An adaptation model for trabecular bone at different mechanical levels

Background  

Bone has the ability to adapt to mechanical usage or other biophysical stimuli in terms of its mass and architecture, indicating that a certain mechanism exists for monitoring mechanical usage and controlling the bone's adaptation behaviors. There are four zones describing different bone adaptation behaviors: the disuse, adaptation, overload, and pathologic overload zones. In different zones, the changes of bone mass, as calculated by the difference between the amount of bone formed and what is resorbed, should be different.     

A genetic approach for building different alphabets for peptide and protein classification

Background  

In this paper, it is proposed an optimization approach for producing reduced alphabets for peptide classification, using a Genetic Algorithm. The classification task is performed by a multi-classifier system where each classifier (Linear or Radial Basis function Support Vector Machines) is trained using features extracted by different reduced alphabets. Each alphabet is constructed by a Genetic Algorithm whose objective function is the maximization of the area under the ROC-curve obtained in several classification problems.     

PseudoGeneQuest – Service for identification of different pseudogene types in the human genome

Background  

Pseudogenes, nonfunctional copies of genes, evolve fast due the lack of evolutionary pressures and thus appear in several different forms. PseudoGeneQuest is an online tool to search the human genome for a given query sequence and to identify different types of pseudogenes as well as novel genes and gene fragments.     

Comparison of fertility results after vaginal insemination using different thawing procedures and packages for frozen ram semen

Background  

The effect of different thawing procedures for ram semen frozen in minitubes and mini straws on the fertility of sheep was tested in a field trial.     

Determination of reference genes for circadian studies in different tissues and mouse strains

Background  

Circadian rhythms have a profound effect on human health. Their disruption can lead to serious pathologies, such as cancer and obesity. Gene expression studies in these pathologies are often studied in different mouse strains by quantitative real time polymerase chain reaction (qPCR). Selection of reference genes is a crucial step of qPCR experiments. Recent studies show that reference gene stability can vary between species and tissues, but none has taken circadian experiments into consideration.     

On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation

Background  

The original spotted array technology with competitive hybridization of two experimental samples and measuring relative expression levels is increasingly displaced by more accurate platforms that allow determining absolute expression values for a single sample (for example, Affymetrix GeneChip and Illumina BeadChip). Unfortunately, cross-platform comparisons show a disappointingly low concordance between lists of regulated genes between the latter two platforms.     

A tool for comparing different statistical methods on identifying differentially expressed genes

Background  

Many different statistical methods have been developed to deal with two group comparison microarray experiments. Most often, a substantial number of genes may be selected or not, depending on which method was actually used. Practical guidance on the application of these methods is therefore required. We developed a procedure based on bootstrap and a criterion to allow viewing and quantifying differences between method-dependent selections. We applied this procedure on three datasets that cover a range of possible sample sizes to compare three well known methods, namely: t-test, LPE and SAM.     

A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips

Background  

In gene expression studies a key role is played by the so called "pre-processing", a series of steps designed to extract the signal and account for the sources of variability due to the technology used rather than to biological differences between the RNA samples. At the moment there is no commonly agreed gold standard pre-processing method and each researcher has the responsibility to choose one method, incurring the risk of false positive and false negative features arising from the particular method chosen.     

Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell

Background  

The characterization of the global functional structure of a cell is a major goal in bioinformatics and systems biology. Gene Ontology (GO) and the protein-protein interaction network offer alternative views of that structure.     

Actin binding domains direct actin-binding proteins to different cytoskeletal locations

Background  

Filamin (FLN) and non-muscle α-actinin are members of a family of F-actin cross-linking proteins that utilize Calponin Homology domains (CH-domain) for actin binding. Although these two proteins have been extensively characterized, little is known about what regulates their binding to F-actin filaments in the cell.     

Abrasions and lameness in piglets born in different farrowing systems with different types of floor

Background  

The quality of the floor is essential to the welfare of piglets as abrasions often are recorded in newborn piglets, and such lesions may lead to lameness. Apart from animal suffering, lameness contributes to losses in form of dead piglets, decreased growth, and increased use of antibiotics and manual labour.     

A decoy set for the thermostable subdomain from chicken villin headpiece,comparison of different free energy estimators

Background  

Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently evaluated by discriminating native or native-like conformations from large ensembles of so-called decoy structures.     

In situ evaluation of surface roughness and micromorphology of temporary soft denture liner materials at different time intervals

Objective

To perform an in situ evaluation of surface roughness and micromorphology of two soft liner materials for dentures at different time intervals.

Background

The surface roughness of materials may influence the adhesion of micro‐organisms and inflammation of the mucosal tissues. The in situ evaluation of surface roughness and the micromorphology of soft liner materials over the course of time may present results different from those of in vitro studies, considering the constant presence of saliva and food, the changes in temperature and the pH level in the oral cavity.

Materials and methods

Forty‐eight rectangular specimens of each of the two soft liner materials were fabricated: a silicone‐based material (Mucopren Soft) and an acrylic resin‐based material (Trusoft). The specimens were placed in the dentures of 12 participants (n = 12), and the materials were evaluated for surface roughness and micromorphology at different time intervals: 0, 7, 30 and 60 days. Roughness (Ra) was evaluated by means of a roughness tester. Surface micromorphology was evaluated by scanning electron microscopy.

Results

Analysis of variance for randomised block design and Tukey's test showed that surface roughness values were lower in the groups using the silicone‐based material at all the time intervals (P < .0001). The average surface roughness was higher at time interval 0 than at the other intervals, for both materials (P < .0001). The surface micromorphology showed that the silicone material presented a more regular and smoother surface than the acrylic resin‐based material.

Conclusion

The surface roughness of acrylic resin‐based and silicone‐based denture soft liner materials decreased after 7 days of evaluation, leading to a smoother surface over time. The silicone‐based material showed lower roughness values and a smoother surface than the acrylic resin‐based material, thereby making it preferred when selecting more appropriate material, due its tendency to promote less biofilm build‐up.     

Lamellipodium extension and membrane ruffling require different SNARE-mediated trafficking pathways

Background  

Intracellular membrane traffic is an essential component of the membrane remodeling that supports lamellipodium extension during cell adhesion. The membrane trafficking pathways that contribute to cell adhesion have not been fully elucidated, but recent studies have implicated SNARE proteins. Here, the functions of several SNAREs (SNAP23, VAMP3, VAMP4 and syntaxin13) are characterized during the processes of cell spreading and membrane ruffling.     

Comparison of different treatment options for palm oil production waste on a life cycle basis

Background, aim, and scope  

Globally, 45 million metric tonnes of palm oil has been produced in 2009. The production of 1 t crude palm oil requires 5 t of fresh fruit bunches (FFB). On average, processing of 1 t FFB in palm oil mills generates 230 kg empty fruit bunches (EFB) and 650 kg palm oil mill effluent (POME) as residues. These residues cause considerable environmental burdens, particularly greenhouse gas emissions. In order to reduce those emissions, four waste management options are compared in the present study using 1,000 kg of FFB as functional unit.     

XRCC1 and PCNA are loading platforms with distinct kinetic properties and different capacities to respond to multiple DNA lesions

Background  

Genome integrity is constantly challenged and requires the coordinated recruitment of multiple enzyme activities to ensure efficient repair of DNA lesions. We investigated the dynamics of XRCC1 and PCNA that act as molecular loading platforms and play a central role in this coordination.     

Evaluating different methods of microarray data normalization

Background  

With the development of DNA hybridization microarray technologies, nowadays it is possible to simultaneously assess the expression levels of thousands to tens of thousands of genes. Quantitative comparison of microarrays uncovers distinct patterns of gene expression, which define different cellular phenotypes or cellular responses to drugs. Due to technical biases, normalization of the intensity levels is a pre-requisite to performing further statistical analyses. Therefore, choosing a suitable approach for normalization can be critical, deserving judicious consideration.     

Maximum static inspiratory and expiratory pressures with different lung volumes

Background  

Maximum pressures developed by the respiratory muscles can indicate the health of the respiratory system, help to determine maximum respiratory flow rates, and contribute to respiratory power development. Past measurements of maximum pressures have been found to be inadequate for inclusion in some exercise models involving respiration.