Big data and other challenges in the quest for orthologs.

Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking. AVAILABILITY AND IMPLEMENTATION: All such materials are available at http://questfororthologs.org. CONTACT: erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac.uk.

Accounting for Big City Growth in Low Paid Occupations: Immigration and/or Service Class Consumption

Growth of 'global cities' in the 1980s was supposed to have involved an occupational polarisation, including growth of low paid service jobs. Though held to be untrue for European cities, at the time, some such growth did emerge in London a decade later than first reported for New York. The question is whether there was simply a delay before London conformed to the global city model, or whether another distinct cause was at work in both cases. This paper proposes that the critical factor in both cases was actually an upsurge of immigration from poor countries providing an elastic supply of cheap labour. This hypothesis and its counterpart based on growth in elite jobs are tested econometrically for the British case with regional data spanning 1975-2008, finding some support for both effects, but with immigration from poor countries as the crucial influence in late 1990s London. Keywords: regional labour markets; wages; employment; international migration; consumer demand JEL Codes: J21, J23, F22, R12

Small changes, big benefits

Being overweight is a major health problem for Northern Ireland. This leaflet helps the public assess whether or not they are overweight and contains useful information on what to do about it, including identifying healthy options, setting targets, getting active and staying motivated.

Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue.

Background: The purpose of the work reported here is to test reliable molecular profiles using routinely processed formalin-fixed paraffin-embedded (FFPE) tissues from participants of the clinical trial BIG 1-98 with a median follow-up of 60 months. Methods: RNA from fresh frozen (FF) and FFPE tumor samples of 82 patients were used for quality control, and independent FFPE tissues of 342 postmenopausal participants of BIG 1-98 with ER-positive cancer were analyzed by measuring prospectively selected genes and computing scores representing the functions of the estrogen receptor (eight genes, ER_8), the progesterone receptor (five genes, PGR_5), Her2 (two genes, HER2_2), and proliferation (ten genes, PRO_10) by quantitative reverse transcription PCR (qRT-PCR) on TaqMan Low Density Arrays. Molecular scores were computed for each category and ER_8, PGR_5, HER2_2, and PRO_10 scores were combined into a RISK_25 score. Results: Pearson correlation coefficients between FF- and FFPE-derived scores were at least 0.94 and high concordance was observed between molecular scores and immunohistochemical data. The HER2_2, PGR_ 5, PRO_10 and RISK_25 scores were significant predictors of disease free-survival (DFS) in univariate Cox proportional hazard regression. PRO_10 and RISK_25 scores predicted DFS in patients with histological grade II breast cancer and in lymph node positive disease. The PRO_10 and PGR_ 5 scores were independent predictors of DFS in multivariate Cox regression models incorporating clinical risk indicators; PRO_10 outperformed Ki-67 labeling index in multivariate Cox proportional hazard analyses. Conclusions: Scores representing the endocrine responsiveness and proliferation status of breast cancers were developed from gene expression analyses based on RNA derived from FFPE tissues. The validation of the molecular scores with tumor samples of participants of the BIG 1-98 trial demonstrates that such scores can serve as independent prognostic factors to estimate disease free survival (DFS) in postmenopausal patients with estrogen receptor positive breast cancer.

The advantage of letrozole over tamoxifen in the BIG 1-98 trial is consistent in younger postmenopausal women and in those with chemotherapy-induced menopause.

Letrozole, an aromatase inhibitor, is ineffective in the presence of ovarian estrogen production. Two subpopulations of apparently postmenopausal women might derive reduced benefit from letrozole due to residual or returning ovarian activity: younger women (who have the potential for residual subclinical ovarian estrogen production), and those with chemotherapy-induced menopause who may experience return of ovarian function. In these situations tamoxifen may be preferable to an aromatase inhibitor. Among 4,922 patients allocated to the monotherapy arms (5 years of letrozole or tamoxifen) in the BIG 1-98 trial we identified two relevant subpopulations: patients with potential residual ovarian function, defined as having natural menopause, treated without adjuvant or neoadjuvant chemotherapy and age ≤ 55 years (n = 641); and those with chemotherapy-induced menopause (n = 105). Neither of the subpopulations examined showed treatment effects differing from the trial population as a whole (interaction P values are 0.23 and 0.62, respectively). Indeed, both among the 641 patients aged ≤ 55 years with natural menopause and no chemotherapy (HR 0.77 [0.51, 1.16]) and among the 105 patients with chemotherapy-induced menopause (HR 0.51 [0.19, 1.39]), the disease-free survival (DFS) point estimate favoring letrozole was marginally more beneficial than in the trial as a whole (HR 0.84 [0.74, 0.95]). Contrary to our initial concern, DFS results for young postmenopausal patients who did not receive chemotherapy and patients with chemotherapy-induced menopause parallel the letrozole benefit seen in the BIG 1-98 population as a whole. These data support the use of letrozole even in such patients.

Big and Little OER

Much of the attention around OERs has been on institutional projects which make explicit learning content available. These can be classified as 'big OER' but another form of OER is that of small scale, individually produced resources using web 2.0 type services, which are classified as 'little OER'. This paper examines some of the differences between the use of these two types of OER to highlight issues in open education. These include attitudes towards reputation, the intentionality of the resource, models of sustainability, the implicit affordances of resources and the context of their hosting sites.

Trisecció de divisors sobre corbes hiperel·líptiques de gènere 2

La criptografia amb corbes el·liptiques i hiperel·líptiques ha adquirit un gran interès en els últims anys. Per a determinar si una corba és bona criptogràficament és necessari, en el cas d'una corba el·liptica trobar el cardinal del grup de punts i, en el cas d'una corba hiperel·líptica trobar el cardinal de la varietat jacobiana. En aquest treball donem mètodes per trobar els trisecats d'un divisor d'una corba de gènere 2. Això ens permetrà determinar el subgrup de 3-Sylow i trobar la major potencia de 3 que divideix al cardinal de la seva Jacobiana, obtenin així informació sobre aquest cardinal.

Big brother is watching you: eavesdropping to resolve family conflicts

Adult animals can eavesdrop on behavioral interactions between potential opponents to assess their competitive ability and motivation to contest resources without interacting directly with them. Surprisingly, eavesdropping is not yet considered as an important factor used to resolve conflicts between family members. In this study, we show that nestling barn owls (Tyto alba) competing for food eavesdrop on nestmates' vocal interactions to assess the dominance status and food needs of opponents. During a first training playback session, we broadcasted to singleton bystander nestlings a simulated vocal interaction between 2 prerecorded individuals, 1 relatively old (i.e., senior) and 1 younger nestling (i.e., junior). One playback individual, the "responder," called systematically just after the "initiator" playback individual, hence displaying a higher hunger level. To test whether nestlings have eavesdropped on this interaction, we broadcasted the same prerecorded individuals separately in a subsequent playback test session. Nestlings vocalized more rapidly after former initiators' than responders' calls and they produced more calls when the broadcasted individual was formerly a junior initiator. They chiefly challenged vocally juniors and initiators against whom the likelihood of winning a vocal contest is higher. Owlets, therefore, identified the age hierarchy between 2 competitors based on their vocalizations. They also memorized the dynamics of competitors' previous vocal interactions, and used this information to optimally adjust signaling level once interacting with only 1 of the competitor. We conclude that siblings eavesdrop on one another to resolve conflicts over parental resources.

The Big Band Theory : català col·loquial i humor científic. Proposta de traducció del capítol pilot

Aquest treball elabora una proposta de traducció per al doblatge del capítol pilot de The Big Bang Theory, que combina llenguatge col•loquial i llenguatge científic.L’objectiu és doble: elaborar un llenguatge col•loquial creïble però a la vegada genuí i emprar els equivalents catalans adequats per als termes científics originals.

Mielikuvien luominen traileroinnilla : tutkimuskohteena Big Brother Suomi

The thesis studies the launch campaign of Big Brother Finland, especially from the viewpoint of on-air promotion. Interest to the subject arose when participating in the campaign as an on-air promotion planner together with Subtv's marketing director, on-air promotion editor and the channel's advertising agency. The launch of the campaign was a challenge due to the format, since not a lot of information can be revealed before the start of the program. When the planning started, all the material consisted of two logos. The first season of the Finnish version of Big Brother begun on Subtv August 2005. The goal of the program was to become a topic of discussion on TV on the fall 2005 and to raise the profile of the channel. The goal of the launch was to get good ratings for the first episode. The launch campaign was also supposed to open up the format to the viewers and to arouse interest in the show. Secrecy and the size of the program were set to be the marketing tones of the launch. Although partly different messages were told via on-air promotion and external media, the campaign was congruent in visual design. In the study, interviews of Subtv's staff, campaign plans and notes were used as research material. From the aspect of affecting images and emotions, the finished campaign promos and other on-air elements were analyzed. In on-air promotion, all choices in audio and visual design affect the outcome and therefore the images that the viewer constructs. The two promo series were made to affect emotions and to awaken curiosity. Other on-air elements were merely used to present program information. The campaign and the series were accepted with enthusiasm. The launch of the second season was even more massive than the first. Participation in the launch campaign of Big Brother Finland was an essential experience in the development of professional identity. When one has taken part in the creation of a massive campaign from scarce materials, tools are given to future assignments in the field of on-air promotion.