bluuebunny/crossref_metadata_2025 huggingface dataset:
The Language of Law and Economics
Authors: Parisi Francesco
Published: July 2017

From a historical perspective, 'law and economics' constituted one of the most influential developments in legal scholarship in the twentieth century; the discipline remains today one of the dominant perspectives on the law, generating a tremendous quantity of new research and discussion. Unfortunately, one consequence of applying the analytical methods of one highly technical field to the historically layered substance of another has been the accumulation of considerable technical overhead, requiring fluency in both the language of economics and the language of the law. Further complicating matters, the field of law and economics has sometimes developed independently, creating new terms, while recasting others from their original economic or legal meanings. In this dictionary of law and economics, Francesco Parisi provides a comprehensive and concise guide to the language and key concepts underlying this fecund interdisciplinary tradition. The first reference work of its kind, it will prove to be an invaluable resource for professionals, students and scholars.
Acoustic streaming: an arbitrary Lagrangian–Eulerian perspective
Authors: Nama Nitesh , Huang Tony Jun , Costanzo Francesco
Published: July 2017

We analyse acoustic streaming flows using an arbitrary Lagrangian Eulerian (ALE) perspective. The formulation stems from an explicit separation of time scales resulting in two subproblems: a first-order problem, formulated in terms of the fluid displacement at the fast scale, and a second-order problem, formulated in terms of the Lagrangian flow velocity at the slow time scale. Following a rigorous time-averaging procedure, the second-order problem is shown to be intrinsically steady, and with exact boundary conditions at the oscillating walls. Also, as the second-order problem is solved directly for the Lagrangian velocity, the formulation does not need to employ the notion of Stokes drift, or any associated post-processing, thus facilitating a direct comparison with experiments. Because the first-order problem is formulated in terms of the displacement field, our formulation is directly applicable to more complex fluid–structure interaction problems in microacoustofluidic devices. After the formulation’s exposition, we present numerical results that illustrate the advantages of the formulation with respect to current approaches.
Cellular flow in a partially filled rotating drum: regular and chaotic advection
Authors: Romanò Francesco , Hajisharifi Arash , Kuhlmann Hendrik C.
Published: July 2017

The topology of the incompressible steady three-dimensional flow in a partially filled cylindrical rotating drum, infinitely extended along its axis, is investigated numerically for a ratio of pool depth to radius of 0.2. In the limit of vanishing Froude and capillary numbers, the liquid–gas interface remains flat and the two-dimensional flow becomes unstable to steady three-dimensional convection cells. The Lagrangian transport in the cellular flow is organised by periodic spiralling-in and spiralling-out saddle foci, and by saddle limit cycles. Chaotic advection is caused by a breakup of a degenerate heteroclinic connection between the two saddle foci when the flow becomes three-dimensional. On increasing the Reynolds number, chaotic streamlines invade the cells from the cell boundary and from the interior along the broken heteroclinic connection. This trend is made evident by computing the Kolmogorov–Arnold–Moser tori for five supercritical Reynolds numbers.
Flow control with rotating cylinders
Authors: Schulmeister James C. , Dahl J. M. , Weymouth G. D. , Triantafyllou M. S.
Published: July 2017

We study the use of small counter-rotating cylinders to control the streaming flow past a larger main cylinder for drag reduction. In a water tunnel experiment at a Reynolds number of 47 000 with a three-dimensional and turbulent wake, particle image velocimetry (PIV) measurements show that rotating cylinders narrow the mean wake and shorten the recirculation length. The drag of the main cylinder was measured to reduce by up to 45 %. To examine the physical mechanism of the flow control in detail, a series of two-dimensional numerical simulations at a Reynolds number equal to 500 were conducted. These simulations investigated a range of control cylinder diameters in addition to rotation rates and gaps to the main cylinder. Effectively controlled simulated flows present a streamline that separates from the main cylinder, passes around the control cylinder, and reattaches to the main cylinder at a higher pressure. The computed pressure recovery from the separation to reattachment points collapses with respect to a new scaling, which indicates that the control mechanism is viscous.
Turbulent thermal convection over rough plates with varying roughness geometries
Authors: Xie Yi-Chao , Xia Ke-Qing
Published: July 2017

We present a systematic investigation of the effects of roughness geometry on turbulent Rayleigh–Bénard convection (RBC) over rough plates with pyramid-shaped and periodically distributed roughness elements. Using a parameter $\unicode[STIX]{x1D706}$ defined as the height of a roughness element over its base width, the heat transport, the flow dynamics and the local temperatures are measured for the Rayleigh number range $7.50\times 10^{7}\leqslant Ra\leqslant 1.31\times 10^{11}$ and Prandtl numbers $Pr$ from 3.57 to 23.34 at four values of $\unicode[STIX]{x1D706}$ (0.5, 1.0, 1.9 and 4.0). It is found that the heat transport scaling, i.e. $Nu\sim Ra^{\unicode[STIX]{x1D6FC}}$ where $Nu$ is the Nusselt number, may be classified into three regimes in turbulent RBC over rough plates. In Regime I, the system is in a dynamically smooth state. The heat transport scaling is the same as that in a smooth cell. In Regimes II and III, the heat transport is enhanced. When $\unicode[STIX]{x1D706}$ is increased from 0.5 to 4.0, $\unicode[STIX]{x1D6FC}$ increases from 0.36 to 0.59 in Regime II and it increases from 0.30 to 0.50 in Regime III. The experiment thus clearly demonstrates that the heat transport scaling in turbulent RBC can be manipulated using $\unicode[STIX]{x1D706}$ in the heat transport enhanced regime. Previous studies suggest that the transition to heat transport enhanced regime, i.e. from Regime I to Regime II, occurs when the thermal boundary layer (BL) thickness becomes smaller than the roughness height. Direct measurements of the viscous BL in the present study suggest that the transition from Regime II to Regime III is likely a result of the viscous BL thickness becoming smaller than the roughness height. The scaling exponent of the Reynolds number $Re$ with respect to $Ra$ changes from 0.471 to 0.551 when $\unicode[STIX]{x1D706}$ is increased from 0.5 to 4.0, suggesting a change of the dynamics of the large-scale circulation. Interestingly, the transition from Regime II to Regime III in terms of the heat transport scaling is not reflected in the $Re$ scaling with $Ra$. It is also found that increasing $\unicode[STIX]{x1D706}$ increases the clustering of thermal plumes which effectively increases the plume lifetime. This leads to a great increase in the probability of observing large temperature fluctuations in the bulk flow, which corresponds to the formation of more coherent plumes or plume clusters that are ultimately responsible for the enhanced heat transport.
A one-dimensional model for tidal array design based on three-scale dynamics
Authors: Gupta Vikrant , Young Anna M.
Published: July 2017

In order to make the extraction of tidal current energy economically viable, the power production per turbine must be optimised in each tidal array. Furthermore, the impact of power extraction on the marine flow environment must be understood. These two aims mean that designers must be able to model different configurations of a tidal array in order to create the most efficient, least invasive arrangement. In this paper, an analytical model is developed for array design in idealised rectangular tidal channels with idealised turbines. The model includes the effects of (i) local blockage, (ii) surface deformation and (iii) added drag due to the installation of the array. While these effects have been accounted for individually in past work, the model presented here is the first to include all three such that the interaction between different effects can be understood. Results are presented for optimal local blockage and turbine resistance as functions of inherent channel drag coefficient, channel length and Froude number at various global blockage values. It will be shown that it is necessary to model the effects of local blockage and added drag simultaneously in order to obtain the design parameters of a tidal array (global blockage, local blockage and turbine resistance), which will maximise the power extraction per turbine. Neglecting either effect will lead to an array design with lower power extraction than the optimum, the addition of unnecessary extra turbines and higher lost power from the array.
The Sadovskii vortex in strain
Authors: Freilich Daniel V. , Llewellyn Smith Stefan G.
Published: July 2017

The point vortex is the simplest model of a two-dimensional vortex with non-zero circulation. The limitations introduced by its lack of core structure have been remedied by using desingularizations such as vortex patches and vortex sheets. We investigate steady states of the Sadovskii vortex in strain, a canonical model for a vortex in a general flow. The Sadovskii vortex is a uniform patch of vorticity surrounded by a vortex sheet. We recover previously known limiting cases of the vortex patch and hollow vortex, and examine the bifurcations away from these families. The result is a solution manifold spanned by two parameters. The addition of the vortex sheet to the vortex patch solutions immediately leads to splits in the solution manifold at certain bifurcation points. The more circular elliptical family remains attached to the family with a single pinch-off, and this family extends all the way to the simpler solution branch for the pure vortex sheet solutions. More elongated families below this one also split at bifurcation points, but these families do not exist in the vortex sheet limit.
Small-scale dynamics of dense gas compressible homogeneous isotropic turbulence
Authors: Sciacovelli L. , Cinnella P. , Grasso F.
Published: July 2017

The present paper investigates the influence of dense gases governed by complex equations of state on the dynamics of homogeneous isotropic turbulence. In particular, we investigate how differences due to the complex thermodynamic behaviour and transport properties affect the small-scale structures, viscous dissipation and enstrophy generation. To this end, we carry out direct numerical simulations of the compressible Navier–Stokes equations supplemented by advanced dense gas constitutive models. The dense gas considered in the study is a heavy fluorocarbon (PP11) that is shown to exhibit an inversion zone (i.e. a region where the fundamental derivative of gas dynamics $\unicode[STIX]{x1D6E4}$ is negative) in its vapour phase, for pressures and temperatures of the order of magnitude of the critical ones. Simulations are carried out at various initial turbulent Mach numbers and for two different initial thermodynamic states, one immediately outside and the other inside the inversion zone. After investigating the influence of dense gas effects on the time evolution of mean turbulence properties, we focus on the statistical properties of turbulent structures. For that purpose we carry out an analysis in the plane of the second and third invariant of the deviatoric strain-rate tensor. The analysis shows a weakening of compressive structures and an enhancement of expanding ones. Strong expansion regions are found to be mostly populated by non-focal convergence structures typical of strong compression regions, in contrast with the perfect gas that is dominated by eddy-like structures. Additionally, the contribution of non-focal expanding structures to the dilatational dissipation is comparable to that of compressed structures. This is due to the occurrence of steep expansion fronts and possibly of expansion shocklets which contribute to enstrophy generation in strong expansion regions and that counterbalance enstrophy destruction by means of the eddy-like structures.
Size segregation of intruders in perpetual granular avalanches
Authors: Marks Benjy , Eriksen Jon Alm , Dumazer Guillaume , Sandnes Bjørnar , Måløy Knut Jørgen
Published: July 2017

Granular flows such as landslides, debris flows and avalanches are systems of particles with a large range of particle sizes that typically segregate while flowing. The physical mechanisms responsible for this process, however, are still poorly understood, and there is no predictive framework for ascertaining the segregation behaviour of a given system of particles. Here, we provide experimental evidence of individual large intruder particles being attracted to a fixed point in a dry two-dimensional flow of particles of otherwise uniform size. A continuum theory is proposed which captures this effect using only a single fitting parameter that describes the rate of segregation, given knowledge of the bulk flow field. Predictions of the continuum theory are compared with the experimental findings, both for the typical location and velocity field of a range of intruder sizes. For large intruder particle sizes, the continuum model successfully predicts that a fixed point attractor will form, where intruders are drawn to a single location.
Working Memory Interventions With Children: Classrooms or Computers?
Authors: Colmar Susan , Double Kit
Published: July 2017

The importance of working memory to classroom functioning and academic outcomes has led to the development of many interventions designed to enhance students’ working memory. In this article we briefly review the evidence for the relative effectiveness of classroom and computerised working memory interventions in bringing about measurable and sustainable benefits to students’ working memory, classroom engagement, and academic performance. Although there is considerable evidence that working memory is significantly linked to academic achievement, virtually no research has been undertaken within the classroom context, nor has the research had an intervention focus, nor has any research involved students themselves. Although there is a large amount of research on computerised working memory training programs, the evidence confirms that such programs rarely provide transferable or sustainable benefits to students’ working memory, classroom functioning, or academic performance. Positive evidence is provided for one classroom intervention specifically designed for personal and independent use by students, with their teachers’ support. Recommendations for classroom practice and directions for further research combining classrooms and computer interventions are discussed.
EXAMINING CHRONOLOGICAL TRENDS IN ANCIENT MAYA DIET AT MINANHA, BELIZE, USING THE STABLE ISOTOPES OF CARBON AND NITROGEN
Authors: Williams Jocelyn S. , Stronge Shannen M. , Iannone Gyles , Longstaffe Fred J.
Published: July 2017

We present the results of stable carbon and nitrogen isotope analyses of bone collagen and bone bioapatite from the ancient Maya center of Minanha, Belize (ca. 100 B.C. to A.D. 1260). The purpose of this research was to reconstruct diet and investigate the influence of sociopolitical and environmental factors. Overall, diet was relatively stable over time, with maize being a staple in all periods. Maize consumption reached its peak in the transitional Early to Middle Classic periods and decreased over time. When isotope data from dry periods were compared to normal periods, there were no significant differences, although comparisons of isotope data by burial location and type suggest that the apical or ruling elite consumed a more diverse diet, with more animal protein, relative to the lesser elites. The temporal variability in maize consumption seems best explained by sociopolitical factors documented at Minanha and within the Vaca Plateau. This study demonstrates the resilience of ancient subsistence practices in the face of climatic instability and highlights the impact that social and political factors can have on diet and subsistence economy.
SHAPING PRECOLONIAL CONCEPTS IN THE ANDES: THEUSHNUFOR LLOCLLAYHUANCUPA (HUAROCHIRÍ, LIMA)
Authors: Ramón Gabriel
Published: July 2017

In precolonial Andean archaeology, specialists frequently deal with objects whose names and functions are unknown. Similarly, early colonial documents from the Andes often mention objects without describing their shapes or functions. How can we articulate these three features—names, shapes, and functions—for objects from precolonial and colonial periods? How can we define these objects while taking into account intra-Andean variability? This article addresses these questions using one section from a well-known document of the early seventeenth century, the Huarochirí Manuscript. This section includes a term extensively discussed in Andean archaeology:husnoorushnu, which has been translated and described in various ways by diverse scholars. Through analysis of the function, form, and translation of the Quechua termushnu, I explore a typological approach to articulate names, shapes, and functions and also propose a redefinition of the concept itself.
Loud ethics and quiet morality among Muslim healers in Eastern Africa
Authors: Parkin David
Published: July 2017

The professional ethics of biomedicine in Eastern Africa are usually sharply distinguished from the everyday moral concerns of patients, who may interpret healthcare treatment differently from their doctors. Biomedical doctors’ pronouncements adhere to the ethical demands of formal training, while ordinary people form their own moral ideas about biomedicine, with the two discourses meeting only during medical-moral crises. The voice of biomedicine, therefore, is metaphorically loud compared with that of everyday talk. This hegemonic duality of biomedicine is less evident in traditional Islamic healing, where patients sometimes negotiate the moral implications of sickness with their healers, and where Islamic medical ethics may be transmitted to younger apprentices interpersonally through life histories and narrative. The differences in volume between healers’ and patients’ moral voices are thus less pronounced, though not absent. Nevertheless, both are subject to the higher authority of Islam, whose holy texts and clerics are the final arbiters of the symptoms, cause and consequences of sickness. It is speculated that the emerging power, influence and stronger voice of radical Wahhabism could create a hegemonic medical ethical duality based more strictly than at present on religiously prescribed practice.
Adult attachment and paranoia: an experimental investigation
Authors: Hutton Jane , Ellett Lyn , Berry Katherine
Published: July 2017

Attachment theory may develop understanding of the occurrence and maintenance of persecutory delusions. This study investigates the role of dispositional attachment and contextually primed secure base attachment representations in the occurrence of paranoid thinking. Sixty participants were randomly allocated to one of three conditions: a secure attachment priming condition, a positive affect condition, or a neutral control condition. Following priming, all participants were exposed to a paranoia induction. State paranoia was measured at baseline and following the paranoia induction. Dispositional insecure attachment was associated with both trait and state paranoid thinking. Contrary to predictions, the secure attachment prime did not appear to buffer paranoid thinking and had a negative impact for participants with high levels of attachment anxiety, highlighting the potentially aversive effects of exposure to secure attachment material in those with existing insecure attachment styles.
A Diagnostic Assay to Detect Herbicide Resistance in Annual Bluegrass (Poa annua)
Authors: Brosnan James T. , Vargas Jose J. , Reasor Eric H. , Viggiani Roberto , Breeden Gregory K. , Zobel John M.
Published: July 2017

Turfgrass managers currently have few readily available means of evaluating herbicide resistance in annual bluegrass during the growing season. Research was conducted to determine if agar-based diagnostic tests developed for agronomic weeds could be used to reliably confirm herbicide resistance in annual bluegrass harvested from golf course turf. Annual bluegrass phenotypes with target-site resistance to acetolactate synthase (ALS; R3, R7), enolpyruvylshikimate-3-phosphate synthase (EPSPS; R5), and photosystem II (PSII; R3, R4) inhibiting herbicides were included in experiments along with an herbicidal susceptible phenotype (S). Single tiller plants were washed free of soil and transplanted into autoclavable polycarbonate plant culture boxes filled with plant tissue culture agar amended with a murashigee-skoog medium and trifloxysulfuron (6.25, 12.5, 25, 50, 75, 100, or 150 μM), glyphosate (0, 6, 12, 25, 50, 100, 200, or 400 μM), or simazine (0, 6, 12, 25, 50, 100, 200, or 400 μM). Mortality in agar was assessed 7 to 10 days after treatment (depending on herbicide) and compared to responses observed after treating individual plants of each phenotype with trifloxysulfuron (28 g ai ha-1), glyphosate (1120 g ae ha-1), or simazine (1120 g ai ha-1) in an enclosed spray chamber. Fisher’s exact test (α = 0.05) determined that mortality in agar with 12.5 μM trifloxysulfuron and 100 μM glyphosate was not significantly different than treating whole plants via traditional spray application. Mortality with all concentrations of simazine in agar was significantly different than that observed after treating resistant and susceptible phenotypes via traditional spray application. Our findings indicate that an agar-based diagnostic assay can be used to detect annual bluegrass resistance to ALS- or EPSPS-inhibiting herbicides in less than 10 days; however, additional research is needed to refine this assay for use with PSII-inhibiting herbicides.
RETRACTED ARTICLE: Inhibition of microRNA-214 promotes epithelial–mesenchymal transition process and induces interstitial cystitis in postmenopausal women by upregulating Mfn2
Authors: Lv Jian-Wei , Wen Wei , Jiang Chen , Fu Qi-Bo , Gu Yin-Jun , Lv Ting-Ting , Li Zhen-Dong , Xue Wei
Published: July 2017

Our study aims to investigate the roles that microRNA-214 (miR-214) plays in the epithelial mesenchymal transition (EMT) process and the development of interstitial cystitis (IC) in postmenopausal women by targeting Mitofusin 2 (Mfn2). IC bladder tissues and adjacent normal bladder tissues were collected from postmenopausal women. Immunohistochemistry (IHC) staining was conducted. The target relationship between miR-214 and Mfn2 was determined by a dual luciferase reporter gene assay. Adipose-derived mesenchymal stem cells (ADMSCs) were extracted from postmenopausal rats and assigned to the blank, mimics, miR-214 inhibitors, mimics negative control (NC), inhibitors NC, Mfn2 siRNA, miR-214 inhibitors and Mfn2 siRNA groups. Exosomes secreted by transfected ADMSCs were instilled into the bladders of postmenopausal rats. The expression of miR-214 and Mfn2 mRNA and EMT markers was assessed by qRT-PCR and western blotting. It was confirmed that Mfn2 was the target gene of miR-214 in IC. Compared with the normal bladder tissues, miR-214 decreased, but Mfn2 increased in IC bladder tissues. Compared with the blank group, the expression of miR-214 and the expression levels of N-cadherin, Fibronectin, Twist1, Snail and Vimentin mRNA and protein increased, whereas the expression levels of Mfn2, E-cadherin and ZO-1 mRNA and protein decreased in the miR-214 mimics and Mfn2 groups. The expression of MiR-214 and the expression levels of N-cadherin, Fibronectin, Twist1, Snail and Vimentin mRNA and protein decreased, whereas the expression levels of Mfn2, E-cadherin and ZO-1 mRNA and protein increased in the miR-214 inhibitors group. Our findings indicate that the inhibition of miR-214 promotes the EMT process and contributes to bladder wall fibrosis by up-regulating Mfn2, thus leading to the occurrence of IC in postmenopausal women.
Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology
Authors: Marine Rachel L , Nasko Daniel J , Wray Jeffrey , Polson Shawn W , Wommack K Eric
Published: July 2017

Chaperonins are protein-folding machinery found in all cellular life. Chaperonin genes have been documented within a few viruses, yet, surprisingly, analysis of metagenome sequence data indicated that chaperonin-carrying viruses are common and geographically widespread in marine ecosystems. Also unexpected was the discovery of viral chaperonin sequences related to thermosome proteins of archaea, indicating the presence of virioplankton populations infecting marine archaeal hosts. Virioplankton large subunit chaperonin sequences (GroELs) were divergent from bacterial sequences, indicating that viruses have carried this gene over long evolutionary time. Analysis of viral metagenome contigs indicated that: the order of large and small subunit genes was linked to the phylogeny of GroEL; both lytic and temperate phages may carry group I chaperonin genes; and viruses carrying a GroEL gene likely have large double-stranded DNA (dsDNA) genomes (>70 kb). Given these connections, it is likely that chaperonins are critical to the biology and ecology of virioplankton populations that carry these genes. Moreover, these discoveries raise the intriguing possibility that viral chaperonins may more broadly alter the structure and function of viral and cellular proteins in infected host cells.
Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor
Authors: Parada Alma E , Fuhrman Jed A
Published: July 2017

Marine archaea are critical contributors to global carbon and nitrogen redox cycles, but their temporal variability and microbial associations across the water column are poorly known. We evaluated seasonal variability of free living (0.2–1 μm size fraction) Thaumarchaea Marine Group I (MGI) and Euryarchaea Marine Group II (MGII) communities and their associations with the microbial community from surface to seafloor (890 m) over 5 years by 16S rRNA V4-V5 gene sequencing. MGI and MGII communities demonstrated distinct compositions at different depths, and seasonality at all depths. Microbial association networks at 150 m, 500 m and 890 m, revealed diverse assemblages of MGI (presumed ammonia oxidizers) and Nitrospina taxa (presumed dominant nitrite oxidizers, completing the nitrification process), suggesting distinct MGI-Nitrospina OTUs are responsible for nitrification at different depths and seasons, and depth- related and seasonal variability in nitrification could be affected by alternating MGI-Nitrospina assemblages. MGII taxa also showed distinct correlations to possibly heterotrophic bacteria, most commonly to members of Marine Group A, Chloroflexi, Marine Group B, and SAR86. Thus, both MGI and MGII likely have dynamic associations with bacteria based on similarities in activity or other interactions that select for distinct microbial assemblages over time. The importance of MGII taxa as members of the heterotrophic community previously reported for photic zone appears to apply throughout the water column.
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation
Authors: Svartström Olov , Alneberg Johannes , Terrapon Nicolas , Lombard Vincent , de Bruijn Ino , Malmsten Jonas , Dalin Ann-Marie , EL Muller Emilie , Shah Pranjul , Wilmes Paul , Henrissat Bernard , Aspeborg Henrik , Andersson Anders F
Published: July 2017

The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.
Uncultivated microbes in need of their own taxonomy
Authors: Konstantinidis Konstantinos T , Rosselló-Móra Ramon , Amann Rudolf
Published: July 2017

The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms. In order to fully realize this potential, standards and guidelines on how to perform these descriptions are needed. Here we aimed to outline these standards and draw the roadmap for a new genome-based taxonomy that, at least initially, would be parallel but highly convergent to the one in existence for isolates. In particular, we recommend the use of DNA genome sequences, recovered by population binning or single-cell techniques, as the basis for (i) identification and phylogenetic placement, (ii) bioinformatics-based functional and thus phenotypic predictions, as well as (iii) type material. We also recommend the implementation of an independent nomenclatural system for uncultivated taxa, following the same nomenclature rules as those for cultured Bacteria and Archaea but with its own list of validly published names. If widely adopted, this system will not only facilitate a comprehensive characterization of the ‘uncultivated majority’, but also provide a unified catalogue of validly published names, thereby avoiding synonyms and confusion. We also suggest that a committee of experts, supported by an international microbiological society, should be formed to govern the new classification system.
A genomic perspective on stoichiometric regulation of soil carbon cycling
Authors: Hartman Wyatt H , Ye Rongzhong , Horwath William R , Tringe Susannah G
Published: July 2017

Similar to plant growth, soil carbon (C) cycling is constrained by the availability of nitrogen (N) and phosphorus (P). We hypothesized that stoichiometric control over soil microbial C cycling may be shaped by functional guilds with distinct nutrient substrate preferences. Across a series of rice fields spanning 5–25% soil C (N:P from 1:12 to 1:70), C turnover was best correlated with P availability and increased with experimental N addition only in lower C (mineral) soils with N:P⩽16. Microbial community membership also varied with soil stoichiometry but not with N addition. Shotgun metagenome data revealed changes in community functions with increasing C turnover, including a shift from aromatic C to carbohydrate utilization accompanied by lower N uptake and P scavenging. Similar patterns of C, N and P acquisition, along with higher ribosomal RNA operon copy numbers, distinguished that microbial taxa positively correlated with C turnover. Considering such tradeoffs in genomic resource allocation patterns among taxa strengthened correlations between microbial community composition and C cycling, suggesting simplified guilds amenable to ecosystem modeling. Our results suggest that patterns of soil C turnover may reflect community-dependent metabolic shifts driven by resource allocation strategies, analogous to growth rate–stoichiometry coupling in animal and plant communities.
Bacterial transcriptome remodeling during sequential co-culture with a marine dinoflagellate and diatom
Authors: Landa Marine , Burns Andrew S , Roth Selena J , Moran Mary Ann
Published: July 2017

In their role as primary producers, marine phytoplankton modulate heterotrophic bacterial activities through differences in the types and amounts of organic matter they release. This study investigates the transcriptional response of bacterium Ruegeria pomeroyi, a member of the Roseobacter clade known to affiliate with diverse phytoplankton groups in the ocean, during a shift in phytoplankton taxonomy. The bacterium was initially introduced into a culture of the dinoflagellate Alexandrium tamarense, and then experienced a change in phytoplankton community composition as the diatom Thalassiosira pseudonana gradually outcompeted the dinoflagellate. Samples were taken throughout the 30-day experiment to track shifts in bacterial gene expression informative of metabolic and ecological interactions. Transcriptome data indicate fundamental differences in the exometabolites released by the two phytoplankton. During growth with the dinoflagellate, gene expression patterns indicated that the main sources of carbon and energy for R. pomeroyi were dimethysulfoniopropionate (DMSP), taurine, methylated amines, and polyamines. During growth with the diatom, dihydroxypropanesulfonate (DHPS), xylose, ectoine, and glycolate instead appeared to fuel the bulk of bacterial metabolism. Expression patterns of genes for quorum sensing, gene transfer agent, and motility suggest that bacterial processes related to cell communication and signaling differed depending on which phytoplankton species dominated the co-culture. A remodeling of the R. pomeroyi transcriptome implicating more than a quarter of the genome occurred through the change in phytoplankton regime.
Genetic and neuronal mechanisms governing the sex-specific interaction between sleep and sexual behaviors in Drosophila
Authors: Chen Dandan , Sitaraman Divya , Chen Nan , Jin Xin , Han Caihong , Chen Jie , Sun Mengshi , Baker Bruce S. , Nitabach Michael N. , Pan Yufeng
Published: July 2017

Animals execute one particular behavior among many others in a context-dependent manner, yet the mechanisms underlying such behavioral choice remain poorly understood. Here we studied how two fundamental behaviors, sex and sleep, interact at genetic and neuronal levels in Drosophila. We show that an increased need for sleep inhibits male sexual behavior by decreasing the activity of the male-specific P1 neurons that coexpress the sex determination genes fru
M
and dsx, but does not affect female sexual behavior. Further, we delineate a sex-specific neuronal circuit wherein the P1 neurons encoding increased courtship drive suppressed male sleep by forming mutually excitatory connections with the fru
M
-positive sleep-controlling DN1 neurons. In addition, we find that FRUM regulates male courtship and sleep through distinct neural substrates. These studies reveal the genetic and neuronal basis underlying the sex-specific interaction between sleep and sexual behaviors in Drosophila, and provide insights into how competing behaviors are co-regulated.
Carbon stocks and changes of dead organic matter in China's forests
Authors: Zhu Jianxiao , Hu Huifeng , Tao Shengli , Chi Xiulian , Li Peng , Jiang Lai , Ji Chengjun , Zhu Jiangling , Tang Zhiyao , Pan Yude , Birdsey Richard A. , He Xinhua , Fang Jingyun
Published: July 2017

Forests play an important role in global carbon cycles. However, the lack of available information on carbon stocks in dead organic matter, including woody debris and litter, reduces the reliability of assessing the carbon cycles in entire forest ecosystems. Here we estimate that the national DOM carbon stock in the period of 2004–2008 is 925 ± 54 Tg, with an average density of 5.95 ± 0.35 Mg C ha−1. Over the past two decades from periods of 1984−1988 to 2004−2008, the national dead organic matter carbon stock has increased by 6.7 ± 2.2 Tg carbon per year, primarily due to increasing forest area. Temperature and precipitation increase the carbon density of woody debris, but decrease that of litter. Additionally, the woody debris increases significantly with above ground biomass and forest age. Our results can improve estimates of the carbon budget in China's forests and for better understanding of effects of climate and stand characteristics on dead organic matter distribution.
Afferent specific role of NMDA receptors for the circuit integration of hippocampal neurogliaform cells
Authors: Chittajallu R. , Wester J. C. , Craig M. T. , Barksdale E. , Yuan X. Q. , Akgül G. , Fang C. , Collins D. , Hunt S. , Pelkey K. A. , McBain C. J.
Published: July 2017

Appropriate integration of GABAergic interneurons into nascent cortical circuits is critical for ensuring normal information processing within the brain. Network and cognitive deficits associated with neurological disorders, such as schizophrenia, that result from NMDA receptor-hypofunction have been mainly attributed to dysfunction of parvalbumin-expressing interneurons that paradoxically express low levels of synaptic NMDA receptors. Here, we reveal that throughout postnatal development, thalamic, and entorhinal cortical inputs onto hippocampal neurogliaform cells are characterized by a large NMDA receptor-mediated component. This NMDA receptor-signaling is prerequisite for developmental programs ultimately responsible for the appropriate long-range AMPAR-mediated recruitment of neurogliaform cells. In contrast, AMPAR-mediated input at local Schaffer-collateral synapses on neurogliaform cells remains normal following NMDA receptor-ablation. These afferent specific deficits potentially impact neurogliaform cell mediated inhibition within the hippocampus and our findings reveal circuit loci implicating this relatively understudied interneuron subtype in the etiology of neurodevelopmental disorders characterized by NMDA receptor-hypofunction.
Cognitive behavioral therapy for insomnia in Parkinson’s disease: a case series
Authors: Humbert Meghan , Findley James , Hernandez-Con Maria , Chahine Lana M.
Published: July 2017

Chronic insomnia is common in patients with Parkinson’s disease. There are limited data to guide its treatment in this patient population, especially in regards to non-pharmacologic interventions, some of which are highly effective in the non-Parkinson’s disease population. The aim of this study is to describe a series of Parkinson’s disease patients who underwent cognitive behavioral therapy for insomnia (CBTi). Parkinson’s disease patients who had undergone a baseline and at least one follow-up CBTi session were identified. Electronic medical records and pre-treatment and post-treatment patient sleep diaries were reviewed. Sleep measures of interest included wake time after sleep onset, sleep efficiency, sleep onset latency, and total sleep time. Pre-treatment and post-treatment values were compared within subjects using paired t-test. Five patients were included. Patients attended an average of eight sessions of CBTi (range 5–12). Significant increases in sleep efficiency (p = 0.02) and decreases in number of awakenings per night (p = 0.02) were found. Our data provide preliminary evidence that cognitive behavioral therapy is an effective treatment for insomnia in Parkinson’s disease, and is well tolerated and well received by patients. Given the limited data supporting use of medications to treat chronic insomnia in Parkinson’s disease, combined with their risks, randomized trials to demonstrate the efficacy of CBTi in Parkinson’s disease are warranted.
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-Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems
Authors: Asmus Josefine , Müller Christian L. , Sbalzarini Ivo F.
Published: July 2017

The design of systems or models that work robustly under uncertainty and environmental fluctuations is a key challenge in both engineering and science. This is formalized in the design-centering problem, which is defined as finding a design that fulfills given specifications and has a high probability of still doing so if the system parameters or the specifications fluctuate randomly. Design centering is often accompanied by the problem of quantifying the robustness of a system. Here we present a novel adaptive statistical method to simultaneously address both problems. Our method, L
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-Adaptation, is inspired by the evolution of robustness in biological systems and by randomized schemes for convex volume computation. It is able to address both problems in the general, non-convex case and at low computational cost. We describe the concept and the algorithm, test it on known benchmarks, and demonstrate its real-world applicability in electronic and biological systems. In all cases, the present method outperforms the previous state of the art. This enables re-formulating optimization problems in engineering and biology as design centering problems, taking global system robustness into account.
Lower Cretaceous fossils from China shed light on the ancestral body plan of crown softshell turtles (Trionychidae, Cryptodira)
Authors: Brinkman Donald , Rabi Márton , Zhao Lijun
Published: July 2017

Pan-trionychids or softshell turtles are a highly specialized and widespread extant group of aquatic taxa with an evolutionary history that goes back to the Early Cretaceous. The earliest pan-trionychids had already fully developed the “classic” softshell turtle morphology and it has been impossible to resolve whether they are stem members of the family or are within the crown. This has hindered our understanding of the evolution of the two basic body plans of crown-trionychids. Thus it remains unclear whether the more heavily ossified shell of the cyclanorbines or the highly reduced trionychine morphotype is the ancestral condition for softshell turtles. A new pan-trionychid from the Early Cretaceous of Zhejiang, China,Perochelys hengshanensissp. nov., allows a revision of softshell-turtle phylogeny. Equal character weighting resulted in a topology that is fundamentally inconsistent with molecular divergence date estimates of deeply nested extant species. In contrast, implied weighting retrieved Lower Cretaceous Perochelysspp. andPetrochelys kyrgyzensisas stem trionychids, which is fully consistent with their basal stratigraphic occurrence and an Aptian-Santonian molecular age estimate for crown-trionychids. These results indicate that the primitive morphology for soft-shell turtles is a poorly ossified shell like that of crown-trionychines and that shell re-ossification in cyclanorbines (including re-acquisition of peripheral elements) is secondary.
Action-based Modeling of Complex Networks
Authors: Arora Viplove , Ventresca Mario
Published: July 2017

Complex networks can model a wide range of complex systems in nature and society, and many algorithms (network generators) capable of synthesizing networks with few and very specific structural characteristics (degree distribution, average path length, etc.) have been developed. However, there remains a significant lack of generators capable of synthesizing networks with strong resemblance to those observed in the real-world, which can subsequently be used as a null model, or to perform tasks such as extrapolation, compression and control. In this paper, a robust new approach we term Action-based Modeling is presented that creates a compact probabilistic model of a given target network, which can then be used to synthesize networks of arbitrary size. Statistical comparison to existing network generators is performed and results show that the performance of our approach is comparable to the current state-of-the-art methods on a variety of network measures, while also yielding easily interpretable generators. Additionally, the action-based approach described herein allows the user to consider an arbitrarily large set of structural characteristics during the generator design process.
Minimal hepatic encephalopathy is associated with expansion and activation of CD4+CD28−, Th22 and Tfh and B lymphocytes
Authors: Mangas-Losada Alba , García-García Raquel , Urios Amparo , Escudero-García Desamparados , Tosca Joan , Giner-Durán Remedios , Serra Miguel Angel , Montoliu Carmina , Felipo Vicente
Published: July 2017

Peripheral inflammation acts synergistically with hyperammonemia in inducing neurological alterations in cirrhotic patients with minimal hepatic encephalopathy (MHE). We hypothesized that appearance of MHE would be associated to some specific qualitative change in peripheral inflammation. The aim of this work was to characterize the changes in peripheral inflammation associated to appearance of MHE. We analyzed it by immunophenotyping and cytokine profile analysis, in cirrhotic patients without or with MHE and controls. The main alterations associated specifically with MHE are: 1) increased activation of all subtypes of CD4+T-lymphocytes, with the increased expression of CD69; 2) increased amount of CD4+CD28−T lymphocytes, associated with increased levels of CX3CL1 and of IL-15; 3) increased differentiation of CD4+T lymphocytes to Th follicular and Th22; 4) increased activation of B lymphocytes and serum IgG. This study has identified some specific alterations of the immune system associated with appearance of the neurological alterations in MHE patients.
Hobit expression by a subset of human liver-resident CD56bright Natural Killer cells
Authors: Lunemann Sebastian , Martrus Gloria , Goebels Hanna , Kautz Tobias , Langeneckert Annika , Salzberger Wilhelm , Koch Martina , J. Bunders Madeleine , Nashan Björn , van Gisbergen Klaas P. J. M. , Altfeld Marcus
Published: July 2017

Immune responses show a high degree of tissue specificity shaped by factors influencing tissue egress and retention of immune cells. The transcription factor Hobit was recently shown to regulate tissue-residency in mice. Whether Hobit acts in a similar capacity in humans remains unknown. Our aim was to assess the expression and contribution of Hobit to tissue-residency of Natural Killer (NK) cells in the human liver. The human liver was enriched for CD56brightNK cells showing increased expression levels of the transcription factor Hobit. HobitposCD56brightNK cells in the liver exhibited high levels of CD49a, CXCR6 and CD69. HobitposCD56brightNK cells in the liver furthermore expressed a unique set of transcription factors with higher frequencies and levels of T-bet and Blimp-1 when compared to HobitnegCD56brightNK cells. Taken together, we show that the transcription factor Hobit identifies a subset of NK cells in human livers that express a distinct set of adhesion molecules and chemokine receptors consistent with tissue residency. These data suggest that Hobit is involved in regulating tissue-residency of human intrahepatic CD56brightNK cells in a subset of NK cells in inflamed livers.