ResearchPad - anisotropy https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Two halves are less than the whole: Evidence of a length bisection bias in fish (<i>Poecilia reticulata</i>)]]> https://www.researchpad.co/article/elastic_article_14632 The horizontal-vertical (HV) illusion is characterized by a tendency to overestimate the length of vertically-arranged objects. Comparative research is primarily confined to primates, a range of species that, although arboreal, often explore their environment moving along the horizontal axis. Such behaviour may have led to the development of asymmetrical perceptual mechanisms to make relative size judgments of objects placed vertically and horizontally. We observed the susceptibility to the HV illusion in fish, whose ability to swim along the horizontal and vertical plane permits them to scan objects’ size equally on both axes. Guppies (Poecilia reticulata) were trained to select the longer orange line to receive a food reward. In the test phase, two arrays, containing two same-sized lines were presented, one horizontally and the other vertically. Black lines were also included in each pattern to generate the perception of an inverted T-shape (where a horizontal line is bisected by a vertical one) or an L-shape (no bisection). No bias was observed in the L-shape, which supports the idea of differential perceptual mechanisms for primates and fish. In the inverted T-shape, guppies estimated the bisected line as shorter, providing the first evidence of a length bisection bias in a fish species.

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<![CDATA[A flexible workflow for simulating transcranial electric stimulation in healthy and lesioned brains]]> https://www.researchpad.co/article/elastic_article_14588 Simulating transcranial electric stimulation is actively researched as knowledge about the distribution of the electrical field is decisive for understanding the variability in the elicited stimulation effect. Several software pipelines comprehensively solve this task in an automated manner for standard use-cases. However, simulations for non-standard applications such as uncommon electrode shapes or the creation of head models from non-optimized T1-weighted imaging data and the inclusion of irregular structures are more difficult to accomplish. We address these limitations and suggest a comprehensive workflow to simulate transcranial electric stimulation based on open-source tools. The workflow covers the head model creation from MRI data, the electrode modeling, the modeling of anisotropic conductivity behavior of the white matter, the numerical simulation and visualization. Skin, skull, air cavities, cerebrospinal fluid, white matter, and gray matter are segmented semi-automatically from T1-weighted MR images. Electrodes of arbitrary number and shape can be modeled. The meshing of the head model is implemented in a way to preserve the feature edges of the electrodes and is free of topological restrictions of the considered structures of the head model. White matter anisotropy can be computed from diffusion-tensor imaging data. Our solver application was verified analytically and by contrasting the tDCS simulation results with that of other simulation pipelines (SimNIBS 3.0, ROAST 3.0). An agreement in both cases underlines the validity of our workflow. Our suggested solutions facilitate investigations of irregular structures in patients (e.g. lesions, implants) or new electrode types. For a coupled use of the described workflow, we provide documentation and disclose the full source code of the developed tools.

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<![CDATA[Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin]]> https://www.researchpad.co/article/5c818e96d5eed0c484cc260a

The high affinity (KD ~ 10−15 M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (kon) is approximately diffusion limited (109 M-1s-1) but recent single molecule and surface binding studies indicate that they are slower than expected (105 to 107 M-1s-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic cycle describes the complex formation, and if there are any functional differences between avidin and streptavidin. We have studied the biotin association by two stopped-flow methodologies using labeled and unlabeled probes: I) fluorescent probes attached to biotin and biocytin; and II) unlabeled biotin and HABA, 2-(4’-hydroxyazobenzene)-benzoic acid. Both native avidin and streptavidin are homo-tetrameric and the association data show no cooperativity between the binding sites. The kon values of streptavidin are faster than avidin but slower than expected for a diffusion limited reaction in both complexes. Moreover, the Arrhenius plots of the kon values revealed strong temperature dependence with large activation energies (6–15 kcal/mol) that do not correspond to a diffusion limited process (3–4 kcal/mol). Accordingly, we propose a simple reaction model with a single transition state for non-immobilized reactants whose forward thermodynamic parameters complete the thermodynamic cycle, in agreement with previously reported studies. Our new understanding and description of the kinetics, thermodynamics, and spectroscopic parameters for these complexes will help to improve purification efficiencies, molecule detection, and drug screening assays or find new applications.

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<![CDATA[Conformational regulation of Escherichia coli DNA polymerase V by RecA and ATP]]> https://www.researchpad.co/article/5c61e917d5eed0c48496f7ea

Mutagenic translesion DNA polymerase V (UmuD′2C) is induced as part of the DNA damage-induced SOS response in Escherichia coli, and is subjected to multiple levels of regulation. The UmuC subunit is sequestered on the cell membrane (spatial regulation) and enters the cytosol after forming a UmuD′2C complex, ~ 45 min post-SOS induction (temporal regulation). However, DNA binding and synthesis cannot occur until pol V interacts with a RecA nucleoprotein filament (RecA*) and ATP to form a mutasome complex, pol V Mut = UmuD′2C-RecA-ATP. The location of RecA relative to UmuC determines whether pol V Mut is catalytically on or off (conformational regulation). Here, we present three interrelated experiments to address the biochemical basis of conformational regulation. We first investigate dynamic deactivation during DNA synthesis and static deactivation in the absence of DNA synthesis. Single-molecule (sm) TIRF-FRET microscopy is then used to explore multiple aspects of pol V Mut dynamics. Binding of ATP/ATPγS triggers a conformational switch that reorients RecA relative to UmuC to activate pol V Mut. This process is required for polymerase-DNA binding and synthesis. Both dynamic and static deactivation processes are governed by temperature and time, in which onoff switching is “rapid” at 37°C (~ 1 to 1.5 h), “slow” at 30°C (~ 3 to 4 h) and does not require ATP hydrolysis. Pol V Mut retains RecA in activated and deactivated states, but binding to primer-template (p/t) DNA occurs only when activated. Studies are performed with two forms of the polymerase, pol V Mut-RecA wt, and the constitutively induced and hypermutagenic pol V Mut-RecA E38K/ΔC17. We discuss conformational regulation of pol V Mut, determined from biochemical analysis in vitro, in relation to the properties of pol V Mut in RecA wild-type and SOS constitutive genetic backgrounds in vivo.

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<![CDATA[Morphological and mechanical properties of the human triceps surae aponeuroses taken from elderly cadavers: Implications for muscle-tendon interactions]]> https://www.researchpad.co/article/5c6730e1d5eed0c484f3829d

The human triceps surae (two gastrocnemii and soleus) has aponeuroses in the proximal and distal aspects, the latter of which insert into the calcaneus by sharing the common Achilles tendon. These tendinous tissues are known to have elasticity and upon muscle contraction the aponeurosis is stretched both longitudinally (along the muscle’s line of action) and transversely. Higher aponeurosis transverse deformability has been documented, but there is a paucity of information on the morphology and mechanical properties of human aponeurosis. This study aimed to identify morphological and mechanical characteristics of the human triceps surae aponeuroses. Twenty-five triceps surae muscle-tendon units were procured from 13 human donors (formalin fixed, 6 males, 7 females) aged 67–91 years. Specimens of aponeuroses were excised from the eight regions (posterior and anterior regions of the gastrocnemius medialis and lateralis, medial and lateral parts of soleus; proximal, middle, and distal sites each, 2–4 cm × 2–4 cm). Aponeurosis thickness was measured using a digital caliper. Uniaxial tensile tests were implemented to determine the mechanical properties of specimens loaded longitudinally (along the muscle’s line of action) and transversely. The aponeurosis thickness showed significant differences between muscles and sites, while Young’s modulus showed direction-dependent (longitudinal vs. transverse) differences within sites. Results show different morphology and mechanical properties of aponeuroses between synergist muscles. The reason for site-dependent differences in stiffness is due to a reduced aponeurosis thickness rather than a reduction in the material property. The anisotropic elastic feature (differences between longitudinal and transverse directions) of the aponeuroses was more pronounced than previous in vivo findings, suggesting inherent material design of the aponeurosis that matches three-dimensional contractile behavior of muscle fibers.

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<![CDATA[Inferring statistical properties of 3D cell geometry from 2D slices]]> https://www.researchpad.co/article/5c5df30ad5eed0c484580bba

Although cell shape can reflect the mechanical and biochemical properties of the cell and its environment, quantification of 3D cell shapes within 3D tissues remains difficult, typically requiring digital reconstruction from a stack of 2D images. We investigate a simple alternative technique to extract information about the 3D shapes of cells in a tissue; this technique connects the ensemble of 3D shapes in the tissue with the distribution of 2D shapes observed in independent 2D slices. Using cell vertex model geometries, we find that the distribution of 2D shapes allows clear determination of the mean value of a 3D shape index. We analyze the errors that may arise in practice in the estimation of the mean 3D shape index from 2D imagery and find that typically only a few dozen cells in 2D imagery are required to reduce uncertainty below 2%. Even though we developed the method for isotropic animal tissues, we demonstrate it on an anisotropic plant tissue. This framework could also be naturally extended to estimate additional 3D geometric features and quantify their uncertainty in other materials.

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<![CDATA[A method for the quantification of phototropic and gravitropic sensitivities of plants combining an original experimental device with model-assisted phenotyping: Exploratory test of the method on three hardwood tree species]]> https://www.researchpad.co/article/5c644898d5eed0c484c2e9dc

Perception of inclination in the gravity field and perception of light direction are two important environmental signals implicated in the control of plant shape and habit. However, their quantitative study in light-grown plants remains a challenge. We present a novel method here to determine the sensitivities to gravitropism and phototropism. The method combines: (i) an original experimental device of isotropic light to disentangle gravitropic and phototropic plant responses; and (ii) model-assisted phenotyping using recent models of tropism perception—the AC model for gravitropism alone and the ArC model for gravitropism combined with phototropism. We first assessed the validity of the AC and ArC models on poplar, the classical species model for woody plants. We then tested the method on three woody species contrasted by their habit and tolerance to shade: poplar (Populus tremula*alba), oak (Quercus petraea) and beech (Fagus sylvatica). The method was found to be effective to quantitatively discriminate the tested species by their ratio of tropistic sensitivities. The method thus appears as an interesting tool to quantitatively determine tropistic sensitivities, a prerequisite for assessing the role of tropisms in the control of the variability of the habit and/or tolerance to shade of woody species in the future.

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<![CDATA[Mechanistic insight into spontaneous transition from cellular alternans to arrhythmia—A simulation study]]> https://www.researchpad.co/article/5c0ae43ed5eed0c484589394

Cardiac electrical alternans (CEA), manifested as T-wave alternans in ECG, is a clinical biomarker for predicting cardiac arrhythmias and sudden death. However, the mechanism underlying the spontaneous transition from CEA to arrhythmias remains incompletely elucidated. In this study, multiscale rabbit ventricular models were used to study the transition and a potential role of INa in perpetuating such a transition. It was shown CEA evolved into either concordant or discordant action potential (AP) conduction alternans in a homogeneous one-dimensional tissue model, depending on tissue AP duration and conduction velocity (CV) restitution properties. Discordant alternans was able to cause conduction failure in the model, which was promoted by impaired sodium channel with either a reduced or increased channel current. In a two-dimensional homogeneous tissue model, a combined effect of rate- and curvature-dependent CV broke-up alternating wavefronts at localised points, facilitating a spontaneous transition from CEA to re-entry. Tissue inhomogeneity or anisotropy further promoted break-up of re-entry, leading to multiple wavelets. Similar observations have also been seen in human atrial cellular and tissue models. In conclusion, our results identify a mechanism by which CEA spontaneously evolves into re-entry without a requirement for premature ventricular complexes or pre-existing tissue heterogeneities, and demonstrated the important pro-arrhythmic role of impaired sodium channel activity. These findings are model-independent and have potential human relevance.

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<![CDATA[Assessing impact of exogenous features on biotic phenomena in the presence of strong spatial dependence: A lake sturgeon case study in natural stream settings]]> https://www.researchpad.co/article/5c117b3dd5eed0c4846985fd

Modeling spatially explicit data provides a powerful approach to identify the effects of exogenous features associated with biological processes, including recruitment of stream fishes. However, the complex spatial and temporal dynamics of the stream and the species’ reproductive and early life stage behaviors present challenges to drawing valid inference using traditional regression models. In these settings it is often difficult to ensure the spatial independence among model residuals—a key assumption that must be met to ensure valid inference. We present statistical models capable of capturing complex residual anisotropic patterns through the addition of spatial random effects within an inferential framework that acknowledges uncertainty in the data and parameters. Proposed models are used to explore the impact of environmental variables on Lake sturgeon (Acipenser fulvescens) reproduction, particularly questions about patterns in egg deposition. Our results demonstrate the need to apply valid statistical methods to identify relationships between response variables, e.g., egg counts, across locations, and environmental covariates in the presence of strong and anisotropic autocorrelation in stream systems. The models may be applied to other settings where gamete distribution or, more generally, other biotic phenomena may be associated with spatially dynamic and anisotropic processes.

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<![CDATA[Anisotropic Crb accumulation, modulated by Src42A, is coupled to polarised epithelial tube growth in Drosophila]]> https://www.researchpad.co/article/5c059de3d5eed0c4849c965b

The control of the size of internal tubular organs, such as the lungs or vascular system, is critical for proper physiological activity and to prevent disease or malformations. This control incorporates the intrinsic physical anisotropy of tubes to generate proportionate organs that match their function. The exact mechanisms underlying tube size control and how tubular anisotropy is translated at the cellular level are still not fully understood. Here we investigate these mechanisms using the Drosophila tracheal system. We show that the apical polarity protein Crumbs transiently accumulates anisotropically at longitudinal cell junctions during tube elongation. We provide evidence indicating that the accumulation of Crumbs in specific apical domains correlates with apical surface expansion, suggesting a link between the anisotropic accumulation of Crumbs at the cellular level and membrane expansion. We find that Src42A is required for the anisotropic accumulation of Crumbs, thereby identifying the first polarised cell behaviour downstream of Src42A. Our results indicate that Src42A regulates a mechanism that increases the fraction of Crb protein at longitudinal junctions, and genetic interaction experiments are consistent with Crb acting downstream of Src42A in controlling tube size. Collectively, our results suggest a model in which Src42A would sense the inherent anisotropic mechanical tension of the tube and translate it into a polarised Crumbs accumulation, which may promote a bias towards longitudinal membrane expansion, orienting cell elongation and, as a consequence, longitudinal growth at the tissue level. This work provides new insights into the key question of how organ growth is controlled and polarised and unveils the function of two conserved proteins, Crumbs and Src42A, with important roles in development and homeostasis as well as in disease, in this biological process.

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<![CDATA[An efficient outlier removal method for scattered point cloud data]]> https://www.researchpad.co/article/5b6da1b2463d7e4dccc5faec

Outlier removal is a fundamental data processing task to ensure the quality of scanned point cloud data (PCD), which is becoming increasing important in industrial applications and reverse engineering. Acquired scanned PCD is usually noisy, sparse and temporarily incoherent. Thus the processing of scanned data is typically an ill-posed problem. In the paper, we present a simple and effective method based on two geometrical characteristics constraints to trim the noisy points. One of the geometrical characteristics is the local density information and another is the deviation from the local fitting plane. The local density based method provides a preprocessing step, which could remove those sparse outlier and isolated outlier. The non-isolated outlier removal in this paper depends on a local projection method, which placing those points onto objects. There is no doubt that the deviation of any point from the local fitting plane should be a criterion to reduce the noisy points. The experimental results demonstrate the ability to remove the noisy point from various man-made objects consisting of complex outlier.

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<![CDATA[Microheterogeneity-induced conduction slowing and wavefront collisions govern macroscopic conduction behavior: A computational and experimental study]]> https://www.researchpad.co/article/5b600750463d7e39c5526203

The incidence of cardiac arrhythmias is known to be associated with tissue heterogeneities including fibrosis. However, the impact of microscopic structural heterogeneities on conduction in excitable tissues remains poorly understood. In this study, we investigated how acellular microheterogeneities affect macroscopic conduction under conditions of normal and reduced excitability by utilizing a novel platform of paired in vitro and in silico studies to examine the mechanisms of conduction. Regular patterns of nonconductive micro-obstacles were created in confluent monolayers of the previously described engineered-excitable Ex293 cell line. Increasing the relative ratio of obstacle size to intra-obstacle strand width resulted in significant conduction slowing up to 23.6% and a significant increase in wavefront curvature anisotropy, a measure of spatial variation in wavefront shape. Changes in bulk electrical conductivity and in path tortuosity were insufficient to explain these observed macroscopic changes. Rather, microscale behaviors including local conduction slowing due to microscale branching, and conduction acceleration due to wavefront merging were shown to contribute to macroscopic phenomena. Conditions of reduced excitability led to further conduction slowing and a reversal of wavefront curvature anisotropy due to spatially non-uniform effects on microscopic slowing and acceleration. This unique experimental and computation platform provided critical mechanistic insights in the impact of microscopic heterogeneities on macroscopic conduction, pertinent to settings of fibrotic heart disease.

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<![CDATA[Impact of tumor position, conductivity distribution and tissue homogeneity on the distribution of tumor treating fields in a human brain: A computer modeling study]]> https://www.researchpad.co/article/5989db5eab0ee8fa60be0a82

Background

Tumor treating fields (TTFields) are increasingly used in the treatment of glioblastoma. TTFields inhibit cancer growth through induction of alternating electrical fields. To optimize TTFields efficacy, it is necessary to understand the factors determining the strength and distribution of TTFields. In this study, we provide simple guiding principles for clinicians to assess the distribution and the local efficacy of TTFields in various clinical scenarios.

Methods

We calculated the TTFields distribution using finite element methods applied to a realistic head model. Dielectric property estimates were taken from the literature. Twentyfour tumors were virtually introduced at locations systematically varied relative to the applied field. In addition, we investigated the impact of central tumor necrosis on the induced field.

Results

Local field “hot spots” occurred at the sulcal fundi and in deep tumors embedded in white matter. The field strength was not higher for tumors close to the active electrode. Left/right field directions were generally superior to anterior/posterior directions. Central necrosis focally enhanced the field near tumor boundaries perpendicular to the applied field and introduced significant field non-uniformity within the tumor.

Conclusions

The TTFields distribution is largely determined by local conductivity differences. The well conducting tumor tissue creates a preferred pathway for current flow, which increases the field intensity in the tumor boundaries and surrounding regions perpendicular to the applied field. The cerebrospinal fluid plays a significant role in shaping the current pathways and funnels currents through the ventricles and sulci towards deeper regions, which thereby experience higher fields. Clinicians may apply these principles to better understand how TTFields will affect individual patients and possibly predict where local recurrence may occur. Accurate predictions should, however, be based on patient specific models. Future work is needed to assess the robustness of the presented results towards variations in conductivity.

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<![CDATA[Preliminary Study of MR Diffusion Tensor Imaging of Pancreas for the Diagnosis of Acute Pancreatitis]]> https://www.researchpad.co/article/5989daeeab0ee8fa60bc0265

Objectives

To evaluate the feasibility of differentiating between acute pancreatitis (AP) and healthy pancreas using diffusion tensor imaging (DTI) and correlate apparent diffusion coefficient (ADC) /fractional anisotropy (FA) values with the severity of AP.

Material and Methods

66 patients diagnosed with AP and 20 normal controls (NC) underwent DTI sequences and routine pancreatic MR sequences on a 3.0T MRI scanner. Average ADC and FA values of the pancreatic were measured. Differences of FA and ADC values between the AP group and the NC group with AP and healthy pancreas were compared by two-sample independent t-test. The severity of AP on MRI was classified into subgroups using MR severity index (MRSI), where the mean FA and ADC values were calculated. Relationship among the FA values, ADC values and MRSI were analyzed using Spearman's rank correlation coefficients.

Results

The pancreatic mean ADC value in the AP group (1.68 ± 0.45×10−3mm2/s) was significantly lower than in the NC group (2.09 ± 0.55×10−3mm2/s) (P = 0.02); the same as mean FA value (0.39 ± 0.23 vs 0.54 ± 0.12, P = 0.00). In the subgroup analysis, the pancreatic ADC and FA value of edema AP patients was significantly higher than necrosis AP patients with P = 0.000 and P = 0.001respectively. In addition, as severity of pancreatitis increased according to MRSI, lower pancreatic ADC (r = -0.635) and FA value (r = -0.654) were noted.

Conclusion

Both FA and ADC value from DTI can be used to differentiate AP patients from NC. Both ADC and FA value of pancreas have a negative correlation with the severity of AP.

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<![CDATA[Concerning the matching of magnetic susceptibility differences for the compensation of background gradients in anisotropic diffusion fibre phantoms]]> https://www.researchpad.co/article/5989db5aab0ee8fa60bdf4d3

Artificial, anisotropic fibre phantoms are nowadays increasingly used in the field of diffusion-weighted MRI. Such phantoms represent useful tools for, among others, the calibration of pulse sequences and validation of diffusion models since they can mimic well-known structural features of brain tissue on the one hand, but exhibit a reduced complexity, on the other. Among all materials, polyethylene fibres have been widely used due to their excellent properties regarding the restriction of water diffusion and surface relaxation properties. Yet the magnetic susceptibility of polyethylene can be distinctly lower than that of distilled water. This difference produces strong microscopic, background field gradients in the vicinity of fibre bundles which are not parallel to the static magnetic field. This, in turn, modulates the MRI signal behaviour. In the present work we investigate an approach to reduce the susceptibility-induced background gradients via reducing the heterogeneity in the internal magnetic susceptibility. An aqueous solution of magnesium chloride hexahydrate (MgCl2·6H2O) is used for this purpose. Its performance is demonstrated in dedicated anisotropic fibre phantoms with different geometrical configurations.

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<![CDATA[Reliable Dual Tensor Model Estimation in Single and Crossing Fibers Based on Jeffreys Prior]]> https://www.researchpad.co/article/5989dab8ab0ee8fa60badad2

Purpose

This paper presents and studies a framework for reliable modeling of diffusion MRI using a data-acquisition adaptive prior.

Methods

Automated relevance determination estimates the mean of the posterior distribution of a rank-2 dual tensor model exploiting Jeffreys prior (JARD). This data-acquisition prior is based on the Fisher information matrix and enables the assessment whether two tensors are mandatory to describe the data. The method is compared to Maximum Likelihood Estimation (MLE) of the dual tensor model and to FSL’s ball-and-stick approach.

Results

Monte Carlo experiments demonstrated that JARD’s volume fractions correlated well with the ground truth for single and crossing fiber configurations. In single fiber configurations JARD automatically reduced the volume fraction of one compartment to (almost) zero. The variance in fractional anisotropy (FA) of the main tensor component was thereby reduced compared to MLE. JARD and MLE gave a comparable outcome in data simulating crossing fibers. On brain data, JARD yielded a smaller spread in FA along the corpus callosum compared to MLE. Tract-based spatial statistics demonstrated a higher sensitivity in detecting age-related white matter atrophy using JARD compared to both MLE and the ball-and-stick approach.

Conclusions

The proposed framework offers accurate and precise estimation of diffusion properties in single and dual fiber regions.

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<![CDATA[Application of Diffusion Tensor Imaging Parameters to Detect Change in Longitudinal Studies in Cerebral Small Vessel Disease]]> https://www.researchpad.co/article/5989da6bab0ee8fa60b92ed1

Cerebral small vessel disease (SVD) is the major cause of vascular cognitive impairment, resulting in significant disability and reduced quality of life. Cognitive tests have been shown to be insensitive to change in longitudinal studies and, therefore, sensitive surrogate markers are needed to monitor disease progression and assess treatment effects in clinical trials. Diffusion tensor imaging (DTI) is thought to offer great potential in this regard. Sensitivity of the various parameters that can be derived from DTI is however unknown. We aimed to evaluate the differential sensitivity of DTI markers to detect SVD progression, and to estimate sample sizes required to assess therapeutic interventions aimed at halting decline based on DTI data. We investigated 99 patients with symptomatic SVD, defined as clinical lacunar syndrome with MRI confirmation of a corresponding infarct as well as confluent white matter hyperintensities over a 3 year follow-up period. We evaluated change in DTI histogram parameters using linear mixed effect models and calculated sample size estimates. Over a three-year follow-up period we observed a decline in fractional anisotropy and increase in diffusivity in white matter tissue and most parameters changed significantly. Mean diffusivity peak height was the most sensitive marker for SVD progression as it had the smallest sample size estimate. This suggests disease progression can be monitored sensitively using DTI histogram analysis and confirms DTI’s potential as surrogate marker for SVD.

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<![CDATA[Dip TIPS as a Facile and Versatile Method for Fabrication of Polymer Foams with Controlled Shape, Size and Pore Architecture for Bioengineering Applications]]> https://www.researchpad.co/article/5989da0cab0ee8fa60b77d39

The porous polymer foams act as a template for neotissuegenesis in tissue engineering, and, as a reservoir for cell transplants such as pancreatic islets while simultaneously providing a functional interface with the host body. The fabrication of foams with the controlled shape, size and pore structure is of prime importance in various bioengineering applications. To this end, here we demonstrate a thermally induced phase separation (TIPS) based facile process for the fabrication of polymer foams with a controlled architecture. The setup comprises of a metallic template bar (T), a metallic conducting block (C) and a non-metallic reservoir tube (R), connected in sequence T-C-R. The process hereinafter termed as Dip TIPS, involves the dipping of the T-bar into a polymer solution, followed by filling of the R-tube with a freezing mixture to induce the phase separation of a polymer solution in the immediate vicinity of T-bar; Subsequent free-drying or freeze-extraction steps produced the polymer foams. An easy exchange of the T-bar of a spherical or rectangular shape allowed the fabrication of tubular, open- capsular and flat-sheet shaped foams. A mere change in the quenching time produced the foams with a thickness ranging from hundreds of microns to several millimeters. And, the pore size was conveniently controlled by varying either the polymer concentration or the quenching temperature. Subsequent in vivo studies in brown Norway rats for 4-weeks demonstrated the guided cell infiltration and homogenous cell distribution through the polymer matrix, without any fibrous capsule and necrotic core. In conclusion, the results show the “Dip TIPS” as a facile and adaptable process for the fabrication of anisotropic channeled porous polymer foams of various shapes and sizes for potential applications in tissue engineering, cell transplantation and other related fields.

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<![CDATA[Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121]]> https://www.researchpad.co/article/5989db50ab0ee8fa60bdbdc2

Major facilitator superfamily (MFS) peptide transporters (typically referred to as PepT, POT or PTR transporters) mediate the uptake of di- and tripeptides, and so play an important dietary role in many organisms. In recent years, a better understanding of the molecular basis for this process has emerged, which is in large part due to a steep increase in structural information. Yet, the conformational transitions underlying the transport mechanism are still not fully understood, and additional data is therefore needed. Here we report in detail the detergent screening, crystallization, experimental MIRAS phasing, and refinement of the peptide transporter PepTSt from Streptococcus thermophilus. The space group is P3121, and the protein is crystallized in a monomeric inward facing form. The binding site is likely to be somewhat occluded, as the lobe encompassing transmembrane helices 10 and 11 is markedly bent towards the central pore of the protein, but the extent of this potential occlusion could not be determined due to disorder at the apex of the lobe. Based on structural comparisons with the seven previously determined P212121 and C2221 structures of inward facing PepTSt, the structural flexibility as well as the conformational changes mediating transition between the inward open and inward facing occluded states are discussed. In conclusion, this report improves our understanding of the structure and conformational cycle of PepTSt, and can furthermore serve as a case study, which may aid in supporting future structure determinations of additional MFS transporters or other integral membrane proteins.

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<![CDATA[A New Variational Approach for Multiplicative Noise and Blur Removal]]> https://www.researchpad.co/article/5989db53ab0ee8fa60bdcb12

This paper proposes a new variational model for joint multiplicative denoising and deblurring. It combines a total generalized variation filter (which has been proved to be able to reduce the blocky-effects by being aware of high-order smoothness) and shearlet transform (that effectively preserves anisotropic image features such as sharp edges, curves and so on). The new model takes the advantage of both regularizers since it is able to minimize the staircase effects while preserving sharp edges, textures and other fine image details. The existence and uniqueness of a solution to the proposed variational model is also discussed. The resulting energy functional is then solved by using alternating direction method of multipliers. Numerical experiments showing that the proposed model achieves satisfactory restoration results, both visually and quantitatively in handling the blur (motion, Gaussian, disk, and Moffat) and multiplicative noise (Gaussian, Gamma, or Rayleigh) reduction. A comparison with other recent methods in this field is provided as well. The proposed model can also be applied for restoring both single and multi-channel images contaminated with multiplicative noise, and permit cross-channel blurs when the underlying image has more than one channel. Numerical tests on color images are conducted to demonstrate the effectiveness of the proposed model.

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