bluuebunny/crossref_metadata_2025 huggingface dataset:
Catalyst-loaded porous WO3 nanofibers using catalyst-decorated polystyrene colloid templates for detection of biomarker molecules
Authors: Choi Seon-Jin , Kim Sang-Joon , Koo Won-Tae , Cho Hee-Jin , Kim Il-Doo
Published: December 2014

A new facile catalyst loading method assisted by layer-by-layer self-assembly as well as pore formation on electrospun nanofibers (NFs) can generate in-depth research for establishing high performance gas sensing composites by exploring diverse catalyst-loaded porous NF composites.
Surface charging behavior of nanoparticles by considering site distribution and density, dielectric constant and pH changes – a Monte Carlo approach
Authors: Clavier Arnaud , Seijo Marianne , Carnal Fabrice , Stoll Serge
Published: December 2014

Monte Carlo simulations are used to describe the charging behavior of metal oxide nanoparticles thus enabling a novel and original approach to predict nanoparticle reactivity and the possible interactions with biological and environmental molecules.
A comparative computational study on the interactions of N719 and N749 dyes with iodine in dye-sensitized solar cells
Authors: Kusama Hitoshi , Sayama Kazuhiro
Published: December 2014

Computational findings in simultaneous multiple interactions of N719 and N749 dyes with an iodide anion and iodine molecules are related closely to both regeneration and recombination reactions, and consequently, dye sensitized solar cell performance.
Switching nuclearity and Co(ii) content through stoichiometry adjustment: {CoII6CoIII3} and {CoIICo4III} mixed valent complexes and a study of their magnetic properties
Authors: Funes Alejandro V. , Carrella Luca , Sorace Lorenzo , Rentschler Eva , Alborés Pablo
Published: December 2014

Controlling the CoII content in polynuclear systems: {CoII6CoIII3} and {CoIICo4III} mixed valent complexes with distinct magnetic behaviours is reported.
Theoretical studies on the AnO2n+(An = U, Np; n = 1, 2) complexes with di-(2-ethylhexyl)phosphoric acid
Authors: Luo Juan , Wang Cong-Zhi , Lan Jian-Hui , Wu Qun-Yan , Zhao Yu-Liang , Chai Zhi-Fang , Nie Chang-Ming , Shi Wei-Qun
Published: December 2014

The AnO2n+(An = U, Np;n= 1, 2) extraction complexes with HDEHP (di-(2-ethylhexyl)phosphoric acid) in nitric acid solutions.
A sensitivity analysis to assess the relative importance of improvements in electrocatalysts, light absorbers, and system geometry on the efficiency of solar-fuels generators
Authors: Chen Yikai , Hu Shu , Xiang Chengxiang , Lewis Nathan S.
Published: December 2014

A sensitivity analysis of the relative importance of reductions in the overpotentials of electrocatalysts and of improvements in the material properties of light absorbers.
Solution-processable metal oxides/chelates as electrode buffer layers for efficient and stable polymer solar cells
Authors: Wang Fuzhi , Tan Zhan'ao , Li Yongfang
Published: December 2014

This review summarizes the recent progress of metal oxides/chelates as interfacial materials for improving the efficiency and stability of PSCs.
Hydrodeoxygenation of lignin-derived phenols into alkanes over carbon nanotube supported Ru catalysts in biphasic systems
Authors: Chen Meng-Yuan , Huang Yao-Bing , Pang Huan , Liu Xin-Xin , Fu Yao
Published: December 2014

Lignin derived phenols and dimers were converted into alkanes through the HDO process over Ru/CNT catalysts in biphasic solvents.
Characterization of syringe-pump-driven induced pressure fluctuations in elastic microchannels
Authors: Zeng Wen , Jacobi Ian , Beck David J. , Li Songjing , Stone Howard A.
Published: December 2014

We study pressure and flow-rate fluctuations in microchannels, where the flow rate is supplied by a syringe pump.
Dissection of metabolic pathways in the Db/Db mouse model by integrative proteome and acetylome analysis
Authors: Hölper Soraya , Nolte Hendrik , Bober Eva , Braun Thomas , Krüger Marcus
Published: December 2014

An in vivo SILAC-based quantitative proteomics approach to analyse protein abundances and acetylation levels under diabetic conditions.
Facilely controlling the Förster energy transfer efficiency of dendron encapsulated conjugated organic molecular wire–CdSe quantum dot nanostructures
Authors: Si Hua-Yan , Wang Le-Jia , Feng Wen-Jie , Zhang Hao-Li , Zhu Hao , Zhao Jin-Jin , Ding Zhan-Lai , Li Yan-Ting
Published: December 2014

On Den-OPE–CdSe nanostructures, as the size of the dendrimer increases, the energy transfer efficiency from Den-OPEs to CdSe QDs enhances.
Cytoprotective nanoparticles by conjugation of a polyhis tagged annexin V to a nanoparticle drug
Authors: Chen Howard H. , Yuan Hushan , Cho Hoonsung , Sosnovik David E. , Josephson Lee
Published: December 2014

Annexin V (red) attached to a Feraheme nanoparticle drug (black) is cytoprotective, preventing plasma membrane rupture and necrosis.
Halide inhibition of the copper-catalysed azide–alkyne cycloaddition
Authors: Moorman Rebekah M. , Collier Matthew B. , Frohock Bram H. , Womble Michael D. , Chalker Justin M.
Published: December 2014

Halides are inhibitors of the copper-catalysed azide–alkyne cycloaddition. Case studies in this inhibition are presented, along with experimental measures useful in accommodating halides in this widely used reaction.
Synthesis of imidazoles via cascade reaction of nitroallylic acetates with amidines and studies on their trypanocidal activity
Authors: Kumar Tarun , Verma Deepti , Menna-Barreto Rubem F. S. , Valença Wagner O. , da Silva Júnior Eufrânio N. , Namboothiri Irishi N. N.
Published: December 2014

Functionalized imidazoles derived from nitroallylic acetates and amidines exhibit potent activity against T. cruzi, the etiological agent of Chagas disease.
Modeling of gas generation from the river adjacent to the manufactured gas plant
Authors: Zhu Tengyi , Fu Dafang , Jafvert Chad T. , Singh Rajendra Prasad
Published: December 2014

Ebullition of gas bubbles through sediment can enhance the migration of gases through the subsurface and potentially affect the emission of important greenhouse gases to the atmosphere.
The aggregation behavior of cellulose micro/nanoparticles in aqueous media
Authors: Qi Wenhui , Xu Hua-Neng , Zhang Lianfu
Published: December 2014

Cellulose micro/nanoparticles were obtained from cotton microcrystalline cellulose. The effect of ionic strength on the aggregation behavior of the cellulose micro/nanoparticles in aqueous media has been investigated by means of rheo-SALS.
Electrophoretic deposited oxide thin films as charge transporting interlayers for solution-processed optoelectronic devices: the case of ZnO nanocrystals
Authors: Bai Sai , He Shasha , Jin Yizheng , Wu Zhongwei , Xia Zhouhui , Sun Baoquan , Wang Xin , Ye Zhizhen , Gao Feng , Shao Shuyan , Zhang Fengling
Published: December 2014

A promising fabrication method of electron transporting interlayers for solution-processed optoelectronic devices by electrophoretic deposition (EPD) of colloidal zinc oxide (ZnO) nanocrystals was demonstrated.
Solid-phase assembly of glycosaminoglycan oligosaccharide precursors
Authors: Guedes Nerea , Kopitzki Sebastian , Echeverria Begoña , Pazos Raquel , Elosegui Elisabete , Calvo Javier , Reichardt Niels-Christian
Published: December 2014

A high yielding procedure for the assembly of heparan and dermatan sulfate oligosaccharide precursors on the solid-phase has been developed.
Effect of SiO2 nanoparticles on the reaction-induced phase separation in dynamically asymmetric epoxy/PEI blends
Authors: Li Weizhen , Xia Zonglian , Li Ao , Ling Yang , Wang Baoyu , Gan Wenjun
Published: December 2014

The scaling coefficient α decreases significantly when the epoxy/PEI blend is filled with certain concentration of MEK–SiO2 nanoparticles, implying that the nanoparticles are forcing the coarsening mechanism towards the diffusion-controlled regime.
Evaluation of nitrates as igniters for microwave-induced combustion: understanding the mechanism of ignition
Authors: Pereira Leticia S. F. , Bizzi Cezar A. , Schmidt Lucas , Mesko Marcia F. , Barin Juliano S. , Flores Erico M. M.
Published: December 2014

Recent studies have reported the use of microwave-induced combustion (MIC) for digestion of several kinds of matrices.
Low temperature and deformation-free bonding of PMMA microfluidic devices with stable hydrophilicity via oxygen plasma treatment and PVA coating
Authors: Yu H. , Chong Z. Z. , Tor S. B. , Liu E. , Loh N. H.
Published: December 2014

A deformation-free bonding method with stable hydrophilicity in PMMA devices has been proposed through oxygen plasma treatment and PVA coating.
Size-controlled growth of cubic boron phosphide nanocrystals
Authors: Sugimoto Hiroshi , Fujii Minoru , Imakita Kenji
Published: December 2014

We report a new synthetic route for cubic boron phosphide (BP) nanocrystals with diameters of 2 to 6 nm.
Multi stimuli-responsive photoluminescent nanocomposite of silver nanoclusters with hyperbranched polyethylenimine derivatives
Authors: Zhu Jia-Li , Liu Yi , Liu Xun-Yong , Liu Hua-Ji , Chen Yu
Published: December 2014

A photoluminescent nanocomposite of AgNC–PEI–TMA was multi stimuli-responsive, including toward temperature, salt, pH, and organic guest.
Metal doped titanate photo catalysts for the mineralization of congo red under visible irradiation
Authors: Joseph Amala Infant Joice , Thiripuranthagan Sivakumar
Published: December 2014

Photomineralisation of textile effluent using highly efficient metal doped titanate catalysts.
Optimal design of superhydrophobic surfaces using a semicircular protrusion microtexture
Authors: Tie Lu , Guo Zhiguang , Li W.
Published: December 2014

The effects of chemistry and all the geometrical parameters for the semicircular microtexture on free energy, contact angle were discussed.
Enhanced CO2 transport properties of membranes by embedding nano-porous zeolite particles into Matrimid®5218 matrix
Authors: Ebadi Amooghin Abtin , Omidkhah Mohammadreza , Kargari Ali
Published: December 2014

A novel mixed matrix membrane (MMM) was fabricated by incorporating micro-sized nano-porous sodium zeolite-Y (NaY zeolite) into Matrimid®5218 matrix.
Synthesis of carbon-incorporated titanium oxide nanocrystals by pulsed solution plasma: electrical, optical investigation and nanocrystals analysis
Authors: Lee Chan Woo , Lee Seok-Geun , Noh Jun Hong , Jung Hyun Suk , Chung Kyoung-Jae , Hong Kug Sun , Kim Dong Wook , Hwang Y. S. , Kim Dong-Wan
Published: December 2014

Titanium oxide/carbon composite nanomaterials were synthesized with a liquid precursor via pulsed solution plasma discharge.
Using halogen⋯halogen interactions or C/N–H⋯Cl hydrogen bonding to direct crystal packing in tetrachlorophthalic acid with N-heterocyclic compounds
Authors: Hu Yanjing , Li Zhiqiang , Zhao Yiran , Yang Yu , Liu Faqian , Wang Lei
Published: December 2014

Hydrogen bonding patterns and halogen⋯halogen interactions, C/N–H⋯Cl hydrogen bonding in a series of multi-component molecular structures constructed by tetrachlorophthalic acid with N-heterocycles were discussed.
Copper hydroxyl sulfate as a heterogeneous catalyst for the catalytic wet peroxide oxidation of phenol
Authors: Huang Kai , Wang Jiejie , Wu Dongfang , Lin Sheng
Published: December 2014

Copper hydroxyl sulfates Cu4(OH)6SO4-A and Cu4(OH)6SO4-B were successfully synthesized by a simple hydrothermal method and applied as heterogeneous catalysts to degrade phenol wastewater in the presence of hydrogen peroxide (H2O2).
The structure effect on the surface and interfacial properties of zwitterionic sulfobetaine surfactants for enhanced oil recovery
Authors: Zhao Jianhui , Dai Caili , Ding Qinfang , Du Mingyong , Feng Haishun , Wei Ziyang , Chen Ang , Zhao Mingwei
Published: December 2014

The molecular structure has an important effect on the surface and interfacial properties of sulfobetaine surfactant at both air–water and crude oil–water interfaces.
Improved photocatalytic activity of g-C3N4 derived from cyanamide–urea solution
Authors: Fan Xiangqian , Xing Zheng , Shu Zhu , Zhang Lingxia , Wang Lianzhou , Shi Jianlin
Published: December 2014

This paper describes the fabrication of g-C3N4 by the polymerization of cyanamide–urea solution at elevated temperatures.
Electrospinning of crystalline MoO3@C nanofibers for high-rate lithium storage
Authors: Li Xiu , Xu Jiantie , Mei Lin , Zhang Zhijia , Cui Chunyu , Liu Huakun , Ma Jianmin , Dou Shixue
Published: December 2014

Due to the advantages of their structure and component, the as-synthesized electrospun MoO3@C nanofibers could maintain a high reversible capacity of 623 and 502 mA h g−1 after 100 cycles at 500 and 1000 mA g−1, respectively.
Activated carbon-based gas sensors: effects of surface features on the sensing mechanism
Authors: Travlou Nikolina A. , Seredych Mykola , Rodríguez-Castellón Enrique , Bandosz Teresa J.
Published: December 2014

Activated carbon chips show great potential for ammonia detection with an adsorption-based reversible sensing mechanism depending on carbon surface chemistry.
Difunctional chemosensor for Cu(ii) and Zn(ii) based on Schiff base modified anthryl derivative with aggregation-induced emission enhancement and piezochromic characteristics
Authors: Yang Mingdi , Zhang Yan , Zhu Weiju , Wang Huizhen , Huang Jing , Cheng Longhuai , Zhou Hongping , Wu Jieying , Tian Yupeng
Published: December 2014

Three new anthryl Schiff base derivatives containing a similar molecular structure were synthesized through a simple method and their fluorescent properties were investigated in detail.
Conserved proline-directed phosphorylation regulates SR protein conformation and splicing function
Authors: Keshwani Malik M. , Aubol Brandon E. , Fattet Laurent , Ma Chen-Ting , Qiu Jinsong , Jennings Patricia A. , Fu Xiang-Dong , Adams Joseph A.
Published: December 2014

The alternative splicing of human genes is dependent on SR proteins, a family of essential splicing factors whose name derives from a signature C-terminal domain rich in arginine–serine dipeptide repeats (RS domains). Although the SRPKs (SR-specific protein kinases) phosphorylate these repeats, RS domains also contain prolines with flanking serines that are phosphorylated by a second family of protein kinases known as the CLKs (Cdc2-like kinases). The role of specific serine–proline phosphorylation within the RS domain has been difficult to assign since CLKs also phosphorylate arginine–serine dipeptides and, thus, display overlapping residue specificities with the SRPKs. In the present study, we address the effects of discrete serine–proline phosphorylation on the conformation and cellular function of the SR protein SRSF1 (SR protein splicing factor 1). Using chemical tagging and dephosphorylation experiments, we show that modification of serine–proline dipeptides broadly amplifies the conformational ensemble of SRSF1. The induction of these new structural forms triggers SRSF1 mobilization in the nucleus and alters its binding mechanism to an exonic splicing enhancer in precursor mRNA. These physical events correlate with changes in the alternative splicing of over 100 human genes based on a global splicing assay. Overall, these studies draw a direct causal relationship between a specific type of chemical modification in an SR protein and the regulation of alternative gene splicing programmes.
Understanding the Landscape of Overruns in Transport Infrastructure Projects
Authors: Love Peter E D , Smith Jim , Simpson Ian , Regan Michael , Olatunji Oluwole
Published: December 2014

Cost and schedule overruns are endemic features of transport infrastructure projects. Despite the considerable amount of research within the field of transport and planning in the past thirty years, limited progress has been made to improving the performance of projects. We contend that this will continue to be an issue as long as research efforts focus on the ‘outside view’ with emphasis being placed upon strategic misrepresentation and optimism bias. Understanding ‘why’ and ‘how’ projects overrun, particularly from both ‘outside’ and ‘inside’ perspectives, is pivotal to reducing their impact and occurrence. Thus, in conjunction with the transport and planning literature, references to cost-overrun studies undertaken within the field of construction and engineering are examined. Our objective is to provide policy makers, industry, voluntary organizations, and the public at large with an ameliorated understanding about time-overrun and cost-overrun phenomena. Suggestions to mitigate overruns based upon recent process and technological innovations are identified and discussed.
ATRX tolerates activity-dependent histone H3 methyl/phos switching to maintain repetitive element silencing in neurons
Authors: Noh Kyung-Min , Maze Ian , Zhao Dan , Xiang Bin , Wenderski Wendy , Lewis Peter W. , Shen Li , Li Haitao , Allis C. David
Published: December 2014

ATRX (the alpha thalassemia/mental retardation syndrome X-linked protein) is a member of the switch2/sucrose nonfermentable2 (SWI2/SNF2) family of chromatin-remodeling proteins and primarily functions at heterochromatic loci via its recognition of “repressive” histone modifications [e.g., histone H3 lysine 9 tri-methylation (H3K9me3)]. Despite significant roles for ATRX during normal neural development, as well as its relationship to human disease, ATRX function in the central nervous system is not well understood. Here, we describe ATRX’s ability to recognize an activity-dependent combinatorial histone modification, histone H3 lysine 9 tri-methylation/serine 10 phosphorylation (H3K9me3S10ph), in postmitotic neurons. In neurons, this “methyl/phos” switch occurs exclusively after periods of stimulation and is highly enriched at heterochromatic repeats associated with centromeres. Using a multifaceted approach, we reveal that H3K9me3S10ph-bound Atrx represses noncoding transcription of centromeric minor satellite sequences during instances of heightened activity. Our results indicate an essential interaction between ATRX and a previously uncharacterized histone modification in the central nervous system and suggest a potential role for abnormal repetitive element transcription in pathological states manifested by ATRX dysfunction.
A history of the potato.
Authors: Brown C. R. , Henfling J. W.
Published: December 2014

This chapter describes the domestication of potato crop, as well as its introduction in Europe and cultivation in North America and Ireland. The breeding and cultivation of new cultivars for resistance to potato late blight are also discussed. The collections of potato and wild potatoes and breeding research are also mentioned.
Tuber development.
Authors: Kloosterman B. , Bachem C.
Published: December 2014

During their life cycle, potato plants develop tuberous organs from underground stems called stolons, which allow the rapid development of daughter plants from sprouts at the beginning of the new growing season. The formation and growth of a potato tuber is a complex process that can be divided into separate physiological events. In recent years, several scientific breakthroughs in the signalling pathway of tuberization have revealed novel tuber identity genes and regulatory pathways. Different signalling pathways leading to tuber initiation either act independently or intersect, but all seem to be, at least in part, under the control of the circadian clock associated with phase transitions during the plant life cycle. This chapter integrates the different signalling pathways underlying the process of potato tuber initiation and subsequent tuber growth in relation to timing, tuber physiology, gene expression, and the hormonal changes impacting these processes.
Commercial potato production and cultural management.
Authors: Pavek M. J.
Published: December 2014

This chapter focuses on the principles and components key to successful commercial potato production. These include market and variety choice, pre-plant preparation, field and soil considerations, pre-plant pest management, integrated pest management, field and seedbed preparation, crop planting, propagation and seed preparation, in-row seed spacing and plant population, planting depth, planter types, planting types and post-planting tillage, growing and harvesting.
Seed potato production.
Authors: Davidson R. D. , Xie K. Y.
Published: December 2014

This chapter compares the formal versus informal method of seed potato production, and describes the true potato seed as well as the diseases and pests of concern. The certification process, sanitation and the early-generation stocks are discussed. Seed potato production is a complicated business. To be successful, there are basic guidelines one must follow, whether using an informal grower-saved seed source or a more formal certification programme. Production of disease-free, high-quality seed potatoes is the first and most important component in the production of high-quality, high-yielding table-stock potatoes. Poor seed quality can financially ruin commercial producers, reduce the food supply, and damage an industry.
Insect pests of potato.
Authors: Waters T. D. , Jensen A. S.
Published: December 2014

This chapter aims to introduce pests and categories of pests of nearly global significance, to discuss important management considerations, and to provide a set of useful references as starting points in the potato entomology literature. The four key principles to integrated pest management (IPM) programmes are described, i.e. pest identification, monitoring, control action guidelines or economic injury levels, and management of the pest. Some general concepts relative to good cultural and chemical pest management as a component of IPM are discussed. Is is suggested that a combination of the general principles of potato insect management and direct observations of local agroecosystems will give crop managers most of the knowledge necessary to minimize crop damage successfully and maintain profitability.
Fungal and bacterial disease aspects in potato production.
Authors: Kirk W. W. , Wharton P. S.
Published: December 2014

This chapter presents the disease cycles for various common and economically significant pathogens of the potato crop and emphasizes where in the cycle interventions are thought to be most effective. Tabulated data are provided on the important bacterial, oomycete, and fungal diseases of potato. The survival, spread and epidemiology of these diseases are described, as well as the role of the tuber in the disease cycle. Some measures to control these diseases (including foliar, seed- and soilborne fungal diseases) are provided. Future prospects, considering climate change, fungicide resistance and molecular disease diagnostics, are mentioned.
Traditional breeding and cultivar development.
Authors: Novy R.
Published: December 2014

This chapter details the contributions that potato breeding and cultivar development have made to the global acceptance of potato as a major food crop, the unique characteristics (including dual reproduction and tetraploidy) of potato that impact its breeding, the emerging issues of importance in cultivar development, and the methodologies used in traditional potato breeding. Traditional breeding allows for the genetic "reshuffling" of genes and their recombination into new genotypes that may carry the desired assemblage of resistance and agronomic traits (such as yield and quality) necessary for release as a new cultivar. Traditional breeding therefore remains the primary source of new potato cultivars, with a greater acceptance and adoption of them by the potato industry.
Molecular breeding of potato in the postgenomic era.
Authors: Veilleux R. E. , Boluarte-Medina T.
Published: December 2014

Since the potato genome was published in 2011 (Potato Genome Sequencing Consortium, 2011), with all of its associated tools, including the genome browser, blast engine, transcriptome with links to other plant genomes, the Infinium 8303 Potato Array, new possibilities have become available for potato breeding that complement the traditional approach. This chapter deals with molecular breeding of potato in the post-genomic era, discussing the development of SNP (single-nucleotide polymorphism) chip for assissting mapping, marker-assisted selection, transcriptomics, proteomics, candidate gene approach, transgenics and comparative genomics. Potato breeders have now been equipped with an enviable array of genomic technologies that can be deployed for cultivar improvement. It is likely that the genetic gains that have already been realized in other crops with more tractable breeding systems can finally become a reality for improvements to potato during the 21st century.
Sustaining soil carbon in bioenergy cropping systems of northern temperate regions.
Authors: Gul S. , Winans K. S. , Leila M. , Whalen J. K.
Published: December 2014

Soil organic carbon (SOC) has an essential role in controlling ecosystem functions associated with soil physical, chemical and biological properties. Maintaining the SOC pool size in agroecosystems is important to sustain food security, protect soil biodiversity and buffer environmental impacts. The SOC pool is dynamic, with losses occurring due to CO
2
mineralization and gains from microbially mediated humification of organic substrates into stable C compounds. Bioenergy production from lignocellulosic feedstock implies that greater amounts of plant residues will be removed from agroecosystems and could deplete the SOC pool, based on empirical models and experimental results from long-term field trials. In northern temperate regions, several management practices are suggested to conserve the SOC pool, such as the application of biochar, judicious use of organic and inorganic fertilizers, crop rotations that include high biomass producing non-bioenergy crops or intercropping systems that combine perennial bioenergy crops with other crops (annuals or trees). Moreover, new technologies such as genetically modified (GM) bioenergy crops are recommended to enhance bioenergy production per unit energy input. Those modifications include GM crops with higher resource-use efficiency (i.e., for water, nutrients and light), GM crops with cellulase/ligninase enzyme systems for biofuel production and GM crops with higher calorific values that release more energy during combustion.
Clinical use of cardiac troponins in dogs.
Authors: Gough A.
Published: December 2014

Cardiac troponins are sensitive and specific markers of myocardial damage. They have been shown to be elevated in a number of primary cardiac and non-cardiac conditions. In cardiomyopathies, they are useful for detecting occult disease, and can provide prognostic information. They can be used to detect myocardial damage caused by the administration of doxorubicin, and have been shown to be elevated in cases of intoxication, as well as after anaesthesia. Other diseases that have been shown to increase troponin levels include gastric dilatation volvulus, pyometra and brachycephalic obstructive syndrome, as well as infectious diseases, including dirofilariasias, babesiosis and ehrlichiosis.
Computational genomics of plants.
Authors: Arunachalam V.
Published: December 2014

This review provides a detailed outline of the developments in the field of computational genomics of plants. Emphasis is laid on research on software, databases and web tools in harnessing the genomic information of plants. The review begins with a short description of developments in complete genome sequencing technologies, platforms, assembly pitfalls and other challenges such as polyploidy and repetitive sequences. Updated literature on computational genomics of two model plants, rice and
Arabidopsis
, is given. A compilation of the available databases and genomic resources in plant families is made. Specific resources available for traits and organelles with potential to understand evolution are listed.
Subgroups generated by two pseudo-Anosov elements in a mapping class group. II. Uniform bound on exponents
Authors: Fujiwara Koji
Published: December 2014

Let

S
S

be a compact orientable surface, and

M
o
d

(
S
)

\mathrm {Mod}(S)

its mapping class group. Then there exists a constant

M
(
S
)

M(S)

, which depends on

S
S

, with the following property. Suppose

a
,
b
∈

M
o
d

(
S
)

a,b \in \mathrm {Mod}(S)

are independent (i.e.,

[

a
n

,

b
m

]
≠
1

[a^n,b^m]\not =1

for any

n
,
m
≠
0

n,m \not =0

) pseudo-Anosov elements. Then for any

n
,
m
≥
M

n,m \ge M

, the subgroup

⟨

a
n

,

b
m

⟩

\langle a^n,b^m \rangle

is a free group freely generated by

a
n

a^n

and

b
m

b^m

, and convex-cocompact in the sense of Farb-Mosher. In particular all non-trivial elements in

⟨

a
n

,

b
m

⟩

\langle a^n,b^m \rangle

are pseudo-Anosov. We also show that there exists a constant

N
N

, which depends on

a
,
b

a,b

, such that

⟨

a
n

,

b
m

⟩

\langle a^n,b^m \rangle

is a free group freely generated by

a
n

a^n

and

b
m

b^m

, and convex-cocompact if

|

n

|

+

|

m

|

≥
N

|n|+|m| \ge N

and

n
m
≠
0

nm \not =0

.
MACE: mutation-oriented profiling of chemical response and gene expression in cancers
Authors: Jeong Euna , He Ningning , Park Hyerin , Song Mee , Kim Nayoung , Lee Seongjoon , Yoon Sukjoon
Published: December 2014

Summary: The mutational status of specific cancer lineages can affect the sensitivity to or resistance against cancer drugs. The MACE database provides web-based interactive tools for interpreting large chemical screening and gene expression datasets of cancer cell lines in terms of mutation and lineage categories. GI50 data of chemicals against individual NCI60 cell lines were normalized and organized to statistically identify mutation- or lineage-specific chemical responses. Similarly, DNA microarray data on NCI60 cell lines were processed to analyze mutation- or lineage-specific gene expression signatures. A combined analysis of GI50 and gene expression data to find potential associations between chemicals and genes is also a capability of this system. This database will provide extensive, systematic information to identify lineage- or mutation-specific anticancer agents and related gene targets.

Availability and implementation: The MACE web database is available at http://mace.sookmyung.ac.kr/.

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact:  yoonsj@sookmyung.ac.kr
Disk-based compression of data from genome sequencing
Authors: Grabowski Szymon , Deorowicz Sebastian , Roguski Łukasz
Published: December 2014

Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be easily captured in the (relatively small) main memory. More interesting solutions for this problem are disk based, where the better of these two, from Cox et al. (2012), is based on the Burrows–Wheeler transform (BWT) and achieves 0.518 bits per base for a 134.0 Gbp human genome sequencing collection with almost 45-fold coverage.

Results: We propose overlapping reads compression with minimizers, a compression algorithm dedicated to sequencing reads (DNA only). Our method makes use of a conceptually simple and easily parallelizable idea of minimizers, to obtain 0.317 bits per base as the compression ratio, allowing to fit the 134.0 Gbp dataset into only 5.31 GB of space.

Availability and implementation:  http://sun.aei.polsl.pl/orcom under a free license.

Contact:  sebastian.deorowicz@polsl.pl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Atherogenic properties of lipoproteins in HIV patients starting atazanavir/ritonavir or darunavir/ritonavir: a substudy of the ATADAR randomized study
Authors: Saumoy Maria , Ordóñez-Llanos Jordi , Martínez Esteban , Ferrer Elena , Domingo Pere , Ribera Esteban , Negredo Eugenia , Curto Jordi , Sánchez-Quesada José Luis , Di Yacovo Silvana , González-Cordón Ana , Podzamczer Daniel
Published: December 2014

Objectives

To assess LDL subfraction phenotype and lipoprotein-associated phospholipase A2 (Lp-PLA2) in naive HIV-infected patients starting atazanavir/ritonavir or darunavir/ritonavir plus tenofovir/emtricitabine.

Methods

This was a substudy of a multicentre randomized study. Standard lipid parameters, LDL subfraction phenotype (by gradient gel electrophoresis) and Lp-PLA2 activity (by 2-thio-PAF) were measured at baseline and weeks 24 and 48. Multivariate regression analysis was performed. Results are expressed as the median (IQR).

Results

Eighty-six (atazanavir/ritonavir, n = 45; darunavir/ritonavir, n = 41) patients were included: age 36 (31–41) years; 89% men; CD4 319 (183–425) cells/mm3; and Framingham score 1% (0%–2%). No differences in demographics or lipid measurements were found at baseline. At week 48, a mild but significant increase in total cholesterol and HDL-cholesterol was observed in both arms, whereas LDL cholesterol increased only in the darunavir/ritonavir arm and triglycerides only in the atazanavir/ritonavir arm. The apolipoprotein A-I/apolipoprotein B ratio increased only in the atazanavir/ritonavir arm. At week 48, the LDL subfraction phenotype improved in the darunavir/ritonavir arm (increase in LDL particle size and in large LDL particles), whereas it worsened in the atazanavir/ritonavir arm (increase in small and dense LDL particles, shift to a greater prevalence of phenotype B); the worsening was related to the greater increase in triglycerides in the atazanavir/ritonavir arm. No changes in total Lp-PLA2 activity or relative distribution in LDL or HDL particles were found at week 48 in either arm.

Conclusions

In contrast with what occurred in the atazanavir/ritonavir arm, the LDL subfraction phenotype improved with darunavir/ritonavir at week 48. This difference was associated with a lower impact on plasma triglycerides with darunavir/ritonavir.
Outpatient parenteral antimicrobial therapy and antimicrobial stewardship: challenges and checklists
Authors: Gilchrist M. , Seaton R. A.
Published: December 2014

Outpatient parenteral antimicrobial therapy (OPAT) has become, for many countries, an established form of healthcare delivery. At the same time, there have been calls to ensure the prudent use of the existing antimicrobial armamentarium. For OPAT, this presents a dilemma. On one hand, stewardship principles look for the most effective agent with minimal collateral effects. In OPAT, whilst the aims of the service are similar, convenience of dosing to optimize early hospital discharge or admission avoidance may take precedence over an agent's spectrum of activity. This brief article aims to highlight the importance and explore the challenges of antimicrobial stewardship in the context of OPAT. Within the UK, the safe and effective use of antimicrobials is modelled around the IDSA/Society for Healthcare Epidemiology of America stewardship practice guidelines with local customization where appropriate. Current UK stewardship practice principles were compared with published good practice recommendations for OPAT to identify how OPAT could support the broader antimicrobial stewardship agenda. It is essential that antimicrobial stewardship teams should understand the challenges faced in the non-inpatient setting and the potential benefits/lower risks associated with avoided admission or shortened hospital stay in this population. Within its limitations, OPAT should practise stewardship principles, including optimization of intravenous to oral switch and the reporting of outcomes, healthcare-associated infections and re-admission rates. OPAT should report to the antimicrobial stewardship team. Ideally the OPAT team should be formally represented within the stewardship framework. A checklist has been proposed to aid OPAT services in ensuring they meet their stewardship agenda.
Seroprevalence of Human T-Cell Lymphotropic Viruses Types 1 and 2 Antibodies in Hepatitis C Virus-Positive Patients: Manitoba, Canada, 2012–2014
Authors: Kadkhoda Kamran , Smart Gerry , Bacon Diane , Casselman Adara , Malloch Laurie , Kim John
Published: December 2014

Human T-cell lymphotropic viruses types 1 and 2 are probably among the most neglected blood-borne pathogens that have experienced significant changes in their epidemiology since discovery, which could be attributed to globalization and intravenous drug use practices as well as enhanced screening recommendations; however, systematic prevalence studies, especially in high-risk populations in North America, are not updated.
FIELD: Automated emission line detection software for Subaru/FMOS near-infrared spectroscopy
Authors: Tonegawa Motonari , Totani Tomonori , Iwamuro Fumihide , Akiyama Masayuki , Dalton Gavin , Glazebrook Karl , Ohta Kouji , Okada Hiroyuki , Yabe Kiyoto
Published: December 2014

We describe the development of automated emission line detection software for the Fiber Multi-Object Spectrograph (FMOS), which is a near-infrared spectrograph fed by 400 fibers from the 0.2 deg2 prime focus field of view of the Subaru Telescope. The software, FIELD (FMOS software for Image-based Emission Line Detection), is developed and tested mainly for the FastSound survey, which is targeting Hα emitting galaxies at z ∼ 1.3 to measure the redshift space distortion as a test of general relativity beyond z ∼ 1. The basic algorithm is to calculate the line signal-to-noise ratio (S/N) along the wavelength direction, given by a 2D convolution of the spectral image and a detection kernel representing a typical emission line profile. A unique feature of FMOS is its use of OH airglow suppression masks, requiring the use of flat-field images to suppress noise around the mask regions. Bad pixels on the detectors and pixels affected by cosmic rays are efficiently removed using the information obtained from the FMOS analysis pipeline. We limit the range of acceptable line-shape parameters for the detected candidates to further improve the reliability of line detection. The final performance of line detection is tested using a subset of the FastSound data; the false detection rate of spurious objects is examined by using inverted frames obtained by exchanging object and sky frames. The false detection rate is < 1% at S/N > 5, allowing an efficient and objective emission line search for FMOS data at the line flux level of ≳ 1.0 × 10−16 erg cm−2 s−1.
Baculovirus infection triggers a positive phototactic response in caterpillars to induce ‘tree-top’ disease
Authors: van Houte Stineke , van Oers Monique M. , Han Yue , Vlak Just M. , Ros Vera I. D.
Published: December 2014

Many parasites manipulate host behaviour to enhance parasite transmission and survival. A fascinating example is baculoviruses, which often induce death in caterpillar hosts at elevated positions (‘tree-top’ disease). To date, little is known about the underlying processes leading to this adaptive host manipulation. Here, we show that the baculovirus
Spodoptera exigua
multiple nucleopolyhedrovirus (SeMNPV) triggers a positive phototactic response in
S. exigua
larvae prior to death and causes the caterpillars to die at elevated positions. This light-dependent climbing behaviour is specific for infected larvae, as movement of uninfected caterpillars during larval development was light-independent. We hypothesize that upon infection, SeMNPV captures a host pathway involved in phototaxis and/or light perception to induce this remarkable behavioural change.
Statistical ecology comes of age
Authors: Gimenez Olivier , Buckland Stephen T. , Morgan Byron J. T. , Bez Nicolas , Bertrand Sophie , Choquet Rémi , Dray Stéphane , Etienne Marie-Pierre , Fewster Rachel , Gosselin Frédéric , Mérigot Bastien , Monestiez Pascal , Morales Juan M. , Mortier Frédéric , Munoz François , Ovaskainen Otso , Pavoine Sandrine , Pradel Roger , Schurr Frank M. , Thomas Len , Thuiller Wilfried , Trenkel Verena , de Valpine Perry , Rexstad Eric
Published: December 2014

The desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1–4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.
Children reject inequity out of spite
Authors: McAuliffe Katherine , Blake Peter R. , Warneken Felix
Published: December 2014

When confronted with inequality, human children and adults sacrifice personal gain to reduce the pay-offs of other individuals, exhibiting apparently spiteful motivations. By contrast, sacrifice of personal gain by non-human animals is often interpreted as frustration. Spite may thus be a uniquely human motivator. However, to date, no empirical study has demonstrated that psychological spite actually drives human behaviour, leaving the motivation for inequity aversion unclear. Here, we ask whether 4- to 9-year-old children and adults reject disadvantageous inequity (less for self, more for peer) out of spite or frustration. We show that children, but not adults, are more likely to reject disadvantageous allocations when doing so deprives their peer of a better reward (spite) than when their peer has already received the better reward (frustration). Spiteful motivations are thus present early in childhood and may be a species-specific component of humans' developing cooperative and competitive behaviour.
Molecular evolution of
Dmrt1
accompanies change of sex-determining mechanisms in reptilia
Authors: Janes Daniel E. , Organ Christopher L. , Stiglec Rami , O'Meally Denis , Sarre Stephen D. , Georges Arthur , Graves Jennifer A. M. , Valenzuela Nicole , Literman Robert A. , Rutherford Kim , Gemmell Neil , Iverson John B. , Tamplin Jeffrey W. , Edwards Scott V. , Ezaz Tariq
Published: December 2014

In reptiles, sex-determining mechanisms have evolved repeatedly and reversibly between genotypic and temperature-dependent sex determination. The gene
Dmrt1
directs male determination in chicken (and presumably other birds), and regulates sex differentiation in animals as distantly related as fruit flies, nematodes and humans. Here, we show a consistent molecular difference in
Dmrt1
between reptiles with genotypic and temperature-dependent sex determination. Among 34 non-avian reptiles, a convergently evolved pair of amino acids encoded by sequence within exon 2 near the DM-binding domain of
Dmrt1
distinguishes species with either type of sex determination. We suggest that this amino acid shift accompanied the evolution of genotypic sex determination from an ancestral condition of temperature-dependent sex determination at least three times among reptiles, as evident in turtles, birds and squamates. This novel hypothesis describes the evolution of sex-determining mechanisms as turnover events accompanied by one or two small mutations.
Ants show a leftward turning bias when exploring unknown nest sites
Authors: Hunt Edmund R. , O'Shea-Wheller Thomas , Albery Gregory F. , Bridger Tamsyn H. , Gumn Mike , Franks Nigel R.
Published: December 2014

Behavioural lateralization in invertebrates is an important field of study because it may provide insights into the early origins of lateralization seen in a diversity of organisms. Here, we present evidence for a leftward turning bias in
Temnothorax albipennis
ants exploring nest cavities and in branching mazes, where the bias is initially obscured by thigmotaxis (wall-following) behaviour. Forward travel with a consistent turning bias in either direction is an effective nest exploration method, and a simple decision-making heuristic to employ when faced with multiple directional choices. Replication of the same bias at the colony level would also reduce individual predation risk through aggregation effects, and may lead to a faster attainment of a quorum threshold for nest migration. We suggest the turning bias may be the result of an evolutionary interplay between vision, exploration and migration factors, promoted by the ants' eusociality.
Magnetoreception in birds: the effect of radio-frequency fields
Authors: Wiltschko Roswitha , Thalau Peter , Gehring Dennis , Nießner Christine , Ritz Thorsten , Wiltschko Wolfgang
Published: December 2014

The avian magnetic compass, probably based on radical pair processes, works only in a narrow functional window around the local field strength, with cryptochrome 1a as most likely receptor molecule. Radio-frequency fields in the MHz range have been shown to disrupt the birds' orientation, yet the nature of this interference is still unclear. In an immuno-histological study, we tested whether the radio-frequency fields interfere with the photoreduction of cryptochrome, but this does not seem to be the case. In behavioural studies, birds were not able to adjust to radio-frequency fields like they are able to adjust to static fields outside the normal functional range: neither a 2-h pre-exposure in a 7.0 MHz field, 480 nT, nor a 7-h pre-exposure in a 1.315 MHz field, 15 nT, allowed the birds to regain their orientation ability. This inability to adjust to radio-frequency fields suggests that these fields interfere directly with the primary processes of magnetoreception and therefore disable the avian compass as long as they are present. They do not have lasting adverse after-effects, however, as birds immediately after exposure to a radio-frequency field were able to orient in the local geomagnetic field.
The role of the surface on microglia function: implications for central nervous system tissue engineering
Authors: Pires Liliana R. , Rocha Daniela N. , Ambrosio Luigi , Pêgo Ana Paula
Published: December 2014

In tissue engineering, it is well accepted that a scaffold surface has a decisive impact on cell behaviour. Here we focused on microglia—the resident immune cells of the central nervous system (CNS)—and on their response to poly(trimethylene carbonate-co-ε-caprolactone) (P(TMC-CL)) fibrous and flat surfaces obtained by electrospinning and solvent cast, respectively. This study aims to provide cues for the design of instructive surfaces that can contribute to the challenging process of CNS regeneration. Cell morphology was evidently affected by the substrate, mirroring the surface main features. Cells cultured on flat substrates presented a round shape, while cells with elongated processes were observed on the electrospun fibres. A higher concentration of the pro-inflammatory cytokine tumour necrosis factor-α was detected in culture media from microglia on fibres. Still, astrogliosis is not exacerbated when astrocytes are cultured in the presence of microglia-conditioned media obtained from cultures in contact with either substrate. Furthermore, a significant percentage of microglia was found to participate in the process of myelin phagocytosis, with the formation of multinucleated giant cells being observed only on films. Altogether, the results presented suggest that microglia in contact with the tested substrates may contribute to the regeneration process, putting forward P(TMC-CL) substrates as supporting matrices for nerve regeneration.