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Search Results: 1 - 10 of 746 matches for " Serena Scollen "
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Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design
Helen I Field, Serena A Scollen, Craig Luccarini, Caroline Baynes, Jonathan Morrison, Alison M Dunning, Douglas F Easton, Paul DP Pharoah
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-180
Abstract: We created Seq4SNPs, a web-based, walk-away software that can process one to several hundred SNPs given rs numbers as input. It outputs a file of fully annotated sequences formatted for one of three proprietary design softwares: TaqMan's Primer-By-Design FileBuilder, Sequenom's iPLEX or SNPstream's Autoprimer, as well as unannotated fasta sequences. We found genotyping assays to be inhibited by repetitive sequences or the presence of additional variations flanking the SNP under test, and in multiplexes, repetitive sequence flanking one SNP adversely affects multiple assays. Assay design software programs avoid such regions if the input sequences are appropriately annotated, so we used Seq4SNPs to provide suitably annotated input sequences, and improved our genotyping success rate. Adjacent SNPs can also be avoided, by annotating sequences used as input for primer design.The accuracy of annotation by Seq4SNPs is significantly better than manual annotation (P < 1e-5).Using Seq4SNPs to incorporate all annotation for additional SNPs and repetitive elements into sequences, for genotyping assay designer software, minimizes assay failure at the design stage, reducing the cost of genotyping. Seq4SNPs provides a rapid route for replacement of poor test SNP sequences. We routinely use this software for assay sequence preparation.Seq4SNPs is available as a service at http://moya.srl.cam.ac.uk/oncology/bio/s4shome.html webcite and http://moya.srl.cam.ac.uk/cgi-bin/oncology/srl/ncbi/seq4snp1.pl webcite, currently for human SNPs, but easily extended to include any species in dbSNP.A survey of single nucleotide polymorphism (SNP) and primer design software reveals several packages that align EST or genome sequences to discover SNPs [1-6]. SNP-VISTA visualizes SNPs from aligned genome sequences [7]. Other packages take a chromosome region then use recorded SNP genotypes, and additional information, to reduce the set of SNPs that need genotyping [[8,9] and references therein]. SNP i
Common variants in the ATM, BRCA1, BRCA2, CHEK2 and TP53 cancer susceptibility genes are unlikely to increase breast cancer risk
Caroline Baynes, Catherine S Healey, Karen A Pooley, Serena Scollen, Robert N Luben, Deborah J Thompson, Paul DP Pharoah, Douglas F Easton, Bruce AJ Ponder, Alison M Dunning, the SEARCH breast cancer study
Breast Cancer Research , 2007, DOI: 10.1186/bcr1669
Abstract: We have attempted a comprehensive, single nucleotide polymorphism (SNP)- and haplotype-tagging association study on each of these five genes in up to 4,474 breast cancer cases from the British, East Anglian SEARCH study and 4,560 controls from the EPIC-Norfolk study, using a two-stage study design. Nine tag SNPs were genotyped in ATM, together with five in BRCA1, sixteen in BRCA2, ten in CHEK2 and five in TP53, with the aim of tagging all other known, common variants. SNPs generating the common amino acid substitutions were specifically forced into the tagging set for each gene.No significant breast cancer associations were detected with any individual or combination of tag SNPs.It is unlikely that there are any other common variants in these genes conferring measurably increased risks of breast cancer in our study population.Four of the genes which lie in the DNA damage-recognition and repair pathway, ATM, BRCA1, BRCA2 and TP53, have mutations that are recognised to increase breast cancer susceptibility with moderate to high penetrance. Such mutations are very rare, and most probably of recent origin. A fifth gene, CHEK2, in the same pathway, has a deletion (1100delC) that reaches polymorphic frequencies (>0.01) in some European countries and doubles the risk of breast cancer in female carriers [1]. Together these mutations account for only a small proportion (2% to 5%) of all breast cancer incidences [2,3]. Breast cancer is, however, a common disease and genetic epidemiological data suggest that there is a low-penetrance genetic contribution to most cases [4,5]. It is likely that at least a part of breast cancer aetiology will fit the common disease-common variant hypothesis, which states that patients with a common, complex disease are likely to share some common, low-penetrance alleles that increase their susceptibility to that disease. This raises the question of whether such common, polymorphic susceptibility alleles exist within these five genes in addition t
You Don’t Know Me But Can I Be Your Friend? Accepting Strangers as Friends in Facebook  [PDF]
Serena Leow, Zuoming Wang
Social Networking (SN) , 2019, DOI: 10.4236/sn.2019.81004
Abstract:
Users in social networking sites, such as Facebook, are increasingly receiving friend requests from strangers. This study examines the effects of the Big Five personality traits (Neurotics vs. Extroversion vs. Openness vs. Conscientiousness vs. Agreeableness) and strangers’ gender in affecting Facebook users’ decisions to accept (or ignore) the stranger’s friend request. Results showed that gender of the stranger and the personality match between participant and stranger jointly affect the decision to accept the stranger as friend on Facebook. Most of the participants accepted the stranger’s friend request based on textual cues that were displayed in the friend request message. This finding supported Social Information Processing theory, suggesting that impression formation of the stranger was not constrained to the lack of nonverbal cues online. Moreover, participants were more likely to accept the stranger’s friend request when the participant’s and stranger’s personalities matched. This effect was more pronounced when the stranger was a female. Participants accepted female stranger’s friend request due to the inflated perception of stereotypical female characteristics, which supports the Hyperpersonal Perspective.
Genes Contributing to Pain Sensitivity in the Normal Population: An Exome Sequencing Study
Frances M. K. Williams,Serena Scollen,Dandan Cao,Yasin Memari,Craig L. Hyde,Baohong Zhang,Benjamin Sidders,Daniel Ziemek,Yujian Shi,Juliette Harris,Ian Harrow,Brian Dougherty,Anders Malarstig,Robert McEwen,Joel C. Stephens,Ketan Patel,Cristina Menni,So-Youn Shin,Dylan Hodgkiss,Gabriela Surdulescu,Wen He,Xin Jin,Stephen B. McMahon,Nicole Soranzo equal contributor,Sally John equal contributor,Jun Wang equal contributor ,Tim D. Spector equal contributor
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1003095
Abstract: Sensitivity to pain varies considerably between individuals and is known to be heritable. Increased sensitivity to experimental pain is a risk factor for developing chronic pain, a common and debilitating but poorly understood symptom. To understand mechanisms underlying pain sensitivity and to search for rare gene variants (MAF<5%) influencing pain sensitivity, we explored the genetic variation in individuals' responses to experimental pain. Quantitative sensory testing to heat pain was performed in 2,500 volunteers from TwinsUK (TUK): exome sequencing to a depth of 70× was carried out on DNA from singletons at the high and low ends of the heat pain sensitivity distribution in two separate subsamples. Thus in TUK1, 101 pain-sensitive and 102 pain-insensitive were examined, while in TUK2 there were 114 and 96 individuals respectively. A combination of methods was used to test the association between rare variants and pain sensitivity, and the function of the genes identified was explored using network analysis. Using causal reasoning analysis on the genes with different patterns of SNVs by pain sensitivity status, we observed a significant enrichment of variants in genes of the angiotensin pathway (Bonferroni corrected p = 3.8×10?4). This pathway is already implicated in animal models and human studies of pain, supporting the notion that it may provide fruitful new targets in pain management. The approach of sequencing extreme exome variation in normal individuals has provided important insights into gene networks mediating pain sensitivity in humans and will be applicable to other common complex traits.
The Abusir Drill Core Survey, Egypt
Serena Love
Papers from the Institute of Archaeology , 2001, DOI: 10.5334/pia.158
Abstract:
Questioning the Location of the Old Kingdom Capital of Memphis, Egypt
Serena Love
Papers from the Institute of Archaeology , 2003, DOI: 10.5334/pia.201
Abstract: The capital city of Memphis was ancient Egypt’s oldest and largest city. However, the city’s origin is shrouded in myth. This study challenges five different references to Memphis, from both classical and historical accounts and concludes that Memphis’ boundary should be redefined. These accounts are reviewed to illustrate the confusion amongst early historians and travellers as to the precise location of Memphis and to highlight the association between the capital and the pyramids of the Giza Plateau. For the Old Kingdom, the urban limits of Memphis should not be restricted to the modern mound of Mit Rahina, but rather the boundaries should be expanded to parallel the Old Kingdom pyramids. Recent archaeological investigations, employing sub-surface sampling techniques, have revealed contemporary Old Kingdom occupational debris scattered throughout the entire Memphite region. The inclusion of archaeological material, in combination with the historical records, will create a different interpretation for Egypt’s Old Kingdom capital city.
The Role of Open Web Standards for Website Development Adhering to the One Web Vision
Serena Pastore
International Journal of Engineering and Technology , 2012,
Abstract: Information dissemination is essential for every organization that needs to increase its visibility. This is valid for educational or research institutes and businesses. Websites are actually the usual way to promote information considering that modern websites are web-based systems composed by several software layers implementing different functionalities. Nowadays, a plethora of web –based content management systems (WCMs), commercial and open-source, provide similar capabilities. The paper highlights the trends in modern website development considering actual open web standards and the particular features of the mobile framework. Approaches include responsive web design techniques and custom mobile sites. Web content should be accessible everywhere, anytime and with whatever devices, which means it should be visualized and processed in the same way regardless of the type of device used, the physical location of the user, and the communication network used at the time. Mobile users’ behavior has a great influence on website development, but open web standards should be adopted in web design to ensure a long-term growth towards the era of the Future Internet.
La situazione attuale della letteratura digitale in Germania
Serena Alcione
LEA : Lingue e Letterature d'Oriente e d'Occidente , 2013,
Abstract:
The Ironies of Comparison : Comparative Literature and the Re-Production of Cultural Difference between East and West
Serena Fusco
Trans : Revue de Littérature Générale et Comparée , 2006,
Abstract: La Littérature Comparée en tant que discipline est aujourd’hui reconnue comme fondamentalement eurocentrique et principalement ancrée dans l’étude des grands canons littéraires européens. Malgré cette tradition, la discipline fait actuellement des efforts pour s’ouvrir à des langues, à des littératures et à des cultures non occidentales. Dans cet article, nous essayerons de comprendre certains enjeux de la Littérature Comparée en tant que discipline potentielle de rencontre entre Est et Ouest, en prenant en considération la Chine comme sujet et objet de discussion. Comparative Literature as a discipline is nowadays recognized as fundamentally Eurocentric and prevalently grounded in the study of “high” European literary canons. In spite of this history, it tries to open itself to non-Western languages, literatures and cultures. In this article, I shall attempt to address some of the stakes of Comparative Literature as a field potentially spanning East and West, taking into consideration China as a subject/object of discourse in its relationship to the discipline. En tanto disciplina, a la literatura comparada se le considera fundamentalmente como eurocéntrica, ancrada sobre todo en el estudio de los “grandes” cánones literarios europeos. A pesar de dicha tradición, la disciplina lleva a cabo un esfuerzo para abrirse a lenguas, a literaturas, a culturas no occidentales. En este artículo intentaremos comprender algunos de los alcances de la Literatura Comparada como disciplina a través de la que se pueden encontrar Oriente y Occidente, tomando a China como tema y objeto de discusión.
The Dance of the Dead Rhino: William Kentridge’s Magic Flute
Serena Guarracino
Altre Modernità , 2010,
Abstract: The article offers a reading of the staging of The Magic Flute by visual artist William Kentridge, focusing on his introduction of the rhino in the visual landscape of the opera as symbol for the silenced subject of violence. Operatic tradition has always been concerned with the staging of death, in particular with the death of its female protagonists, and recent scholarship has highlighted the complicity of the genre with the ideology of Western patriarchy and colonial violence. In this light, Kentridge's appropriation stages Mozart's opera as both voice of colonial Europe and place of resistance for the postcolonial artist. Kentridge moves the setting of the opera to colonial Africa, and the Flute becomes haunted with the massacre of the Herero people in South West Africa by the German army led by general von Trotha (1904-1907). The African white rhino, a species under the threat of extinction, works in this work as proxy for the missing corpses of the Herero people; in its being subject to humiliation and ruthless murder, it recalls Judith Butler's recent attempt at a different categorization of human life as both a continuous exposure to violence and what can be mourned after death. With its silence among the powerful sounds of Mozart's opera, the body of the dead, dancing rhino stands at the centre of Kentridge's work, which becomes a ceremony of mourning where the Western canon can be made to "resonate differently" (Trinh T. Minh-ha).
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