-
Journal of Evolutionary Biology Jun 2021Research on the genomics of adaptation is rapidly changing. In the last few decades, progress in this area has been driven by methodological advances, not only in the...
Research on the genomics of adaptation is rapidly changing. In the last few decades, progress in this area has been driven by methodological advances, not only in the way increasingly large amounts of molecular data are generated (e.g. with high-throughput sequencing), but also in the way these data are analysed. This includes a growing appreciation and quantitative treatment of covariation among units within the same data type (e.g. genes) or across data types (e.g. genes and phenotypes). The development and adoption of more and more integrative tools have resulted in richer and more interesting empirical work. This special issue - comprising methodological, empirical, and review papers - aims to capture a 'snapshot' of this rapidly evolving field. We discuss in particular three important themes in the study of adaptation: the genetic architecture of adaptive variation, protein-coding and regulatory changes, and parallel evolution. We highlight how more traditional key themes in the study of genetic architecture (e.g. the number of loci underlying adaptive traits and the distribution of their effects) are now being complemented by other factors (e.g. how patterns of linkage and number of loci interact to affect the ability to adapt). Similarly, apart from addressing the relative importance of protein-coding and regulatory changes, we now have the tools to look in-depth at specific types of regulatory variation to gain a clearer picture of regulatory networks. Finally, parallel evolution has always been central to the study of adaptation, but now we are often able to address the question of whether - and to what extent - parallelism at the organismal or phenotypic level is matched by parallelism at the genetic level. Perhaps most importantly, we can now determine what mechanisms are driving parallelism (or lack thereof) across levels of biological organization. All these recent methodological developments open up new directions for future studies of adaptive changes across traits, levels of biological organization, demographic contexts and time scales.
Topics: Adaptation, Biological; Biological Evolution; Genetic Variation; Genomics
PubMed: 34145685
DOI: 10.1111/jeb.13871 -
Frontiers in Neuroscience 2015Multi-modal magnetic resonance imaging (MRI) techniques are widely applied in human brain studies. To obtain specific brain measures of interest from MRI datasets, a... (Review)
Review
Multi-modal magnetic resonance imaging (MRI) techniques are widely applied in human brain studies. To obtain specific brain measures of interest from MRI datasets, a number of complex image post-processing steps are typically required. Parallel workflow tools have recently been developed, concatenating individual processing steps and enabling fully automated processing of raw MRI data to obtain the final results. These workflow tools are also designed to make optimal use of available computational resources and to support the parallel processing of different subjects or of independent processing steps for a single subject. Automated, parallel MRI post-processing tools can greatly facilitate relevant brain investigations and are being increasingly applied. In this review, we briefly summarize these parallel workflow tools and discuss relevant issues.
PubMed: 26029043
DOI: 10.3389/fnins.2015.00171 -
Physical Review. E, Statistical,... Mar 2015We study the thermodynamic properties of the three-dimensional Blume-Capel model on the simple cubic lattice by means of computer simulations. In particular, we...
We study the thermodynamic properties of the three-dimensional Blume-Capel model on the simple cubic lattice by means of computer simulations. In particular, we implement a parallelized variant of the multicanonical approach and perform simulations by keeping a constant temperature and crossing the phase boundary along the crystal-field axis. We obtain numerical data for several temperatures in both the first- and second-order regime of the model. Finite-size scaling analyses provide us with transition points and the dimensional scaling behavior in the numerically demanding first-order regime, as well as a clear verification of the expected Ising universality in the respective second-order regime. Finally, we discuss the scaling behavior in the vicinity of the tricritical point.
PubMed: 25871073
DOI: 10.1103/PhysRevE.91.032126 -
European Journal of Dental Education :... Nov 2023Narrative medicine is a novel approach aimed at attending to the socio-emotional aspects of illness and care. Parallel charts represent one of the tools of narrative... (Observational Study)
Observational Study
INTRODUCTION
Narrative medicine is a novel approach aimed at attending to the socio-emotional aspects of illness and care. Parallel charts represent one of the tools of narrative medicine and are brief accounts of care in which practitioners can express their feelings and emotions towards patients and treatments. They are, therefore, intended to collect practitioners' feedback in the form of "narrative" tools to encourage reflection.
MATERIALS AND METHODS
This is a single-centre observational pilot study comprising the setting up and analysis of parallel charts in two classes of 5th and 6th year students in a Paediatric Dentistry Department in France. Forty-four students completed 126 parallel charts. A qualitative, thematic, analysis was conducted and the charts were also classified according to the three types of description of illness made by Arthur Kleinman.
RESULTS
This work showed that dental students mainly compiled parallel charts from a disease-centred perspective. The qualitative analysis identified the various themes addressed by the student: relationship with patients and managing children's anxiety, student stress, relationship with the environment or with lecturers.
CONCLUSION
The qualitative analysis highlighted the usefulness of compiling parallel charts by the students to allow them to express both positive and negative feelings, and thus to adopt a self-evaluative approach regarding their practices based on emotional impact. Parallel charts may improve patient-practitioner relationship, but more extensive studies over longer periods of time need to be undertaken.
Topics: Humans; Anxiety; Education, Dental; Emotions; Qualitative Research; Students, Dental; Adult
PubMed: 36651688
DOI: 10.1111/eje.12892 -
Orthopaedics & Traumatology, Surgery &... Oct 2021Since its introduction in the early 1960s, the multiple cannulated screw fixation method has been developed for use in femoral neck fractures (FNFs); however, the... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Since its introduction in the early 1960s, the multiple cannulated screw fixation method has been developed for use in femoral neck fractures (FNFs); however, the parallelism of screws remains controversial.
MATERIALS AND METHODS
MEDLINE, Embase, and the Cochrane Library were systematically searched for studies published before June 2, 2020, that compared the use of parallel and non-parallel screw fixation for the treatment of FNF. The pooled analysis was designed to identify differences between the two groups and focused on postoperative complications, including fracture nonunion and osteonecrosis of the femoral head (ONFH).
RESULTS
Over four studies, we enrolled 445 patients, including 195 patients with fixed FNF with parallel trajectory screws and 250 patients with fixed FNF with non-parallel screws. The pooled analysis showed no difference in the nonunion rates (odds ratio (OR)=0.91; 95% confidence interval (CI), 0.24-3.44; p=0.89) and no significant difference in the incidence of ONFH between parallel and non-parallel screw fixation (OR=0.74; 95% CI: 0.21-2.63; p=0.64).
CONCLUSIONS
The results of this meta-analysis reveal that screw parallelism in multiple cannulated screw fixation of FNF has no relationship with either the fracture nonunion rate or the incidence of postoperative ONFH.
LEVEL OF EVIDENCE
III; meta-analysis.
Topics: Bone Screws; Femoral Neck Fractures; Fracture Fixation, Internal; Fractures, Ununited; Humans; Postoperative Complications
PubMed: 34217865
DOI: 10.1016/j.otsr.2021.103005 -
Biology Letters Feb 2022Parallelism between evolutionary trajectories in a trait space is often seen as evidence for repeatability of phenotypic evolution, and angles between trajectories play... (Review)
Review
Parallelism between evolutionary trajectories in a trait space is often seen as evidence for repeatability of phenotypic evolution, and angles between trajectories play a pivotal role in the analysis of parallelism. However, properties of angles in multidimensional spaces have not been widely appreciated by biologists. To remedy this situation, this study provides a brief overview on geometric and statistical aspects of angles in multidimensional spaces. Under the null hypothesis that trajectory vectors have no preferred directions (i.e. uniform distribution on hypersphere), the angle between two independent vectors is concentrated around the right angle, with a more pronounced peak in a higher-dimensional space. This probability distribution is closely related to - and beta distributions, which can be used for testing the null hypothesis concerning a pair of trajectories. A recently proposed method with eigenanalysis of a vector correlation matrix can be connected to the test of no correlation or concentration of multiple vectors, for which simple test procedures are available in the statistical literature. Concentration of vectors can also be examined by tools of directional statistics such as the Rayleigh test. These frameworks provide biologists with baselines to make statistically justified inferences for (non)parallel evolution.
Topics: Biological Evolution; Phenotype
PubMed: 35168376
DOI: 10.1098/rsbl.2021.0638 -
Frontiers in Plant Science 2020Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants...
Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. , a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbor the alpine ecotype and used SNP genotyping to test for repeated alpine colonization. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makes a promising candidate for studying genomic basis of adaptation.
PubMed: 33363550
DOI: 10.3389/fpls.2020.561526 -
Journal of Evolutionary Biology Nov 2022Examples of parallel evolution have been crucial for our understanding of adaptation via natural selection. However, strong parallelism is not always observed even in... (Review)
Review
Examples of parallel evolution have been crucial for our understanding of adaptation via natural selection. However, strong parallelism is not always observed even in seemingly similar environments where natural selection is expected to favour similar phenotypes. Leveraging this variation in parallelism within well-researched study systems can provide insight into the factors that contribute to variation in adaptive responses. Here we analyse the results of 36 studies reporting 446 average trait values in Trinidadian guppies, Poecilia reticulata, from different predation regimes. We examine how the extent of predator-driven phenotypic parallelism is influenced by six factors: sex, trait type, rearing environment, ecological complexity, evolutionary history, and time since colonization. Analyses show that parallel evolution in guppies is highly variable and weak on average, with only 24.7% of the variation among populations being explained by predation regime. Levels of parallelism appeared to be especially weak for colour traits, and parallelism decreased with increasing complexity of evolutionary history (i.e., when estimates of parallelism from populations within a single drainage were compared to estimates of parallelism from populations pooled between two major drainages). Suggestive - but not significant - trends that warrant further research include interactions between the sexes and different trait categories. Quantifying and accounting for these and other sources of variation among evolutionary 'replicates' can be leveraged to better understand the extent to which seemingly similar environments drive parallel and nonparallel aspects of phenotypic divergence.
Topics: Animals; Poecilia; Biological Evolution; Predatory Behavior; Adaptation, Physiological; Selection, Genetic
PubMed: 36098479
DOI: 10.1111/jeb.14086 -
Current Topics in Medicinal Chemistry 2018Molecular docking, as one of the widely used virtual screening methods, aims to predict the binding-conformations of small molecule ligands to the appropriate target... (Review)
Review
Molecular docking, as one of the widely used virtual screening methods, aims to predict the binding-conformations of small molecule ligands to the appropriate target binding site. Because of the computational complexity and the arrival of the big data era, molecular docking requests High- Performance Computing (HPC) to improve its performance and accuracy. We discuss, in detail, the advances in accelerating molecular docking software in parallel, based on the different common HPC platforms, respectively. Not only the existing suitable programs have been optimized and ported to HPC platforms, but also many novel parallel algorithms have been designed and implemented. This review focuses on the techniques and methods adopted in parallelizing docking software. Where appropriate, we refer readers to exemplary case studies.
Topics: Molecular Conformation; Molecular Docking Simulation; Small Molecule Libraries; Software
PubMed: 30129415
DOI: 10.2174/1568026618666180821145215 -
Science Advances Jul 2022pH controls a large repertoire of chemical and biochemical processes in water. Densely arrayed pH microenvironments would parallelize these processes, enabling their...
pH controls a large repertoire of chemical and biochemical processes in water. Densely arrayed pH microenvironments would parallelize these processes, enabling their high-throughput studies and applications. However, pH localization, let alone its arrayed realization, remains challenging because of fast diffusion of protons in water. Here, we demonstrate arrayed localizations of picoliter-scale aqueous acids, using a 256-electrochemical cell array defined on and operated by a complementary metal oxide semiconductor (CMOS)-integrated circuit. Each cell, comprising a concentric pair of cathode and anode with their current injections controlled with a sub-nanoampere resolution by the CMOS electronics, creates a local pH environment, or a pH "voxel," via confined electrochemistry. The system also monitors the spatiotemporal pH profile across the array in real time for precision pH control. We highlight the utility of this CMOS pH localizer-imager for high-throughput tasks by parallelizing pH-gated molecular state encoding and pH-regulated enzymatic DNA elongation at any selected set of cells.
PubMed: 35895813
DOI: 10.1126/sciadv.abm6815