Biobanking with Big Data: A Need for Developing “Big Data Metrics”

The term “big data” has often been used as an all-encompassing phrase for research that involves the use of large-scale data sets. However, the use of the term does little to signify the underlying complexity of definitions, of data sets, and of the requirements that need to be taken into consideration for sustainable research and the estimation of downstream impact. In particular, “big data” is frequently connected with biobanks and biobank networks as the institutions involved in tissue preservation are increasingly and perhaps unavoidably linked to the de facto preservation of information. “Big data” is commonly defined as collections of data sets so large and complex that its manipulation and management present significant logistical challenges (Oxford English Dictionary, 2013). Within the sphere of clinically oriented research, the term is often synonymous to electronic patient records from large hospitals, clinical trials, and/or -omics-based consortia and their associated banked samples. These data can be structured or unstructured, generated from diverse sources (sometimes in real time), and in very large volumes

Re: A review of continuous vs intermittent androgen deprivation therapy: Redefining the gold standard in the treatment of advanced prostate cancer. Myths, facts and new data on a ?perpetual dispute?

Objectives: To review the literature and present new data of continuous androgen deprivation therapy (ADT) vs intermittent androgen deprivation (IAD) as therapies for prostate cancer in terms of survival and quality of life and clarify practical issues in the use of IAD. Materials and Methods: We conducted a systematic search on Medline and Embase databases using “prostatic neoplasm” and “intermittent androgen deprivation” as search terms. We reviewed meta-analyses, randomised controlled trials, reviews, clinical trials and practise guidelines written in English from 2000 and onwards until 01/04/2013. Ten randomized controlled trials were identified. Seven of them published extensive data and results randomizing 4675 patients to IAD versus CAD. Data from the other three randomized trials were limited. Results: Over the last years studies confirmed that IAD is an effective alternative approach to hormonal deprivation providing simultaneously several potential benefits in terms of quality of life and cost effectiveness. Thus, in patients with non metastatic, advanced prostate cancer IAD could be used as standard treatment, while in metastatic prostate cancer IAD role still remains ambiguous. Conclusions: Nowadays, revaluation of the gold standard of ADT in advanced prostate cancer appears essential. Recent data established that IAD should no longer be considered as investigational, since its effectiveness has been proven, especially in patients suffering from non-metastatic advanced prostate cancer

Synchronous Primary Adenocarcinoma and Ancient Schwannoma in the Colon: An Unusual Case Report

Gastrointestinal schwannomas are uncommon stromal tumors of the intestinal tract and colon schwannomas are extremely rare. We report a rare case of ascending colon schwannoma with associated synchronous adenocarcinoma of the sigmoid colon. A 68-year-old man presented with a 20-day history of bleeding per rectum. Colonoscopy revealed a mass of 4.2 cm in diameter with endoluminal protrusion in the sigmoid colon and a second submucosal tumor in the ascending colon. Surgical intervention was suggested and ileo-hemicolectomy was done. Microscopically, the submucosal tumor of 4 cm in diameter showed features of schwannoma with degenerative change (ancient schwannoma). Lesional cells were positive for S100p and negative for actin, desmin, CD34, CD117, and pankeratin. The mass showed features of an invasive moderately differentiated adenocarcinoma. Colon schwannoma is a rare submucosal tumor, and the incidental occurrence with adenocarcinoma has not been well described in the literature

Giant mediastinal mature teratoma with increased exocrine pancreatic activity presenting in a young woman: a case report

Abstract Introduction Mediastinal mature teratoma is a benign, slow-growing tumor typically affecting 20- to 40-year-old adults. Fluid examination from the cystic masses rarely shows enzymatic activity as we describe in this report. Case presentation We report a case of a giant mediastinal germ cell tumor (measuring 15 cm × 14 cm × 8 cm) detected in a 35-year-old Caucasian woman. Microscopic examination showed that the lesion resembled a mature cystic teratoma with areas of pancreatic tissue with mature ductal and acinar structures intermixed with islets of Langerhans. Fluid from the cysts in the mass was examined after removal showed amylase activity of 599 U/l despite normal serum levels. The post-operative period was free of complications, and the patient was discharged on post-operative day 10. Conclusion Complete surgical removal is the treatment of choice for mature cystic teratomas, with optimal results and acceptable surgical risk. Exocrine pancreatic function may be an aid to pre-operative or intra-operative diagnosis; however, these findings have no impact on survival or the therapeutic pathway.</p

Sequential and switchable patterning for studying cellular processes under spatiotemporal control

Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science

European 1 MW, 170 GHz CW Gyrotron Prototype for ITER - long-pulse operation at KIT -

The upgraded EU 1 MW, 170 GHz continuous wave (CW) industrial prototype gyrotron (TH1509U) for Electron Cyclotron Resonance Heating and Current Drive (ECRH&CD) in ITER was tested at the Karlsruhe Institute of Technology (KIT). The gyrotron surpassed the performance of the previous TH1509 tube. In particular, TH1509U delivered (i) 0.9 MW in 180 s pulses (max. pulse length of the KIT test stand) and (ii) more than 1 MW at a pulse length limited to 40 s, due to a problem with the test stand cooling circuit at that time. In addition, it was possible to demonstrate gyrotron operation at (iii) 0.5 MW in 1600 s pulses

Cost-effective external interference for promoting the evolution of cooperation.

The problem of promoting the evolution of cooperative behaviour within populations of self-regarding individuals has been intensively investigated across diverse fields of behavioural, social and computational sciences. In most studies, cooperation is assumed to emerge from the combined actions of participating individuals within the populations, without taking into account the possibility of external interference and how it can be performed in a cost-efficient way. Here, we bridge this gap by studying a cost-efficient interference model based on evolutionary game theory, where an exogenous decision-maker aims to ensure high levels of cooperation from a population of individuals playing the one-shot Prisoner's Dilemma, at a minimal cost. We derive analytical conditions for which an interference scheme or strategy can guarantee a given level of cooperation while at the same time minimising the total cost of investment (for rewarding cooperative behaviours), and show that the results are highly sensitive to the intensity of selection by interference. Interestingly, we show that a simple class of interference that makes investment decisions based on the population composition can lead to significantly more cost-efficient outcomes than standard institutional incentive strategies, especially in the case of weak selection.</p

Adrenocortical oncocytic carcinoma with recurrent metastases: a case report and review of the literature

<p>Abstract</p> <p>Background</p> <p>Adrenal cortex oncocytic carcinoma (AOC) represents an exceptional pathological entity, since only 22 cases have been documented in the literature so far.</p> <p>Case presentation</p> <p>Our case concerns a 54-year-old man with past medical history of right adrenal excision with partial hepatectomy, due to an adrenocortical carcinoma. The patient was admitted in our hospital to undergo surgical resection of a left lung mass newly detected on chest Computed Tomography scan. The histological and immunohistochemical study revealed a metastatic AOC. Although the patient was given mitotane orally in adjuvant basis, he experienced relapse with multiple metastases in the thorax twice in the next year and was treated with consecutive resections. Two and a half years later, a right hip joint metastasis was found and concurrent chemoradiation was given. Finally, approximately five years post disease onset, the patient died due to massive metastatic disease. A thorough review of AOC and particularly all diagnostic difficulties are extensively stated.</p> <p>Conclusion</p> <p>Histological classification of adrenocortical oncocytic tumours has been so far a matter of debate. There is no officially established histological scoring system regarding these rare neoplasms and therefore many diagnostic difficulties occur for pathologists.</p

An integrated open-coastal biogeochemistry, ecosystem and biodiversity observatory of the eastern Mediterranean – the Cretan Sea component of the POSEIDON system

There is a general scarcity of oceanic observations that concurrently examine air–sea interactions, coastal–open-ocean processes and physical–biogeochemical processes, in appropriate spatiotemporal scales and under continuous, long-term data acquisition schemes. In the Mediterranean Sea, the resulting knowledge gaps and observing challenges increase due to its oligotrophic character, especially in the eastern part of the basin. The oligotrophic open Cretan Sea's biogeochemistry is considered to be representative of a greater Mediterranean area up to 106&thinsp;km2, and understanding its features may be useful on even larger oceanic scales, since the Mediterranean Sea has been considered a miniature model of the global ocean. The spatiotemporal coverage of biogeochemical (BGC) observations in the Cretan Sea has progressively increased over the last decades, especially since the creation of the POSEIDON observing system, which has adopted a multiplatform, multivariable approach, supporting BGC data acquisition. The current POSEIDON system's status includes open and coastal sea fixed platforms, a Ferrybox (FB) system and Bio-Argo autonomous floats that remotely deliver fluorescence as a proxy of chlorophyll-a (Chl-a), O2, pH and pCO2 data, as well as BGC-related physical variables. Since 2010, the list has been further expanded to other BGC (nutrients, vertical particulate matter fluxes), ecosystem and biodiversity (from viruses up to zooplankton) variables, thanks to the addition of sediment traps, frequent research vessel (R/V) visits for seawater–plankton sampling and an acoustic Doppler current profiler (ADCP) delivering information on macrozooplankton–micronekton vertical migration (in the epipelagic to mesopelagic layer). Gliders and drifters are the new (currently under integration to the existing system) platforms, supporting BGC monitoring. Land-based facilities, such as data centres, technical support infrastructure, calibration laboratory and mesocosms, support and give added value to the observatory. The data gathered from these platforms are used to improve the quality of the BGC-ecosystem model predictions, which have recently incorporated atmospheric nutrient deposition processes and assimilation of satellite Chl-a data. Besides addressing open scientific questions at regional and international levels, examples of which are presented, the observatory provides user-oriented services to marine policy makers and the society, and is a technological test bed for new and/or cost-efficient BGC sensor technology and marine equipment. It is part of European and international observing programs, playing a key role in regional data handling and participating in harmonization and best practices procedures. Future expansion plans consider the evolving scientific and society priorities, balanced with sustainable management.</p