bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of ALMA Band 4 (125–163 GHz) receiver
Authors: Asayama Shin’ichiro , Takahashi Toshikazu , Kubo Kouichi , Ito Tetsuya , Inata Motoko , Suzuki Takakiyo , Wada Toru , Soga Tomio , Kamada Chiyoshi , Karatsu Miki , Fujii Yumi , Obuchi Yoshiyuki , Kawashima Susumu , Iwashita Hiroyuki , Uzawa Yoshinori 
Published: June 2014

Abstract
We have developed a dual-polarization receiver for Band 4 of the Atacama Large Millimeter/submillimeter Array (ALMA). Band 4, which covers the 125 to 163 GHz spectral window, is one of the ten bands that form the ALMA Front End. The Band 4 receiver consists of three elements: a warm optics, a cold cartridge assembly, and a warm cartridge assembly. The cold cartridge includes a feed horn, an orthomode transducer, sideband-separating (2SB) superconductor–insulator–superconductor mixers, cold intermediate frequency (IF) amplifiers, IF isolators, bias-protection circuit boards, and component interconnections. The IF bandwidth is 4–8 GHz. The first eight receivers manufactured as preproduction models have demonstrated excellent performance within the stringent ALMA requirements. Stable astronomical fringes and closure phase have been successfully achieved during field performance tests of the Band 4 receivers installed in the ALMA antennas. Our well-established Band 4 receivers will contribute to various fields of astronomical research, such as the detection of high-redshift galaxies, characterization of cold molecular medium in normal field galaxies, and astrochemistry including observations of deuterated species.
A comparative study of infrared asteroid surveys: IRAS, AKARI, and WISE
Authors: Usui Fumihiko , Hasegawa Sunao , Ishiguro Masateru , Müller Thomas G. , Ootsubo Takafumi 
Published: June 2014

Abstract
We present a comparative study of three infrared asteroid surveys based on the size and albedo data from the Infrared Astronomical Satellite (IRAS), the Japanese infrared satellite AKARI, and the Wide-field Infrared Survey Explorer (WISE). Our study showed that: (i) the total number of asteroids detected with diameter and albedo information with these three surveyors is 138285, which is largely contributed by WISE; (ii) the diameters and albedos measured by the three surveyors for 1993 commonly detected asteroids are in good agreement, and within ±10% in diameter and ±22% in albedo at 1 σ deviation level. It is true that WISE offers size and albedo of a large fraction (&gt; 20%) of known asteroids down to bodies of a few km, but we would suggest that the IRAS and AKARI catalogs compensate for larger asteroids up to several hundred km, especially in the main belt region. We discuss the complementarity of these three catalogs in order to facilitate the use of these data sets for characterizing the physical properties of minor planets.
Cyclosporine Protects the Heart during Aortic Valve Surgery
Authors: Chiari Pascal , Angoulvant Denis , Mewton Nathan , Desebbe Olivier , Obadia Jean-François , Robin Jacques , Farhat Fadi , Jegaden Olivier , Bastien Olivier , Lehot Jean-Jacques , Ovize Michel 
Published: June 2014

Abstract

Background:
Part of the myocardial damage occurring during cardiac surgery is a consequence of reperfusion injury. Cyclosporine, a potent inhibitor of the opening of the mitochondrial permeability transition pore, attenuates reperfusion injury in patients with acute ST-segment elevation myocardial infarction. This study investigated whether the administration of cyclosporine just before the aortic cross-unclamping would reduce myocardial injury in patients undergoing aortic valve surgery.

Methods:
This study was a monocentric, prospective, randomized, single-blinded, controlled trial. Sixty-one patients, scheduled for elective aortic valve surgery, were randomly assigned (computer-generated randomization sequence) to receive either an intravenous bolus of cyclosporine (2.5 mg/kg, cyclosporine group, n = 30) or normal saline (control group, n = 31) 10 min before aortic cross-unclamping. The primary endpoint was the 72-h area under the curve for cardiac troponin I.

Results:
Both groups were similar with respect to baseline characteristics and aortic cross-clamping duration. A significant 35% reduction of area under the curve for cardiac troponin I was observed in the cyclosporine group compared with the control group (242 ± 225 vs. 155 ± 71 arbitrary units, mean ± SD; mean difference, −86.2 ± 42.5; 95% CI, −172.3 to −0.1; P = 0.03). Cyclosporine beneficial effect remained significant after adjustment for aortic cross-clamping duration in each group (mean difference, −88 ± 34, 95% CI, −157 to −19; P = 0.01). None of the treated patients had significant side effects (odds ratio, 0.64; 95% CI, 0.16 to 2.55; P = 0.52).

Conclusions:
Cyclosporine administration at the time of reperfusion protects against reperfusion injury in patients undergoing aortic valve surgery. The clinical benefit of this protection requires confirmation in a larger clinical trial.
Effects of Dexamethasone on Cognitive Decline after Cardiac Surgery
Authors: Ottens Thomas H. , Dieleman Jan M. , Sauër Anne-Mette C. , Peelen Linda M. , Nierich Arno P. , de Groot Welmer J. , Nathoe Hendrik M. , Buijsrogge Marc P. , Kalkman Cor J. , van Dijk Diederik 
Published: June 2014

Abstract

Background:
Cardiac surgery can be complicated by postoperative cognitive decline (POCD), which is characterized by impaired memory function and intellectual ability. The systemic inflammatory response that is induced by major surgery and cardiopulmonary bypass may play an important role in the etiology of POCD. Prophylactic corticosteroids to attenuate the inflammatory response may therefore reduce the risk of POCD. The authors investigated the effect of intraoperative high-dose dexamethasone on the incidence of POCD at 1 month and 12 months after cardiac surgery.

Methods:
This multicenter, randomized, double-blind, placebo-controlled trial is a preplanned substudy of the DExamethasone for Cardiac Surgery trial. A total of 291 adult patients undergoing cardiac surgery with cardiopulmonary bypass were recruited in three hospitals and randomized to receive dexamethasone 1 mg/kg (n = 145) or placebo (n = 146). The main outcome measures were incidence of POCD at 1- and 12-month follow-up, defined as a decline in neuropsychological test performance beyond natural variability, as measured in a control group.

Results:
At 1-month follow-up, 19 of 140 patients in the dexamethasone group (13.6%) and 10 of 138 patients in the placebo group (7.2%) fulfilled the diagnostic criteria for POCD (relative risk, 1.87; 95% CI, 0.90 to 3.88; P = 0.09). At 12-month follow-up, 8 of 115 patients in the dexamethasone group (7.0%) and 4 of 114 patients (3.5%) in the placebo group had POCD (relative risk, 1.98; 95% CI, 0.61 to 6.40; P = 0.24).

Conclusion:
Intraoperative high-dose dexamethasone did not reduce the risk of POCD after cardiac surgery.
Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq
Authors: Gonzàlez-Porta Mar , Brazma Alvis 
Published: June 2014

AbstractIn the past years, RNA sequencing has become the method of choice for the study of transcriptome composition. When working with this type of data, several tools exist to quantify differences in splicing across conditions and to address the significance of those changes. However, the number of genes predicted to undergo differential splicing is often high, and further interpretation of the results becomes a challenging task. Here we present SwitchSeq, a novel set of tools designed to help the users in the interpretation of differential splicing events that affect protein coding genes. More specifically, we provide a framework to identify switch events,i.e.,cases where, for a given gene, the identity of the most abundant transcript changes across conditions. The identified events are then annotated by incorporating information from several public databases and third-party tools, and are further visualised in an intuitive manner with the independent R package tviz. All the results are displayed in a self-contained HTML document, and are also stored in txt and json format to facilitate the integration with any further downstream analysis tools. Such analysis approach can be used complementarily to Gene Ontology and pathway enrichment analysis, and can also serve as an aid in the validation of predicted changes in mRNA and protein abundance.Availability: The latest version of SwitchSeq, including installation instructions and use cases, can be found athttps://github.com/mgonzalezporta/SwitchSeq. Additionally, the plot capabilities are provided as an independent R package athttps://github.com/mgonzalezporta/tviz.
Avoiding test set bias with rank-based prediction
Authors: Patil Prasad , Bachant-Winner Pierre-Olivier , Haibe-Kains Benjamin , Leek Jeffrey T. 
Published: June 2014

AbstractBackgroundPrior to applying genomic predictors to clinical samples, the genomic data must be properly normalized. The most effective normalization methods depend on the data from multiple patients. From a biomedical perspective this implies that predictions for a single patient may change depending on which other patient samples they are normalized with. This test set bias will occur when any cross-sample normalization is used before clinical prediction.MethodsWe developed a new prediction modeling framework based on the relative ranks of features within a sample in order to prevent the need for cross-sample normalization, therefore effectively avoiding test set bias. We employed modeling with previously published Top-Scoring Pairs (TSPs) methodology to build the rank-based predictors. We further investigated the robustness of the rank-based models in case of heterogeneous datasets using diverse microarray technologies.ResultsWe demonstrated that results from existing genetic signatures which rely on normalizing test data may be unreproducible when the patient population changes composition or size. Using pairwise comparisons of features, we produced a ten gene, platform-robust, and interpretable alternative to the PAM50 subtyping signature and evaluated the robustness of our signature across 6,297 patients samples from 28 curated breast cancer microarray datasets spanning 15 different platforms.ConclusionWe propose a new approach to developing genomic signatures that avoids test set bias through the robustness of rank-based features. Our small, interpretable alternative to PAM50 produces comparable predictions and patient survival differentiation to the original signature. Additionally, we are able to ensure that the same patient will be classified the same way in every context.
iRAP - an integrated RNA-seq Analysis Pipeline
Authors: Fonseca Nuno A. , Petryszak Robert , Marioni John C. , Brazma Alvis 
Published: June 2014

AbstractRNA-sequencing (RNA-Seq) has become the technology of choice for whole-transcriptome profiling. However, processing the millions of sequence reads generated requires considerable bioinformatics skills and computational resources. At each step of the processing pipeline many tools are available, each with specific advantages and disadvantages. While using a specific combination of tools might be desirable, integrating the different tools can be time consuming, often due to specificities in the formats of input/output files required by the different programs.Here we present iRAP, an integrated RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression, testing for differential expression. iRAP also includes multiple tools for gene set enrichment analysis and generates web browsable reports of the results obtained in the different stages of the pipeline. Depending upon the application, iRAP can be used to quantify expression at the gene, exon or transcript level. iRAP is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line. Despite this, it also provides more advanced users with the ability to customise the options used by their chosen tools.iRAP is available under General Public License 3 (GPLv3) and although it should be portable to any POSIX-compliant operating system, several third party programs only run on Linux. iRAP can be obtained fromhttp://code.google.com/p/irap.
Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression
Authors: Frazee Alyssa C. , Jaffe Andrew E. , Langmead Ben , Leek Jeffrey T. 
Published: June 2014

AbstractMotivationStatistical methods development for differential expression analysis of RNA sequencing (RNA-seq) requires software tools to assess accuracy and error rate control. Since true differential expression status is often unknown in experimental datasets, artificially-constructed datasets must be utilized, either by generating costly spike-in experiments or by simulating RNA-seq data.ResultsPolyesteris an R package designed to simulate RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads. Its main advantage is the ability to simulate reads indicating isoform-level differential expression across biological replicates for a variety of experimental designs. Data generated by Polyester is a reasonable approximation to real RNA-seq data and standard differential expression workflows can recover differential expression set in the simulation by the user.Availability and ImplementationPolyesteris freely available from Bioconductor (http://bioconductor.org/).Contactjtleek@gmail.comSupplementary InformationSupplementary figures are available online.
Testing the Toxicofera: comparative reptile transcriptomics casts doubt on the single, early evolution of the reptile venom system
Authors: Hargreaves Adam D , Swain Martin T , Logan Darren W , Mulley John F 
Published: June 2014

AbstractBackgroundThe identification of apparently conserved gene complements in the venom and salivary glands of a diverse set of reptiles led to the development of the Toxicofera hypothesis – the idea that there was a single, early evolution of the venom system in reptiles. However, this hypothesis is based largely on relatively small scale EST-based studies of only venom or salivary glands and toxic effects have been assigned to only some of these putative Toxcoferan toxins in some species. We set out to investigate the distribution of these putative venom toxin transcripts in order to investigate to what extent conservation of gene complements may reflect a bias in previous sampling efforts.ResultsWe have carried out the first large-scale test of the Toxicofera hypothesis and found it lacking in a number of regards. Our quantitative transcriptomic analyses of venom and salivary glands and other body tissues in five species of reptile, together with the use of available RNA-Seq datasets for additional species shows that the majority of genes used to support the establishment and expansion of the Toxicofera are in fact expressed in multiple body tissues and most likely represent general maintenance or “housekeeping” genes. The apparent conservation of gene complements across the Toxicofera therefore reflects an artefact of incomplete tissue sampling. In other cases, the identification of a non-toxic paralog of a gene encoding a true venom toxin has led to confusion about the phylogenetic distribution of that venom component.ConclusionsVenom has evolved multiple times in reptiles. In addition, the misunderstanding regarding what constitutes a toxic venom component, together with the misidentification of genes and the classification of identical or near-identical sequences as distinct genes has led to an overestimation of the complexity of reptile venoms in general, and snake venom in particular, with implications for our understanding of (and development of treatments to counter) the molecules responsible for the physiological consequences of snakebite.
A comparison of the gobiid fauna between a shoal and an island habitat in the central Visayas (Philippines)
Authors: Stiefel Klaus M. , Merrifield Alistair , Reed Matt , Joyce David B. 
Published: June 2014

We surveyed the marine gobies of Malapascua island (Philippines), the surrounding islets and the nearby Monad shoal. We found 59 species in 19 genera, including 2 undescribed species of the genusTrimma, and 3 geographic and 6 depth range expansions. Furthermore we describe a new type of mimicry between the gobyKoumasetta hectoriand the cardinalfishApogon nigrofasciatus. The comparison of the island versus shoal goby fauna showed a lesser species richness of shrimp-associated gobies at the shoal. This likely reflects the fact that hydrodynamic features of the environment play a dominant role in selecting which gobiid species, or their symbiotic shrimp, will be found in a certain location. We also observed a bias towards hovering species (of the genusTrimma) and away from shrimp-associated gobies at greater depths. These findings are in accord with the suspected shift of gobies towards planctotrophy with increasing depth.We furthermore compare this study to previous surveys of goby faunas, and plot the recorded species numbers against the survey areas. This species-area plot provides support for the notion of high speciation rates in gobies due to their low mobility.
Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function
Authors: Mulley John F , Hargreaves Adam D , Hegarty Matthew J , Heller R. Scott , Swain Martin T 
Published: June 2014

AbstractBackgroundUnderstanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles, although the lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancreas, particularly with respect to their “unusual” energy metabolism (where ketone bodies and amino acids are the main oxidative fuel source) and their paradoxical ability to both maintain stable blood glucose levels and tolerate extensive periods of hypoglycemia. In order to shed light on some of these processes we have carried out the first large-scale comparative transcriptomic survey of multiple cartilaginous fish tissues: the pancreas, brain and liver of the lesser spotted catshark,Scyliorhinus canicula.ResultsWe generated a mutli-tissue assembly comprising 86,006 contigs, of which 44,794 were assigned to a particular tissue or combination of tissue based on mapping of sequencing reads. We have characterised transcripts encoding genes involved in insulin regulation, glucose sensing, transcriptional regulation, signaling and digestion, as well as many peptide hormone precursors and their receptors for the first time. Comparisons to published mammalian pancreas transcriptomes reveals that mechanisms of glucose sensing and insulin regulation used to establish and maintain a stable internal environment are conserved across jawed vertebrates and likely pre-date the vertebrate radiation. Conservation of pancreatic hormones and genes encoding digestive proteins support the single, early evolution of a distinct pancreatic gland with endocrine and exocrine functions in vertebrates, although the peptide diversity of the early vertebrate pancreas has been overestimated as a result of the use of cross-reacting antisera in earlier studies. A three hormone islet organ is therefore the basal vertebrate condition, later elaborated upon only in the tetrapod lineage.ConclusionsThe cartilaginous fish are a great untapped resource for the reconstruction of patterns and processes of vertebrate evolution and new approaches such as those described in this paper will greatly facilitate their incorporation into the rank of “model organism”.
Efficient isolation of specific genomic regions retaining molecular interactions by the iChIP system using recombinant exogenous DNA-binding proteins
Authors: Fujita Toshitsugu , Fujii Hodaka 
Published: June 2014

AbstractBackgroundComprehensive understanding of mechanisms of genome functions requires identification of molecules interacting with genomic regions of interestin vivo. We have developed the insertional chromatin immunoprecipitatin (iChIP) technology to isolate specific genomic regions retaining molecular interactions and identify their associated molecules. iChIP consists of locus-tagging and affinity purification. The recognition sequences of an exogenous DNA-binding protein such as LexA are inserted into a genomic region of interest in the cell to be analyzed. The exogenous DNA-binding protein fused with a tag(s) is expressed in the cell and the target genomic region is purified with antibody against the tag(s). In this study, we developed the iChIP system using recombinant DNA-binding proteins to make iChIP more straightforward.ResultsIn this system, recombinant 3xFNLDD-D (r3xFNLDD-D) consisting of the 3xFLAG-tag, a nuclear localization signal, the DNA-binding domain plus the dimerization domain of the LexA protein, and the Dock-tag is used for isolation of specific genomic regions. 3xFNLDD-D was expressed using a silkworm-baculovirus expression system and purified by affinity purification. iChIP using r3xFNLDD-D could efficiently isolate the single-copy chickenPax5(cPax5) locus, in which LexA binding elements were inserted, with negligible contamination of other genomic regions. In addition, we could detect RNA associated with the cPax5locus using this form of the iChIP system combined with RT-PCR.ConclusionsThe iChIP system using r3xFNLDD-D can isolate specific genomic regions retaining molecular interactions without expression of the exogenous DNA-binding protein in the cell to be analyzed. iChIP using r3xFNLDD-D would be more straightforward and useful for analysis of specific genomic regions to elucidate their functions.
Polyamine Oxidase5 Regulates Arabidopsis Growth through Thermospermine Oxidase Activity
Authors: Kim Dong Wook , Watanabe Kanako , Murayama Chihiro , Izawa Sho , Niitsu Masaru , Michael Anthony J. , Berberich Thomas , Kusano Tomonobu 
Published: June 2014

Abstract
The major plant polyamines (PAs) are the tetraamines spermine (Spm) and thermospermine (T-Spm), the triamine spermidine, and the diamine putrescine. PA homeostasis is governed by the balance between biosynthesis and catabolism; the latter is catalyzed by polyamine oxidase (PAO). Arabidopsis (Arabidopsis thaliana) has five PAO genes, AtPAO1 to AtPAO5, and all encoded proteins have been biochemically characterized. All AtPAO enzymes function in the back-conversion of tetraamine to triamine and/or triamine to diamine, albeit with different PA specificities. Here, we demonstrate that AtPAO5 loss-of-function mutants (pao5) contain 2-fold higher T-Spm levels and exhibit delayed transition from vegetative to reproductive growth compared with that of wild-type plants. Although the wild type and pao5 are indistinguishable at the early seedling stage, externally supplied low-dose T-Spm, but not other PAs, inhibits aerial growth of pao5 mutants in a dose-dependent manner. Introduction of wild-type AtPAO5 into pao5 mutants rescues growth and reduces the T-Spm content, demonstrating that AtPAO5 is a T-Spm oxidase. Recombinant AtPAO5 catalyzes the conversion of T-Spm and Spm to triamine spermidine in vitro. AtPAO5 specificity for T-Spm in planta may be explained by coexpression with T-Spm synthase but not with Spm synthase. The pao5 mutant lacking T-Spm oxidation and the acl5 mutant lacking T-Spm synthesis both exhibit growth defects. This study indicates a crucial role for T-Spm in plant growth and development.