bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAGNA: Maximizing Accuracy in Global Network Alignment
Authors: Saraph Vikram , Milenković Tijana 
Published: July 2014

Abstract
Motivation : Biological network alignment aims to identify similar regions between networks of different species. Existing methods compute node similarities to rapidly identify from possible alignments the high-scoring alignments with respect to the overall node similarity. But, the accuracy of the alignments is then evaluated with some other measure that is different than the node similarity used to construct the alignments. Typically, one measures the amount of conserved edges. Thus, the existing methods align similar nodes between networks hoping to conserve many edges ( after the alignment is constructed!).
Results : Instead, we introduce MAGNA to directly ‘optimize’ edge conservation while the alignment is constructed, without decreasing the quality of node mapping. MAGNA uses a genetic algorithm and our novel function for ‘crossover’ of two ‘parent’ alignments into a superior ‘child’ alignment to simulate a ‘population’ of alignments that ‘evolves’ over time; the ‘fittest’ alignments survive and proceed to the next ‘generation’, until the alignment accuracy cannot be optimized further. While we optimize our new and superior measure of the amount of conserved edges, MAGNA can optimize any alignment accuracy measure, including a combined measure of both node and edge conservation. In systematic evaluations against state-of-the-art methods (IsoRank, MI-GRAAL and GHOST), on both synthetic networks and real-world biological data, MAGNA outperforms all of the existing methods, in terms of both node and edge conservation as well as both topological and biological alignment accuracy.
Availability : Software: http://nd.edu/∼cone/MAGNA
Contact : tmilenko@nd.edu
Supplementary information : Supplementary data are available at Bioinformatics online.
GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination
Authors: Gotz Lou , Abrahams Jodie L. , Mariethoz Julien , Rudd Pauline M. , Karlsson Niclas G. , Packer Nicolle H. , Campbell Matthew P. , Lisacek Frederique 
Published: July 2014

Abstract
Summary: Sequencing oligosaccharides by exoglycosidases, either sequentially or in an array format, is a powerful tool to unambiguously determine the structure of complex N- and O- link glycans. Here, we introduce GlycoDigest, a tool that simulates exoglycosidase digestion, based on controlled rules acquired from expert knowledge and experimental evidence available in GlycoBase. The tool allows the targeted design of glycosidase enzyme mixtures by allowing researchers to model the action of exoglycosidases, thereby validating and improving the efficiency and accuracy of glycan analysis.
Availability and implementation: http://www.glycodigest.org .
Contact: matthew.campbell@mq.edu.au or frederique.lisacek@isb-sib.ch
Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression
Authors: Cheng Chun-Pei , Kuo I-Ying , Alakus Hakan , Frazer Kelly A. , Harismendy Olivier , Wang Yi-Ching , Tseng Vincent S. 
Published: July 2014

Abstract
Motivation: A rapid progression of esophageal squamous cell carcinoma (ESCC) causes a high mortality rate because of the propensity for metastasis driven by genetic and epigenetic alterations. The identification of prognostic biomarkers would help prevent or control metastatic progression. Expression analyses have been used to find such markers, but do not always validate in separate cohorts. Epigenetic marks, such as DNA methylation, are a potential source of more reliable and stable biomarkers. Importantly, the integration of both expression and epigenetic alterations is more likely to identify relevant biomarkers.
Results: We present a new analysis framework, using ESCC progression-associated gene regulatory network (GRN escc ), to identify differentially methylated CpG sites prognostic of ESCC progression. From the CpG loci differentially methylated in 50 tumor–normal pairs, we selected 44 CpG loci most highly associated with survival and located in the promoters of genes more likely to belong to GRN escc . Using an independent ESCC cohort, we confirmed that 8/10 of CpG loci in the promoter of GRN escc genes significantly correlated with patient survival. In contrast, 0/10 CpG loci in the promoter genes outside the GRN escc were correlated with patient survival. We further characterized the GRN escc network topology and observed that the genes with methylated CpG loci associated with survival deviated from the center of mass and were less likely to be hubs in the GRN escc . We postulate that our analysis framework improves the identification of bona fide prognostic biomarkers from DNA methylation studies, especially with partial genome coverage.
Contact: tsengsm@mail.ncku.edu.tw or ycw5798@mail.ncku.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
A new approach for detecting riboswitches in DNA sequences
Authors: Havill Jessen T. , Bhatiya Chinmoy , Johnson Steven M. , Sheets Joseph D. , Thompson Jeffrey S. 
Published: July 2014

Abstract
Motivation : Riboswitches are short sequences of messenger RNA that can change their structural conformation to regulate the expression of adjacent genes. Computational prediction of putative riboswitches can provide direction to molecular biologists studying riboswitch-mediated gene expression.
Results : The Denison Riboswitch Detector (DRD) is a new computational tool with a Web interface that can quickly identify putative riboswitches in DNA sequences on the scale of bacterial genomes. Riboswitch descriptions are easily modifiable and new ones are easily created. The underlying algorithm converts the problem to a ‘heaviest path’ problem on a multipartite graph, which is then solved using efficient dynamic programming. We show that DRD can achieve ∼88–99% sensitivity and &gt;99.99% specificity on 13 riboswitch families.
Availability and implementation : DRD is available at http://drd.denison.edu .
Contact : havill@denison.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing
Authors: Calabrese Claudia , Simone Domenico , Diroma Maria Angela , Santorsola Mariangela , Guttà Cristiano , Gasparre Giuseppe , Picardi Ernesto , Pesole Graziano , Attimonelli Marcella 
Published: July 2014

Abstract
Motivation: The increasing availability of mitochondria-targeted and off-target sequencing data in whole-exome and whole-genome sequencing studies (WXS and WGS) has risen the demand of effective pipelines to accurately measure heteroplasmy and to easily recognize the most functionally important mitochondrial variants among a huge number of candidates. To this purpose, we developed MToolBox, a highly automated pipeline to reconstruct and analyze human mitochondrial DNA from high-throughput sequencing data.
Results: MToolBox implements an effective computational strategy for mitochondrial genomes assembling and haplogroup assignment also including a prioritization analysis of detected variants. MToolBox provides a Variant Call Format file featuring, for the first time, allele-specific heteroplasmy and annotation files with prioritized variants. MToolBox was tested on simulated samples and applied on 1000 Genomes WXS datasets.
Availability and implementation: MToolBox package is available at https://sourceforge.net/projects/mtoolbox/ .
Contact: marcella.attimonelli@uniba.it
Supplementary information: Supplementary data are available at Bioinformatics online.
The China power grid: a network science perspective
Authors: Chen Guanrong (Ron) 
Published: July 2014

Abstract
Power grid is a very large scale and highly non-linear dynamical system, and its stable and reliable operation poses a great challenge to scientists and engineers. As a complex dynamic network has a tendency of catastrophic failure, sophisticated analysis and control are required. In an interview with NSR, Professor Yusheng Xue, member of the Chinese Academy of Engineering, Honorary President of China's State Grid Electric Power Research Institute, talked about the economic impact, technical challenges, and future development of power grid in China.
Alexandria
Authors: Taylor Joan 
Published: July 2014

Founded by Alexander the Great in 331 bce, Alexandria under the Ptolemaic dynasty soon became a unique cultural center that led the Hellenistic world. Cultural interchange created a milieu in which some of the most important Jewish and Christian thinkers would thrive. The Septuagint (lxx) was produced here, largely in the 3rd century bce. With the vibrant intellectual hubs of the Alexandrian museon and library, a distinctive Alexandrian school of philosophy, science, and medicine developed that included such figures as Eratosthenes and Ptolemy. It is likely that many works of Jewish literature written in Greek were composed here, though their provenance cannot be established with certainty. There was a Jewish school of allegorical exegesis, evidenced in the work of Aristobulus and Philo. Paul’s influential associate Apollos came from this city (Acts 18: 24–8). After the uprising of 115–17 ce, when the Alexandrian Jewish community was decimated, allegorical exegesis was continued in the Christian catechetical school, headed by Pantaenus, Clement, and then Origen. Christian teachers such as Basilides, Valentinus, and Isidore were also active in the city. Traditionally the evangelist Mark was said to have died in Alexandria (see, for example, Eusebius, Hist. Eccles. 2: 16, 24), where his tomb was venerated for centuries before his remains were brought to Venice in 828 ce. A useful bibliographical Internet resource for the site may be found online. A remarkable 3-D tour of ancient Alexandria is also provided online.
Caterina Sforza
Authors: de Vries Joyce 
Published: July 2014

Caterina Sforza (b. 1462/63–d. 1509) was the daughter of Galeazzo Maria Sforza (b. 1444–d. 1476), duke of Milan (r. 1467–1476), and his mistress Lucrezia Landriani (b. 1440/45–d. 1507). In 1477, she married Girolamo Riario (b. 1443–d. 1488), nephew of Pope Sixtus IV and ruler of Imola since 1473. He gained possession of Forlì in 1480. Sforza bore at least eight children with Riario, six of whom survived infancy, and she became regent for her son Ottaviano (b. 1479–d. 1533) when Riario was assassinated in 1488. She survived several conspiracies against her rule of Imola and Forlì in the 1490s, and she was deposed only when Cesare Borgia (b. 1475/76–d. 1507) invaded the Romagna region in late 1499. Taken prisoner in early 1500, she was released in July 1501. Sforza moved to Florence, where she plotted to retake the family territories. Neither she nor the Riario family ever resumed power and she died after a long illness in 1509. She was buried in the Murate convent, where she had maintained a cell for spiritual retreat. Sforza’s political cunning and forceful rule fascinated many in early modern Italy, including Niccolò Machiavelli, who came to Forlì in 1499 to negotiate her son Ottaviano’s military contract with Florence. In The Prince, Machiavelli highlights Sforza’s use of fortresses for protection. His version of her actions after Riario’s assassination in 1488 did much to promote her reputation as a sexually bold and merciless ruler. By all accounts, when Sforza entered the Rocca di Ravaldino to facilitate its surrender to the rebels, she instead mounted the ramparts with the intention to rule and challenged her enemies to kill her children, who were hostages. According to Machiavelli, in the Discourses, she then lifted her skirts to reveal her genitals, a gesture meant to emphasize her claim that she could bear more children, who would eventually avenge Riario’s murder. This purported act is an exaggeration of her actions, but this version of the events remains influential as part of her legend. Sforza has often been cast as an exceptional woman not only because of her long regency, but also because of her sexual independence during her widowhood and regency. Without a husband or father to patrol her sexuality, Sforza inspired many rumors about possible sexual partners. During her widowhood, she did indeed maintain relationships with at least two men, whom she claimed after their deaths to have married. Giacomo Feo (b. 1470–d. 1495) achieved much power in her court and was assassinated. They had a son, Carlo (b. 1490–d. 1550s). The second, Giovanni di Pierfrancesco de’ Medici (b. 1467–d. 1498), of the cadet branch of the Florentine family, did not gain political power and died of natural causes. During her final years in Florence, Sforza won custody of their son, Giovanni (b. 1498–d. 1526). She then oversaw his education and estates, and he grew up to became a famous military commander in Italy, known as Giovanni dalle Bande Nere, and father of the future duke of Florence, Cosimo I de’ Medici (b. 1519–d. 1574). Sforza’s Medici connections augmented her fame after her death.
Low Multiplicity of HIV-1 Infection and No Vaccine Enhancement in VAX003 Injection Drug Users
Authors: Sterrett Sarah , Learn Gerald H. , Edlefsen Paul T. , Haynes Barton F. , Hahn Beatrice H. , Shaw George M. , Bar Katharine J. 
Published: July 2014

AbstractBackground.  We performed human immunodeficiency virus type 1 (HIV-1) transmitted/founder (T/F) virus analysis of the VAX003 vaccine efficacy trial participants to characterize the transmission bottleneck and test for vaccine-associated reduction or enhancement of infection in this injection drug user (IDU) cohort.Methods.  We performed single genome sequencing of plasma vRNA from 50 subjects sampled in early HIV infection. Sequences were analyzed phylogenetically, T/F viruses enumerated, and a sieve analysis performed.Results.  Eight of 19 (42%) placebo recipients were productively infected by more than 1 virus (range 1–5, median 1, mean 1.7). This frequency of multiple virus transmission was greater than reported for heterosexual cohorts (19%, P = .03) but not statistically different from vaccine recipients (22.6%, P &gt; .05), where the range was 1–3, median 1, and mean 1.3 (P &gt; .05 for all comparisons). An atypical sieve effect was detected in Env V2 but was not associated with reduction or enhancement of virus acquisition.Conclusions.  The number of T/F viruses in IDUs was surprising low, with 95% of individuals infected by only 1–3 viruses. This finding suggests that a successful vaccine or other prevention modality generally needs to protect against only one or a few viruses regardless of risk behavior. T/F analysis ide.jpegied an atypical genetic sieve in the V2 region of Envelope and found no evidence for vaccine-mediated enhancement in VAX003.
Discovery of an overlapping cluster in the Abell 1674 field with Suzaku
Authors: Inoue Shota , Hayashida Kiyoshi , Akamatsu Hiroki , Ueda Shutaro , Nagino Ryo , Tsunemi Hiroshi , Tawa Noriaki , Koyama Katsuji 
Published: July 2014

Abstract
We present the results of a Suzaku observation of Abell 1674, an optically very rich (richness class 3) cluster cataloged as z = 0.1066. We discover the He-like Fe K-shell line from the central region for the first time, and find that the X-ray spectrum yields a high redshift of $0.215^{+0.007}_{-0.006}$. On the other hand, the spectrum of the south-western region is fitted with a redshift of 0.11 ± 0.02 by the He-like Fe L-shell lines, consistent with the optically determined value. The gas temperature, metal abundance, and core radius of the X-ray emission in the central region are 3.8 ± 0.2 keV, 0.20 ± 0.05 Z⊙, and 450 ± 40 kpc, respectively, while those in the south-western region are 2.0 ± 0.2 keV, $0.41^{+0.17}_{-0.13}\,Z$⊙, and $220^{+90}_{-70}$ kpc, respectively. These parameters are typical for clusters. We thus conclude that Abell 1674 consists of two independent clusters, A 1674-C at z ∼ 0.22 and A 1674-SW at z ∼ 0.11, overlapping along the line of sight. The X-ray luminosity of A 1674-C within r = 2 Mpc is (15.9 ± 0.6) × 1043 erg s−1 in the 0.1–2.4 keV energy band, while that for A 1674-SW is (1.25 ± 0.07) × 1043 erg s−1. Both are consistent with those expected from the L–T relation of clusters within a factor of 2. This is another supporting factor for our conclusion.
A plea for evidence in ecosystem service science: a framework and its application
Authors: Mupepele Anne-Christine , Dormann Carsten F. 
Published: July 2014

AbstractThe ecosystem service concept is at the interface of ecology, economics and politcs, with scientific results rapidly translated into management or political action. This emphasises the importance ofreliable recommendationsprovided by scientist. We propose to use evidence-based practice in ecosystem service science in order to evaluate and improve the reliability of scientific statements. For this purpose, we introduce a level-of-evidence scale ranking study designs (e.g. review, case-control, descriptive) in combination with a study quality checklist. For illustration, the concept was directly applied to 12 case studies. We also review criticisms levered against evidence-based practice and how it applies to ecosystem services science. We further discuss who should use the evidence-based concept and suggest important next steps, with a focus on the development of guidelines for methods used in ecosystem service assessments.
Chromosomal distribution of cyto-nuclear genes in a dioecious plant with sex chromosomes
Authors: Hough Josh , Ågren J. Arvid , Barrett Spencer C. H. , Wright Stephen I. 
Published: July 2014

AbstractThe coordination between nuclear and organellar genes is essential to many aspects of eukaryotic life, including basic metabolism, energy production, and ultimately, organismal fitness. Whereas nuclear genes are bi-parentally inherited, mitochondrial and chloroplast genes are almost exclusively maternally inherited, and this asymmetry may lead to a bias in the chromosomal distribution of nuclear genes whose products act in the mitochondria or chloroplasts. In particular, because X-linked genes have a higher probability of co-transmission with organellar genes (2/3) compared to autosomal genes (1/2), selection for co-adaptation has been predicted to lead to an over-representation of nuclear-mitochondrial and nuclear-chloroplast genes on the X chromosome relative to autosomes. In contrast, the occurrence of sexually antagonistic organellar mutations might lead to selection for movement of cyto-nuclear genes from the X chromosome to autosomes to reduce male mutation load. Recent broad-scale comparative studies of N-mt distributions in animals have found evidence for these hypotheses in some species, but not others. Here, we use transcriptome sequences to conduct the first study of the chromosomal distribution of cyto-nuclear interacting genes in a plant species with sex chromosomes (Rumex hastatulus; Polygonaceae). We found no evidence of under- or over-representation of either N-mt or N-cp genes on the X chromosome, and thus no support for either the co-adaptation or the sexual-conflict hypothesis. We discuss how our results from a species with recently evolved sex chromosomes fit into an emerging picture of the evolutionary forces governing the chromosomal distribution of nuclear-mitochondrial and nuclear-chloroplast genes.
Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI’s RNA-seq archive
Authors: Olarerin-George Anthony O. , Hogenesch John B. 
Published: July 2014

ABSTRACTMycoplasmas are notorious contaminants of cell culture and can have profound effects on host cell biology by depriving cells of nutrients and inducing global changes in gene expression. Because they are small, they can escape filtration in culture media. Because they lack cell walls, they are resistant to commonly used antibiotics. Over the last two decades, sentinel testing has revealed wide-ranging contamination rates in mammalian culture. To obtain an unbiased assessment from hundreds of labs, we analyzed sequence data from 9395 rodent and primate samples from 884 series (or projects) in the NCBI Sequence Read Archive. We found 11% of these series were contaminated (defined as ≥ 100 reads/million mapping to mycoplasma in one or more samples). Ninety percent of mycoplasma-mapped reads aligned to ribosomal RNA. Interestingly, series using poly(A)-selection, which should bias against mycoplasma detection, had comparable contamination rates as non-poly(A)-selected series. We also examined the relationship between mycoplasma contamination and host gene expression in a single cell RNA-seq dataset and found 61 host genes (P< 0.001) were significantly associated with mycoplasma-mapped read counts. Lastly, to estimate the potential economic cost of this widespread contamination, we queried NIH RePORTER to find grants with the terms “cell culture” or “cell lines”. Funding for these totaled over $3 billion, suggesting hundreds of millions of dollars in research are potentially affected. In all, this study suggests mycoplasma contamination is still prevalent today and poses substantial risk to research quality, with considerable financial consequences.
Ligation-anchored PCR unveils immune repertoire of TCR-beta from whole blood
Authors: Gao Fan , Wang Kai 
Published: July 2014

AbstractBackgroundAs one of the genetic mechanisms for adaptive immunity, V(D)J recombination generates an enormous repertoire of T-cell receptors (TCRs). With the development of high-throughput sequencing techniques, systematic exploration of V(D)J recombination becomes possible. Multiplex PCR method has been previously developed to assay immune repertoire, however the usage of primer pools has inherent bias in target amplification. In our study, we developed a ligation-anchored PCR method to unbiasedly amplify the repertoire.ResultsBy utilizing a universal primer paired with a single primer targeting the conserved constant region, we amplified TCR-beta (TRB) variable regions from total RNA extracted from blood. Next-generation sequencing libraries were then prepared for Illumina HiSeq 2500 sequencer, which provided 151 bp read length to cover the entire V(D)J recombination region. We evaluated this approach on blood samples from patients with malignant and benign meningiomas. Mapping of sequencing data showed 64% to 91% of mapped TCRV-containing reads belong to TRB subtype. An increased usage of TRBV29-1 was observed in malignant meningiomas. Also distinct signatures were identified from CDR3 sequence logos, with predominant subset as 42 nt for benign and 45 nt for malignant samples, respectively.ConclusionsIn summary, we report an integrative approach to monitor immune repertoire in a systematic manner.
Discovery of a bifunctional acyltransferase responsible for ornithine lipid synthesis in Serratia proteamaculans
Authors: Vences‐Guzmán Miguel Ángel , Guan Ziqiang , Escobedo‐Hinojosa Wendy Itzel , Bermúdez‐Barrientos José Roberto , Geiger Otto , Sohlenkamp Christian 
Published: July 2014

SummaryOrnithine lipids (OLs) are phosphorus‐free membrane lipids that can be formed by many bacteria but that are absent from archaea and eukaryotes. A function for OLs in stress conditions and in host–bacteria interactions has been shown in some bacteria. Some bacterial species have been described that can form OLs, but lack the known genes (olsBA) involved in its biosynthesis, which implied the existence of a second pathway. Here we describe the bifunctional protein OlsF from Serratia proteamaculans involved in OL formation. Expression of OlsF and its homologue from Flavobacterium johnsoniae in Escherichia coli causes OL formation. Deletion of OlsF in S. proteamaculans caused the absence of OL formation. Homologues of OlsF are widely distributed among γ‐, δ‐ and ε‐Proteobacteria and in the Cytophaga‐Flavobacterium‐Bacteroidetes group of bacteria, including several well‐studied pathogens for which the presence of OLs has not been suspected, such as for example Vibrio cholerae and Klebsiella pneumonia. Using genomic data, we predict that about 50% of bacterial species can form OLs.