scholarly journals Deep Learning For Denoising Hi-C Chromosomal Contact Data

2019 ◽  
Author(s):  
Max Highsmith ◽  
Oluwatosin Oluwadare ◽  
Jianlin Cheng
Keyword(s):  
Deep Learning ◽  
Signal To Noise Ratio ◽  
Pearson Correlation ◽  
3D Structure ◽  
Three Dimensional ◽  
Yeast Genome ◽  
Chromosome Conformation ◽  
Contact Matrix ◽  
The Impact

AbstractMotivationThe three-dimensional (3D) organization of an organism’s genome and chromosomes plays a significant role in many biological processes. Currently, methods exist for modeling chromosomal 3D structure using contact matrices generated via chromosome conformation capture (3C) techniques such as Hi-C. However, the effectiveness of these methods is inherently bottlenecked by the quality of the Hi-C data, which may be corrupted by experimental noise. Consequently, it is valuable to develop methods for eliminating the impact of noise on the quality of reconstructed structures.ResultsWe develop unsupervised and semi-supervised deep learning algorithms (i.e. deep convolutional autoencoders) to denoise Hi-C contact matrix data and improve the quality of chromosome structure predictions. When applied to noisy synthetic contact matrices of the yeast genome, our network demonstrates consistent improvement across metrics for contact matrix similarity including: Pearson Correlation, Spearman Correlation and Signal-to-Noise Ratio. Positive improvement across these metrics is seen consistently across a wide space of parameters to both gaussian and poisson noise [email protected] and [email protected]

Cryomicroscopy of crotoxin complex crystals at 400 KV

1989 ◽  
Vol 47 ◽  
pp. 826-827
Author(s):  
Jaap Brink ◽  
Wah Chiu
Keyword(s):  
Signal To Noise Ratio ◽  
3D Structure ◽  
Three Dimensional ◽  
Carbon Films ◽  
Depth Of Field ◽  
Basic Subunit ◽  
Ewald Sphere ◽  
Diffraction Patterns ◽  
Complex Crystals ◽  
Acidic Subunit

The crotoxin complex is a potent neurotoxin composed of a basic subunit (Mr = 12,000) and an acidic subunit (M = 10,000). The basic subunit possesses phospholipase activity whereas the acidic subunit shows no enzymatic activity at all. The complex's toxocity is expressed both pre- and post-synaptically. The crotoxin complex forms thin crystals suitable for electron crystallography. The crystals diffract up to 0.16 nm in the microscope, whereas images show reflections out to 0.39 nm2. Ultimate goal in this study is to obtain a three-dimensional (3D-) structure map of the protein around 0.3 nm resolution. Use of 100 keV electrons in this is limited; the unit cell's height c of 25.6 nm causes problems associated with multiple scattering, radiation damage, limited depth of field and a more pronounced Ewald sphere curvature. In general, they lead to projections of the unit cell, which at the desired resolution, cannot be interpreted following the weak-phase approximation. Circumventing this problem is possible through the use of 400 keV electrons. Although the overall contrast is lowered due to a smaller scattering cross-section, the signal-to-noise ratio of especially higher order reflections will improve due to a smaller contribution of inelastic scattering. We report here our preliminary results demonstrating the feasability of the data collection procedure at 400 kV.Crystals of crotoxin complex were prepared on carbon-covered holey-carbon films, quench frozen in liquid ethane, inserted into a Gatan 626 holder, transferred into a JEOL 4000EX electron microscope equipped with a pair of anticontaminators operating at −184°C and examined under low-dose conditions. Selected area electron diffraction patterns (EDP's) and images of the crystals were recorded at 400 kV and −167°C with dose levels of 5 and 9.5 electrons/Å, respectively.

scholarly journals Impact of Partially Treated Wastewater on Downstream Water Quality of Notwane River in Botswana

2018 ◽  
pp. 1-9
Author(s):  
Gilbert K. Gaboutloeloe ◽  
Gugu Molokwe ◽  
Benedict Kayombo
Keyword(s):  
Water Quality ◽  
Pearson Correlation ◽  
Oxygen Demand ◽  
Ammonia Nitrogen ◽  
Treated Wastewater ◽  
Nitrate N ◽  
River Stretch ◽  
Ph Range ◽  
The Impact

The impact of partially treated wastewater on the water quality of Notwane river stretch in the Gaborone region of Botswana was investigated. Water samples collected at effluent discharge point and three other sampling sites downstream were analyzed for pH, temperature, Biological Oxygen Demand (BOD5), Ammonia-nitrogen (Ammonia-N) and Nitrate-nitrogen (Nitrate-N). Sampling was conducted bi-weekly between February 2013 and April 2013. The ranges of measured parameters were:  pH (7.6-8.5), temperature (22-23ºC), BOD5 (11.2-27.0 mg/l), Ammonia-N (2.4-60.5 mg/l), Nitrate-N (20.6-28.6 mg/l). Analysis of variance, Games-Howel multiple comparisons and Pearson correlation were used to separate variable means. The results signal river non-point pollution due to runoff inflow of organics mainly from land use and domestic waste dumping by nearby dwellings. Temperature, BOD5, and pH range values were all within the Botswana Bureau of Standards (BOBS) limit while the maximum Ammonia-N and Nitrate-N were above BOBS limit by 50.5 mg/l and 6.6 mg/l, respectively. Regulations on indiscriminate waste dumping and discharge standards adherence should be enforced.

Online quality evaluation of tissue paper structure on new generation tissue machines

2018 ◽  
Vol 33 (1) ◽  
pp. 133-141 ◽  
Author(s):  
Jukka-Pekka Raunio ◽  
Tommi Löyttyniemi ◽  
Risto Ritala
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Surface Profile ◽  
Absorption Capacity ◽  
Tissue Paper ◽  
Paper Manufacturing ◽  
Residual Variation ◽  
Residual Variances ◽  
New Generation

Abstract At present, the tissue paper manufacturing is mostly based on the dry crepe technology. During the last decade, the manufacturers have introduced new tissue machines concepts that increase the softness, bulk, and absorption capacity. Such machines produce a strong regular three-dimensional (3D) structure to the sheet before the Yankee cylinder. At present, the quality of the 3D structure is not evaluated, or it is evaluated only subjectively at the mill. This is mostly because of the difficulties to separate reliably the regular 3D pattern from other variations. This paper introduces a frequency analysis based method which separates the surface profile variances in tissue paper to the creping, to the regular 3D pattern and to the residual variation. The 3D surface profiles and their variances were determined online with the photometric stereo method. We show that the introduced analysis method evaluates the variance portions reliably and the results are consistent with the visual perception of the 3D surfaces. In one particular product, the regular 3D pattern explains 74 % of total surface variance; the creping explains 10 % and residual variations 16 %. Furthermore, the creping and residual variances are quite stable over time whereas the variance of the regular 3D pattern fluctuates significantly.

Perceptions of nurses on the impact of accreditation on quality of care

2014 ◽  
Vol 19 (2) ◽  
pp. 69-82 ◽  
Author(s):  
Ahmet Yildiz ◽  
Sidika Kaya
Keyword(s):  
Regression Analysis ◽  
Patient Satisfaction ◽  
Quality Of Care ◽  
Positive Impact ◽  
Pearson Correlation ◽  
High Rate ◽  
Content Type ◽  
Independent Variables ◽  
The Impact

Purpose – This article aims to investigate perceptions of Turkish nurses on the impact of accreditation on quality of care and the effect of accreditation on quality results. Design/methodology/approach – This study was performed as a cross-sectional, questionnaire-based survey on 258 nurses who started working in the hospital before it was accredited and continued to work during and after accrediation and who therefore knew both the hospital's pre-accrediation and post-accreditation periods. In this study, descriptive statistical analyses (means and standard deviations) were carried out to explore the views of the participants on “quality results,” “benefits of accreditation” and “participation of employees.” “Quality results” was considered to be the dependent variable, while “benefits of accreditation” and “participation of employees” were accepted as the independent variables. The relationship between the dependent variable and the independent variables was tested using Pearson correlation and multiple regression analysis. External patient satisfaction data collected by the quality department of the hospital before and after accreditation were also investigated. Findings – It was found that nurses had generally high scores for the items concerning the benefits of accreditation. There was a statistically significant positive correlation between the dependent variable (quality results) and the independent variables (benefits of accreditation and participation of employees). Regression analysis indicated that R2=0.461 and the extent to which the independent variables explained the dependent variable was 46.1 per cent, which is a high rate. Patient satisfaction scores increased after accreditation. Practical implications – Our study suggest that providing support for nurses, especially nurses with administrative responsibilities and incorporating employees into the process are important for exercising quality standards. Originality/value – Hospital accreditation has a positive impact on quality results especially on quality of care provided to patients and patient satisfaction. Study findings could guide policy makers and hospital managers in Turkey and in other countries who are preparing or implementing accreditation.

scholarly journals Classroom acoustics: Listening problems in children

2019 ◽  
Vol 27 (1) ◽  
pp. 47-59 ◽  
Author(s):  
Flavia Gheller ◽  
Elisa Lovo ◽  
Athena Arsie ◽  
Roberto Bovo
Keyword(s):  
Auditory Processing ◽  
Signal To Noise Ratio ◽  
Cognitive Effort ◽  
Listening Skills ◽  
Noisy Environments ◽  
Acoustic Characteristics ◽  
Classroom Acoustics ◽  
Acoustic Quality ◽  
The Impact

The acoustic quality of classrooms is crucial for children’s listening skills and consequently for their learning. Listening abilities in kids are still developing, and an environment with inadequate acoustic characteristics may create additional problems in speech perception and phonetic recognition. Background noise or reverberation may cause auditory processing problems and greater cognitive effort. There are also other elements which can make difficulty in listening and understanding in noisy environments an even more serious problem, such as learning disabilities, mild to severe hearing loss or bilingualism. Therefore, it is important to improve the acoustic quality of the classrooms, taking into account the specific needs of children in terms of signal-to-noise ratio and reverberation time, in order to ensure a proper quality of listening. The aim of this work is to analyse, through the review of previous studies, the impact that the acoustic of classrooms has on children’s listening skills and learning activities.

scholarly journals The impact of technical parameters on the perception quality of three-dimensional content

2020 ◽  
Vol 29 (4) ◽  
pp. 13-18
Author(s):  
Fabijan Nushi ◽  
◽  
Vladimir Cviljušac ◽  
Lidija Mandić ◽  
◽  
...  
Keyword(s):  
Three Dimensional ◽  
Technical Parameters ◽  
The Impact

scholarly journals The dynamic three-dimensional organization of the diploid yeast genome

2016 ◽  
Author(s):  
Seungsoo Kim ◽  
Ivan Liachko ◽  
Donna G Brickner ◽  
Kate Cook ◽  
William S Noble ◽  
...  
Keyword(s):  
Nuclear Periphery ◽  
Three Dimensional ◽  
Culture Conditions ◽  
Yeast Genome ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Chromosome Conformation ◽  
Homolog Pairing ◽  
Pore Complexes ◽  
Eukaryotic Genomes

AbstractThe budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes. Even in this well-studied model, it is unclear how homolog pairing in diploids and environment-induced gene relocalization influence overall genome organization. Here, we performed high-throughput chromosome conformation capture on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid yeasts. After controlling for the Rabl-like orientation, we observe significant homolog proximity that increased in saturated culture conditions. Surprisingly, we observe a localized increase in homologous interactions between the HAS1 alleles specifically under galactose induction and saturated growth, mediated by association with nuclear pore complexes at the nuclear periphery. Together, these results reveal that the diploid yeast genome has a dynamic and complex 3D organization.

scholarly journals Data mining and machine learning methods for chromosome conformation data analysis

2019 ◽  
Author(s):  
◽  
Oluwatosin Oluwadare
Keyword(s):  
Data Analysis ◽  
Human Genome ◽  
Structure Prediction ◽  
Learning Algorithm ◽  
3D Structure ◽  
Three Dimensional ◽  
Gene Clusters ◽  
Research Field ◽  
Chromosome Conformation ◽  
Graphical Tool

Sixteen years after the sequencing of the human genome, the Human Genome Project (HGP), and 17 years after the introduction of Chromosome Conformation Capture (3C) technologies, three-dimensional (3-D) inference and big data remains problematic in the field of genomics, and specifically, in the field of 3C data analysis. Three-dimensional inference involves the reconstruction of a genome's 3D structure or, in some cases, ensemble of structures from contact interaction frequencies extracted from a variant of the 3C technology called the Hi-C technology. Further questions remain about chromosome topology and structure; enhancer-promoter interactions; location of genes, gene clusters, and transcription factors; the relationship between gene expression and epigenetics; and chromosome visualization at a higher scale, among others. In this dissertation, four major contributions are described, first, 3DMax, a tool for chromosome and genome 3-D structure prediction from H-C data using optimization algorithm, second, GSDB, a comprehensive and common repository that contains 3D structures for Hi-C datasets from novel 3D structure reconstruction tools developed over the years, third, ClusterTAD, a method for topological associated domains (TAD) extraction from Hi-C data using unsupervised learning algorithm. Finally, we introduce a tool called, GenomeFlow, a comprehensive graphical tool to facilitate the entire process of modeling and analysis of 3D genome organization. It is worth noting that GenomeFlow and GSDB are the first of their kind in the 3D chromosome and genome research field. All the methods are available as software tools that are freely available to the scientific community.

scholarly journals Synthetic OCT data in challenging conditions: three-dimensional OCT and presence of abnormalities

2021 ◽  
Author(s):  
Hajar Danesh ◽  
Keivan Maghooli ◽  
Alireza Dehghani ◽  
Rahele Kafieh
Keyword(s):  
Deep Learning ◽  
3D Structure ◽  
Three Dimensional ◽  
Synthetic Data ◽  
Texture Features ◽  
3D Data ◽  
Original Dataset ◽  
Straight Line ◽  
Training Stage ◽  
Kolmogorov Smirnov

AbstractNowadays, retinal optical coherence tomography (OCT) plays an important role in ophthalmology and automatic analysis of the OCT is of real importance: image denoising facilitates a better diagnosis and image segmentation and classification are undeniably critical in treatment evaluation. Synthetic OCT was recently considered to provide a benchmark for quantitative comparison of automatic algorithms and to be utilized in the training stage of novel solutions based on deep learning. Due to complicated data structure in retinal OCTs, a limited number of delineated OCT datasets are already available in presence of abnormalities; furthermore, the intrinsic three-dimensional (3D) structure of OCT is ignored in many public 2D datasets. We propose a new synthetic method, applicable to 3D data and feasible in presence of abnormalities like diabetic macular edema (DME). In this method, a limited number of OCT data is used during the training step and the Active Shape Model is used to produce synthetic OCTs plus delineation of retinal boundaries and location of abnormalities. Statistical comparison of thickness maps showed that synthetic dataset can be used as a statistically acceptable representative of the original dataset (p > 0.05). Visual inspection of the synthesized vessels was also promising. Regarding the texture features of the synthesized datasets, Q-Q plots were used, and even in cases that the points have slightly digressed from the straight line, the p-values of the Kolmogorov–Smirnov test rejected the null hypothesis and showed the same distribution in texture features of the real and the synthetic data. The proposed algorithm provides a unique benchmark for comparison of OCT enhancement methods and a tailored augmentation method to overcome the limited number of OCTs in deep learning algorithms. Graphical abstract

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