SNPs detection in 5’-UTR region of the MC4R gene in Garut sheep

The melanocortin-4 receptor (MC4R) gene has been linked to controlling feeding behavior and body weight. The objective of this study was to detect the polymorphism within the 5’-UTR region of the MC4R gene in Garut sheep. A total of 36 blood samples were isolated and amplified using primers (forward: 5’-TTCGTTTGGGGCAAGTCAAG-3’ and reverse: 5’-GGAAACGCTCACCAACATGT-3’). Two SNPs, g.396C/T and g.399C/G, were discovered in the 5‘UTR region based on sequence alignment (position number based on Genbank acc no. NC_040274). For both SNPs, only two genotypes were found in the samples. Both SNPs had identical allele and genotype frequencies. The C allele (86%, n=26) was higher than the T (g.396C/T) and G allele (g.399C/G) (14%, n=10). The homozygous CC genotype has a higher frequency (72%) in both SNP g.396C/T and g.399C/G, followed by CT and CG genotype (28%), respectively. The Hardy-Weinberg equilibrium analysis resulted in the sample population did not deviate (χ2<5.59). Further analysis could be suggested to provide an overview of this polymorphism effect in Garut sheep’s growth traits.

Photonic crystal nanobeam cavities with lateral fins

We present the design, fabrication, and characterization of suspended arrays of small volume, high quality factor (Q) silicon nitride photonic crystal nanobeam (PCNB) cavities with lateral nanorod fin structures. By controlling the alignment position of the fins with respect to the air holes, the resonance wavelength and Q-factor of the PCNB cavities can be tuned to realize the desired performance. Measured tunable range of 2 × 104 and 10 nm is achieved for Q-factor and resonance wavelength, respectively, with the highest Q-factor measured at 2.5 × 104. Incorporating such nanorod fins into the nanobeam cavity is demonstrated to provide improved mechanical support, thermal transport, and channels of lateral carrier injection for the suspended PCNB. The proposed PCNB cavities with lateral fins are advantageous for energy efficient, ultra-compact lasers, modulators, filters, and sensors.

Inspection System for Vehicle Headlight Defects Based on Convolutional Neural Network

This paper proposes a method to detect the defects in the region of interest (ROI) based on a convolutional neural network (CNN) after alignment (position and rotation calibration) of a manufacturer’s headlights to determine whether the vehicle headlights are defective. The results were compared with an existing method for distinguishing defects among the previously proposed methods. One hundred original headlight images were acquired for each of the two vehicle types for the purpose of this experiment, and 20,000 high quality images and 20,000 defective images were obtained by applying the position and rotation transformation to the original images. It was found that the method proposed in this paper demonstrated a performance improvement of more than 0.1569 (15.69% on average) as compared to the existing method.

SWAV: a web-based visualization browser for sliding window analysis

Sliding window analysis has been extensively applied in evolutionary biology. With the development of the high-throughput DNA sequencing of organisms at the population level, an application that is dedicated to visualizing population genetic test statistics at the genomic level is needed. We have developed the sliding window analysis viewer (SWAV), which is a web-based program that can be used to integrate, view and browse test statistics and perform genome annotation. In addition to browsing, SAV can mark, generate and customize statistical images and search by sequence alignment, position or gene name. These features facilitate the effectiveness of sliding window analysis. As an example application, yeast and silkworm resequencing data are analyzed with SWAV. The SWAV package, user manual and usage demo are available at http://swav.popgenetics.net.

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers

Background Unique Molecular Identifiers (UMI) are used in many experiments to find and remove PCR duplicates. There are many tools for solving the problem of deduplicating reads based on their finding reads with the same alignment coordinates and UMIs. However, many tools either cannot handle substitution errors, or require expensive pairwise UMI comparisons that do not efficiently scale to larger datasets. Results We reformulate the problem of deduplicating UMIs in a manner that enables optimizations to be made, and more efficient data structures to be used. We implement our data structures and optimizations in a tool called UMICollapse, which is able to deduplicate over one million unique UMIs of length 9 at a single alignment position in around 26 s, using only a single thread and much less than 10 GB of memory. Conclusions We present a new formulation of the UMI deduplication problem, and show that it can be solved faster, with more sophisticated data structures.

Defect Inspection in Display Panel Using Concentrated Auto Encoder

In this paper, concentrated auto encoder (CAE) is proposed for aligning photo spacer (PS) and for local inspection of PS. The CAE method has two characteristics. First, unaligned images can be moved to the same alignment position, which makes it possible to move the measured PS images to the same position in order to directly compare the images. Second, the characteristics of the abnormal PS are maintained even if the PS is aligned by the CAE method. The abnormal PS obtained through CAE has the same alignment as the reference PS and has its abnormal characteristics. The presence or absence of defects and the location of defects were identified without precisely measuring the height of the PS and critical dimension (CD). Also, alignment and defect inspection were performed simultaneously, which shortened the inspection time. Finally, inspection performance parameters and inspection time were analyzed to confirm the validity of the CAE method and were compared with the image similarity comparison methods used for defect inspection.

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers

BackgroundUnique Molecular Identifiers (UMI) are used in many experiments to find and remove PCR duplicates. Although there are many tools for solving the problem of deduplicating reads based on their finding reads with the same alignment coordinates and UMIs, many tools either cannot handle substitution errors, or require expensive pairwise UMI comparisons that do not efficiently scale to larger datasets.ResultsWe formulate the problem of deduplicating UMIs in a manner that enables optimizations to be made, and more efficient data structures to be used. We implement our data structures and optimizations in a tool called UMICollapse, which is able to deduplicate over one million unique UMIs of length 9 at a single alignment position in around 26 seconds.ConclusionsWe present a new formulation of the UMI deduplication problem, and show that it can be solved faster, with more sophisticated data structures.

Alignment position method for SPAD detector calibration and homogeneity

<p><strong>Background:</strong> Over the last decade have seen a drastically increase of interest in the Single photon avalanche diode (SPAD) detectors applications at many variety of quantum experiments where the detection efficiency at single-photon level is required. The calibration of such detectors involves predominantly the determination of the detection efficiency.</p><p><strong>Methods:</strong> The present study was carried out at Department of Photometry and Applied Radiometry, Physikalisch-Technische Bundesanstalt (PTB), National Metrology Institute of Germany. This work is focused in a reproducible and close-to-ideal alignment position method of the SPAD detectors to the incident beam for achieving low measurement uncertainty.</p><p><strong>Results:</strong> A dominantly Gaussian profile is obtained when the diameter of the detector is smaller than the beam diameter, whereas in case then the detector is larger than the beam, a dominantly rectangular scan is obtained. The optimal position (X/Y/Z) for setting the SPAD detector correspond to X_center = 235.11 mm, Y_center<em> </em>= 6.28 mm and Z_position = 14.6 mm. Homogeneity of the detection efficiency depends on the beam size and evaluated regions.</p><p><strong>Conclusions:</strong> The experimental set-up and experimental results needed for optimization of the SPAD detector position were described. This analysis gives important information in how to carry out the optimization of the detector position for the calibration of the SPAD and analysis of quantum detection homogeneity.</p>

Traveling Wave Excitation: A Method to Produce Consistent Experimental Results

This paper describes the experimental framework to establish consistent, repeatable results associated with a traveling wave excitation system. The experiment is employed to ascertain the forced response and mistuning patterns for rotors. Several items attributing to existing experimental inconsistencies were identified and their effects were realized during this research. These experimental items were signal input locations, response measurement locations, and rotor alignment position. Accounting for these experimental variables, this paper develops a process which enables consistent rotor forced response results, independent of its orientation on the test stand.

THE ACROBOT® SYSTEM FOR ROBOTIC MIS TOTAL KNEE AND UNI-CONDYLAR ARTHROPLASTY

The concept of the Acrobot® system is described. The technical details of the complete system are then outlined, including the pre-operative planner which incorporates 3D CT models together with CAD models of prostheses that can be used to plan the leg alignment, position the prostheses, plan the shape of the cuts required and generate the regions within which cuts must be constrained. The robotic system is also described, together with the methods for locating and clamping the patient. An outline is given of the means by which the preoperative model is registered or aligned to the intra-operative position of the patient and of the robot, without the need for fiducial markers. Post-operative results are given, for both total knee replacement and also for the more recent clinical trials using a minimally invasive robotic procedure for uni-condylar arthroplasty.