bluuebunny/crossref_metadata_2025 huggingface dataset:
Communication: Optimal parameters for basin-hopping global optimization based on Tsallis statistics
Authors: Shang C. , Wales D. J.
Published: August 2014

A fundamental problem associated with global optimization is the large free energy barrier for the corresponding solid-solid phase transitions for systems with multi-funnel energy landscapes. To address this issue we consider the Tsallis weight instead of the Boltzmann weight to define the acceptance ratio for basin-hopping global optimization. Benchmarks for atomic clusters show that using the optimal Tsallis weight can improve the efficiency by roughly a factor of two. We present a theory that connects the optimal parameters for the Tsallis weighting, and demonstrate that the predictions are verified for each of the test cases.
Density functional theory calculations of stability and diffusion mechanisms of impurity atoms in Ge crystals
Authors: Maeta Takahiro , Sueoka Koji
Published: August 2014

Ge-based substrates are being developed for applications in advanced nano-electronic devices because of their higher intrinsic carrier mobility than Si. The stability and diffusion mechanism of impurity atoms in Ge are not well known in contrast to those of Si. Systematic studies of the stable sites of 2nd to 6th row element impurity atoms in Ge crystal were undertaken with density functional theory (DFT) and compared with those in Si crystal. It was found that most of the impurity atoms in Ge were stable at substitutional sites, while transition metals in Si were stable at interstitial sites and the other impurity atoms in Si were stable at substitutional sites. Furthermore, DFT calculations were carried out to clarify the mechanism responsible for the diffusion of impurity atoms in Ge crystals. The diffusion mechanism for 3d transition metals in Ge was found to be an interstitial-substitutional diffusion mechanism, while in Si this was an interstitial diffusion mechanism. The diffusion barriers in the proposed diffusion mechanisms in Ge and Si were quantitatively verified by comparing them to the experimental values in the literature.
Strain-induced long range ferroelectric order and linear electro-optic effect in epitaxial relaxor thin films
Authors: Scarisoreanu N. D. , Craciun F. , Birjega R. , Andrei A. , Ion V. , Negrea R. F. , Ghica C. , Dinescu M.
Published: August 2014

Relaxor ferroelectrics have neither long range ferroelectric order nor structural transformation down to the lowest temperatures, and display isotropic optical properties like quadratic electro-optic effect. However, if an anisotropy is forced through an external agent, like electric field or uniaxial strain, a ferroelectric and structural long range order can be induced in these materials. Here, we show that epitaxial strain in relaxor ferroelectric thin films can be employed to induce a linear electro-optic effect, opening the path to new strain-controlled electro-optic materials. Epitaxial thin films with Pb1-3x/2LaxZr0.2Ti0.8O3 (x = 0.22) composition grown by pulsed laser deposition on (001) SrRuO3/SrTiO3 single crystal heterostructures become tetragonal below the susceptibility peak, which occurs at a temperature 140 K higher as compared to bulk. These films show piezoelectric properties and almost linear electro-optic behaviour.
Dimensional scale effects on surface enhanced Raman scattering efficiency of self-assembled silver nanoparticle clusters
Authors: Fasolato C. , Domenici F. , Sennato S. , Mura F. , De Angelis L. , Luongo F. , Costantini F. , Bordi F. , Postorino P.
Published: August 2014

A study of the Surface Enhanced Raman Scattering (SERS) from micrometric metallic nanoparticle aggregates is presented. The sample is obtained from the self-assembly on glass slides of micro-clusters of silver nanoparticles (60 and 100 nm diameter), functionalized with the organic molecule 4-aminothiophenol in water solution. For nanoparticle clusters at the micron scale, a maximum enhancement factor of 109 is estimated from the SERS over the Raman intensity ratio normalized to the single molecule contribution. Atomic force microscopy, correlated to spatially resolved Raman measurements, allows highlighting the connection between morphology and efficiency of the plasmonic system. The correlation between geometric features and SERS response of the metallic structures reveals a linear trend of the cluster maximum scattered intensity as a function of the surface area of the aggregate. On given clusters, the intensity turns out to be also influenced by the number of stacking planes of the aggregate, thus suggesting a plasmonic waveguide effect. The linear dependence results weakened for the largest area clusters, suggesting 30 μm2 as the upper limit for exploiting the coherence over large scale of the plasmonic response.
Ferromagnetism and the electronic band structure in (Ga,Mn)(Bi,As) epitaxial layers
Authors: Yastrubchak O. , Sadowski J. , Gluba L. , Domagala J. Z. , Rawski M. , Żuk J. , Kulik M. , Andrearczyk T. , Wosinski T.
Published: August 2014

Impact of Bi incorporation into (Ga,Mn)As layers on their electronic- and band-structures as well as their magnetic and structural properties has been studied. Homogenous (Ga,Mn)(Bi,As) layers of high structural perfection have been grown by the low-temperature molecular-beam epitaxy technique. Post-growth annealing treatment of the layers results in an improvement of their structural and magnetic properties and an increase in the hole concentration in the layers. The modulation photoreflectance spectroscopy results are consistent with the valence-band model of hole-mediated ferromagnetism in the layers. This material combines the properties of (Ga,Mn)As and Ga(Bi,As) ternary compounds and offers the possibility of tuning its electrical and magnetic properties by controlling the alloy composition.
Quantum beats from the coherent interaction of hole states with surface state in near-surface quantum well
Authors: Khan Salahuddin , Jayabalan J. , Chari Rama , Pal Suparna , Porwal Sanjay , Sharma Tarun Kumar , Oak S. M.
Published: August 2014

We report tunneling assisted beating of carriers in a near-surface single GaAsP/AlGaAs quantum well using transient reflectivity measurement. The observed damped oscillating signal has a period of 120 ± 6 fs which corresponds to the energy difference between lh1 and hh2 hole states in the quantum well. Comparing the transient reflectivity signal at different photon energies and with a buried quantum well sample, we show that the beating is caused by the coherent coupling between surface state and the hole states (lh1 and hh2) in the near-surface quantum well. The dependence of decay of coherence of these tunneling carriers on the excitation fluence is also reported. This observation on the coherent tunneling of carrier is important for future quantum device applications.
Toward epitaxially grown two-dimensional crystal hetero-structures: Single and double MoS2/graphene hetero-structures by chemical vapor depositions
Authors: Lin Meng-Yu , Chang Chung-En , Wang Cheng-Hung , Su Chen-Fung , Chen Chi , Lee Si-Chen , Lin Shih-Yen
Published: August 2014

Uniform large-size MoS2/graphene hetero-structures fabricated directly on sapphire substrates are demonstrated with layer-number controllability by chemical vapor deposition (CVD). The cross-sectional high-resolution transmission electron microscopy (HRTEM) images provide the direct evidences of layer numbers of MoS2/graphene hetero-structures. Photo-excited electron induced Fermi level shift of the graphene channel are observed on the single MoS2/graphene hetero-structure transistors. Furthermore, double hetero-structures of graphene/MoS2/graphene are achieved by CVD fabrication of graphene layers on top of the MoS2, as confirmed by the cross-sectional HRTEM. These results have paved the possibility of epitaxially grown multi-hetero-structures for practical applications.
Cyclotron-undulator cooling of a free-electron-laser beam
Authors: Bandurkin I. V. , Kuzikov S. V. , Savilov A. V.
Published: August 2014

We propose methods of fast cooling of an electron beam, which are based on wiggling of particles in an undulator in the presence of an axial magnetic field. We use a strong dependence of the axial electron velocity on the oscillatory velocity, when the electron cyclotron frequency is close to the frequency of electron wiggling in the undulator field. The abnormal character of this dependence (when the oscillatory velocity increases with the increase of the input axial velocity) can be a basis of various methods for fast cooling of moderately relativistic (several MeV) electron beams.
A simplified hollow-core microstructured optical fibre laser with microring resonators and strong radial emission
Authors: Li Zhi-Li , Liu Yan-Ge , Yan Min , Zhou Wen-Yuan , Ying Cui-Feng , Ye Qing , Tian Jian-Guo
Published: August 2014

A simplified hollow-core microstructured optical fibre (SHMOF) laser with microring resonators and strong radial emission is demonstrated. We propose that a submicron thickness silica ring embedded in the SHMOF can act as a microring resonator, with the advantages of being both compact and solid. Furthermore, the microfluidics can be easily controlled with a side pumping scheme. We also obtained a highly stable and tunable laser. The attractive possibility of developing microfluidic dye lasers within single SHMOFs presents opportunities for integrated optics applications and biomedical analysis.
Phase lag deduced information in photo-thermal actuation for nano-mechanical systems characterization
Authors: Bijster R. J. F. , de Vreugd J. , Sadeghian H.
Published: August 2014

In photo-thermal actuation, heat is added locally to a micro-cantilever by means of a laser. A fraction of the irradiation is absorbed, yielding thermal stresses and deformations in the structure. Harmonic modulation of the laser power causes the cantilever to oscillate. Moreover, a phase lag is introduced which is very sensitive to the spot location and the cantilever properties. This phase lag is theoretically predicted and experimentally verified. Combined with thermo-mechanical properties of the cantilever and its geometry, the location of the laser spot, the thermal diffusivity, and the layer thicknesses of the cantilever can be extracted.
Characteristic time scales of coalescence of silver nanocomposite and nanoparticle films induced by continuous wave laser irradiation
Authors: Paeng Dongwoo , Lee Daeho , Grigoropoulos Costas P.
Published: August 2014

In-situ optical probing has been performed to analyze and compare the characteristic coalescence time scales of silver ion-doped polyvinylalcohol nanocomposite (Ag-PVA NC) and polyvinylpyrrolidone-capped silver nanoparticle (Ag-PVP NP) films subjected to continuous wave laser irradiation. The Ag-PVA NC yielded conductive metallic patterns by photothermal reduction of PVA, formation of nanoparticles from silver ions and their subsequent coalescence. On the other hand, Ag-PVP NP thin films produced conductive patterns through only coalescence of nanoparticles. Upon laser irradiation, Ag-PVA NC and Ag-PVP NP films exhibited different coalescence characteristics.
Graphene/GaN diodes for ultraviolet and visible photodetectors
Authors: Lin Fang , Chen Shao-Wen , Meng Jie , Tse Geoffrey , Fu Xue-Wen , Xu Fu-Jun , Shen Bo , Liao Zhi-Min , Yu Da-Peng
Published: August 2014

The Schottky diodes based on graphene/GaN interface are fabricated and demonstrated for the dual-wavelength photodetection of ultraviolet (UV) and green lights. The physical mechanisms of the photoelectric response of the diodes with different light wavelengths are different. For UV illumination, the photo-generated carriers lower the Schottky barrier and increase the photocurrent. For green light illumination, as the photon energy is smaller than the bandgap of GaN, the hot electrons excited in graphene via internal photoemission are responsible for the photoelectric response. Using graphene as a transparent electrode, the diodes show a ∼mS photoresponse, providing an alternative route toward multi-wavelength photodetectors.
Regionalization of Planned S&T Parks: The Case of Daedeok S&T Park in Daejeon, South Korea
Authors: Kim Hyungjoo , Lee Yong-Sook , Hwang Hye-Ran
Published: August 2014

This study examines how the Daedeok Science and Technology (S&T) Park, built as a national R&D center, has evolved over time from the perspective of a complex adaptive system. We argue that the Daedeok S&T Park—a planned park exhibiting path-dependent, self-reinforcing trajectories led by the government—has gradually evolved over time, undergoing some tension between nationalizing and regionalizing forces instead of encountering an imminent and radical transformation through the replication of a new model each time. The state's role is highlighted as a creator that ironically leads to the process of the planned park's evolution toward a more cluster-based park by strengthening regional actors' capabilities and changing the structure of governance. The study contributes to the literature on S&T parks by providing an in-depth analysis of an S&T park from an evolutionary perspective, and not from a typical static evaluation, and is based on archival analyses and case studies of ten firms as well as on in-depth interviews with key actors.
Comparing Subjective Contours for Kanizsa Squares and Linear Edge Alignments (‘New York Titanic’ Figures)
Authors: Gillam Barbara , Marlow Phillip J
Published: August 2014

One current view is that subjective contours may involve high-level detection of a salient shape with back propagation to early visual areas where small receptive fields allow for scrutiny of relevant details. This idea applies to Kanizsa-type figures. However, Gillam and Chan (2002 Psychological Science, 13, 279–282) using figures based on Gillam's graphic ‘New York Titanic’ (Gillam, 1997 Thresholds: Limits of perception. New York: Arts Magazine) showed that strong subjective contours can be seen along the linearly aligned edges of a set of shapes if occlusion cues of ‘extrinsic edge’ and ‘entropy contrast’ are strong. Here we compared ratings of the strength of subjective contours along linear alignments with those seen in Kanizsa figures. The strongest subjective contour for a single set of linearly aligned shapes was similar in strength to the edges of a Kanizsa square (controlling for support ratio) despite the lack of a salient region. The addition of a second set of linearly aligned inducers consistent with a common surface increased subjective-contour strength, as did having four rather than two ‘pacmen’ in the Kanizsa figure, indicating a role for surface support. We argue that linear subjective contours allow for the investigation of certain occlusion cues and the interactions between them that are not easily explored with Kanizsa figures.
Phenotyping novel stay-green traits to capture genetic variation in senescence dynamics
Authors: Christopher John T. , Veyradier Mathieu , Borrell Andrew K. , Harvey Greg , Fletcher Susan , Chenu Karine
Published: August 2014

Stay-green plants retain green leaves longer after anthesis and can have improved yield, particularly under water limitation. As senescence is a dynamic process, genotypes with different senescence patterns may exhibit similar final normalised difference vegetative index (NDVI). By monitoring NDVI from as early as awn emergence to maturity, we demonstrate that analysing senescence dynamics improves insight into genotypic stay-green variation. A senescence evaluation tool was developed to fit a logistic function to NDVI data and used to analyse data from three environments for a wheat (Triticum aestivum L.) population whose lines contrast for stay-green. Key stay-green traits were estimated including, maximum NDVI, senescence rate and a trait integrating NDVI variation after anthesis, as well as the timing from anthesis to onset, midpoint and conclusion of senescence. The integrative trait and the timing to onset and mid-senescence exhibited high positive correlations with yield and a high heritability in the three studied environments. Senescence rate was correlated with yield in some environments, whereas maximum NDVI was associated with yield in a drought-stressed environment. Where resources preclude frequent measurements, we found that NDVI measurements may be restricted to the period of rapid senescence, but caution is required when dealing with lines of different phenology. In contrast, regular monitoring during the whole period after flowering allows the estimation of senescence dynamics traits that may be reliably compared across genotypes and environments. We anticipate that selection for stay-green traits will enhance genetic progress towards high-yielding, stay-green germplasm.
Response of floret fertility and individual grain weight of wheat to high temperature stress: sensitive stages and thresholds for temperature and duration
Authors: Prasad P. V. Vara , Djanaguiraman Maduraimuthu
Published: August 2014

Short episodes of high temperature (HT) stress during reproductive stages of crop development cause significant yield losses in wheat (Triticum aestivum L.). Wheat plants of cultivar Chinese Spring were grown at various temperature regimes at several stages of reproductive development for different durations. The objectives of this research were to (i) identify the stage(s) most sensitive to HT stress during reproductive development, and (ii) determine threshold temperature and duration of HT stress that decrease floret fertility and individual grain weight. Two periods (first at 8–6 days before anthesis and second at 2–0 days before anthesis) during reproductive development were most sensitive to short episodes (2 or 5 days) of HT stress, causing maximum decreases in floret fertility. Short episodes (5 days) of mean daily temperatures >24°C imposed at start of heading quadratically decreased floret fertility, with the values reaching close to 0% around mean daily temperature of 35°C; and floret fertility and individual grain weight decreased linearly with increasing duration (in the range from 2 to 30 days) of HT stress when imposed at start of heading or start of grain filling respectively. HT stress caused morphological abnormalities in pollen, stigma and style. The combination of lower floret fertility (leading to decreased grain numbers) and decreased individual grain weights can cause significant decreases in grain yield. Further research to search for genetic variability for these traits and use them in breeding programs to develop tolerant genotypes that can provide yield stability under current and future climates is warranted.
Climate change poised to threaten hydrologic connectivity and endemic fishes in dryland streams
Authors: Jaeger Kristin L. , Olden Julian D. , Pelland Noel A.
Published: August 2014

Significance

We provide the first demonstration to our knowledge that projected changes in regional climate regimes will have significant consequences for patterns of intermittence and hydrologic connectivity in dryland streams of the American Southwest. By simulating fine-resolution streamflow responses to forecasted climate change, we simultaneously evaluate alterations in local flow continuity over time and network flow connectivity over space and relate how these changes may challenge the persistence of a globally endemic fish fauna. Given that human population growth in arid regions will only further increase surface and groundwater extraction during droughts, we expect even greater likelihood of flow intermittence and loss of habitat connectivity in the future.
Introgression in hybrid ants is favored in females but selected against in males
Authors: Kulmuni Jonna , Pamilo Pekka
Published: August 2014

Significance

Hybridization in animals has commonly been considered rare. In contrast, recent studies suggest hybridization to play a central role in both speciation and adaptation. This work highlights a complex process resulting from hybridization; exchange of genomic regions between species in
Formica
wood ants is at the same time selected for and against, leading to an intragenomic conflict and extremely strong natural selection. The results suggest that the genomic regions acquired through hybridization harbor both incompatibilities and adaptive genetic variation. Our study has implications for the genomic architecture of speciation and argues for incorporating adaptive introgression into the current models of genomic divergence.
Robustness against serum neutralization of a poliovirus type 1 from a lethal epidemic of poliomyelitis in the Republic of Congo in 2010
Authors: Drexler Jan Felix , Grard Gilda , Lukashev Alexander N. , Kozlovskaya Liubov I. , Böttcher Sindy , Uslu Gökhan , Reimerink Johan , Gmyl Anatoly P. , Taty-Taty Raphaël , Lekana-Douki Sonia Etenna , Nkoghe Dieudonné , Eis-Hübinger Anna M. , Diedrich Sabine , Koopmans Marion , Leroy Eric M. , Drosten Christian
Published: August 2014

Significance

In 2010, a large outbreak of poliomyelitis involving 445 laboratory-confirmed cases occurred in the Republic of Congo. The 47% case-fatality rate was unusually high. Outbreak severity was attributed to low immunization coverage but vaccine-mediated immunity against the outbreak virus was never investigated. We isolated the poliovirus type 1 responsible for the outbreak and located its evolutionary origins to Southeast Asia. Fatal cases showed evidence for previous vaccination against polioviruses and the outbreak virus was refractive against neutralization by monoclonal and vaccine-derived antibodies. This pointed to immune escape contributing to the severity of the outbreak. Sustained vaccination regimens in polio-free regions, together with clinical and environmental poliovirus surveillance will be necessary to combat antigenetically variant polioviruses in the poliomyelitis eradication endgame.
History of vaccination
Authors: Plotkin Stanley
Published: August 2014

Vaccines have a history that started late in the 18th century. From the late 19th century, vaccines could be developed in the laboratory. However, in the 20th century, it became possible to develop vaccines based on immunologic markers. In the 21st century, molecular biology permits vaccine development that was not possible before.
Vaccines against poverty
Authors: MacLennan Calman A. , Saul Allan
Published: August 2014

With the 2010s declared the Decade of Vaccines, and Millennium Development Goals 4 and 5 focused on reducing diseases that are potentially vaccine preventable, now is an exciting time for vaccines against poverty, that is, vaccines against diseases that disproportionately affect low- and middle-income countries (LMICs). The Global Burden of Disease Study 2010 has helped better understand which vaccines are most needed. In 2012, US$1.3 billion was spent on research and development for new vaccines for neglected infectious diseases. However, the majority of this went to three diseases: HIV/AIDS, malaria, and tuberculosis, and not neglected diseases. Much of it went to basic research rather than development, with an ongoing decline in funding for product development partnerships. Further investment in vaccines against diarrheal diseases, hepatitis C, and group A
Streptococcus
could lead to a major health impact in LMICs, along with vaccines to prevent sepsis, particularly among mothers and neonates. The Advanced Market Commitment strategy of the Global Alliance for Vaccines and Immunisation (GAVI) Alliance is helping to implement vaccines against rotavirus and pneumococcus in LMICs, and the roll out of the MenAfriVac meningococcal A vaccine in the African Meningitis Belt represents a paradigm shift in vaccines against poverty: the development of a vaccine primarily targeted at LMICs. Global health vaccine institutes and increasing capacity of vaccine manufacturers in emerging economies are helping drive forward new vaccines for LMICs. Above all, partnership is needed between those developing and manufacturing LMIC vaccines and the scientists, health care professionals, and policy makers in LMICs where such vaccines will be implemented.
Systems vaccinology: Probing humanity’s diverse immune systems with vaccines
Authors: Pulendran Bali
Published: August 2014

Homo sapiens
are genetically diverse, but dramatic demographic and socioeconomic changes during the past century have created further diversification with respect to age, nutritional status, and the incidence of associated chronic inflammatory disorders and chronic infections. These shifting demographics pose new challenges for vaccination, as emerging evidence suggests that age, the metabolic state, and chronic infections can exert major influences on the immune system. Thus, a key public health challenge is learning how to reprogram suboptimal immune systems to induce effective vaccine immunity. Recent advances have applied systems biological analysis to define molecular signatures induced early after vaccination that correlate with and predict the later adaptive immune responses in humans. Such “systems vaccinology” approaches offer an integrated picture of the molecular networks driving vaccine immunity, and are beginning to yield novel insights about the immune system. Here we discuss the promise of systems vaccinology in probing humanity’s diverse immune systems, and in delineating the impact of genes, the environment, and the microbiome on protective immunity induced by vaccination. Such insights will be critical in reengineering suboptimal immune systems in immunocompromised populations.
Development of in-group favoritism in children’s third-party punishment of selfishness
Authors: Jordan Jillian J. , McAuliffe Katherine , Warneken Felix
Published: August 2014

Significance

Humans are unique among animals in their willingness to cooperate with friends and strangers. Costly punishment of unfair behavior is thought to play a key role in promoting cooperation by deterring selfishness. Importantly, adults sometimes show in-group favoritism in their punishment. To our knowledge, our study is the first to document this bias in children. Furthermore, our results suggest that from its emergence in development, children’s costly punishment shows in-group favoritism, highlighting that group membership provides critical context for understanding the enforcement of fairness norms. However, 8-y-old children show attenuated bias relative to 6-y-olds, perhaps reflecting a motivation for impartially. Our findings thus demonstrate that in-group favoritism has an important influence on human fairness and morality, but can be partially overcome with age.
Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria
Authors: Palovaara Joakim , Akram Neelam , Baltar Federico , Bunse Carina , Forsberg Jeremy , Pedrós-Alió Carlos , González José M. , Pinhassi Jarone
Published: August 2014

Significance

Bacteria control biogeochemical cycles of elements and fluxes of energy in the ocean. Discovery of a membrane photoprotein widespread in marine bacteria—proteorhodopsin—expanded their potential importance for global energy budgets, providing a novel mechanism to harness light energy. Yet, how proteorhodopsin-derived energy is used for cell metabolism remains largely unexplored. We combined experiments in a model marine bacterium with gene expression analyses. Light-stimulated growth coincided with a shift in carbon acquisition pathways, with anaplerotic CO
2
fixation providing up to one-third of the cell carbon. Exposure to light resulted in the up-regulation of several central metabolism genes, including the glyoxylate shunt. Thus, light provides proteorhodopsin-containing bacteria with wider means to adapt to environmental variability than previously recognized.
Illegal killing for ivory drives global decline in African elephants
Authors: Wittemyer George , Northrup Joseph M. , Blanc Julian , Douglas-Hamilton Iain , Omondi Patrick , Burnham Kenneth P.
Published: August 2014

Significance

Illegal harvest for commercial trade has recently surged to become a major threat to some of the world’s most endangered and charismatic species. Unfortunately, the cryptic nature of illegal killing makes estimation of rates and impacts difficult. Applying a model based on field census of carcasses, to our knowledge we provide the first detailed assessment of African elephant illegal killing rates at population, regional, and continental scales. Illegal harvest for commercial trade in ivory has recently surged, coinciding with increases in illegal ivory seizures and black market ivory prices. As a result, the species declined over the past 4 y, during which tens of thousands of elephants have been killed annually across the continent. Solutions to this crisis require global action.
Does aquaculture add resilience to the global food system?
Authors: Troell Max , Naylor Rosamond L. , Metian Marc , Beveridge Malcolm , Tyedmers Peter H. , Folke Carl , Arrow Kenneth J. , Barrett Scott , Crépin Anne-Sophie , Ehrlich Paul R. , Gren Åsa , Kautsky Nils , Levin Simon A. , Nyborg Karine , Österblom Henrik , Polasky Stephen , Scheffer Marten , Walker Brian H. , Xepapadeas Tasos , de Zeeuw Aart
Published: August 2014

Aquaculture is the fastest growing food sector and continues to expand alongside terrestrial crop and livestock production. Using portfolio theory as a conceptual framework, we explore how current interconnections between the aquaculture, crop, livestock, and fisheries sectors act as an impediment to, or an opportunity for, enhanced resilience in the global food system given increased resource scarcity and climate change. Aquaculture can potentially enhance resilience through improved resource use efficiencies and increased diversification of farmed species, locales of production, and feeding strategies. However, aquaculture’s reliance on terrestrial crops and wild fish for feeds, its dependence on freshwater and land for culture sites, and its broad array of environmental impacts diminishes its ability to add resilience. Feeds for livestock and farmed fish that are fed rely largely on the same crops, although the fraction destined for aquaculture is presently small (∼4%). As demand for high-value fed aquaculture products grows, competition for these crops will also rise, as will the demand for wild fish as feed inputs. Many of these crops and forage fish are also consumed directly by humans and provide essential nutrition for low-income households. Their rising use in aquafeeds has the potential to increase price levels and volatility, worsening food insecurity among the most vulnerable populations. Although the diversification of global food production systems that includes aquaculture offers promise for enhanced resilience, such promise will not be realized if government policies fail to provide adequate incentives for resource efficiency, equity, and environmental protection.
Optogenetic neuronal stimulation promotes functional recovery after stroke
Authors: Cheng Michelle Y. , Wang Eric H. , Woodson Wyatt J. , Wang Stephanie , Sun Guohua , Lee Alex G. , Arac Ahmet , Fenno Lief E. , Deisseroth Karl , Steinberg Gary K.
Published: August 2014

Significance

Stroke is the leading cause of disability in the United States and has very limited treatment options. Brain stimulation techniques that promote recovery after stroke are a promising area of research; however, current stimulation techniques nonspecifically activate/inhibit the target area, which not only leads to undesired side effects but also makes it difficult to understand which cell types and mechanisms drive recovery. We used the optogenetic technique to specifically stimulate only neurons after stroke and demonstrate that selective neuronal stimulations can activate beneficial mechanisms and promote recovery. Understanding the cell type and mechanisms driving recovery may identify potential drug targets for stroke treatment, as well as ultimately help develop precise brain stimulation techniques for stroke therapy.
Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose
Authors: Socha Aaron M. , Parthasarathi Ramakrishnan , Shi Jian , Pattathil Sivakumar , Whyte Dorian , Bergeron Maxime , George Anthe , Tran Kim , Stavila Vitalie , Venkatachalam Sivasankari , Hahn Michael G. , Simmons Blake A. , Singh Seema
Published: August 2014

Significance

Ionic liquids (ILs) have unique properties applicable to a variety of industrial processes. Nearly universal solvating capabilities, low vapor pressures, and high thermal stabilities make these compounds ideal substitutes for a wide range of organic solvents. To date, the best performing ILs are derived from nonrenewable sources such as petroleum or natural gas. Due to their potential for large-scale deployment, ILs derived from inexpensive, renewable reagents are highly desirable. Herein, we describe a process for synthesizing ILs from materials derived from lignin and hemicellulose, major components of terrestrial plant biomass. With respect to overall sugar yield, experimental evaluation of these compounds showed that they perform comparably to traditional ILs in biomass pretreatment.
Crystal structure of a nematode-infecting virus
Authors: Guo Yusong R. , Hryc Corey F. , Jakana Joanita , Jiang Hongbing , Wang David , Chiu Wah , Zhong Weiwei , Tao Yizhi J.
Published: August 2014

Significance

Since the discovery of Orsay, the first virus that naturally infects nematodes, it has been widely expected that
Caenorhabditis elegans
-Orsay would serve as a highly tractable model for studying viral pathogenesis. Here we report the crystal structure of the Orsay virus. The Orsay capsid contains 180 copies of the capsid protein, each consisting of a jelly-roll β-barrel and a protrusion domain. Although sequence analyses indicate that Orsay is related to nodaviruses, the structure reveals substantial differences compared with the insect-infecting alphanodaviruses. Small plant RNA viruses are the closest homologs for Orsay when their β-barrel domains are compared. Our results have not only shed light on the evolutionary lineage of Orsay but have also provided a framework for further studies of Orsay–host interaction.
(
R
)-PFI-2 is a potent and selective inhibitor of SETD7 methyltransferase activity in cells
Authors: Barsyte-Lovejoy Dalia , Li Fengling , Oudhoff Menno J. , Tatlock John H. , Dong Aiping , Zeng Hong , Wu Hong , Freeman Spencer A. , Schapira Matthieu , Senisterra Guillermo A. , Kuznetsova Ekaterina , Marcellus Richard , Allali-Hassani Abdellah , Kennedy Steven , Lambert Jean-Philippe , Couzens Amber L. , Aman Ahmed , Gingras Anne-Claude , Al-Awar Rima , Fish Paul V. , Gerstenberger Brian S. , Roberts Lee , Benn Caroline L. , Grimley Rachel L. , Braam Mitchell J. S. , Rossi Fabio M. V. , Sudol Marius , Brown Peter J. , Bunnage Mark E. , Owen Dafydd R. , Zaph Colby , Vedadi Masoud , Arrowsmith Cheryl H.
Published: August 2014

Significance

Protein methyltransferases constitute an emerging but undercharacterized class of therapeutic targets with diverse roles in normal human biology and disease. Small-molecule “chemical probes” can be powerful tools for the functional characterization of such enzymes, and here we report the discovery of (
R
)-PFI-2—a first-in-class, potent, highly selective, and cell-active inhibitor of the methyltransferase activity of SETD7 [SET domain containing (lysine methyltransferase) 7]—and two related compounds for control and chemoproteomics studies. We used these compounds to characterize the role of SETD7 in signaling, in the Hippo pathway, that controls cell growth and organ size. Our work establishes a chemical biology tool kit for the study of the diverse roles of SETD7 in cells and further validates protein methyltransferases as a druggable target class.
Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel
Authors: Boiteux Céline , Vorobyov Igor , French Robert J. , French Christopher , Yarov-Yarovoy Vladimir , Allen Toby W.
Published: August 2014

Significance

Voltage-gated sodium (Nav) channels control neuronal signaling and are key targets for local anesthetics, antiepileptics, and therapeutics for a range of disorders. Multimicrosecond Anton simulations have provided completely unbiased molecular-level views of the interactions of lipophilic drugs with the recently solved bacterial channel, NavAb fromArcobacter butzleri. Newly parameterized benzocaine and phenytoin molecules exhibit different membrane partition coefficients, crossing rates and distributions around the channel, leading to the identification of distinct high- and low-affinity sites. We observe a minimum free energy pathway through membrane-bound fenestrations to a pore-blocking location, or from aqueous solution directly through the (closed) intracellular gate. These observations help explain experimental data and provide insight into Navinhibition processes that will assist future drug development.
Adaptive optoelectronic camouflage systems with designs inspired by cephalopod skins
Authors: Yu Cunjiang , Li Yuhang , Zhang Xun , Huang Xian , Malyarchuk Viktor , Wang Shuodao , Shi Yan , Gao Li , Su Yewang , Zhang Yihui , Xu Hangxun , Hanlon Roger T. , Huang Yonggang , Rogers John A.
Published: August 2014

Significance

Artificial systems that replicate functional attributes of the skins of cephalopods could offer capabilities in visual appearance modulation with potential utility in consumer, industrial, and military applications. Here we demonstrate a complete set of materials, components, fabrication approaches, integration schemes, bioinspired designs, and coordinated operational modes for adaptive optoelectronic camouflage sheets. These devices are capable of producing black-and-white patterns that spontaneously match those of the surroundings, without user input or external measurement. Systematic experimental, computational, and analytical studies of the optical, electrical, thermal, and mechanical properties reveal the fundamental aspects of operation and also provide quantitative design guidelines that are applicable to future embodiments.
Mutation of
Plekha7
attenuates salt-sensitive hypertension in the rat
Authors: Endres Bradley T. , Priestley Jessica R. C. , Palygin Oleg , Flister Michael J. , Hoffman Matthew J. , Weinberg Brian D. , Grzybowski Michael , Lombard Julian H. , Staruschenko Alexander , Moreno Carol , Jacob Howard J. , Geurts Aron M.
Published: August 2014

Significance

Zinc-finger nuclease (ZFN)-mediated mutagenesis has now enabled researchers to manipulate specific genes to test their function in animal models other than mice. Applying ZFNs to rats, we can now test the role of specific human genome-wide association studies (GWAS)-nominated genes for hypertension in a well-characterized hypertensive rat model, the Dahl salt-sensitive rat. This study provides the first functional evidence that the GWAS-nominated gene
Plekha7
plays an essential role in blood pressure regulation and cardiovascular function by modulating vascular function. Our results indicate that
Plekha7
plays a role in the regulation of intracellular calcium, nitric oxide bioavailability, and the response of the vasculature to increased flow.
A wave-mechanical model of incoherent quasielastic scattering in complex systems
Authors: Frauenfelder Hans , Fenimore Paul W. , Young Robert D.
Published: August 2014

Significance

Quasielastic incoherent neutron scattering (QENS) is a key tool for the exploration of complex systems, such as liquids, polymers, glasses, and biomolecules. A considerable number of neutron facilities exist and more are being planned. Understanding QENS is important, both for comprehending and applying the science and making efficient use of the facilities. We claim that the present explanation of QENS is incomplete. We propose a wave-mechanical model, consistent with neutron diffraction. It is based on the free-energy landscape and treats the neutrons as de Broglie wave packets. The model is supported by experiments and has predictive power. It provides significant insight into the dynamics of proteins and may lead to a better understanding of biological processes.
Formation and structures of GroEL:GroES
2
chaperonin footballs, the protein-folding functional form
Authors: Fei Xue , Ye Xiang , LaRonde Nicole A. , Lorimer George H.
Published: August 2014

Significance

Symmetric, football-shaped GroEL:GroES
2
particles are the species involved in assisted protein folding. Here we show that the two rings of GroEL are simultaneously functional. The GroEL–GroES nanomachine is thus a parallel-processing device and not an alternating engine as previously thought. Crystals of the GroEL:GroES
2
particles containing the ATP analog ADP-BeF
3
were prepared both with and without an encapsulated molecule of substrate protein (Rubisco) in each of the central chambers. The structures of both of these GroEL:GroES
2
particles have been solved to ∼3.7-Å resolution. Structural changes in the equatorial plate suggest a mechanism for directly linking the ATP-binding sites of the two rings, thus accounting for inter-ring negative cooperativity.
Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam
Authors: Sawaya Michael R. , Cascio Duilio , Gingery Mari , Rodriguez Jose , Goldschmidt Lukasz , Colletier Jacques-Philippe , Messerschmidt Marc M. , Boutet Sébastien , Koglin Jason E. , Williams Garth J. , Brewster Aaron S. , Nass Karol , Hattne Johan , Botha Sabine , Doak R. Bruce , Shoeman Robert L. , DePonte Daniel P. , Park Hyun-Woo , Federici Brian A. , Sauter Nicholas K. , Schlichting Ilme , Eisenberg David S.
Published: August 2014

Significance

In vivo microcrystals have been observed in prokaryotic and eukaryotic cells. With rare exception, however, the ∼100,000 biological structures determined by X-ray crystallography to date have required the macromolecule under study to be extracted from the cells that produced it and crystallized in vitro. In vivo crystals present a challenge for structure determination and pose the question of the extent to which in vivo macromolecular structures are similar to those of extracted and recrystallized macromolecules. Here we show that serial femtosecond crystallography enabled by a free-electron laser yields the structure of in vivo crystals, as they exist in a living cell, and in this case the in vivo structure is essentially identical to the structure of extracted and recrystallized protein.
A sharp T-cell antigen receptor signaling threshold for T-cell proliferation
Authors: Au-Yeung Byron B. , Zikherman Julie , Mueller James L. , Ashouri Judith F. , Matloubian Mehrdad , Cheng Debra A. , Chen Yiling , Shokat Kevan M. , Weiss Arthur
Published: August 2014

Significance

Biochemical signals triggered by the T-cell receptor (TCR) are required for stimulating T cells and can be initiated within seconds. However, a hallmark of T-cell activation, cell division, occurs hours after TCR signaling has begun, implying that T cells require a minimum duration and/or accumulate TCR signaling events to drive proliferation. To visualize the accumulated signaling experienced by T cells, we used a fluorescent reporter gene that is activated by TCR stimulation. This technique showed a threshold between dividing and nondividing T cells for TCR signaling that does not change with stronger or weaker TCR signaling or the presence of growth factor. Together these data may have implications for the development of T-cell–targeted therapies for autoimmunity.
Immune evasion mediated by tumor-derived lactate dehydrogenase induction of NKG2D ligands on myeloid cells in glioblastoma patients
Authors: Crane Courtney A. , Austgen Kathryn , Haberthur Kristen , Hofmann Carly , Moyes Kara White , Avanesyan Lia , Fong Lawrence , Campbell Michael J. , Cooper Stewart , Oakes Scott A. , Parsa Andrew T. , Lanier Lewis L.
Published: August 2014

Significance

This study describes a mechanism of immune escape in which glioblastoma cells produce a soluble protein, lactate dehydrogenase 5 (LDH5), that induces the expression of Natural killer group 2, member D (NKG2D) ligands on the surface of healthy myeloid cells. Expression of NKG2D ligands by myeloid cells causes the down-modulation of the activating NKG2D receptor on natural killer cells, thereby preventing their recognition of NKG2D ligand-bearing tumors and impairing their ability to attack and eliminate tumors. The discovery that monocytes in patients with several types of cancer also express NKG2D ligands suggests that LDH5 production by tumors may represent a common mechanism of immune evasion. Blocking LDH5 might improve recognition of tumors in cancer patients.
From construction candidates to constructicon entries
Authors: Forsberg Markus , Johansson Richard , Bäckström Linnéa , Borin Lars , Lyngfelt Benjamin , Olofsson Joel , Prentice Julia
Published: August 2014

We present an experiment where natural language processing tools are used to automatically identify potential constructions in a corpus. The experiment was conducted as part of the ongoing efforts to develop a Swedish constructicon. Using an automatic method to suggest constructions has advantages not only for efficiency but also methodologically: it forces the analyst to look more objectively at the constructions actually occurring in corpora, as opposed to focusing on “interesting” constructions only. As a heuristic for identifying potential constructions, the method has proved successful, yielding about 200 (out of 1,200) highly relevant construction candidates.
Regime-building, identity-making and foreign policy: neo-Eurasianist rhetoric in post-Soviet Kazakhstan
Authors: Anceschi Luca
Published: August 2014

This article illustrates the evolution experienced by the identity-making strategies pursued through the propagandistic exploitation of Kazakhstani foreign policy. Periodical readjustments in the focus of foreign policy rhetoric led the Kazakhstani regime to reshape the identity of the population, in order to promote forms of self-perception almost exclusively associable with the leadership that ruled the country in the post-Soviet era. Identity-making, in this context, became a crucial link in (and a key driver for) the progressive subjugation of foreign policy rhetoric to the logic of regime-building, intended here as the ensemble of concerted efforts aimed to increase the population's compliance with the leaderships' authoritarian outlooks.
VLA-4 blockade promotes differential routes into human CNS involving PSGL-1 rolling of T cells and MCAM-adhesion of TH17 cells
Authors: Schneider-Hohendorf Tilman , Rossaint Jan , Mohan Hema , Böning Daniel , Breuer Johanna , Kuhlmann Tanja , Gross Catharina C. , Flanagan Ken , Sorokin Lydia , Vestweber Dietmar , Zarbock Alexander , Schwab Nicholas , Wiendl Heinz
Published: August 2014

The focus of this study is the characterization of human T cell blood–brain barrier migration and corresponding molecular trafficking signatures. We examined peripheral blood and cerebrospinal fluid immune cells from patients under long-term anti–very late antigen-4 (VLA-4)/natalizumab therapy (LTNT) and from CNS specimens. LTNT patients’ cerebrospinal fluid T cells exhibited healthy central-/effector-memory ratios, but lacked CD49d and showed enhanced myeloma cell adhesion molecule (MCAM) expression. LTNT led to an increase of PSGL-1 expression on peripheral T cells. Although vascular cell adhesion molecule-1 (VLA-4 receptor) was expressed at all CNS barriers, P-selectin (PSGL-1-receptor) was mainly detected at the choroid plexus. Accordingly, in vitro experiments under physiological flow conditions using primary human endothelial cells and LTNT patients’ T cells showed increased PSGL-1–mediated rolling and residual adhesion, even under VLA-4 blockade. Adhesion of MCAM+/TH17 cells was not affected by VLA-4 blocking alone, but was abrogated when both VLA-4 and MCAM were inhibited. Consistent with these data, MCAM+ cells were detected in white matter lesions, and in gray matter of multiple sclerosis patients. Our data indicate that lymphocyte trafficking into the CNS under VLA-4 blockade can occur by using the alternative adhesion molecules, PSGL-1 and MCAM, the latter representing an exclusive pathway for TH17 cells to migrate over the blood–brain barrier.