bluuebunny/crossref_metadata_2025 huggingface dataset:
p53 suppression partially rescues the mutant phenotype in mouse models of DiGeorge syndrome
Authors: Caprio Cinzia , Baldini Antonio
Published: September 2014

Significance

The 22q11.2 deletion is the most common known genetic cause of congenital heart disease (CHD). The haploinsufficiency of
TBX1
has been identified as the cause of CHD. Using mouse models of the disease, we found that reduced dosage of p53 suppresses the
Tbx1
mutant phenotype. Tbx1 and p53 proteins coregulate the gene
Gbx2
, which is required for cardiovascular development.
Gbx2
expression is positively regulated by Tbx1, whereas suppression of p53 results in reduced levels of the repressive chromatin mark H3K27me3 at a genetic element occupied by both Tbx1 and p53. These data illustrate a mechanism by which reduced p53, by genetic or pharmacological means, can counterbalance the consequences of reduced dosage of Tbx1.
Children’s strategic theory of mind
Authors: Sher Itai , Koenig Melissa , Rustichini Aldo
Published: September 2014

Significance

Human interaction requires reasoning not only about other people’s observed behavior and mental states but also about their incentives and goals. The development of children’s strategic thinking is not well understood, leaving open critical questions about early human capacity for strategic interaction. We investigated strategic reasoning in 3- to 9-y-old children and adults in two strategic games that represent prevalent aspects of social interaction: incentives to mislead and competition. We find that despite strategic differences in the two games, by the age of 7 y, children’s behavior is similar to that of adults. Our findings also show an early sophisticated ability to think strategically about others in both static and repeated interactions.
Quantifying the benefits of vehicle pooling with shareability networks
Authors: Santi Paolo , Resta Giovanni , Szell Michael , Sobolevsky Stanislav , Strogatz Steven H. , Ratti Carlo
Published: September 2014

Significance

Recent advances in information technologies have increased our participation in “sharing economies,” where applications that allow networked, real-time data exchange facilitate the sharing of living spaces, equipment, or vehicles with others. However, the impact of large-scale sharing on sustainability is not clear, and a framework to assess its benefits quantitatively is missing. For this purpose, we propose the method of shareability networks, which translates spatio-temporal sharing problems into a graph-theoretic framework that provides efficient solutions. Applying this method to a dataset of 150 million taxi trips in New York City, our simulations reveal the vast potential of a new taxi system in which trips are routinely shareable while keeping passenger discomfort low in terms of prolonged travel time.
Oxygenic photosynthesis without galactolipids
Authors: Awai Koichiro , Ohta Hiroyuki , Sato Naoki
Published: September 2014

Significance

Cyanobacteria, as well as chloroplasts of plants and algae, are the sites of photosynthesis that produces oxygen. Photosynthetic membranes, also known as thylakoid membranes, in these organisms contain galactolipids, without exception, as the major components. Galactolipids are thus believed to be important for photosynthesis or at least for the formation of the flattened shape of thylakoid membranes. The biosynthetic pathway of galactolipids is definitely different in plants and cyanobacteria. Here we identified the final piece of the long-sought gene for the galactolipid synthesis in cyanobacteria, namely monoglucosyldiacylglycerol epimerase, which converts glucolipid to galactolipid. Cyanobacterial mutants in which this gene is disrupted still formed authentic thylakoid membranes without galactolipids and kept the ability to grow photosynthetically, indicating that galactolipids are not essential for either oxygenic photosynthesis or the development of the thylakoid membrane structure.
Epigenetic role for the conserved Fe-S cluster biogenesis protein AtDRE2 in
Arabidopsis thaliana
Authors: Buzas Diana Mihaela , Nakamura Miyuki , Kinoshita Tetsu
Published: September 2014

Significance

Eukaryotic nuclear genomes store epigenetic information independent of DNA sequence, for example, in the form of 5-methylcytosine (5mC). In organisms as diverse as mammals and flowering plants, removal of 5mC profoundly impacts transcription and reproductive development. We found that the highly conserved protein DRE2 in
Arabidopsis
controls maternal gene expression and seed development by reducing DNA methylation in the maternal, central cell gamete. An antiapoptotic factor, essential from yeast to human, Dre2 is best known as an assembly component for iron and sulfur into cofactors termed Fe-S clusters and has continually emerging biological roles and functions. To our knowledge, we demonstrate the first epigenetic role for Dre2 in any organism.
A
TNFSF15
disease-risk polymorphism increases pattern-recognition receptor-induced signaling through caspase-8–induced IL-1
Authors: Hedl Matija , Abraham Clara
Published: September 2014

Significance

This study describes a role for tumor necrosis factor ligand superfamily member 15 (TNFSF15), a molecule being considered for therapy in inflammatory diseases. We identify that death receptor 3 (DR3) is clearly expressed on human macrophages and define a new role for TNFSF15:DR3 signaling in mediating innate immune outcomes in human myeloid-derived cells, as well as mechanisms mediating these outcomes. We further define the disease-relevant, functional consequences of polymorphisms in the
TNFSF15
region, one of the 163 inflammatory bowel disease risk loci. To our knowledge, our studies highlight a previously unknown mechanism through which TNFSF15:DR3 can contribute to intestinal inflammation, namely by enhancing signaling and cytokine secretion upon stimulation of a broad range of pattern-recognition-receptors, mycobacterial components, and live bacteria.
Transcription factor EKLF (KLF1) recruitment of the histone chaperone HIRA is essential for β-globin gene expression
Authors: Soni Shefali , Pchelintsev Nikolay , Adams Peter D. , Bieker James J.
Published: September 2014

Significance

The β-like globin locus has provided a long-standing model for the study of cell-specific and developmental control of transcription and chromatin structure. We have previously shown that the replication-independent histone H3.3 variant is enriched at the active adult β-globin promoter. Although the erythroid Krüppel-like factor (EKLF), which is also known as Krüppel-like factor 1 (KLF1), transcription factor interacts with histone H3, it does not distinguish between the H3.1 or H3.3 variants. We now show that EKLF interacts with the H3.3 chaperone named histone cell cycle regulation defective homolog A (HIRA) and that this enables its selective recruitment of HIRA to the promoter. To our knowledge, our studies implicate HIRA for the first time in establishment of erythropoiesis and explain how critical protein interactions can lead to directed changes in histone variants at restricted sites.
Prospects for detecting oxygen, water, and chlorophyll on an exo-Earth
Authors: Brandt Timothy D. , Spiegel David S.
Published: September 2014

Significance

One of NASA’s most important long-term goals is to detect and characterize terrestrial exoplanets, and to search their spectra for signs of life. This overarching goal is currently driving concepts for a future high-contrast flagship mission. We determine the fidelity with which such a mission would need to measure an exo-Earth’s spectrum to detect oxygen, water, and chlorophyll. Our results suggest that a well-designed space mission could detect O
2
and H
2
O in a nearby Earth twin, but that it would need to be significantly more sensitive (or very lucky) to see chlorophyll. We suggest designing the instrument with an eye toward oxygen, and perhaps looking for chlorophyll around one or a few exceptional targets.
Mu transpososome and RecBCD nuclease collaborate in the repair of simple Mu insertions
Authors: Choi Wonyoung , Jang Sooin , Harshey Rasika M.
Published: September 2014

Significance

Transposition is not finished until the gaps left in the target in the wake of transposition are repaired, yet this is the least understood aspect of transposition. This study describes to our knowledge the first in vitro assay for repair of Mu insertions, which shows that repair is controlled by both transpososome and host factors. The long flanking DNA (FD) attached to Mu is shortened in two stages, requiring collaboration between the transpososome and RecBCD at both stages. The transpososome initially regulates the timing of RecBCD entry into the FD, and then exploits RecBCD action on this DNA to promote endonucleolytic cleavage within the transpososome. The final product has short flanks, and is likely the substrate for gap repair by a host polymerase.
Ultrafast phase-change logic device driven by melting processes
Authors: Loke Desmond , Skelton Jonathan M. , Wang Wei-Jie , Lee Tae-Hoon , Zhao Rong , Chong Tow-Chong , Elliott Stephen R.
Published: September 2014

Significance

The ever-increasing demand for faster computers is tackled by reducing the size of devices, but this is becoming almost impossible to continue. To improve the speed of computers, a solution is to increase the number of operations performed per device. Numerous operations in phase-change–based “in-memory” logic devices have previously been achieved using crystallization, but they show slow speeds, mostly due to a trade-off between the crystallization speed and stability of the initialized-glassy states. Here, we instead control melting processes to perform logic operations. Ultrafast melting speeds and diverse operations were achieved. Computer simulations and electrical measurements show the origin and kinetics of melting. These advances open the doorway for developing computers that can perform calculations at well beyond current processing rates.
Cell cycle-dependent adaptor complex for ClpXP-mediated proteolysis directly integrates phosphorylation and second messenger signals
Authors: Smith Stephen C. , Joshi Kamal K. , Zik Justin J. , Trinh Katherine , Kamajaya Aron , Chien Peter , Ryan Kathleen R.
Published: September 2014

Significance

Controlled degradation of specific proteins is used by all organisms to change cell behavior in response to internal or external cues. Because ATP-dependent proteases, such as ClpXP, have a broad range of targets, accessory proteins called adaptors are often necessary for selective substrate proteolysis. Here we show that three proteins work together as a multicomponent adaptor to stimulate the degradation of a key regulatory protein, CtrA, in
Caulobacter crescentus
. The adaptor is only functional when one of the components, CpdR, is unphosphorylated and when another component, PopA, is bound to the signaling molecule cyclic diguanylate. These features ensure that CtrA is only proteolyzed during a specific window in the
Caulobacter
cell-division cycle.
Highly sensitive detection of nanoparticles with a self-referenced and self-heterodyned whispering-gallery Raman microlaser
Authors: Özdemir Şahin Kaya , Zhu Jiangang , Yang Xu , Peng Bo , Yilmaz Huzeyfe , He Lina , Monifi Faraz , Huang Steven He , Long Gui Lu , Yang Lan
Published: September 2014

Significance

To date, loss compensation in optical microresonators has been done using rare-earth ions, which requires additional processing steps and costs and raises biocompatibility concerns. An alternative to integrating rare-earth ions for loss compensation is the use of intrinsic gain mechanisms such as Raman and parametric gain present in the materials from which resonators are fabricated. Here, we report the first implementation to our knowledge of Raman gain-induced loss compensation in silica whispering-gallery-mode (WGM) resonators for improved detection and the first demonstration to our knowledge of mode splitting in a WGM Raman microlaser for detecting and counting single nanoparticles down to 10 nm. This intrinsically self-referenced, self-heterodyned, and biocompatible scheme has enabled achieving record-high polarizability sensitivity (down to 3.82 × 10
−6
μm
3
) without using plasmonic effects, passive or active stabilization, or frequency locking.
Antiinfective therapy with a small molecule inhibitor of
Staphylococcus aureus
sortase
Authors: Zhang Jie , Liu Hongchuan , Zhu Kongkai , Gong Shouzhe , Dramsi Shaynoor , Wang Ya-Ting , Li Jiafei , Chen Feifei , Zhang Ruihan , Zhou Lu , Lan Lefu , Jiang Hualiang , Schneewind Olaf , Luo Cheng , Yang Cai-Guang
Published: September 2014

Significance

Antiinfectives, drugs that inhibit virulence strategies of microbial pathogens without affecting bacterial growth, may prevent hospital-acquired infections caused by antibiotic-resistant
Staphylococcus aureus
. We used virtual screening and synthetic optimization to identify 3,6-disubstituted triazolothiadiazole compounds as inhibitors of sortase, an enzyme that incorporates surface proteins into the staphylococcal envelope. Other Gram-positive bacteria also use sortase for protein assembly in the envelope and disease pathogenesis, suggesting that sortase inhibitors could protect high-risk patients against infection with many nosocomial pathogens.
Clearance of pathological antibodies using biomimetic nanoparticles
Authors: Copp Jonathan A. , Fang Ronnie H. , Luk Brian T. , Hu Che-Ming J. , Gao Weiwei , Zhang Kang , Zhang Liangfang
Published: September 2014

Significance

The selective depletion of disease-causing antibodies using nanoparticles offers a new model in the management of type II immune hypersensitivity reactions. The demonstration of pathophysiologically inspired nanoengineering serves as a valuable prototype for additional therapeutic improvements with the goal of minimizing therapy-related adverse effects. Through the use of cell membrane-cloaked nanoparticles, nanoscale decoys with strong affinity to pathological antibodies can be administered to disrupt disease processes in a minimally toxic manner. These biomimetic nanoparticles enable indiscriminate absorption of pathological antibodies regardless of their epitope specificities. This particular approach offers much promise in treating antibody-mediated autoimmune diseases, in which target antigens on susceptible cells can vary from patient to patient.
Ebf2 is a selective marker of brown and beige adipogenic precursor cells
Authors: Wang Wenshan , Kissig Megan , Rajakumari Sona , Huang Li , Lim Hee-woong , Won Kyoung-Jae , Seale Patrick
Published: September 2014

Significance

High levels of brown/beige fat activity protects animals against metabolic disease, but there has been little known about the precursor cells that mediate the expansion of brown or beige fat. We discovered that early B-cell factor 2 (Ebf2), a transcription factor, is selectively expressed in brown and beige fat cell precursors. Through purification of
Ebf2
+
cells, we identified a gene profile of brown fat precursors that can be used to distinguish these cells from other developmentally related cell types. Importantly, Ebf2 was also found to regulate the gene expression profile of brown fat precursor cells. Taken together, this study identifies Ebf2 as a highly specific marker of brown and beige preadipose cells and reveals that Ebf2 functions to control brown preadipose cell identity.
Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley
Authors: Dai Fei , Chen Zhong-Hua , Wang Xiaolei , Li Zefeng , Jin Gulei , Wu Dezhi , Cai Shengguan , Wang Ning , Wu Feibo , Nevo Eviatar , Zhang Guoping
Published: September 2014

Significance

Archaeological, historic, and molecular studies have indicated that the Fertile Crescent in the Near East is a major center of origin and domestication of cultivated barley. However, growing evidence in recent years supports the theory of a polyphyletic origin of barley. To our knowledge, this is the first attempt using RNA sequencing techniques and genomic similarity analysis to study the domestication of barley. We confirmed the polyphyletic origin of cultivated barley and our results revealed the genomic origin of modern cultivated barley is from both the Near East and Tibet, with different contributions on each chromosome. These findings advance our understanding of the early spread of agrarian culture, and are expected to be of wide interest to evolutionary geneticists and plant breeders.
Structural insight into the molecular mechanism of allosteric activation of human cystathionine β-synthase by
S
-adenosylmethionine
Authors: Ereño-Orbea June , Majtan Tomas , Oyenarte Iker , Kraus Jan P. , Martínez-Cruz Luis Alfonso
Published: September 2014

Significance

Cystathionine β-synthase (CBS), the pivotal enzyme of the transsulfuration pathway, regulates flux through the pathway to yield compounds, such as cysteine, glutathione, taurine, and H
2
S, that control cellular redox status and signaling. Our crystal structure of an engineered human CBS construct bound to
S
-adenosylmethionine (AdoMet) reveals the unique binding site of the allosteric activator and the architecture of the human CBS enzyme in its activated conformation. Together with the basal conformation that we reported earlier, these structures unravel the molecular mechanism of human CBS activation by AdoMet. Current knowledge will allow for modeling of numerous pathogenic mutations causing inherited homocystinuria and for design of compounds modulating CBS activity.
Crystal structure of the γ-secretase component nicastrin
Authors: Xie Tian , Yan Chuangye , Zhou Rui , Zhao Yanyu , Sun Linfeng , Yang Guanghui , Lu Peilong , Ma Dan , Shi Yigong
Published: September 2014

Significance

γ-Secretase is a four-component intramembrane protease associated with the onset of Alzheimer's disease. Nicastrin is the putative substrate-recruiting component of the γ-secretase complex, but no atomic-resolution structure had been identified on γ-secretase or any of its four components. Here we report the first atomic-resolution crystal structure of a eukaryotic nicastrin which shares significant sequence homology with human nicastrin. This structure reveals the fine details of nicastrin and allows structure modeling of human nicastrin. Analysis of the structural details yields a working model showing how nicastrin might function to recruit substrate protein. The nicastrin structure also allows reevaluation of the previously proposed transmembrane helix assignment in the γ-secretase complex. Our structural analysis provides insights into the assembly and function of γ-secretase.
Xylella fastidiosa
outer membrane vesicles modulate plant colonization by blocking attachment to surfaces
Authors: Ionescu Michael , Zaini Paulo A. , Baccari Clelia , Tran Sophia , da Silva Aline M. , Lindow Steven E.
Published: September 2014

Significance

Release of outer membrane vesicles (OMVs) is a general feature of Gram-negative bacteria. Most studies have addressed the mechanisms of their formation or the cargo they can carry, but other roles remain to be explored further. Here we provide evidence for a novel role for OMVs in
Xylella fastidiosa
, a bacterial pathogen that colonizes the xylem of important crop plants. OMVs, whose production is suppressed by a quorum-sensing system, serve as an autoinhibitor of cell adhesion to surfaces, thereby blocking attachment-driven biofilm formation that would restrict movement within the xylem and thus colonization of plants. The ubiquity of OMV formation in the bacterial world suggests that these extracellular products may have alternative roles that might modulate movement and biofilm formation.
Distinctive signature of indium gallium nitride quantum dot lasing in microdisk cavities
Authors: Woolf Alexander , Puchtler Tim , Aharonovich Igor , Zhu Tongtong , Niu Nan , Wang Danqing , Oliver Rachel , Hu Evelyn L.
Published: September 2014

Significance

The III-nitride family of materials has already demonstrated tremendous optical efficiency and versatility for devices across a broad range of wavelengths. Quantum dots formed in these materials, with advantages such as improved carrier confinement, should offer even greater device efficiency. They are also important constituents for fundamental studies of light−matter interaction. However, that promise has been far from realized, and this is a complex problem to address. This work, through a comparative study of quantum dot, quantum well, and fragmented quantum well gain media in compact microdisk cavities, allows better understanding of the limitations to lasing for the quantum dot samples. These results allow both improved device efficiency and fundamental insights into quantum dot−cavity interactions in these materials.
Synthesis of (±)-terpendole E
Authors: Teranishi Takaaki , Murokawa Tetsuro , Enomoto Masaru , Kuwahara Shigefumi
Published: September 2014

The first synthesis of the racemate of terpendole E, a specific inhibitor of the mitotic kinesin Eg5, has been achieved from a known tricyclic dihydroxy ketone by a 13-step sequence that involves diastereoselective installation of its C3 quaternary stereocenter via a cyclopropyl ketone intermediate and Pd-mediated two-step construction of the indole ring moiety as the key transformations.
National Wage Trends and Migration in a Chinese Village Economy: A Micro Level Modeling Approach Based on a Composite Utility Function
Authors: Kleinwechter Ulrich , Grethe Harald
Published: September 2014

China's economy is experiencing a regime shift away from a fully elastic supply of labor from a large pool of rural surplus labor and toward a situation of increasing labor scarcity and rising wage rates. Moreover, faster wage increases in the regions of origin of many rural–urban migrants are likely to affect the dynamics of inter‐regional migration. These wage trends have implications at the local level, in particular in a setting in which migration connects rural communities to the national labor market and in which migration is of high importance for the livelihoods of rural households. Taking a village perspective, this article develops a village computable general equilibrium model to study local impacts of current wage trends in China. As a central piece of the model, the role of access to migration for household livelihoods is recognized. Access to migration is linked to household demographics and included in the model through a composite utility function that captures household preferences and disutilities associated with alternative off‐farm activities. Simulation results illustrate how households’ utility considerations affect migration responses to national wage changes. Statements about possible impacts on village level labor supply, land use, and agricultural production are made. When migration wages and local off‐farm wages are simulated to increase, an overall increase in household and village migration and a higher supply of labor to local off‐farm labor markets is accompanied by a contraction of farm production. Although land is reallocated between households with different migration responses, total agricultural output declines.
Transaction Costs in Payment for Environmental Service Contracts
Authors: Peterson Jeffrey M. , Smith Craig M. , Leatherman John C. , Hendricks Nathan P. , Fox John A.
Published: September 2014

Payment for environmental service contracts commonly require actions beyond adoption of a practice, such as undergoing specified enrollment procedures, granting consent to being monitored, and paying penalties for violations. These provisions are a bundle of attributes a landholder must accept with contract enrollment, leading to transaction costs in the contracting process. This article develops a principal–agent framework to study the links between these transaction costs and the well‐known information asymmetries between the landholders and the government agency offering contracts. Using stated choice data collected from a sample of farmers, we estimate a mixed logit model to quantify the contribution of different contract attributes on contract willingness‐to‐accept (WTA). More stringent provisions in contracts were found to raise individual WTA by widely differing amounts across farmers, but the average effects imply that overall contract supply is sensitive to stringency. From a series of microsimulations based on the estimated model, we find that transaction costs create a significant drain on the cost‐effectiveness of contracting from the agency's point of view, similar in magnitude to the inefficiency created by hidden information. Although stringent contractual terms raise program expenditures, they may be justified if they raise compliance rates enough to offset the added cost. We also simulate an implicit frontier to trace out the change in compliance needed to justify a given increase in stringency. For environmental benefits in the range of previous estimates, this analysis suggests that stringent terms would need to substantially raise compliance rates to be cost effective.
Nutritional Efficiency Wages and Unemployment: Where's the Beef?
Authors: Powell Benjamin , Murphy Ryan
Published: September 2014

We modify the standard nutritional efficiency wage model to allow for the fact that employers can directly provide calories to their workers rather than paying a higher wage to induce employees to spend more on their own caloric consumption. We derive the various theoretical outcomes that are possible depending on the assumptions about the transaction costs of directly providing calories. We argue that in most real‐world situations the ability of employers to directly provide calories undermines the traditional efficiency wage theory as a cause of equilibrium unemployment.
ballaxy: web services for structural bioinformatics
Authors: Hildebrandt Anna Katharina , Stöckel Daniel , Fischer Nina M. , de la Garza Luis , Krüger Jens , Nickels Stefan , Röttig Marc , Schärfe Charlotta , Schumann Marcel , Thiel Philipp , Lenhof Hans-Peter , Kohlbacher Oliver , Hildebrandt Andreas
Published: September 2014

Motivation: Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together.

Results: In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling.

Availability and implementation:  ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy . Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/ . ballaxy is licensed under the terms of the GPL.

Supplementary information : Supplementary data are available at Bioinformatics online.

Contact:  anna.hildebrandt@bioinf.uni-sb.de or andreas.hildebrandt@uni-mainz.de
String graph construction using incremental hashing
Authors: Ben-Bassat Ilan , Chor Benny
Published: September 2014

Motivation : New sequencing technologies generate larger amount of short reads data at decreasing cost. De novo sequence assembly is the problem of combining these reads back to the original genome sequence, without relying on a reference genome. This presents algorithmic and computational challenges, especially for long and repetitive genome sequences. Most existing approaches to the assembly problem operate in the framework of de Bruijn graphs. Yet, a number of recent works use the paradigm of string graph , using a variety of methods for storing and processing suffixes and prefixes, like suffix arrays, the Burrows–Wheeler transform or the FM index. Our work is motivated by a search for new approaches to constructing the string graph, using alternative yet simple data structures and algorithmic concepts.

Results : We introduce a novel hash-based method for constructing the string graph. We use incremental hashing, and specifically a modification of the Karp–Rabin fingerprint, and Bloom filters. Using these probabilistic methods might create false-positive and false-negative edges during the algorithm’s execution, but these are all detected and corrected. The advantages of the proposed approach over existing methods are its simplicity and the incorporation of established probabilistic techniques in the context of de novo genome sequencing. Our preliminary implementation is favorably comparable with the first string graph construction of Simpson and Durbin (2010) (but not with subsequent improvements). Further research and optimizations will hopefully enable the algorithm to be incorporated, with noticeable performance improvement, in state-of-the-art string graph-based assemblers.

Availability and implementation : A beta version of all source code used in this work can be downloaded from http://www.cs.tau.ac.il/~bchor/StringGraph/

Contact: ilanbb@gmail.com or benny@cs.tau.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
First Report of Bursaphelenchus yongensis on Pinus rigida in Korea
Authors: Han H.
Published: September 2014

During a pinewood nematode survey in 2011, a dead pitch pine (Pinus rigida) was found in Daejeon city, Korea. Samples were taken from several regions of the trunk and nematodes were extracted from the wood samples by a modified Baermann funnel method (1). Recovered nematodes were then cultured on Botrytis cinerea grown in potato dextrose agar (PDA) medium. Males and females (n = 10) were examined under an inverted light microscope. Morphologically, these nematodes were identified as Bursaphelenchus yongensis sharing the characters of the genus Bursaphelenchus including a large median bulb, offset cephalic region, a well-developed stylet with small basal knobs, female with vulva at 70% of body length, and males with terminal bursa. Females of B. yongensis were similar to B. muconatus and B. fraudulentus by presence of tail mucron, but they were differentiated by a smaller vulval flap. Males had spicules with small cucullus, pointed rostrum, and with strongly dorsally bent condylus. The identity of the nematode was confirmed through molecular diagnosis. DNA was extracted from each of 10 nematodes using commercial DNeasy kits (Qiagen, Valencia, CA) and the ITS regions were amplified with a primer set by PCR (Bio Rad, US/PTC-0220) (3,5). Amplified ITS DNA was cloned and sequenced, and the sequence data was deposited to GenBank (Accession No. KJ857070). The ITS sequence of Korean isolate (KJ857070) showed 99% similarity to that from Chinese isolate in GenBank (AM180513). ITS-RFLP patterns using five different restriction enzymes, RsaI, HaeIII, MspI, HinfI, and AluI, matched 100% with those previously reported for B. yongensis (2,4). Host pathogenicity tests were conducted from June to August on saplings of five native and introduced conifer species found in Korea (Abies sp., Larix leptolepsis, P. koraiensis, P. strobus, and P. thunbergii). All saplings were 5 to 6 years old and 15 saplings were inoculated for each species. B. yongensis was cultures on B. cinerea for 10 days at 25°C and the inoculum concentration was calibrated at 5,000 nematodes/50 μl sterile water. Nematodes were artificially inoculated by making a 1-cm-long incision into the stem using a sterile razor blade. B. yongensis was pathogenic on L. leptolepsis, causing wilt and death in all inoculated saplings; however, the nematode had no effect on P. thunbergii, P. koraiensis, Abies sp., or P. strobus. To our knowledge, this is the first report of B. yongensis in Korea. This nematode is a potential threat to L. leptolepsis; however, the role of B. yongensis in the mortality of P. rigida is uncertain at this time.

References: (1) S. M. Ayoub. Plant Nematology in Agricultural Training Aid. Department of Food and Agriculture, Division of Plant Industry, Sacramento, CA, 1977. (2) W. Burgermeister et al. Nematology 11:649, 2009. (3) V. R. Ferris et al. Fund. Appl. Nematol. 16:177, 1993. (4) J. Gu et al. Russian J. Nematol. 14:91, 2006. (5) T. C. Vrain. J. Nematol. 25:361, 1993.
First Report of Leaf Spot Disease in Coconut Seedling Caused by Bipolaris setariae in China
Authors: Niu X.-Q. , Yu F.-Y. , Zhu H. , Qin W.-Q.
Published: September 2014

Coconut (Cocos nucifera L.), an important oilseed as well as a multipurpose perennial plantation crop, is distributed and planted in humid tropical areas. In October 2012, a new leaf spot disease was observed on 3-year-old coconut seedlings in Wenchang, Hainan Province, China. The symptom first appeared as spindly or elliptical and brown flecks with water-soaked lesions that became yellow with the progress of the disease. In the later stage of the disease, the lesions merged together, gradually expanding to the leaf apex. In recent years, the disease has been prevalent in all the nursery gardens surveyed. Once young leaves got infected and nearly all the leaves of the tree showed diseased symptoms, the coconut eventually became defoliated. The pathogen was isolated from the lesion margin, surface sterilized with 75% ethanol and 0.1% mercury bichloride, washed by sterile distilled water, and then placed excising pieces of leaves from the leision margin onto potato dextrose agar (PDA). Plates were incubated at 25°C for 4 days. After 7 days, the colony was grayish black and produced black pigment in the medium. Aerial mycelium was fluffy, septate, and branched, the conidiophores were slightly flexuous or straight, 5 to 11 μm thick, and produced curved, spindle-shaped, or fusiform, septate conidia with 4 to 10 septa, measuring 39 to 86 × 9 to 16 μm, with a slightly protuberant hilum, truncated. Based on the symptoms and mycelial and conidial characters above, the fungus was identified as Bipolaris setariae (1). The pathogenicity was established and repeated for six times by following Koch's postulates. Two 1-year-old coconut seedlings were washed with sterilized water and six leaves were wounded with a sterile needle and then inoculated by spraying them with a suspension of conidia of the isolate. The seedlings were kept in two incubators at 25°C for 12 days. Inoculated leaves showed typical symptoms similar to those described above. The pathogen was re-isolated from inoculated leaves. Morphological characteristics were identical to the original isolated fungus. In contrast, the control leaves did not show any symptoms. The genomic DNA of this fungus was extracted, amplification of the internal transcribed spacer (ITS) region was performed with primer ITS1 and ITS4, and the purified PCR product was sequenced (GenBank Accession No. KJ605157). BLASTn analysis revealed 99% sequence similarity with four B. setariae isolates (HE792936.1, JX462256, GU073108.1, and FJ606786.1). Morphologic characters and sequence analysis of the ITS rDNA confirmed that the pathogen was B. setariae. Bipolaris incurvata has been reported causing disease on coconut (2), but B. setariae was not previously reported on coconut. So far, this is the first report of B. setariae caused coconut seedling leaf spot disease in Hainan, China.

References: (1) K. C. da Cunha et al. J. Clin. Microbiol. 50:4061, 2012. (2) A. Kamalakannan et al. New Dis. Rep. 12:18, 2005.
Transcriptional Reprogramming of the Mycoparasitic FungusAmpelomyces quisqualisDuring the Powdery Mildew Host-Induced Germination
Authors: Siozios Stefanos , Tosi Lorenzo , Ferrarini Alberto , Ferrari Alessandro , Tononi Paola , Bellin Diana , Maurhofer Monika , Gessler Cesare , Delledonne Massimo , Pertot Ilaria
Published: September 2014

Ampelomyces quisqualis is a mycoparasite of a diverse range of phytopathogenic fungi associated with the powdery mildew disease. Among them are several Erysiphaceae species with great economic impact on high-value crops such as grape. Due to its ability to parasitize and prevent the spread of powdery mildews, A. quisqualis has received considerable attention for its biocontrol potential. However, and in sharp contrast to the extensively studied biocontrol species belonging to the genus Trichoderma, little is known about the biology of A. quisqualis at the molecular and genetic levels. We present the first genome-wide transcription profiling in A. quisqualis during host-induced germination. A total of 1,536 putative genes showed significant changes in transcription during the germination of A. quisqualis. This finding denotes an extensive transcriptional reprogramming of A. quisqualis induced by the presence of the host. Several upregulated genes were predicted to encode for putative mycoparasitism-related proteins such as secreted proteases, virulence factors, and proteins related to toxin biosynthesis. Our data provide the most comprehensive sequence resource currently available for A. quisqualis in addition to offering valuable insights into the biology of A. quisqualis and its mycoparasitic lifestyle. Eventually, this may improve the biocontrol capacity of this mycoparasite.
A Case of Orbital Histoplasmosis
Authors: Krakauer Mark , Prendes Mark Armando , Wilkes Byron , Lee Hui Bae Harold , Fraig Mostafa , Nunery William R.
Published: September 2014

Histoplasma capsulatum var capsulatum is a dimorphic fungus endemic to the Ohio and Mississippi River Valleys of the United States. In this case report, a 33-year-old woman who presented with a right orbital mass causing progressive vision loss, diplopia, and facial swelling is described. Lateral orbitotomy with lateral orbital wall bone flap was performed for excisional biopsy of the lesion. The 1.5 × 1.8 × 2.3 cm cicatricial mass demonstrated a granulomatous lesion with necrosis and positive staining consistent with Histoplasma capsulatum var capsulatum infection. To the authors’ knowledge, this is the first case of orbital histoplasmosis to be reported in the United States and the first case worldwide of orbital histoplasmosis due to Histoplasma capsulatum var capsulatum.
An agent-based model of cancer stem cell initiated avascular tumour growth and metastasis: the effect of seeding frequency and location
Authors: Norton Kerri-Ann , Popel Aleksander S.
Published: September 2014

It is very important to understand the onset and growth pattern of breast primary tumours as well as their metastatic dissemination. In most cases, it is the metastatic disease that ultimately kills the patient. There is increasing evidence that cancer stem cells are closely linked to the progression of the metastatic tumour. Here, we investigate stem cell seeding to an avascular tumour site using an agent-based stochastic model of breast cancer metastatic seeding. The model includes several important cellular features such as stem cell symmetric and asymmetric division, migration, cellular quiescence, senescence, apoptosis and cell division cycles. It also includes external features such as stem cell seeding frequency and location. Using this model, we find that cell seeding rate and location are important features for tumour growth. We also define conditions in which the tumour growth exhibits decremented and exponential growth patterns. Overall, we find that seeding, senescence and division limit affect not only the number of stem cells, but also their spatial and temporal distribution.
Some new addition formulae for Weierstrass elliptic functions
Authors: Eilbeck J. Chris , England Matthew , Ônishi Yoshihiro
Published: September 2014

We present new addition formulae for the Weierstrass functions associated with a general elliptic curve. We prove the structure of the formulae in
n
-variables and give the explicit addition formulae for the 2- and 3-variable cases. These new results were inspired by new addition formulae found in the case of an equianharmonic curve, which we can now observe as a specialization of the results here. The new formulae, and the techniques used to find them, also follow the recent work for the generalization of Weierstrass functions to curves of higher genus.
Subglacial swamps
Authors: Kyrke-Smith T. M. , Fowler A. C.
Published: September 2014

The existence of both water and sediment at the bed of ice streams is well documented, but there is a lack of fundamental understanding about the mechanisms of ice, water and sediment interaction. We pose a model to describe subglacial water flow below ice sheets, in the presence of a deformable sediment layer. Water flows in a rough-bedded film; the ice is supported by larger clasts, but there is a millimetric water layer submerging the smaller particles. Partial differential equations describing the water film are derived from a description of the dynamics of ice, water and mobile sediment. We assume that sediment transport is possible, either as fluvial bedload, but more significantly by ice-driven shearing and by internal squeezing. This provides an instability mechanism for rivulet formation; in the model, downstream sediment transport is compensated by lateral squeezing of till towards the incipient streams. We show that the model predicts the formation of shallow, swamp-like streams, with a typical depth of the order of centimetres. The swamps are stable features, typically with a width of the order of tens to hundreds of metres.
Computer simulation of metal co-doping in lithium niobate
Authors: Araujo Romel M. , Valerio Mário E. G. , Jackson Robert A.
Published: September 2014

Lithium niobate, LiNbO
3
, is an important technological material with good electro-optic, acousto-optic, elasto-optic, piezoelectric and nonlinear properties. Computer modelling provides a useful means of determining the properties of the material, including its defect chemistry, and the effect of doping on the structure. In this work, double-doped LiNbO
3
was studied, and the energetics of the solid-state reactions leading to incorporation of the dopants was calculated. The following combinations of dopants were studied: Fe and Cu; Ce and Cu; Ce and Mn; Fe and Rh; and Ru and Fe. For most of these combinations, the co-doping process decreases the energy required for incorporation of the dopants, and the final defect configurations are consistent with experimental results, where available.
Thermophysical and anion diffusion properties of (U

x

,Th

1−
x

)O
2
Authors: Cooper Michael W. D. , Murphy Samuel T. , Fossati Paul C. M. , Rushton Michael J. D. , Grimes Robin W.
Published: September 2014

Using molecular dynamics, the thermophysical properties of the (U

x

,Th

1−
x

)O
2
system have been investigated between 300 and 3600 K. The thermal dependence of lattice parameter, linear thermal expansion coefficient, enthalpy and specific heat at constant pressure is explained in terms of defect formation and diffusivity on the oxygen sublattice. Vegard's law is approximately observed for solid solution thermal expansion below 2000 K. Different deviations from Vegard's law above this temperature occur owing to the different temperatures at which the solid solutions undergo the superionic transition (2500–3300 K). Similarly, a spike in the specific heat, associated with the superionic transition, occurs at lower temperatures in solid solutions that have a high U content. Correspondingly, oxygen diffusivity is higher in pure UO
2
than in pure ThO
2
. Furthermore, at temperatures below the superionic transition, oxygen mobility is notably higher in solid solutions than in the end members. Enhanced diffusivity is promoted by lower oxygen-defect enthalpies in (U

x

,Th

1−
x

)O
2
solid solutions. Unlike in UO
2
and ThO
2
, there is considerable variety of oxygen vacancy and oxygen interstitial sites in solid solutions generating a wide range of property values. Trends in the defect enthalpies are discussed in terms of composition and the lattice parameter of (U

x

,Th

1−
x

)O
2
.
Shifts and disruptions in resource-use trait syndromes during the evolution of herbaceous crops
Authors: Milla Rubén , Morente-López Javier , Alonso-Rodrigo J. Miguel , Martín-Robles Nieves , Stuart Chapin F.
Published: September 2014

Trait-based ecology predicts that evolution in high-resource agricultural environments should select for suites of traits that enable fast resource acquisition and rapid canopy closure. However, crop breeding targets specific agronomic attributes rather than broad trait syndromes. Breeding for specific traits, together with evolution in high-resource environments, might lead to reduced phenotypic integration, according to predictions from the ecological literature. We provide the first comprehensive test of these hypotheses, based on a trait-screening programme of 30 herbaceous crops and their wild progenitors. During crop evolution plants became larger, which enabled them to compete more effectively for light, but they had poorly integrated phenotypes. In a subset of six herbaceous crop species investigated in greater depth, competitiveness for light increased during early plant domestication, whereas diminished phenotypic integration occurred later during crop improvement. Mass-specific leaf and root traits relevant to resource-use strategies (e.g. specific leaf area or tissue density of fine roots) changed during crop evolution, but in diverse and contrasting directions and magnitudes, depending on the crop species. Reductions in phenotypic integration and overinvestment in traits involved in competition for light may affect the chances of upgrading modern herbaceous crops to face current climatic and food security challenges.
Cortical networks for face perception in two-month-old infants
Authors: Nakano Tamami , Nakatani Kazuko
Published: September 2014

Newborns have an innate system for preferentially looking at an upright human face. This face preference behaviour disappears at approximately one month of age and reappears a few months later. However, the neural mechanisms underlying this U-shaped behavioural change remain unclear. Here, we isolate the functional development of the cortical visual pathway for face processing using S-cone-isolating stimulation, which blinds the subcortical visual pathway. Using luminance stimuli, which are conveyed by both the subcortical and cortical visual pathways, the preference for upright faces was not observed in two-month-old infants, but it was observed in four- and six-month-old infants, confirming the recovery phase of the U-shaped development. By contrast, using S-cone stimuli, two-month-old infants already showed a preference for upright faces, as did four- and six-month-old infants, demonstrating that the cortical visual pathway for face processing is already functioning at the bottom of the U-shape at two months of age. The present results suggest that the transient functional deterioration stems from a conflict between the subcortical and cortical functional pathways, and that the recovery thereafter involves establishing a level of coordination between the two pathways.