bluuebunny/crossref_metadata_2025 huggingface dataset:
Sexual behaviour, drug use and health service use by young Noongar people in Western Australia: a snapshot
Authors: Williams Robyn , Lawrence Chris , Wilkes Edward , Shipp Maurice , Henry Barbara , Eades Sandra , Mathers Bradley , Kaldor John , Maher Lisa , Gray Dennis
Published: December 2014

Background
This study aimed to describe sexual health behaviour, alcohol and other drug use, and health service use among young Noongar people in the south-west of Western Australia. Method: A cross-sectional survey was undertaken among a sample of 244 Noongar people aged 16−30 years. Results: The sample was more disadvantaged than the wider Noongar population. Sexual activity was initiated at a young age, 18% had two or more casual sex partners in the previous 12 months, with men more likely to have done so than women (23% vs 14%). Condoms were always or often carried by 57% of men and 37% of women, and 36% of men and 23% of women reported condom use at last sex with a casual partner. Lifetime sexually transmissible infection diagnosis was 14%. Forty percent currently smoked tobacco and 25% reported risky alcohol consumption on a weekly and 7% on an almost daily basis. Cannabis was used by 37%, 12% used drugs in addition to cannabis and 11% reported recently injecting drugs. In the previous 12 months, 66% had a health check and 31% were tested for HIV or sexually transmissible infections. Additionally, 25% sought advice or assistance for mental health or alcohol and other drug issues. Discussion: Although some respondents engaged in risky sexual behaviour, alcohol and other drug use or both, most did not. Particularly encouraging was the engagement of respondents with the health care system, especially among those engaging in risky behaviours. The results confound negative stereotypes of Aboriginal people and demonstrate a level of resilience among respondents.
Life cycle air quality impacts of conventional and alternative light-duty transportation in the United States
Authors: Tessum Christopher W. , Hill Jason D. , Marshall Julian D.
Published: December 2014

Significance

Our assessment of the life cycle air quality impacts on human health of 10 alternatives to conventional gasoline vehicles finds that electric vehicles (EVs) powered by electricity from natural gas or wind, water, or solar power are best for improving air quality, whereas vehicles powered by corn ethanol and EVs powered by coal are the worst. This work advances the current debate over the environmental impacts of conventional versus alternative transportation options by combining detailed spatially and temporally explicit emissions inventories with state-of-the-science air quality impact analysis using advanced chemical transport modeling. Our results reinforce previous findings that air quality-related health damages from transportation are generally comparable to or larger than climate change-related damages.
Myosin binding protein-C activates thin filaments and inhibits thick filaments in heart muscle cells
Authors: Kampourakis Thomas , Yan Ziqian , Gautel Mathias , Sun Yin-Biao , Irving Malcolm
Published: December 2014

Significance

Myosin binding protein-C (MyBP-C) is a regulatory protein of heart muscle. Mutations in MyBP-C are frequently associated with heart disease, but the mechanism of action of MyBP-C is poorly understood. By characterizing the effects of its N-terminal domains on the structures of the thin and thick filaments in contracting heart muscle cells, we showed that MyBP-C stabilizes the ON state of thin filaments and the OFF state of thick filaments. The results lead to a model for the control of heart muscle contraction in which the regulatory functions of the thin and thick filaments are coordinated by MyBP-C, providing an integrated framework for the design and development of therapeutic interventions in heart disease.
Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma
Authors: Perry Jennifer A. , Kiezun Adam , Tonzi Peter , Van Allen Eliezer M. , Carter Scott L. , Baca Sylvan C. , Cowley Glenn S. , Bhatt Ami S. , Rheinbay Esther , Pedamallu Chandra Sekhar , Helman Elena , Taylor-Weiner Amaro , McKenna Aaron , DeLuca David S. , Lawrence Michael S. , Ambrogio Lauren , Sougnez Carrie , Sivachenko Andrey , Walensky Loren D. , Wagle Nikhil , Mora Jaume , de Torres Carmen , Lavarino Cinzia , Dos Santos Aguiar Simone , Yunes Jose Andres , Brandalise Silvia Regina , Mercado-Celis Gabriela Elisa , Melendez-Zajgla Jorge , Cárdenas-Cardós Rocío , Velasco-Hidalgo Liliana , Roberts Charles W. M. , Garraway Levi A. , Rodriguez-Galindo Carlos , Gabriel Stacey B. , Lander Eric S. , Golub Todd R. , Orkin Stuart H. , Getz Gad , Janeway Katherine A.
Published: December 2014

Significance

We present, to our knowledge, the first comprehensive next-generation sequencing of osteosarcoma in combination with a functional genomic screen in a genetically defined mouse model of osteosarcoma. Our data provide a strong rationale for targeting the phosphatidylinositol 3-kinase/mammalian target of rapamycin pathway in osteosarcoma and a foundation for rational clinical trial design. These findings present an immediate clinical opportunity because multiple inhibitors of this pathway are currently in clinical trials.
Auxin depletion from leaf primordia contributes to organ patterning
Authors: Qi Jiyan , Wang Ying , Yu Ting , Cunha Alexandre , Wu Binbin , Vernoux Teva , Meyerowitz Elliot , Jiao Yuling
Published: December 2014

Significance

Stem cells not only initiate organs, but may also contribute to organ patterning, at least in the shoot apex of flowering plants: classical microsurgical experiments imply that the shoot apical meristem promotes development of the leaf adaxial side, i.e., the upper side. In this study, we show the existence of a transient low auxin zone in the adaxial side that contributes to adaxial development. We further find that this adaxial low auxin zone results from auxin transport from leaves to the shoot apex. Thus, it is not a positive signal from stem cells, but departure of a signaling molecule from primordia to stem cells, that delivers polarity information—opposite to what is generally assumed.
Structural dynamics inside a functionalized metal–organic framework probed by ultrafast 2D IR spectroscopy
Authors: Nishida Jun , Tamimi Amr , Fei Honghan , Pullen Sonja , Ott Sascha , Cohen Seth M. , Fayer Michael D.
Published: December 2014

Significance

A unique aspect of metal–organic frameworks (MOFs) is their structural flexibility coexisting with a degree of regularity. Adsorbed guest molecules can cause MOF pore shapes to deform. Pore shape changes may be related to the high capacity and selectivity of the MOFs for gas adsorption and other processes. MOF flexibility and other properties are influenced by fast dynamics of the framework. Direct measurements to characterize fast motions of the MOFs have not been applied previously. We show that 2D IR spectroscopy can be performed on functionalized MOFs. We use 2D IR and other ultrafast IR methods to elucidate the timescales for ultrafast structural fluctuations and how they are influenced by a solvent filling the pores.
Estrogen-related receptor α is required for efficient human cytomegalovirus replication
Authors: Hwang Jesse , Purdy John G. , Wu Kai , Rabinowitz Joshua D. , Shenk Thomas
Published: December 2014

Significance

Viruses use the host cell’s resources, including numerous cellular metabolites, to successfully replicate and produce progeny. Here, we report that estrogen-related receptor α (ERRα), an orphan nuclear receptor and transcriptional regulator, supports the expression of multiple metabolic enzymes that contribute to the metabolic program induced by human cytomegalovirus in cultured primary fibroblasts. Loss or inhibition of ERRα impedes the viral replication cycle at multiple levels, leading to a reduction in progeny virus. Our findings identify ERRα as a host factor that is manipulated by the virus for its replicative needs and establish its potential as a pharmacological target for treatment of cytomegalovirus infection.
I love chips and (h)ate them too: the role of ambivalence and contextual cues on attitudinally based eating behaviour / Me encantan las patatas fritas, las como y (también) las odio: el papel de la ambivalencia y de las claves contextuales en el comportamiento alimentario basado en la actitud
Authors: Batista Maria T. , Lima Maria-Luísa , Pereira Cícero , Alves Hélder
Published: December 2014

Although past work proposed ambivalence as moderating the consistency between attitudes and behaviours, empirical evidence is mixed. We address this matter by taking into account social influence processes and observing actual eating behaviour. We predicted that less ambivalent attitudes are more consistent with behaviours independently of context cues. In two studies, we first evaluated participants’ ambivalence towards the target food. A week later we observed their eating behaviour (Study 1), and analysed the influence of context cues on it (Study 2). Results showed that only less ambivalent attitudes are good predictors of actual behaviour. Importantly, context cues only influenced behaviour among individuals with ambivalent attitudes.
Ramalin inhibits VCAM-1 expression and adhesion of monocyte to vascular smooth muscle cells through MAPK and PADI4-dependent NF-kB and AP-1 pathways
Authors: Park Bongkyun , Yim Joung-Han , Lee Hong-Kum , Kim Byung-Oh , Pyo Suhkneung
Published: December 2014

Cell adhesion molecules play a critical role in inflammatory processes and atherosclerosis. In this study, we investigated the effect of ramalin, a chemical compound from the Antarctic lichen Ramalina terebrata, on vascular cell adhesion molecule-1 (VCAM-1) expression induced by TNF-α in vascular smooth muscular cells (VSMCs). Pretreatment of VSMCs with ramalin (0.1–10 μg/mL) concentration-dependently inhibited TNF-α-induced VCAM-1 expression. Additionally, ramalin inhibited THP-1 (human acute monocytic leukemia cell line) cell adhesion to TNF-α-stimulated VSMCs. Ramalin suppressed TNF-α-induced production of reactive oxygen species (ROS), PADI4 expression, and phosphorylation of p38, ERK, and JNK. Moreover, ramalin inhibited TNF-α-induced translocation of NF-κB and AP-1. Inhibition of PADI4 expression by small interfering RNA or the PADI4-specific inhibitor markedly attenuated TNF-α-induced activation of NF-κB and AP-1 and VCAM-1 expression in VSMCs. Our study provides insight into the mechanisms underlying ramalin activity and suggests that ramalin may be a potential therapeutic agent to modulate inflammation within atherosclerosis.
High-level expression of tamavidin 2 in human cells by codon-usage optimization
Authors: Takakura Yoshimitsu , Katayama Sakurako , Nagata Yuki
Published: December 2014

Tamavidin 2 is a fungal protein that binds to biotin with an extremely high affinity. Tamavidin 2 is superior to avidin or streptavidin in terms of its low-level non-specific binding and high-level thermal stability. However, the gene for tamavidin 2 is highly expressed in Escherichia coli but not in mammalian cells, restricting its application as an affinity tag in mammalian cells. Here, we optimized the codon usage of tamavidin 2 for human cells and found that the resultant mutant expressed tamavidin 2 at approximately 30-fold higher level compared with the native gene. The protein thus produced in human cells could be purified by iminobiotin affinity chromatography, bound tightly to biotin, and was stable at high temperature (82 °C). This powerful technology for high-level expression of tamavidin 2 in mammalian cells will be of value in evaluating various fusion proteins produced in mammalian cells for numerous applications.
Evolution in action: adaptation and incipient sympatric speciation with gene flow across life at “Evolution Canyon”, Israel
Authors: Nevo Eviatar
Published: December 2014

Various major evolutionary problems are still open, controversial or unsettled. These include even the basic evolutionary processes of adaptation and speciation. The “Evolution Canyon” model is a microscale natural laboratory that can highlight some of the basic problems requiring clarification (Nevo list of “Evolution Canyon” publications athttp://evolution.haifa.ac.il). This is especially true if an interdisciplinary approach is practiced including ecological functional genomics, transcriptomics, proteomics, metabolomics and phenomics. Here I overview and reanalyze theincipient sympatric adaptive ecological speciationof five model organisms at “Evolution Canyon”, across life: the soil bacterium,Bacillus simplex; wild barley, the progenitor of cultivated barley,Hordeum spontaneum; the tiny beetleOryzaephilus surinamensis; the cosmopolitan fruit-fly,Drosophila melanogaster, and the Africa-originated spiny mouse,Acomys cahirinus. All five models of organisms displayevolution in action of microclimatic adaptation and incipient sympatric adaptive ecological speciationon the tropical and temperate abutting slopes, separated on average by only 250 meters. Some distant species converge in theirmicro-climatic adaptations to the hot and dry “African”, south-facing slope (SFS or AS) and to the cool and humid “European”, north-facing slope (NSF or ES). Natural selection overrules ongoing inter-slope gene-flow between the free interbreeding populations within and between slopes, and leads toadaptive incipient sympatric ecological speciationon the dramatically opposite abutting xeric savannoid and mesic forested slopes.
THE CONTINUED OPTICAL TO MID-INFRARED EVOLUTION OF V838 MONOCEROTIS*
Authors: Loebman S. R. , Wisniewski J. P. , Schmidt S. J. , Kowalski A. F. , Barry R. K. , Bjorkman K. S. , Hammel H. B. , Hawley S. L. , Hebb L. , Kasliwal M. M. , Lynch D. K. , Russell R. W. , Sitko M. L. , Szkody P.
Published: December 2014

The eruptive variable V838 Monocerotis (V838 Mon) gained notoriety in 2002 when it brightened nine magnitudes in a series of three outbursts and then rapidly evolved into an extremely cool supergiant. We present optical, near-infrared (near-IR), and mid-IR spectroscopic and photometric observations of V838 Mon obtained between 2008 and 2012 at the Apache Point Observatory 3.5 m, NASA IRTF 3 m, and Gemini South 8 m telescopes. We contemporaneously analyze the optical and IR spectroscopic properties of V838 Mon to arrive at a revised spectral type L3 supergiant and effective temperature

–2200 K. Because there are no existing optical observational data for L supergiants, we speculate that V838 Mon may represent the prototype for L supergiants in this wavelength regime. We find a low level of Hα emission present in the system, consistent with interaction between V838 Mon and its B3V binary; however, we cannot rule out a stellar collision as the genesis event, which could result in the observed Hα activity. Based upon a two-component blackbody fit to all wavelengths of our data, we conclude that, as of 2009, a shell of ejecta surrounded V838 Mon at a radius of

AU with a temperature of

K. This result is consistent with IR interferometric observations from the same era and predictions from the Lynch et al. model of the expanding system, which provides a simple framework for understanding this complicated system.
A FRAMEWORK FOR COLLABORATIVE REVIEW OF CANDIDATE EVENTS IN HIGH DATA RATE STREAMS: THE V-FASTR EXPERIMENT AS A CASE STUDY
Authors: Hart Andrew F. , Cinquini Luca , Khudikyan Shakeh E. , Thompson David R. , Mattmann Chris A. , Wagstaff Kiri , Lazio Joseph , Jones Dayton
Published: December 2014

“Fast radio transients” are defined here as bright millisecond pulses of radio-frequency energy. These short-duration pulses can be produced by known objects such as pulsars or potentially by more exotic objects such as evaporating black holes. The identification and verification of such an event would be of great scientific value. This is one major goal of the Very Long Baseline Array (VLBA) Fast Transient Experiment (V-FASTR), a software-based detection system installed at the VLBA. V-FASTR uses a “commensal” (piggy-back) approach, analyzing all array data continually during routine VLBA observations and identifying candidate fast transient events. Raw data can be stored from a buffer memory, which enables a comprehensive off-line analysis. This is invaluable for validating the astrophysical origin of any detection. Candidates discovered by the automatic system must be reviewed each day by analysts to identify any promising signals that warrant a more in-depth investigation. To support the timely analysis of fast transient detection candidates by V-FASTR scientists, we have developed a metadata-driven, collaborative candidate review framework. The framework consists of a software pipeline for metadata processing composed of both open source software components and project-specific code written expressly to extract and catalog metadata from the incoming V-FASTR data products, and a web-based data portal that facilitates browsing and inspection of the available metadata for candidate events extracted from the VLBA radio data.
Answer to a question of Kolmogorov
Authors: Balka Richárd , Elekes Márton , Máthé András
Published: December 2014

More than 80 years ago Kolmogorov asked the following question. Let

E
⊆

R

2

E\subseteq \mathbb {R}^{2}

be a measurable set with

λ

2

(
E
)
>
∞

\lambda ^{2}(E)>\infty

, where

λ
2

\lambda ^2

denotes the two-dimensional Lebesgue measure. Does there exist for every

ε
>
0

\varepsilon >0

a contraction

f
:
E
→

R

2

f\colon E\to \mathbb {R}^{2}

such that

λ

2

(
f
(
E
)
)
≥

λ

2

(
E
)
−
ε

\lambda ^{2}(f(E))\geq \lambda ^{2}(E)-\varepsilon

and

f
(
E
)

f(E)

is a polygon? We answer this question in the negative by constructing a bounded, simply connected open counterexample. Our construction can easily be modified to yield an analogous result in higher dimensions.
The four-dimensional Perfect-Mirsky Conjecture
Authors: Levick Jeremy , Pereira Rajesh , Kribs David
Published: December 2014

We verify the Perfect-Mirsky Conjecture on the structure of the set of eigenvalues for all

n
×
n

n \times n

doubly stochastic matrices in the four-dimensional case. The

n
=
1
,
2
,
3

n=1,2,3

cases have been established previously and the

n
=
5

n=5

case has been shown to be false. Our proof is direct and uses basic tools from matrix theory and functional analysis. Based on this analysis we formulate new conjectures for the general case.
Prevalence, Determinants, and Clinical Significance of Masked Hypertension in a Population-Based Sample of African Americans: The Jackson Heart Study
Authors: Diaz Keith M. , Veerabhadrappa Praveen , Brown Michael D. , Whited Matthew C. , Dubbert Patricia M. , Hickson DeMarc A.
Published: December 2014

BACKGROUND

The disproportionate rates of cardiovascular disease in African Americans may, in part, be due to suboptimal assessment of blood pressure (BP) with clinic BP measurements alone. To date, however, the prevalence of masked hypertension in African Americans has not been fully delineated. The purpose of this study was to evaluate masked hypertension prevalence in a large population-based sample of African Americans and examine its determinants and association with indices of target organ damage (TOD).

METHODS

Clinic and 24-hour ambulatory BP monitoring were conducted in 972 African Americans enrolled in the Jackson Heart Study. Common carotid artery intima-media thickness, left ventricular mass index, and the urinary albumin:creatinine excretion ratio were evaluated as indices of TOD.

RESULTS

Masked hypertension prevalence was 25.9% in the overall sample and 34.4% in participants with normal clinic BP. All indices of TOD were significantly higher in masked hypertensives compared to sustained normotensives and were similar between masked hypertensives and sustained hypertensives. Male gender, smoking, diabetes, and antihypertensive medication use were independent determinants of masked hypertension in multivariate analyses.

CONCLUSIONS

In this population-based cohort of African Americans, approximately one-third of participants with presumably normal clinic BP had masked hypertension when BP was assessed in their daily environment. Masked hypertension was accompanied by a greater degree of TOD in this cohort.
Identifying cancer-related microRNAs based on gene expression data
Authors: Zhao Xing-Ming , Liu Ke-Qin , Zhu Guanghui , He Feng , Duval Béatrice , Richer Jean-Michel , Huang De-Shuang , Jiang Chang-Jun , Hao Jin-Kao , Chen Luonan
Published: December 2014

Motivation: MicroRNAs (miRNAs) are short non-coding RNAs that play important roles in post-transcriptional regulations as well as other important biological processes. Recently, accumulating evidences indicate that miRNAs are extensively involved in cancer. However, it is a big challenge to identify which miRNAs are related to which cancer considering the complex processes involved in tumors, where one miRNA may target hundreds or even thousands of genes and one gene may regulate multiple miRNAs. Despite integrative analysis of matched gene and miRNA expression data can help identify cancer-associated miRNAs, such kind of data is not commonly available. On the other hand, there are huge amount of gene expression data that are publicly accessible. It will significantly improve the efficiency of characterizing miRNA’s function in cancer if we can identify cancer miRNAs directly from gene expression data.

Results: We present a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles without requiring either miRNA expression data or the matched gene and miRNA expression data. The results on multiple cancer datasets show that our proposed method can effectively identify cancer-related miRNAs with higher precision compared with other popular approaches. Furthermore, some of our novel predictions are validated by both differentially expressed miRNAs and evidences from literature, implying the predictive power of our proposed method. In addition, we construct a cancer-miRNA-pathway network, which can help explain how miRNAs are involved in cancer.

Availability and implementation: The R code and data files for the proposed method are available at http://comp-sysbio.org/miR_Path/

Contact:  liukeq@gmail.com

Supplementary information:  supplementary data are available at Bioinformatics online.
JEPEG: a summary statistics based tool for gene-level joint testing of functional variants
Authors: Lee Donghyung , Williamson Vernell S. , Bigdeli T. Bernard , Riley Brien P. , Fanous Ayman H. , Vladimirov Vladimir I. , Bacanu Silviu-Alin
Published: December 2014

Motivation: Gene expression is influenced by variants commonly known as expression quantitative trait loci (eQTL). On the basis of this fact, researchers proposed to use eQTL/functional information univariately for prioritizing single nucleotide polymorphisms (SNPs) signals from genome-wide association studies (GWAS). However, most genes are influenced by multiple eQTLs which, thus, jointly affect any downstream phenotype. Therefore, when compared with the univariate prioritization approach, a joint modeling of eQTL action on phenotypes has the potential to substantially increase signal detection power. Nonetheless, a joint eQTL analysis is impeded by (i) not measuring all eQTLs in a gene and/or (ii) lack of access to individual genotypes.

Results: We propose joint effect on phenotype of eQTL/functional SNPs associated with a gene (JEPEG), a novel software tool which uses only GWAS summary statistics to (i) impute the summary statistics at unmeasured eQTLs and (ii) test for the joint effect of all measured and imputed eQTLs in a gene. We illustrate the behavior/performance of the developed tool by analysing the GWAS meta-analysis summary statistics from the Psychiatric Genomics Consortium Stage 1 and the Genetic Consortium for Anorexia Nervosa.

Conclusions: Applied analyses results suggest that JEPEG complements commonly used univariate GWAS tools by: (i) increasing signal detection power via uncovering (a) novel genes or (b) known associated genes in smaller cohorts and (ii) assisting in fine-mapping of challenging regions, e.g. major histocompatibility complex for schizophrenia.

Availability and implementation: JEPEG, its associated database of eQTL SNPs and usage examples are publicly available at http://code.google.com/p/jepeg/.

Contact:  dlee4@vcu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sputnik: ad hoc distributed computation
Authors: Völkel Gunnar , Lausser Ludwig , Schmid Florian , Kraus Johann M. , Kestler Hans A.
Published: December 2014

Motivation: In bioinformatic applications, computationally demanding algorithms are often parallelized to speed up computation. Nevertheless, setting up computational environments for distributed computation is often tedious. Aim of this project were the lightweight ad hoc set up and fault-tolerant computation requiring only a Java runtime, no administrator rights, while utilizing all CPU cores most effectively.

Results: The Sputnik framework provides ad hoc distributed computation on the Java Virtual Machine which uses all supplied CPU cores fully. It provides a graphical user interface for deployment setup and a web user interface displaying the current status of current computation jobs. Neither a permanent setup nor administrator privileges are required. We demonstrate the utility of our approach on feature selection of microarray data.

Availability and implementation: The Sputnik framework is available on Github http://github.com/sysbio-bioinf/sputnik under the Eclipse Public License.

Contact: hkestler@fli-leibniz.de or hans.kestler@uni-ulm.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Response to the comment on ‘protein-protein binding affinity prediction from amino acid sequence’
Authors: Yugandhar K. , Gromiha M. Michael
Published: December 2014

Contact:  gromiha@iitm.ac.in
Epock: rapid analysis of protein pocket dynamics
Authors: Laurent Benoist , Chavent Matthieu , Cragnolini Tristan , Dahl Anna Caroline E. , Pasquali Samuela , Derreumaux Philippe , Sansom Mark S.P. , Baaden Marc
Published: December 2014

Summary: The volume of an internal protein pocket is fundamental to ligand accessibility. Few programs that compute such volumes manage dynamic data from molecular dynamics (MD) simulations. Limited performance often prohibits analysis of large datasets. We present Epock, an efficient command-line tool that calculates pocket volumes from MD trajectories. A plugin for the VMD program provides a graphical user interface to facilitate input creation, run Epock and analyse the results.

Availability and implementation: Epock C++ source code, Python analysis scripts, VMD Tcl plugin, documentation and installation instructions are freely available at http://epock.bitbucket.org.

Contact:  benoist.laurent@gmail.com or baaden@smplinux.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Detection of circular permutations within protein structures using CE-CP
Authors: Bliven Spencer E. , Bourne Philip E. , Prlić Andreas
Published: December 2014

Motivation: Circular permutation is an important type of protein rearrangement. Natural circular permutations have implications for protein function, stability and evolution. Artificial circular permutations have also been used for protein studies. However, such relationships are difficult to detect for many sequence and structure comparison algorithms and require special consideration.

Results: We developed a new algorithm, called Combinatorial Extension for Circular Permutations (CE-CP), which allows the structural comparison of circularly permuted proteins. CE-CP was designed to be user friendly and is integrated into the RCSB Protein Data Bank. It was tested on two collections of circularly permuted proteins. Pairwise alignments can be visualized both in a desktop application or on the web using Jmol and exported to other programs in a variety of formats.

Availability and implementation: The CE-CP algorithm can be accessed through the RCSB website at http://www.rcsb.org/pdb/workbench/workbench.do. Source code is available under the LGPL 2.1 as part of BioJava 3 (http://biojava.org; http://github.com/biojava/biojava).

Contact:  sbliven@ucsd.edu or info@rcsb.org.
HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins
Authors: Rezaei-Ghaleh Nasrollah , Klama Frederik , Munari Francesca , Zweckstetter Markus
Published: December 2014

Motivation: A large fraction of eukaryotic proteins contain unstructured tails or linkers. The presence of flexible regions allows these systems to experience a high level of mobility facilitating their biological function. The complex nature of protein rotation in such flexible modular systems precludes a straightforward application of hydrodynamic methods to calculate their rotational motional properties. We describe the workflow of HYdrodynamic CoUpling of Domains (HYCUD), a program for prediction of effective rotational correlation times in multidomain proteins. The usage of HYCUD is demonstrated by its application to the ribosomal protein L7/L12. Rotational correlation times predicted by HYCUD might be used to detect molecular switch events mediated by disorder–order transitions in interdomain linkers.

Availability and implementation: The source code and documentation are available at www.mpibpc.mpg.de/106144/software.

Contact:  mzwecks@gwdg.de or nare@nmr.mpibpc.mpg.de

Supplementary information:  Supplementary material is available at Bioinformatics online.
Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier
Authors: Navarro-Gomez Daniel , Leipzig Jeremy , Shen Lishuang , Lott Marie , Stassen Alphons P.M. , Wallace Douglas C. , Wiggs Janey L. , Falk Marni J. , van Oven Mannis , Gai Xiaowu
Published: December 2014

Motivation: All current mitochondrial haplogroup classification tools require variants to be detected from an alignment with the reference sequence and to be properly named according to the canonical nomenclature standards for describing mitochondrial variants, before they can be compared with the haplogroup determining polymorphisms. With the emergence of high-throughput sequencing technologies and hence greater availability of mitochondrial genome sequences, there is a strong need for an automated haplogroup classification tool that is alignment-free and agnostic to reference sequence.

Results: We have developed a novel mitochondrial genome haplogroup-defining algorithm using a k-mer approach namely Phy-Mer. Phy-Mer performs equally well as the leading haplogroup classifier, HaploGrep, while avoiding the errors that may occur when preparing variants to required formats and notations. We have further expanded Phy-Mer functionality such that next-generation sequencing data can be used directly as input.

Availability and implementation: Phy-Mer is publicly available under the GNU Affero General Public License v3.0 on GitHub (https://github.com/danielnavarrogomez/phy-mer).

Contact:  Xiaowu_Gai@meei.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
diXa: a data infrastructure for chemical safety assessment
Authors: Hendrickx Diana M. , Aerts Hugo J.W.L. , Caiment Florian , Clark Dominic , Ebbels Timothy M.D. , Evelo Chris T. , Gmuender Hans , Hebels Dennie G.A.J. , Herwig Ralf , Hescheler Jürgen , Jennen Danyel G.J. , Jetten Marlon J.A. , Kanterakis Stathis , Keun Hector C. , Matser Vera , Overington John P. , Pilicheva Ekaterina , Sarkans Ugis , Segura-Lepe Marcelo P. , Sotiriadou Isaia , Wittenberger Timo , Wittwehr Clemens , Zanzi Antonella , Kleinjans Jos C.S.
Published: December 2014

Motivation: The field of toxicogenomics (the application of ‘-omics’ technologies to risk assessment of compound toxicities) has expanded in the last decade, partly driven by new legislation, aimed at reducing animal testing in chemical risk assessment but mainly as a result of a paradigm change in toxicology towards the use and integration of genome wide data. Many research groups worldwide have generated large amounts of such toxicogenomics data. However, there is no centralized repository for archiving and making these data and associated tools for their analysis easily available.

Results: The Data Infrastructure for Chemical Safety Assessment (diXa) is a robust and sustainable infrastructure storing toxicogenomics data. A central data warehouse is connected to a portal with links to chemical information and molecular and phenotype data. diXa is publicly available through a user-friendly web interface. New data can be readily deposited into diXa using guidelines and templates available online. Analysis descriptions and tools for interrogating the data are available via the diXa portal.

Availability and implementation:  http://www.dixa-fp7.eu

Contact:  d.hendrickx@maastrichtuniversity.nl; info@dixa-fp7.eu

Supplementary information:  Supplementary data are available at Bioinformatics online.
3Dmol.js: molecular visualization with WebGL
Authors: Rego Nicholas , Koes David
Published: December 2014

Summary: 3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites.

Availability and implementation: 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu

Contact:  dkoes@pitt.edu
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy
Authors: Lee Woonghee , Tonelli Marco , Markley John L.
Published: December 2014

Summary: SPARKY (Goddard and Kneller, SPARKY 3) remains the most popular software program for NMR data analysis, despite the fact that development of the package by its originators ceased in 2001. We have taken over the development of this package and describe NMRFAM-SPARKY, which implements new functions reflecting advances in the biomolecular NMR field. NMRFAM-SPARKY has been repackaged with current versions of Python and Tcl/Tk, which support new tools for NMR peak simulation and graphical assignment determination. These tools, along with chemical shift predictions from the PACSY database, greatly accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format interconversion for interfacing with a variety of web servers including, PECAN , PINE, TALOS-N, CS-Rosetta, SHIFTX2 and PONDEROSA-C/S.

Availability and implementation: The software package, along with binary and source codes, if desired, can be downloaded freely from http://pine.nmrfam.wisc.edu/download_packages.html. Instruction manuals and video tutorials can be found at http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm.

Contact:  whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bayesian depletion model estimates of spiny lobster abundance at two marine protected areas in Belize with or without in-season recruitment
Authors: Babcock Elizabeth A. , Harford William J. , Coleman Robin , Gibson Janet , Maaz Julio , Foley James R. , Gongora Mauro
Published: December 2014

In Belize, beginning in 2011 at Glover's Reef Marine Reserve, and in 2012 at Port Honduras Marine Reserve, fishers have been required to keep logbooks to document their catch and effort. A Bayesian depletion model including in-season recruitment was applied to the standardized catch per unit effort (cpue) of Caribbean spiny lobster (Panulirus argus) from the logbooks to estimate the abundance and fishing mortality of lobsters at both sites. Two alternative subsets of the cpue data were used to account for changes in targeting caused by the opening and closing of the queen conch (Strombus gigas) season. At Glover's Reef, a typical model estimated abundance ∼66–79 000 lobsters. Of these, ∼60–85% were present at the beginning of the season and the rest recruited into the fished population later in the season. The depletion model applied to data from the 2012 season at Port Honduras found an abundance of ∼12 000 lobsters, and in-season recruitment was not supported by the data. That in-season recruitment was present at Glover's Reef and not at Port Honduras may be explained by the fact that Glover's Reef has more unfished areas that could serve as a source of adult lobsters during the season. Glover's Reef has a larger no-take zone (20% of the reserve area, compared with 5% at Port Honduras), and it is surrounded by a deep wall reef where lobsters are found below the depth accessible to fishers. The models estimated a harvest fraction of ∼70% in both reserves.
The reversal of the SF–density relation in a massive, X-ray-selected galaxy cluster at z = 1.58: results from Herschel
Authors: Santos J. S. , Altieri B. , Valtchanov I. , Nastasi A. , Böhringer H. , Cresci G. , Elbaz D. , Fassbender R. , Rosati P. , Tozzi P. , Verdugo M.
Published: December 2014

Dusty, star-forming galaxies have a critical role in the formation and evolution of massive galaxies in the Universe. Using deep far-infrared imaging in the range 100–500 μm obtained with the Herschel telescope, we investigate the dust-obscured star formation (SF) in the galaxy cluster XDCP J0044.0-2033 at z = 1.58, the most massive cluster at z > 1.5, with a measured mass M200 = 4.7$^{+1.4}_{-0.9}$ × 1014 M⊙. We perform an analysis of the spectral energy distributions (SEDs) of 12 cluster members (5 spectroscopically confirmed) detected with ≥3σ significance in the PACS maps, all ultraluminous infrared galaxies. The individual star formation rates (SFRs) lie in the range 155–824 M⊙ yr−1, with dust temperatures of 24–35 K. We measure a strikingly high amount of SF in the cluster core, SFR (<250 kpc) ≥ 1875 ± 158 M⊙ yr−1, four times higher than the amount of SF in the cluster outskirts. This scenario is unprecedented in a galaxy cluster, showing for the first time a reversal of the SF–density relation at z ∼ 1.6 in a massive cluster.
The nature of ULX source M101 X-1: optically thick outflow from a stellar mass black hole
Authors: Shen Rong-Feng , Barniol Duran Rodolfo , Nakar Ehud , Piran Tsvi
Published: December 2014

The nature of ultraluminous X-ray sources (ULXs) has long been plagued by an ambiguity about whether the central compact objects are intermediate-mass (IMBH, ≳103 M⊙) or stellar-mass (a few tens M⊙) black holes (BHs). The high-luminosity (≃1039 erg s−1) and supersoft spectrum (T ≃ 0.1 keV) during the high state of the ULX source X-1 in the galaxy M101 suggest a large emission radius (≳109 cm), consistent with being an IMBH accreting at a sub-Eddington rate. However, recent kinematic measurement of the binary orbit of this source and identification of the secondary as a Wolf–Rayet star suggest a stellar-mass BH primary with a super-Eddington accretion. If that is the case, a hot, optically thick outflow from the BH can account for the large emission radius and the soft spectrum. By considering the interplay of photons’ absorption and scattering opacities, we determine the radius and mass density of the emission region of the outflow and constrain the outflow mass-loss rate. The analysis presented here can be potentially applied to other ULXs with thermally dominated spectra, and to other super-Eddington accreting sources.
Stable isotope analysis of vertebrae reveals ontogenetic changes in habitat in an endothermic pelagic shark
Authors: Carlisle Aaron B. , Goldman Kenneth J. , Litvin Steven Y. , Madigan Daniel J. , Bigman Jennifer S. , Swithenbank Alan M. , Kline Thomas C. , Block Barbara A.
Published: December 2014

Ontogenetic changes in habitat are driven by shifting life-history requirements and play an important role in population dynamics. However, large portions of the life history of many pelagic species are still poorly understood or unknown. We used a novel combination of stable isotope analysis of vertebral annuli, Bayesian mixing models, isoscapes and electronic tag data to reconstruct ontogenetic patterns of habitat and resource use in a pelagic apex predator, the salmon shark (
Lamna ditropis
). Results identified the North Pacific Transition Zone as the major nursery area for salmon sharks and revealed an ontogenetic shift around the age of maturity from oceanic to increased use of neritic habitats. The nursery habitat may reflect trade-offs between prey availability, predation pressure and thermal constraints on juvenile endothermic sharks. The ontogenetic shift in habitat coincided with a reduction of isotopic niche, possibly reflecting specialization upon particular prey or habitats. Using tagging data to inform Bayesian isotopic mixing models revealed that adult sharks primarily use neritic habitats of Alaska yet receive a trophic subsidy from oceanic habitats. Integrating the multiple methods used here provides a powerful approach to retrospectively study the ecology and life history of migratory species throughout their ontogeny.
Does early learning drive ecological divergence during speciation processes in parasitoid wasps?
Authors: König Kerstin , Krimmer Elena , Brose Sören , Gantert Cornelia , Buschlüter Ines , König Christian , Klopfstein Seraina , Wendt Ingo , Baur Hannes , Krogmann Lars , Steidle Johannes L. M.
Published: December 2014

Central to the concept of ecological speciation is the evolution of ecotypes, i.e. groups of individuals occupying different ecological niches. However, the mechanisms behind the first step of separation, the switch of individuals into new niches, are unclear. One long-standing hypothesis, which was proposed for insects but never tested, is that early learning causes new ecological preferences, leading to a switch into a new niche within one generation. Here, we show that a host switch occurred within a parasitoid wasp, which is associated with the ability for early learning and the splitting into separate lineages during speciation.Lariophagus distinguendusconsists of two genetically distinct lineages, most likely representing different species. One attacks drugstore beetle larvae (Stegobium paniceum(L.)), which were probably the ancestral host of both lineages. The drugstore beetle lineage has an innate host preference that cannot be altered by experience. In contrast, the second lineage is found onSitophilusweevils as hosts and changes its preference by early learning. We conclude that a host switch has occurred in the ancestor of the second lineage, which must have been enabled by early learning. Because early learning is widespread in insects, it might have facilitated ecological divergence and associated speciation in this hyperdiverse group.
Long sperm fertilize more eggs in a bird
Authors: Bennison Clair , Hemmings Nicola , Slate Jon , Birkhead Tim
Published: December 2014

Sperm competition, in which the ejaculates of multiple males compete to fertilize a female's ova, results in strong selection on sperm traits. Although sperm size and swimming velocity are known to independently affect fertilization success in certain species, exploring the relationship between sperm length, swimming velocity and fertilization success still remains a challenge. Here, we use the zebra finch (Taeniopygia guttata), where sperm size influences sperm swimming velocity, to determine the effect of sperm total length on fertilization success. Sperm competition experiments, in which pairs of males whose sperm differed only in length and swimming speed, revealed that males producing long sperm were more successful in terms of (i) the number of sperm reaching the ova and (ii) fertilizing those ova. Our results reveal that although sperm length is the main factor determining the outcome of sperm competition, complex interactions between male and female reproductive traits may also be important. The mechanisms underlying these interactions are poorly understood, but we suggest that differences in sperm storage and utilization by females may contribute to the outcome of sperm competition.
Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond
Authors: Jørgensen Peter Søgaard , Barraquand Frédéric , Bonhomme Vincent , Curran Timothy J , Cieraad Ellen , Ezard Thomas , Gherardi Laureano , Hayes R. Andrew , Poisot Timothée , Salguero-Gómez Roberto , DeSoto Lucía , Swartz Brian , Talbot Jennifer M. , Wee Brian , Zimmerman Naupaka
Published: December 2014

We present a case for using global community innovation platforms (GCIPs), an approach to improve innovation and knowledge exchange in international scientific communities through a common and open online infrastructure. We highlight the value of GCIPs by focusing on recent efforts targeting the ecological sciences, where GCIPs are of high relevance given the urgent need for interdisciplinary, geographical, and cross-sector collaboration to cope with growing challenges to the environment as well as the scientific community itself. Amidst the emergence of new international institutions, organizations, and dedicated meetings, GCIPs provide a stable international infrastructure for rapid and long-term coordination that can be accessed by any individual. The accessibility can be particularly important for researchers early in their careers. Recent examples of early career GCIPs complement an array of existing options for early career scientists to improve skill sets, increase academic and social impact, and broaden career opportunities. In particular, we provide a number of examples of existing early career initiatives that incorporate elements from the GCIPs approach, and highlight an in-depth case study from the ecological sciences: the International Network of Next-Generation Ecologists (INNGE), initiated in 2010 with support from the International Association for Ecology and 18 member institutions from six continents.
Limits to adaptation along environmental gradients
Authors: Polechová Jitka , Barton Nick
Published: December 2014

Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: while it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that when the environment varies across space, ?swamping? by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. Yet, current deterministic theory shows that when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary time scales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment, and ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.