Marker-based C-arm self-calibration with unknown calibration pattern.

Background: Accurate tomographic reconstructions require the knowledge of the actual acquisition geometry. Many mobile C-arm CT scanners have poorly reproducible acquisition geometries and thus need acquisition-specific calibration procedures. Most of geometric self-calibration methods based on projection data either need prior information or are limited to the estimation of a low number of geometric calibration parameters.

Consecutive action of two BAHD acyltransferases promotes tetracoumaroyl spermine accumulation in chicory.

Fully substituted phenolamide accumulation in the pollen coat of Eudicotyledons is a conserved evolutionary chemical trait. Interestingly, spermidine derivatives are replaced by spermine derivatives as the main phenolamide accumulated in the Asteraceae family. Here, we show that the full substitution of spermine in chicory (Cichorium intybus) requires the successive action of two enzymes, that is spermidine hydroxycinnamoyl transferase-like proteins 1 and 2 (CiSHT1 and CiSHT2), two members of the BAHD enzyme family.

Leveraging historical data to optimize the number of covariates and their explained variance in the analysis of randomized clinical trials.

The amount of data collected from patients involved in clinical trials is continuously growing. All baseline patient characteristics are potential covariates that could be used to improve clinical trial analysis and power. However, the limited number of patients in phases I and II studies restricts the possible number of covariates included in the analyses.

Aging at Evolutionary Crossroads: Longitudinal Gene Co-expression Network Analyses of Proximal and Ultimate Causes of Aging in Bats.

How, when, and why do organisms, their tissues, and their cells age remain challenging issues, although researchers have identified multiple mechanistic causes of aging, and three major evolutionary theories have been developed to unravel the ultimate causes of organismal aging. A central hypothesis of these theories is that the strength of natural selection decreases with age. However, empirical evidence on when, why, and how organisms age is phylogenetically limited, especially in natural populations.

Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods.

Inferring phylogenetic relationships among hundreds or thousands of microbial genomes is an increasingly common task. The conventional phylogenetic approach adopts multiple sequence alignment to compare gene-by-gene, concatenated multigene or whole-genome sequences, from which a phylogenetic tree would be inferred. These alignments follow the implicit assumption of full-length contiguity among homologous sequences.

MeJA Elicitation of Chicory Hairy Roots Promotes Efficient Increase of 3,5-diCQA Accumulation, a Potent Antioxidant and Antibacterial Molecule.

L. () is an important industrial crop, as well as a medicinal plant which produces some bioactive compounds implicated in various biological effects with potential applications in human health. Particularly, roots produce hydroxycinnamic acids like 5-caffeoyquinic acid and 3,5-dicaffeoylquinic acid (di-CQA).

Computational fluid dynamics simulation from microCT stacks of commercial biomaterials usable for bone grafting.

Granules of calcium/phosphate biomaterials are used to fill small bone defects in oral and maxilla-facial surgery. Granules of natural (e.g.

Online mobile C-arm calibration using inertial sensors: a preliminary study in order to achieve CBCT.

Purpose: Cone beam computed tomography (CBCT) became increasingly popular over the last years. It allows more accurate diagnosis and treatment planning with a lower effective radiation dose. However, volume reconstruction algorithms require a very precise knowledge of the imaging geometry.

Maxillary sinus floor elevation using Beta-Tricalcium-Phosphate (beta-TCP) or natural bone: same inflammatory response.

Sinus elevation is a common procedure to increase bone volume in the atrophic maxilla to allow placement of dental implants. Autogenous bone is the gold standard but is limited in quantity and causes morbidity at the donor site. β-TCP is a synthetic biomaterial commonly used in that purpose.

Benchmarking of alignment-free sequence comparison methods.

Background: Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment.

Results: Here, we present a community resource (http://afproject.

The diversity of benthic diatoms affects ecosystem productivity in heterogeneous coastal environments.

The current decrease in biodiversity affects all ecosystems, and the impacts of diversity on ecosystem functioning need to be resolved. So far, marine studies about diversity-ecosystem productivity-relationships have concentrated on small-scale, controlled experiments, with often limited relevance to natural ecosystems. Here, we provide a real-world study on the effects of microorganismal diversity (measured as the diversity of benthic diatom communities) on ecosystem productivity (using chlorophyll a concentration as a surrogate) in a heterogeneous marine coastal archipelago.

Efficient Genome Editing Using CRISPR/Cas9 Technology in Chicory.

CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated with protein CAS9) is a genome-editing tool that has been extensively used in the last five years because of its novelty, affordability, and feasibility. This technology has been developed in many plant species for gene function analysis and crop improvement but has never been used in chicory ( L.).

-mer Similarity, Networks of Microbial Genomes, and Taxonomic Rank.

Microbial genomes have been shaped by parent-to-offspring (vertical) descent and lateral genetic transfer. These processes can be distinguished by alignment-based inference and comparison of phylogenetic trees for individual gene families, but this approach is not scalable to whole-genome sequences, and a tree-like structure does not adequately capture how these processes impact microbial physiology. Here we adopted alignment-free approaches based on -mer statistics to infer phylogenomic networks involving 2,783 completely sequenced bacterial and archaeal genomes and compared the contributions of rRNA, protein-coding, and plasmid sequences to these networks.

A BAHD neofunctionalization promotes tetrahydroxycinnamoyl spermine accumulation in the pollen coat of the Asteraceae family.

In eudicotyledons, accumulation of trihydroxycinnamoyl spermidine that is restricted to the pollen wall constitutes an evolutionary conserved trait. However, the role of this compound, which is synthetized by the BAHD enzyme spermidine hydroxycinnamoyl transferase (SHT), is still a matter of debate. Here, we show that this particular phenolamide is replaced by tetrahydroxycinnamoyl spermine in the pollen coat of the Asteraceae.

Biomaterial granules used for filling bone defects constitute 3D scaffolds: porosity, microarchitecture and molecular composition analyzed by microCT and Raman microspectroscopy.

Biomaterials are used in the granular form to fill small bone defects. Granules can be prepared with a grinder from trabecular bone samples or provided as synthetic biomaterials by industry. Granules occupy the 3D-space and create a macroporosity allowing invasion of vascular and bone cells when the inter-granular pores are larger than 300 µm.

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery.

Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology.

Alignment-free inference of hierarchical and reticulate phylogenomic relationships.

We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA.

Maxillary Sinus Lift with Beta-Tricalcium Phosphate (β-TCP) in Edentulous Patients: A Nanotomographic and Raman Study.

Sinus lift elevation restores bone mass at the maxilla in edentulate patients before the placement of dental implants. It consists of opening the lateral side of the sinus and grafting beta-tricalcium phosphate granules (β-TCP) under the olfactory membrane. Bone biopsies were obtained in five patients after 60 weeks.

Asymmetric bone remodeling in mandibular and maxillary tori.

Objectives: Tori are frequent paucisymptomatic bony outgrowths of the oral cavity in three locations: torus palatinus (TP), mandibularis (TM), and maxillaris (TMax). Their usually described histological characteristics are unspecific: normal cortical bone with more or less trabecular bone. The aim of this study was to describe tori's specific morphological and histomorphometric characteristics.

Recapitulating phylogenies using -mers: from trees to networks.

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution.

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.

Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement.

Experimental Assessment of the Effects of Temperature and Food Availability on Particle Mixing by the Bivalve Abra alba Using New Image Analysis Techniques.

The effects of temperature and food addition on particle mixing in the deposit-feeding bivalve Abra alba were assessed using an experimental approach allowing for the tracking of individual fluorescent particle (luminophore) displacements. This allowed for the computations of vertical profiles of a set of parameters describing particle mixing. The frequency of luminophore displacements (jumps) was assessed through the measurement of both waiting times (i.

Effects of NO3 (-) and PO4 (3-) on the release of geogenic arsenic and antimony in agricultural wetland soil: a field and laboratory approach.

The dynamics of arsenic (As) and antimony (Sb) in wetland soil periodically submitted to agricultural pressure as well as the impact of soil enrichment with NO3 (-) (50 mg L(-1)) and PO4 (3-) (20 mg L(-1)) on As and Sb release were evaluated at both field and laboratory scales. The results showed that As and Sb exhibited different temporal behaviors, depending on the study scale. At field scale, As release (up to 93 μg L(-1)) occurred under Fe-reducing conditions, whereas Sb release was favored under oxidizing conditions (up to 5 μg L(-1)) and particularity when dissolved organic carbon (DOC) increased in soil pore water (up to 92.