Relative abundance of diatom species in surface samples from the Southern Ocean, major open ocean species

Diatom assemblages from 228 core-top samples were investigated to determine the modern geographic distributions of 10 major open ocean species or species groups in the Atlantic and Indian sectors of the Southern Ocean. Our study gives a more comprehensive view of the relationships between diatom distribution and environmental pressures than previous studies, as our modern database covers a much wider area, and additionally highlights the relationships with sea ice cover and concentration. The 10 species or species categories can mainly be lumped into three groupings. First, a cool open ocean grouping composed of Rhizosolenia pointed group, Thalassiosira gracilis group and Trichotoxon reinboldii with maximum relative abundances occurring within the maximum winter sea-ice edge. Second, a pelagic open ocean grouping composed of Fragilariopsis kerguelensis, Thalassiosira lentiginosa, Thalassiosira oliverana and Thalassiothrix spp. group with maximum occurrences at the Antarctic Polar Front. Third, a warm open ocean grouping with maximum abundances observed within the Polar Front Zone and composed of the Rhizosolenia rounded group, the Thalassionema nitzschioides var. nitzschioides group and the Thalassionema nitzschioides var. lanceolata. Comparisons of the abovementioned 10 species or species groups with modern February sea-surface temperatures and sea-ice duration and concentration reveal species-specific sedimentary distributions regulated both by sea-surface temperatures and sea ice conditions that support the use of diatom remains to reconstruct past variations of these environmental parameters via qualitative and transfer function approaches.

Mesocosm experiment on warming and acidification effects in 2012: Microzooplankton data

Global warming and ocean acidification are among the most important stressors for aquatic ecosystems in the future. To investigate their direct and indirect effects on a near-natural plankton community, a multiple-stressor approach is needed. Hence, we set up mesocosms in a full-factorial design to study the effects of both warming and high CO2 on a Baltic Sea autumn plankton community, concentrating on the impacts on microzooplankton (MZP). MZP abundance, biomass, and species composition were analysed over the course of the experiment. We observed that warming led to a reduced time-lag between the phytoplankton bloom and an MZP biomass maximum. MZP showed a significantly higher growth rate and an earlier biomass peak in the warm treatments while the biomass maximum was not affected. Increased pCO2 did not result in any significant effects on MZP biomass, growth rate, or species composition irrespective of the temperature, nor did we observe any significant interactions between CO2 and temperature. We attribute this to the high tolerance of this estuarine plankton community to fluctuations in pCO2, often resulting in CO2 concentrations higher than the predicted end-of-century concentration for open oceans. In contrast, warming can be expected to directly affect MZP and strengthen its coupling with phytoplankton by enhancing its grazing pressure.

Oceanographic data, oxygen and methane concentrations, and C-CH4 isotope ratios measured at Jaco Scar

Methane (CH4) concentrations and CH4 stable carbon isotopic composition (d13CCH4) were investigated in the water column within Jaco Scar. It is one of several scars formed by massive slides resulting from the subduction of seamounts offshore Costa Rica, a process that can open up structural and stratigraphical pathways for migrating CH4. The release of large amounts of CH4 into the adjacent water column was discovered at the outcropping lowermost sedimentary sequence of the hanging wall in the northwest corner of Jaco Scar, where concentrations reached up to 1,500 nmol L-1. There CH4-rich fluids seeping from the sedimentary sequence stimulate both growth and activity of a dense chemosynthetic community. Additional point sources supplying CH4 at lower concentrations were identified in density layers above and below the main plume from light carbon isotope ratios. The injected CH4 is most likely a mixture of microbial and thermogenic CH4 as suggested by d13CCH4 values between -50 and -62 per mil Vienna Pee Dee Belemnite. This CH4 spreads along isopycnal surfaces throughout the whole area of the scar, and the concentrations decrease due to mixing with ocean water and microbial oxidation. The supply of CH4 appears to be persistent as repeatedly high CH4 concentrations were found within the scar over 6 years. The maximum CH4 concentration and average excess CH4 concentration at Jaco Scar indicate that CH4 seepage from scars might be as significant as seepage from other tectonic structures in the marine realm. Hence, taking into account the global abundance of scars, such structures might constitute a substantial, hitherto unconsidered contribution to natural CH4 sources at the seafloor.

Model simulation output data (CCSM3) related to uplift of Africa and Himalaya/Tibet Plateau and the influence on tropical African vegetation

Hominid evolution in the late Miocene has long been hypothesized to be linked to the retreat of the tropical rainforest in Africa. One cause for the climatic and vegetation change often considered was uplift of Africa, but also uplift of the Himalaya and the Tibetan Plateau was suggested to have impacted rainfall distribution over Africa. Recent proxy data suggest that in East Africa open grassland habitats were available to the common ancestors of hominins and apes long before their divergence and do not find evidence for a closed rainforest in the late Miocene. We used the coupled global general circulation model CCSM3 including an interactively coupled dynamic vegetation module to investigate the impact of topography on African hydro-climate and vegetation. We performed sensitivity experiments altering elevations of the Himalaya and the Tibetan Plateau as well as of East and Southern Africa. The simulations confirm the dominant impact of African topography for climate and vegetation development of the African tropics. Only a weak influence of prescribed Asian uplift on African climate could be detected. The model simulations show that rainforest coverage of Central Africa is strongly determined by the presence of elevated African topography. In East Africa, despite wetter conditions with lowered African topography, the conditions were not favorable enough to maintain a closed rainforest. A discussion of the results with respect to other model studies indicates a minor importance of vegetation-atmosphere or ocean-atmosphere feedbacks and a large dependence of the simulated vegetation response on the land surface/vegetation model.

Estimate of the (R)USLE rainfall erosivity factor from monthly precipitation data in mainland Spain

The need for continuous recording rain gauges makes it difficult to determine the rainfall erosivity factor (R-factor) of the (R)USLE model in areas without good temporal data coverage. In mainland Spain, the Nature Conservation Institute (ICONA) determined the R-factor at few selected pluviographs, so simple estimates of the R-factor are definitely of great interest. The objectives of this study were: (1) to identify a readily available estimate of the R-factor for mainland Spain; (2) to discuss the applicability of a single (global) estimate based on analysis of regional results; (3) to evaluate the effect of record length on estimate precision and accuracy; and (4) to validate an available regression model developed by ICONA. Four estimators based on monthly precipitation were computed at 74 rainfall stations throughout mainland Spain. The regression analysis conducted at a global level clearly showed that modified Fournier index (MFI) ranked first among all assessed indexes. Applicability of this preliminary global model across mainland Spain was evaluated by analyzing regression results obtained at a regional level. It was found that three contiguous regions of eastern Spain (Catalonia, Valencian Community and Murcia) could have a different rainfall erosivity pattern, so a new regression analysis was conducted by dividing mainland Spain into two areas: Eastern Spain and plateau-lowland area. A comparative analysis concluded that the bi-areal regression model based on MFI for a 10-year record length provided a simple, precise and accurate estimate of the R-factor in mainland Spain. Finally, validation of the regression model proposed by ICONA showed that R-ICONA index overpredicted the R-factor by approximately 19%.

Sweat Lodges in Iron Age Iberian Peninsula: New Data, Typologies and Interpretations

Three questions on the study of NO Iberian Peninsula sweat lodges are posed. First, the new sauna of Monte Ornedo (Cantabria), the review of the one of Armea (Ourense), and the Cantabrian pedra formosa type are discussed. Second, the known types of sweat lodges are reconsidered underlining the differences between the Cantabrian and the Douro - Minho groups as these differences contribute to a better assessment of the saunas located out of those territories, such as those of Monte Ornedo or Ulaca. Third, a richer record demands a more specific terminology, a larger use of archaeometric analysis and the application of landscape archaeology or art history methodologies. In this way the range of interpretation of the sweat lodges is opened, as an example an essay is proposed that digs on some already known proposals and suggests that the saunas are material metaphors of wombs whose rationale derives from ideologies and ritual practices of Indo-European tradition.

Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line

Here, we describe gene expression compositional assignment (GECA), a powerful, yet simple method based on compositional statistics that can validate the transfer of prior knowledge, such as gene lists, into independent data sets, platforms and technologies. Transcriptional profiling has been used to derive gene lists that stratify patients into prognostic molecular subgroups and assess biomarker performance in the pre-clinical setting. Archived public data sets are an invaluable resource for subsequent in silico validation, though their use can lead to data integration issues. We show that GECA can be used without the need for normalising expression levels between data sets and can outperform rank-based correlation methods. To validate GECA, we demonstrate its success in the cross-platform transfer of gene lists in different domains including: bladder cancer staging, tumour site of origin and mislabelled cell lines. We also show its effectiveness in transferring an epithelial ovarian cancer prognostic gene signature across technologies, from a microarray to a next-generation sequencing setting. In a final case study, we predict the tumour site of origin and histopathology of epithelial ovarian cancer cell lines. In particular, we identify and validate the commonly-used cell line OVCAR-5 as non-ovarian, being gastrointestinal in origin. GECA is available as an open-source R package.

Epirubicin, oxaliplatin, and capecitabine with or without panitumumab for patients with previously untreated advanced oesophagogastric cancer (REAL3): a randomised, open-label phase 3 trial.

BACKGROUND: EGFR overexpression occurs in 27-55% of oesophagogastric adenocarcinomas, and correlates with poor prognosis. We aimed to assess addition of the anti-EGFR antibody panitumumab to epirubicin, oxaliplatin, and capecitabine (EOC) in patients with advanced oesophagogastric adenocarcinoma. METHODS: In this randomised, open-label phase 3 trial (REAL3), we enrolled patients with untreated, metastatic, or locally advanced oesophagogastric adenocarcinoma at 63 centres (tertiary referral centres, teaching hospitals, and district general hospitals) in the UK. Eligible patients were randomly allocated (1:1) to receive up to eight 21-day cycles of open-label EOC (epirubicin 50 mg/m(2) and oxaliplatin 130 mg/m(2) on day 1 and capecitabine 1250 mg/m(2) per day on days 1-21) or modified-dose EOC plus panitumumab (mEOC+P; epirubicin 50 mg/m(2) and oxaliplatin 100 mg/m(2) on day 1, capecitabine 1000 mg/m(2) per day on days 1-21, and panitumumab 9 mg/kg on day 1). Randomisation was blocked and stratified for centre region, extent of disease, and performance status. The primary endpoint was overall survival in the intention-to-treat population. We assessed safety in all patients who received at least one dose of study drug. After a preplanned independent data monitoring committee review in October, 2011, trial recruitment was halted and panitumumab withdrawn. Data for patients on treatment were censored at this timepoint. This study is registered with ClinicalTrials.gov, number NCT00824785. FINDINGS: Between June 2, 2008, and Oct 17, 2011, we enrolled 553 eligible patients. Median overall survival in 275 patients allocated EOC was 11.3 months (95% CI 9.6-13.0) compared with 8.8 months (7.7-9.8) in 278 patients allocated mEOC+P (hazard ratio [HR] 1.37, 95% CI 1.07-1.76; p=0.013). mEOC+P was associated with increased incidence of grade 3-4 diarrhoea (48 [17%] of 276 patients allocated mEOC+P vs 29 [11%] of 266 patients allocated EOC), rash (29 [11%] vs two [1%]), mucositis (14 [5%] vs none), and hypomagnesaemia (13 [5%] vs none) but reduced incidence of haematological toxicity (grade ≥ 3 neutropenia 35 [13%] vs 74 [28%]). INTERPRETATION: Addition of panitumumab to EOC chemotherapy does not increase overall survival and cannot be recommended for use in an unselected population with advanced oesophagogastric adenocarcinoma. FUNDING: Amgen, UK National Institute for Health Research Biomedical Research Centre.

The MOOC Dashboard: Visualising MOOC data for everyone

Abstract Massive Open Online Courses (MOOCs) generate enormous amounts of data. The University of Southampton has run and is running dozens of MOOC instances. The vast amount of data resulting from our MOOCs can provide highly valuable information to all parties involved in the creation and delivery of these courses. However, analysing and visualising such data is a task that not all educators have the time or skills to undertake. The recently developed MOOC Dashboard is a tool aimed at bridging such a gap: it provides reports and visualisations based on the data generated by learners in MOOCs. Speakers Manuel Leon is currently a Lecturer in Online Teaching and Learning in the Institute for Learning Innovation and Development (ILIaD). Adriana Wilde is a Teaching Fellow in Electronics and Computer Science, with research interests in MOOCs and Learning Analytics. Darron Tang (4th Year BEng Computer Science) and Jasmine Cheng (BSc Mathematics & Actuarial Science and starting MSc Data Science shortly) have been working as interns over this Summer (2016) as have been developing the MOOC Dashboard.

Quasilinear elliptic systems with measure data

We study the existence of solutions of quasilinear elliptic systems involving $N$ equations and a measure on the right hand side, with the form $$\left\{\begin{array}{ll} -\sum_{i=1}^n \frac{\partial}{\partial x_i}\left(\sum\limits_{\beta=1}^{N}\sum\limits_{j=1}^{n}% a_{i,j}^{\alpha,\beta}\left( x,u\right)\frac{\partial}{\partial x_j}u^\beta\right)=\mu^\alpha& \mbox{ in }\Omega ,\\ u=0 & \mbox{ on }\partial\Omega, \end{array}\right.$$ where $\alpha\in\{1,\dots,N\}$ is the equation index, $\Omega$ is an open bounded subset of $\mathbb{R}^{n}$, $u:\Omega\rightarrow\mathbb{R}^{N}$ and $\mu$ is a finite Randon measure on $\mathbb{R}^{n}$ with values into $\mathbb{R}^{N}$. Existence of a solution is proved for two different sets of assumptions on $A$. Examples are provided that satisfy our conditions, but do not satisfy conditions required on previous works on this matter.

Federated architecture for biomedical data integration

The last decades have been characterized by a continuous adoption of IT solutions in the healthcare sector, which resulted in the proliferation of tremendous amounts of data over heterogeneous systems. Distinct data types are currently generated, manipulated, and stored, in the several institutions where patients are treated. The data sharing and an integrated access to this information will allow extracting relevant knowledge that can lead to better diagnostics and treatments. This thesis proposes new integration models for gathering information and extracting knowledge from multiple and heterogeneous biomedical sources. The scenario complexity led us to split the integration problem according to the data type and to the usage specificity. The first contribution is a cloud-based architecture for exchanging medical imaging services. It offers a simplified registration mechanism for providers and services, promotes remote data access, and facilitates the integration of distributed data sources. Moreover, it is compliant with international standards, ensuring the platform interoperability with current medical imaging devices. The second proposal is a sensor-based architecture for integration of electronic health records. It follows a federated integration model and aims to provide a scalable solution to search and retrieve data from multiple information systems. The last contribution is an open architecture for gathering patient-level data from disperse and heterogeneous databases. All the proposed solutions were deployed and validated in real world use cases.

Laparoscopic versus open appendectomy for the treatment of complicated appendicitis

Aim. Laparoscopic Appendectomy (LA) is widely performed for the treatment of acute appendicitis. However the use of laparoscopic approach for complicated appendicitis is controversial, in particular because it has been reported an increased risk of postoperative IntraAbdominal Abscess (IAA). The aim of this study was to compare the outcomes of LA versus Open Appendectomy (OA) in the treatment of complicated appendicitis, especially with regard to the incidence of postoperative IAA. Patients and Methods. A retrospective study of all patients treated at our institution for complicated appendicitis, from May 2004 to June 2009, was performed. Data collection included demographic characteristics, postoperative complications, conversion rate, and length of hospital stay. Results. Thirty-eight patients with complicated appendicitis were analysed. Among these, 18 (47,3%) had LA and 20 (52,7%) had OA. There were no statistical differences in characteristics between the two groups. The incidence of postoperative IAA was higher (16,6%), although not statistically significant, in the LA compared with OA group (5%). On the other hand the rate of wound infection was lower (5%) in the LA versus OA (20%). Conclusion. Our study indicated that LA should be utilised with caution in case of perforated appendicitis, because it is associated with an increased risk of postoperative IAA compared with OA.

Linking electronic journals - Lessons from the Open Journal project

The Open Journal project has completed its three year period of funding by the UK Electronic Libraries (eLib) programme (Rusbridge 1998). During that time, the number of journals that are available electronically leapt from a few tens to a few thousand. Some of these journals are now developing the sort of features the project has been advocating, in particular the use of links within journals, between different primary journals, with secondary journals data, and to non-journal sources. Assessing the achievements of the project and considering some of the difficulties it faced, we report on the different approaches to linking that the project developed, and summarise the important user responses that indicate what works and what does not. Looking ahead, there are signs of change, not just to simple linking within journals but to schemes in which links are the basis of "distributed" journals, where information may be shared and documents built from different sources. The significance has yet to be appreciated, but this would be a major change from printed journals. If projects such as this and others have provided the initial impetus, the motivation for distributed journals comes, perhaps surprisingly, from within certain parts of the industry, as the paper shows.

The impact of Open Access outside of European Universities

The Open Access movement has encouraged the availability of publicly-funded research papers, data and learning content for barrier-free use of that content without payment by the user. The impact of increasing availability of content to researchers in European universities is understood in terms of easier access to previous research and greater exposure for new research results, bringing benefits to the research community itself. A new culture of informal sharing is evident within the teaching and learning communities and to some extent also within the research community, but as yet the growth in informal sharing has not had a major effect upon the use of formal publication choices. This briefing paper explores the impact of open access upon potential users of research outputs outside the walls of research-led European universities, where the economic value of open access may be even greater than the academic value within universities. The potential impact of open access is understood in many communities but requires a greater volume of open access content to be available for the full potential to be realised. More open access content will become available as the opportunities in open, internet-based digital scholarship are understood. This briefing paper was written in cooperation with SPARC Europe. All links provided in footnotes in this Briefing Paper are to studies available in open access.