bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competition between the centrifugal and strato-rotational instabilities in the stratified Taylor–Couette flow
Authors: Park Junho , Billant Paul , Baik Jong-Jin , Seo Jaemyeong Mango 
Published: February 2018

The stably stratified Taylor–Couette flow is investigated experimentally and numerically through linear stability analysis. In the experiments, the stability threshold and flow regimes have been mapped over the ranges of outer and inner Reynolds numbers: $-2000<Re_{o}<2000$ and $0<Re_{i}<3000$, for the radius ratio $r_{i}/r_{o}=0.9$ and the Brunt–Väisälä frequency $N\approx 3.2~\text{rad}~\text{s}^{-1}$. The corresponding Froude numbers $F_{o}$ and $F_{i}$ are always much smaller than unity. Depending on $Re_{o}$ (or equivalently on the angular velocity ratio $\unicode[STIX]{x1D707}=\unicode[STIX]{x1D6FA}_{o}/\unicode[STIX]{x1D6FA}_{i}$), three different regimes have been identified above instability onset: a weakly non-axisymmetric mode with low azimuthal wavenumber $m=O(1)$ is observed for $Re_{o}<0$ ($\unicode[STIX]{x1D707}<0$), a highly non-axisymmetric mode with $m\sim 12$ occurs for $Re_{o}>840$ ($\unicode[STIX]{x1D707}>0.57$) while both modes are present simultaneously in the lower and upper parts of the flow for $0\leqslant Re_{o}\leqslant 840$ ($0\leqslant \unicode[STIX]{x1D707}\leqslant 0.57$). The destabilization of these primary modes and the transition to turbulence as $Re_{i}$ increases have been also studied. The linear stability analysis proves that the weakly non-axisymmetric mode is due to the centrifugal instability while the highly non-axisymmetric mode comes from the strato-rotational instability. These two instabilities can be clearly distinguished because of their distinct dominant azimuthal wavenumber and frequency, in agreement with the recent results of Park et al. (J. Fluid Mech., vol. 822, 2017, pp. 80–108). The stability threshold and the characteristics of the primary modes observed in the experiments are in very good agreement with the numerical predictions. Moreover, we show that the centrifugal and strato-rotational instabilities are observed simultaneously for $0\leqslant Re_{o}\leqslant 840$ in the lower and upper parts of the flow, respectively, because of the variations of the local Reynolds numbers along the vertical due to the salinity gradient.
Deep time diversity of metatherian mammals: implications for evolutionary history and fossil-record quality
Authors: Bennett C. Verity , Upchurch Paul , Goin Francisco J. , Goswami Anjali 
Published: February 2018

AbstractDespite a global fossil record, Metatheria are now largely restricted to Australasia and South America. Most metatherian paleodiversity studies to date are limited to particular subclades, time intervals, and/or regions, and few consider uneven sampling. Here, we present a comprehensive new data set on metatherian fossil occurrences (Barremian to end Pliocene). These data are analyzed using standard rarefaction and shareholder quorum subsampling (including a new protocol for handling Lagerstätte-like localities).Global metatherian diversity was lowest during the Cretaceous, and increased sharply in the Paleocene, when the South American record begins. Global and South American diversity rose in the early Eocene then fell in the late Eocene, in contrast to the North American pattern. In the Oligocene, diversity declined in the Americas, but this was more than offset by Oligocene radiations in Australia. Diversity continued to decrease in Laurasia, with final representatives in North America (excluding the later entry ofDidelphis virginiana) and Europe in the early Miocene, and Asia in the middle Miocene. Global metatherian diversity appears to have peaked in the early Miocene, especially in Australia. Following a trough in the late Miocene, the Pliocene saw another increase in global diversity. By this time, metatherian biogeographic distribution had essentially contracted to that of today.Comparison of the raw and sampling-corrected diversity estimates, coupled with evaluation of “coverage” and number of prolific sites, demonstrates that the metatherian fossil record is spatially and temporally extremely patchy. Therefore, assessments of macroevolutionary patterns based on the raw fossil record (as in most previous studies) are inadvisable.
Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota
Authors: Serena Carolina , Ceperuelo-Mallafré Victoria , Keiran Noelia , Queipo-Ortuño Maria Isabel , Bernal Rosa , Gomez-Huelgas Ricardo , Urpi-Sarda Mireia , Sabater Mónica , Pérez-Brocal Vicente , Andrés-Lacueva Cristina , Moya Andres , Tinahones Francisco J , Fernández-Real Jose Manuel , Vendrell Joan , Fernández-Veledo Sonia 
Published: February 2018

Abstract
Gut microbiota-related metabolites are potential clinical biomarkers for cardiovascular disease (CVD). Circulating succinate, a metabolite produced by both microbiota and the host, is increased in hypertension, ischemic heart disease, and type 2 diabetes. We aimed to analyze systemic levels of succinate in obesity, a major risk factor for CVD, and its relationship with gut microbiome. We explored the association of circulating succinate with specific metagenomic signatures in cross-sectional and prospective cohorts of Caucasian Spanish subjects. Obesity was associated with elevated levels of circulating succinate concomitant with impaired glucose metabolism. This increase was associated with specific changes in gut microbiota related to succinate metabolism: a higher relative abundance of succinate-producing Prevotellaceae (P) and Veillonellaceae (V), and a lower relative abundance of succinate-consuming Odoribacteraceae (O) and Clostridaceae (C) in obese individuals, with the (P + V/O + C) ratio being a main determinant of plasma succinate. Weight loss intervention decreased (P + V/O + C) ratio coincident with the reduction in circulating succinate. In the spontaneous evolution after good dietary advice, alterations in circulating succinate levels were linked to specific metagenomic signatures associated with carbohydrate metabolism and energy production with independence of body weight change. Our data support the importance of microbe–microbe interactions for the metabolite signature of gut microbiome and uncover succinate as a potential microbiota-derived metabolite related to CVD risk.
Plasma density limits for hole boring by intense laser pulses
Authors: Iwata Natsumi , Kojima Sadaoki , Sentoku Yasuhiko , Hata Masayasu , Mima Kunioki 
Published: February 2018

AbstractHigh-power lasers in the relativistic intensity regime with multi-picosecond pulse durations are available in many laboratories around the world. Laser pulses at these intensities reach giga-bar level radiation pressures, which can push the plasma critical surface where laser light is reflected. This process is referred to as the laser hole boring (HB), which is critical for plasma heating, hence essential for laser-based applications. Here we derive the limit density for HB, which is the maximum plasma density the laser can reach, as a function of laser intensity. The time scale for when the laser pulse reaches the limit density is also derived. These theories are confirmed by a series of particle-in-cell simulations. After reaching the limit density, the plasma starts to blowout back toward the laser, and is accompanied by copious superthermal electrons; therefore, the electron energy can be determined by varying the laser pulse length.
Residential energy use emissions dominate health impacts from exposure to ambient particulate matter in India
Authors: Conibear Luke , Butt Edward W. , Knote Christoph , Arnold Stephen R. , Spracklen Dominick V. 
Published: February 2018

AbstractExposure to ambient fine particulate matter (PM2.5) is a leading contributor to diseases in India. Previous studies analysing emission source attributions were restricted by coarse model resolution and limited PM2.5 observations. We use a regional model informed by new observations to make the first high-resolution study of the sector-specific disease burden from ambient PM2.5 exposure in India. Observed annual mean PM2.5 concentrations exceed 100 μg m−3 and are well simulated by the model. We calculate that the emissions from residential energy use dominate (52%) population-weighted annual mean PM2.5 concentrations, and are attributed to 511,000 (95UI: 340,000–697,000) premature mortalities annually. However, removing residential energy use emissions would avert only 256,000 (95UI: 162,000–340,000), due to the non-linear exposure–response relationship causing health effects to saturate at high PM2.5 concentrations. Consequently, large reductions in emissions will be required to reduce the health burden from ambient PM2.5 exposure in India.
Sustained micellar delivery via inducible transitions in nanostructure morphology
Authors: Karabin Nicholas B. , Allen Sean , Kwon Ha-Kyung , Bobbala Sharan , Firlar Emre , Shokuhfar Tolou , Shull Kenneth R. , Scott Evan A. 
Published: February 2018

AbstractNanocarrier administration has primarily been restricted to intermittent bolus injections with limited available options for sustained delivery in vivo. Here, we demonstrate that cylinder-to-sphere transitions of self-assembled filomicelle (FM) scaffolds can be employed for sustained delivery of monodisperse micellar nanocarriers with improved bioresorptive capacity and modularity for customization. Modular assembly of FMs from diverse block copolymer (BCP) chemistries allows in situ gelation into hydrogel scaffolds following subcutaneous injection into mice. Upon photo-oxidation or physiological oxidation, molecular payloads within FMs transfer to micellar vehicles during the morphological transition, as verified in vitro by electron microscopy and in vivo by flow cytometry. FMs composed of multiple distinct BCP fluorescent conjugates permit multimodal analysis of the scaffold’s non-inflammatory bioresorption and micellar delivery to immune cell populations for one month. These scaffolds exhibit highly efficient bioresorption wherein all components participate in retention and transport of therapeutics, presenting previously unexplored mechanisms for controlled nanocarrier delivery.
CellCycleTRACER accounts for cell cycle and volume in mass cytometry data
Authors: Rapsomaniki Maria Anna , Lun Xiao-Kang , Woerner Stefan , Laumanns Marco , Bodenmiller Bernd , Martínez María Rodríguez 
Published: February 2018

AbstractRecent studies have shown that cell cycle and cell volume are confounding factors when studying biological phenomena in single cells. Here we present a combined experimental and computational method, CellCycleTRACER, to account for these factors in mass cytometry data. CellCycleTRACER is applied to mass cytometry data collected on three different cell types during a TNFα stimulation time-course. CellCycleTRACER reveals signaling relationships and cell heterogeneity that were otherwise masked.
Direct measurement of superdiffusive energy transport in disordered granular chains
Authors: Kim Eunho , Martínez Alejandro J. , Phenisee Sean E. , Kevrekidis P. G. , Porter Mason A. , Yang Jinkyu 
Published: February 2018

AbstractEnergy transport properties in heterogeneous materials have attracted scientific interest for more than half of a century, and they continue to offer fundamental and rich questions. One of the outstanding challenges is to extend Anderson theory for uncorrelated and fully disordered lattices in condensed-matter systems to physical settings in which additional effects compete with disorder. Here we present the first systematic experimental study of energy transport and localization properties in simultaneously disordered and nonlinear granular crystals. In line with prior theoretical studies, we observe in our experiments that disorder and nonlinearity—which individually favor energy localization—can effectively cancel each other out, resulting in the destruction of wave localization. We also show that the combined effect of disorder and nonlinearity can enable manipulation of energy transport speed in granular crystals. Specifically, we experimentally demonstrate superdiffusive transport. Furthermore, our numerical computations suggest that subdiffusive transport should be attainable by controlling the strength of the system’s external precompression force.
Non-equivalent antigen presenting capabilities of dendritic cells and macrophages in generating brain-infiltrating CD8 + T cell responses
Authors: Malo Courtney S. , Huggins Matthew A. , Goddery Emma N. , Tolcher Heather M. A. , Renner Danielle N. , Jin Fang , Hansen Michael J. , Pease Larry R. , Pavelko Kevin D. , Johnson Aaron J. 
Published: February 2018

AbstractThe contribution of antigen-presenting cell (APC) types in generating CD8+T cell responses in the central nervous system (CNS) is not fully defined, limiting the development of vaccines and understanding of immune-mediated neuropathology. Here, we generate a transgenic mouse that enables cell-specific deletion of the H-2Kb MHC class I molecule. By deleting H-2Kbon dendritic cells and macrophages, we compare the effect of each APC in three distinct models of neuroinflammation: picornavirus infection, experimental cerebral malaria, and a syngeneic glioma. Dendritic cells and macrophages both activate CD8+T cell responses in response to these CNS immunological challenges. However, the extent to which each of these APCs contributes to CD8+T cell priming varies. These findings reveal distinct functions for dendritic cells and macrophages in generating CD8+T cell responses to neurological disease.
Glacigenic sedimentation pulses triggered post-glacial gas hydrate dissociation
Authors: Karstens Jens , Haflidason Haflidi , Becker Lukas W. M. , Berndt Christian , Rüpke Lars , Planke Sverre , Liebetrau Volker , Schmidt Mark , Mienert Jürgen 
Published: February 2018

AbstractLarge amounts of methane are stored in continental margins as gas hydrates. They are stable under high pressure and low temperature, but react sensitively to environmental changes. Bottom water temperature and sea level changes were considered as main contributors to gas hydrate dynamics after the last glaciation. However, here we show with numerical simulations that pulses of increased sedimentation dominantly controlled hydrate stability during the end of the last glaciation offshore mid-Norway. Sedimentation pulses triggered widespread gas hydrate dissociation and explains the formation of ubiquitous blowout pipes in water depths of 600 to 800 m. Maximum gas hydrate dissociation correlates spatially and temporally with the formation or reactivation of pockmarks, which is constrained by radiocarbon dating of Isorropodon nyeggaensis bivalve shells. Our results highlight that rapid changes of sedimentation can have a strong impact on gas hydrate systems affecting fluid flow and gas seepage activity, slope stability and the carbon cycle.
High throughput protease profiling comprehensively defines active site specificity for thrombin and ADAMTS13
Authors: Kretz Colin A. , Tomberg Kärt , Van Esbroeck Alexander , Yee Andrew , Ginsburg David 
Published: February 2018

AbstractWe have combined random 6 amino acid substrate phage display with high throughput sequencing to comprehensively define the active site specificity of the serine protease thrombin and the metalloprotease ADAMTS13. The substrate motif for thrombin was determined by >6,700 cleaved peptides, and was highly concordant with previous studies. In contrast, ADAMTS13 cleaved only 96 peptides (out of >107 sequences), with no apparent consensus motif. However, when the hexapeptide library was substituted into the P3-P3′ interval of VWF73, an exosite-engaging substrate of ADAMTS13, 1670 unique peptides were cleaved. ADAMTS13 exhibited a general preference for aliphatic amino acids throughout the P3-P3′ interval, except at P2 where Arg was tolerated. The cleaved peptides assembled into a motif dominated by P3 Leu, and bulky aliphatic residues at P1 and P1′. Overall, the P3-P2′ amino acid sequence of von Willebrand Factor appears optimally evolved for ADAMTS13 recognition. These data confirm the critical role of exosite engagement for substrates to gain access to the active site of ADAMTS13, and define the substrate recognition motif for ADAMTS13. Combining substrate phage display with high throughput sequencing is a powerful approach for comprehensively defining the active site specificity of proteases.
Graphene based room temperature flexible nanocomposites from permanently cross-linked networks
Authors: Hameed Nishar , Dumée Ludovic F. , Allioux Francois-Marie , Reghat Mojdeh , Church Jeffrey S. , Naebe Minoo , Magniez Kevin , Parameswaranpillai Jyotishkumar , Fox Bronwyn L. 
Published: February 2018

AbstractGraphene based room temperature flexible nanocomposites were prepared using epoxy thermosets for the first time. Flexible behavior was induced into the epoxy thermosets by introducing charge transfer complexes between functional groups within cross linked epoxy and room temperature ionic liquid ions. The graphene nanoplatelets were found to be highly dispersed in the epoxy matrix due to ionic liquid cation–π interactions. It was observed that incorporation of small amounts of graphene into the epoxy matrix significantly enhanced the mechanical properties of the epoxy. In particular, a 0.6 wt% addition increased the tensile strength and Young’s modulus by 125% and 21% respectively. The electrical resistance of nanocomposites was found to be increased with graphene loading indicating the level of self-organization between the ILs and the graphene sheets in the matrix of the composite. The graphene nanocomposites were flexible and behave like ductile thermoplastics at room temperature. This study demonstrates the use of ionic liquid as a compatible agent to induce flexibility in inherently brittle thermoset materials and improve the dispersion of graphene to create high performance nanocomposite materials.
Generation of a Dual-Target, Safe, Inexpensive Microbicide that Protects Against HIV-1 and HSV-2 Disease
Authors: Farr Zuend Christina , Nomellini John F. , Smit John , Horwitz Marc S. 
Published: February 2018

AbstractHSV-2 infection is a significant health problem and a major co-morbidity factor for HIV-1 acquisition, increasing risk of infection 2–4 fold. Condom based prevention strategies for HSV-2 and HIV-1 have not been effective at stopping the HIV-1 pandemic, indicating that alternative prevention strategies need to be investigated. We have previously developed an inexpensive HIV-1 specific microbicide that utilizes the S-layer mediated display capabilities of Caulobacter crescentus, and have shown that recombinant C. crescentus displaying HIV entry blocking proteins are able to provide significant protection from HIV-1 infection in vitro. Here we demonstrate that recombinant C. crescentus are safe for topical application and describe 5 new recombinant C. crescentus that provide protection from HIV-1 infection in vitro. Further, we demonstrate protection from disease following intravaginal infection with HSV-2 in a murine model using C. crescentus expressing the anti-viral lectins Cyanovirin-N and Griffithsin, as well as α-1-antitrypsin and indolicidin. Interestingly, C. crescentus alone significantly reduced HSV-2 replication in vaginal lavage fluid. Protection from HSV-2 disease was strongly associated with early cytokine production in the vaginal tract. Our data support the potential for a dual-target microbicide that can protect against both HIV-1 and HSV-2, which could have an enormous impact on public health.
Urban stormwater runoff negatively impacts lateral line development in larval zebrafish and salmon embryos
Authors: Young Alexander , Kochenkov Valentin , McIntyre Jenifer K. , Stark John D. , Coffin Allison B. 
Published: February 2018

AbstractAfter a storm, water often runs off of impervious urban surfaces directly into aquatic ecosystems. This stormwater runoff is a cocktail of toxicants that have serious effects on the ecological integrity of aquatic habitats. Zebrafish that develop in stormwater runoff suffer from cardiovascular toxicity and impaired growth, but the effects of stormwater on fish sensory systems are not understood. Our study investigated the effect of stormwater on hair cells of the lateral line in larval zebrafish and coho salmon. Our results showed that although toxicants in stormwater did not kill zebrafish hair cells, these cells did experience damage. Zebrafish developing in stormwater also experienced impaired growth, fewer neuromasts in the lateral line, and fewer hair cells per neuromast. A similar reduction in neuromast number was observed in coho salmon reared in stormwater. Bioretention treatment, intended to filter out harmful constituents of stormwater, rescued the lateral line defects in zebrafish but not in coho salmon, suggesting that not all of the harmful constituents were removed by the filtration media and that salmonids are particularly sensitive to aquatic toxicants. Collectively, these data demonstrate that sub-lethal exposure to stormwater runoff negatively impacts a fish sensory system, which may have consequences for organismal fitness.
Luminescence resonance energy transfer between genetically encoded donor and acceptor for protein-protein interaction studies in the molecular chaperone HSP70/HSP90 complexes
Authors: Bhattacharya Kaushik , Bernasconi Lilia , Picard Didier 
Published: February 2018

AbstractComplex patterns of protein-protein interactions (PPInts) are involved in almost all cellular processes. This has stimulated the development of a wide range of methods to characterize PPInts in detail. Methods with fluorescence resonance energy transfer can be technically challenging and suffer from several limitations, which could be overcome by switching to luminescence resonance energy transfer (LRET) with lanthanide ions such as Tb3+. With LRET, energy transfer between PPInt partners works over a larger distance and with less topological constraints; moreover, the long-lived luminescence of lanthanides allows one to bypass the short-lived background fluorescence. We have developed a novel LRET method to investigate PPInts between partners expressed as fusion proteins with genetically encoded donor and acceptor moieties. Upon UV excitation of a tryptophan within a lanthanide binding peptide, the Tb3+ luminescence is harnessed to excite either a green or a red fluorescent protein. We demonstrate the usefulness of the LRET assay by applying it to analyze the interactions of the molecular chaperones HSP70 and HSP90 with their common co-chaperone HOP/Sti1. We recapitulate the previously described interaction specificities between the HSP70/HSP90 C-termini and tetratricopeptide repeat domains of HOP/Sti1 and demonstrate the impact of single point mutants on domain-domain interactions.