Critical test of bead–spring model to resolve the scaling laws of polymer melts: a molecular dynamics study

Abstract

To examine the intrinsic nature of the bead–spring Kremer–Grest (KG) model, long-time molecular dynamics simulations are performed. Certain scaling laws for representative polymer properties are compared with theoretical predictions. The results for static properties satisfy the expected static Gaussian nature, irrespective of the chain length. In contrast, the results for the dynamic properties of short chains show a clear discrepancy from theoretical predictions that assume ideal chain motion. This is clear evidence that the Gaussian nature of the dynamics of short chains is not necessarily established for the actual KG model, despite it being designed to have Gaussian characteristics by virtue of its stochastic equations of motion. This intrinsic nature of the KG model should be considered carefully when using this model for applications that involve relatively short chains.     

Egg size in relation to body size in rotifers: an indication of reproductive strategy?

Egg sizes and body sizes of 43 egg-bearing rotifer species of numerous, mostly tropical, general have been recorded. Larger absolute egg volumes have been found for larger rotifer species, but the increase was lower than expected in proportion to body size, i.e. the relative egg volume decreased with increasing body size. Obviously the relative investment per offspring is smaller in larger rotifer species.     

Elasticity and geometry: a computational model of the Heineke–Mikulicz strictureplasty

Crohn’s disease is a challenging inflammatory process with a propensity for focal gastro-intestinal tract inflammation and stricture. Surgically, Crohn’s is often treated with resection. However, a subtype of diffuse disease with multiple strictures is treated by strictureplasty procedures in hope of avoiding short-gut syndrome. Prior work by Pocivavsek et al. defined the geometry of a Heineke–Mikulicz strictureplasty. Here, we bring this analysis one step closer to clinical and biological relevance by calculating the mechanical stresses and strains that the strictureplasty deformation generates on a model intestinal wall. The small bowel is simulated as a linearly elastic isotropic deformable cylindrical shell using finite element modeling. Data show a divergence in elastic response between the anti-mesenteric and mesenteric halves. The anti-mesenteric surface shows a bending dominated elastic response that correlates with the prior purely geometric analysis. However, the mesenteric half is not a neutral bystander during strictureplasty formation, as geometric arguments predict. Strong in-plane stretching strains develop in a rim around the image of the transverse closure, which may impact local perfusion and serve as sites of disease recurrence. Lastly, nearly all the deformation energy is stored in the central vertex stitch, placing this part at highest risk of dehiscence. This study enhances our understanding of mechanical response in complex nonlinear cylindrical geometries like the surgically manipulated intestinal tract. The developed framework serves as a platform for future addition of more complex clinically relevant parameters to our model, including real tissue properties, anisotropy, blood supply modeling, and patient deriver anatomic factors.     

Tentative identification of a vasopressin–neurophysin and an oxytocin–neurophysin in the rat

1. Rat neurohypophysial extracts have been examined by polyacrylamide-gel electrophoresis. 2. Three of the proteins were tentatively identified as neurophysins by their acidic nature and their disappearance after dehydration of the animals. 3. These proteins were radioactive 24h after intracisternal injection of [(35)S]cysteine. 4. Two of the proteins were present in much greater quantities than the third, and these two were present in the gland in the same ratio as the hormones vasopressin and oxytocin. 5. One of these proteins was absent from glands of rats homozygous for diabetes insipidus but present in heterozygous animals. 6. It is suggested that these two proteins are the vasopressin-neurophysin and oxytocin-neurophysin of the rat.     

Is the island biogeography model a poor predictor of biodiversity patterns in shallow lakes?

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The effect of the entry and re-entry size in the aortic dissection: a two-way fluid–structure interaction simulation

Biomechanics and Modeling in Mechanobiology - Aortic dissection (AD) is one of the most catastrophic cardiovascular diseases. AD occurs when a layer inside the aorta is disrupted and gives rise to...     

Scaling VOI size in 3D μCT studies of trabecular bone: a test of the over-sampling hypothesis

For comparative 3D microCT studies of trabecular bone, the use of a volume of interest (VOI) scaled to body size may avoid over-sampling the trabecular mass in smaller versus larger-bodied taxa and comparison of regions that are not functionally homologous (Fajardo and Müller: Am J Phys Anthropol 115 (2001) 327-336), though the influence on quantitative analyses using scaled versus nonscaled VOIs remains poorly characterized. We compare trabecular architectural properties reflecting mass, organization, and orientation from three volumes of interest (large, scaled, and small) obtained from the distal first metacarpal in a sample of Homo (n = 10) and Pan (n = 12). We test the null hypotheses that neither absolute VOI size, nor scaling of the VOI to metacarpal size as a proxy for body size, biases intraspecific analyses nor impacts the detection of interspecific differences. These hypotheses were only partially supported. While certain properties (e.g., bone volume fraction or trabecular thickness) were not affected by varying VOI size within taxa, others were significantly impacted (e.g., intersection surface, connectivity, and structure). In comparing large versus scaled VOIs, we found that the large VOI inflated the number and/or magnitude of significant differences between Homo and Pan. In summary, our results support the use of scaled VOIs in studies of trabecular architecture.     

Establishment of a pancreatic β cell proliferation model in vitro and a platform for diabetes drug screening

Diabetes, a disease resulting from loss of functional β cells, is globally an increasingly important condition. Based on the islet-differentiation ability of ductal epithelial cells and stimulating β cell proliferation ability of the Reg Iα gene, we aimed to establish an in vitro pancreatic β cell proliferation model for screening therapeutic drugs of diabetes in the future. Pancreatic ductal epithelial cells were isolated from male Wistar rats, and induced to differentiate into pancreatic β cells. Immunofluorescence staining assay, western blot, RT-PCR analysis, and dithizone staining were used to characterize the cells. Rat Reg Iα protein was transiently expressed in vitro by transfection of HEK 293 cells with the PCMV6-entry-REG Ia plasmid, and expression was verified by RT-PCR analysis, proliferation assay, and apoptosis assay. The pancreatic β cell proliferation model was further validated by a proliferation assay using differentiated pancreatic β cells treated with transfection supernatant. Finally, we have successfully established an in vitro pancreatic β cells proliferation model using transiently expressed rat Reg Iα protein and differentiated pancreatic β cells from pancreatic ductal epithelial cells. This model could be used as a platform to screen new drugs for islet neogenesis to cure diabetes, especially Chinese herbal drugs in the future.     

Spatio-temporal pattern formation in Rosenzweig–MacArthur model: Effect of nonlocal interactions

Spatio-temporal pattern formation in reaction–diffusion models of interacting populations is an active area of research due to various ecological aspects. Instability of homogeneous steady-states can lead to various types of patterns, which can be classified as stationary, periodic, quasi-periodic, chaotic, etc. The reaction–diffusion model with Rosenzweig–MacArthur type reaction kinetics for prey–predator type interaction is unable to produce Turing patterns but some non-Turing patterns can be observed for it. This scenario changes if we incorporate non-local interactions in the model. The main objective of the present work is to reveal possible patterns generated by the reaction–diffusion model with Rosenzweig–MacArthur type prey–predator interaction and non-local consumption of resources by the prey species. We are interested in the existence of Turing patterns in this model and in the effect of the non-local interaction on the periodic travelling wave and spatio-temporal chaotic patterns. Global bifurcation diagrams are constructed to describe the transition from one pattern to another one.     

Evaluating DMS measurements and model results in the Northeast subarctic Pacific from 1996–2010

About a decade of dimethylsulphide (DMS) measurements in the North East Pacific are summarized and compared to model simulations. Bottle samples at various depths have been taken three times per year along Line P from the British Columbia coast to Ocean Station Papa (145°?W, 50°?N). Despite the long timeseries, DMS measurements are still sparse and the data show large variabilities in concentrations both spatially and temporally. DMS concentrations in late summer have been consistently high, while spring measurements at the offshore stations suggest a downward trend over the past years. Low values in spring, however, have also been recorded in the late 1990s, which might hint to interannual variability in the onset of the spring bloom and/or plankton assemblage rather than to a response to recent climate change. Some of the variability, both short-term and interannual, can be caused by regional or local preconditioning of the physical environment. The model simulations provide examples where periods of low winds, shallow mixed layers and sometimes high irradiance follow a mixing event and cause DMS peaks on various time scales as well as consistently elevated DMS concentrations for longer timeperiods. The model in its current configuration, which has been calibrated with measurements in the late 1990s/early 2000s, is not able to capture the low values in winter and spring observed in recent years. We suggest that this is due to missing or misrepresented links in the biogeochemical parameterizations of the model, e.g., an incomplete representation of variations in the phytoplankton assemblage. Including a seasonally varying S:N ratio to account for the absence of dinoflagellates in winter and spring significantly improves the simulation. Variability in DMS concentrations can also be induced by natural iron fertilization, which the model reproduces when timing is specified. For example, the model can reproduce the effects of natural volcanic Fe fertilization on surface water plankton dynamics and mixed layer DMS accumulation. The model also shows that the amplitude of the short term variability (days) increases when DMSP producing phytoplankton are less iron limited.     

The dynamics of the lynx–hare system: an application of the Lotka–Volterra model

The Lotka–Volterra model of predator–prey dynamics was used for approximation of the wellknown empirical time series on the lynx–hare system in Canada that was collected by the Hudson Bay Company in 1845–1935. The model was assumed to demonstrate satisfactory data approximation if the sets of deviations of the model and empirical data for both time series satisfied a number of statistical criteria (for the selected significance level). The frequency distributions of deviations between the theoretical (model) trajectories and empirical datasets were tested for symmetry (with respect to the Y-axis; the Kolmogorov–Smirnov and Lehmann–Rosenblatt tests) and the presence or absence of serial correlation (the Swed–Eisenhart and “jumps up–jumps down” tests). The numerical calculations show that the set of points of the space of model parameters, when the deviations satisfy the statistical criteria, is not empty and, consequently, the model is suitable for describing empirical data.     

‘An island of socialism in a capitalist country’: Postsocialist Russian science and the culture of the state

Through a comparison of privatization programs in two physics institutes, this article explores the ways in which scientists in the Siberian science city of Akademgorodok adapted to the low levels of state funding available to them in the 1990s. Scientists transformed structures that were available under socialism into hybrid state-private ventures. Rather than ‘freeing’ Russian science from its former dependence on the state, however, these changes have reconfigured, and in some cases even strengthened, the relationship between state power and the production of knowledge. Seeing ‘the state’ as it is constituted in Russian scientists' discourse challenges Western models of the autonomy of science.     

Is the remodeling of the polyp prepattern in a hydrozoan planula a function of larval age or size and is it of “adaptive” significance?

Eggs of medusae develop into lecithotrophic planulae that undergo metamorphosis at different ages to form polyps. As planulae age they decrease in size as their yolk stores are utilized. The planulae of most Phialidium medusae develop into polyps where there is a decrease in the size of the holdfast region and a relative increase in the size of the hydranth region as they age. These changes occur independently of the decrease in planula size. In planulae with a decrease in the size of the holdfast region and an increase in the size of the hydranth-forming region there was a 50% decline in polyps that successfully stayed attached to the substrate after metamorphosis. These aged planulae produced an initial hydranth with the same number of tentacles as polyps from full-sized young planulae while young half-sized planulae produced hydranths where the tentacle number was smaller. The first phase of polyp colony growth with a small initial hydranth was slower than growth of a colony with a larger initial hydranth. Predation during this period led to more death in colonies with a small initial hydranth. The decline in successful attachment in aged planulae was not offset by the higher rate of growth and a smaller window of time where predation leads to death, suggesting that this age-related developmental change in planulae was not adaptive.     

Application of an in vitro digestion model to study the metabolic profile changes of an herbal extract combination by UHPLC–HRMS

BackgroundSTW 5 is a fixed herbal combination containing extracts from nine medicinal plants: bitter candytuft, greater celandine, garden angelica roots, lemon balm leaves, peppermint leaves, caraway fruits, licorice roots, chamomile flowers, and milk thistle fruit. STW 5 is a clinically proven treatment for functional dyspepsia and irritable bowel syndrome.PurposeUsing a static in vitro method, we simulated oral, gastric, and small intestinal digestion and analyzed the metabolic profile changes by UHPLC–HRMS to determine the impact of oro-gastro-intestinal digestion on STW 5 constituents.Study Design and MethodsSTW 5 was incubated according to the InfoGest consensus method. Samples of each digestive phase were analyzed by UHPLC–HRMS in ESI positive and negative modes. After data processing, background subtraction, and normalization, the peak areas of detectable compounds were compared to untreated reference samples and recovery ratios were calculated to monitor the metabolic profile of STW 5 during simulated digestion.ResultsAlthough the levels of some constituents were reduced, we did not observe complete degradation of any of the constituents of STW 5 upon in vitro digestion. We did not detect any new metabolites beyond increased levels of caffeic acid and liquiritigenin due to degradation of progenitor compounds. Changes observed in intestinal bioaccessibility ratios were mainly a result of isomerization, hydrolysis, protein binding, and low water solubility.ConclusionThe majority of STW 5 constituents are stable towards simulated in vitro digestion and can reach the colon to interact with gut microbiota if they remain unabsorbed in the upper intestinal tract.     

Structure of the UreD–UreF–UreG–UreE complex in Helicobacter pylori: a model study

The molecular details of the protein complex formed by UreD, UreF, UreG, and UreE, accessory proteins for urease activation in the carcinogenic bacterium Helicobacter pylori, have been elucidated using computational modeling. The calculated structure of the complex supports the hypothesis of UreF acting as a GTPase activation protein that facilitates GTP hydrolysis by UreG during urease maturation, and provides a rationale for the design of new drugs against infections by ureolytic bacterial pathogens.     

Epithelial–mesenchymal transition in the formation of hypertrophic scars and keloids

Abnormal wound healing is likely to induce the formation of hypertrophic scars and keloids, which leads to dysfunction, deformity, and mental problem in the patients. Despite the advances in prevention and management of hypertrophic scar and keloids, the mechanism underlying scar and keloid formation has not been fully elucidated. Recent insights into the role of the epithelial–mesenchymal transition (EMT) in development, wound healing, stem cell regulation, fibrosis, and tumorigenesis have increased our understanding of the pathophysiology of hypertrophic scarring and keloids and suggested new therapeutic targets. This review summarizes recent progress in the elucidation of the role of EMT in physiologic wound healing and pathologic scar formation. This knowledge will facilitate an understanding of EMT roles in scar formation and shed new light on the modulation and potential treatment of hypertrophic scars and keloids.     

Does prey size matter? Novel observations of feeding in the leatherback turtle (Dermochelys coriacea) allow a test of predator–prey size relationships

Optimal foraging models predict that large predators should concentrate on large prey in order to maximize their net gain of energy intake. Here, we show that the largest species of sea turtle, Dermochelys coriacea, does not strictly adhere to this general pattern. Field observations combined with a theoretical model suggest that a 300 kg leatherback turtle would meet its energetic requirements by feeding for 3-4 h a day on 4 g jellyfish, but only if prey were aggregated in high-density patches. Therefore, prey abundance rather than prey size may, in some cases, be the overriding parameter for foraging leatherbacks. This is a classic example where the presence of small prey in the diet of a large marine predator may reflect profitable foraging decisions if the relatively low energy intake per small individual prey is offset by high encounter rates and minimal capture and handling costs. This study provides, to our knowledge, the first quantitative estimates of intake rate for this species.