Template Pattern Research Articles

A drop array culture for patterning adherent mouse embryonic stem cell-derived neurospheres.

New therapeutic approaches for repairing an injured or degenerating nervous system have accelerated the development of methods to generate populations of neurons derived from various stem cell sources efficiently. Many of these methods require the generation of neurospheres. Here a simple technique is described for creating an array of adherent mouse embryonic stem cell (mESC)-derived neurospheres using a conventional plastic culture dish and a patterning template. mESC-derived neurospheres are confined to circular (4-mm diameter), gel-coated regions within an array. The adherent neurosphere arrays require 3days to prepare from an mESC source; they can be maintained in 15μl drops of medium, and exhibit extensive neurite elaboration after 8days of cultivation. Additionally, the potential of treating the adherent neurospheres in selected drops of an array is demonstrated with a variety of differentiation-inducing reagents and subsequently individually analysing such neurospheres for gene expression, protein levels and morphological development. Copyright © 2016 John Wiley & Sons, Ltd.

A 5-mC Dot Blot Assay Quantifying the DNA Methylation Level of Chondrocyte Dedifferentiation <em>In Vitro</em>

The dedifferentiation of hyaline chondrocytes into fibroblastic chondrocytes often accompanies monolayer expansion of chondrocytes in vitro. The global DNA methylation level of chondrocytes is considered to be a suitable biomarker for the loss of the chondrocyte phenotype. However, results based on different experimental methods can be inconsistent. Therefore, it is important to establish a precise, simple, and rapid method to quantify global DNA methylation levels during chondrocyte dedifferentiation. Current genome-wide methylation analysis techniques largely rely on bisulfite genomic sequencing. Due to DNA degradation during bisulfite conversion, these methods typically require a large sample volume. Other methods used to quantify global DNA methylation levels include high-performance liquid chromatography (HPLC). However, HPLC requires complete digestion of genomic DNA. Additionally, the prohibitively high cost of HPLC instruments limits HPLC's wider application. In this study, genomic DNA (gDNA) was extracted from human chondrocytes cultured with varying number of passages. The gDNA methylation level was detected using a methylation-specific dot blot assay. In this dot blot approach, a gDNA mixture containing the methylated DNA to be detected was spotted directly onto an N+ membrane as a dot inside a previously drawn circular template pattern. Compared with other gel electrophoresis-based blotting approaches and other complex blotting procedures, the dot blot method saves significant time. In addition, dot blots can detect overall DNA methylation level using a commercially available 5-mC antibody. We found that the DNA methylation level differed between the monolayer subcultures, and therefore could play a key role in chondrocyte dedifferentiation. The 5-mC dot blot is a reliable, simple, and rapid method to detect the general DNA methylation level to evaluate chondrocyte phenotype.

Phonological patterns (templates) in 5p deletion syndrome

ABSTRACTWhole word phonological patterns (templates) in utterances produced by children with 5p deletion syndrome are analysed, addressing four questions: (1) Are children with 5p deletion syndrome able to generalise over words? (2) How does the template score of children with 5p deletion syndrome relate to those of typically developing children and of the target language? (3) How do the template scores relate to other phonological measures, PCC and consonant variegation? (4) What can the relationship between template scores and phonological measures tell us about templates? Children with 5p deletion syndrome are able to generalise over words, some to a target like extent, others generalise more than expected for their age. The template scores relate to other phonological measures, with two exceptions. The exceptions indicate that the template score of a child with articulatory difficulties may reflect more detailed representations of the words in memory than she is able to express.

A Channel Rejection Method for Attenuating Motion-Related Artifacts in EEG Recordings during Walking.

Recording scalp electroencephalography (EEG) during human motion can introduce motion artifacts. Repetitive head movements can generate artifact patterns across scalp EEG sensors. There are many methods for identifying and rejecting bad channels and independent components from EEG datasets, but there is a lack of methods dedicated to evaluate specific intra-channel amplitude patterns for identifying motion-related artifacts. In this study, we proposed a template correlation rejection (TCR) as a novel method for identifying and rejecting EEG channels and independent components carrying motion-related artifacts. We recorded EEG data from 10 subjects during treadmill walking. The template correlation rejection method consists of creating templates of amplitude patterns and determining the fraction of total epochs presenting relevant correlation to the template. For EEG channels, the template correlation rejection removed channels presenting the majority of epochs (>75%) correlated to the template, and presenting pronounced amplitude in comparison to all recorded channels. For independent components, the template correlation rejection removed components presenting the majority of epochs correlated to the template. Evaluation of scalp maps and power spectra confirmed low neural content for the rejected components. We found that channels identified for rejection contained ~60% higher delta power, and had spectral properties locked to the gait phases. After rejecting the identified channels and running independent component analysis on the EEG datasets, the proposed method identified 4.3 ± 1.8 independent components (out of 198 ± 12) with substantive motion-related artifacts. These results indicate that template correlation rejection is an effective method for rejecting EEG channels contaminated with motion-related artifact during human locomotion.

Well-dated fluvial sequences as templates for patterns of handaxe distribution: Understanding the record of Acheulean activity in the Thames and its correlatives

The use of Acheulean (handaxe) typology as a cultural and temporal marker has been a topic of controversy in recent decades, with many archaeologists continuing to reject such an approach out of hand. Much of the controversy stems, however, from difficulties in reconciling the archaeological record from Quaternary sediments with a flawed and overly simplified chronostratigraphical template. With the adoption of the ‘expanded chronology’ based on the marine oxygen isotope record, underpinned by biostratigraphical and geochronological dating, has come the recognition of a meaningful progression of artefact types, such as the first appearance of Levallois technique, attributed to MIS 9–8 over widespread parts of the Old World. More recently it has been established that assemblages in Britain with twisted ovate handaxes in significant numbers represent MIS 11 occupation, while those with significant proportions of cleavers and ‘ficron’ handaxes appear to be correlated with deposits formed at around the time of the MIS 9 interglacial. The recognition of such patterns stems largely from the well-dated Thames sequence; it should not be confused with the previous use, in the mid-20th century, of archaeological typology as a crude dating indicator based on a relative refinement of tool making. Key means of age constraint for the Thames sequence have been mammalian assemblage zones representing the last four interglacial cycles, molluscan biostragraphy and amino acid racemization dating of molluscan material, especially the calcitic opercula of the gastropod Bithynia tentaculata, thus providing a framework within which the archaeological patterns can be identified.

Beyond Conventional Patterns: New Electrochemical Lithography with High Precision for Patterned Film Materials and Wearable Sensors.

We report a simple, low-cost, and brand-new electrochemical lithography technique for replicating the template pattern with high resolution at ∼2 μm. The developed method is that the electroactive material is first deposited on the patterned conductive template by the electrochemical technique and then peeled by an adhesive tape/material. The resulting film with the precise pattern shows excellent mechanical and electronic properties and promises high prospect in designing flexible electronics. This interesting approach can be performed at ambient conditions and easily generalized to pattern various electroactive materials covering metal, alloy, nonmetal, salt, oxide, and composite on different types of substrates in several seconds to a few minutes, making the mass production of flexible/rigid/stretchable patterned thin films quite possible.

Efficient Pattern-Based Aggregation on Sequence Data

A Sequence OLAP (S-OLAP) system provides a platform on which pattern-based aggregate (PBA) queries on a sequence database are evaluated. In its simplest form, a PBA query consists of a pattern template $T$ and an aggregate function $F$ . A pattern template is a sequence of variables, each is defined over a domain. Each variable is instantiated with all possible values in its corresponding domain to derive all possible patterns of the template. Sequences are grouped based on the patterns they possess. The answer to a PBA query is a sequence cuboid (s-cuboid), which is a multidimensional array of cells. Each cell is associated with a pattern instantiated from the query's pattern template. The value of each s-cuboid cell is obtained by applying the aggregate function $F$ to the set of data sequences that belong to that cell. Since a pattern template can involve many variables and can be arbitrarily long, the induced s-cuboid for a PBA query can be huge. For most analytical tasks, however, only iceberg cells with very large aggregate values are of interest. This paper proposes an efficient approach to identifying and evaluating iceberg cells of s-cuboids. Experimental results show that our algorithms are orders of magnitude faster than existing approaches.

Uwagi polemiczne do pracy Marquity Volken „Archaeological Footwear. Development of shoe patterns and styles from Prehistory till the 1600’s”1

One of the newest works on shoemaking was written in the Swiss Musee de la Chaussure in Lausanne. The author of the work, Marquita Volken, presented her own original way to organize source materials known mainly from archaeological excavations, but also from iconographic sources and old collections. The system is intended to be used primarily by novice researchers dealing with issues of development of shoemaking in Europe. In essence, the author has achieved her goal – she presented the development of footwear from prehistory to the seventeenth century, therefore this is another attempt to summarize the existing research results. However, the publication by M. Volken, despite the bulk of work involved, especially the careful preparation of the graphic part, contains a number of controversial statements and conclusions. The author attempts to define the styles of footwear, basic pattern templates, as well as the seams and stitches. A discussion on the diversity of footwear’s names and on suggestions as to their unification is a very important part of the work. M. Volken’s suggestions are certainly interesting, but the systematization and periodization model presented by her brings a lot of doubts. In the opinion of the Author, a new method was created, combining styles and pattern templates, reflecting fashion and stylistic and cultural aspects

Development of coagulate map formation algorithms to carry out treatment by laser coagulation

The eye’s fundus is a complex object with a high density of filling vessels. The procedure of fundus treatment requires a lot of experience and skill from the physician. The basic tool in fundus treatment is laser coagulation, when a series of metered microscopic thermal wounds – laser coagulates – are applied in edema on the eye’s retina. Currently available software packages are focused first on the use of the specified template (pattern) for coagulate location. Effects of the pattern application are caused by irregular coagulate location by reason of high variability in edema and vasculature forms. The paper presents algorithms for calculating a coagulate map within the framework of the solution of the sphere close-packing problem in a random region and research results for developed algorithms. For automatic coagulate arrangement, we proposed a software package including the proposed algorithms.

Low-cost fabrication of nanoimprint templates with tunable feature sizes at a constant pitch

Nanoimprint lithography (NIL) templates are in general costly, especially for large area and small feature sizes. With a simple shrinking technique using a serial of well-known technologies, it has been feasibly realized to produce high-quality soft NIL templates with widely tunable feature sizes at a constant pitch from a single master at very low-cost and in a short processing cycle. The master featuring at sub-micron range has been replicated to new silicon NIL templates with feature sizes at, but not limited to, sub-200nm. soft UV-NIL combined with a dry etch process, were employed to fabricate an intermediate template of nanocone patterns that is further used for an imprint on the final substrate. The feature size of the SiO2 etch mask on the final substrate can be adjusted by varying the duration of mask formation etching. The final patterning of the template is realized by cryogenic etching based on SF6/O2 chemistry. Silicon NIL templates featuring nanopillar patterns with diameters of 150nm, 200nm and 250nm, respectively, have been fabricated on wafer level from the same master with 450nm feature size. The presented process flow avoids the time-consuming and cost-intensive electron beam writings and gives more flexibility in the fabrication of nanopatterns. The fabrication cycle for such NIL working templates with tunable feature sizes is maintained short and at a low cost. Moreover, the technique allows the fabrication of wafer level products at a constant pitch, which is of importance as well for the stacked large-area imprintings with varying feature sizes.

Dietary regimes and the nutrition transition: bridging disciplinary domains

The nutrition transition concept developed by Popkin has gained wide currency within the nutritional sciences literature as a way of understanding population wide changes to diet and energy balance and their related health outcomes in society. It offers a useful template of different nutritional patterns societies progress through, but it has not provided a comprehensive understanding of the why and how of dietary change. Building on insights from the literature on food regimes in the social sciences, this paper argues the concept of dietary regimes can augment the nutrition transition model and can serve as a bridge between social and health sciences around nutrition and dietary change. The political economy analysis of the dietary regime approach provides insights into the historical degradation of food and the diffusion of nutrient-poor products throughout food environments today. It also engages analysis of the key actors shaping food environments and diets in the industrial era. The dietary regime approach can provide fruitful directions with respect to concrete policy options to address the major issue of population wide weight gain that the nutrition transition model has sought to confront in recent iterations.

General Template Units for the Finite Volume Method in Box-Shaped Domains

In this work, we develop an extension of the Curiously Recurring Template Pattern (CRTP), which allows us to organize three related concepts in a class hierarchy. Generalizations, specializations and special procedures are the concepts that we use to define and implement several tools. We call these tools general template units because they are well-defined building blocks (units) for numerically solving partial differential equations (PDEs), are based on the use of templates of the C++ language, and can be applied in the solution of different kinds of problems. We focus on the solution of PDEs using the Finite Volume Method (FVM) in box-shaped domains. The three concepts just mentioned are intensively used to generate optimized codes for each case study. The convenience of our approach is highlighted in the numerical solutions of the examples of application, including laminar thermal convection, turbulent thermal convection, as well as a two-phase flow model in porous media, all of them in one, two, and three dimensions. The mathematical models of these examples were obtained using the axiomatic formulation, which provides generality, simplicity, and clarity to tackle any continuum mechanics application. The ideas explained in this work are quite simple but powerful in solving fluid dynamics problems, in which the conservativeness of the FVM is an important feature. The techniques developed in this work allow us to swap easily between numerical schemes for computing the coefficients obtained by applying the FVM.

Image database of printed fabric with repeating dot patterns part (I) – image archiving

An image database of printed fabrics with repeating dot patterns was created to alleviate issues associated with management of and searches for numerous dot printed fabrics in the printing industry. The function of the database is to archive and allow retrieval of images. First, we discuss image archiving of repeating pattern-based dot printed fabrics. The color image was scanned by resolution of 200 dpi. The wavelet transformation was used to preprocess the image to obtain a scanned image 1/16 of the size of the original to be the stored image. To acquire images with repeating pattern color and repeating pattern template, the binary image of each pattern was obtained using the Sobel edge detection method and a morphological operation. Then pattern elements identical to the target pattern element were screened out. Afterwards, the centroid positions of these identical pattern elements were used to subdivide the repeating pattern color image and repeating pattern template image using a vertical vector method. Finally, the RGB 512-color histogram was used as the color feature of the dot printed fabrics, and the geometric and moment invariant feature values of the repeating pattern template image were used as the pattern feature of the dot printed fabrics. Our experimental results show that images can be acquired that are suitable for use in a dot printed fabric image database. The color and template images of the repeating patterns, which represent the image content of the printed fabrics, were obtained to create an image database of repeating pattern-based dot printed fabrics. This image database contains data on 300 printed fabrics which can be used for subsequent research on database image retrieval.

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems.

Spatial normalization of brain images and beyond

The deformable atlas paradigm has been at the core of computational anatomy during the last two decades. Spatial normalization is the variant endowing the atlas with a coordinate system used for voxel-based aggregation of images across subjects and studies. This framework has largely contributed to the success of brain mapping. Brain spatial normalization, however, is still ill-posed because of the complexity of the human brain architecture and the lack of architectural landmarks in standard morphological MRI. Multi-atlas strategies have been developed during the last decade to overcome some difficulties in the context of segmentation. A new generation of registration algorithms embedding architectural features inferred for instance from diffusion or functional MRI is on the verge to improve the architectural value of spatial normalization. A better understanding of the architectural meaning of the cortical folding pattern will lead to use some sulci as complementary constraints. Improving the architectural compliance of spatial normalization may impose to relax the diffeomorphic constraint usually underlying atlas warping. A two-level strategy could be designed: in each region, a dictionary of templates of incompatible folding patterns would be collected and matched in a way or another using rare architectural information, while individual subjects would be aligned using diffeomorphisms to the closest template. Manifold learning could help to aggregate subjects according to their morphology. Connectivity-based strategies could emerge as an alternative to deformation-based alignment leading to match the connectomes of the subjects rather than images.

Fan fault diagnosis based on symmetrized dot pattern analysis and image matching

To detect the mechanical failure of fans, a new diagnostic method based on the symmetrized dot pattern (SDP) analysis and image matching is proposed. Vibration signals of 13 kinds of running states are acquired on a centrifugal fan test bed and reconstructed by the SDP technique. The SDP pattern templates of each running state are established. An image matching method is performed to diagnose the fault. In order to improve the diagnostic accuracy, the single template, multiple templates and clustering fault templates are used to perform the image matching.

Harmonic modulation of acoustic standing wave fields for tissue engineering

Acoustic standing wave fields can be used to produce virtual, scaffold-less templates for tissue patterning and engineering. To date, only simple tissue patterns have been attempted and achieved such as layered microstructures. This is due in large part to the use of single-frequency standing waves transmitted from a single source, producing planar nodes and antinodes in the cell/growth medium suspension. The purpose of this study was to explore with computational models the possibility of generating complex tissue microstructures using multiple sources with multiple frequency capabilities. The models simulated multifrequency standing waves (i.e., modulated by higher harmonics), multiple acoustic sources at various angles to each other, and corresponding acoustic cavities. The simulations demonstrated that interference patterns of standing waves could be produced with a three-dimensional complexity similar to that of natural biological structures. Such patterns included alveolar structures (thin, membrane-like walls encapsulating open cavities), lobular structures (cell clusters interlaced with duct- and vascular-like channels), and radial structures (iris-like patterns). Experiments for rendering these models to actual tissue structures have also begun, including the development of multifrequency transducers, using multiple transducers to generate a square lattice of cell walls and channels, and methods to reproduce natural tissue structures with high fidelity.

Effect of defects in oxide templates on Non-catalytic growth of GaN nanowires for high-efficiency light-emitting diodes

Two kinds of oxide templates, one with and one without undercuts, are employed to study the effect of defects in oxide templates on non-catalytic growth of GaN nanowires (NWs). GaN NWs abnormally grown from the templates containing undercuts exhibit two types of patterns: earlystage growth of premature NWs and abnormally-overgrown (~2 μm) NWs. GaN NWs grown on perfectly-symmetric template patterns are highly crystalline and have high aspect ratios (2 ~ 5), and their tops are shaped as pyramids with semipolar facets, clearly indicating hexagonal symmetry. The internal quantum efficiency of the well-grown NWs is 10% larger than that of the deformed NWs, as estimated by using photoluminescence. These results suggest that our technique is an effective approach for growing large-area-patterned, vertically-aligned, hexagonal GaN NWs without catalysts, in strong contrast to catalytic vapor-liquid-solid growth, and that good formation of the oxide templates is crucial for the growth of high-quality GaN NWs.

Use of Self Organizing Map to Obtain ECG Data Templates for Its Compression and Reconstruction

An electrocardiogram (ECG) is a recording of electrical impulses generated by the electrical activity of the heart and is used as a diagnostic tool to analyze various heart diseases. For economical storage and fast transmission over low-bandwidth channels, ECG data need to be compressed. For the efficient compression of ECG signals, the topology preservation feature of self-organizing maps (SOM) is used. It is observed that a compression ratio up to 1:20 can be achieved with a very low-percentage root-mean-square difference, i.e. below 1.6, by creating templates of ECG patterns in the form of weight vectors of neurons. The templates obtained in this manner are then used to reconstruct the ECG signal. This analysis shows that the reconstructed signal is perfectly matched to the original signal.

Fast Mode Decision in the HEVC Video Coding Standard by Exploiting Region with Dominated Motion and Saliency Features.

The emerging High Efficiency Video Coding (HEVC) standard introduces a number of innovative and powerful coding tools to acquire better compression efficiency compared to its predecessor H.264. The encoding time complexities have also increased multiple times that is not suitable for realtime video coding applications. To address this limitation, this paper employs a novel coding strategy to reduce the time complexity in HEVC encoder by efficient selection of appropriate block-partitioning modes based on human visual features (HVF). The HVF in the proposed technique comprise with human visual attention modelling-based saliency feature and phase correlation-based motion features. The features are innovatively combined through a fusion process by developing a content-based adaptive weighted cost function to determine the region with dominated motion/saliency (RDMS)- based binary pattern for the current block. The generated binary pattern is then compared with a codebook of predefined binary pattern templates aligned to the HEVC recommended block-paritioning to estimate a subset of inter-prediction modes. Without exhaustive exploration of all modes available in the HEVC standard, only the selected subset of modes are motion estimated and motion compensated for a particular coding unit. The experimental evaluation reveals that the proposed technique notably down-scales the average computational time of the latest HEVC reference encoder by 34% while providing similar rate-distortion (RD) performance for a wide range of video sequences.