Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach

The unparalleled heterogeneity in genetic causes of hearing loss along with remarkable differences in prevalence of causative variants among ethnic groups makes single gene tests technically inefficient. Although hundreds of genes have been reported to be associated with nonsyndromic hearing loss (NSHL), GJB2, GJB6, SLC26A4, and mitochondrial (mt) MT-RNR1 and MTTS are the major contributors. In order to provide a faster, more comprehensive and cost effective assay, we constructed a DNA fluidic array, CapitalBioMiamiOtoArray, for the detection of sequence variants in five genes that are common in most populations of European descent. They consist of c.35delG, p.W44C, p.L90P, c.167delT (GJB2); 309kb deletion (GJB6); p.L236P, p.T416P (SLC26A4); and m.1555A>G, m.7444G>A (mtDNA). We have validated our hearing loss array by analyzing a total of 160 DNAs samples. Our results show 100% concordance between the fluidic array biochip-based approach and the established Sanger sequencing method, thus proving its robustness and reliability at a relatively low cost

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Application of deep learning in Mandarin Chinese lip-reading recognition

Abstract Lip-reading is an emerging technology in recent years, and it can be applied to the field of language recovery, criminal investigation, identity authentication, etc. We aim to recognize what the speaker is saying without audio but only video. Because of the different mouth shapes and the influence of homophones, the current Mandarin Chinese lip-reading network is proposed, an end-to-end model based on long short-term memory (LSTM) encoder-decoder architecture. The model incorporates the LSTM encoder-decode architecture, the spatiotemporal convolutional neural network (STCNN), Word2Vec, and the Attention model. The STCNN captures continuously encoded motion information, Word2Vec converts words into word vectors for feature encoding, and the Attention model assigns weights to the target words. Based on the video dataset we built, we completed training and testing. Experiments have proved that the accuracy of the Mandarin Chinese lip-reading model is about 72%. Therefore, MCLRN can be used to identify the words spoken by the speaker

Loop Closure Detection in RGB-D SLAM by Utilizing Siamese ConvNet Features

Loop closure detection is a key challenge in visual simultaneous localization and mapping (SLAM) systems, which has attracted significant research interest in recent years. It entails correctly determining whether a scene has previously been visited by a mobile robot and completely establishing the consistent maps of motion. There are many loop closure detection methods that have been proposed, but most of these algorithms are handcrafted features-based and perform weak robustness to illumination variations. In this paper, we investigate a Siamese Convolutional Neural Network (SCNN) to solve the task of loop closure detection in RGB-D SLAM. Firstly, we use a pre-trained SCNN model to extract features as image descriptors; then, the L2 norm distance is adopted as a similarity metric between descriptors. In terms of the learned features for matching, there are two key issues for discussion: (1) how to define an appropriate loss as supervision (utilizing the cross-entropy loss, the contrastive loss, or the combination of two); and (2) how to combine the appearance information in RGB images and position information in depth images (utilizing early fusion, mid-level fusion or late fusion). We compare our proposed method of different baseline by experiments carried out on two public datasets (New College and NYU), and our performance outperforms the state-of-the-art

Application of global phase filtering method in multi frequency measurement

In reverse engineering, reconstruction of 3D point cloud data is the key step to acquire the final profile of the object. However, the quality of 3D reconstruction is influenced by noise in the three-dimensional measurement. This paper aims to tackle the issue of removing the noisy data from the complex point cloud data. The 3D-GPF (Three Dimensional Global Phase Filtering) global phase filtering method is proposed based on the study of phase filtering method, consisting of the steps below. Firstly, the six-step phase shift profilometry is used to obtain the local phase information, and encoding the obtained phase information. Through the global phase unwrapping method, the global phase can be acquired. Secondly, 3D-GPF method is used for the obtained global phase. Finally, the effect of 3D reconstruction is analyzed after the global phase filtering. Experimental results indicate that the noisy points of three-dimensional graphics is reduced 98.02%, the speed of 3D reconstruction is raised 12%.The effect of the proposed global phase filtering method is better than DCT and GSM methods. It is high precision and fast speed, and can be widely used in other 3D reconstruction application

A color phase shift profilometry for the fabric defect detection

For fabric defect identification in the textile industry, a three-dimensional (3D) color phase shift profilometry (CPSP) method is proposed. The detecting system is mainly composed of one CCD camera and one digital-light-processing (DLP) projector. Before detection, the system should be calibrated to make sure the camera parameters. The CPSP color grating is projected to the measured fabric by DLP projector, and then it is collected by CCD camera to obtain the grating phase. The 3D measurement can be completed by the grating phase difference. In image acquisition, only invariable grating is projected to the object. In order to eliminate the interference from background light during the image acquisition, the brightness correction method is researched for improving the detection accuracy. The experimental results show that the false rate of detecting the fabric defects is 5.78%, the correct rates of detecting the fabric defects of hole and qualified fabric are both 100%, and the correct rates of detecting the fabric defect of scratch and fold are 98% and 96%, respectively. The experiment proves that the proposed method can accurately identify fabric defects

A Structural Gap in Dpo4 Supports Mutagenic Bypass of a Major Bbenzo[a]pyrene dG Adduct in DNA through Template Misalignment

Erroneous replication of lesions in DNA by DNA polymerases leads to elevated mutagenesis. To understand the molecular basis of DNA damage-induced mutagenesis, we have determined the x-ray structures of the Y-family polymerase, Dpo4, in complex with a DNA substrate containing a bulky DNA lesion and incoming nucleotides. The DNA lesion is derived from an environmentally widespread carcinogenic polycyclic aromatic hydrocarbon, benzo[a]pyrene (BP). The potent carcinogen BP is metabolized to diol epoxides that form covalent adducts with cellular DNA. In the present study, the major BP diol epoxide adduct in DNA, BP-N(2)-deoxyguanosine (BP-dG), was placed at a template-primer junction. Three ternary complexes reveal replication blockage, extension past a mismatched lesion, and a -1 frameshift mutation. In the productive structures, the bulky adduct is flipped/looped out of the DNA helix into a structural gap between the little finger and core domains. Sequestering of the hydrophobic BP adduct in this new substrate-binding site permits the DNA to exhibit normal geometry for primer extension. Extrusion of the lesion by template misalignment allows the base 5\u27 to the adduct to serve as the template, resulting in a -1 frameshift. Subsequent strand realignment produces a mismatched base opposite the lesion. These structural observations, in combination with replication and mutagenesis data, suggest a model in which the additional substrate-binding site stabilizes the extrahelical nucleotide for lesion bypass and generation of base substitutions and -1 frameshift mutations

Evaluating the Roles of sCD14 and sCD14-ST in Diagnosing COPD and Predicting an Acute Exacerbation of COPD

Abstract Aim To evaluate the roles of plasma soluble cluster of differentiation 14 (sCD14) and sCD14 subtype (sCD14-ST) in the diagnosis of chronic obstructive pulmonary disease (COPD) and in the prediction of an acute exacerbation of COPD (AECOPD). Methods We quantified the levels of white blood cell count (WBC), C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), interleukin (IL)-6, IL-8, sCD14, and sCD14-ST in patients with COPD and healthy controls. The relationships between sCD14 or sCD14-ST and inflammatory markers were analyzed in each group. We used receiver operating characteristics (ROC) curves to evaluate the potential roles of sCD14 and sCD14-ST in the diagnosis of COPD and in predicting AECOPD. Results A total of 62 subjects were recruited, including 15 controls and 47 COPD patients, with the latter including 32 stable COPD and 15 AECOPD. WBC, IL-8, sCD14, and sCD14-ST were significantly higher in COPD than in the controls (all P < 0.05). WBC, CRP, ESR, IL-6, IL-8, sCD14, and sCD14-ST were higher in AECOPD than in the controls (all P < 0.05). In the COPD group, sCD14 levels were positively correlated with WBC, IL-8, and sCD14-ST (P < 0.05), and sCD14-ST levels were positively correlated with WBC and IL-8 (P < 0.05). In the AECOPD group, sCD14 was positively correlated with WBC, CRP, IL-8, and sCD14-ST (P < 0.05); sCD14-ST was positively correlated with WBC, IL-6, and IL-8 (P < 0.05). Discrimination between COPD and controls was tested by calculating areas under the ROC curve (AUCs) for sCD14 and sCD14-ST showing scores of 0.765 (95% CI 0.648–0.883) and 0.735 (95% CI 0.537–0.933) respectively. Similarly, discrimination between AECOPD and controls using sCD14 and sCD14-ST showed scores of 0.862 (95% CI 0.714–1.000) and 0.773 (95% CI 0.587–0.960), respectively. Conclusion Our study suggests that the inflammatory markers sCD14 and sCD14-ST might play an important diagnostic role in COPD and help predict AECOPD