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1.
Benjamin B Wheatley Gregory M Odegard Kenton R Kaufman Tammy L Haut Donahue 《Biomechanics and modeling in mechanobiology》2017,16(3):1011-1022
The passive properties of skeletal muscle are often overlooked in muscle studies, yet they play a key role in tissue function in vivo. Studies analyzing and modeling muscle passive properties, while not uncommon, have never investigated the role of fluid content within the tissue. Additionally, intramuscular pressure (IMP) has been shown to correlate with muscle force in vivo and could be used to predict muscle force in the clinic. In this study, a novel model of skeletal muscle was developed and validated to predict both muscle stress and IMP under passive conditions for the New Zealand White Rabbit tibialis anterior. This model is the first to include fluid content within the tissue and uses whole muscle geometry. A nonlinear optimization scheme was highly effective at fitting model stress output to experimental stress data (normalized mean square error or NMSE fit value of 0.993) and validation showed very good agreement to experimental data (NMSE fit values of 0.955 and 0.860 for IMP and stress, respectively). While future work to include muscle activation would broaden the physiological application of this model, the passive implementation could be used to guide surgeries where passive muscle is stretched. 相似文献
2.
3.
BackgroundInterphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chromatin states, up to multi-megabase-scale domains associated with nuclear positioning, replication timing and other qualities. However, we have lacked detailed, quantitative models to understand the interactions between these different strata.ResultsHere we collate large collections of matched locus-level chromatin features and Hi-C interaction data, representing higher-order organization, across three human cell types. We use quantitative modeling approaches to assess whether locus-level features are sufficient to explain higher-order structure, and identify the most influential underlying features. We identify structurally variable domains between cell types and examine the underlying features to discover a general association with cell-type-specific enhancer activity. We also identify the most prominent features marking the boundaries of two types of higher-order domains at different scales: topologically associating domains and nuclear compartments. We find parallel enrichments of particular chromatin features for both types, including features associated with active promoters and the architectural proteins CTCF and YY1.ConclusionsWe show that integrative modeling of large chromatin dataset collections using random forests can generate useful insights into chromosome structure. The models produced recapitulate known biological features of the cell types involved, allow exploration of the antecedents of higher-order structures and generate testable hypotheses for further experimental studies.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0661-x) contains supplementary material, which is available to authorized users. 相似文献4.
Objectives
To investigate whether polyomaviruses contribute to interstitial cystitis pathogenesis.Subjects and Methods
A prospective study was performed with 50 interstitial cystitis cases compared with 50 age-matched, disease-free controls for the frequency of polyomaviruria. Associations between polyomaviruria and disease characteristics were analysed in cases. Polyomavirus in urine and bladder tissue was detected with species (JC virus vs. BK virus) specific, real-time PCR.Results
Case patients were reflective of interstitial cystitis epidemiology with age range from 26–88 years (median 58) and female predominance (41/50 F). There was a significant increase in the frequency of polyomavirus shedding between cases and controls (p<0.02). Polyomavirus shedding, in particular BK viruria, was associated with vesical ulceration, a marker of disease severity, among interstitial cystitis cases after adjustment for age and sex (OR 6.8, 95% CI 1.89–24.4). There was a significant association among cases between the presence of BK viruria and response to intravesical Clorpactin therapy (OR 4.50, 95% CI 1.17–17.4).Conclusion
The presence of polyomaviruria was found to be associated with the ulcerative form of interstitial cystitis. Clorpactin, which has anti-DNA virus activity, was more likely to improve symptoms in the presence of BK viruria. These data from this pilot study suggest associations between polyomaviruria and interstitial cystitis warranting further investigation. 相似文献5.
Benjamin T. Dunkley Paul A. Sedge Sam M. Doesburg Richard J. Grodecki Rakesh Jetly Pang N. Shek Margot J. Taylor Elizabeth W. Pang 《PloS one》2015,10(4)
Post-traumatic stress disorder (PTSD) is a mental health injury characterised by re-experiencing, avoidance, numbing and hyperarousal. Whilst the aetiology of the disorder is relatively well understood, there is debate about the prevalence of cognitive sequelae that manifest in PTSD. In particular, there are conflicting reports about deficits in executive function and mental flexibility. Even less is known about the neural changes that underlie such deficits. Here, we used magnetoencephalography to study differences in functional connectivity during a mental flexibility task in combat-related PTSD (all males, mean age = 37.4, n = 18) versus a military control (all males, mean age = 33.05, n = 19) group. We observed large-scale increases in theta connectivity in the PTSD group compared to controls. The PTSD group performance was compromised in the more attentionally-demanding task and this was characterised by ''late-stage'' theta hyperconnectivity, concentrated in network connections involving right parietal cortex. Furthermore, we observed significant correlations with the connectivity strength in this region with a number of cognitive-behavioural outcomes, including measures of attention, depression and anxiety. These findings suggest atypical coordination of neural synchronisation in large scale networks contributes to deficits in mental flexibility for PTSD populations in timed, attentionally-demanding tasks, and this propensity toward network hyperconnectivity may play a more general role in the cognitive sequelae evident in this disorder. 相似文献
6.
Jonathan H. Clarke Judith I. Laurie Harry J. Gilbert Geoffrey P. Hazlewood 《FEMS microbiology letters》1991,83(3):305-309
Cellulomonas fimi genomic DNA encoding xylanase activity has been cloned and expressed in Escherichia coli. As judged by DNA hybridization and restriction analysis, twelve xylanase-positive clones carried a minimum of four different xylanase (xyn) genes. The encoded enzymes were devoid of cellulase activity but three of the four bound to Avicel. 相似文献
7.
The zebrafish is rapidly increasing in popularity with developmental biologists. Driving this interest are the elegant methods for in vivo observations and recovery of early developmental mutations. The past year has seen the introduction of additional methods for in vivo manipulation of identified cells and the application of these methods to mutant analysis. 相似文献
8.
Relationship between Legionella pneumophila and Acanthamoeba polyphaga: physiological status and susceptibility to chemical inactivation. 总被引:4,自引:0,他引:4
J Barker M R Brown P J Collier I Farrell P Gilbert 《Applied and environmental microbiology》1992,58(8):2420-2425
Survival studies were conducted on Legionella pneumophila cells that had been grown intracellularly in Acanthamoeba polyphaga and then exposed to polyhexamethylene biguanide (PHMB), benzisothiazolone (BIT), and 5-chloro-N-methylisothiazolone (CMIT). Susceptibilities were also determined for L. pneumophila grown under iron-sufficient and iron-depleted conditions. BIT was relatively ineffective against cells grown under iron depletion; in contrast, iron-depleted conditions increased the susceptibilities of cells to PHMB and CMIT. The activities of all three biocides were greatly reduced against L. pneumophila grown in amoebae. PHMB (1 x MIC) gave 99.99% reductions in viability for cultures grown in broth within 6 h and no detectable survivors at 24 h but only 90 and 99.9% killing at 6 h and 24 h, respectively, for cells grown in amoebae. The antimicrobial properties of the three biocides against A. polyphaga were also determined. The majority of amoebae recovered from BIT treatment, but few, if any, survived CMIT treatment or exposure to PHMB. This study not only shows the profound effect that intra-amoebal growth has on the physiological status and antimicrobial susceptibility of L. pneumophila but also reveals PHMB to be a potential biocide for effective water treatment. In this respect, PHMB has significant activity, below its recommended use concentrations, against both the host amoeba and L. pneumophila. 相似文献
9.
Benjamin T. Hutchins 《Biodiversity and Conservation》2018,27(2):475-501
Biodiversity conservation requires an objective and consistent method for evaluating the conservation status of species. Conservation status assessments can identify conservation priorities and can highlight data gaps, effective conservation strategies, and groups of taxa that are underrepresented in conservation efforts relative to charismatic flagship and umbrella species. Groundwater invertebrates have a suite of traits that make them inherently vulnerable. But they go largely unnoticed by the general public and conservation practitioners, and comprehensive conservation status assessments are lacking for most species. In this article, the conservation status of all sixty-nine described groundwater-obligate invertebrates recorded from Texas, U.S.A. was assessed using NatureServe methodology. Some of the smallest taxa (e.g. copepods, ostracods, and mites) are too poorly known to evaluate their conservation status. Species restricted to springs were generally more at risk than species in other groundwater habitats, and beetles and snails were the most imperiled taxonomic groups. Most species faced low or medium severity threats, and only seven percent faced high or very high magnitude threats. Threat level varied among aquifers and among sites within aquifers and was primarily dependent on human population density and the adequacy of regulatory mechanisms protecting groundwater quality and quantity. Regardless of threat severity, fifty-five percent of evaluated species were ranked as imperiled or critically imperiled, largely due to extreme small-range endemism. Relative to other regions, Texas’ groundwater fauna is not unique in terms of rarity and threat, suggesting that as an ecological group, groundwater-obligate species are probably among the world’s most imperiled taxa. 相似文献
10.
Haselmair-Gosch Christian Nitarska Daria Walliser Benjamin Flachowsky Henryk Marinovic Silvija Halbwirth Heidi 《Plant Cell, Tissue and Organ Culture》2020,140(2):415-429
Plant Cell, Tissue and Organ Culture (PCTOC) - Somatic embryogenesis is a biotechnological tool with high application potential in the in vitro propagation and regeneration of crop plants, such as... 相似文献