037), IL-12 (0·048) and IL-10 (P=0·010) than the GG genotype. The -308A allele carriers also had lower levels of plasma palmitoleic acid (P=0·009), oleic acid (P=0·039), total MUFA (P=0·014), stearoyl-CoA desaturase (SCD) activity index-16 (P=0·007), SCD-18 (P=0·020) and higher levels of PUFA (P=0·046) and DHA (P=0·044). Significant interactions modifying the risk of belonging to the INF cluster were observed with inflammatory cluster as outcome between -857C/T and plasma α-linolenic acid (P=0·026), and also between -308G/A and plasma stearic acid (P=0·044) and total SFA (P=0·040). Our study contributes to knowledge on TNF-α SNP and their association with inflammatory biomarker levels, plasma FA and the interaction among them, of particular interest for the Brazilian population.
Dietary gap assessment: an approach for evaluating whether a country’s food supply can support healthy diets at the population level
Authors: Kuyper Edye M , Engle-Stone Reina , Arsenault Joanne E , Arimond Mary , Adams Katherine P , Dewey Kathryn G 
Published: June 2017

AbstractObjectiveDietary diversity, and in particular consumption of nutrient-rich foods including fruits, vegetables, nuts, beans and animal-source foods, is linked to greater nutrient adequacy. We developed a ‘dietary gap assessment’ to evaluate the degree to which a nation’s food supply could support healthy diets at the population level.Design/SettingIn the absence of global food-based dietary guidelines, we selected the Dietary Approaches to Stop Hypertension (DASH) diet as an example because there is evidence it prevents diet-related chronic disease and supports adequate micronutrient intakes. We used the DASH guidelines to shape a hypothetical ‘healthy’ diet for the test country of Cameroon. Food availability was estimated using FAO Food Balance Sheet data on country-level food supply. For each of the seven food groups in the ‘healthy’ diet, we calculated the difference between the estimated national supply (in kcal, edible portion only) and the target amounts.ResultsIn Cameroon, dairy and other animal-source foods were not adequately available to meet healthy diet recommendations: the deficit was −365 kcal (–1527 kJ)/capita per d for dairy products and −185 kcal (–774 kJ)/capita per d for meat, poultry, fish and eggs. Adequacy of fruits and vegetables depended on food group categorization. When tubers and plantains were categorized as vegetables and fruits, respectively, supply nearly met recommendations. Categorizing tubers and plantains as starchy staples resulted in pronounced supply shortfalls: −109 kcal (–457 kJ)/capita per d for fruits and −94 kcal (–393 kJ)/capita per d for vegetables.ConclusionsThe dietary gap assessment illustrates an approach for better understanding how food supply patterns need to change to achieve healthier dietary patterns.
Optogenetic activation of Plexin-B1 reveals contact repulsion between osteoclasts and osteoblasts
Authors: Deb Roy Abhijit , Yin Taofei , Choudhary Shilpa , Rodionov Vladimir , Pilbeam Carol C. , Wu Yi I. 
Published: June 2017

AbstractDuring bone remodelling, osteoclasts induce chemotaxis of osteoblasts and yet maintain spatial segregation. We show that osteoclasts express the repulsive guidance factor Semaphorin 4D and induce contact inhibition of locomotion (CIL) in osteoblasts through its receptor Plexin-B1. To examine causality and elucidate how localized Plexin-B1 stimulation may spatiotemporally coordinate its downstream targets in guiding cell migration, we develop an optogenetic tool for Plexin-B1 designated optoPlexin. Precise optoPlexin activation at the leading edge of migrating osteoblasts readily induces local retraction and, unexpectedly, distal protrusions to steer cells away. These morphological changes are accompanied by reorganization of Myosin II, PIP3, adhesion and active Cdc42. We attribute the resultant repolarization to RhoA/ROCK-mediated redistribution of β-Pix, which activates Cdc42 and promotes protrusion. Thus, our data demonstrate a causal role of Plexin-B1 for CIL in osteoblasts and reveals a previously unknown effect of Semaphorin signalling on spatial distribution of an activator of cell migration.
Cellulose-based magnetoelectric composites
Authors: Zong Yan , Zheng Tian , Martins Pedro , Lanceros-Mendez S. , Yue Zhilian , Higgins Michael J. 
Published: June 2017

AbstractSince the first magnetoelectric polymer composites were fabricated more than a decade ago, there has been a reluctance to use piezoelectric polymers other than poly(vinylidene fluoride) and its copolymers due to their well-defined piezoelectric mechanism and high piezoelectric coefficients that lead to superior magnetoelectric coefficients of >1 V cm−1 Oe−1. This is the current situation despite the potential for other piezoelectric polymers, such as natural biopolymers, to bring unique, added-value properties and functions to magnetoelectric composite devices. Here we demonstrate a cellulose-based magnetoelectric laminate composite that produces considerable magnetoelectric coefficients of ≈1.5 V cm−1 Oe−1, comprising a Fano resonance that is ubiquitous in the field of physics, such as photonics, though never experimentally observed in magnetoelectric composites. The work successfully demonstrates the concept of exploring new advances in using biopolymers in magnetoelectric composites, particularly cellulose, which is increasingly employed as a renewable, low-cost, easily processable and degradable material.
The emergence and transient behaviour of collective motion in active filament systems
Authors: Suzuki Ryo , Bausch Andreas R. 
Published: June 2017

AbstractMost living systems, ranging from animal flocks, self-motile microorganisms to the cytoskeleton rely on self-organization processes to perform their own specific function. Despite its importance, the general understanding of how individual active constituents initiate the intriguing pattern formation phenomena on all these different length scales still remains elusive. Here, using a high density actomyosin motility assay system, we show that the observed collective motion arises from a seeding process driven by enhanced acute angle collisions. Once a critical size is reached, the clusters coarsen into high and low density phases each with fixed filament concentrations. The steady state is defined by a balance of collision induced randomization and alignment effects of the filaments by multi-filament collisions within ordered clusters.
Phonon engineering in proximity enhanced superconductor heterostructures
Authors: Tang Yong-Chao , Kwon Sangil , Mohebbi Hamid R. , Cory David G. , Miao Guo-Xing 
Published: June 2017

AbstractIn this research, we tailor the phonon density of states (DOS) in thin superconducting films to suppress quasiparticle losses. We examine a model system of a proximity-enhanced three-layered Al/Nb/Al heterostructure and show that the local quantized phonon spectrum of the ultrathin Al cladding layers in the heterostructure has a pronounced effect on the superconducting resonator’s quality factors. Instead of a monotonic increase of quality factors with decreasing temperatures, we observe the quality factor reaches a maximum at 1.2 K in 5/50/5 nm Al/Nb/Al microstrip resonators, because of a quantized phonon ladder. The phonon DOS may be engineered to enhance the performance of quantum devices.
Long-term cilostazol treatment reduces gliovascular damage and memory impairment in a mouse model of chronic cerebral hypoperfusion
Authors: Kitamura Akihiro , Manso Yasmina , Duncombe Jessica , Searcy James , Koudelka Juraj , Binnie Margaret , Webster Scott , Lennen Ross , Jansen Maurits , Marshall Ian , Ihara Masafumi , Kalaria Raj N. , Horsburgh Karen 
Published: June 2017

AbstractChronic cerebral hypoperfusion is a major cause of age-related vascular cognitive impairment. A well-characterised mouse model has shown that hypoperfusion results in gliovascular and white matter damage and impaired spatial working memory. In this study, we assessed whether cilostazol, a phosphodiesterase III inhibitor, could protect against these changes. Adult, male C57Bl/6J mice were subjected to bilateral common carotid artery stenosis or a sham operation and fed normal or cilostazol diet for three months. Cilostazol treatment reduced the impairment in working memory and white matter function after hypoperfusion. Endothelial adhesion molecules and gliosis, increased after hypoperfusion, were ameliorated with cilostazol treatment. Interestingly, the improvement in working memory was closely correlated with reduced microglia and endothelial adhesion molecules. Further, the number of stroke lesions after hypoperfusion was reduced in the cilostazol-treated group. Altogether cilostazol showed potential to ameliorate the gliovascular damage and working memory impairments after hypoperfusion possibly via endothelial protection supporting its potential use in the treatment of vascular cognitive impairment.
Multiple introns in a deep-sea Annelid (Decemunciger: Ampharetidae) mitochondrial genome
Authors: Bernardino Angelo F. , Li Yuanning , Smith Craig R. , Halanych Kenneth M. 
Published: June 2017

AbstractWood falls provide episodic fluxes of energy to the sea floor that are degraded by a species-rich benthic fauna. Part of this rich diversity includes annelid polychaetes but unfortunately, our understanding of such fauna is limited and their genetic variability and evolutionary origins remain poorly known. In this study, we sequenced complete mitochondrial genomes from three congeneric Decemunciger (Ampharetidae) individuals that had colonized multiple wood falls in the deep (~1600 m) NE Pacific Ocean. Mitochondrial gene order within Decemunciger was similar to the three other available Terebellomorpha genomes, consistent with the relatively conserved nature of mitochondrial genomes within annelids. Unexpectedly, we found introns within the cox1, nad1 and nad4 genes of all three genomes assembled. This is the greatest number of introns observed in annelid mtDNA genomes, and possibly in bilaterians. Interestingly, the introns were of variable sizes suggesting possible evolutionary differences in the age and origins of introns. The sequence of the introns within cox1 is similar to Group II introns previously identified, suggesting that introns in the mitochondrial genome of annelids may be more widespread then realized. Phylogenetically, Decemunciger appears to be a sister clade among current vent and seep deep-sea Ampharetinae.
Effect of high fat diet on phenotype, brain transcriptome and lipidome in Alzheimer’s model mice
Authors: Nam Kyong Nyon , Mounier Anais , Wolfe Cody M. , Fitz Nicholas F. , Carter Alexis Y. , Castranio Emilie L. , Kamboh Hafsa I. , Reeves Valerie L. , Wang Jianing , Han Xianlin , Schug Jonathan , Lefterov Iliya , Koldamova Radosveta 
Published: June 2017

AbstractWe examined the effect of chronic high fat diet (HFD) on amyloid deposition and cognition of 12-months old APP23 mice, and correlated the phenotype to brain transcriptome and lipidome. HFD significantly increased amyloid plaques and worsened cognitive performance compared to mice on normal diet (ND). RNA-seq results revealed that in HFD mice there was an increased expression of genes related to immune response, such as Trem2 and Tyrobp. We found a significant increase of TREM2 immunoreactivity in the cortex in response to HFD, most pronounced in female mice that correlated to the amyloid pathology. Down-regulated by HFD were genes related to neuron projections and synaptic transmission in agreement to the significantly deteriorated neurite morphology and cognition in these mice. To examine the effect of the diet on the brain lipidome, we performed Shotgun Lipidomics. While there was no difference in the total amounts of phospholipids of each class, we revealed that the levels of 24 lipid sub-species in the brain were significantly modulated by HFD. Network visualization of correlated lipids demonstrated overall imbalance with most prominent effect on cardiolipin molecular sub-species. This integrative approach demonstrates that HFD elicits a complex response at molecular, cellular and system levels in the CNS.
Effects of habitat constraints on soil microbial community function
Authors: Nunan Naoise , Leloup Julie , Ruamps Léo S. , Pouteau Valérie , Chenu Claire 
Published: June 2017

AbstractAn underlying assumption of most soil carbon (C) dynamics models is that soil microbial communities are functionally similar; in other words, that microbial activity under given conditions is not dependent on the composition or diversity of the communities. Although a number of studies have indicated that microbial communities are not intrinsically functionally similar, most soil C dynamics models can adequately describe C dynamics without explicitly describing microbial functioning. Here, we provide a mechanistic basis for reconciling this apparent discrepancy. In a reciprocal transplant experiment, we show that the environmental context (soil and pore-network properties) of microbial communities can constrain the activity of functionally different communities to such an extent that their activities are indistinguishable. The data also suggest that when microbial activity is less constrained, the intrinsic functional differences among communities can be expressed. We conclude that soil C dynamics may depend on microbial community structure or diversity in environments where their activity is less constrained, such as the rhizosphere or the litter layer, but not in oligotrophic environments such as the mineral layers of soil.
Comparative proteome analysis between C
. briggsae embryos and larvae reveals a role of chromatin modification proteins in embryonic cell division
Authors: An Xiaomeng , Shao Jiaofang , Zhang Huoming , Ren Xiaoliang , Ho Vincy Wing Sze , Li Runsheng , Wong Ming-Kin , Zhao Zhongying 
Published: June 2017

AbstractCaenorhabditis briggsae has emerged as a model for comparative biology against model organism C. elegans. Most of its cell fate specifications are completed during embryogenesis whereas its cell growth is achieved mainly in larval stages. The molecular mechanism underlying the drastic developmental changes is poorly understood. To gain insights into the molecular changes between the two stages, we compared the proteomes between the two stages using iTRAQ. We identified a total of 2,791 proteins in the C. briggsae embryos and larvae, 247 of which undergo up- or down-regulation between the two stages. The proteins that are upregulated in the larval stages are enriched in the Gene Ontology categories of energy production, protein translation, and cytoskeleton; whereas those upregulated in the embryonic stage are enriched in the categories of chromatin dynamics and posttranslational modification, suggesting a more active chromatin modification in the embryos than in the larva. Perturbation of a subset of chromatin modifiers followed by cell lineage analysis suggests their roles in controlling cell division pace. Taken together, we demonstrate a general molecular switch from chromatin modification to metabolism during the transition from C. briggsae embryonic to its larval stages using iTRAQ approach. The switch might be conserved across metazoans.
Novel insights into mitochondrial gene rearrangement in thrips (Insecta: Thysanoptera) from the grass thrips, Anaphothrips obscurus
Authors: Liu Hangrui , Li Hu , Song Fan , Gu Wenyi , Feng Jinian , Cai Wanzhi , Shao Renfu 
Published: June 2017

AbstractWe sequenced the mitochondrial (mt) genome of the grass thrips, Anaphothrips obscurus, which is highly rearranged and differs from the four thrips species reported previously in the arrangement of both tRNA genes and a protein-coding gene, nad3, and in the copy number of the control region (CR). We reconstructed the phylogeny of the thrips with mt genome sequences, and used it as a framework to gain insights into mt genome evolution in thrips. It is evident that A. obscurus is less rearranged in mt genome organization than the other four known thrips. nad3 is in its ancestral location in A. obscurus but was translocated in other four thrips. Also, A. obscurus has one CR, which is ancestral to hexapods whereas other thrips have two or three CRs. All of the five thrips whose mt genomes have been sequenced to date are from the subfamily Thripinae, which represents about a quarter of the species richness in the order Thysanoptera. The high variation in mt genome organization observed in a subfamily challenges our knowledge about animal mt genomes. It remains to be investigated why mt genomes evolved so fast in the subfamily Thripinae and how mt genomes evolved in other lineages of thrips.