bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hierarchically structured nanowires on and nanosticks in ZnO microtubes
Authors: Rivaldo-Gómez C. M. , Cabrera-Pasca G. A. , Zúñiga A. , Carbonari A. W. , Souza J. A. 
Published: October 2015

AbstractWe report both coaxial core-shell structured microwires and ZnO microtubes with growth of nanosticks in the inner and nanowires on the outer surface as a novel hierarchical micro/nanoarchitecture. First, a core-shell structure is obtained—the core is formed by metallic Zn and the semiconducting shell is comprised by a thin oxide layer covered with a high density of nanowires. Such Zn/ZnO core-shell array showed magnetoresistance effect. It is suggested that magnetic moments in the nanostructured shell superimposes to the external magnetic field enhancing the MR effect. Second, microtubes decorated with nanowires on the external surface are obtained. In an intermediate stage, a hierarchical morphology comprised of discrete nanosticks in the inner surface of the microtube has been found. Hyperfine interaction measurements disclosed the presence of confined metallic Zn regions at the interface between linked ZnO grains forming a chain and a ZnO thicker layer. Surprisingly, the metallic clusters form highly textured thin flat regions oriented parallel to the surface of the microtube as revealed by the electrical field gradient direction. The driving force to grow the internal nanosticks has been ascribed to stress-induced migration of Zn ions due to compressive stress caused by the presence of these confined regions.
Novel anticancer agent, SQAP, binds to focal adhesion kinase and modulates its activity
Authors: Izaguirre-Carbonell Jesus , Kawakubo Hirofumi , Murata Hiroshi , Tanabe Atsushi , Takeuchi Toshifumi , Kusayanagi Tomoe , Tsukuda Senko , Hirakawa Takeshi , Iwabata Kazuki , Kanai Yoshihiro , Ohta Keisuke , Miura Masahiko , Sakaguchi Kengo , Matsunaga Sachihiro , Sahara Hiroeki , Kamisuki Shinji , Sugawara Fumio 
Published: October 2015

AbstractSQAP is a novel and promising anticancer agent that was obtained by structural modifications from a natural compound. SQAP inhibits angiogenesis in vivo resulting in increased hypoxia and reduced tumor volume. In this study, the mechanism by which SQAP modifies the tumor microenvironment was revealed through the application of a T7 phage display screening. This approach identified five SQAP-binding proteins including sterol carrier protein 2, multifunctional enzyme type 2, proteasomal ubiquitin receptor, UV excision repair protein and focal adhesion kinase (FAK). All the interactions were confirmed by surface plasmon resonance analysis. Since FAK plays an important role in cell turnover and angiogenesis, the influence of SQAP on FAK was the principal goal of this study. SQAP decreased FAK phosphorylation and cell migration in human umbilical vein endothelial cells and A549 cancer cells. These findings suggest that inhibition of FAK phosphorylation works as the mechanism for the anti-angiogenesis activity of SQAP.
Phase Diagram and Transformations of Iron Pentacarbonyl to nm Layered Hematite and Carbon-Oxygen Polymer under Pressure
Authors: Ryu Young Jay , Kim Minseob , Yoo Choong-Shik 
Published: October 2015

AbstractWe present the phase diagram of Fe(CO)5, consisting of three molecular polymorphs (phase I, II and III) and an extended polymeric phase that can be recovered at ambient condition. The phase diagram indicates a limited stability of Fe(CO)5 within a pressure-temperature dome formed below the liquid- phase II- polymer triple point at 4.2 GPa and 580 K. The limited stability, in turn, signifies the temperature-induced weakening of Fe-CO back bonds, which eventually leads to the dissociation of Fe-CO at the onset of the polymerization of CO. The recovered polymer is a composite of novel nm-lamellar layers of crystalline hematite Fe2O3 and amorphous carbon-oxygen polymers. These results, therefore, demonstrate the synthesis of carbon-oxygen polymer by compressing Fe(CO)5, which advocates a novel synthetic route to develop atomistic composite materials by compressing organometallic compounds.
Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space
Authors: Kaushik Swati , Nair Anu G. , Mutt Eshita , Subramanian Hari Prasanna , Sowdhamini Ramanathan 
Published: October 2015

Abstract
Motivation: In the post-genomic era, automatic annotation of protein sequences using computational homology-based methods is highly desirable. However, often protein sequences diverge to an extent where detection of homology and automatic annotation transfer is not straightforward. Sophisticated approaches to detect such distant relationships are needed. We propose a new approach to identify deep evolutionary relationships of proteins to overcome shortcomings of the available methods.
Results: We have developed a method to identify remote homologues more effectively from any protein sequence database by using several cascading events with Hidden Markov Models (C-HMM). We have implemented clustering of hits and profile generation of hit clusters to effectively reduce the computational timings of the cascaded sequence searches. Our C-HMM approach could cover 94, 83 and 40% coverage at family, superfamily and fold levels, respectively, when applied on diverse protein folds. We have compared C-HMM with various remote homology detection methods and discuss the trade-offs between coverage and false positives.
Availability and implementation: A standalone package implemented in Java along with a detailed documentation can be downloaded from https://github.com/RSLabNCBS/C-HMM
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: mini@ncbs.res.in
FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction
Authors: Khosraviani Mehrshad , Saheb Zamani Morteza , Bidkhori Gholamreza 
Published: October 2015

Abstract
Motivation: A fundamental computational problem in the area of metabolic engineering is finding metabolic pathways between a pair of source and target metabolites efficiently. We present an approach, namely FogLight, for searching metabolic networks utilizing Boolean (AND-OR) operations represented in matrix notation to efficiently reduce the search space. This enables the enumeration of all pathways between metabolites that are too distant for the application of brute-force methods.
Results: Benchmarking tests run with FogLight show that it can reduce the search space by up to 98%, after which the accelerated search for high accurate results is guaranteed. Using FogLight, several pathways between eight given pairs of metabolites are found of which the pathways from CO2 to ethanol are specifically discussed. Additionally, in comparison with three path-finding tools, namely PHT, FMM and RouteSearch, FogLight can find shorter and more pathways for attempted source-target metabolite pairs.
Contact: szamani@aut.ac.ir, gholamreza.bidkhori@vtt.fi
Supplementary information: Supplementary data are available at Bioinformatics online.
I-PV: a CIRCOS module for interactive protein sequence visualization
Authors: Tanyalcin Ibrahim , Al Assaf Carla , Gheldof Alexander , Stouffs Katrien , Lissens Willy , Jansen Anna C. 
Published: October 2015

Abstract
Summary: Today’s genome browsers and protein databanks supply vast amounts of information about proteins. The challenge is to concisely bring together this information in an interactive and easy to generate format.
Availability and implementation: We have developed an interactive CIRCOS module called i-PV to visualize user supplied protein sequence, conservation and SNV data in a live presentable format. I-PV can be downloaded from http://www.i-pv.org.
Contact: ibrahim.tanyalcin@i-pv.org, itanyalc@vub.ac.be or support@i-pv.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic
Authors: Brown Peter , Pullan Wayne , Yang Yuedong , Zhou Yaoqi 
Published: October 2015

Abstract
Motivation: The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique.
Results: The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments.
Availability and implementation: SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org
Contact: yaoqi.zhou@griffith.edu.au
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition
Authors: Wang Chao , Zhang Haicang , Zheng Wei-Mou , Xu Dong , Zhu Jianwei , Wang Bing , Ning Kang , Sun Shiwei , Li Shuai Cheng , Bu Dongbo 
Published: October 2015

Abstract
Summary: The protein structure prediction approaches can be categorized into template-based modeling (including homology modeling and threading) and free modeling. However, the existing threading tools perform poorly on remote homologous proteins. Thus, improving fold recognition for remote homologous proteins remains a challenge. Besides, the proteome-wide structure prediction poses another challenge of increasing prediction throughput.
In this study, we presented FALCON@home as a protein structure prediction server focusing on remote homologue identification. The design of FALCON@home is based on the observation that a structural template, especially for remote homologous proteins, consists of conserved regions interweaved with highly variable regions. The highly variable regions lead to vague alignments in threading approaches. Thus, FALCON@home first extracts conserved regions from each template and then aligns a query protein with conserved regions only rather than the full-length template directly. This helps avoid the vague alignments rooted in highly variable regions, improving remote homologue identification.
We implemented FALCON@home using the Berkeley Open Infrastructure of Network Computing (BOINC) volunteer computing protocol. With computation power donated from over 20 000 volunteer CPUs, FALCON@home shows a throughput as high as processing of over 1000 proteins per day. In the Critical Assessment of protein Structure Prediction (CASP11), the FALCON@home-based prediction was ranked the 12th in the template-based modeling category. As an application, the structures of 880 mouse mitochondria proteins were predicted, which revealed the significant correlation between protein half-lives and protein structural factors.
Availability and implementation: FALCON@home is freely available at http://protein.ict.ac.cn/FALCON/.
Contact: shuaicli@cityu.edu.hk, dbu@ict.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis
Authors: Patel Parth , Ramachandruni S. Deepthi , Kakrana Atul , Nakano Mayumi , Meyers Blake C. 
Published: October 2015

Abstract
Summary: We describe miTRATA, the first web-based tool for microRNA Truncation and Tailing Analysis—the analysis of 3′ modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. miTRATA is implemented in Python (version 3) and employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets. It utilizes miRBase, currently version 21, as a source of known microRNAs for analysis. miTRATA notifies user(s) via email to download as well as visualize the results online. miTRATA’s strengths lie in (i) its biologist-focused web interface, (ii) improved scalability via parallel processing and (iii) its uniqueness as a webtool to perform microRNA truncation and tailing analysis.
Availability and implementation: miTRATA is developed in Python and PHP. It is available as a web-based application from https://wasabi.dbi.udel.edu/∼apps/ta/.
Contact: meyers@dbi.udel.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
Authors: Silva Genivaldo Gueiros Z. , Green Kevin T. , Dutilh Bas E. , Edwards Robert A. 
Published: October 2015

Abstract
Summary: Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools.
Availability and implementation: SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS.
Contact: redwards@mail.sdsu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Automatic semantic classification of scientific literature according to the hallmarks of cancer
Authors: Baker Simon , Silins Ilona , Guo Yufan , Ali Imran , Högberg Johan , Stenius Ulla , Korhonen Anna 
Published: October 2015

Abstract
Motivation: The hallmarks of cancer have become highly influential in cancer research. They reduce the complexity of cancer into 10 principles (e.g. resisting cell death and sustaining proliferative signaling) that explain the biological capabilities acquired during the development of human tumors. Since new research depends crucially on existing knowledge, technology for semantic classification of scientific literature according to the hallmarks of cancer could greatly support literature review, knowledge discovery and applications in cancer research.
Results: We present the first step toward the development of such technology. We introduce a corpus of 1499 PubMed abstracts annotated according to the scientific evidence they provide for the 10 currently known hallmarks of cancer. We use this corpus to train a system that classifies PubMed literature according to the hallmarks. The system uses supervised machine learning and rich features largely based on biomedical text mining. We report good performance in both intrinsic and extrinsic evaluations, demonstrating both the accuracy of the methodology and its potential in supporting practical cancer research. We discuss how this approach could be developed and applied further in the future.
Availability and implementation: The corpus of hallmark-annotated PubMed abstracts and the software for classification are available at: http://www.cl.cam.ac.uk/∼sb895/HoC.html .
Contact: simon.baker@cl.cam.ac.uk
CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads
Authors: Borozan Ivan , Ferretti Vincent 
Published: October 2015

Abstract
Summary: Sequence comparison of genetic material between known and unknown organisms plays a crucial role in genomics, metagenomics and phylogenetic analysis. The emerging long-read sequencing technologies can now produce reads of tens of kilobases in length that promise a more accurate assessment of their origin. To facilitate the classification of long and short DNA sequences, we have developed a Python package that implements a new sequence classification model that we have demonstrated to improve the classification accuracy when compared with other state of the art classification methods. For the purpose of validation, and to demonstrate its usefulness, we test the combined sequence similarity score classifier (CSSSCL) using three different datasets, including a metagenomic dataset composed of short reads.
Availability and implementation: Package’s source code and test datasets are available under the GPLv3 license at https://github.com/oicr-ibc/cssscl.
Contact: ivan.borozan@oicr.on.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Jflow: a workflow management system for web applications
Authors: Mariette Jérôme , Escudié Frédéric , Bardou Philippe , Nabihoudine Ibouniyamine , Noirot Céline , Trotard Marie-Stéphane , Gaspin Christine , Klopp Christophe 
Published: October 2015

Abstract
Summary: Biologists produce large data sets and are in demand of rich and simple web portals in which they can upload and analyze their files. Providing such tools requires to mask the complexity induced by the needed High Performance Computing (HPC) environment. The connection between interface and computing infrastructure is usually specific to each portal. With Jflow, we introduce a Workflow Management System (WMS), composed of jQuery plug-ins which can easily be embedded in any web application and a Python library providing all requested features to setup, run and monitor workflows.
Availability and implementation: Jflow is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/jflow. The package is coming with full documentation, quick start and a running test portal.
Contact: Jerome.Mariette@toulouse.inra.fr
Seascape genetics of saithe (Pollachius virens) across the North Atlantic using single nucleotide polymorphisms
Authors: Saha Atal , Hauser Lorenz , Kent Matthew , Planque Benjamin , Neat Francis , Kirubakaran Tina Graceline , Huse Irene , Homrum Eydna Í. , Fevolden Svein-Erik , Lien Sigbjørn , Johansen Torild 
Published: October 2015

AbstractThe identification of isolated populations in widely distributed marine species is often impeded by low levels of genetic differentiation. However, modern genetic approaches now allow for the efficient detection of potentially large numbers of novel genetic variations, thereby improving the power to identify biologically meaningful management units. To investigate the genetic structuring of saithe (Pollachius virens L.), we applied seascape genetic approaches to 131 single nucleotide polymorphism loci genotyped in 584 fish collected from 11 locations across the North Atlantic. Wombling analysis and the Monmonier algorithm revealed four genetic clusters (Barents Sea, Central Northeast Atlantic, Rockall, and Canada) across the species distribution range. These results imply that genetic structuring in saithe may be influenced by abiotic factors such as geographical distance, and bathymetry as well as biotic factors such as sex-biased migration, and natal homing. The results suggest a potential mismatch between management and biological units across the Northeast Atlantic, which may have implications for sustainable exploitation of the species.
Intuitionistic ancestral logic
Authors: Cohen Liron , Constable Robert L 
Published: October 2015

Abstract
In this article we define pure intuitionistic Ancestral Logic ( iAL ), extending pure intuitionistic First-Order Logic ( iFOL ). This logic is a dependently typed abstract programming language with computational functionality beyond iFOL given by its realizer for the transitive closure, TC . We derive this operator from the natural type theoretic definition of TC using intersection. We show that provable formulas in iAL are uniformly realizable, thus iAL is sound with respect to constructive type theory. We further show that iAL subsumes Kleene Algebras with tests and thus serves as a natural programming logic for proving properties of program schemes. We also extract schemes from proofs that iAL specifications are solvable.
Continuing Decline in Varicella Incidence After the 2-Dose Vaccination Recommendation—Connecticut, 2009–2014
Authors: Mullins Jocelyn , Kudish Kathy , Sosa Lynn , Hadler Jim 
Published: October 2015

Abstract
Background.  Varicella is a highly contagious vaccine-preventable illness. In 1996, the Advisory Committee for Immunization Practices recommended 1 dose of vaccine for children, and in 2006 it recommended 2 doses; Connecticut required 1 dose for school entry in 2000 and 2 doses for school entry starting in 2011. Connecticut varicella incidence overall and among persons aged 1–14 years declined during 2005–2008. We analyzed varicella surveillance data for 2009–2014 to characterize overall and age group-specific trends in the setting of the 2-dose requirement.
Methods.  Passive surveillance was used to collect data and identify incidence trends and changes in proportions, and these were assessed by χ2 tests for trend and proportion, respectively.
Results.  Varicella incidence decreased from 13.8 cases/100 000 persons during 2009 to 5.1 cases/100 000 persons during 2014 (P &lt; .001); significant declines in incidence occurred among children aged 1–4, 5–9, and 10–14 years (P &lt; .01 for each age group). Cases classified as preventable decreased from 44% during 2009 to 25% during 2014 (P &lt; .01); significant declines in percentages of preventable cases occurred only among those aged 5–9 years (P &lt; .05) and 10–14 (P &lt; .01) years.
Conclusions.  Varicella incidence continued to decline in Connecticut in the setting of the 2-dose school-entry program. Continued surveillance is needed to assess the full influence of the 2-dose recommendation.