bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of circular permutations within protein structures using CE-CP
Authors: Bliven Spencer E. , Bourne Philip E. , Prlić Andreas 
Published: December 2014

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractIn 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

Abstract
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 &gt; 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 (&lt;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

Abstract
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.
The utility of visual estimation of cover for rapid assessment of graminoid abundance in forest and grassland habitats in studies of animal foraging
Authors: Gautam Hansraj , Potdar G. G. , Vidya T.N.C. 
Published: December 2014

AbstractQuestionsTo assess the feasibility of using visually-estimated cover in rapid assessment of herbivore food species abundance in the grass layer, we asked the following questions: 1) What is the relationship between total graminoid cover and biomass in forests, and does height improve the prediction of biomass from cover? 2) How does total cover relate to biomass in a grassland habitat? 3) How does elephant food species graminoid cover relate to individual species biomass? 4) How well does species diversity of forest understorey grass layer, calculated from cover data, mirror that calculated from biomass data?LocationNagarahole National Park, India.MethodsWe estimated the abundance of graminoids through visual estimation of cover and weighted harvested biomass in forest and grassland plots. In forests, two estimates of total graminoid abundance, total graminoid cover and sum of species covers, were used. In the grassland, only total graminoid abundance was measured. We examined the relationship between cover estimates and biomass, and the additional utility of height in predicting biomass, using multiple regressions and AIC-based model selection. We also assessed similarity in cover- and biomass-based Simpson’s and Shannon-Wiener diversity indices using regressions.ResultsGraminoid cover explained a large portion of variation in total graminoid biomass in forest and grassland habitats. The sum of species covers was better than total cover in estimating total graminoid biomass in the forest. The benefit of including height to estimate total biomass was moderate in forests but substantial in grassland. Cover estimates were good proxies of food species biomass, and the addition of height did not yield better models for most species. Species diversity indices calculated from cover largely matched those based on biomass.ConclusionsVisual estimation of species cover is a good alternative to biomass harvesting for rapid assessment of abundance of graminoids consumed by generalist herbivores, like elephants.
More Signal, Less Noise: Single-primer Adenylation Method (SAM) for the Efficient Preparation of DNA for Transposon Sequencing (TnSeq)
Authors: Willcocks S , Stabler R , Wren B 
Published: December 2014

ABSTRACTTransposon Sequencing (TnSeq) is a cutting-edge tool that allows quantitative, genome-wide genetic analysis of a given population in an experimental condition. TnSeq utilises next generation sequencing that is designed to perform optimally when all of the input material is of interest, therefore TnSeq is inefficient since only a small portion of nucleic acid fragments contain the transposon target site for primer annealing. We describe an innovative modification to standard transposon library preparation protocols that provides a significant improvement to the quality of sequencing data recovered.
Molecular characterization of the skin fungal microbiome in patients with psoriasis
Authors: Takemoto Akemi , Cho Otomi , Morohoshi Yuka , Sugita Takashi , Muto Masahiko 
Published: December 2014

AbstractThe skin surface is colonized by a wide variety of fungi and bacteria. While many of these organisms, including Malassezia, Candida, Streptococcus and Staphylococcus species, are associated with provocation and/or exacerbation of psoriasis, a detailed analysis of the cutaneous fungal microbiome in psoriatic patients has yet to be performed. To identify the disease‐specific fungal microbiota on psoriatic scale samples, fungal rRNA gene sequences from 12 psoriatic patients and 12 healthy controls were analyzed by pyrosequencing. A total of 317 806 high‐quality sequences were obtained, representing 142 genera. Malassezia species were the most abundant sequences in both populations (46.9 ± 14.0% in psoriasis vs 76.0 ± 14.6% for healthy controls). Principal coordinate analysis revealed that the fungal microbiomes were independent. Although an association between the cutaneous fungal microbiome and psoriasis has yet to be established, our data indicate that the microbiome in patients with psoriasis is independent of that in healthy controls.
Alien and native plant species play different roles in plant community structure
Authors: Bernard‐Verdier Maud , Hulme Philip E. 
Published: December 2014

Summary

Although impacts of alien plants on species richness are widely reported, it remains unclear how common such effects might be and whether they differ from those due to native species. To date, too few studies have examined the impacts of a wide enough spectrum of native and alien species to address the importance of geographic origin on the richness of plant communities.

We investigated how total plant species richness, as well as its separate alien and native components, varied with the abundance of 115 alien and 146 native plant species across Banks Peninsula in New Zealand. Using null models, we tested whether significant correlations between the abundance of each focal species and species richness were more frequent than expected by chance. Examination of the differences in the relationships with species abundance found for native and alien richness can shed light as to whether alien species might be acting as drivers of biodiversity change or passengers responding to external environmental factors.

Significant relationships were rarely found for total richness due to contrasting trends of native and alien richness with species abundance. In contrast to natives, an increase in the abundance of an alien species revealed more frequent negative relationships with native richness and positive correlations with alien richness.

The relationship with species abundance found for native and alien components of richness differed between grasslands and woodlands. While we found putative support for negative impacts on native richness for several alien species in grasslands, the similar negative correlations in woodlands were more likely to reflect the shade intolerance of alien grasses where native species richness was high.

Synthesis. Our analyses reveal that widespread alien and native species play different roles in the plant communities in which they co‐occur. Separately analysing the relationship with species abundance for alien and native components of richness can help distinguish between situations where aliens may be acting as the primary drivers in plant community changes or simply passengers. This is an essential first step in designing further experimental studies to determine the underlying ecological processes and potential ecosystem impacts of alien species.
Insects as a model system for aging studies
Authors: Lee Hye‐Yeon , Lee Shin‐Hae , Min Kyung‐Jin 
Published: December 2014

AbstractAs the human lifespan has increased dramatically in recent decades, the amount of aging research has correspondingly increased. To investigate mechanisms of aging, an efficient model system is required. Although mammalian animal models are essential for aging studies, they are sometimes inappropriate due to their long lifespans and high maintenance costs. In this regard, insects can be effective alternative model systems for aging studies, as insects have a relatively short lifespan and cost less to maintain. Many species of insects have been used as model systems for aging studies, especially fruit flies, silkworm moths and several social insects. Fruit flies are most commonly used for aging studies due to the wide availability of abundant resources such as mutant stocks, databases and genetic tools. Silkworm moths are also good tools for studying aging at the tissue level due to their relatively large size. Last, social insects such as ants and bees are good for investigating lifespan determinants, as their lifespans significantly differ according to caste despite a constant genotype among the population. In this review, we discuss the current status and future prospects of aging research using insect model systems.
Risk of tuberculosis, serious infection and lymphoma with disease‐modifying biologic drugs in rheumatoid arthritis patients in Taiwan
Authors: Chiu Ying‐Ming , Lang Hui‐Chu , Lin Hsiao‐Yi , Yang Ming‐Ta , Fang Chi‐Hui , Yang Ya‐Wen , Schabert Vernon F. , Tang Boxiong 
Published: December 2014

AbstractAimTo determine the risk of adverse events in rheumatoid arthritis (RA) patients treated with biological disease‐modifying anti‐rheumatic drugs (bDMARD) versus traditional DMARDs (tDMARD).MethodThis retrospective study used Taiwan's National Health Insurance Research Database to capture data for adult patients diagnosed with RA between 1 January 1999 and 31 December 2009 and treated with tDMARD or bDMARD. The endpoints were patients with cases of an inpatient serious bacterial infection (SBI), diagnosis of tuberculosis (TB) or lymphoma. Within the bDMARD cohort, individual bDMARDS with adequate data were also compared (adalimumab and etanercept). Propensity‐score matching was used to adjust for significant (P ≤ 0.05) patient characteristics. Incidence rate ratios (IRR) of SBI/TB/lymphoma cases versus non‐cases were adjusted for exposure time (rate per 100 000 patient‐years) and 95% confidence intervals were constructed to assess whether IRRs differed from 1.0.ResultsOf 34 947 potential patients, 7888 tDMARD, 3459 bDMARD (including 1492 etanercept and 746 adalimumab) patients were matched for analysis. A total of 2150 cases were identified and of these 1711 were SBI, 406 as TB and 33 as lymphoma. For all cases except SBI, the IRR (95% CI) was higher for bDMARD versus tDMARD (SBI 1.04 [0.89–1.19]; TB 2.67 [2.12–3.34]; lymphoma 3.24 [1.37–7.06]). Excepting lymphoma, IRR was higher for adalimumab versus etanercept (SBI 1.83 [1.19–2.77]; TB 2.35 [1.29–4.15]; lymphoma 1.49 [0.03–18.66]).ConclusionsThere was a higher risk for specified infections and lymphoma with bDMARD versus tDMARD and adalimumab versus etanercept.