MarBEF publishing revisited

Networking and integration served within a partnership approach and covered with a delicious sauce of free and open access to data and information is MarBEF’s main dish, and it is this recipe that has helped MarBEF to successfully bring marine biodiversity research to a European level. Numerous meetings, workshops, training courses and Responsive Mode Projects (RMPs) have brought together many scientists. This integration has created endless new possibilities for new initiatives – the MarBEF Publication Series and the MarBEF Open Archive, to mention just two. So, is this having any effect on the way we publish as a network today

Publish wisely or perish? an open archive for MarBEF

While scientists are publishing around two million papers annually (Odlyzko, 1998), it is surprising to notice that this growing resource of information is seldom easily accessible, even to those scientists. Basically, it is the community at large that funds almost all research, so all information resulting from this research should in principle be publicly available. However, in reality, too many barriers (mostly installed by the publisher) are blocking free and open access to scientific information

Biodiversity's big wet secret: the global distribution of marine biological records reveals chronic under-exploration of the deep pelagic ocean

Background: Understanding the distribution of marine biodiversity is a crucial first step towards the effective and sustainable management of marine ecosystems. Recent efforts to collate location records from marine surveys enable us to assemble a global picture of recorded marine biodiversity. They also effectively highlight gaps in our knowledge of particular marine regions. In particular, the deep pelagic ocean - the largest biome on Earth - is chronically under-represented in global databases of marine biodiversity. Methodology/Principal Findings: We use data from the Ocean Biogeographic Information System to plot the position in the water column of ca 7 million records of marine species occurrences. Records from relatively shallow waters dominate this global picture of recorded marine biodiversity. In addition, standardising the number of records from regions of the ocean differing in depth reveals that regardless of ocean depth, most records come either from surface waters or the sea bed. Midwater biodiversity is drastically under-represented. Conclusions/Significance: The deep pelagic ocean is the largest habitat by volume on Earth, yet it remains biodiversity's big wet secret, as it is hugely under-represented in global databases of marine biological records. Given both its value in the provision of a range of ecosystem services, and its vulnerability to threats including overfishing and climate change, there is a pressing need to increase our knowledge of Earth's largest ecosystem

Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)

Background: Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies produce ad hoc solutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets. Furthermore, the implementations described here can be of significant interest to expert bioinformaticians or R developers. Therefore, our goals can be summarized as: (i) description of a complete methodology for the analysis of large datasets by combining capabilities of diverse R packages, (ii) presentation of their application through a virtual R laboratory (RvLab) that makes execution of complex functions and visualization of results easy and readily available to the end-user. New information: In this paper, the novelty stems from implementations of parallel methodologies which rely on the processing of data on different levels of abstraction and the availability of these processes through an integrated portal. Parallel implementation R packages, such as the pbdMPI (Programming with Big Data – Interface to MPI) package, are used to implement Single Program Multiple Data (SPMD) parallelization on primitive mathematical operations, allowing for interplay with functions of the vegan package. The dplyr and RPostgreSQL R packages are further integrated offering connections to dataframe like objects (databases) as secondary storage solutions whenever memory demands exceed available RAM resources. The RvLab is running on a PC cluster, using version 3.1.2 (2014-10-31) on a x86_64-pc-linux-gnu (64-bit) platform, and offers an intuitive virtual environmet interface enabling users to perform analysis of ecological and microbial communities based on optimized vegan functions. A beta version of the RvLab is available after registration at: https://portal.lifewatchgreece.eu

Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field

COMPARATIVE STUDY OF THREE TRANSECT METHODS TO ASSESS CORAL 29 Comparative Study of Three Transect Methods to Assess Coral Cover, Richness and Diversity

Abstract-Three different transect methods were compared at two different sites in Kenya, on their efficiency to estimate hard coral cover, genus richness and Shannon diversity index. For a modified line transect method (LTM), the line intercept method (LIT) and a linear point intercept (LPI) method the relative efficiency of the three methods was calculated with respect to the tested parameters. The three methods were examined along identical transect lines (10 m) and a total of 27 transect triplets were recorded in Vipingo and 21 in Mombasa. The correlation coefficients for all three ecological parameters were calculated for the three possible pairs of methods, and the accumulation curves plotted for each of the parameters using number of transects as the independent variable. Results from the three methods were virtually indistinguishable. When the parameters were plotted using measuring time on the x axis, the curves for the LPI method converged twice as fast as those for LTM, while LIT time was intermediate. It is suggested that the LPI method might be most suitable for assessing coral cover, richness and diversity where time and effort are significant constraints

Bridging disciplines to address complex questions: The need for data publication

SCOPUS: ar.jinfo:eu-repo/semantics/publishe