Automatic alignment of stacks of filament data

We present a fast and robust method for the alignment of image stacks containing filamentous structures. Such stacks are usually obtained by physical sectioning a specimen, followed by an optical sectioning of each slice. For reconstruction, the filaments have to be traced and the sub-volumes aligned. Our algorithm takes traced filaments as input and matches their endpoints to find the optimal transform. We show that our method is able to quickly and accurately align sub-volumes containing neuronal processes, acquired using brightfield microscopy. Our method also makes it possible to align traced microtubuli, obtained from electron tomography data, which are extremely difficult to align manually

Defining genes: a computational framework

The precise elucidation of the gene concept has become the subject of intense discussion in light of results from several, large high-throughput surveys of transcriptomes and proteomes. In previous work, we proposed an approach for constructing gene concepts that combines genomic heritability with elements of function. Here, we introduce a definition of the gene within a computational framework of cellular interactions. The definition seeks to satisfy the practical requirements imposed by annotation, capture logical aspects of regulation, and encompass the evolutionary property of homology

Does Amazon forest leaf phenology mediate transpiration seasonality and hence, ecoclimate teleconnections?

Abstract OOS 11-5

Age-dependent leaf function and consequences for carbon uptake of leaves, branches, and the canopy during the dry season in an Amazon evergreen forest.

Abstract COS 124-3

SynBlast: Assisting the analysis of conserved synteny information

<p>Abstract</p> <p>Motivation</p> <p>In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information.</p> <p>Results</p> <p>Here we present the <monospace>SynBlast</monospace> pipeline that is designed to construct and evaluate local synteny information. <monospace>SynBlast</monospace> uses the genomic region around a focal reference gene to retrieve candidates for homologous regions from a collection of target genomes and ranks them in accord with the available evidence for homology. The pipeline is intended as a tool to aid high quality manual annotation in particular in those cases where automatic procedures fail. We demonstrate how <monospace>SynBlast</monospace> is applied to retrieving orthologous and paralogous clusters using the vertebrate <it>Hox </it>and <it>ParaHox </it>clusters as examples.</p> <p>Software</p> <p>The <monospace>SynBlast</monospace> package written in <monospace>Perl</monospace> is available under the GNU General Public License at <url>http://www.bioinf.uni-leipzig.de/Software/SynBlast/</url>.</p

“Genes”

In order to describe a cell at molecular level, a notion of a “gene” is neither necessary nor helpful. It is sufficient to consider the molecules (i.e., chromosomes, transcripts, proteins) and their interactions to describe cellular processes. The downside of the resulting high resolution is that it becomes very tedious to address features on the organismal and phenotypic levels with a language based on molecular terms. Looking for the missing link between biological disciplines dealing with different levels of biological organization, we suggest to return to the original intent behind the term “gene”. To this end, we propose to investigate whether a useful notion of “gene” can be constructed based on an underlying notion of function, and whether this can serve as the necessary link and embed the various distinct gene concepts of biological (sub)disciplines in a coherent theoretical framework. In reply to the Genon Theory recently put forward by Klaus Scherrer and Jürgen Jost in this journal, we shall discuss a general approach to assess a gene definition that should then be tested for its expressiveness and potential cross-disciplinary relevance

Consensus statement: loneliness in older adults, the 21st century social determinant of health?

© Author(s) (or their employer(s)) 2020. Objective The purpose of this consensus statement is to determine the state of the field of loneliness among older people, highlighting key issues for researchers, policymakers and those designing services and interventions. Methods In December 2018, an international meeting on loneliness was held in Belfast with leaders from across the USA and Europe. A summary of the conclusions reached at this event is presented following a consensus-building exercise conducted both during this event after each presentation as well as after the event through the drafting, reviewing and agreement of this statement by all authors for over 6 months. Results This meeting resulted in an agreement to produce a consensus statement on key issues including definitions of loneliness, measurement, antecedents, consequences and interventions. Discussion There has been an exponential growth in research on loneliness among older adults. However, differing measurements and definitions of loneliness mean the incidence and prevalence, associated risk factors and health consequences are often conflicting or confusing especially for those developing policy and services