Root morphology and biomechanical characteristics of high altitude alpine plant species and their potential application in soil stabilization

Glacial forefields host young, poorly developed soils with highly unstable environmental conditions. Root system contribution to soil stabilization is a well-known phenomenon. Identifying the functional traits and root morphology of pioneer vegetation that establish on forefields can provide information useful in the practical application of plants in land restoration of high altitude mountain sites.This study aims to gather information on the root morphology and biomechanical characteristics of the 10 most dominant pioneer plant species of the forefield of Lys Glacier (NW Italian Alps).X-ray Computed Tomography (X-ray CT) was used to visualize and quantify non-destructively the root architecture of the studied species. Samples were cored directly from the forefield. Data on root traits such as total root length, rooting depth, root diameter, root length density and number of roots in relation to diameter classes as well as plant height were determined and compared between species. Roots were also tested for their tensile strength resistance.X-ray CT technology allowed us to visualize the 3D root architecture of species intact in their natural soil system. X-ray CT technology provided a visual representation of root-soil interface and information on the exact position, orientation and elongation of the root system in the soil core. Root architecture showed high variability among the studied species. For all species the majority of roots consisted of roots smaller than 0.5. mm in diameter. There were also considerable differences found in root diameter and total root length although these were not statistically significant. However, significant differences were found in rooting depth, root length density, plant height and root tensile strength between species and life forms (dwarf shrub, forb, graminoid). In all cases, root tensile strength decreased with increasing root diameter. The highest tensile strength was recorded for graminoids such as Luzula spicata (L.) DC. and Poa laxa Haenke and the lowest for Epilobium fleischeri Hochst.The differences in root properties among the studied species highlight the diverse adaptive and survival strategies plants employ to establish on and thrive in the harsh and unstable soil conditions of a glacier forefield. The data determined in this study could provide a significant contribution to a database that allow those who are working in land restoration and preservation of high altitude mountain sites to employ native species in a more efficient, effective and informed manner

Describing the content of trial recruitment interventions using the TIDieR Reporting Checklist : A systematic methodology review

Peer reviewe

Quail Genomics: a knowledgebase for Northern bobwhite

<p>Abstract</p> <p>Background</p> <p>The Quail Genomics knowledgebase (<url>http://www.quailgenomics.info</url>) has been initiated to share and develop functional genomic data for Northern bobwhite (<it>Colinus virginianus</it>). This web-based platform has been designed to allow researchers to perform analysis and curate genomic information for this non-model species that has little supporting information in GenBank.</p> <p>Description</p> <p>A multi-tissue, normalized cDNA library generated for Northern bobwhite was sequenced using 454 Life Sciences next generation sequencing. The Quail Genomics knowledgebase represents the 478,142 raw ESTs generated from the sequencing effort in addition to assembled nucleotide and protein sequences including 21,980 unigenes annotated with meta-data. A normalized MySQL relational database was established to provide comprehensive search parameters where meta-data can be retrieved using functional and structural information annotation such as gene name, pathways and protein domain. Additionally, blast hit cutoff levels and microarray expression data are available for batch searches. A Gene Ontology (GO) browser from Amigo is locally hosted providing 8,825 unigenes that are putative orthologs to chicken genes. In an effort to address over abundance of Northern bobwhite unigenes (71,384) caused by non-overlapping contigs and singletons, we have built a pipeline that generates scaffolds/supercontigs by aligning partial sequence fragments against the indexed protein database of chicken to build longer sequences that can be visualized in a web browser. </p> <p>Conclusion</p> <p>Our effort provides a central repository for storage and a platform for functional interrogation of the Northern bobwhite sequences providing comprehensive GO annotations, meta-data and a scaffold building pipeline. The Quail Genomics knowledgebase will be integrated with Japanese quail (<it>Coturnix coturnix</it>) data in future builds and incorporate a broader platform for these avian species. </p

Efficient algorithms for reconstructing gene content by co-evolution

<p>Abstract</p> <p>Background</p> <p>In a previous study we demonstrated that co-evolutionary information can be utilized for improving the accuracy of ancestral gene content reconstruction. To this end, we defined a new computational problem, the Ancestral Co-Evolutionary (ACE) problem, and developed algorithms for solving it.</p> <p>Results</p> <p>In the current paper we generalize our previous study in various ways. First, we describe new efficient computational approaches for solving the ACE problem. The new approaches are based on reductions to classical methods such as linear programming relaxation, quadratic programming, and min-cut. Second, we report new computational hardness results related to the ACE, including practical cases where it can be solved in polynomial time.</p> <p>Third, we generalize the ACE problem and demonstrate how our approach can be used for inferring parts of the genomes of <it>non-ancestral</it> organisms. To this end, we describe a heuristic for finding the portion of the genome ('dominant set’) that can be used to reconstruct the rest of the genome with the lowest error rate. This heuristic utilizes both evolutionary information and co-evolutionary information.</p> <p>We implemented these algorithms on a large input of the ACE problem (95 unicellular organisms, 4,873 protein families, and 10, 576 of co-evolutionary relations), demonstrating that some of these algorithms can outperform the algorithm used in our previous study. In addition, we show that based on our approach a ’dominant set’ cab be used reconstruct a major fraction of a genome (up to 79%) with relatively low error-rate (<it>e.g.</it> 0.11). We find that the ’dominant set’ tends to include metabolic and regulatory genes, with high evolutionary rate, and low protein abundance and number of protein-protein interactions.</p> <p>Conclusions</p> <p>The <it>ACE</it> problem can be efficiently extended for inferring the genomes of organisms that exist today. In addition, it may be solved in polynomial time in many practical cases. Metabolic and regulatory genes were found to be the most important groups of genes necessary for reconstructing gene content of an organism based on other related genomes.</p

Linguistic validation, validity and reliability of the British English versions of the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire and QuickDASH in people with rheumatoid arthritis

Background: Although the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire is widely used in the UK, no British English version is available. The aim of this study was to linguistically validate the DASH into British English and then test the reliability and validity of the British English DASH, (including the Work and Sport/Music DASH) and QuickDASH, in people with rheumatoid arthritis (RA). Methods: The DASH was forward translated, reviewed by an expert panel and cognitive debriefing interviews undertaken with 31 people with RA. Content validity was evaluated using the ICF Core Set for RA. Participants with RA (n=340) then completed the DASH, Health Assessment Questionnaire (HAQ), Short Form Health Survey v2 (SF36v2) and Measure of Activity Performance of the Hand (MAPHAND). We examined internal consistency and concurrent validity for the DASH, Work and Sport/Music DASH modules and QuickDASH. Participants repeated the DASH to assess test-retest reliability. Results: Minor wording changes were made as required. The DASH addresses a quarter of Body Function and half of Activities and Participation codes in the ICF RA Core Set. Internal consistency for DASH scales were consistent with individual use (Cronbach’s alpha = 0.94-0.98). Concurrent validity was strong with the HAQ (rs = 0.69-0.91), SF36v2 Physical Function (rs = -0.71 - -0.85), Bodily Pain (rs = -0.71 - -0.74) scales and MAPHAND (rs =0.71-0.93). Test-retest reliability was good (rs = 0.74-0.95). Conclusions: British English versions of the DASH, QuickDASH and Work and Sport/Music modules are now available to evaluate upper limb disabilities in the UK. The DASH, QuickDASH, Work and Sport/Music modules are reliable and valid to use in clinical practice and research with British people with RA

ACL injuries identifiable for pre-participation imagiological analysis: Risk factors

Identification of pre-participation risk factors for noncontact anterior cruciate ligament (ACL) injuries has been attracting a great deal of interest in the sports medicine and traumatology communities. Appropriate methods that enable predicting which patients could benefit from pre- ventive strategies are most welcome. This would enable athlete-specific training and conditioning or tailored equipment in order to develop appropriate strategies to reduce incidence of injury. In order to accomplish these goals, the ideal system should be able to assess both anatomic and functional features. Complementarily, the screening method must be cost-effective and suited for widespread application. Anatomic study protocol requiring only standard X rays could answer some of such demands. Dynamic MRI/CT evaluation and electronically assisted pivot-shift evaluation can be powerful tools providing complementary information. These upcoming insights, when validated and properly combined, envision changing pre-participation knee examination in the near future. Herein different methods (validated or under research) aiming to improve the capacity to identify persons/athletes with higher risk for ACL injury are overviewed.

MaGe: A Monte Carlo framework for the Gerda and Majorana double beta decay experiments

The Gerda [1] and Majorana [2] projects, both searching for the neutrinoless double beta-decay of 76Ge, are developing a joint Monte-Carlo simulation framework called MaGe. Such an approach has many benefits: the workload for the development of general tools is shared between more experts, the code is tested in more detail, and more experimental data is made available for validation

MaGe: a Monte Carlo framework for the Gerda and Majorana double beta decay experiments

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