bluuebunny/crossref_metadata_2025_split huggingface dataset:
A method for finding consensus breakpoints in the cancer genome from copy number data
Authors: Toloşi Laura , Theißen Jessica , Halachev Konstantin , Hero Barbara , Berthold Frank , Lengauer Thomas 
Published: May 2013

Abstract
Motivation: Recurrent DNA breakpoints in cancer genomes indicate the presence of critical functional elements for tumor development. Identifying them can help determine new therapeutic targets. High-dimensional DNA microarray experiments like arrayCGH afford the identification of DNA copy number breakpoints with high precision, offering a solid basis for computational estimation of recurrent breakpoint locations.
Results: We introduce a method for identification of recurrent breakpoints (consensus breakpoints) from copy number aberration datasets. The method is based on weighted kernel counting of breakpoints around genomic locations. Counts larger than expected by chance are considered significant. We show that the consensus breakpoints facilitate consensus segmentation of the samples. We apply our method to three arrayCGH datasets and show that by using consensus segmentation we achieve significant dimension reduction, which is useful for the task of prediction of tumor phenotype based on copy number data. We use our approach for classification of neuroblastoma tumors from different age groups and confirm the recent recommendation for the choice of age cut-off for differential treatment of 18 months. We also investigate the (epi)genetic properties at consensus breakpoint locations for seven datasets and show enrichment in overlap with important functional genomic regions.
Availability: Implementation in R of our approach can be found at http://www.mpi-inf.mpg.de/ ∼laura/FeatureGrouping.html.
Contact: laura@mpi-inf.mpg.de.
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Leaf Spot Disease Caused by Glomerella magna on Lobelia chinensis in China
Authors: Li Q. L. , Mo J. Y. , Huang S. P. , Guo T. X. , Pan Z. B. , Ning P. , Hsiang T. 
Published: May 2013

Lobelia chinensis is a perennial herbaceous plant in the family Campanulaceae that is native to China, where it grows well in moist to wet soils. It is commonly used as a Chinese herbal medicine. In May 2012, symptoms of leaf spot were observed on leaves of L. chinensis in Nanning, Guangxi Zhuang Autonomous Region, China. The leaf lesions began as small, water-soaked, pale greenish to grayish spots, which enlarged to gray to pale yellowish spots, 4 to 6 mm in diameter. At later stages, numerous acervuli appeared on the lesions. Acervuli were mostly epiphyllous, and 40 to 196 μm in diameter. On potato dextrose agar (PDA), a fungus was consistently recovered from symptomatic leaf samples, with a 93% isolation rate from 60 leaf pieces that were surface sterilized in 75% ethanol for 30 s and then in 0.1% mercuric chloride for 45 s. Three single-spore isolates were used to evaluate cultural and morphological characteristics of the pathogen. Setae were two to three septate, dark brown at the base, acicular, and up to 90 μm long. Conidia were long oblong-elliptical, guttulate, hyaline, and 11 to 20 × 4.1 to 6.3 μm (mean 15.2 × 5.1 μm). These morphological characteristics of the fungus were consistent with the description of Colletotrichum magna (teleomorph Glomerella magna Jenkins & Winstead) (1). The rDNA internal transcribed spacer (ITS) region of one isolate, LC-1, was sequenced (GenBank Accession No. KC815123), and it showed 100% identity to G. magna, GenBank HM163187.1, an isolate from Brazil cultured from papaya (2). Although KC815123 was identified as G. magna, it shows 99% identity to GenBank sequences from isolates of C. magna, and more research is needed to elucidate the relationships between these taxa, especially with consideration to host specificity. Pathogenicity tests were performed with each of the three isolates by spraying conidial suspensions (1 × 106 conidia/ml) containing 0.1% Tween 20 onto the surfaces of leaves of 30-day-old and 6- to 8-cm-high plants. For each isolate, 30 leaves from five replicate plants were treated. Control plants were treated with sterilized water containing 0.1% Tween 20. All plants were incubated for 36 h at 25°C and 90% relative humidity in an artificial climate chamber, and then moved into a greenhouse. Seven days after inoculation, gray spots typical of field symptoms were observed on all inoculated leaves, but no symptoms were seen on water-treated control plants. Koch's postulates were fulfilled by reisolation of G. magna from diseased leaves. To our knowledge, this is the first report of G. magna infecting L. chinensis worldwide. References: (1) M. Z. Du et al. Mycologia 97:641, 2005. (2) R. J. Nascimento et al. Plant Dis. 94:1506, 2010.
First Report of ‘Candidatus Phytoplasma solani’ Strains Associated with Grapevine Bois Noir in Jordan
Authors: Salem N. M. , Quaglino F. , Abdeen A. , Casati P. , Bulgari D. , Alma A. , Bianco P. A. 
Published: May 2013

During a survey carried out in Jordanian vineyards in August and October 2012, grapevine (Vitis vinifera L.) plants showing typical grapevine yellows (GY) disease symptoms, including leaf discoloration and curling, berry shriveling, and irregular maturation of wood, were observed. In the same vineyards, bindweed (Convolvulus arvensis L.) plants showing stunting and leaf chromatic alteration were found, suggesting the involvement of phytoplasmas in the disease etiology. Using a CTAB method, total DNA was extracted from leaf veins of 25 symptomatic and two asymptomatic grapevines, and from five symptomatic and two asymptomatic bindweeds for PCR analysis. DNAs from periwinkle (Catharanthus roseus (L.) G. Don) plants infected by ‘Ca. Phytoplasma asteris’ strain SAY (group 16SrI), ‘Ca. Phytoplasma solani’ strain STOL (group 16SrXII), and ‘Ca. Phytoplasma ulmi’ strain EY1 (group 16SrV), were used as positive controls. DNAs from healthy periwinkle and reactions without template DNA were employed as negative controls. 16S rDNA nested PCRs, carried out using the primer pairs P1/P7, followed by R16F2n/R16R2 (1), yielded an amplicon of the expected size (1,250-bp) in three grapevine and in five bindweed samples, and in positive controls. Amplicons were not produced with DNA from 22 symptomatic grapevines (probably because samples were collected late in the growing season and phytoplasma distribution in plants was non-uniform [2]); nor from asymptomatic plants and negative controls. PCR products were sequenced by commercial services in Italy (Primm, Milan) and Korea (Macrogen Inc., Soul). Representative 16S rDNA nucleotide sequences were deposited in NCBI GenBank with accessions KC835139 (from grapevine) and KC835140 (from bindweed). The 16S rDNA nucleotide sequences of phytoplasmas identified in grapevine and bindweed in Jordan shared >99.5% sequence identity with ‘Ca. Phytoplasma solani’ reference strain STOL (AF248959), and carried identical STOL-unique signature sequences and distinguishing sequence blocks (3). Phylogenetic and in silico RFLP analyses confirmed the affiliation of phytoplasma strains identified in grapevine and bindweed in Jordan to the species ‘Ca. Phytoplasma solani’ (subgroup 16SrXII-A), opening an avenue to future studies on the dissemination and impact of Bois noir (BN) in Jordan. These studies may add new information about BN, previously reported in neighboring countries (4). Further studies will investigate the role of Hyalesthes obsoletus Signoret, a polyphagous Cixiidae responsible for the BN phytoplasma transmission in Europe, and other possible insect vector(s) in the BN spread in Jordan. References: (1) I.-M. Lee et al. Int. J. Syst. Bact. 48:1153, 1998. (2) F. E. Constable et al. Plant Pathol. 52:267, 2003. (3) F. Quaglino et al. Int. J. Syst. Evol. Microb. 63:2879. (4) E. Choueiri et al. Plant Dis. 86:697, 2002.
First Report of Sweet potato leaf curl Georgia virus on Sweet Potato in China
Authors: Qin Y. , Zhang Z. , Qiao Z. , Qiao Q. , Zhang D. , Tian Y. , Wang S. 
Published: May 2013

Begomoviruses infecting sweet potato (Ipomoea batatas) are phylogenetically distinct from other members of the genus Begomovirus, and have been named “sweepoviruses” (1). Sweepoviruses cause sweet potato yield losses and cultivar decline, and have been found in China (1,3). In 2011, a survey was conducted to determine the incidence, genetic diversity, and distribution of sweepoviruses in China. Thirty sweet potato cuttings showing upward leaf curl, leaf roll, chlorosis, and stunting were collected from fields in Jiangsu, Guangxi, Guizhou, Shanxi, Henan, and Hebei Provinces. Five-leaf growth stage I. setosa plants were inoculated by side-grafting with scions from these samples, and grown in an insect-proof greenhouse in 20-cm-diameter clay pots. Each sample was grafted onto three replicate plants. Healthy, non-grafted I. setosa plants were used as the negative control treatment. Total nucleic acids were extracted from 100 mg fresh leaves harvested 30 days post-inoculation (dpi) from symptomatic and negative control plants using the Universal Genomic DNA Extraction Kit (TaKaRa, Dalian, China). Universal primers for amplification of Geminiviruses (BM-V [5′-KSGGGTCGACGTCATCAATGACGTTRTAC-3′] and BM-C [5′-AARGAATTCATKGGGGCCCARARRGACTGGC-3′]) (2) were used to amplify the begomovirus A component by PCR assay. A DNA fragment of the expected size (2.8 kb) was obtained from grafted leaf samples of the Hebei Province plant, and was cloned into the pMD-19T vector (TaKaRa). The recombinant plasmid was transformed into competent cells of Escherichia coli strain JM109, and the inserted fragment sequenced. The nucleotide sequence obtained (GenBank Accession No. JX448368) was 2,785 nt long, and contained two open reading frames (ORFs) in the virion sense, and four ORFs in the complementary sense, similar to other monopartite begomoviruses (1). The sequence was compared with sequences in GenBank using BLAST. The results revealed the greatest nucleotide sequence identity, 90.8%, with that of the Sweet potato leaf curl Georgia virus (SPLCGV) from Georgia, United States (AF326775). The sequence also shared identities of <89% with other sweepoviruses, and was therefore designated SPLCGV-China: Hebei: 2011. Comparison of the complete genome sequence of SPLCGV-China: Hebei: 2011 with SPLCGV revealed an 18 nucleotide insertion between AV-1 and AC-3. The results confirmed that the sweet potato sample from which SPLCGV-China: Hebei: 2011 was obtained was infected with SPLCGV. To our knowledge, this is the first report of the natural occurrence of SPLCGV in China. This study will assist with understanding the presence of this virus and genetic diversity of sweepoviruses in China. References: (1) H. P. Bi and P. Zhang. Arch. Virol. 157:441, 2012. (2) R. W. Briddon and P. G. Markham. Mol. Biotechnol. 1:202, 1994. (3) Y. S. Luan et al. Virus Genes 35:379, 2007.
Towards tacit knowledge sharing over social web tools
Authors: Panahi Sirous , Watson Jason , Partridge Helen 
Published: May 2013

PurposeResearchers debate whether tacit knowledge sharing through information technology (IT) is actually possible. However, with the advent of social web tools, it has been argued that most shortcomings of tacit knowledge sharing are likely to disappear. The purpose of this paper is two‐fold: first, to demonstrate the existing debates in the literature regarding tacit knowledge sharing using IT; and second, to identify key research gaps that lay the foundations for future research into tacit knowledge sharing using the social web.Design/methodology/approachThis paper reviews current literature on IT‐mediated tacit knowledge sharing and opens a discussion on tacit knowledge sharing through the use of the social web.FindingsFirst, the existing schools of thought in regards to IT ability for tacit knowledge sharing are introduced. Next, difficulties of sharing tacit knowledge through the use of IT are discussed. Then, potentials and pitfalls of social web tools are presented. Finally, the paper concludes that whilst there are significant theoretical arguments supporting the notion that the social web facilitates tacit knowledge sharing there is a lack of empirical evidence to support these arguments and further work is required.Research limitations/implicationsThe limitations of the review include: covering only papers that were published in English, issues of access to full texts of some resources, and the possibility of missing some resources due to search strings used or limited coverage of databases searched.Originality/valueThe paper contributes to the fast growing literature on the intersection of KM and IT particularly by focusing on tacit knowledge sharing in social media space. The paper highlights the need for further studies in this area by discussing the current situation in the literature and disclosing the emerging questions and gaps for future studies.
Study on enterprise knowledge sharing in ESN perspective: a Chinese case study
Authors: Zhao Rong‐ying , Chen Bi‐kun 
Published: May 2013

PurposeAn enterprise social network (ESN) is part of the landscape of information reform by enterprises, using Web 2.0. In terms of the marketing targets of typical Web 2.0 techniques, enterprise knowledge sharing in Web 2.0 can be classified into different types (individual interaction type, group interaction type, social interaction type, real‐time interaction type and delay interaction type). The purpose of this paper is to summarize the features and modes of different enterprises' knowledge sharing and study enterprise knowledge sharing quantitatively from an ESN perspective by selecting real‐time interaction type as the case.Design/methodology/approachBecause of the area of research, the authors supplemented social network analysis (SNA) with a mathematical modeling method and additional in‐depth interviews.FindingsThe Web 2.0 era provides the opportunity to quantify knowledge sharing. Also, SNA can quantitatively and visually diagnose the knowledge sharing status of the enterprise and guide the enterprise's knowledge‐sharing process.Research limitations/implicationsOnly a case study regarding real‐time interaction type is presented; other types of interaction are not studied empirically.Practical implicationsSNA, combined with a mathematical modeling method and additional in‐depth interviews with team leaders or key managers in organizations, can diagnose quantitatively, visually and comprehensively the knowledge‐sharing status of the enterprise.Originality/valueThis paper systematically summarizes the features and modes of Web 2.0 enterprise knowledge sharing, and the multiple‐method research design represents a sound approach to targeting enterprise knowledge sharing.
The biomechanical basis of evolutionary change in a territorial display
Authors: Ord Terry J. , Collar David C. , Sanger Thomas J. 
Published: May 2013

SummaryFew studies have examined how the anatomy of an animal signal contributes to, or limits, the evolution of signal differentiation among closely related species.InAnolislizards, adult males extend a large, conspicuous dewlap as part of a territorial advertisement display. Males of species from the island of Jamaica rely on the rapid extension of the dewlap to facilitate display detection by territorial neighbours and conspecific females. Males of other species on the island of Puerto Rico extend the dewlap at considerably slower speeds and instead rely on other strategies to maintain an effective display. What initially prompted this divergence in display between the islands is unknown, but evidence suggests that it may have something to do with the way the dewlap is extended during display.Our goal was to determine whether an innovation in the dewlap lever in Jamaican lineages, but absent in Puerto Rican lineages, accounted for the evolution of the high‐speed dewlap on Jamaica. We began by modelling the performance of theAnolisdewlap as a first‐order lever system. We then simulated changes to this system relating to its morphology, articulation and input force in biologically realistic ways to predict how such changes impact dewlap speed. Finally, we compared these predictions with data on the morphology of the dewlap lever system from museum specimens and actual dewlap speed recorded for lizards in the field.This investigation revealed that changes to the dewlap lever have affected the performance of the dewlap display in at least two ways. Within islands, structural changes to the hyoid morphology seem to have led to differences in dewlap speed among species. Between islands, however, differences in dewlap speed were most likely the result of a major increase in muscle contraction velocity that powers the dewlap extension in Jamaican species, but has not originated in species on Puerto Rico.Our study shows how the biomechanics of a social signal can have important implications for understanding why closely related species might differ in signal behaviour, despite apparent similarities in the selection pressures that act on the signal.
Forensic Facial Comparison: Issues of Admissibility in the Development of Novel Analytical Technique
Authors: Mallett Xanthé , Evison Martin P. 
Published: May 2013

AbstractMuch contemporary debate in forensic science concerns validity and admissibility of scientific evidence in court. In this paper, three current approaches to facial identification—image superimposition, photogrammetry, and morphological analysis—are considered with regard to criteria for scientific evidence in the United States, and England, and Wales. The aim of the paper is to assess the extent to which facial image comparison meets criteria of admissibility in these jurisdictions. The method used is a comparative evaluation of the methods of facial image comparison and their underlying premises against the range of admissibility criteria reported in court rulings and relevant judicial and scientific inquiries in the United States and the United Kingdom. While the techniques of facial image comparison are generally accepted within their practitioner communities, they are not tested, and their error rates are unknown. On that basis, the methods of facial image comparison would appear not to meet the anticipated standards. They are, nevertheless, admitted in court in the United States, and England, and Wales. This paper concludes that further research in science and law will be necessary to more definitively establish admissibility of facial image comparison evidence, as it will for other nascent and novel methods that are potentially influential in court proceedings.
The all‐ceramic, inlay supported fixed partial denture. Part 4. Fracture surface analyses of an experimental model, all‐ceramic, inlay supported fixed partial denture
Authors: Thompson MC , Sornsuwan T , Swain MV 
Published: May 2013

AbstractBackgroundIn the previous three papers, the authors sought to conduct a thorough analysis of the feasibility for the use of zirconia in inlay supported, fixed partial dentures via finite element analysis (FEA). Correlating the response of the numerical model against the experimental model has never been satisfactorily performed for an anatomically accurate ceramic bridge; such validation is crucial if the results from the FEA are to be confidently relied upon. Part 4 of this series is a detailed fractographic analysis of the zirconia bridge that was the model for the experimental validation, performed in order to confirm the fracture origin/s and fracture trajectory as predicted from the FEA.MethodsEstablished fractographic techniques involving optical examination followed by examination with scanning electron microscopy were conducted. The porous, granular surface of zirconia (both partially and fully sintered) does not lend itself to easy surface analysis but the classic fractographic signs (hackle lines, wake hackle lines and compression curl) are present. Use of linear fracture elastic mechanics allowed the calculation of theoretical critical flaw size and a comparison to two defects or inclusions found at the primary origin of fracture.ResultsExcellent agreement between the fracture sites and paths of travel as predicted in the numerical analysis exist with fractographic analysis. Furthermore, the calculated critical flaw size of 30 μm to 40 μm equates very well with defects seen at the general vicinity of the primary fracture origin and the general observed size of critical flaws in machined ceramics which range between 20 μm to 50 μm, thus providing further confirmation.ConclusionsThe fractographic analysis detailed in this study provides validation of the ‘zones of failure’ as predicted in our FEA. Additionally, the excellent correlation between the calculated critical flaw size and the defects observed at the primary fracture site demonstrates that field of experimental mechanics is a powerful predictive tool.
Parental knowledge and attitudes towards dental radiography for children
Authors: Chiri R , Awan S , Archibald S , Abbott PV 
Published: May 2013

AbstractBackgroundRadiographs are an essential part of most clinical dental examinations and diagnoses. The aim of the study was to assess the knowledge and attitudes of parents towards dental radiographs for their children.MethodsA 21‐item questionnaire, covering parental level of radiation knowledge and socio‐demographics was applied. Sliding scales were used to assess attitude towards dental radiographs.ResultsThere were 1467 questionnaires distributed between five primary schools in the Perth (Western Australia) metropolitan area, with 309 surveys (21%) returned for collection. Most parents displayed a low level of knowledge, but had a positive attitude towards dental radiographs. Parents with children who have previously had dental radiographs perceived dental radiographs as ‘good’, ‘useful’ and ‘pleasant’. A higher level of education and parents with children who have previously had radiographs were significantly associated with a higher level of knowledge about dental radiography. Parents who had higher scores on questions assessing radiation knowledge were more likely to perceive dental radiographs as ‘safe’ and ‘beneficial’.ConclusionsMost parents have a positive attitude towards dental radiographs on their children. However, the majority of parents lack knowledge regarding dental radiography, especially regarding the risks involved.
Transarterial chemoembolization in hepatocellular carcinoma with vascular invasion or extrahepatic metastasis: A systematic review
Authors: Zhao Yan , Cai Guohong , Zhou Lin , Liu Lei , Qi Xingshun , Bai Ming , Li Yongping , Fan Daiming , Han Guohong 
Published: May 2013

AbstractAimsAdvanced hepatocellular carcinoma (HCC) with vascular invasion or extrahepatic metastasis has been considered a contraindication for transarterial chemoembolization (TACE) treatment according to Barcelona Clinic Liver Cancer (BCLC) staging classification. However, real clinical practice varies among different countries. In recent years another opinion has been developing that considers that TACE can be safely performed in advanced HCC patients.MethodsAll studies on the efficacy of TACE for patients with advanced HCC were identified via the PubMed database. The primary items were TACE and HCC.ResultsWe identified 15 studies in the treatment of TACE in advanced HCC patients. Most adverse events reported were treated successfully and in these studies there were no procedure‐related deaths within 4 weeks of the TACE treatment. Four controlled studies reported that TACE increased survival rate and prolonged overall survival compared with conservative management. The most frequent prognostic factors were liver function and the degree of portal vein tumor thrombosis.ConclusionTACE can be safely performed in advanced HCC patients with vascular invasion or extrahepatic spread and may improve their overall survival. Patients with portal vein branch invasion and well‐preserved liver function seemed to derive optimal benefit from treatment with TACE. Further studies are needed to provide strong evidence of the efficacy of TACE for advanced HCC patients to update the BCLC staging system.