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Showing papers by "University of California published in 2012"


PatentDOI
03 Nov 2012-Nature
TL;DR: Hybrid plasmonic waveguides as discussed by the authors employ a high-gain semiconductor nanostructure functioning as a gain medium that is separated from a metal substrate surface by a nanoscale thickness thick low-index gap.
Abstract: Hybrid plasmonic waveguides are described that employ a high-gain semiconductor nanostructure functioning as a gain medium that is separated from a metal substrate surface by a nanoscale thickness thick low-index gap. The waveguides are capable of efficient generation of sub-wavelength high intensity light and have the potential for large modulation bandwidth >1 THz.

2,060 citations


PatentDOI
TL;DR: In this article, a chemical approach to immobilize sulfur and lithium polysulfides via the reactive functional groups on graphene oxide was proposed, which obtains a uniform and thin (˜tens of nanometers) sulfur coating.
Abstract: The loss of sulfur cathode material as a result of polysulfide dissolution causes significant capacity fading in rechargeable lithium/sulfur cells. Embodiments of the invention use a chemical approach to immobilize sulfur and lithium polysulfides via the reactive functional groups on graphene oxide. This approach obtains a uniform and thin (˜tens of nanometers) sulfur coating on graphene oxide sheets by a chemical reaction-deposition strategy and a subsequent low temperature thermal treatment process. Strong interaction between graphene oxide and sulfur or polysulfides demonstrate lithium/sulfur cells with a high reversible capacity of 950-1400 mAh g −1 , and stable cycling for more than 50 deep cycles at 0.1 C.

1,350 citations


Book ChapterDOI
01 Jan 2012
TL;DR: In this article, the authors argue that success lies in being able to communicate, share, and use information to solve complex problems, in adapting and innovating in response to new demands and changing circumstances, in marshaling and expanding the power of technology to create new knowledge, and in expanding human capacity and productivity.
Abstract: As the previous chapter indicates, there has been a significant shift in advanced economies from manufacturing to information and knowledge services. Knowledge itself is growing ever more specialized and expanding exponentially. Information and communication technology is transforming the nature of how work is conducted and the meaning of social relationships. Decentralized decision making, information sharing, teamwork, and innovation are key in today’s enterprises. No longer can students look forward to middle class success in the conduct of manual labor or use of routine skills – work that can be accomplished by machines. Rather, whether a technician or a professional person, success lies in being able to communicate, share, and use information to solve complex problems, in being able to adapt and innovate in response to new demands and changing circumstances, in being able to marshal and expand the power of technology to create new knowledge, and in expanding human capacity and productivity.

1,056 citations


Journal ArticleDOI
TL;DR: A high-quality reference genome sequence for foxtail millet (Setaria italica) is generated and regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion are identified.
Abstract: We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

758 citations


Journal ArticleDOI
TL;DR: The first 1 fb−1 of LHC searches have set impressive limits on new colored particles decaying to missing energy, and the implication of these searches for naturalness in supersymmetry (SUSY) is addressed in this paper.
Abstract: The first 1 fb−1 of LHC searches have set impressive limits on new colored particles decaying to missing energy. We address the implication of these searches for naturalness in supersymmetry (SUSY). General bottom-up considerations of natural electroweak symmetry breaking show that higgsinos, stops, and the gluino should not be too far above the weak scale. The rest of the spectrum, including the squarks of the first two generations, can be heavier and beyond the current LHC reach. We have used collider simulations to determine the limits that all of the 1 fb−1 searches pose on higgsinos, stops, and the gluino. We find that stops and the left-handed sbottom are starting to be constrained and must be heavier than about 200–300 GeV when decaying to higgsinos. The gluino must be heavier than about 600–800 GeV when it decays to stops and sbottoms. While these findings point toward scenarios with a lighter third generation split from the other squarks, we do find that moderately-tuned regions remain, where the gluino is just above 1 TeV and all the squarks are degenerate and light. Among all the searches, jets plus missing energy and same-sign dileptons often provide the most powerful probes of natural SUSY. Overall, our results indicate that natural SUSY has survived the first 1 fb−1 of data. The LHC is now on the brink of exploring the most interesting region of SUSY parameter space.

573 citations


Patent
04 Dec 2012
TL;DR: In this paper, an expert system manages a power grid wherein charging stations are connected to the power grid, with electric vehicles connected to charging stations, whereby the expert system selectively backfills power from connected electric vehicles to the grid through a grid tie inverter (if present) within the charging stations.
Abstract: An expert system manages a power grid wherein charging stations are connected to the power grid, with electric vehicles connected to the charging stations, whereby the expert system selectively backfills power from connected electric vehicles to the power grid through a grid tie inverter (if present) within the charging stations. In more traditional usage, the expert system allows for electric vehicle charging, coupled with user preferences as to charge time, charge cost, and charging station capabilities, without exceeding the power grid capacity at any point. A robust yet accurate state of charge (SOC) calculation method is also presented, whereby initially an open circuit voltage (OCV) based on sampled battery voltages and currents is calculated, and then the SOC is obtained based on a mapping between a previously measured reference OCV (ROCV) and SOC. The OCV-SOC calculation method accommodates likely any battery type with any current profile.

455 citations


Journal ArticleDOI
TL;DR: This review sets out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues.
Abstract: Despite the efforts that bioengineers have exerted in designing and constructing biological processes that function according to a predetermined set of rules, their operation remains fundamentally circumstantial. The contextual situation in which molecules and single-celled or multi-cellular organisms find themselves shapes the way they interact, respond to the environment and process external information. Since the birth of the field, synthetic biologists have had to grapple with contextual issues, particularly when the molecular and genetic devices inexplicably fail to function as designed when tested in vivo. In this review, we set out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues.

438 citations


Book ChapterDOI
27 Feb 2012
TL;DR: In this paper, the authors perform an in-depth investigation to understand what made Bitcoin so successful, while decades of research on cryptographic e-cash has not lead to a large-scale deployment.
Abstract: Bitcoin is a distributed digital currency which has attracted a substantial number of users. We perform an in-depth investigation to understand what made Bitcoin so successful, while decades of research on cryptographic e-cash has not lead to a large-scale deployment. We ask also how Bitcoin could become a good candidate for a long-lived stable currency. In doing so, we identify several issues and attacks of Bitcoin, and propose suitable techniques to address them.

430 citations


Journal ArticleDOI
06 Jul 2012-Planta
TL;DR: The different sources of ROS that are present in plant cells and their role in the oxidative burst are discussed, and two well-studied ROS generating systems are described, the NADPH oxidase and apoplastic peroxidase proteins, and their roles as the primary producers of ROS during pathogen invasion.
Abstract: Harnessing the toxic properties of reactive oxygen species (ROS) to fight off invading pathogens can be considered a major evolutionary success story. All aerobic organisms have evolved the ability to regulate the levels of these toxic intermediates, whereas some have evolved elaborate signalling pathways to dramatically increase the levels of ROS and use them as weapons in mounting a defence response, a process commonly referred to as the oxidative burst. The balance between steady state levels of ROS and the exponential increase in these levels during the oxidative burst has begun to shed light on complex signalling networks mediated by these molecules. Here, we discuss the different sources of ROS that are present in plant cells and review their role in the oxidative burst. We further describe two well-studied ROS generating systems, the NADPH oxidase and apoplastic peroxidase proteins, and their role as the primary producers of ROS during pathogen invasion. We then discuss what is known about the metabolic and proteomic fluxes that occur in plant cells during the oxidative burst and after pathogen recognition, and try to highlight underlying biochemical processes that may provide more insight on the complex regulation of ROS in plants.

425 citations


Journal ArticleDOI
TL;DR: In this article, the naturalness of a Higgs boson with a mass near 125 GeV is explored in a variety of weak-scale supersymmetric models, showing that a mass of this size strongly points towards a non-minimal implementation of supersymmetry.
Abstract: The naturalness of a Higgs boson with a mass near 125 GeV is explored in a variety of weak-scale supersymmetric models. A Higgs mass of this size strongly points towards a non-minimal implementation of supersymmetry. The Minimal Supersymmetric Standard Model now requires large A-terms to avoid multi-TeV stops. The ne-tuning is at least 1% for low messenger scales, and an order of magnitude worse for high messenger scales. Naturalness is signicantly improved in theories with a singlet supereld

417 citations


Journal ArticleDOI
TL;DR: The addition of bevacizumab to neoadjuvant chemotherapy significantly increased the rate of pathological complete response, which was the primary end point of this study.
Abstract: A B S T R AC T BACKGROUND Bevacizumab and the antimetabolites capecitabine and gemcitabine have been shown to improve outcomes when added to taxanes in patients with metastatic breast cancer. The primary aims of this trial were to determine whether the addition of capecitabine or gemcitabine to neoadjuvant chemotherapy with docetaxel, followed by doxorubicin plus cyclophosphamide, would increase the rates of pathological complete response in the breast in women with operable, human epidermal growth factor receptor 2 (HER2)–negative breast cancer and whether adding bevacizumab to these chemotherapy regimens would increase the rates of pathological complete response. METHODS

Journal ArticleDOI
TL;DR: The findings indicate that students tended to be more engaged in courses where the instructor consistently signaled an openness to student questions and recognizes her/his role in helping students succeed.
Abstract: The lack of academic engagement in introductory science courses is considered by some to be a primary reason why students switch out of science majors. This study employed a sequential, explanatory mixed methods approach to provide a richer understanding of the relationship between student engagement and introductory science instruction. Quantitative survey data were drawn from 2,873 students within 73 introductory science, technology, engineering, and mathematics (STEM) courses across 15 colleges and universities, and qualitative data were collected from 41 student focus groups at eight of these institutions. The findings indicate that students tended to be more engaged in courses where the instructor consistently signaled an openness to student questions and recognizes her/his role in helping students succeed. Likewise, students who reported feeling comfortable asking questions in class, seeking out tutoring, attending supplemental instruction sessions, and collaborating with other students in the course were also more likely to be engaged. Instructional implications for improving students' levels of academic engagement are discussed.

Journal ArticleDOI
TL;DR: In this paper, a new numerical algorithm based on semidefinite programming was introduced to efficiently compute bounds on operator dimensions, central charges, and OPE coefficients in 4D conformal and superconformal field theories.
Abstract: We introduce a new numerical algorithm based on semidefinite programming to efficiently compute bounds on operator dimensions, central charges, and OPE coefficients in 4D conformal and $$ \mathcal{N} = 1 $$ superconformal field theories. Using our algorithm, we dramatically improve previous bounds on a number of CFT quantities, particularly for theories with global symmetries. In the case of SO(4) or SU(2) symmetry, our bounds severely constrain models of conformal technicolor. In $$ \mathcal{N} = 1 $$ superconformal theories, we place strong bounds on dim(Φ†Φ), where Φ is a chiral operator. These bounds asymptote to the line dim(Φ†Φ) ≤ 2 dim(Φ) near dim(Φ) ≃ 1, forbidding positive anomalous dimensions in this region. We also place novel upper and lower bounds on OPE coefficients of protected operators in the Φ × Φ OPE. Finally, we find examples of lower bounds on central charges and flavor current two-point functions that scale with the size of global symmetry representations. In the case of $$ \mathcal{N} = 1 $$ theories with an SU(N) flavor symmetry, our bounds on current two-point functions lie within an O(1) factor of the values realized in supersymmetric QCD in the conformal window.

Journal ArticleDOI
TL;DR: Random phase approximation (RPA) is a promising post-Kohn-Sham method to treat electron correlation in molecules, surfaces, and solids as mentioned in this paper, and it has been applied to various molecular and solid-state properties, including relative energies of conformers, reaction energies involving weak and covalent interactions.
Abstract: In the past decade, the random phase approximation (RPA) has emerged as a promising post-Kohn–Sham method to treat electron correlation in molecules, surfaces, and solids. In this review, we explain how RPA arises naturally as a zero-order approximation from the adiabatic connection and the fluctuation-dissipation theorem in a density functional context. This is contrasted to RPA with exchange (RPAX) in a post-Hartree–Fock context. In both methods, RPA and RPAX, the correlation energy may be expressed as a sum over zero-point energies of harmonic oscillators representing collective electronic excitations, consistent with the physical picture originally proposed by Bohm and Pines. The extra factor 1/2 in the RPAX case is rigorously derived. Approaches beyond RPA are briefly summarized. We also review computational strategies implementing RPA. The combination of auxiliary expansions and imaginary frequency integration methods has lead to recent progress in this field, making RPA calculations affordable for systems with over 100 atoms. Finally, we summarize benchmark applications of RPA to various molecular and solid-state properties, including relative energies of conformers, reaction energies involving weak and covalent interactions, diatomic potential energy curves, ionization potentials and electron affinities, surface adsorption energies, bulk cohesive energies and lattice constants. RPA barrier heights for an extended benchmark set are presented. RPA is an order of magnitude more accurate than semi-local functionals such as B3LYP for non-covalent interactions rivaling the best empirically parametrized methods. Larger but systematic errors are observed for processes that do not conserve the number of electron pairs, such as atomization and ionization.

PatentDOI
26 Dec 2012-Science
TL;DR: The use of chiral cation salts as phase-transfer catalysts for anionic reagents has enabled a vast set of enantioselective transformations as discussed by the authors, such as the fluorocyclization of olefins and dearomatization of aromatic systems with a cationic electrophile transferring (e.g., fluorinating) agent and a chiral phosphate catalyst.
Abstract: The discovery of distinct modes of asymmetric catalysis has the potential to rapidly advance chemists' ability to build enantioenriched molecules. As an example, the use of chiral cation salts as phase-transfer catalysts for anionic reagents has enabled a vast set of enantioselective transformations. A largely overlooked analogous mechanism wherein a chiral anionic catalyst brings a cationic species into solution is itself a powerful method. The concept is broadly applicable to a number of different reaction pathways, including to the enantioselective fluorocyclization of olefins, and dearomatization of aromatic systems with a cationic electrophile-transferring (e.g., fluorinating) agent and a chiral phosphate catalyst. The reactions proceed in high yield and stereoselectivity. The compounds and methods of the invention are of particular value, especially considering the scarcity of alternative approaches.

Journal ArticleDOI
TL;DR: In this article, it was shown that the positron fraction measured by PAMELA and the peculiar spectral features reported in the total electron-positron flux measured by ATIC have a very natural explanation in the injected electron positron pairs produced by nearby pulsars.
Abstract: We argue that both the positron fraction measured by PAMELA and the peculiar spectral features reported in the total electron-positron flux measured by ATIC have a very natural explanation in electron-positron pairs produced by nearby pulsars. While this possibility was pointed out a long time ago, the greatly improved quality of current data potentially allow to reverse-engineer the problem: given the regions of pulsar parameter space favored by PAMELA and by ATIC, are there known pulsars that explain the data with reasonable assumptions on the injected electron-positron pairs? In the context of simple benchmark models for estimating the electron-positron output, we consider all known pulsars, as listed in the most complete available catalogue. We find that it is unlikely that a single pulsar be responsible for both the PAMELA positron fraction anomaly and for the ATIC excess, although two single sources are in principle enough to explain both experimental results. The PAMELA excess positrons likely come from a set of mature pulsars (age ∼ × 106 yr), with a distance of 0.8–1 kpc, or from a single, younger and closer source like Geminga. The ATIC data require a larger (and less plausible) energy output, and favor an origin associated to powerful, more distant (1–2 kpc) and younger (age ∼ × 5 × 105 yr) pulsars. We list several candidate pulsars that can individually or coherently contribute to explain the PAMELA and ATIC data. Although generally suppressed, we find that the contribution of pulsars more distant than 1–2 kpc could contribute for the ATIC excess. Finally, we stress the multi-faceted and decisive role that Fermi-LAT will play in the very near future by (1) providing us with an exquisite measurement of the electron-positron flux, (2) unveiling the existence of as yet undetected gamma-ray pulsars, and (3) searching for anisotropies in the arrival direction of high-energy electrons and positrons.

Journal ArticleDOI
TL;DR: A unified nomenclature for variants of all five classes of histones is proposed that uses consistent but flexible naming conventions to produce names that are informative and readily searchable and incorporates phylogenetic relationships, which are strong predictors of structure and function.
Abstract: Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for them has led to a variety of naming styles, multiple synonyms and misleading homographs that obscure variant relationships and complicate database searches. We propose here a unified nomenclature for variants of all five classes of histones that uses consistent but flexible naming conventions to produce names that are informative and readily searchable. The nomenclature builds on historical usage and incorporates phylogenetic relationships, which are strong predictors of structure and function. A key feature is the consistent use of punctuation to represent phylogenetic divergence, making explicit the relationships among variant subtypes that have previously been implicit or unclear. We recommend that by default new histone variants be named with organism-specific paralog-number suffixes that lack phylogenetic implication, while letter suffixes be reserved for structurally distinct clades of variants. For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure.

Book ChapterDOI
10 Sep 2012
TL;DR: DNADroid, a tool that detects Android application copying, or “cloning”, by robustly computing the similarity between two applications is presented, which achieves this by comparing program dependency graphs between methods in candidate applications.
Abstract: We present DNADroid, a tool that detects Android application copying, or “cloning”, by robustly computing the similarity between two applications. DNADroid achieves this by comparing program dependency graphs between methods in candidate applications. Using DNADroid, we found at least 141 applications that have been the victims of cloning, some as many as seven times. DNADroid has a very low false positive rate — we manually confirmed that all the applications detected are indeed clones by either visual or behavioral similarity. We present several case studies that give insight into why applications are cloned, including localization and redirecting ad revenue. We describe a case of malware being added to an application and show how DNADroid was able to detect two variants of the same malware. Lastly, we offer examples of an open source cracking tool being used in the wild.

Journal ArticleDOI
TL;DR: In this article, the authors review the emerging field of high energy atmospheric physics, including the production of runaway electrons, the production and propagation of energetic radiation, and the effects of both on atmospheric electrodynamics.
Abstract: It is now well established that both thunderclouds and lightning routinely emit x-rays and gamma-rays. These emissions appear over wide timescales, ranging from sub-microsecond bursts of x-rays associated with lightning leaders, to sub-millisecond bursts of gamma-rays seen in space called terrestrial gamma-ray flashes, to minute long glows from thunderclouds seen on the ground and in or near the cloud by aircraft and balloons. In particular, terrestrial gamma-ray flashes (TGFs), which are thought to be emitted by thunderclouds, are so bright that they sometimes saturate detectors on spacecraft hundreds of kilometers away. These TGFs also generate energetic secondary electrons and positrons that are detected by spacecraft in the inner magnetosphere. It is generally believed that these x-ray and gamma-ray emissions are generated, via bremsstrahlung, by energetic runaway electrons that are accelerated by electric fields in the atmosphere. In this paper, we review this newly emerging field of High-Energy Atmospheric Physics, including the production of runaway electrons, the production and propagation of energetic radiation, and the effects of both on atmospheric electrodynamics.

Journal ArticleDOI
Allan Bradley1, Konstantinos Anastassiadis2, Abdelkader Ayadi, James F. Battey3, Cindy Bell4, Marie-Christine Birling, Joanna Bottomley1, Steve D.M. Brown, Antje Bürger5, Carol J. Bult, Wendy Bushell1, Francis S. Collins3, Christian Desaintes, Brendan Doe, Aris N. Economides6, Janan T. Eppig, Richard H. Finnell7, Richard H. Finnell8, Colin Fletcher3, Martin Fray, David Frendewey6, Roland H. Friedel9, Roland H. Friedel5, Frank Grosveld10, Jens Hansen5, Yann Herault, Geoffrey G. Hicks11, Andreas Hörlein5, Richard Houghton1, Martin Hrabé de Angelis, Danny Huylebroeck12, Vivek Iyer1, Pieter J. de Jong13, James A. Kadin, Cornelia Kaloff5, Karen Kennedy1, Manousos Koutsourakis1, Kevin C K Lloyd14, Susan Marschall, Jeremy Mason, Colin McKerlie, Michael P. McLeod8, Harald von Melchner15, Mark Moore3, Alejandro O. Mujica6, Alejandro O. Mujica1, Andras Nagy9, Mikhail Nefedov13, Lauryl M. J. Nutter, Guillaume Pavlovic, Jane Peterson3, Jonathan D. Pollock16, Ramiro Ramirez-Solis1, Derrick E. Rancourt17, Marcello Raspa, Jacques E. Remacle, Martin Ringwald, Barry Rosen1, Nadia Rosenthal18, Janet Rossant, Patricia Ruiz Noppinger19, Edward Ryder1, Joel Schick5, Frank Schnütgen15, Paul N. Schofield20, Claudia Seisenberger5, Mohammed Selloum, Elizabeth M. Simpson21, William C. Skarnes1, Damian Smedley18, Damian Smedley1, William L. Stanford22, A. Francis Stewart2, Kevin R. Stone, Kate Swan4, Hamsa D. Tadepally, Lydia Teboul, Glauco P. Tocchini-Valentini, David M. Valenzuela6, Anthony P. West1, Ken Ichi Yamamura23, Yuko Yoshinaga13, Wolfgang Wurst5, Wolfgang Wurst24 
TL;DR: The IKMC materials considerably enhance functional gene annotation of the mammalian genome and will have a major impact on future biomedical research.
Abstract: In 2007, the International Knockout Mouse Consortium (IKMC) made the ambitious promise to generate mutations in virtually every protein-coding gene of the mouse genome in a concerted worldwide action. Now, 5 years later, the IKMC members have developed high-throughput gene trapping and, in particular, gene-targeting pipelines and generated more than 17,400 mutant murine embryonic stem (ES) cell clones and more than 1,700 mutant mouse strains, most of them conditional. A common IKMC web portal (www.knockoutmouse.org) has been established, allowing easy access to this unparalleled biological resource. The IKMC materials considerably enhance functional gene annotation of the mammalian genome and will have a major impact on future biomedical research.

Journal ArticleDOI
TL;DR: Based on the same data source of Landsat TM/ETM+ in 1990s, 2000s and 2010s, all urban built-up areas in China are mapped mainly by human interpretation as mentioned in this paper.
Abstract: Based on the same data source of Landsat TM/ETM+ in 1990s, 2000s and 2010s, all urban built-up areas in China are mapped mainly by human interpretation. Mapping results were checked and refined by the same analyst with the same set of criteria. The results show during the last 20 years urban areas in China have increased exponentially more than 2 times. The greatest area of urbanization changed from Northeastern provinces in 1990s to the Southeast coast of China in Jiangsu, Guangdong, Shandong, and Zhejiang in 2010s. Urban areas are mostly converted from croplands in China. Approximately 17750 km2 croplands were converted into urban lands. Furthermore, the conversion from 2000 to 2010 doubled that from 1990 to 2000. During the 20 years, the most urbanized provinces are Jiangsu, Guangdong, Shandong and Zhejiang. We also analyzed built-up areas, gross domestic production (GDP) and population of 147 cities with a population of greater than 500000 in 2009. The result shows coastal cities and resource-based cities are with high economic efficiency per unit of built-up areas, resource-based cities have the highest population density, and the economic efficiency of most coastal provinces are lower than central provinces and Guangdong. The newly created urban expansion dataset is useful in many fields including trend analysis of urbanization in China; simulation of urban development dynamics; analysis of the relationship among urbanization, population growth and migration; studies of carbon emissions and climate change; adaptation of climate change; as well as land use and urban planning and management.

Journal ArticleDOI
TL;DR: A 454-based whole genome shotgun sequence has been assembled, which covers 69% of the predicted genome size and 96% of protein-coding gene space, and an efficient genotyping-by-sequencing (GBS) approach is being developed to catalog SNPs both within the mapping population and among diverse African farmer-preferred varieties of cassava.
Abstract: The starchy swollen roots of cassava provide an essential food source for nearly a billion people, as well as possibilities for bioenergy, yet improvements to nutritional content and resistance to threatening diseases are currently impeded. A 454-based whole genome shotgun sequence has been assembled, which covers 69% of the predicted genome size and 96% of protein-coding gene space, with genome finishing underway. The predicted 30,666 genes and 3,485 alternate splice forms are supported by 1.4 M expressed sequence tags (ESTs). Maps based on simple sequence repeat (SSR)-, and EST-derived single nucleotide polymorphisms (SNPs) already exist. Thanks to the genome sequence, a high-density linkage map is currently being developed from a cross between two diverse cassava cultivars: one susceptible to cassava brown streak disease; the other resistant. An efficient genotyping-by-sequencing (GBS) approach is being developed to catalog SNPs both within the mapping population and among diverse African farmer-preferred varieties of cassava. These resources will accelerate marker-assisted breeding programs, allowing improvements in disease-resistance and nutrition, and will help us understand the genetic basis for disease resistance.

Journal ArticleDOI
TL;DR: In this paper, the authors consider branes in refined topological strings and show that their wave-functions satisfy a Schrodinger equation depending on multiple times and prove this in the case where the topological string has a dual matrix model description.
Abstract: We consider branes in refined topological strings We argue that their wave-functions satisfy a Schrodinger equation depending on multiple times and prove this in the case where the topological string has a dual matrix model description Furthermore, in the limit where one of the equivariant rotations approaches zero, the brane partition function satisfies a time-independent Schrodinger equation We use this observation, as well as the back reaction of the brane on the closed string geometry, to offer an explanation of the connection between integrable systems and N = 2 gauge systems in four dimensions observed by Nekrasov and Shatashvili

Proceedings Article
01 May 2012
TL;DR: This paper presents the Internet Argument Corpus, a set of 390,704 posts in 11,800 discussions extracted from the online debate site 4forums.com, and discusses the relationship between discourse marker pragmatics, agreement, emotionality, and sarcasm in the IAC corpus.
Abstract: Deliberative, argumentative discourse is an important component of opinion formation, belief revision, and knowledge discovery; it is a cornerstone of modern civil society. Argumentation is productively studied in branches ranging from theoretical artificial intelligence to political rhetoric, but empirical analysis has suffered from a lack of freely available, unscripted argumentative dialogs. This paper presents the Internet Argument Corpus (IAC), a set of 390,704 posts in 11,800 discussions extracted from the online debate site 4forums.com. A 2866 thread/130,206 post extract of the corpus has been manually sided for topic of discussion, and subsets of this topic-labeled extract have been annotated for several dialogic and argumentative markers: degrees of agreement with a previous post, cordiality, audience-direction, combativeness, assertiveness, emotionality of argumentation, and sarcasm. As an application of this resource, the paper closes with a discussion of the relationship between discourse marker pragmatics, agreement, emotionality, and sarcasm in the IAC corpus.

Journal ArticleDOI
TL;DR: The authors conducted a meta-analysis of 42 published microbial responses to fire and found that fire reduced microbial abundance by an average of 33.2% in boreal and temperate forests but not following grasslands fires.
Abstract: Soil microbes regulate the transfer of carbon (C) from ecosystems to the atmosphere and in doing so influence feedbacks between terrestrial ecosystems and global climate change. Fire is one element of global change that may influence soil microbial communities and, in turn, their contribution to the C dynamics of ecosystems. In order to improve our understanding of how fire influences belowground communities, we conducted a meta-analysis of 42 published microbial responses to fire. We hypothesized that microbial biomass as a whole, and fungal biomass specifically, would be altered following fires. Across all studies, fire reduced microbial abundance by an average of 33.2% and fungal abundance by an average of 47.6%. However, microbial responses to fire differed significantly among biomes and fire types. For example, microbial biomass declined following fires in boreal and temperate forests but not following grasslands fires. In addition, wildfires lead to a greater reduction in microbial biomass than prescribed burns. These differences are likely attributable to differences in fire severity among biomes and fire types. Changes in microbial abundance were significantly correlated with changes in soil CO2 emissions. Altogether, these results suggest that fires may significantly decrease microbial abundance, with corresponding consequences for soil CO2 emissions.

Journal ArticleDOI
TL;DR: This review describes how holocentricity may be identified through cytological and molecular methods and how extensive genome sequencing and experiments in nonmodel organisms may allow Holocentric chromosomes to shed light on general principles of chromosome segregation.
Abstract: In most eukaryotes, the kinetochore protein complex assembles at a single locus termed the centromere to attach chromosomes to spindle microtubules. Holocentric chromosomes have the unusual property of attaching to spindle microtubules along their entire length. Our mechanistic understanding of holocentric chromosome function is derived largely from studies in the nematode Caenorhabditis elegans, but holocentric chromosomes are found over a broad range of animal and plant species. In this review, we describe how holocentricity may be identified through cytological and molecular methods. By surveying the diversity of organisms with holocentric chromosomes, we estimate that the trait has arisen at least 13 independent times (four times in plants and at least nine times in animals). Holocentric chromosomes have inherent problems in meiosis because bivalents can attach to spindles in a random fashion. Interestingly, there are several solutions that have evolved to allow accurate meiotic segregation of holocentric chromosomes. Lastly, we describe how extensive genome sequencing and experiments in nonmodel organisms may allow holocentric chromosomes to shed light on general principles of chromosome segregation.

Journal ArticleDOI
TL;DR: Wang et al. as mentioned in this paper analyzed the 2008 wetland distribution in China and discussed wetland changes and their drivers over the past 30 years using four wetland maps for all China have been produced, based on Landsat and CBERS-02B remote sensing data.
Abstract: Four wetland maps for all China have been produced, based on Landsat and CBERS-02B remote sensing data between 1978 and 2008 (1978, 1990, 2000 and 2008). These maps were mainly developed by manual interpretation and validated by substantial field investigation in 2009. Based on these maps, we analyzed the 2008 wetland distribution in China and discussed wetland changes and their drivers over the past 30 years. (i) There were about 324097 km(2) of wetlands in 2008, for which inland marshes or swamps were the most common wetland type (35%), with lakes (26%) second. Most of the wetlands were in Heilongjiang, Inner Mongolia, Qinghai and Tibet, occupying about 55% of the national wetland area. (ii) From 1978 to 2008, China's wetland area continually and significantly decreased, by about 33% based on changes in the wetland map. This was in sharp contrast to the increase in artificial wetlands, which increased by about 122%. Inland marshes accounted for the main loss of total wetlands from 1978 to 2000. From 2000 through 2008, riverine and lacustrine wetlands constituted the main wetland loss. Fortunately however, the rate of wetland loss decreased from 5523 to 831 km(2)/a. (iii) The change ratio of lost natural wetlands (including inland and coastal wetlands) to non-wetlands has decreased slightly over the past 30 years. From 1978 to 1990, nearly all natural wetlands (98%) lost were transformed into non-wetlands. However, the ratio declined to 86% from 1990 to 2000, and to 77% from 2000 to 2008. (iv) All Chinese provinces were divided into three groups according to patterns of wetland changes, which could relate to the driving forces of such changes. Tibet was completely different from other provinces, as it was one representative example in which there was a net wetland increase, because of global warming and decreased human activity since 1990. Increased economic development caused considerable wetland loss in most eastern provinces, and artificial wetlands increased.

Book ChapterDOI
01 Jan 2012
TL;DR: In this article, instead of looking at dispersion relative to a fixed point, the authors consider the spread of a random variable throughout its distribution, which does not require the assumption of symmetry but which even in the symmetric case does not coincide with the concept considered in BL III.
Abstract: Ordering by spread. In the preceding paper of this series [1] (to which we refer as BL III) we studied the dispersion of a symmetric distribution about its center of symmetry. In the present paper we study a related aspect of dispersion, which does not require the assumption of symmetry but which even in the symmetric case does not coincide with the concept considered in BL III. Roughly speaking, instead of looking at dispersion relative to a fixed point, we now consider the spread of a random variable throughout its distribution. The difference is perhaps best explained in terms of an example.

Journal ArticleDOI
TL;DR: This overview addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies on the impacts of climate change on plant health, using Sudden Oak Death as an introductory case study.
Abstract: There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases. This overview addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies ontheimpactsofclimatechangeonplant health.Sudden Oak Death is used as an introductory case study: Cali- fornian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronic- ity between host cambium activity and pathogen colonization rate. A summary of observed and pre- dicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Predic- tion and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertain- ty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to in- terdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in moun- tain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (includ- ing our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycor- rhiza, using long-term and large-scale datasets and considering various plant disease control methods.

Journal ArticleDOI
TL;DR: In this paper, a measure of holographic information based on a causal wedge construction is proposed to quantify the amount of information contained in a given spatial region in field theory, which is an extremal surface on the boundary of the bulk causal wedge.
Abstract: We propose a measure of holographic information based on a causal wedge construction. The motivation behind this comes from an attempt to understand how boundary field theories can holographically reconstruct spacetime. We argue that given the knowledge of the reduced density matrix in a spatial region of the boundary, one should be able to reconstruct at least the corresponding bulk causal wedge. In attempt to quantify the ‘amount of information’ contained in a given spatial region in field theory, we consider a particular bulk surface (specifically a co-dimension two surface in the bulk spacetime which is an extremal surface on the boundary of the bulk causal wedge), and propose that the area of this surface, measured in Planck units, naturally quantifies the information content. We therefore call this area the causal holographic information. We also contrast our ideas with earlier studies of holographic entanglement entropy. In particular, we establish that the causal holographic information, whilst not being a von Neumann entropy, curiously enough agrees with the entanglement entropy in all cases where one has a microscopic understanding of entanglement entropy.