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Irish Journal of Medical Science Dec 2023The tibial tuberosity-trochlear groove (TTTG) distance is used to assess patellofemoral instability (PFI) and the likelihood of the development of patellofemoral...
BACKGROUND
The tibial tuberosity-trochlear groove (TTTG) distance is used to assess patellofemoral instability (PFI) and the likelihood of the development of patellofemoral disorders. The current gold standard in the assessment of the TTTG is computed tomography (CT) or magnetic resonance imaging (MRI). The current image software used for viewing these CT images does not allow for easy assessment of the TTTG.
AIMS
This study presents a simple method to measure the TTTG on any image software, utilizing easily available and affordable stationary.
METHODS
Four consecutive patients with no known knee pathologies were selected from recent studies at our institution. Their TTTGs were measured using this study's method and validated using the standard, freely available image analysis software Fiji. Pre-defined anatomical landmarks were located and marked using adhesive pieces of paper. The TTTG was defined as the distance between parallel lines through the apex of the tibial tuberosity and trough of the trochlear groove, where each of these lines is perpendicular to the Dorsal Condylar Line.
RESULTS
The TTTG measured using this study's method was found to be in agreement with the measurements made using Fiji software.
CONCLUSIONS
This study demonstrates that the TTTG can be simply and quickly assessed using readily available and affordable stationery, without the need for expensive or complex secondary analysis software. This could allow for the assessment of PFI in the outpatient clinic whilst the patient is present, offering valuable assistance to the orthopaedic surgeon in clinical decision making.
Topics: Humans; Tibia; Knee Joint; Tomography, X-Ray Computed; Magnetic Resonance Imaging; Joint Instability
PubMed: 36787029
DOI: 10.1007/s11845-023-03302-z -
SN Applied Sciences 2021In this study we present the new power electronic circuit implementation to create the arbitrary near-rectangular electromagnetic pulse. To this end, we develop a...
UNLABELLED
In this study we present the new power electronic circuit implementation to create the arbitrary near-rectangular electromagnetic pulse. To this end, we develop a parallel- Insulated-gate bipolar transistors (IGBT)-based magnetic pulse generator utilizing the H-bridge architecture. This approach effectively reduces the current stress on the power switches while maintaining a simple structure using a single DC source and energy storage capacitor. Experimental results from the circuit characterization show that the proposed circuit is capable of repeatedly generating near-rectangular magnetic pulses and enables the generation of configurable and stable magnetic pulses without causing excessive device stresses. The introduced device enables the production of near-rectangular pulse trains for modulated magnetic stimuli. The maximum positive pulse width in the proposed neurostimulator is up to 600 µs, which is adjustable by the operator at the step resolution of 10 µs. The maximum transferred energy to the treatment coil was measured to be 100.4 J. The proposed transcranial magnetic stimulator (TMS) device enables more flexible magnetic stimulus shaping by H-bridge architecture and parallel IGBTs, which can effectively mitigate the current stress on power switches for repetitive treatment protocols.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s42452-021-04420-y.
PubMed: 33748674
DOI: 10.1007/s42452-021-04420-y -
Brain and Language Oct 2010Songbirds share a number of parallels with humans that make them an attractive model system for studying the behavioral and neurobiological mechanisms that underlie the... (Review)
Review
Songbirds share a number of parallels with humans that make them an attractive model system for studying the behavioral and neurobiological mechanisms that underlie the learning and processing of vocal communication signals. Here we review the perceptual and cognitive mechanisms of audition in birds, and emphasize the behavioral and neural basis of song recognition. Where appropriate, we point out a number of intersections with human vocal communication behavior that suggest common mechanisms amenable to further study, and limitations of birdsong as a model for human language.
Topics: Animals; Auditory Pathways; Auditory Perception; Brain; Discrimination, Psychological; Hearing; Humans; Language; Recognition, Psychology; Songbirds; Vocalization, Animal
PubMed: 20471673
DOI: 10.1016/j.bandl.2009.09.008 -
Theory in Biosciences = Theorie in Den... Jun 2023Recent results have shown that the human malaria-resistant hemoglobin S mutation originates de novo more frequently in the gene and in the population where it is of... (Review)
Review
Recent results have shown that the human malaria-resistant hemoglobin S mutation originates de novo more frequently in the gene and in the population where it is of adaptive significance, namely, in the hemoglobin subunit beta gene compared to the nonresistant but otherwise identical 20A[Formula: see text]T mutation in the hemoglobin subunit delta gene, and in sub-Saharan Africans, who have been subject to intense malarial pressure for many generations, compared to northern Europeans, who have not. This finding raises a fundamental challenge to the traditional notion of accidental mutation. Here, we address this finding with the replacement hypothesis, according to which preexisting genetic interactions can lead directly and mechanistically to mutations that simplify and replace them. Thus, an evolutionary process under selection can gradually hone in on interactions of importance for the currently evolving adaptations, from which large-effect mutations follow that are relevant to these adaptations. We exemplify this hypothesis using multiple types of mutation, including gene fusion mutations, gene duplication mutations, A[Formula: see text]G mutations in RNA-edited sites and transcription-associated mutations, and place it in the broader context of a system-level view of mutation origination called interaction-based evolution. Potential consequences include that similarity of mutation pressures may contribute to parallel evolution in genetically related species, that the evolution of genome organization may be driven by mutational mechanisms, that transposable element movements may also be explained by replacement, and that long-term directed mutational responses to specific environmental pressures are possible. Such mutational phenomena need to be further tested by future studies in natural and artificial settings.
Topics: Humans; Selection, Genetic; Mutation; Genome; Adaptation, Physiological; Hemoglobin Subunits
PubMed: 36899155
DOI: 10.1007/s12064-023-00387-z -
Ecology and Evolution Dec 2022Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have...
Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e., microbiotas), which are crucial for their hosts' ecology and evolution. Determining the extent of microbiota parallelism in nature can improve our ability to identify the factors that are associated with (putatively adaptive) shifts in microbial communities. While it has been emphasized that (non)parallel evolution is better considered as a quantitative continuum rather than a binary phenomenon, quantitative approaches have rarely been used to study microbiota parallelism. We advocate using multivariate vector analysis (i.e., phenotypic change vector analysis) to quantify direction and magnitude of microbiota changes and discuss the applicability of this approach for studying parallelism, and we compiled an R package for multivariate vector analysis of microbial communities ('multivarvector'). We exemplify its use by reanalyzing gut microbiota data from multiple fish species that exhibit parallel shifts in trophic ecology. We found that multivariate vector analysis results were largely consistent with other statistical methods, parallelism estimates were not affected by the taxonomic level at which the microbiota is studied, and parallelism might be stronger for gut microbiota function compared to taxonomic composition. This approach provides an analytical framework for quantitative comparisons across host lineages, thereby providing the potential to advance our capacity to predict microbiota changes. Hence, we emphasize that the development and application of quantitative measures, such as multivariate vector analysis, should be further explored in microbiota research in order to better understand the role of microbiota dynamics during their hosts' adaptive evolution, particularly in settings of parallel evolution.
PubMed: 36590339
DOI: 10.1002/ece3.9674 -
Science Advances Nov 2021Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated...
Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish . While morphological differentiation was continuously distributed across different lake-stream population pairs, we found that there were two categories with respect to genomic differentiation, suggesting a “gray zone” of speciation at ~0.1% net nucleotide divergence. Genomic differentiation was increased in the presence of divergent selection and drift compared to drift alone. The quantification of phenotypic and genetic parallelism in four cichlid species occurring along a lake-stream environmental contrast revealed parallel and antiparallel components in rapid adaptive divergence, and morphological convergence in species replicates inhabiting the same environments. Furthermore, we show that the extent of parallelism was higher when ancestral populations were more similar. Our study highlights the complementary roles of divergent selection and drift on speciation and parallel evolution.
PubMed: 34731007
DOI: 10.1126/sciadv.abg5391 -
PloS One 2012This study sought to synthesize survival outcomes from trials of laparoscopic and open colorectal cancer surgery, and to determine whether expert acceptance of this... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
This study sought to synthesize survival outcomes from trials of laparoscopic and open colorectal cancer surgery, and to determine whether expert acceptance of this technology in the literature has parallel cumulative survival evidence.
STUDY DESIGN
A systematic review of randomized trials was conducted. The primary outcome was survival, and meta-analysis of time-to-event data was conducted. Expert opinion in the literature (published reviews, guidelines, and textbook chapters) on the acceptability of laparoscopic colorectal cancer was graded using a 7-point scale. Pooled survival data were correlated in time with accumulating expert opinion scores.
RESULTS
A total of 5,800 citations were screened. Of these, 39 publications pertaining to 23 individual trials were retained. As well, 414 reviews were included (28 guidelines, 30 textbook chapters, 20 systematic reviews, 336 narrative reviews). In total, 5,782 patients were randomized to laparoscopic (n = 3,031) and open (n = 2,751) colorectal surgery. Survival data were presented in 16 publications. Laparoscopic surgery was not inferior to open surgery in terms of overall survival (HR = 0.94, 95% CI 0.80, 1.09). Expert opinion in the literature pertaining to the oncologic acceptability of laparoscopic surgery for colon cancer correlated most closely with the publication of large RCTs in 2002-2004. Although increasingly accepted since 2006, laparoscopic surgery for rectal cancer remained controversial.
CONCLUSIONS
Laparoscopic surgery for colon cancer is non-inferior to open surgery in terms of overall survival, and has been so since 2004. The majority expert opinion in the literature has considered these two techniques to be equivalent since 2002-2004. Laparoscopic surgery for rectal cancer has been increasingly accepted since 2006, but remains controversial. Knowledge translation efforts in this field appear to have paralleled the accumulation of clinical trial evidence.
Topics: Colorectal Neoplasms; Expert Testimony; Humans; Laparoscopy; Randomized Controlled Trials as Topic; Survival Rate; Treatment Outcome
PubMed: 22532846
DOI: 10.1371/journal.pone.0035292 -
PloS One 2023As a powerful but computationally intensive method, hybrid computational models study the dynamics of multicellular systems by evolving discrete cells in reacting and...
As a powerful but computationally intensive method, hybrid computational models study the dynamics of multicellular systems by evolving discrete cells in reacting and diffusing extracellular microenvironments. As the scale and complexity of studied biological systems continuously increase, the exploding computational cost starts to limit large-scale cell-based simulations. To facilitate the large-scale hybrid computational simulation and make it feasible on easily accessible computational devices, we develop Gell (GPU Cell), a fast and memory-efficient open-source GPU-based hybrid computational modeling platform for large-scale system modeling. We fully parallelize the simulations on GPU for high computational efficiency and propose a novel voxel sorting method to further accelerate the modeling of massive cell-cell mechanical interaction with negligible additional memory footprint. As a result, Gell efficiently handles simulations involving tens of millions of cells on a personal computer. We compare the performance of Gell with a state-of-the-art paralleled CPU-based simulator on a hanging droplet spheroid growth task and further demonstrate Gell with a ductal carcinoma in situ (DCIS) simulation. Gell affords ~150X acceleration over the paralleled CPU method with one-tenth of the memory requirement.
Topics: Algorithms; Computer Simulation; Cell Communication; Computer Graphics
PubMed: 37463167
DOI: 10.1371/journal.pone.0288721 -
Genome Biology and Evolution Oct 2023Animals abandoned their marine niche and successfully adapted to life on land multiple times throughout evolution, providing a rare opportunity to study the mechanisms...
Animals abandoned their marine niche and successfully adapted to life on land multiple times throughout evolution, providing a rare opportunity to study the mechanisms driving large scale macroevolutionary convergence. However, the genomic factors underlying this process remain largely unknown. Here, we investigate the macroevolutionary dynamics of gene repertoire evolution during repeated transitions out of the sea in mollusks, a lineage that has transitioned to freshwater and terrestrial environments multiple independent times. Through phylogenomics and phylogenetic comparative methods, we examine ∼100 genomic data sets encompassing all major molluskan lineages. We introduce a conceptual framework for identifying and analyzing parallel and convergent evolution at the orthogroup level (groups of genes derived from a single ancestral gene in the species in question) and explore the extent of these mechanisms. Despite deep temporal divergences, we found that parallel expansions of ancient gene families played a major role in facilitating adaptation to nonmarine habitats, highlighting the relevance of the preexisting genomic toolkit in facilitating adaptation to new environments. The expanded functions primarily involve metabolic, osmoregulatory, and defense-related systems. We further found functionally convergent lineage-exclusive gene gains, while family contractions appear to be driven by neutral processes. Also, genomic innovations likely contributed to fuel independent habitat transitions. Overall, our study reveals that various mechanisms of gene repertoire evolution-parallelism, convergence, and innovation-can simultaneously contribute to major evolutionary transitions. Our results provide a genome-wide gene repertoire atlas of molluskan terrestrialization that paves the way toward further understanding the functional and evolutionary bases of this process.
Topics: Animals; Phylogeny; Biological Evolution; Evolution, Molecular; Genomics; Mollusca; Ecosystem
PubMed: 37793176
DOI: 10.1093/gbe/evad176 -
Genes Feb 2019Studying parallel and convergent amino acid replacements in protein evolution is frequently used to assess adaptive evolution at the molecular level. Identifying...
Studying parallel and convergent amino acid replacements in protein evolution is frequently used to assess adaptive evolution at the molecular level. Identifying parallel and convergent replacements involves multiple steps and computational routines, such as multiple sequence alignment, phylogenetic tree inference, ancestral state reconstruction, topology tests, and simulation of sequence evolution. Here, we present , a Python 3 package that provides a common interface for users to process molecular data and identify parallel and convergent amino acid replacements in orthologous protein sequences. By integrating several widely used programs for computational biology, implements general functions for handling multiple sequence alignment, ancestral-state reconstruction, maximum-likelihood phylogenetic tree inference, and sequence simulation. also contains a built-in pipeline that automates all these sequential steps, and enables quick identification of observed and expected parallel and convergent amino acid replacements under different evolutionary assumptions. The most up-to-date version of , including scripts containing user tutorials, the full API reference and documentation are publicly and freely available under an open source MIT License via GitHub. The latest stable release is also available on PyPI (the Python Package Index).
Topics: Amino Acid Sequence; Computational Biology; Evolution, Molecular; Phylogeny; Software
PubMed: 30813627
DOI: 10.3390/genes10030181