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Identifying EGFR mutation-induced drug resistance based on alpha shape model analysis of the dynamics

Identifying EGFR mutation-induced drug resistance based on alpha shape model analysis of the dynamics

Results: We analyzed the EGFR mutation-induced drug resistance based on the motion trajectories obtained from MD simulation. We computed alpha shape model of all the trajectory frames for each mutation type. Solid angle was used to characterize the curvature of the atoms at the drug binding site. We measured the knob level of the drug binding pocket of each mutant from two ways and analyzed its relationship with the drug response level. Results show that 90 % of the mutants can be grouped correctly by setting a certain knob level threshold. Conclusions: There is a strong correlation between the geometric properties of the drug binding pocket of the EGFR mutants and the corresponding drug responses, which can be used to predict the response of a new EGFR mutant to a drug molecule.

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Application of the Alpha Shape Method to Visualize and Analyze Surgical Motion

Application of the Alpha Shape Method to Visualize and Analyze Surgical Motion

Alpha shape algorithm is a method derived from Delaunay triangulation (DT) methods [20] [21]. The major difference between DT and the alpha shape algo- rithm is the additional constraint in the latter—the radius of each circle passing through the three vertices of the triangles must be less than a predefined value, alpha ( α ) (Figure 1). The alpha value ranges from zero to infinity, and generates different shapes, called alpha shape, depending on the alpha value. For α = 0, the alpha shape is the point itself. When α is chosen large enough (infinity), the al- pha shape is a convex hull which is the output of the DT algorithm. The alpha value can be determined experimentally to achieve a balance between size and shape/surface contours. Alternatively, a pre-determined alpha value can be set to allow the comparison of sizes and shape/surface of reconstructed data sets.

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Application of the morphological alpha shape method to the extraction of topographical features from engineering surfaces

Application of the morphological alpha shape method to the extraction of topographical features from engineering surfaces

It is reported that in comparison to roughness and waviness components, the wear rates of surfaces in the operational service is more affected by topographical features like pits, valleys, scratches [22]. From the functional evaluation point of view, these topographical features will impact directly on wear mechanics and physical properties of the component, such as the cylinder liner of the engine system and the femoral head of the hip joint replacement system. Using the morphological method based on the alpha shape, topographical features on the surfaces presented in Fig. 8(a) – Fig. 11(a) are properly extracted with no distortions.

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Conformal Alpha Shape-based Multi-scale Curvature Estimation from Point Clouds

Conformal Alpha Shape-based Multi-scale Curvature Estimation from Point Clouds

In the rest of the paper, we estimate curvatures of surface reconstructed with conformal alpha shape. In Section 2, we describe conformal alpha shapes largely following Edelsbrunner [9] and Cazals [5]. In Section 3, we describe the curvatures estimation on conformal alpha shapes with works of Dong [8] and Seibert [20]. In Section 4, we present an algorithm to compute internal alpha scale parameters and to estimate surface curvature of conformal alpha shapes. In Section 5, we discuss results on the sample of Stanford Bunny. In this work, we are primarily interested in estimating face-based curvatures on 3D conformal alpha shapes. One of our key motivating applications is the matching of molecular surface regions to identify potentially similar chemical functionality.

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Prediction of DNA-binding protein based on statistical and geometric features and support vector machines

Prediction of DNA-binding protein based on statistical and geometric features and support vector machines

An important step before extracting geometric fea- tures from the alpha shape model is the definition of interface surface which contains most of the information need to predict protein-DNA interaction. In the alpha shape model, the vertices correspond to the surface atoms of the original protein-DNA structure. Using this characteristic, the interface atoms of the protein-DNA structure can be defined as follows. First, we calculate the alpha shape of the protein-DNA complex and obtain the surface atom set {Complex}. Then, we calculate the alpha shape of the protein independently (with the DNA part removed) and obtain the protein surface atom set {Protein}. Finally, the interface atoms set can be obtained by retaining the atoms which are in { Protein } but not in { Complex }.

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Shape Simplification Through Graph Sparsification

Shape Simplification Through Graph Sparsification

Similarly Fig. 3 shows the 1-skeletons of five alpha shapes that were con- structed over various point clouds, also varying the α value. These correspond to two different versions of the abstract shape already shown in 2(a), two alpha shapes of the deer model in 2(c) and an alpha shape from the cow point set that correspond to 2(e). The choice of these alpha shapes is motivated by the presence of small and larger handles and features that alpha shapes have diffi- culty capturing with a single choice of the parameter α, as previously discussed. The results in Table 2 report the number of edges of the 1-skeleton of the alpha shape when the value of the ǫ parameter increases. From these experiment, we think that with sparsification would be possible to overcome the limitations of alpha shapes in the sense that we hope that it will be possible to commence from a quite large value of the parameters α and then to remove the redun- dant edges by using sparsification, thus implementing a connected, progressive, geometrical-topological peeling of the shape.

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An Efficient Divide and Conquer Algorithm for Morphological Filters

An Efficient Divide and Conquer Algorithm for Morphological Filters

Following the three typical steps of the divide-and- conquer paradigm, i.e. divide, conquer, combine, at each level of the recursion, the details of each step are illustrated below. Fig 6 presents an example surface (100 x 100 points) as well as its boundary alpha shape facets computed by the alpha shape method. The example surface is then divided into four small sub-surfaces with 50 x 50 points for individual each one (see Fig 7). The search of contact points on these sub-surfaces is conquered by applying the alpha shape method. Fig 8 graphs the contact points and the boundary alpha shape facets of four sub-surfaces respectively. Finally the contact points of four sub-surfaces are merged together and the alpha shape method is applied on the combined contact points set to generate the final boundary alpha shape facets (see Fig 9). It could be noticed in the figure Fig. 6. An example surface and it boundary alpha shape facets. (a) Example surface; (b) Boundary facets superimposed on the surface

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Geometric computation theory for morphological filtering on freeform surfaces

Geometric computation theory for morphological filtering on freeform surfaces

Surfaces govern functional behaviours of geometrical products, especially high precision and high added-value products. Compared to the mean-line based filters, morphological filters, evolved from the traditional E-system, are relevant to functional performance of surfaces. The conventional implementation of morphological filters based on image processing does not work for state-of-the-art surfaces, for example freeform surfaces. A set of novel geometric computation theory is developed by applying the alpha shape to the computation. Divide and conquer optimisation is employed to speed up the computational performance of the alpha shape method and reduce memory usage. To release the dependence of the alpha shape method on the Delaunay triangulation, a set of definitions and propositions for the search of contact points is presented and mathematically proved based on alpha shape theory, which are applicable to both circular and horizontal flat structuring elements. The developed methods are verified through experimentation.

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Nanobiomechanical Properties of Microtubules

Nanobiomechanical Properties of Microtubules

Microtubules, the active filaments with tubular shapes, play important roles in a wide range of cellular functions, including structural supports, mitosis, cytokinesis, and vesicular transport, which are essential for the growth and division of eukaryotic cells. Finding properties of microtubules is one of the main concerns of scientists. This work helps to obtain mechanical properties of microtubule. For this aim, interaction energy in alpha-beta, beta-alpha, alpha- alpha and beta-beta dimers was calculated using the molecular dynamic simulation and GROMACS software package. Force-distance diagrams for these dimers were obtained using the relation between potential energy and force. Each dimer has nearly 8500 atoms. There are more than 100 tubulins in a microtubule with 13 protofilaments and 0.1 µm length. So, molecular dynamic simulation of a microtubule will be a very difficult task. Then, it would be better to build a structural mechanic model which has rather similar properties with microtubule. The first and most important step for this process is to obtain the interaction force between tubulins. Therefore, instead of the each tubulin we can consider one sphere with 55 kDa weights that connect to another tubulin with a nonlinear connection such as nonlinear spring. The mechanical model of microtubule was used to calculate Young’s modulus based on finite element method. The Young’s modulus has good agreement with previous works.

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Shape memory polymers and shape memory  alloys: use in smart textiles

Shape memory polymers and shape memory alloys: use in smart textiles

Some biological evaluations were made in order to prove the compatibility of fabrics containing shape memory fiber with human body. These initiated the applications of shape memory effect fabrics in biological and medical areas. For the effective application of shape memory fabrics in medical textiles, corselets were foreseen. For instance, therapeutic clothes for burned skins, sport clothes skin and some casual dresses including female lingerie (Hu et al., 2012; Meng et al., 2009). With the usage of shape memory polymers in medical area as controlled drug release, biodegradable sewing yarn, stent, implants, the relevant studies have been increasing (Lendlein and Langer, 2002; Wache et al., 2003; Lendlein et al., 2010; Goraltchouk et al., 2011). In this area, sewing yarns with biodegradable shape memory feature was studied. With the increase in temperature, filament presses the scar and enables it to be closed (Figure 3). In addition, SMP’s having minimal temporary shape can be implanted into the body from the small scars and take their original shape with body temperature. The shape memory products of the medical area need to be supported with such controlled features as biodegradability and drug release (Lendlein et al., 2010).

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In Vitro Antidiabetic Effect of Neohesperidin

In Vitro Antidiabetic Effect of Neohesperidin

500 gm of malted whole wheat flour was added slowly with stirring to 1 liter of 0.2% calcium acetate solution at room temperature and continuously stirred for 2 hours on a stirrer. The suspension was then centrifuged at 40ºC at 12000 rpm for 10 minutes. The resultant clear brown supernatant was stored at 2°C to 3°C prior to heat treatment. Then inactivates β-amylase by heat treatment, since beta amylase interferes with the enzymatic determination of alpha amylase it was inactivated by heating the extract at 70°C for 15 minutes. Alpha amylase is resistant to inactivation by this treatment at pH between 6.5 and 8.0. The pH of the extract was first adjusted to pH 6.6 with cold 4% ammonium hydroxide. Heat treatment was carried out at 85°C to 90°C and other at 72°C to 74°C using a water bath with continuous stirring. The extract was then cooled to 2°C to 3°C until use.

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A panel of glycoproteins as candidate biomarkers for early diagnosis and treatment evaluation of B-cell acute lymphoblastic leukemia

A panel of glycoproteins as candidate biomarkers for early diagnosis and treatment evaluation of B-cell acute lymphoblastic leukemia

Results: A total of 96 proteins were identified. Leucine-rich alpha-2-glycoprotein 1 (LRG1), Clusterin (CLU), thrombin (F2), heparin cofactor II (SERPIND1), alpha-2-macroglobulin (A2M), alpha-2-antiplasmin (SERPINF2), Alpha-1 antitrypsin (SERPINA1), Complement factor B (CFB) and Complement C3 (C3) were identified as candidate biomarkers for early diagnosis of B-ALL, as they were upregulated in the B-ALL group relative to the control and AIT groups. Expression levels of the candidate biomarkers did not differ significantly between the AIT and control groups, providing further evidence that the candidate biomarkers are present only in the disease state, as all patients achieved complete remission after treatment.

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Pushover Analysis on Plan Irregular Buildings

Pushover Analysis on Plan Irregular Buildings

The performance point in different shape of building such as square shape, rectangular shape, L shape, T shape, H shape, plus shape and C shape has been found from sap2000 software of spectral displacement and bargraph is plotted spectral displacement vs. shape of building for push x and push y as shown as bellow. While comparing the spectral displacement in square shape of building is less compared to another shape building and is more in plus shape.

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Comparative Study of Combinatorial 3D Reconstruction Algorithms

Comparative Study of Combinatorial 3D Reconstruction Algorithms

In this section, we will make an empirical comparison between the four methods of combinatorial reconstruction: the Poisson surface reconstruction method [10], the Alpha-Shape method [16], the Marching Cube method [17] and the Ball-Pivoting algorithm [14]. The comparison between these methods is conducted from the point of view of computation time and mesh quality (TABLE I) and the number of triangles per mesh (TABLE II).

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Synthesis of alpha substituted amino acids.

Synthesis of alpha substituted amino acids.

Since the decomposition product, m.p. 147 - l48 (dec.), could not be identified, and since its yield and that of the hydrolysis product were very small resulting in an overall yield of suspected amino acid of less than ten percent, this phase of the study was terminated. (The main purpose of the synthesis of o(-phenylalanine had been the determination of a convenient method of preparation of alpha substituted cystines having large, bulky groups in the alpha position.)

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Mindfulness Meditation versus EEG-Alpha Neurofeedback: The Role of EEG-Alpha Enhancement in Attentional Control

Mindfulness Meditation versus EEG-Alpha Neurofeedback: The Role of EEG-Alpha Enhancement in Attentional Control

between these studies and ours should be noted. For example, Bazanova et al. (2007) implemented an Alpha-NFB protocol that concurrently involved electromyographic (EMG) biofeedback training for muscle relaxation. Although significant increases in alpha amplitude were seen after just one session of Alpha-NFB/EMG-Biofeedback training, this cannot be unequivocally attributed to NFB training of the alpha rhythm alone. The most salient feature distinguishing the NFB paradigm used in our study from others is that of an eyes-closed vs. eyes- open NFB training protocol, where these previous single-session studies have used the latter condition. The alpha amplitude is normally seen as a function of reduced sensory input from the thalamic nuclei to the cortex (Vernon et al., 2009). Keeping the eyes open will naturally increase sensory input and thus suppress alpha amplitude by default. Therefore, NFB training with eyes open provides a lower baseline from which to attempt to increase the alpha amplitude and as such may be more amenable to positive effects from NFB. In contrast, alpha amplitude at parietal-occipital regions, where NFB training is typically conducted, is greater when eyes are closed. Aware of such considerations, we nevertheless elected to conduct NFB with eyes-closed to insure comparability with MM which is most often practiced with eyes-closed. Despite this we acknowledge that training the enhancement of EEG-Alpha during an eyes-closed condition may be more challenging and require multiple sessions to be successful.

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Compensatory increase in alpha 1 globin gene expression in individuals heterozygous for the alpha thalassemia 2 deletion

Compensatory increase in alpha 1 globin gene expression in individuals heterozygous for the alpha thalassemia 2 deletion

normal individuals and in individuals heterozygous for the common 3.7-kilobase deletion within the alpha-globin gene cluster that removes the alpha 2-globin gene (the rightward type alpha-Thal-2 deletion). To quantitate accurately the ratio of the two alpha-globin mRNAs, we have modified a previously reported S1 nuclease assay to include the use of 32P end-labeled probes isolated from alpha 1- and alpha 2-globin complementary DNA recombinant plasmids. In individuals with a normal alpha-globin genotype (as determined by Southern blot analysis [alpha alpha/alpha alpha]), alpha 2-globin mRNA is present at an average 2.8-fold excess to alpha 1. In individuals heterozygous for the rightward type alpha- Thal-2 deletion (-alpha/alpha alpha) the alpha 2/alpha 1 mRNA ratio is 1:1. These results suggest that the loss of the alpha 2-globin gene […]

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<p>New Patient-Centric Approaches to the Management of Alpha-1 Antitrypsin Deficiency</p>

<p>New Patient-Centric Approaches to the Management of Alpha-1 Antitrypsin Deficiency</p>

IV self-administration has been utilized in other therapy areas such as hereditary angioedema, and has demonstrated bene fi ts in terms of reducing time off work, and reducing healthcare visits and episodes of hospitalization. 60 Therefore, in a subset of patients with AATD, self-administration of AAT therapy has the potential to improve the convenience of weekly infusions. However, although self-administration has been shown to be feasible in AATD, 55 there has been a lack of data concerning the frequency of self-administration utilization, and patients ’ satisfaction with this therapeutic strategy. Therefore, AlphaNet, a US-based not-for-pro fi t organization that provides customized patient care through the Alpha-1 Disease Management and Prevention (ADMAP) program, 61 sought to evaluate the utilization of and patients ’ satisfaction with self- administration. 62 Of the 555 patients surveyed, 44 (7.9%) reported that they were actively self-administering their AAT therapy, and all patients self-infusing were either “ very satis- fi ed ” (95.4%) or “ satis fi ed ” (4.6%) with their treatment overall. In addition, very few adverse events were reported related to self-administration. The most frequently cited reason for patients not choosing self-administration was that they were satis fi ed with their current regimens, which highlights that self- administration is not suitable for all patients (Figure 5). However, it is notable that many patients merely lacked the con fi dence to self-administer, suggesting that a further section

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Portable wireless neurofeedback system of EEG alpha rhythm enhances memory

Portable wireless neurofeedback system of EEG alpha rhythm enhances memory

A portable system based on low-power wireless Bluetooth technology was developed for NFT of EEG’s alpha rhythm. The proposed portable system utilized a modern smart- phone to control the training procedure and visual feedback of 1-channel EEG infor- mation. The present study provided evidence that neurofeedback can be implemented in a tiny size of EEG signal device with the mobility of a smartphone. The NFT system increased alpha power and alpha duration throughout the training in the Alpha group exclusively. The Alpha group had significant elevation of memory in terms of the word- pair task and backward digital span task compared to the control group. The findings demonstrate the effect of alpha rhythm on both working memory and episodic mem- ory, which extends the findings on enhancement of working memory and attention in

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Effect of exercise and/or reduced calorie dietary interventions on breast cancer related endogenous sex hormones in healthy postmenopausal women

Effect of exercise and/or reduced calorie dietary interventions on breast cancer related endogenous sex hormones in healthy postmenopausal women

The studies in this meta-analysis mostly showed benefi- cial effects of exercise and/or caloric restriction on endogenous sex hormones, although the magnitude of effects varied. There are several underlying factors that can explain this variation. First, varying types, doses, and dur- ation of interventions might be responsible for differences between studies. Second, inclusion criteria across studies were largely comparable, but differences in baseline BMI and other differences in study populations might have con- tributed to varying results on endogenous sex hormones. The SHAPE-1, the ALPHA trial, and the study of Orsatti et al. included normal-weight women [3, 24, 25], while the other studies excluded these women. Women with normal weight might have less room for improvement in sex hor- mone levels since this change depends on the amount of fat mass. Similarly, although all studies included “inactive” women, the definition of “inactive” varied between studies. Third, the studies varied by the mean weight loss in the intervention group(s), with larger weight loss in the stud- ies that explicitly aimed for weight loss. On average, stron- ger effects were found in the NEW trial and in the SHAPE-2 study [17, 18]. Contrary to the ALPHA, PATH, and SHAPE-1 trials, the interventions in the NEW and SHAPE-2 trials targeted weight loss, with goals of − 10% of body weight and 5 to 6 kg, respectively [3, 17, 18, 22–24]. This difference might explain the larger effects since all studies found that women who lost larger amounts of weight showed larger effects on sex hormone levels [16, 28, 29]. Results of the trials studying the effect of exercise without aiming for weight loss show that exercise only is not sufficient to affect the hormone levels substantially [3, 17, 18, 22–24]. After stratifying for fat loss, the SHAPE-1 and PATH trials both reported larger effects on hormone levels in women who lost > 2% of body fat [3, 22, 23]. Hence, it is important to achieve weight loss to affect sex

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