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American Journal of Veterinary Research May 2013To characterize medial femoral condyle (MFC) morphometrics and subchondral bone density patterns in Thoroughbred racehorses and to determine whether these variables...
OBJECTIVE
To characterize medial femoral condyle (MFC) morphometrics and subchondral bone density patterns in Thoroughbred racehorses and to determine whether these variables differ between left and right limbs.
SAMPLE
Stifle joints harvested from 6 Thoroughbred racehorses euthanized for reasons other than hind limb lameness.
PROCEDURES
The distal portion of the left and right femurs of each cadaver was scanned via CT. Hounsfield units were converted to dipotassium phosphate equivalent densities through use of a phantom on each specimen. Medial femoral condyle width, length, height, and curvature; subchondral bone plate densities; and subchondral trabecular bone densities were analyzed in multiple sections in 5 frontal planes and 3 sagittal planes and were compared between left and right MFCs.
RESULTS
MFC width, length, and height did not differ between left and right limbs. Regions of interest in the right caudoaxial subchondral bone plate and subchondral trabecular bone were significantly denser than their corresponding left regions of interest in the frontal and sagittal planes. A concavity in the otherwise convex articular surface of the cranial aspect of the MFC was identified in 11 of 12 specimens.
CONCLUSIONS AND CLINICAL RELEVANCE
A disparity was identified between left and right subchondral bone density patterns at the caudoaxial aspect of the MFC, which could be attributable to the repetitive asymmetric cyclic loading that North American Thoroughbred racehorses undergo as they race in a counterclockwise direction. The uneven region at the cranial aspect of the MFC could be associated with the development of subchondral bone cysts in horses.
Topics: Animals; Bone Density; Cadaver; Femur; Horses; Stifle
PubMed: 23627381
DOI: 10.2460/ajvr.74.5.691 -
Bioinformation 2023It is of interest to explore the correlation between preoperative bone density, assessed via CBCTT, and primary stability of dental implants, assessed by torque ratchet....
It is of interest to explore the correlation between preoperative bone density, assessed via CBCTT, and primary stability of dental implants, assessed by torque ratchet. A total of 100 patients who had implant placed were taken a sample for this retrospective study. The Hounsfield units (HU) derived preoperative bone densities at implant sites that were acquired with the help of the CBCT and the primary stability was achieved during the day of surgery. Both were compared to optimum bone densities. Statistical correlation was done between the HU and Bone density. Data suggests that evaluating HU values, along with other parameters, before performing implant surgery could lead to better primary implant stability.
PubMed: 37822826
DOI: 10.6026/97320630019495 -
Journal of Applied Crystallography Dec 2017A procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP...
A procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP essentially is obtained by inverse Fourier transform of the dynamic structure factors of the total charge density corresponding to the independent atom model, the multipole model or maximum-entropy densities, employing dedicated software that will be part of the software package. Our approach is also discussed with respect to the Ewald summation method. It is argued that a meaningful ESP can only be obtained if identical thermal smearing is applied to the nuclear (positive) and electronic (negative) parts of the dynamic charge densities. The method is applied to structure models of dl-serine at three different temperatures of 20, 100 and 298 K. The ESP at locations near the atomic nuclei exhibits a drastic reduction with increasing temperature, the largest difference between the ESP from the static charge density and the ESP of the dynamic charge density being at = 20 K. These features demonstrate that zero-point vibrations are sufficient for changing the spiky nature of the ESP at the nuclei into finite values. On 0.5 e Å isosurfaces of the electron densities (taken as the molecular surface relevant to intermolecular interactions), the dynamic ESP is surprisingly similar at all temperatures, while the static ESP of a single molecule has a slightly larger range and is shifted towards positive potential values.
PubMed: 29217990
DOI: 10.1107/S1600576717013802 -
FEMS Microbiology Ecology Apr 2020Larval crowding represents a complex stressful situation arising from inter-individual competition for time- and space-limited resources. The foraging of a large number...
Larval crowding represents a complex stressful situation arising from inter-individual competition for time- and space-limited resources. The foraging of a large number of individuals may alter the chemical and bacterial composition of food and in turn affect individual's traits. Here we used Drosophila melanogaster to explore these assumptions. First, we used a wide larval density gradient to investigate the impact of crowding on phenotypical traits. We confirmed that high densities increased development time and pupation height, and decreased viability and body mass. Next, we measured concentrations of common metabolic wastes (ammonia, uric acid) and characterized bacterial communities, both in food and in larvae, for three contrasting larval densities (low, medium and high). Ammonia concentration increased in food from medium and high larval densities, but remained low in larvae regardless of the larval density. Uric acid did not accumulate in food but was detected in larvae. Surprisingly, bacterial composition remained stable in guts of larvae whatever their rearing density, although it drastically changed in the food. Overall, these results indicate that crowding deeply affects individuals, and also their abiotic and biotic surroundings. Environmental bacterial communities likely adapt to altered nutritional situations resulting from crowding, putatively acting as scavengers of larval metabolic wastes.
Topics: Animals; Drosophila melanogaster; Gastrointestinal Microbiome; Humans; Larva; Phenotype; Population Density
PubMed: 32221589
DOI: 10.1093/femsec/fiaa055 -
BMC Bioinformatics May 2016Several tools are available for visualizing genomic data. Some, such as Gbrowse and Jbrowse, are very efficient for small genomic regions, but they are not suitable for...
BACKGROUND
Several tools are available for visualizing genomic data. Some, such as Gbrowse and Jbrowse, are very efficient for small genomic regions, but they are not suitable for entire genomes. Others, like Phenogram and CViT, can be used to visualise whole genomes, but are not designed to display very dense genomic features (eg: interspersed repeats). We have therefore developed DensityMap, a lightweight Perl program that can display the densities of several features (genes, ncRNA, cpg, etc.) along chromosomes on the scale of the whole genome. A critical advantage of DensityMap is that it uses GFF annotation files directly to compute the densities of features without needing additional information from the user. The resulting picture is readily configurable, and the colour scales used can be customized for a best fit to the data plotted.
RESULTS
DensityMap runs on Linux architecture with few requirements so that users can easily and quickly visualize the distributions and densities of genomic features for an entire genome. The input is GFF3-formated data representing chromosomes (linkage groups or pseudomolecules) and sets of features which are used to calculate representations in density maps. In practise, DensityMap uses a tilling window to compute the density of one or more features and the number of bases covered by these features along chromosomes. The densities are represented by colour scales that can be customized to highlight critical points. DensityMap can compare the distributions of features; it calculates several chromosomal density maps in a single image, each of which describes a different genomic feature. It can also use the genome nucleotide sequence to compute and plot a density map of the GC content along chromosomes.
CONCLUSIONS
DensityMap is a compact, easily-used tool for displaying the distribution and density of all types of genomic features within a genome. It is flexible enough to visualize the densities of several types of features in a single representation. The images produced are readily configurable and their SVG format ensures that they can be edited.
Topics: Animals; Base Composition; Drosophila melanogaster; Exons; Genetic Linkage; Genome; Genomics; Long Interspersed Nucleotide Elements; RNA, Untranslated; Retroelements; Software
PubMed: 27153821
DOI: 10.1186/s12859-016-1055-0 -
Journal of Chemical Ecology Dec 2020Western flower thrips (WFT), Frankliniella occidentalis, is a serious insect pest of Chrysanthemum [Chrysanthemum × morifolium Ramat. (Asteraceae)]. Here we have...
Western flower thrips (WFT), Frankliniella occidentalis, is a serious insect pest of Chrysanthemum [Chrysanthemum × morifolium Ramat. (Asteraceae)]. Here we have investigated whether genotypic variation in constitutive and inducible resistance to WFT correlates with phenotypic differences in leaf trichome density and the activity of the defense-related enzyme polyphenol oxidase (PPO) in chrysanthemum. Non-glandular and glandular leaf trichome densities significantly varied among ninety-five chrysanthemum cultivars. Additional analyses in a subset of these cultivars, differing in leaf trichome density, revealed significant variation in PPO activities and resistance to WFT as well. Constitutive levels of trichome densities and PPO activity, however, did not correlate with chrysanthemum resistance to WFT. Further tests showed that exogenous application of the phytohormone jasmonic acid (JA) increased non-glandular trichome densities, PPO activity and chrysanthemum resistance to WFT, and that these effects were cultivar dependent. In addition, no tradeoff between constitutive and inducible resistance to WFT was observed. JA-mediated induction of WFT resistance, however, did not correlate with changes in leaf trichome densities nor PPO activity levels. Taken together, our results suggest that chrysanthemum can display both high levels of constitutive and inducible resistance to WFT, and that leaf trichome density and PPO activity may not play a relevant role in chrysanthemum defenses against WFT.
Topics: Animals; Catechol Oxidase; Chrysanthemum; Cyclopentanes; Genotype; Host-Parasite Interactions; Insect Control; Insect Repellents; Oxylipins; Plant Extracts; Plant Growth Regulators; Thysanoptera; Trichomes
PubMed: 33089352
DOI: 10.1007/s10886-020-01222-1 -
Poultry Science Sep 2017Free-range laying hen systems are increasing in number within Australia. Variation in outdoor stocking densities has led to development of a national information...
Free-range laying hen systems are increasing in number within Australia. Variation in outdoor stocking densities has led to development of a national information standard on free-range egg labeling, including setting a maximum density of 10,000 hens per hectare. However, there are few data on the impacts of differing outdoor densities on production and egg quality. ISA Brown hens in small (150 hens) flocks were housed in identical indoor pens, each with access (from 21 weeks) to different sized ranges simulating one of three outdoor stocking densities (2 replicates each: 2,000 hens/hectare (ha), 10,000 hens/ha, 20,000 hens/ha). Hen-day production was tracked from 21 through 35 weeks with eggs visually graded daily for external deformities. All eggs laid on one day were weighed each week. Eggs were collected from each pen at 25, 30, and 36 weeks and analyzed for egg quality. There were no effects of outdoor stocking density on average hen-day percentage production (P = 0.67), egg weight (P = 0.09), percentages of deformed eggs (P = 0.30), shell reflectivity (P = 0.74), shell breaking strength (P = 0.07), shell deformation (P = 0.83), or shell thickness (P = 0.24). Eggs from hens in the highest density had the highest percentage shell weight (P = 0.004) and eggs from the lowest density had the highest yolk color score (P < 0.001). The amount of cuticle present did not differ between densities (P = 0.95) but some aspects of shell colors (P ≤ 0.01) and location of protoporphyrin IX (P = 0.046) varied. Hen age affected the majority of measurements. Stocking density differences may be related to hen diet as previous radio-frequency identification tracking of individual hens in these flocks showed birds used the range for longer in the lowest density and the least in the highest density, including depleting the range of vegetation sooner in the smaller ranges. An additional study assessing the relationship between individual hen range use, nutrition, and egg quality is warranted.
Topics: Animal Husbandry; Animals; Chickens; Egg Shell; Female; Housing, Animal; New South Wales; Ovum; Population Density; Protoporphyrins; Reproduction
PubMed: 28431098
DOI: 10.3382/ps/pex107 -
Insights Into Imaging Sep 2019Cervical component of thymus is noted more in children and young adults than in older age group. CT texture (lobules of soft tissue interspersed with fat), similarity...
OBJECTIVES
Cervical component of thymus is noted more in children and young adults than in older age group. CT texture (lobules of soft tissue interspersed with fat), similarity with CT density of mediastinal thymus and continuity with mediastinal thymus on sagittal/coronal images, are given as the criteria for diagnosis of the cervical thymus. But CT densities of cervical and mediastinal components of the thymus may vary. The purpose of our study was to compare CT densities of cervical and mediastinal parts of the thymus, in cases where ultrasonography correlation was available.
METHODS
We retrospectively identified 22 patients who had undergone CT between May 2015 and May 2017 and in whom ultrasonography (USG) correlation was available. CT densities of cervical and mediastinal components of thymus were measured.
RESULTS
1. CT density of cervical thymus is lower than the CT density of mediastinal thymus by ~ 25 HU. 2. There is a moderate positive correlation between CT densities of cervical and mediastinal parts of the thymus. 3. CT densities of both cervical and mediastinal thymus were found to reduce with age, but the reduction was statistically significant only in the cervical thymus in this study.
CONCLUSIONS
CT densities of cervical and mediastinal components of the thymus may vary, with CT density of cervical thymus being lower. There is a positive correlation between CT densities of cervical and mediastinal parts of the thymus. CT density of cervical thymus reduces with age. Understanding these may help avoid confusion on CT and avoid the need for correlative USG, saving time and effort.
PubMed: 31565757
DOI: 10.1186/s13244-019-0781-z -
Journal of the Royal Society, Interface Apr 2020Scratch assays are routinely used to study collective cell behaviour . Typical experimental protocols do not vary the initial density of cells, and typical mathematical...
Scratch assays are routinely used to study collective cell behaviour . Typical experimental protocols do not vary the initial density of cells, and typical mathematical modelling approaches describe cell motility and proliferation based on assumptions of linear diffusion and logistic growth. Jin (Jin . 2016 , 136-145 (doi:10.1016/j.jtbi.2015.10.040)) find that the behaviour of cells in scratch assays is density-dependent, and show that standard modelling approaches cannot simultaneously describe data initiated across a range of initial densities. To address this limitation, we calibrate an individual-based model to scratch assay data across a large range of initial densities. Our model allows proliferation, motility, and a direction bias to depend on interactions between neighbouring cells. By considering a hierarchy of models where we systematically and sequentially remove interactions, we perform model selection analysis to identify the minimum interactions required for the model to simultaneously describe data across all initial densities. The calibrated model is able to match the experimental data across all densities using a single parameter distribution, and captures details about the spatial structure of cells. Our results provide strong evidence to suggest that motility is density-dependent in these experiments. On the other hand, we do not see the effect of crowding on proliferation in these experiments. These results are significant as they are precisely the opposite of the assumptions in standard continuum models, such as the Fisher-Kolmogorov equation and its generalizations.
Topics: Cell Line, Tumor; Cell Movement; Cell Proliferation; Diffusion; Models, Biological
PubMed: 32343933
DOI: 10.1098/rsif.2020.0143 -
Journal of Vision Jul 2017Texture density has previously been thought of as a scalar attribute on the assumption that texture density adaptation only reduces, not enhances, perceived density...
Texture density has previously been thought of as a scalar attribute on the assumption that texture density adaptation only reduces, not enhances, perceived density (Durgin & Huk, 1997). This "unidirectional" property of density adaptation is in contradistinction to the finding that simultaneous density contrast (SDC) is "bidirectional"; that is, not only do denser surrounds reduce the perceived density of a lower density region, but sparser surrounds enhance it (Sun, Baker, & Kingdom, 2016). Here we reexamine the directionality of density adaptation using random dot patterns and a two-alternative forced choice task in which observers compare the perceived density of adapted test patches with unadapted match stimuli. In the first experiment, we observed a unidirectional density aftereffect when test and match were presented simultaneously as in previous studies. However, when they were presented sequentially, bidirectionality was obtained. This bidirectional aftereffect remained when the presentation order of test and match was reversed (second experiment). In the third experiment, we used sequential presentation to measure the density aftereffect for a wide range of adaptor densities (0-73 dots/deg2) and test densities (1.6, 6.4, and 25.6 dots/deg2). We found bidirectionality for all combinations of adaptor and test densities, consistent with our previous SDC results. This evidence supports the idea that there are multiple channels selective to texture density in human vision.
Topics: Adaptation, Ocular; Choice Behavior; Contrast Sensitivity; Field Dependence-Independence; Humans; Pattern Recognition, Visual; Psychometrics
PubMed: 28719913
DOI: 10.1167/17.8.9