bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient conducting channels formed by the π-π stacking in single [2,2]paracyclophane molecules
Authors: Bai Meilin , Liang Jinghong , Xie Liqiang , Sanvito Stefano , Mao Bingwei , Hou Shimin
Published: March 2012

The electronic transport properties of single [2,2]paracyclophane molecules directly connected to gold and platinum electrodes have been investigated both theoretically and experimentally by using first-principles quantum transport simulations and break-junction experiments. For comparison, investigations on [3,3]- and [4,4]-paracyclophanes have also been performed. Our calculations show that the strength of the π-π interaction in paracyclophanes is critically dependent on the inter-ring distance. In contrast to [4,4]paracyclophane in which the π-π interaction is very weak due to the large inter-ring distance, the π-π interaction in [2,2]- and [3,3]-paracyclophanes is rather strong and dominates the electronic transport properties. In particular, for the asymmetric Au-[2,2]paracyclophane-Au junction in which the [2,2]paracyclophane molecule is connected to each gold electrode through a Au adatom and the two Au adatoms are attached in η1-fashion to two carbon atoms in the benzene backbones connecting with different ethylene groups, the transmission coefficient at the Fermi level is calculated to be 1.0 × 10−2, in excellent agreement with experiments. When the gold electrodes are replaced by platinum, the calculated transmission coefficient at the Fermi level of the symmetric Pt-[2,2]paracyclophane-Pt junction with one Pt adatom used as the linker group is increased to 0.83, demonstrating that the π-π stacking in [2,2]paracyclophane is efficient for electron transport when the molecule-electrode interfaces are electronically transparent. This is confirmed by our preliminary experimental studies on the Pt-[2,2]paracyclophane-Pt junctions, for which the low-bias junction conductance has reached 0.40 ± 0.02 G0 (G0 is the conductance quantum). These findings are helpful for the design of molecular electronic devices incorporating π-π stacking molecular systems.
Analysis of the contrast mechanism in bimodal atomic force microscopy combining amplitude modulation and band excitation
Authors: Solares Santiago D.
Published: March 2012

A new bimodal method of scanning probe microscopy was recently introduced in which one cantilever eigenmode is driven using the conventional tapping mode (amplitude modulation) technique while another one is driven using a broadband excitation signal, such that its transfer function can be measured throughout the full spectrum and used to infer material properties from changes in the resonance frequency and quality factor as the surface is scanned. This paper explores computationally the fundamental mechanisms underlying the observed contrast as well as the most relevant aspects of the cantilever dynamics. The objective is to place the new multifrequency method in the context of previous work in the field, describing in detail the type of information it provides, as well as the conditions that lead to meaningful measurements or measurements affected by artifacts.
Structure related hardness and elastic modulus of bulk metallic glass
Authors: Song M. , Sun Y. Y. , He Y. H. , Guo S. F.
Published: March 2012

In this paper, the structure (free volume) related hardness and elastic modulus of a typical Cu36Zr48Al8Ag8 bulk metallic glass have been investigated. It is found that the cooling rate during sample preparation affects significantly the concentration of the free volume and thus the interatomic distance. The central region of the specimen has a much lower cooling rate and concentration of the free volume, which decreases the nucleation density of the shear bands, leading to higher hardness and elastic modulus.
Communication: Self-assembly of semiflexible-flexible block copolymers
Authors: Kumar N. Arun , Ganesan Venkat
Published: March 2012

We apply the methodology of self-consistent Brownian dynamics simulations to study the self-assembly behavior in melts of semiflexible-flexible diblock copolymers as a function of the persistence length of the semiflexible block. Our results reveal a novel progression of morphologies in transitioning from the case of flexible-coil to rod-coil copolymers. At even moderate persistence lengths, the morphologies in the semiflexible-block rich region of the phase diagram transform to liquid crystalline phases. In contrast, the phases in the flexible-block rich region of the phase diagram persist up to much larger persistence lengths. Our analysis suggests that the development of orientational order in the semiflexible block to be a critical factor influencing the morphologies of self-assembly.
Photoluminescence associated with basal stacking faults in c-plane ZnO epitaxial film grown by atomic layer deposition
Authors: Yang S. , Kuo C. C. , Liu W.-R. , Lin B. H. , Hsu H.-C. , Hsu C.-H. , Hsieh W. F.
Published: March 2012

Basal plane stacking faults (BSFs) with density of ∼1 × 106 cm−1 are identified as the dominant defect in the annealed ZnO thin films grown on c-plane sapphire by atomic layer deposition. The dominant peak centered at 3.321 eV in low-temperature photoluminescence measurements is attributed to the emission from the BSFs. The emission mechanism is considered to be the confined indirect excitons in the region of quantum-well-like structure formed by the BSFs. The observed energy shift of 19 meV with respect to the BSF-bounded exciton at low temperature may be caused by the localization effect associated with the coupling between BSF quantum wells.
Investigation of defect states in heavily dislocated thin silicon films
Authors: Mchedlidze T. , Kittler M.
Published: March 2012

Deep level transient spectroscopy (DLTS) and photoluminescence (PL) were applied for investigation of defect states in thin crystalline silicon (Si) films deposited on glass. The films were fabricated by solid phase crystallization of amorphous Si layers and subsequently were subjected either to rapid thermal annealing or/and to hydrogenation. The study revealed presence of carrier traps and radiative recombination centers characteristic for dislocations in Si. Density of the traps strongly varied depending on the fabrication processes applied to the film. This allowed to link formation of the defects with applied fabrication processes and suggested origins for the traps. Passivation of the dislocation-related defect states by hydrogen was observed and appearance of hydrogen-related traps for the dislocated structures was detected. An increase in intensity of dislocation-related luminescence well correlated with the decrease in density of deep dislocation-related traps.
Temperature dependent thermal conductivity of pure silica MEL and MFI zeolite thin films
Authors: Fang Jin , Huang Yi , Lew Christopher M. , Yan Yushan , Pilon Laurent
Published: March 2012

This paper reports the temperature dependent cross-plane thermal conductivity of pure silica zeolite (PSZ) MFI and MEL thin films measured using the 3ω method between 30 and 315 K. PSZ MFI thin films were b-oriented, fully crystalline, and had a 33% microporosity. PSZ MEL thin films consisted of MEL nanoparticles embedded in a nonuniform and porous silica matrix. They featured porosity, relative crystallinity, and particle size ranging from 40% to 59%, 23% to 47%, and 55 to 80 nm, respectively. Despite their crystallinity, MFI films had smaller thermal conductivity than that of amorphous silica due to strong phonon scattering by micropores. In addition, the effects of increased relative crystallinity and particle size on thermal conductivity of MEL thin films were compensated by the simultaneous increase in porosity. Finally, thermal conductivity of MFI zeolite was predicted and discussed using the Callaway model based on the Debye approximation.
Effect of ferroelectric parameters on ferroelectric diodes
Authors: Ge Chen , Jin Kui-juan , Wang Can , Lu Hui-bin , Wang Cong , Yang Guo-zhen
Published: March 2012

We investigate the effect of various ferroelectric parameters, such as the doping density, the permittivity, and the thickness, on ferroelectric diodes based on the proposed self-consistent numerical model. Our calculations clarify the dependence of the band diagrams, the charge density distributions, and the I–V curves on these important ferroelectric parameters in metal/ferroelectrics/metal structures. The calculated results reveal that the ON/OFF ratio of the ferroelectric diodes decreases with the increase of the doping density, the permittivity, and the thickness in the ferroelectric film, respectively.
An “acoustical camera” for in vitro characterization of contrast agent microbubble vibrations
Authors: Renaud G. , Bosch J. G. , van der Steen A. F. W. , de Jong N.
Published: March 2012

An acoustical method was developed to retrieve the radial response of single microbubbles to a pressure wave by means of a low-amplitude probing wave. If the frequency of the latter is much higher than the spherical resonance frequency of the microbubble, the relative amplitude modulation in the signal scattered in response to the probing wave is quasi-equal to the radial strain induced by the pressure wave. A reference probe signal before and after the transmission of the pressure wave allows us to assess asymmetry in microbubble oscillations. Among 138 lipid-coated microbubbles, 8% and 7% showed compression-only and expansion-only behaviors, respectively.
An expanded molecular phylogeny of the southern bluebells (Wahlenbergia, Campanulaceae) from Australia and New Zealand
Authors: Prebble Jessica M. , Meudt Heidi M. , Garnock-Jones Phil J.
Published: March 2012

We used nuclear and chloroplast DNA markers to examine relationships and test the current morphology-based taxonomy of several species and subspecies of Australian and New Zealand Wahlenbergia. We sampled nuclear ribosomal ITS regions and the chloroplast regions trnL–F and trnK–psbA from 105 individuals, representing 29 of the 46 species and subspecies currently recognised in New Zealand and Australia. Our phylogeny was incompletely resolved because of low levels of genetic variation in all three markers and some conflict between ITS and chloroplast markers. The New Zealand rhizomatous species appear to have radiated in New Zealand after a single long-distance dispersal event from Australia, but it is unclear to which species in Australia they are most closely related. The New Zealand radicate species do not form a clade; instead they are shown to be very closely related to many Australian radicate species. The four species in the New Zealand lowland radicate W. gracilis complex may all belong to the same morphologically variable species. In contrast, the other New Zealand radicate species, W. vernicosa, is probably a separately evolving lineage, and is not conspecific with the W. gracilis complex, nor the Australian W. littoricola, as previously hypothesised. Two of the New Zealand rhizomatous species, W. albomarginata and W. pygmaea, may be conspecific. By contrast, the morphologically distinctive New Zealand rhizomatous W. cartilaginea, W. matthewsii and W. congesta subsp. haastii each formed monophyletic groups. Samples of two recently described Australian species (W. rupicola and W. telfordii) formed monophyletic groups consistent with their recognition.
Revision of Pichonia (Sapotaceae) in New Caledonia
Authors: Swenson Ulf , Munzinger Jérôme
Published: March 2012

Pichonia Pierre (Sapotaceae, Chrysophylloideae) is a small genus of 10 species in Australasia, of which seven are endemic to New Caledonia. We revise the genus for New Caledonia and describe one new species (P. grandiflora), resurrect another (P. dubia) and make two new combinations because of nomenclatural priority (P. balansae, P. deplanchei). P. balansae has been known for decades as P. calomeris, a name that in fact has never been validly published. The members are mainly found in Grande Terre, the main island of New Caledonia, but two species extend to Belep Islands in the north and to Isle of Pines in the south of the archipelago. Most grow in maquis vegetation at low altitudes, on ultramafic soils, preferably serpentinite. The exceptions are P. balansana, confined to limestone areas, and P. dubia that is a large canopy tree of the humid forest on ultramafic soil. Pichonia is distinguished by a character combination of an areolate higher venation, staminodes, a single-seeded fruit, plano-convex cotyledons and absence of endosperm. Because of being restricted to ultramafic soils, they are subsequently sensitive to present and future mining activities in New Caledonia. Hence, preliminary IUCN Red List assessments for all members are provided. P. balansana, P. daenikeri and P. lecomtei are all naturally uncommon, do not occur in any protected area and are proposed the IUCN status of Vulnerable. The herein described species P. grandiflora is rare in nature, known only from the Boulinda–Paéoua–Kopéto Mountains, and is in urgent need of protection. It is therefore assigned a preliminary status of Endangered.
Morphological evaluation of the Drosera peltata complex (Droseraceae)
Authors: Gibson Robert , Conn Barry J. , Bruhl Jeremy J.
Published: March 2012

A phenetic study of morphological characters of the Drosera peltata complex (Droseraceae) supports the recognition of the following taxa: D. peltata from wetlands of south-eastern Australia; D. auriculata from south-eastern Australia and New Zealand; the morphologically variable D. hookeri from south-eastern Australia and northern New Zealand; the widespread D. lunata from southern and South-East Asia, as well as northern and north-eastern Australia; and the new species D. yilgarnensis R.P.Gibson & B.J.Conn is here described, from around granite outcrops of south-western Australia. D. bicolor from south-western Australia is recognised as a distinct species outside of the D. peltata complex. D. insolita, considered until recently as a distinct species, is reduced to synonymy of D. lunata. Phenotypic plasticity, vegetative similarity and fleetingly produced diagnostic floral and seed characters within the complex pose significant challenges in understanding the taxonomy of these taxa.
The effect of wildfires on vegetation cover and dune activity in Australia's desert dunes: a multisensor analysis
Authors: Levin N. , Levental S. , Morag H.
Published: March 2012

Most of Australia’s desert dune fields are stable; however, wildfires may reduce vegetation and biological soil crust cover so that sand movement may take place until vegetation recovers. In this study, we aimed to study the recovery rate of vegetation cover in spinifex (Triodia)-dominated desert dunes following wildfires using satellite imagery-derived spectral indices to: (1) determine for how long after fire these dunes may be active until critical levels of vegetation cover are attained; (2) determine which spectral index is the most suitable for monitoring vegetation recovery in this area. We have used a combination of MODIS, Landsat, Aster and QuickBird images to analyse vegetation cover following fire at various spatial and temporal scales, in the Great Victoria Desert, WA. The following spectral indices were compared: Brightness Index, Biological Soil Crust Index (BSCI), Crust Index, Enhanced Vegetation Index, Normalised Burn Ratio, Normalised Difference Vegetation Index, Soil Adjusted Vegetation Index and the Stress-related Vegetation Index. The BSCI was found to outperform the other spectral indices in monitoring vegetation cover in this area. Whereas full recovery of vegetation following wildfires in the study area was attained only after 25–30 years, critical thresholds of vegetation cover limiting sand movement were attained after just 1–5 years. The frequency and intensity of wildfires is therefore an important factor controlling dune activity in Australia’s deserts.
Estimation of wildfire size and risk changes due to fuels treatments
Authors: Cochrane M. A. , Moran C. J. , Wimberly M. C. , Baer A. D. , Finney M. A. , Beckendorf K. L. , Eidenshink J. , Zhu Z.
Published: March 2012

Human land use practices, altered climates, and shifting forest and fire management policies have increased the frequency of large wildfires several-fold. Mitigation of potential fire behaviour and fire severity have increasingly been attempted through pre-fire alteration of wildland fuels using mechanical treatments and prescribed fires. Despite annual treatment of more than a million hectares of land, quantitative assessments of the effectiveness of existing fuel treatments at reducing the size of actual wildfires or how they might alter the risk of burning across landscapes are currently lacking. Here, we present a method for estimating spatial probabilities of burning as a function of extant fuels treatments for any wildland fire-affected landscape. We examined the landscape effects of more than 72 000 ha of wildland fuel treatments involved in 14 large wildfires that burned 314 000 ha of forests in nine US states between 2002 and 2010. Fuels treatments altered the probability of fire occurrence both positively and negatively across landscapes, effectively redistributing fire risk by changing surface fire spread rates and reducing the likelihood of crowning behaviour. Trade offs are created between formation of large areas with low probabilities of increased burning and smaller, well-defined regions with reduced fire risk.
Antiparallel β-sheet architecture in Iowa-mutant β-amyloid fibrils
Authors: Qiang Wei , Yau Wai-Ming , Luo Yongquan , Mattson Mark P. , Tycko Robert
Published: March 2012

Wild-type, full-length (40- and 42-residue) amyloid β-peptide (Aβ) fibrils have been shown by a variety of magnetic resonance techniques to contain cross-β structures in which the β-sheets have an in-register parallel supramolecular organization. In contrast, recent studies of fibrils formed in vitro by the Asp23-to-Asn mutant of 40-residue Aβ (D23N-A
β
1–40
), which is associated with early onset neurodegeneration, indicate that D23N-A
β
1–40
fibrils can contain either parallel or antiparallel β-sheets. We report a protocol for producing structurally pure antiparallel D23N-A
β
1–40
fibril samples and a series of solid state nuclear magnetic resonance and electron microscopy measurements that lead to a specific model for the antiparallel D23N-A
β
1–40
fibril structure. This model reveals how both parallel and antiparallel cross-β structures can be constructed from similar peptide monomer conformations and stabilized by similar sets of interactions, primarily hydrophobic in nature. We find that antiparallel D23N-A
β
1–40
fibrils are thermodynamically metastable with respect to conversion to parallel structures, propagate less efficiently than parallel fibrils in seeded fibril growth, and therefore must nucleate more efficiently than parallel fibrils in order to be observable. Experiments in neuronal cell cultures indicate that both antiparallel and parallel D23N-A
β
1–40
fibrils are cytotoxic. Thus, our antiparallel D23N-A
β
1–40
fibril model represents a specific “toxic intermediate” in the aggregation process of a disease-associated Aβ mutant.
Interaction of soybean and
Phakopsora pachyrhizi
, the cause of soybean rust.
Authors: Hartman G. L. , Hill C. B. , Twizeyimana M. , Miles M. R. , Bandyopadhyay R.
Published: March 2012

Soybean rust, caused by
Phakopsora pachyrhizi
Syd., is a major disease limiting soybean [
Glycine max
(L.) Merr.] production in many areas of the world. Yield losses of up to 80% have been reported in experimental plots in Taiwan. Although the disease is not always yield limiting, it has the potential under conducive conditions to cause major losses in most soybean-producing countries in the world. The threat of
P. pachyrhizi
to soybean production in the Western Hemisphere began in Paraguay in 2001, where the disease was found in a limited number of soybean fields in the Parana River basin bordering Brazil. Later, in 2004,
P. pachyrhizi
was found in the continental USA. There are approximately 150 species in 53 genera the family Fabaceae known to be hosts of
P. pachyrhizi
. Approximately 120 of the known hosts occur in North and Central America and could become important in the epidemiology of the disease, serving as a bridge or over-wintering host between soybean crops. The interaction between soybean genotypes and
P. pachyrhizi
isolates appears to follow gene-for-gene theory, with resistance genes controlling resistance to specific pathotypes. In addition to soybean, pathotype-specific resistance has also been found in a number of perennial
Glycine
species. Dominant genes controlling pathotype-specific resistance to soybean rust have been identified and mapped to five loci in the soybean genome, with multiple alleles at four loci. Many of the resistance genes have become ineffective over time in different geographic areas following their deployment into soybean production. The search for more durable soybean rust resistance will include research on non-host and/or engineered resistance.
Detection and measurement of plant disease symptoms using visible-wavelength photography and image analysis.
Authors: Bock C. H. , Nutter F. W., Jr.
Published: March 2012

Plant disease detection and severity assessment are required for many purposes, including predicting yield loss, monitoring and forecasting epidemics, judging host resistance and for studying fundamental biological host-pathogen processes. If assessments of disease severity are inaccurate and/or imprecise, incorrect conclusions might be drawn and incorrect actions taken. Image analysis based on digital images made using visible wavelengths is one of the several methods used to detect and quantify disease; it offers advantages compared with visual assessment or other methods. Over the last 30 years, major advances have been made to improve reliability, precision and accuracy of image analysis for detecting and measuring plant disease. Although the equipment and software continue to become more sophisticated, these technologies are also becoming easier to use. As a result, image analysis to measure plant disease is becoming increasingly widely used, and has now been applied in the study of numerous plant diseases. This review describes the history, technology and application of visible-wavelength photography and image analysis, and progress towards realizing the full potential of these systems in plant disease detection and assessment.
Symbiotic nitrogen fixation and the delivery of multiple ecosystem services: a global change perspective.
Authors: Fornara D.
Published: March 2012

A key challenge facing humanity in the coming decades will be ensuring food supply to a growing human population without compromising the sustainability of many agro-ecosystems worldwide. Although agricultural soils remain firmly at the foundation of human life-support systems, human domination of terrestrial ecosystems over the last century has greatly affected their long-term sustainability as well as reducing soil biological diversity. This has mainly occurred through widespread land-use changes and through the chronic deposition of biologically available nutrients, such as nitrogen (N) and phosphorous (P). Here I argue that a better understanding of the ecological role of symbiotic N-fixers could help in developing more sustainable multifunctional agro-ecosystems. N-fixers are beneficial for the delivery of multiple ecosystem services such as greater primary productivity (i.e. increased crop yields), increased soil carbon (C) and N sequestration, and higher soil biological diversity. Understanding the ecological mechanisms responsible for the provision of these ecosystem services may also be critical for reducing the global-warming potential of many agricultural practices worldwide.
Nutrients that kill: is fructose guilty of causing the obesity epidemic?
Authors: Purcell K. , Priya Sumithran Priya Sumithran , Haywood C. , Proietto J.
Published: March 2012

Obesity has become a major health issue throughout the world. Between 1960 and 2000, fructose consumption has increased at a similar rate to that of obesity. For this reason, fructose has been postulated to contribute to obesity. This paper reviews several possible mechanisms by which dietary fructose may be linked to obesity, and examines the currently available data on the interaction of dietary fructose with the increase in rates of obesity. The majority of studies reviewed in this paper support a link between fructose consumption and obesity. However, studies that are controlled for sugar intake do not appear to support a specific effect of fructose (as opposed to glucose) in the development of obesity. At least one study suggests that fructose ingestion gives a worse metabolic profile when compared with glucose.
Life Satisfaction, Self-Determination, and Consumption Adequacy at the Bottom of the Pyramid
Authors: Martin Kelly D. , Paul Hill Ronald
Published: March 2012

Concentration on consumption in material environments characterized by too much rather than too little creates important gaps in the understanding of how much of the earth’s population navigates the marketplace. This study investigates bottom-of-the-pyramid, or impoverished, consumers to better comprehend the relationship between societal poverty and individual life satisfaction as moderated by psychological need deprivation and described by self-determination theory. Data were gathered from more than 77,000 individuals in 51 of the world’s poorest countries. Using hierarchical linear models, results show that relatedness and autonomy improve poverty’s negative influence on life satisfaction, but only if basic life necessities are available, described as consumption adequacy. Findings illustrate that without consumption adequacy, psychological need fulfillment has little effect on the poverty–well-being relationship, emphasizing the hopelessness of individuals living in extreme poverty. Findings also suggest to researchers that impoverished consumers not only face different circumstances but actually respond to those circumstances in unique ways.
Lenses of the Heart: How Actors’ and Observers’ Perspectives Influence Emotional Experiences
Authors: Hung Iris W. , Mukhopadhyay Anirban
Published: March 2012

This research examines how the visual perspectives that people take to appraise an event, that is, whether they view themselves as actors in the situation or observers of it, influence the intensities of the emotions they experience. We predict that in a situation that elicits emotions, greater attention to the self (if using an observer’s perspective) leads to greater intensity of self-conscious emotions such as pride, guilt, and embarrassment, whereas greater attention to the situation (if using an actor’s perspective) leads to greater intensity of hedonic emotions such as joy, sorrow, and excitement. In this way, visual perspectives can act as situational antecedents that shape the use of emotion appraisals. Three experiments support these propositions and demonstrate the mediating role of appraisals, across a variety of emotion-eliciting contexts, that were visualized as well as recalled.
Visible light responsive titania-based nanostructures for photocatalytic, photovoltaic and photoelectrochemical applications
Authors: Nguyen Van Hieu , Nguyen Bich Ha
Published: March 2012

This work presents a topical review of selected articles on visible light responsive titania-based nanostructures used for fabricating the photoanodes of the photocatalytic and photoelectrical cells for hydrogen production by water splitting or fuel decomposition, electricity generation by fuel decomposition and pollutant degradation under illumination by sunlight as well as for fabricating dye-sensitized and quantum dot-sensitized solar cells. Three main types of related nanostructures are reviewed: anion-doped titania nanomaterials, cation-doped titania nanomaterials and titania-based nanostructures sensitized by dyes and quantum dots. After the presentation of the obtained results, the prospective further research works to achieve the successful fabrication of visible light responsive photocatalytic, photoelectrochemical or photovoltaic devices with high performance are discussed.
The synthesis of α-MnO2nanorods using hydrothermal homogeneous precipitation
Authors: Hlaing Aye Aye , Win Phyu Phyu
Published: March 2012

Clear and uniform one-dimensional (1D) α-MnO2nanorods with diameters of 30–50 nm were prepared by hydrothermal treatment of homogeneous solution of hydratedMnSO4andKMnO4with a littleH2O2. Upon control of hydrothermal conditions (reaction temperature and duration time), an excellent crystalline phase ofMnO2was obtained and its morphology was investigated. The crystal structures of as-synthesizedMnO2products have been characterized by x-ray diffraction (XRD). The morphology of the product was examined by scanning electron microscopy (SEM) and the chemical composition was analyzed using energy dispersive spectroscopy (EDS) along with SEM. The Mn concentration was determined by the chemical titration method.
YOABS: yet other aligner of biological sequences—an efficient linearly scaling nucleotide aligner
Authors: Galinsky V. L.
Published: March 2012

Motivation: Explosive growth of short-read sequencing technologies in the recent years resulted in rapid development of many new alignment algorithms and programs. But most of them are not efficient or not applicable for reads ≳200 bp because these algorithms specifically designed to process short queries with relatively low sequencing error rates. However, the current trend to increase reliability of detection of structural variations in assembled genomes as well as to facilitate de novo sequencing demand complimenting high-throughput short-read platforms with long-read mapping. Thus, algorithms and programs for efficient mapping of longer reads are becoming crucial. However, the choice of long-read aligners effective in terms of both performance and memory are limited and includes only handful of hash table (BLAT, SSAHA2) or trie (Burrows-Wheeler Transform - Smith-Waterman (BWT-SW), Burrows-Wheeler Alignerr - Smith-Waterman (BWA-SW)) based algorithms.

Results: New O(n) algorithm that combines the advantages of both hash and trie-based methods has been designed to effectively align long biological sequences (≳200 bp) against a large sequence database with small memory footprint (e.g. ~2 GB for the human genome). The algorithm is accurate and significantly more fast than BLAT or BWT-SW, but similar to BWT-SW it can find all local alignments. It is as accurate as SSAHA2 or BWA-SW, but uses 3+ times less memory and 10+ times faster than SSAHA2, several times faster than BWA-SW with low error rates and almost two times less memory.

Availability and implementation: The prototype implementation of the algorithm will be available upon request for non-commercial use in academia (local hit table binary and indices are at ftp://styx.ucsd.edu).

Contact:  vit@ucsd.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
2-Phenyl-1H-imidazol-3-ium hydrogen fumarate–fumaric acid (2/1)
Authors: Guo Hong , Zhang Xin , Li Jian-Xia
Published: March 2012

The asymmetric unit of the title compound, C9H9N2+·C4H3O4−·0.5C4H4O4, consists of one 2-phenylimidazolium cation, one hydrogen fumarate anion and half a fumaric acid molecule, which lies on an inversion center. N—H...O and O—H...O hydrogen bonds connect the cations, anions and fumaric acid molecules into sheets parallel to the (102) plane.
(Acetylacetonato-κ2O,O′)carbonyl[tris(naphthalen-1-yl)phosphane-κP]rhodium(I) acetone hemisolvate
Authors: Ogutu Hezron , Meijboom Reinout
Published: March 2012

The title compound, [Rh(C5H7O2)(C30H21P)(CO)]·0.5C3H6O, has two different complex molecules in the asymmetric unit, with the RhIatoms in slightly distorted square-planar coordination environments. The molecules are packed as two monomeric molecules with one acetone solvent molecule sitting at the centre.
6β-Methyl-3,20-dioxopregn-4-en-17-yl acetate
Authors: Chen Longran , Liu Xuefen , Yang Peng
Published: March 2012

The title compound, C24H34O4, is a precursor of Megestrol acetate. RingAhas a half-chair conformation [Q= 0.446 (3) Å, θ = 54.6 (4)° and φ = 9.5 (4)°]. RingDadopts a 13β-envelope conformation [Q= 0.463 (2) Å and φ = 188.2 (3)°].
5-{2-(4-Chlorophenyl)-1-[2-(4-chlorophenyl)-1-(3,4,5-trimethoxyphenyl)ethoxy]ethyl}-1,2,3-trimethoxybenzene
Authors: Fu Ying , Yuan Mu , Hu Xuemei , Yang Yanshou , Hou Hongxia
Published: March 2012

The title compound, C34H36Cl2O7, is a by-product from the reaction of 4-chlorobenzylzinc chloride with 3,4,5-trimethoxybenzaldehyde. In each of the two 1,2-diphenylethyl moieties, the two benzene rings are arranged in atransconformation and make Car—C—C—Cartorsion angles of 163.64 (19) and 174.43 (18)°. The crystal structure is stabilized by van der Waals interactions only.
Rubrene endoperoxide acetone monosolvate
Authors: Shinashi Kiyoaki , Uchida Akira
Published: March 2012

The title acetone solvate, C42H28O2·C3H6O [systematic name: 1,3,10,12-tetraphenyl-19,20-dioxapentacyclo[10.6.2.02,11.04,9.013,18]icosa-2(11),3,5,7,9,13,15,17-octaene acetone monosolvate], is a photooxygenation product of rubrene (systematic name: 5,6,11,12-tetraphenyltetracene). The molecule bends at the bridgehead atoms, which are linked by the O—O transannular bond, with a dihedral angle of 49.21 (6)° between the benzene ring and the naphthalene ring system of the tetracene unit. In the crystal, the rubrene molecules are linked by C—H...O hydrogen bonds into a column along thecaxis. The acetone solvent molecules form a dimer around a crystallographic inversion centre through a carbonyl–carbonyl dipolar interaction. A C—H...O hydrogen bond between the rubrene and acetone molecules is also observed.
N-(4-Chlorobutanoyl)-N′-[2-(trifluoromethyl)phenyl]thiourea
Authors: Yusof Mohd Sukeri Mohd , Embong Nur Farhana , Arshad Suhana , Razak Ibrahim Abdul
Published: March 2012

In the title compound, C12H12ClF3N2OS, the dihedral angle between the benzene ring and the thiourea fragment is 69.41 (5)°. The thiourea N—H atoms adopt ananticonformation, such that one of them forms an intramolecular N—H...O hydrogen bond, generating anS(6) ring. In the crystal, both N—H groups form inversion dimers, oneviaa pair of N—H...S hydrogen bonds and oneviaa pair of N—H...O hydrogen bonds. These lead toR22(8) andR22(12) loops, respectively. Weak C—H...Cl, C—H...F, C—H...S and π–π [centroid–centroid separation = 3.7098 (6)Å and slippage = 1.853 Å] interactions also occur.
2-Amino-4-(4-chlorophenyl)-6-(pyrrolidin-1-yl)pyridine-3,5-dicarbonitrile
Authors: Inglebert S. Antony , Kamalraja Jayabal , Sethusankar K. , Vasuki Gnanasambandam
Published: March 2012

In the title compound, C17H14ClN5, two C atoms and their attached H atoms of the pyrrolidine ring are disordered over two sets of sites with an occupancy ratio of 0.638 (10):0.362 (10). The benzene and pyridine rings are inclined to one another by 60.57 (8)°. In the crystal, the amino group forms an N—H...N hydrogen bond with one of the cyano groups, linking the molecules into chains along [010].
(E)-N′-(4-Isopropylbenzylidene)isonicotinohydrazide monohydrate
Authors: Bhat Mashooq A. , Abdel-Aziz Hatem A. , Ghabbour Hazem A. , Hemamalini Madhukar , Fun Hoong-Kun
Published: March 2012

In the title compound, C16H17N3O·H2O, the isonicotinohydrazide molecule adopts anEconformation about the central C=N double bond. The dihedral angle between the pyridine and the benzene rings is 54.56 (15)°. In the crystal, molecules are connectedviaN—H...O, O—H...N and O—H...O hydrogen bonds, forming a three-dimensional network.
2-Amino-3-chloro-5-nitrobenzamide
Authors: Wardell James L. , Tiekink Edward R. T.
Published: March 2012

The amide group in the title compound, C7H6ClN3O3, is significantly twisted out of the plane of the benzene ring [C—C—C—O = 34.2 (5)°] whereas the nitro group is almost co-planar [O—N—C—C = 4.0 (5)°] with the ring. Intramolecular N—H...O and N—H...Cl hydrogen bonds occur. In the crystal, the molecules are linked by N—H...O hydrogen bonds, generating layers propagating in theabplane.
4-[3,4-Dimethyl-1-(4-methylphenyl)-5-oxo-4,5-dihydro-1H-pyrazol-4-yl]-3,4-dimethyl-1-(4-methylphenyl)-4,5-dihydro-1H-pyrazol-5-one
Authors: Wardell Solange M. S. V. , Howie Alan H. , Tiekink Edward R. T. , Wardell James L.
Published: March 2012

In the title compound, C24H26N4O2, the complete molecule is generated by the application of twofold symmetry. The pyrazole ring is approximately planar [r.m.s. deviation = 0.026 Å] and the benzene ring is twisted out of this plane [dihedral angle = 21.94 (7)°]. A twist in the molecule about the central C—C bond [1.566 (3) Å] is also evident [C—C—C—C torsion angle = 44.30 (14)°]. Supramolecular layers in thebcplane are formed in the crystal packingviaC—H...O and C—H...π interactions.
4-{2-[4-(Dimethylamino)phenyl]ethenyl}-1-methylpyridinium 4-nitrobenzenesulfonate
Authors: Li Liang , Dai Yiqiang , Jin Yun , Yang Huai , Yang Zhou
Published: March 2012

The asymmetric unit of the title salt, C16H19N2+. C6H4NO5S−, consists of two cations and two anions. The crystal structure is stabilized by π–π interactions between the pyridyl and phenyl rings of the cations, with a centroid–centroid distance of 3.7323 (6) Å.
Marbofloxacin
Authors: Shen Jin , Qian Jing-Jing , Gu Jian-Ming , Hu Xiu-Rong
Published: March 2012

In the title compound, [systematic name: 9-fluoro-2,3-dihydro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-7H-pyrido[1,2,3-ij][1,2,4]benzoxadiazine-6-carboxylic acid], C17H19FN4O4, the carbonyl and carboxyl groups are coplanar with the quinoline ring, making a dihedral angle of 2.39 (2)°. The piperazine ring adopts a chair conformation and the oxadiazinane ring displays an envelope conformation with the CH2group at the flap displaced by 0.650 (2) Å from the plane through the other five atoms. The molecular structure exhibits anS(6) ring motif, owing to an intramolecular O—H...O hydrogen bond. In the crystal, weak C—H...F hydrogen bonds link molecules into layers parallel to theabplane.
{4,4′,6,6′-Tetrabromo-2,2′-[(2,2-dimethylpropane-1,3-diyl)bis(nitrilomethanylylidene)]diphenolato}copper(II)
Authors: Kargar Hadi , Kia Reza , Haghshenas Mahbubeh , Tahir Muhammad Nawaz
Published: March 2012

In the title compound, [Cu(C19H16Br4N2O2)], the CuIIion and the substituted C atom of the diamine fragment lie on a crystallographic twofold rotation axis. The geometry around the CuIIion is distorted square-planar, which is defined by the N2O2donor atoms of the coordinated Schiff base ligand. The dihedral angle between the symmetry-related substituted benzene rings is 25.33 (14)°. The crystal structure is stabilized by an intermolecular π–π interaction [centroid–centroid distance = 3.8891 (18) Å].
N-(2-Formylphenyl)-4-toluenesulfonamide: a second monoclinic polymorph
Authors: Murugavel S. , Manikandan N. , Kannan D. , Bakthadoss M.
Published: March 2012

The title compound, C14H13NO3S, (I), is a second monoclinic polymorph. The original polymorph, (II), was reported by Mahíaet al.[Acta Cryst.(1999), C55, 2158–2160]. Polymorph (II) crystalllized in the space groupP21/c(Z= 4), whereas the title polymorph (I) occurs in the space groupP21/n(Z= 4). The dihedral angle between the two aromatic rings is 75.9 (1)° in (I) compared to 81.9 (1)° for (II). In both polymorphs, twoS(6) rings are generated by intramolecular N—H...O and C—H...O hydrogen bonds, resulting in similar molecular geometries. However, the two polymorphs differ concerning their crystal packing. In (I), molecules are linked intoC(8) zigzag chains along thebaxis by C—H...O hydrogen bonds, whereas in (II) molecules are linked by C—H...O hydrogen bonds, formingC(7) chains along thebaxis. The title polymorph is further stabilized by intermolecular C—H...π and π–π interactions [centroid–centroid distance = 3.814 (1) Å]. These interactions are not evident in polymorph (II).
3-(3-Methoxybenzylidene)chroman-4-one
Authors: Gopaul Kaalin , Shaikh Mahidansha , Ramjugernath Deresh , Koorbanally Neil A. , Omondi Bernard
Published: March 2012

In the title compound, C17H14O3, the dihedral angle between the methoxybenzene unit and the benzene ring of the chromanone system is 64.12 (3)°. The crystal structure is stabilized by weak C—H...O interactions.
1,3-Diphenyl-4,5-dihydro-1H-pyrazol-5-one
Authors: Baddeley Thomas C. , Wardell Solange M. S. V. , Tiekink Edward R. T. , Wardell James L.
Published: March 2012

In the title pyrazolone derivative, C15H12N2O, the five-membered ring is approximately planar (r.m.s. deviation = 0.018 Å), and the N- and C-bound benzene rings are inclined to this plane [dihedral angles = 21.45 (10) and 6.96 (10)°, respectively] and form a dihedral angle of 20.42 (10)° with each other. Supramolecular layers are formed in the crystal structureviaC—H...O and C—H...N interactions, and these are assembled into double layers by C—H...π and π–π interactions between the pyrazole and C-bound benzene rings [ring centroid–centroid distance = 3.6476 (12) Å]. The double layers stack along theaaxis being connected by π–π interactions between the N- and C-bound benzene rings [ring centroid–centroid distance = 3.7718 (12) Å].
3,5-Dimethyl-1-(4-nitrophenyl)-1H-pyrazole
Authors: Tiekink Edward R. T. , Wardell Solange M. S. V. , Wardell James L.
Published: March 2012

In the title pyrazole derivative, C11H11N3O2, the benzene ring is twisted [dihedral angle = 31.38 (12)°] with respect to the pyrazole ring (r.m.s. deviation = 0.009 Å). The nitro group is effectively coplanar with the benzene ring to which it is attached [O—N—C—C torsion angle = −6.5 (3)°]. Supramolecular chains along thebaxis are formed owing to π–π interactions [3.8653 (2) Å] between translationally related molecules involving both the five- and six-membered rings.
catena-Poly[[[triaquacobalt(II)]-μ-10-methylphenothiazine-3,7-dicarboxylato] monohydrate]
Authors: Hu Yun-Xia , Zhou Yan , Wang Fang-Ming , Zhang Wen-Wei
Published: March 2012

The polymeric title compound, {[Co(C15H9NO4S)(H2O)3]·H2O}n, consists of chains along [001] made up from Co2+ions bridged by 10-methylphenothiazine-3,7-dicarboxylate anions. The Co2+ion, coordinated by three O atoms from two different carboxylate groups and three water molecules, displays a distorted octahedral environment. In the crystal, π–π interchain interactions, with centroid–centroid distances of 3.656 (2) and 3.669 (2) Å between the benzene rings of the ligands, assemble the chains into sheets parallel to (100). O—H...O hydrogen-bonding interactions between the coordinating water molecules and carboxylate O atoms link the sheets into a three-dimensional network.
2,2,2-Trifluoro-N-(4-methyl-2-oxo-2H-chromen-7-yl)acetamide
Authors: Li Hong-Da , Yin Bing-Zhu
Published: March 2012

In the title molecule, C12H8F3NO3, the trifluoromethyl group is rotationally disordered over three orientations in a 0.5:0.3:0.2 ratio. In the crystal, N—H...O hydrogen bonds link the molecules related by translation into chains along thecaxis. The crystal packing exhibits π–π interactions between the pyran rings of neighboring molecules [centroid–centroid distance = 3.462 (4) Å] and short C...O contacts of 3.149 (4) Å.
4,7,8-Trimethyl-2H-chromen-2-one
Authors: Yang Jian-Xin , Tan Xue-Mei , Wang Xiang-Hui , Wang Yin
Published: March 2012

The molecule of the title compound, C12H12O2, is essentially planar, with a maximum deviation from the mean plane of all non-H atoms of 0.038 (1) Å for the methyl C atom in the 8-position. The crystal structure is characterized by antiparallel π–π stacking along thecaxis, with centroid–centroid distances as short as 3.866 (1) Å. In the crystal, C—H...O hydrogen bonds connect the molecules across the stacks into ribbons in thea-axis direction.
Chlordiazepoxide dichloromethane monosolvate
Authors: Fischer Andreas
Published: March 2012

In the title compound (systematic name: 7-chloro-2-methylamino-5-phenyl-3H-1,4-benzodiazepine 4-oxide dichloromethane monosolvate), C16H14ClN3O·CH2Cl2, the seven-membered ring adopts a boat conformation with the CH2group as the prow and the two aromatic C atoms as the stern. The dihedral angle between the benzene rings is 75.25 (6)°. The crystal structure features centrosymmetric pairs of chlordiazepoxide molecules linked by pairs of N—H...O hydrogen bonds, which generateR22(12) loops.
Bis(μ-nitrito-κ2O:O)bis[bis(1-methyl-1H-imidazole-κN3)(nitrito-κO)copper(II)]
Authors: Zhu Run-Qiang
Published: March 2012

In the binuclear title compound, [Cu2(NO2)4(C4H6N2)4], centrosymmetrically related complex molecules are linkedviaweak Cu—O interactions, forming dimeric units. The CuIIatom displays an elongated square-pyramidal CuN2O3coordination geometry with a slight tetrahedral distortion of the basal plane [maximum deviation = 0.249 (2) Å]. The dihedral angle formed by the imidazole rings is 26.20 (10)°.
(E)-4-Amino-N-(1,2-dihydropyridin-2-ylidene)benzenesulfonamide nitromethane monosolvate
Authors: Ghorab Mostafa M. , Al-Said Mansour S. , Ghabbour Hazem A. , Chantrapromma Suchada , Fun Hoong-Kun
Published: March 2012

In the title solvate, C11H11N3O2S·CH3NO2, the dihedral angle between the benzene ring and the N-containing ring is 85.94 (11)°, and an approximate V shape arises for the sulfonamide molecule. In the crystal, N—H...O and N—H...N hydrogen bonds and weak C—H...O interactions link the sulfonamide molecules into a three-dimensional network. The nitromethane solvent molecules are located in the interstitial sites in the sulfonamide network.
rac-18-Methoxycoronaridine hydrochloride
Authors: Kuehne Martin E. , Waterman Rory
Published: March 2012

In the crystal structure of the racemic title compound, C22H29N2O3+·Cl−, both NH groups form N—H...Cl hydrogen bonds with the chloride counter-ion, forming translational chains along theaaxis.
(E)-4-[(1,5-Dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)iminomethyl]-2-methoxyphenyl 4-bromobenzenesulfonate
Authors: Duan Zhong-Yu , Ma Guo-Li , Yang Li-Ping
Published: March 2012

In the title compound, C25H22BrN3O5S, the central benzene ring makes dihedral angles of 4.41 (10), 67.09 (9) and 62.05 (10)°, respectively, with the pyrazolone, bromobenzene and terminal phenyl rings. The dihedral angle between the pyrazolone and phenyl rings is 57.75 (11)°. In the crystal, two pairs of C—H...O hydrogen bonds link the molecules into inversion dimers. A weak intramolecular C—H...O hydrogen bonds is also observed.
trans-Dichloridobis[dicyclohexyl(phenyl)phosphane-κP]palladium(II)
Authors: Burgoyne Andrew R. , Meijboom Reinout , Ogutu Hezron
Published: March 2012

The title compound, [PdCl2{P(C6H11)2(C6H5)}2], forms a monomeric complex with atrans-square-planar geometry. The Pd—P bond lengths are 2.3343 (5) Å, as the Pd atom lies on an inversion centre, while the Pd—Cl bond lengths are 2.3017 (4) Å. The observed structure was found to be closely related to [PdCl2{P(C6H11)3}2] [Grushinet al.(1994).Inorg. Chem.33, 4804–4806], [PdBr2{P(C6H11)3}2] [Clarkeet al.(2003).Dalton Trans.pp. 4393–4394] and [PdCl2P(C6H11)2(C7H7)}2] [Vuotiet al.(2008).Eur. J. Inorg. Chem.pp. 397–407] (C6H11is cyclohexyl and C7H7iso-tolyl). One of the cyclohexyl rings is disordered with the phenyl ring in a 0.587 (9):413 (9) ratio. Five long-range C—H...Cl interactions were observed within the structure.
Triprolidinium dichloranilate–chloranilic acid–methanol–water (2/1/2/2)
Authors: Dayananda A. S. , Butcher Ray J. , Akkurt Mehmet , Yathirajan H. S. , Narayana B.
Published: March 2012

In the triprolidinium cation of the title compound {systematic name: 2-[1-(4-methylphenyl)-3-(pyrrolidin-1-ium-1-yl)prop-1-en-1-yl]pyridin-1-ium bis(2,5-dichloro-4-hydroxy-3,6-dioxocyclohexa-1,4-dien-1-olate)–2,5-dichloro-3,6-dihydroxycyclohexa-2,5-diene-1,4-dione–methanol–water (2/1/2/2)}, C19H24N22+·2C6HCl2O4−·0.5C6H2Cl2O4·CH3OH·H2O, the N atoms on both the pyrrolidine and pyridine groups are protonated. The neutral chloranilic acid molecule is on an inversion symmetry element and its hydroxy H atoms are disordered over two positions with site-occupancy factors of 0.53 (6) and 0.47 (6). The methanol solvent molecule is disordered over two positions in a 0.836 (4):0.164 (4) ratio. In the crystal, N—H...O, O—H...O and C—H...O interactions link the components. The crystal structure also features π–π interactions between the benzene rings [centroid–centroid distances = 3.5674 (15), 3.5225 (15) and 3.6347 (15) Å].