bluuebunny/crossref_metadata_2025 huggingface dataset:
Pyrroloquinoline Quinone Ethanol Dehydrogenase in Methylobacterium extorquens AM1 Extends Lanthanide-Dependent Metabolism to Multicarbon Substrates
Authors: Good Nathan M. , Vu Huong N. , Suriano Carly J. , Subuyuj Gabriel A. , Skovran Elizabeth , Martinez-Gomez N. Cecilia
Published: August 2016

Lanthanides are utilized by microbial methanol dehydrogenases, and it has been proposed that lanthanides may be important for other type I alcohol dehydrogenases. A triple mutant strain (
mxaF xoxF1 xoxF2
; named MDH-3), deficient in the three known methanol dehydrogenases of the model methylotroph
Methylobacterium extorquens
AM1, is able to grow poorly with methanol if exogenous lanthanides are added to the growth medium. When the gene encoding a putative quinoprotein ethanol dehydrogenase,
exaF
, was mutated in the MDH-3 background, the quadruple mutant strain could no longer grow on methanol in minimal medium with added lanthanum (La
3+
). ExaF was purified from cells grown with both calcium (Ca
2+
) and La
3+
and with Ca
2+
only, and the protein species were studied biochemically. Purified ExaF is a 126-kDa homodimer that preferentially binds La
3+
over Ca
2+
in the active site. UV-visible spectroscopy indicates the presence of pyrroloquinoline quinone (PQQ) as a cofactor. ExaF purified from the Ca
2+
-plus-La
3+
condition readily oxidizes ethanol and has secondary activities with formaldehyde, acetaldehyde, and methanol, whereas ExaF purified from the Ca
2+
-only condition has minimal activity with ethanol as the substrate and activity with methanol is not detectable. The
exaF
mutant is not affected for growth with ethanol; however, kinetic and
in vivo
data show that ExaF contributes to ethanol metabolism when La
3+
is present, expanding the role of lanthanides to multicarbon metabolism.

IMPORTANCE
ExaF is the most efficient PQQ-dependent ethanol dehydrogenase reported to date and, to our knowledge, the first non-XoxF-type alcohol oxidation system reported to use lanthanides as a cofactor, expanding the importance of lanthanides in biochemistry and bacterial metabolism beyond methanol dehydrogenases to multicarbon metabolism. These results support an earlier proposal that an aspartate residue near the catalytic aspartate residue may be an indicator of rare-earth element utilization by type I alcohol dehydrogenases.
Interrupting Biosynthesis of O Antigen or the Lipopolysaccharide Core Produces Morphological Defects in Escherichia coli by Sequestering Undecaprenyl Phosphate
Authors: Jorgenson Matthew A. , Young Kevin D.
Published: August 2016

Undecaprenyl phosphate (Und-P) is a member of the family of essential polyprenyl phosphate lipid carriers and in the Gram-negative bacterium
Escherichia coli
is required for synthesizing the peptidoglycan (PG) cell wall, enterobacterial common antigen (ECA), O antigen, and colanic acid. Previously, we found that interruption of ECA biosynthesis indirectly alters PG synthesis by sequestering Und-P via dead-end intermediates, causing morphological defects. To determine if competition for Und-P was a more general phenomenon, we determined if O-antigen intermediates caused similar effects. Indeed, disrupting the synthesis of O antigen or the lipopolysaccharide core oligosaccharide induced cell shape deformities, which were suppressed by preventing the initiation of O-antigen biosynthesis or by manipulating Und-P metabolism. We conclude that accumulation of O-antigen intermediates alters PG synthesis by sequestering Und-P. Importantly, many previous experiments addressed the physiological functions of various oligosaccharides and glycoconjugates, but these studies employed mutants that accumulate deleterious intermediates. Thus, conclusions based on these experiments must be reevaluated to account for possible indirect effects of Und-P sequestration.

IMPORTANCE
Bacteria use long-chain isoprenoids like undecaprenyl phosphate (Und-P) as lipid carriers to assemble numerous glycan polymers that comprise the cell envelope. In any one bacterium, multiple oligosaccharide biosynthetic pathways compete for a common pool of Und-P, which means that disruptions in one pathway may produce secondary consequences that affect the others. Using the Gram-negative bacterium
Escherichia coli
as a model, we demonstrate that interruption of the biogenesis of O antigen, a major outer membrane component, indirectly impairs peptidoglycan synthesis by sequestering Und-P into dead-end intermediates. These results strongly argue that the functions of many Und-P-utilizing pathways must be reevaluated, because much of our current understanding is based on experiments that did not control for these unintended secondary effects.
Growth and nutrition in children with ataxia telangiectasia
Authors: Stewart Emma , Prayle Andrew P , Tooke Alison , Pasalodos Sara , Suri Mohnish , Bush Andy , Bhatt Jayesh M
Published: August 2016

Background

Ataxia telangiectasia (A-T) is a rare multisystem disease with high early mortality from lung disease and cancer. Nutritional failure adversely impacts outcomes in many respiratory diseases. Several factors influence nutrition in children with A-T. We hypothesised that children with A-T have progressive growth failure and that early gastrostomy tube feeding (percutaneous endoscopic gastrostomy, PEG) is a favourable management option with good nutritional outcomes.

Methods

Data were collected prospectively on weight, height and body mass index (BMI) at the national paediatric A-T clinic. Adequacy and safety of oral intake was assessed. Nutritional advice was given at each multidisciplinary review.

Results

101 children (51 girls) had 222 measurements (32 once, 32 twice, 24 thrice) between 2009 and 2016. Median (IQR) age was 9.3 (6.4 to 13.1) years. Mean (SD) weight, height and BMI Z-scores were respectively −1 (1.6), −1.2 (1.2) and −0.4 (1.4). 35/101 children had weight Z-scores below −2 on at least one occasion. Weight, height and BMI Z-scores declined over time. Decline was most obvious after 8 years of age. 14/101 (14%) children had a PEG, with longitudinal data available for 12. In a nested case control study, there was a trend for improvement in weight in those with a PEG (p=0.10).

Conclusions

Patients with A-T decline in growth over time. There is an urgent need for new strategies, including an understanding of why growth falters. We suggest early proactive consideration of PEG from age 8 years onwards to prevent progressive growth failure.
Advanced Endoscopic Ultrasound Management Techniques for Preneoplastic Pancreatic Cystic Lesions
Authors: Arshad Hafiz Muhammad Sharjeel , Bharmal Sheila , Duman Deniz Guney , Liangpunsakul Suthat , Turner Brian G
Published: August 2016

Pancreatic cystic lesions can be benign, premalignant or malignant. The recent increase in detection and tremendous clinical variability of pancreatic cysts has presented a significant therapeutic challenge to physicians. Mucinous cystic neoplasms are of particular interest given their known malignant potential. This review article provides a brief but comprehensive review of premalignant pancreatic cystic lesions with advanced endoscopic ultrasound (EUS) management approaches. A comprehensive literature search was performed using PubMed, Cochrane, OVID and EMBASE databases. Preneoplastic pancreatic cystic lesions include mucinous cystadenoma and intraductal papillary mucinous neoplasm. The 2012 International Sendai Guidelines guide physicians in their management of pancreatic cystic lesions. Some of the advanced EUS management techniques include ethanol ablation, chemotherapeutic (paclitaxel) ablation, radiofrequency ablation and cryotherapy. In future, EUS-guided injections of drug-eluting beads and neodymium:yttrium aluminum agent laser ablation is predicted to be an integral part of EUS-guided management techniques. In summary, International Sendai Consensus Guidelines should be used to make a decision regarding management of pancreatic cystic lesions. Advanced EUS techniques are proving extremely beneficial in management, especially in those patients who are at high surgical risk.
‘Limbitless Solutions’: the Prosthetic Arm, Iron Man and the Science Fiction of Technoscience
Authors: Smith Susan
Published: August 2016

Early last year, a non-profit organisation called ‘Limbitless Solutions’ modelled a 3D printed prosthetic arm on a fighting suit that features in the popular superhero film series,Iron Man(2008–2013). In addition, ‘Limbitless Solutions’ resourcefully deployed the fictional character and inventor of the Iron Man suit, weapons specialist and philanthropist, Tony Stark, played by Robert Downey Jr, in a celebrity/superhero endorsed promotional short film, showing ‘Tony’, the ‘real Iron Man’, gifting the futuristic military styled ‘gauntlet’ to Alex, a 7-year-old boy with a partially developed right arm. Engaging with scholarly work on the science fiction of technoscience, prostheses and the posthuman, and disability and DIY assistive technology, I analyse ‘Limbitless Solutions’ use of science fiction in a high-profile media event that problematically portrays an impaired child ‘in need’ of ‘repair’ and subsequently ‘fixed’ by technology. Overall, the aim is to integrate science fiction tropes, such as the wounded hero, the fighting suit and prosthetic arm, with disability studies, to highlight the sustained challenges that emerging theories of disability and technology face as contemporary economic, political and ideological forces endorse and promote militarised images of cyborg assimilation over human variation and physical difference.
Multi-directional force–displacement response of underground pipe in sand
Authors: Jung Jai K. , O’Rourke Thomas D. , Argyrou Christina
Published: August 2016

A methodology is presented to evaluate multi-directional force–displacement relationships for soil–pipeline interaction analysis and design. Large-scale tests of soil reaction to pipe lateral and uplift movement in dry and partially saturated sand are used to validate plane strain, finite element (FE) soil, and pipe continuum models. The FE models are then used to characterize force versus displacement performance for lateral, vertical upward, vertical downward, and oblique orientations of pipeline movement in soil. Using the force versus displacement relationships, the analytical results for pipeline response to strike-slip fault rupture are shown to compare favorably with the results of large-scale tests in which strike-slip fault movement was imposed on 250 and 400 mm diameter high-density polyethylene pipelines in partially saturated sand. Analytical results normalized with respect to maximum lateral force are provided on 360° plots to predict maximum pipe loads for any movement direction. The resulting methodology and dimensionless plots are applicable for underground pipelines and conduits at any depth, subjected to relative soil movement in any direction in dry or saturated and partially saturated medium to very dense sands.
Hyperfine structure and isotope shifts in Mo II
Authors: Rosner S.D. , Holt R.A.
Published: August 2016

We have applied fast-ion-beam laser-fluorescence spectroscopy to measure the hyperfine structures of seven even-parity and six odd-parity levels in Mo II and the isotope shifts of nine transitions in the wavelength range 424.5–443.4 nm. These are the first measurements of these parameters and almost the first such measurements in Mo II. These atomic data are essential for astrophysical studies of chemical abundances, allowing correction for saturation and the effects of blended lines. They also provide important constraints on stellar diffusion modeling, particularly in chemically peculiar (CP) stars, and serve as valuable input to semi-empirical theoretical models of hyperfine structure and isotope shifts.
K–ϵ model for rotating homogeneous decaying turbulence
Authors: Marzougui Hamed
Published: August 2016

In the present work, we propose a modification to the standard K–ϵ model for simulating homogeneous decaying turbulence subjected to uniform rotation. In this modification, the dissipation rate equation is formulated in terms of the rotation rate Ω, the integral length scales along the axis of rotation [Formula: see text], and its isotropic value [Formula: see text]. The comparison of our results with the corresponding direct numerical simulations proves that the new model reproduces in an excellent way the decay rate of the turbulent kinetic energy.
DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests
Authors: Ashfaq Muhammad , Hebert Paul D.N.
Published: August 2016

Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.
Fungal DNA barcoding
Authors: Xu Jianping
Published: August 2016

Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.
Genomic study of the Type IVC secretion system in Clostridium difficile: understanding C. difficile evolution via horizontal gene transfer
Authors: Zhang Wen , Cheng Ying , Du Pengcheng , Zhang Yuanyuan , Jia Hongbing , Li Xianping , Wang Jing , Han Na , Qiang Yujun , Chen Chen , Lu Jinxing
Published: August 2016

Clostridium difficile, the etiological agent of Clostridium difficile infection (CDI), is a gram-positive, spore-forming bacillus that is responsible for ∼20% of antibiotic-related cases of diarrhea and nearly all cases of pseudomembranous colitis. Previous data have shown that a substantial proportion (11%) of the C. difficile genome consists of mobile genetic elements, including seven conjugative transposons. However, the mechanism underlying the formation of a mosaic genome in C. difficile is unknown. The type-IV secretion system (T4SS) is the only secretion system known to transfer DNA segments among bacteria. We searched genome databases to identify a candidate T4SS in C. difficile that could transfer DNA among different C. difficile strains. All T4SS gene clusters in C. difficile are located within genomic islands (GIs), which have variable lengths and structures and are all conjugative transposons. During the horizontal-transfer process of T4SS GIs within the C. difficile population, the excision sites were altered, resulting in different short-tandem repeat sequences among the T4SS GIs, as well as different chromosomal insertion sites and additional regions in the GIs.
Archimedes force on Casimir apparatus
Authors: Shevchenko Vladimir , Shevrin Efim
Published: August 2016

This paper addresses a problem of Casimir apparatus in dense medium, put in weak gravitational field. The falling of the apparatus has to be governed by the equivalence principle with proper account for contributions to the weight of the apparatus from its material part and from distorted quantum fields. We discuss general expression for the corresponding force in metric with cylindrical symmetry. By way of example, we compute explicit expression for Archimedes force, acting on the Casimir apparatus of finite size, immersed into thermal bath of free scalar field. It is shown that besides universal term, proportional to the volume of the apparatus, there are non-universal quantum corrections, depending on the boundary conditions.
Symmetric Fold/Super-Hopf Bursting, Chaos and Mixed-Mode Oscillations in Pernarowski Model of Pancreatic Beta-Cells
Authors: Fallah Haniyeh
Published: August 2016

Pancreatic beta-cells produce insulin to regularize the blood glucose level. Bursting is important in beta cells due to its relation to the release of insulin. Pernarowski model is a simple polynomial model of beta-cell activities indicating bursting oscillations in these cells. This paper presents bursting behaviors of symmetric type in this model. In addition, it is shown that the current system exhibits the phenomenon of period doubling cascades of canards which is a route to chaos. Canards are also observed symmetrically near folds of slow manifold which results in a chaotic transition between [Formula: see text] and [Formula: see text] spikes symmetric bursting. Furthermore, mixed-mode oscillations (MMOs) and combination of symmetric bursting together with MMOs are illustrated during the transition between symmetric bursting and continuous spiking.
Chimera States in Star Networks
Authors: Meena Chandrakala , Murali K. , Sinha Sudeshna
Published: August 2016

We consider star networks of chaotic oscillators, with all end-nodes connected only to the central hub node, under diffusive coupling, conjugate coupling and mean-field diffusive coupling. We observe the existence of chimeras in the end-nodes, which are identical in terms of the coupling environment and dynamical equations. Namely, the symmetry of the end-nodes is broken and coexisting groups with different synchronization features and attractor geometries emerge. Surprisingly, such chimera states are very wide-spread in this network topology, and large parameter regimes of moderate coupling strengths evolve to chimera states from generic random initial conditions. Further, we verify the robustness of these chimera states in analog circuit experiments. Thus it is evident that star networks provide a promising class of coupled systems, in natural or engineered contexts, where chimeras are prevalent.
Deciphering Dynamics of Recent Epidemic Spread and Outbreak in West Africa: The Case of Ebola Virus
Authors: Upadhyay Ranjit Kumar , Roy Parimita
Published: August 2016

Recently, the 2014 Ebola virus (EBOV) outbreak in West Africa was the largest outbreak to date. In this paper, an attempt has been made for modeling the virus dynamics using an SEIR model to better understand and characterize the transmission trajectories of the Ebola outbreak. We compare the simulated results with the most recent reported data of Ebola infected cases in the three most affected countries Guinea, Liberia and Sierra Leone. The epidemic model exhibits two equilibria, namely, the disease-free and unique endemic equilibria. Existence and local stability of these equilibria are explored. Using central manifold theory, it is established that the transcritical bifurcation occurs when basic reproduction number passes through unity. The proposed Ebola epidemic model provides an estimate to the potential number of future cases. The model indicates that the disease will decline after peaking if multisectorial and multinational efforts to control the spread of infection are maintained. Possible implication of the results for disease eradication and its control are discussed which suggests that proper control strategies like: (i) transmission precautions, (ii) isolation and care of infectious Ebola patients, (iii) safe burial, (iv) contact tracing with follow-up and quarantine, and (v) early diagnosis are needed to stop the recurrent outbreak.
A New Simple Chaotic Circuit Based on Memristor
Authors: Wu Renping , Wang Chunhua
Published: August 2016

In this paper, a new memristor is proposed, and then an emulator built from off-the-shelf solid state components imitating the behavior of the proposed memristor is presented. Multisim simulation and breadboard experiment are done on the emulator, exhibiting a pinched hysteresis loop in the voltage–current plane when the emulator is driven by a periodic excitation voltage. In addition, a new simple chaotic circuit is designed by using the proposed memristor and other circuit elements. It is exciting that this circuit with only a linear negative resistor, a capacitor, an inductor and a memristor can generate a chaotic attractor. The dynamical behaviors of the proposed chaotic system are analyzed by Lyapunov exponents, phase portraits and bifurcation diagrams. Finally, an electronic circuit is designed to implement the chaotic system. For the sake of simple circuit topology, the proposed chaotic circuit can be easily manufactured at low cost.
Invariant Sets for Monotone Local Dendrite Maps
Authors: Abdelli Hafedh , Marzougui Habib
Published: August 2016

Let [Formula: see text] be a local dendrite and let [Formula: see text] be a monotone map. Denote by [Formula: see text], RR[Formula: see text], UR[Formula: see text], [Formula: see text] the set of periodic (resp., regularly recurrent, uniformly recurrent, recurrent) points and [Formula: see text] the union of all [Formula: see text]-limit sets of [Formula: see text]. We show that if [Formula: see text] is nonempty, then (i) [Formula: see text]. (ii) R[Formula: see text] if and only if every cut point is a periodic point. If [Formula: see text] is empty, then (iii) [Formula: see text]. (iv) R[Formula: see text] if and only if [Formula: see text] is a circle and [Formula: see text] is topologically conjugate to an irrational rotation of the unit circle [Formula: see text]. On the other hand, we prove that [Formula: see text] has no Li–Yorke pair. Moreover, we show that the family of all [Formula: see text]-limit sets of [Formula: see text] is closed with respect to the Hausdorff metric.
Periodic Orbits Analysis in a Class of Planar Liénard Systems with State-Triggered Jumps
Authors: Jiang Fangfang , Lu Wei D. , Sun Jitao
Published: August 2016

In this paper, we investigate the existence problem of periodic orbits for a planar Liénard system, whose solution mappings are interrupted by abrupt changes of state. We first present the geometrical properties of solutions for the planar Liénard system with state impulses, then by using Bendixson theorem of impulsive differential equations and successor function method, several new criteria on the closed orbits and discontinuous periodic orbits are established in the impulsive Liénard system.
Structural Perspectives on Axon Guidance
Authors: Seiradake Elena , Jones E. Yvonne , Klein Rüdiger
Published: August 2016

Axon guidance relies on a combinatorial code of receptor and ligand interactions that direct adhesive/attractive and repulsive cellular responses. Recent structural data have revealed many of the molecular mechanisms that govern these interactions and enabled the design of sophisticated mutant tools to dissect their biological functions. Here, we discuss the structure/function relationships of four major classes of guidance cues (ephrins, semaphorins, slits, netrins) and examples of morphogens (Wnt, Shh) and of cell adhesion molecules (FLRT). These cell signaling systems rely on specific modes of receptor-ligand binding that are determined by selective binding sites; however, defined structure-encoded receptor promiscuity also enables cross talk between different receptor/ligand families and can also involve extracellular matrix components. A picture emerges in which a multitude of highly context-dependent structural assemblies determines the finely tuned cellular behavior required for nervous system development.
Patterns, Causes, and Consequences of Anthropocene Defaunation
Authors: Young Hillary S. , McCauley Douglas J. , Galetti Mauro , Dirzo Rodolfo
Published: August 2016

Anthropocene defaunation, the global extinction of faunal species and populations and the decline in abundance of individuals within populations, has been predominantly documented in terrestrial ecosystems, but indicators suggest defaunation has been more severe in freshwater ecosystems. Marine defaunation is in a more incipient stage, yet pronounced effects are already apparent and its rapid acceleration seems likely. Defaunation now impacts the planet's wildlife with profound cascading consequences, ranging from local to global coextinctions of interacting species to the loss of ecological services critical for humanity. Slowing defaunation will require aggressively reducing animal overexploitation and habitat destruction; mitigating climate disruption; and stabilizing the impacts of human population growth and uneven resource consumption. Given its omnipresence, defaunation should receive status of major global environmental change and should be addressed with the same urgency as deforestation, pollution, and climatic change. Global action is needed to prevent defaunation's current trajectory from catalyzing the planet's sixth major extinction.
A Genomic Perspective on the Generation and Maintenance of Genetic Diversity in Herbivorous Insects
Authors: Gloss Andrew D. , Groen Simon C. , Whiteman Noah K.
Published: August 2016

Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales—from variation within populations to divergence among populations—to form a comprehensive view of adaptation in herbivorous insects.
Structure and Functioning of Dryland Ecosystems in a Changing World
Authors: Maestre Fernando T. , Eldridge David J. , Soliveres Santiago , Kéfi Sonia , Delgado-Baquerizo Manuel , Bowker Matthew A. , García-Palacios Pablo , Gaitán Juan , Gallardo Antonio , Lázaro Roberto , Berdugo Miguel
Published: August 2016

Understanding how drylands respond to ongoing environmental change is extremely important for global sustainability. In this review, we discuss how biotic attributes, climate, grazing pressure, land cover change, and nitrogen deposition affect the functioning of drylands at multiple spatial scales. Our synthesis highlights the importance of biotic attributes (e.g., species richness) in maintaining fundamental ecosystem processes such as primary productivity, illustrates how nitrogen deposition and grazing pressure are impacting ecosystem functioning in drylands worldwide, and highlights the importance of the traits of woody species as drivers of their expansion in former grasslands. We also emphasize the role of attributes such as species richness and abundance in controlling the responses of ecosystem functioning to climate change. This knowledge is essential to guide conservation and restoration efforts in drylands, as biotic attributes can be actively managed at the local scale to increase ecosystem resilience to global change.
Infectious Disease Dynamics in Heterogeneous Landscapes
Authors: Parratt Steven R. , Numminen Elina , Laine Anna-Liisa
Published: August 2016

Infectious diseases dynamics are affected by both spatial and temporal heterogeneity in their environments. Our ability to quantify and predict how this heterogeneity impacts risks of infection and disease emergence is the key to successful disease prevention efforts. Here, we review the literature on infectious diseases from human, agricultural, and wildlife ecosystems to describe the rapid ecological and evolutionary responses in pathogens to environmental heterogeneity, with expected impacts on their epidemiology. To date, the underlying network structures through which disease transmission proceeds have been notoriously difficult to quantify because of this variation. We show that with recent advances in statistical methods and genomic approaches, it is now more feasible than ever to trace disease transmission networks, the molecular underpinning of infection, and the environmental variation relevant to disease dynamics. We end by identifying major new opportunities and challenges in understanding disease dynamics in an ever-changing world.
Reputation and Feedback Systems in Online Platform Markets
Authors: Tadelis Steven
Published: August 2016

Online marketplaces have become ubiquitous, as sites such as eBay, Taobao, Uber, and Airbnb are frequented by billions of users. The success of these marketplaces is attributed to not only the ease in which buyers can find sellers, but also the trust that these marketplaces help facilitate through reputation and feedback systems. I begin by briefly describing the basic ideas surrounding the role of reputation in facilitating trust and trade, and offer an overview of how feedback and reputation systems work in online marketplaces. I then describe the literature that explores the effects of reputation and feedback systems on online marketplaces and highlight some of the problems of bias in feedback and reputation systems as they appear today. I discuss ways to address these problems to improve the practical design of online marketplaces and suggest some directions for future research.
Transformative Environmental Governance
Authors: Chaffin Brian C. , Garmestani Ahjond S. , Gunderson Lance H. , Benson Melinda Harm , Angeler David G. , Arnold Craig Anthony (Tony) , Cosens Barbara , Craig Robin Kundis , Ruhl J.B. , Allen Craig R.
Published: August 2016

Transformative governance is an approach to environmental governance that has the capacity to respond to, manage, and trigger regime shifts in coupled social-ecological systems (SESs) at multiple scales. The goal of transformative governance is to actively shift degraded SESs to alternative, more desirable, or more functional regimes by altering the structures and processes that define the system. Transformative governance is rooted in ecological theories to explain cross-scale dynamics in complex systems, as well as social theories of change, innovation, and technological transformation. Similar to adaptive governance, transformative governance involves a broad set of governance components, but requires additional capacity to foster new social-ecological regimes including increased risk tolerance, significant systemic investment, and restructured economies and power relations. Transformative governance has the potential to actively respond to regime shifts triggered by climate change, and thus future research should focus on identifying system drivers and leading indicators associated with social-ecological thresholds.
Corporate Environmentalism: Motivations and Mechanisms
Authors: Chrun Elizabeth , Dolšak Nives , Prakash Aseem
Published: August 2016

Corporate environmentalism (CE) pertains to firm-level efforts to reduce pollution and resource use along with protecting natural habitats. Importantly, firms pledge to undertake these actions beyond the requirements of the law. Although historically CE efforts focused on resource conservation, their contemporary focus is on pollution reduction to reduce direct harm to humans and their communities and on the protection of environmental sinks. We review two broad categories of CE: direct CE and indirect CE. Direct CE, whether undertaken unilaterally or collectively, pertains to firms themselves adopting policies that reduce the environmental impact of their activities, or disclosing information about their environmental performance. Indirect CE refers to policies of actors (such as financial institutions) that encourage firms seeking their resources (through loans, venture capital, etc.) to commit to environmental stewardship policies. Three key lessons emerge. First, firm-level characteristics, particularly size and economic performance, encourage CE. Second, although pressure from external stakeholders, especially environmental nongovernmental organizations (NGOs), has played an important role in discouraging policies that harm the environment, its effect on encouraging proenvironmental activities remains unclear. Third, the literature is ripe with serious methodological issues. The endogeneity between firms’ economic and environmental record and their CE efforts poses difficulty in drawing causal inferences.
Impact on Granular Beds
Authors: van der Meer Devaraj
Published: August 2016

The impact of an object on a granular solid is an ubiquitous phenomenon in nature, the scale of which ranges from the impact of a raindrop onto sand all the way to that of a large asteroid on a planet. Despite the obvious relevance of these impact events, the study of the underlying physics mechanisms that guide them is relatively young, with most work concentrated in the past decade. Upon impact, an object starts to interact with a granular bed and experiences a drag force from the sand. This ultimately leads to phenomena such as crater formation and the creation of a transient cavity that upon collapse may cause a jet to appear from above the surface of the sand. This review provides an overview of research that targets these phenomena, from the perspective of the analogous but markedly different impact of an object on a liquid. It successively addresses the drag an object experiences inside a granular bed, the expansion and collapse of the cavity created by the object leading to the formation of a jet, and the remarkable role played by the air that resides within the pores between the grains.
Physics and Measurement of Aero-Optical Effects: Past and Present
Authors: Jumper Eric J. , Gordeyev Stanislav
Published: August 2016

The field of aero-optics is devoted to the study of the effects of turbulent flow fields on laser beams projected from airborne laser systems. This article reviews the early and present periods of research in aero-optics. Both periods generated impressive amounts of research activity; however, the types and amount of data differ greatly in accuracy, quality, and type owing to the development of new types of instrumentation available to collect and analyze the aberrated wave fronts of otherwise collimated laser beams projected through turbulent compressible flow fields of the type that form over beam directors. This review traces the activities and developments associated with both periods but particularly focuses on the development of modern high-bandwidth wave-front sensors used in the present research period. We describe how these modern wave-front data are collected and analyzed and the fluid mechanic information that can be gleaned from them; the use of these data in the fundamental study of turbulence is emphasized.
Sex-Biased Gene Expression
Authors: Grath Sonja , Parsch John
Published: August 2016

Methods of transcriptional profiling have made it possible to compare gene expression between females and males on a genome-wide scale. Such studies have revealed that sex-biased gene expression is abundant in many species, although its extent may vary greatly among tissues or developmental stages. In species with genetic sex determination, sex chromosome–specific processes, such as dosage compensation, also may influence sex-biased gene expression. Sex-biased genes, especially those with male-biased expression, often show elevated rates of both protein sequence and gene expression divergence between species, which could have a number of causes, including sexual selection, sexual antagonism, and relaxed selective constraint. Here, we review our current knowledge of sex-biased gene expression in both model and nonmodel organisms, as well as the biological and technical factors that should be considered when analyzing sex-biased expression. We also discuss current approaches to uncover the evolutionary forces that govern the evolution of sex-biased genes.
The Count/Mass Distinction in Grammar and Cognition
Authors: Doetjes Jenny
Published: August 2016

The count/mass distinction is a domain of human language that is strongly related to human cognition. This review starts with an overview of recent research on individuation in relation to core knowledge systems (in particular the systems of object representation, agent representation, and number representation), followed by a brief overview of the role these representations play in the acquisition of count meaning. I then discuss linguistic aspects of individuation and the count/mass distinction in more detail. I distinguish between the grammatical systems of languages and the lexical properties of nouns, focusing on crosslinguistic variation. Languages vary substantially in the grammatical conditions that quantity expressions impose on the nouns they combine with, as well as in the exact lexical and grammatical properties of nouns. At the same time, individuation and counting seem to play a role in all languages, and similar counting strategies show up in unrelated languages.
Advances in the Application of Surface Drifters
Authors: Lumpkin Rick , Özgökmen Tamay , Centurioni Luca
Published: August 2016

Surface drifting buoys, or drifters, are used in oceanographic and climate research, oil spill tracking, weather forecasting, search and rescue operations, calibration and validation of velocities from high-frequency radar and from altimeters, iceberg tracking, and support of offshore drilling operations. In this review, we present a brief history of drifters, from the message in a bottle to the latest satellite-tracked, multisensor drifters. We discuss the different types of drifters currently used for research and operations as well as drifter designs in development. We conclude with a discussion of the various properties that can be observed with drifters, with heavy emphasis on a critical process that cannot adequately be observed by any other instrument: dispersion in the upper ocean, driven by turbulence at scales from waves through the submesoscale to the large-scale geostrophic eddies.
Structure, Function, and Evolution of Coronavirus Spike Proteins
Authors: Li Fang
Published: August 2016

The coronavirus spike protein is a multifunctional molecular machine that mediates coronavirus entry into host cells. It first binds to a receptor on the host cell surface through its S1 subunit and then fuses viral and host membranes through its S2 subunit. Two domains in S1 from different coronaviruses recognize a variety of host receptors, leading to viral attachment. The spike protein exists in two structurally distinct conformations, prefusion and postfusion. The transition from prefusion to postfusion conformation of the spike protein must be triggered, leading to membrane fusion. This article reviews current knowledge about the structures and functions of coronavirus spike proteins, illustrating how the two S1 domains recognize different receptors and how the spike proteins are regulated to undergo conformational transitions. I further discuss the evolution of these two critical functions of coronavirus spike proteins, receptor recognition and membrane fusion, in the context of the corresponding functions from other viruses and host cells.
Benzimidazole derivative small-molecule 991 enhances AMPK activity and glucose uptake induced by AICAR or contraction in skeletal muscle
Authors: Bultot Laurent , Jensen Thomas E. , Lai Yu-Chiang , Madsen Agnete L. B. , Collodet Caterina , Kviklyte Samanta , Deak Maria , Yavari Arash , Foretz Marc , Ghaffari Sahar , Bellahcene Mohamed , Ashrafian Houman , Rider Mark H. , Richter Erik A. , Sakamoto Kei
Published: August 2016

AMP-activated protein kinase (AMPK) plays diverse roles and coordinates complex metabolic pathways for maintenance of energy homeostasis. This could be explained by the fact that AMPK exists as multiple heterotrimer complexes comprising a catalytic α-subunit (α1 and α2) and regulatory β (β1 and β2)- and γ (γ1, γ2, γ3)-subunits, which are uniquely distributed across different cell types. There has been keen interest in developing specific and isoform-selective AMPK-activating drugs for therapeutic use and also as research tools. Moreover, establishing ways of enhancing cellular AMPK activity would be beneficial for both purposes. Here, we investigated if a recently described potent AMPK activator called 991, in combination with the commonly used activator 5-aminoimidazole-4-carboxamide riboside or contraction, further enhances AMPK activity and glucose transport in mouse skeletal muscle ex vivo. Given that the γ3-subunit is exclusively expressed in skeletal muscle and has been implicated in contraction-induced glucose transport, we measured the activity of AMPKγ3 as well as ubiquitously expressed γ1-containing complexes. We initially validated the specificity of the antibodies for the assessment of isoform-specific AMPK activity using AMPK-deficient mouse models. We observed that a low dose of 991 (5 μM) stimulated a modest or negligible activity of both γ1- and γ3-containing AMPK complexes. Strikingly, dual treatment with 991 and 5-aminoimidazole-4-carboxamide riboside or 991 and contraction profoundly enhanced AMPKγ1/γ3 complex activation and glucose transport compared with any of the single treatments. The study demonstrates the utility of a dual activator approach to achieve a greater activation of AMPK and downstream physiological responses in various cell types, including skeletal muscle.
Inventory Control by Multiple Service Levels under Unreliable Supplying Condition
Authors: Na Byungsoo , Lee Jinpyo , Ahn Hyung Jun
Published: August 2016

We consider an inventory system where there is random demand from customers as well as unreliable supplying capacity from supplier. In many real-world cases, supplier might fail to satisfy the amount of order from retailers or producers so that only partial proportion of order is satisfied or even fail to deliver all of the order. Moreover, recently a concern regarding unreliable supplying capacity has been increasing since the globalization makes the retailer or producer face the extended supply network with complicated and risky supplying capacity. Also, we consider two classified customers, of which one is willing to pay extra charge for expedited delivery service but the other is not reluctant to delay the delivery without any extra charge. We show that there exists an optimal threshold for inventory and price for each service level in the following sense: if the inventory level is less than the predetermined threshold, then the retailer or producer needs to order up to the threshold level and offer threshold price corresponding to service level. Otherwise, the retailer does not need to order. The risk of stockout due to unreliable supplying capacity can be mitigated by the dynamic pricing and inventory control with multiple service levels.
Stability and Hopf Bifurcation Analysis of an Epidemic Model by Using the Method of Multiple Scales
Authors: Wang Wanyong , Chen Lijuan
Published: August 2016

A delayed epidemic model with nonlinear incidence rate which depends on the ratio of the numbers of susceptible and infectious individuals is considered. By analyzing the corresponding characteristic equations, the effects of time delay on the stability of the equilibria are studied. By choosing time delay as bifurcation parameter, the critical value of time delay at which a Hopf bifurcation occurs is obtained. In order to derive the normal form of the Hopf bifurcation, an extended method of multiple scales is developed and used. Then, the amplitude of bifurcating periodic solution and the conditions which determine the stability of the bifurcating periodic solution are obtained. The validity of analytical results is shown by their consistency with numerical simulations.
Design of UAVs-Based 3D Antenna Arrays for a Maximum Performance in Terms of Directivity and SLL
Authors: Garza Jesus , Panduro Marco A. , Reyna Alberto , Romero Gerardo , Rio Carlos del
Published: August 2016

This paper presents a design of UAVs-based 3D antenna arrays for a maximum performance in terms of directivity and side lobe level (SLL). This paper illustrates how to model the UAVs formation flight using 3D nonuniform antenna arrays. This design of 3D antenna arrays considers the optimization of the positions of the antenna elements to model the UAVs formation flight. In this case, a disk patch antenna is chosen to be used as element in each UAV. The disk patch antenna is formulated by the well-known cavity model. The synthesis process is carried out by the method of Differential Evolution for Multiobjective Optimization (DEMO). Furthermore, a comparison of the performance of 3D nonuniform antenna arrays is provided with respect to the most conventional arrays (circular, planar, linear, and the cubic) for UAVs formation flight.
Developing an On-Demand Cloud-Based Sensing-as-a-Service System for Internet of Things
Authors: Kim Mihui , Asthana Mihir , Bhargava Siddhartha , Iyyer Kartik Krishnan , Tangadpalliwar Rohan , Gao Jerry
Published: August 2016

The increasing number of Internet of Things (IoT) devices with various sensors has resulted in a focus on Cloud-based sensing-as-a-service (CSaaS) as a new value-added service, for example, providing temperature-sensing data via a cloud computing system. However, the industry encounters various challenges in the dynamic provisioning of on-demand CSaaS on diverse sensor networks. We require a system that will provide users with standardized access to various sensor networks and a level of abstraction that hides the underlying complexity. In this study, we aim to develop a cloud-based solution to address the challenges mentioned earlier. Our solution, SenseCloud, includes asensor virtualizationmechanism that interfaces with diverse sensor networks, amultitenancymechanism that grants multiple users access to virtualized sensor networks while sharing the same underlying infrastructure, and adynamic provisioningmechanism to allow the users to leverage the vast pool of resources on demand and on a pay-per-use basis. We implement a prototype of SenseCloud by using real sensors and verify the feasibility of our system and its performance. SenseCloud bridges the gap between sensor providers and sensor data consumers who wish to utilize sensor data.