bluuebunny/crossref_metadata_2025 huggingface dataset:
New species and new records of the lichen genusPorpidia(Lecideaceae) from western China
Authors: WANG Xin Yu , ZHANG Lu Lu , JOSHI Yogesh , WANG Hai Ying , HUR Jae Seoun
Published: August 2012

A taxonomic study of the genusPorpidiain western China revealed two species hitherto unknown to science,Porpidia squamosaandP. shangrila, along with three new records for the country:P. flavicunda, P. soredizodesandP. thomsonii. Detailed taxonomic descriptions, ecological and chemical characters, and illustrations are provided for the new taxa, and brief taxonomic descriptions provided for the newly reported taxa. A key to all known ChinesePorpidiaspecies is also provided.
Presence of three distinct genotypes within the Paragonimus westermani complex in northeastern India
Authors: DEVI K. REKHA , NARAIN KANWAR , MAHANTA JAGADISH , NIRMOLIA TULIKA , BLAIR DAVID , SAIKIA SIDHARTHA P. , AGATSUMA TAKESHI
Published: August 2012

The name Paragonimus westermani (Kerbert, 1878) is commonly applied to members of a species complex that includes the well-known Asian lung fluke of medical and veterinary importance. Unambiguous molecular and morphological evidence showing the presence of a member of the complex in India has recently been published. In the present study we report the occurrence of 2 more members of the P. westermani complex in northeastern (NE) India. Surveys of the freshwater crabs Maydelliatelphusa lugubris in NE India revealed 2 morphologically distinct types of lung fluke metacercariae. Phylogenetic analyses, using DNA sequences from ITS2, 28S and cox1 gene regions indicate that these lung metacercariae belong to P. westermani complex. Type 1 metacercariae have a more basal position within the complex whereas type 2 metacercariae are closely related to the relatively derived forms of P. westermani from NE Asia (Japan, Korea, China) and Vietnam. A third type of metacercaria (type 3), detected in another crab host, Sartoriana spinigera in Assam, was phylogenetically close to P. siamensis, also a member of the P. westermani group. Molecular evidence has demonstrated the existence of 3 genotypes of lung flukes within the Paragonimus westermani complex in NE India. Two of these were previously unknown.
Towards a new, ecologically targeted approach to monitoring wild bird populations for avian influenza viruses
Authors: SCHOENE C. U. R. , STAUBACH C. , GRUND C. , GLOBIG A. , KRAMER M. , WILKING H. , BEER M. , CONRATHS F. J. , HARDER T. C. ,   the BL Monitoring Group
Published: August 2012

Prevalence monitoring of avian influenza in wild bird populations is important to estimate risks for the occurrence of potentially zoonotic and economically disastrous outbreaks of highly pathogenic avian influenza virus (AIV) in poultry worldwide. A targeted, cost-effective monitoring method for AIV in wild birds was developed, which is based on monitoring results for AIV in Germany and information on the distribution and abundance of wild bird species in selected habitat types. Spatial data were combined with virological and outbreak data for the period of 1 January 2006 to 31 December 2010. Using Germany as an example, we identified 11 indicator species. By concentrating monitoring efforts on these species in spatially confined locations, we propose a targeted and more cost-effective risk-based AIV monitoring approach that can be adapted universally for the identification of wild bird indicator species worldwide with the perspective of reducing sample sizes (and costs) without impairing the validity of the results.
Worldwide implementation of the WHO Child Growth Standards
Authors: de Onis Mercedes , Onyango Adelheid , Borghi Elaine , Siyam Amani , Blössner Monika , Lutter Chessa
Published: August 2012

Objective

To describe the worldwide implementation of the WHO Child Growth Standards (‘WHO standards’).

Design

A questionnaire on the adoption of the WHO standards was sent to health authorities. The questions concerned anthropometric indicators adopted, newly introduced indicators, age range, use of sex-specific charts, previously used references, classification system, activities undertaken to roll out the standards and reasons for non-adoption.

Setting

Worldwide.

Subjects

Two hundred and nineteen countries and territories.

Results

By April 2011, 125 countries had adopted the WHO standards, another twenty-five were considering their adoption and thirty had not adopted them. Preference for local references was the main reason for non-adoption. Weight-for-age was adopted almost universally, followed by length/height-for-age (104 countries) and weight-for-length/height (eighty-eight countries). Several countries (thirty-six) reported newly introducing BMI-for-age. Most countries opted for sex-specific charts and the Z-score classification. Many redesigned their child health records and updated recommendations on infant feeding, immunization and other health messages. About two-thirds reported incorporating the standards into pre-service training. Other activities ranged from incorporating the standards into computerized information systems, to providing supplies of anthropometric equipment and mobilizing resources for the standards’ roll-out.

Conclusions

Five years after their release, the WHO standards have been widely scrutinized and implemented. Countries have adopted and harmonized best practices in child growth assessment and established the breast-fed infant as the norm against which to assess compliance with children's right to achieve their full genetic growth potential.
On estimation and attribution of long‐term temperature trends in the thermosphere
Authors: Akmaev R. A.
Published: August 2012

Recent analyses of long‐term time series of ion temperature from two midlatitude incoherent‐scatter radars have revealed very strong cooling, which is substantially greater than predicted by models for neutral temperature. There is also an indication that the cooling has substantially accelerated after a breakpoint around 1979 when the ozone hole was discovered. This has prompted a hypothesis that the accelerated cooling might have resulted from the ozone depletion and associated reduction in daytime radiative heating in the stratosphere. A lively discussion on relative roles of different cooling mechanisms has followed. The purpose of this note is to contribute to this discussion from a theoretical and modeling perspective. In particular, a possible misinterpretation of the modeling results behind the ozone hypothesis is clarified. It is also shown that model predictions of neutral temperature trends in the thermosphere agree well with, and hence are tightly constrained by, independent observations including trends in heights of ionospheric layers and in neutral density from satellite drag. However, they are up to an order of magnitude smaller than the observational estimates of trends in ion temperature. These widely different results cannot be quantitatively reconciled regardless of what known cooling mechanisms are invoked. This stark discrepancy should be addressed on the data analysis and theoretical fronts.
Coseismic and postseismic elastic wave velocity variations caused by the 2008 Iwate‐Miyagi Nairiku earthquake, Japan
Authors: Hobiger M. , Wegler U. , Shiomi K. , Nakahara H.
Published: August 2012

We analyze coseismic and postseismic velocity variations caused by the June 13, 2008 Iwate‐Miyagi Nairiku earthquake (MW= 6.9) using Passive Image Interferometry (PII). Seismic noise is correlated in order to reconstruct the Green's function between two sensors. Shear wave velocity changes are determined by relating the coda parts of the daily Green's functions to a long‐term reference Green's function. Our study extends from January 2008 to August 2010 and includes the correlations for 190 station pairs in three different frequency ranges from 0.125 to 1.0 Hz. We show that combining the 9 different component cross‐correlation functions stabilizes the velocity change estimation and increases analysis resolution. The observed velocity change curves can be fitted by model time series consisting of a coseismic velocity drop followed by logarithmic postseismic recovery and seasonal velocity variations. The coseismic velocity drops are stronger at higher frequencies and are concentrated in the southern part of the fault zone. A tomography algorithm was developed to reproject the observed velocity variations of the different sensor pairs onto the single sensors. The depth distribution of coseismic changes was modeled for the three stations with the largest velocity drops. At two stations, the coseismic velocity changes are located in the upper several hundred meters. The third station shows indications for deeper changes, in the order of kilometers. Postseismic recovery takes significantly longer than the analyzed two year period. Seasonal velocity variations with periods of one year are observed at all analyzed frequencies for most station pairs.
Birth of ball lightning
Authors: Lowke J. J. , Smith D. , Nelson K. E. , Crompton R. W. , Murphy A. B.
Published: August 2012

Many observations of ball lightning report a ball of light, about 10 cm in diameter, moving at about walking speed, lasting up to 20 s and frequently existing inside of houses and even aeroplanes. The present paper reports detailed observations of the initiation or birth of ball lightning. In two cases, navigation crew of aircraft saw ball lightning form at the windscreen inside the cockpit of their planes. In the first case, the ball lightning occurred during a thunderstorm, with much lightning activity outside of the plane. In the second case, large “horns” of electrical corona were seen outside of the plane at the surface of the radome, just prior to the formation of the ball lightning. A third case reports ball lightning formed inside of a house, during a thunderstorm, at a closed glass window. It is proposed, based on two‐dimensional calculations of electron and ion transport, that ball lightning in these cases is driven and formed by atmospheric ions impinging and collecting on the insulating surface of the glass or Perspex windows. This surface charge can produce electric fields inside of the cockpit or room sufficient to sustain an electric discharge. Charges of opposite sign to those outside of the window accumulate on the inside surface of the glass, leaving a ball of net charge moving inside of the cockpit or room to produce a pulsed discharge on a microsecond time scale.
Phase transitions in thermally annealed films of Alq3
Authors: Baldacchini G. , Chiacchiaretta P. , Pode R. B. , Vincenti M. A. , Wang Q.-M.
Published: August 2012

Organic light emitting devices have improved greatly in recent years, so they are now widely used in displays and lighting. Annealing processes in different atmospheres strongly affect their performance, as when the active material is the small molecule Alq3. In particular, a significant increase in the photoluminescence is observed in thin films of this molecule between 150 and 180 °C, before physical destruction of the films sets in at higher temperatures. This phenomenon is attributed to a phase transition to a novel morphological aggregation of the molecules in the film, which has yielded a much improved optical material for luminescence applications, and seems to apply to other molecules as well.
Photodissociation and photochemistry of V+(H2O)n, n = 1–4, in the 360–680 nm region
Authors: Scharfschwerdt Björn , van der Linde Christian , Petru Balaj O. , Herber Ina , Schütze Doreen , Beyer Martin K.
Published: August 2012

Photodissociation and photochemistry of V+(H2O)n, n = 1–4, was studied in 360–680 nm region using a Fourier transform ion cyclotron resonance mass spectrometer. The light of a high pressure mercury arc lamp was filtered using a set of bandpass filters with the center wavelengths from 360 to 680 nm in steps of 20 nm. The bandwidth of the filters, defined as full width at half maximum, was 10 nm. Photodissociation channels were attributed to loss of water molecules as well as atomic or molecular hydrogen, possibly accompanied by loss of water molecules. The most intense absorptions were red-shifted with increasing hydration. Theoretical spectra were calculated using time-dependent density functional theory. Calculations reproduced all the features of the experimental spectra, including the red shift with increasing hydration shell and the overall pattern of strong and weak absorption peaks.
Radiolysis of astrophysical ices by heavy ion irradiation: Destruction cross section measurement
Authors: de Barros A. L. F. , Boduch P. , Domaracka A. , Rothard H. , da Silveira E. F.
Published: August 2012

Many solar system objects, such as planets and their satellites, dust grains in rings, and comets, are known to either be made of ices or to have icy surfaces. These ices are exposed to ionizing radiation including keV, MeV and GeV ions from solar wind or cosmic rays. Moreover, icy dust grains are present in interstellar space and, in particular, in dense molecular clouds. Radiation effects include radiolysis (the destruction of molecules leading to formation of radicals), the formation of new molecules following radiolysis, the desorption or sputtering of atoms or molecules from the surface, compaction of porous ices, and phase changes. This review discusses the application of infrared spectroscopy FTIR to study the evolution of the chemical composition of ices containing the most abundant molecular species found in the solar system and interstellar medium, such as H2O, CO, CO2 and hydrocarbons. We focus on the evolution of chemical composition with ion fluence in order to deduce the corresponding destruction and formation cross sections. Although initial approach focused on product identification, it became increasingly necessary to work toward a comprehensive understanding of ice chemistry. The abundances of these molecules in different phases of ice mantles provide important clues to the chemical processes in dense interstellar clouds, and therefore it is of importance to accurately measure the quantities such as dissociation and formation cross sections of the infrared features of these molecules. We also are able to obtain the scaling of these cross sections with deposited energy.
Intermolecular vibrations of fluorobenzene-Ar up to 130 cm−1 in the ground electronic state
Authors: Gascooke Jason R. , Alexander Ula N. , Lawrance Warren D.
Published: August 2012

Sixteen intermolecular vibrational levels of the S0 state of the fluorobenzene-Ar van der Waals complex have been observed using dispersed fluorescence. The levels range up to ∼130 cm−1 in vibrational energy. The vibrational energies have been modelled using a complete set of harmonic and quartic anharmonic constants and a cubic anharmonic coupling between the stretch and long axis bend overtone that becomes near ubiquitous at higher energies. The constants predict the observed band positions with a root mean square deviation of 0.04 cm−1. The set of vibrational levels predicted by the constants, which includes unobserved bands, has been compared with the predictions of ab initio calculations, which include all vibrational levels up to 70–75 cm−1. There are small differences in energy, particularly above 60 cm−1, however, the main differences are in the assignments and are largely due to the limitations of assigning the ab initio wavefunctions to a simple stretch, bend, or combination when the states are mixed by the cubic anharmonic coupling. The availability of these experimental data presents an opportunity to extend ab initio calculations to higher vibrational energies to provide an assessment of the accuracy of the calculated potential surface away from the minimum. The intermolecular modes of the fluorobenzene-Ar2 trimer complex have also been investigated by dispersed fluorescence. The dominant structure is a pair of bands with a ∼35 cm−1 displacement from the origin band. Based on the set of vibrational modes calculated from the fluorobenzene-Ar frequencies, they are assigned to a Fermi resonance between the symmetric stretch and symmetric short axis bend overtone. The analysis of this resonance provides a measurement of the coupling strength between the stretch and short axis bend overtone in the dimer, an interaction that is not directly observed. The coupling matrix elements determined for the fluorobenzene-Ar stretch-long axis bend overtone and stretch-short axis bend overtone couplings are remarkably similar (3.8 cm−1 cf. 3.2 cm−1). Several weak features seen in the fluorobenzene-Ar2 spectrum have also been assigned.
Electronic spectroscopy, stimulated emission, and persistent spectral hole burning of cryogenic nitrogen matrices doped with tetrabenzoporphin
Authors: Arabei S. M. , Galaup J.-P. , McCaffrey J. G. , Shafizadeh N. , Crépin C.
Published: August 2012

This paper deals with our on-going work on the electronic spectroscopy of tetrapyrrole molecules embedded in cryogenic hosts. Under nanosecond laser excitation of free-base tetrabenzoporphin molecules in a nitrogen matrix at 8 K, increasing laser pulse energy results in essential enhancement of the intensity of one or several vibronic emission lines in the fine-structure fluorescence spectrum. Some characteristics of stimulated radiation are realized in the observed intense monochromatic radiation as a result of a transition from the purely electronic S1 level to a vibrational sublevel of the S0 state, corresponding to the excitation of C–C stretching vibrations of tetrapyrrole methane bridges. We also report on persistent spectral hole-burning effects. Hole and antihole formation analysis gives some insight on the photochemical properties of tetrabenzoporphin in a nitrogen matrix.
Orientational glassification in fullerite C60 saturated with H2: Photoluminescence studies
Authors: Zinoviev P. V. , Zoryansky V. N. , Silaeva N. B. , Stetsenko Yu. E. , Strzhemechny M. A. , Yagotintsev K. A.
Published: August 2012

Using one-photon excitation we studied photoluminescence of C60 saturated with molecular hydrogen over a temperature range from 10 to 230 K. Saturation of samples was done at 30 atm and at temperatures low enough (T < 250 °C) to exclude chemical sorption. The samples were saturated during periods of varied duration τ to reach different occupancy levels. To check the reliability of our luminescence results and their interpretation, our spectra for pure C60 were compared with data known in the art, demonstrating good compatibility. The luminescence spectra were attributed according to the approach of Akimoto and Kan’no by separating the total spectra into two components of different origin. The A-type spectra, associated with exciton transport to deep traps, become prevalent over the B-type emission above 70 K. The integrated intensity I as a function of the temperature T of the luminescence measurements I(T) remained at a constant level up to the orientational vitrification point of about 100 K when the saturation times exceeded a certain value (for one, 50 h for a saturation temperature of 200 °C); then I(T) went down rather steeply with increasing T. However, at longer τ the intensity I(Τ) persisted consistently to higher T (the higher, the longer τ) and then dropped with increasing T. This finding made us reexamine the lattice parameter vs. saturation time dependence for saturation temperatures of 200 and 230 °C. As a result, additional evidence allowed us to infer that after the completion of the single-molecule filling of O-voids (specifically, after roughly 50 h at Tsat = 200 °C) a slower process of double filling sets in. Double filling entails an anisotropic deformation of the octahedral cage, which modifies rotational dynamics more than single filling. Further, we argue that singlet exciton transport to traps (which is responsible for the A-type emission) can be crucially hampered by rotational jumps of one of the molecules, over which a travelling exciton is spread. Such jumps break coherence, and the exciton stops, thereby increasing the probability of emissionless deactivation. If so, then the temperature at which the rotational jumps occur sufficiently frequently may be by inference considered to be the unfreezing point for the orientational glass state (essentially coinciding with the inverse critical point Tg, where the rotational system freezes into the orientational glass). This treatment of Tg differs from that existing in the art, according to which the glass state is destroyed owing to the increased density of phonon states. Keeping to our reasoning, we conclude that the orientational glass state does not disappear but, instead, is conserved almost unchanged under one-molecule filling and persists to appreciably higher temperatures in the case of double filling, which has a stronger effect on exciton dynamics.
Reverse engineering of complex dynamical networks in the presence of time-delayed interactions based on noisy time series
Authors: Wang Wen-Xu , Ren Jie , Lai Ying-Cheng , Li Baowen
Published: August 2012

Reverse engineering of complex dynamical networks is important for a variety of fields where uncovering the full topology of unknown networks and estimating parameters characterizing the network structure and dynamical processes are of interest. We consider complex oscillator networks with time-delayed interactions in a noisy environment, and develop an effective method to infer the full topology of the network and evaluate the amount of time delay based solely on noise-contaminated time series. In particular, we develop an analytic theory establishing that the dynamical correlation matrix, which can be constructed purely from time series, can be manipulated to yield both the network topology and the amount of time delay simultaneously. Extensive numerical support is provided to validate the method. While our method provides a viable solution to the network inverse problem, significant difficulties, limitations, and challenges still remain, and these are discussed thoroughly.
Detection of type 2 diabetes: what role for associated risk and protective factors and socioeconomic status?
Authors: Comino Elizabeth J. , Harris Mark F. , Shaw Jonathan E. , Jayasinghe Upali W.
Published: August 2012

Objectives. This study explored associations between demographic, socioeconomic, behavioural risk, and health factors (study factors) and detection of type 2 diabetes. Methods. A secondary analysis of data extracted from the AusDiab study was undertaken. Participants were classified as known diabetes (KDM), newly detected diabetes (NDDM), impaired fasting glucose (IFG), impaired glucose tolerance (IGT), or normal according to results of a glucose tolerance test. Results. The weighted prevalence of diabetes was 6.9%; 49.6% of participants with diabetes (NDDM + KDM) were classified as NDDM. Although study factors were associated with diabetes prevalence, most were not associated with proportion of diabetic participants classified as NDDM. Among participants with diabetes, NDDM was more likely among those who spoke English at home, were in good general health and did not report past history of cardiovascular disease. Conclusions. Although a range of personal and socioeconomic factors are associated with diabetes prevalence, these factors are not similarly associated with prior detection of diabetes. These findings highlight the importance of systematic approaches to screening for diabetes risk focussed on the whole population, with selective screening based on multi-factorial assessment of diabetes risk using the AUSDRISK Assessment Tool. What is known about the topic? Type 2 diabetes is an increasing public health problem and early detection is associated with improved outcomes. About half of the participants with diabetes in the AusDiab study had been diagnosed previously with diabetes, with the remainder being newly diagnosed in the study. What does this paper add? A range of demographic, socioeconomic, behavioural risk and health factors were associated with increased risk of diabetes. However, these factors did not differentiate between those with a prior diagnosis of diabetes and those with newly diagnosed diabetes. Among participants with diabetes, NDDM was more likely among those who spoke English at home, were in good general health or reported no past history of cardiovascular disease. What are the implications for practitioners? Screening for type 2 diabetes should be broadly focussed on the whole population, with selective blood testing based on multi-factorial assessment of diabetes risk using the AUSDRISK Assessment Tool.
Collective many-body van der Waals interactions in molecular systems
Authors: DiStasio Robert A. , von Lilienfeld O. Anatole , Tkatchenko Alexandre
Published: August 2012

Van der Waals (vdW) interactions are ubiquitous in molecules and condensed matter, and play a crucial role in determining the structure, stability, and function for a wide variety of systems. The accurate prediction of these interactions from first principles is a substantial challenge because they are inherently quantum mechanical phenomena that arise from correlations between many electrons within a given molecular system. We introduce an efficient method that accurately describes the nonadditive many-body vdW energy contributions arising from interactions that cannot be modeled by an effective pairwise approach, and demonstrate that such contributions can significantly exceed the energy of thermal fluctuations—a critical accuracy threshold highly coveted during molecular simulations—in the prediction of several relevant properties. Cases studied include the binding affinity of ellipticine, a DNA-intercalating anticancer agent, the relative energetics between the A- and B-conformations of DNA, and the thermodynamic stability among competing paracetamol molecular crystal polymorphs. Our findings suggest that inclusion of the many-body vdW energy is essential for achieving chemical accuracy and therefore must be accounted for in molecular simulations.
ECM microenvironment regulates collective migration and local dissemination in normal and malignant mammary epithelium
Authors: Nguyen-Ngoc Kim-Vy , Cheung Kevin J. , Brenot Audrey , Shamir Eliah R. , Gray Ryan S. , Hines William C. , Yaswen Paul , Werb Zena , Ewald Andrew J.
Published: August 2012

Breast cancer progression involves genetic changes and changes in the extracellular matrix (ECM). To test the importance of the ECM in tumor cell dissemination, we cultured epithelium from primary human breast carcinomas in different ECM gels. We used basement membrane gels to model the normal microenvironment and collagen I to model the stromal ECM. In basement membrane gels, malignant epithelium either was indolent or grew collectively, without protrusions. In collagen I, epithelium from the same tumor invaded with protrusions and disseminated cells. Importantly, collagen I induced a similar initial response of protrusions and dissemination in both normal and malignant mammary epithelium. However, dissemination of normal cells into collagen I was transient and ceased as laminin 111 localized to the basal surface, whereas dissemination of carcinoma cells was sustained throughout culture, and laminin 111 was not detected. Despite the large impact of ECM on migration strategy, transcriptome analysis of our 3D cultures revealed few ECM-dependent changes in RNA expression. However, we observed many differences between normal and malignant epithelium, including reduced expression of cell-adhesion genes in tumors. Therefore, we tested whether deletion of an adhesion gene could induce sustained dissemination of nontransformed cells into collagen I. We found that deletion of P-cadherin was sufficient for sustained dissemination, but exclusively into collagen I. Our data reveal that metastatic tumors preferentially disseminate in specific ECM microenvironments. Furthermore, these data suggest that breaks in the basement membrane could induce invasion and dissemination via the resulting direct contact between cancer cells and collagen I.
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment
Authors: Ma Haisu , Zhao Hongyu
Published: August 2012

Motivation: It is well recognized that the effects of drugs are far beyond targeting individual proteins, but rather influencing the complex interactions among many relevant biological pathways. Genome-wide expression profiling before and after drug treatment has become a powerful approach for capturing a global snapshot of cellular response to drugs, as well as to understand drugs’ mechanism of action. Therefore, it is of great interest to analyze this type of transcriptomic profiling data for the identification of pathways responsive to different drugs. However, few computational tools exist for this task.

Results: We have developed FacPad, a Bayesian sparse factor model, for the inference of pathways responsive to drug treatments. This model represents biological pathways as latent factors and aims to describe the variation among drug-induced gene expression alternations in terms of a much smaller number of latent factors. We applied this model to the Connectivity Map data set (build 02) and demonstrated that FacPad is able to identify many drug–pathway associations, some of which have been validated in the literature. Although this method was originally designed for the analysis of drug-induced transcriptional alternation data, it can be naturally applied to many other settings beyond polypharmacology.

Availability and implementation: The R package ‘FacPad’ is publically available at: http://cran.open-source-solution.org/web/packages/FacPad/

Contact:  hongyu.zhao@yale.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Positive-unlabeled learning for disease gene identification
Authors: Yang Peng , Li Xiao-Li , Mei Jian-Ping , Kwoh Chee-Keong , Ng See-Kiong
Published: August 2012

Background: Identifying disease genes from human genome is an important but challenging task in biomedical research. Machine learning methods can be applied to discover new disease genes based on the known ones. Existing machine learning methods typically use the known disease genes as the positive training set P and the unknown genes as the negative training set N (non-disease gene set does not exist) to build classifiers to identify new disease genes from the unknown genes. However, such kind of classifiers is actually built from a noisy negative set N as there can be unknown disease genes in N itself. As a result, the classifiers do not perform as well as they could be.

Result: Instead of treating the unknown genes as negative examples in N, we treat them as an unlabeled set U. We design a novel positive-unlabeled (PU) learning algorithm PUDI (PU learning for disease gene identification) to build a classifier using P and U. We first partition U into four sets, namely, reliable negative set RN, likely positive set LP, likely negative set LN and weak negative set WN. The weighted support vector machines are then used to build a multi-level classifier based on the four training sets and positive training set P to identify disease genes. Our experimental results demonstrate that our proposed PUDI algorithm outperformed the existing methods significantly.

Conclusion: The proposed PUDI algorithm is able to identify disease genes more accurately by treating the unknown data more appropriately as unlabeled set U instead of negative set N. Given that many machine learning problems in biomedical research do involve positive and unlabeled data instead of negative data, it is possible that the machine learning methods for these problems can be further improved by adopting PU learning methods, as we have done here for disease gene identification.

Availability and implementation: The executable program and data are available at http://www1.i2r.a-star.edu.sg/∼xlli/PUDI/PUDI.html.

Contact:  xlli@i2r.a-star.edu.sg or yang0293@e.ntu.edu.sg

Supplementary information:  Supplementary Data are available at Bioinformatics online.
RazerS 3: Faster, fully sensitive read mapping
Authors: Weese David , Holtgrewe Manuel , Reinert Knut
Published: August 2012

Motivation: During the past years, next-generation sequencing has become a key technology for many applications in the biomedical sciences. Throughput continues to increase and new protocols provide longer reads than currently available. In almost all applications, read mapping is a first step. Hence, it is crucial to have algorithms and implementations that perform fast, with high sensitivity, and are able to deal with long reads and a large absolute number of insertions and deletions.

Results: RazerS is a read mapping program with adjustable sensitivity based on counting q-grams. In this work, we propose the successor RazerS 3, which now supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers’ bit-vector algorithm for verification, memory-saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular, long reads with many errors. We extensively compare RazerS 3 with other popular read mappers and show that its results are often superior to them in terms of sensitivity while exhibiting practical and often competitive run times. In addition, RazerS 3 works without a pre-computed index.

Availability and Implementation: Source code and binaries are freely available for download at http://www.seqan.de/projects/razers. RazerS 3 is implemented in C++ and OpenMP under a GPL license using the SeqAn library and supports Linux, Mac OS X and Windows.

Contact:  david.weese@fu-berlin.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis
Authors: Kumar Sudhir , Stecher Glen , Peterson Daniel , Tamura Koichiro
Published: August 2012

Summary: There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA’s graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis.

Availability:  http://www.megasoftware.net/

Contact:  s.kumar@asu.edu
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes
Authors: Kumar Narendra , Skolnick Jeffrey
Published: August 2012

Summary: High-quality enzyme function annotation is essential for understanding the biochemistry, metabolism and disease processes of organisms. Previously, we developed a multi-component high-precision enzyme function predictor, EFICAz2 (enzyme function inference by a combined approach). Here, we present an updated improved version, EFICAz2.5, that is trained on a significantly larger data set of enzyme sequences and PROSITE patterns. We also present the results of the application of EFICAz2.5 to the enzyme reannotation of 396 genomes cataloged in the ENSEMBL database.

Availability: The EFICAz2.5 server and database is freely available with a use-friendly interface at http://cssb.biology.gatech.edu/EFICAz2.5.

Contact:  skolnick@gatech.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Optimal timepoint sampling in high-throughput gene expression experiments
Authors: Rosa Bruce A. , Zhang Ji , Major Ian T. , Qin Wensheng , Chen Jin
Published: August 2012

Motivation: Determining the best sampling rates (which maximize information yield and minimize cost) for time-series high-throughput gene expression experiments is a challenging optimization problem. Although existing approaches provide insight into the design of optimal sampling rates, our ability to utilize existing differential gene expression data to discover optimal timepoints is compelling.

Results: We present a new data-integrative model, Optimal Timepoint Selection (OTS), to address the sampling rate problem. Three experiments were run on two different datasets in order to test the performance of OTS, including iterative-online and a top-up sampling approaches. In all of the experiments, OTS outperformed the best existing timepoint selection approaches, suggesting that it can optimize the distribution of a limited number of timepoints, potentially leading to better biological insights about the resulting gene expression patterns.

Availability: OTS is available at www.msu.edu/∼jinchen/OTS.

Contact:  wqin@lakeheadu.ca; jinchen@msu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
COMPADRE: an R and web resource for pathway activity analysis by component decompositions
Authors: Ramos-Rodriguez Roberto-Rafael , Cuevas-Diaz-Duran Raquel , Falciani Francesco , Tamez-Peña Jose-Gerardo , Trevino Victor
Published: August 2012

Summary: The analysis of biological networks has become essential to study functional genomic data. Compadre is a tool to estimate pathway/gene sets activity indexes using sub-matrix decompositions for biological networks analyses. The Compadre pipeline also includes one of the direct uses of activity indexes to detect altered gene sets. For this, the gene expression sub-matrix of a gene set is decomposed into components, which are used to test differences between groups of samples. This procedure is performed with and without differentially expressed genes to decrease false calls. During this process, Compadre also performs an over-representation test. Compadre already implements four decomposition methods [principal component analysis (PCA), Isomaps, independent component analysis (ICA) and non-negative matrix factorization (NMF)], six statistical tests (t- and f-test, SAM, Kruskal–Wallis, Welch and Brown–Forsythe), several gene sets (KEGG, BioCarta, Reactome, GO and MsigDB) and can be easily expanded. Our simulation results shown in Supplementary Information suggest that Compadre detects more pathways than over-representation tools like David, Babelomics and Webgestalt and less false positives than PLAGE. The output is composed of results from decomposition and over-representation analyses providing a more complete biological picture. Examples provided in Supplementary Information show the utility, versatility and simplicity of Compadre for analyses of biological networks.

Availability and implementation: Compadre is freely available at http://bioinformatica.mty.itesm.mx:8080/compadre. The R package is also available at https://sourceforge.net/p/compadre.

Contact:  vtrevino@itesm.mx

Supplementary information: Supplementary Data are available at Bioinformatics online
Bayesian Inference of Signaling Network Topology in a Cancer Cell Line
Authors: Hill Steven M. , Lu Yiling , Molina Jennifer , Heiser Laura M. , Spellman Paul T. , Speed Terence P. , Gray Joe W. , Mills Gordon B. , Mukherjee Sach
Published: August 2012

Motivation: Protein signaling networks play a key role in cellular function, and their dysregulation is central to many diseases, including cancer. To shed light on signaling network topology in specific contexts, such as cancer, requires interrogation of multiple proteins through time and statistical approaches to make inferences regarding network structure.

Results: In this study, we use dynamic Bayesian networks to make inferences regarding network structure and thereby generate testable hypotheses. We incorporate existing biology using informative network priors, weighted objectively by an empirical Bayes approach, and exploit a connection between variable selection and network inference to enable exact calculation of posterior probabilities of interest. The approach is computationally efficient and essentially free of user-set tuning parameters. Results on data where the true, underlying network is known place the approach favorably relative to existing approaches. We apply these methods to reverse-phase protein array time-course data from a breast cancer cell line (MDA-MB-468) to predict signaling links that we independently validate using targeted inhibition. The methods proposed offer a general approach by which to elucidate molecular networks specific to biological context, including, but not limited to, human cancers.

Availability:  http://mukherjeelab.nki.nl/DBN (code and data).

Contact:  s.hill@nki.nl; gmills@mdanderson.org; s.mukherjee@nki.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data
Authors: Feng Jianxing , Meyer Clifford A. , Wang Qian , Liu Jun S. , Shirley Liu X. , Zhang Yong
Published: August 2012

Motivation: RNA-seq has been widely used in transcriptome analysis to effectively measure gene expression levels. Although sequencing costs are rapidly decreasing, almost 70% of all the human RNA-seq samples in the gene expression omnibus do not have biological replicates and more unreplicated RNA-seq data were published than replicated RNA-seq data in 2011. Despite the large amount of single replicate studies, there is currently no satisfactory method for detecting differentially expressed genes when only a single biological replicate is available.

Results: We present the GFOLD (generalized fold change) algorithm to produce biologically meaningful rankings of differentially expressed genes from RNA-seq data. GFOLD assigns reliable statistics for expression changes based on the posterior distribution of log fold change. In this way, GFOLD overcomes the shortcomings of P-value and fold change calculated by existing RNA-seq analysis methods and gives more stable and biological meaningful gene rankings when only a single biological replicate is available.

Availability: The open source C/C++ program is available at http://www.tongji.edu.cn/∼zhanglab/GFOLD/index.html

Contact: xsliu@jimmy.harvard.edu or yzhang@tongji.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
The GlycomeAtlas tool for visualizing and querying glycome data
Authors: Konishi Yoshitsugu , Aoki-Kinoshita Kiyoko F.
Published: August 2012

Motivation: The development of glycomics technologies in recent years has produced a sufficient amount of data to begin analyzing the glycan structures present in various organisms and tissues. In particular, glycan profiling using mass spectrometry (MS) and tandem MS has generated a large amount of data that are waiting to be analyzed. The Consortium for Functional Glycomics (CFG) has provided a web resource for obtaining such glycan profiling data easily. Although an interactive spectrum viewer is provided on the website as a Java applet, it is not necessarily easy to search for particular glycans or to find commonalities between different tissues in a single organism, for example. Therefore, to allow users to better take advantage of the valuable glycome data that can be obtained from mass spectra and other leading technologies, we have developed a tool called Glycome Atlas which is pre-loaded with the data from the CFG and is also able to visualize local glycan profiling data for human and mouse.

Results: We have developed a tool to allow users to visualize and perform queries of glycome data. This tool, called GlycomeAtlas, is pre-loaded with glycome data as provided by the CFG. Moreover, users can load their own local glycome data into this tool to visualize and perform queries on their own data.

Availability: This tool is available at the following URL: http://www.rings.t.soka.ac.jp/GlycomeAtlas/GUI.html.

Contact:  kkiyoko@soka.ac.jp
Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone
Authors: Kumar Sudhir , Boccia Kelly , McCutchan Michael , Ye Jieping
Published: August 2012

Mobile technologies provide unique opportunities for ubiquitous distribution of scientific information through user-friendly interfaces. Therefore, we have developed a new FlyExpress mobile application that makes available a growing collection (>100 000) of standardized in situ hybridization images containing spatial patterns of gene expression from Drosophila melanogaster (fruit fly) embryogenesis. Using this application, scientists can visualize and compare expression patterns of >4000 developmentally relevant genes. The FlyExpress app displays the expression patterns of the selected gene for different visual projections (e.g. lateral) and displays them according to their developmental stages, which shows a gene’s progression of spatial expression over developmental time. Ultimately, we envision the use of FlyExpress app in the laboratory where scientists may wish to immediately conduct a visual comparison of a known expression pattern with the one observed on the bench top or to display expression patterns of interest during scientific discussions at large.

Availability: Search “FlyExpress” on the Apple iTunes store

Contact:  s.kumar@asu.edu
HiTC: exploration of high-throughput ‘C’ experiments
Authors: Servant Nicolas , Lajoie Bryan R. , Nora Elphège P. , Giorgetti Luca , Chen Chong-Jian , Heard Edith , Dekker Job , Barillot Emmanuel
Published: August 2012

Summary: The R/Bioconductor package HiTC facilitates the exploration of high-throughput 3C-based data. It allows users to import and export ‘C’ data, to transform, normalize, annotate and visualize interaction maps. The package operates within the Bioconductor framework and thus offers new opportunities for future development in this field.

Availability and implementation: The R package HiTC is available from the Bioconductor website. A detailed vignette provides additional documentation and help for using the package.

Contact:  nicolas.servant@curie.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.