scholarly journals COPILOT: a Containerised wOrkflow for Processing ILlumina genOtyping daTa

2021 ◽  
Author(s):  
Hamel Patel ◽  
Sang-Hyuck Lee ◽  
Gerome Breen ◽  
Stephen Menzel ◽  
Oyesola Ojewunmi ◽  
...  
Keyword(s):  
Call Rate ◽  
Initial Sample ◽  
Bioinformatics Analyses ◽  
Daunting Task ◽  
Ancestry Estimation ◽  
Related Individuals ◽  
Gender Discrepancies ◽  
Image Format ◽  
Rate Threshold ◽  
Average Sample

Background: The Illumina genotyping microarrays generate data in image format, which is processed by the platform-specific software GenomeStudio, followed by an array of complex bioinformatics analyses. This process can be time-consuming, lead to reproducibility errors, and be a daunting task for novice bioinformaticians. Results: Here we introduce the COPILOT (Containerised wOrkflow for Processing ILlumina genOtyping daTa) protocol, which provides an in-depth and clear guide to process raw Illumina genotype data in GenomeStudio, followed by a containerised workflow to automate an array of complex bioinformatics analyses involved in a GWAS quality control (QC). The COPILOT protocol was applied to two independent cohorts consisting of 2791 and 479 samples genotyped on the Infinium Global Screening (GSA) array with Multi-disease (MD) drop-in (~750,000 markers) and the Infinium H3Africa consortium array (~2,200,000 markers) respectively. Following the COPILOT protocol, an average sample quality improvement of 1.24% was observed across sample call rates, with notable improvement for low-quality samples. For example, from the 3270 samples processed, 141 samples had an initial sample call rate below 98%, averaging 96.6% (95% CI 95.6-97.7%), which is considered below the acceptable sample call rate threshold for a typical GWAS analysis. However, following the COPILOT protocol, all 141 samples had a call rate above 98% after QC and averaged 99.6% (95% CI 99.5-99.7%). In addition, the COPILOT pipeline automatically identified potential data issues, including gender discrepancies, heterozygosity outliers, related individuals, and population outliers through ancestry estimation. Conclusions: The COPILOT protocol makes processing Illumina genotyping data transparent, effortless and reproducible. The container is deployable on multiple platforms, improves data quality, and the end product is analysis-ready PLINK formatted data, with a comprehensive and interactive summary report to guide the user for further data analyses.

Experience With Grant Writing: Where Do I Even Begin?

2010 ◽  
Vol 11 (1) ◽  
pp. 21-24
Author(s):  
Nicole M. Mancini
Keyword(s):  
Lessons Learned ◽  
Economic Situation ◽  
Grant Writing ◽  
Personal Journey ◽  
Know How ◽  
Daunting Task

Abstract At first, grant writing may look like a daunting task. You may ask yourself, “Is it really worth the time and effort?” With today's economic situation, teachers and therapists need ways to supplement their programs and grants provide such an opportunity. However, many of us do not know how to get started. After a few experiences and many lessons learned, I have come to enjoy researching and writing grants to supplement my students' learning. It is well worth the time and effort. This article provides information about a personal journey, lessons learned, and resources to get you started.

Audience effects on food call rate and structure in brown capuchins

2003 ◽  
Author(s):  
Amy S. Pollick ◽  
Frans B. M. de Waal ◽  
Harold Gouzoules
Keyword(s):  
Call Rate ◽  
Food Call ◽  
Audience Effects

Energetic properties of peat saturated with petroleum products

2020 ◽  
Vol 13 (2) ◽  
pp. 105-109
Author(s):  
E. S. Dremicheva
Keyword(s):  
Crude Oil ◽  
Diesel Fuel ◽  
Energy Use ◽  
Experimental Studies ◽  
Calorific Value ◽  
Petroleum Products ◽  
Ash Content ◽  
Motor Oil ◽  
Initial Sample

This paper presents a method of sorption using peat for elimination of emergency spills of crude oil and petroleum products and the possibility of energy use of oil-saturated peat. The results of assessment of the sorbent capacity of peat are presented, with waste motor oil and diesel fuel chosen as petroleum products. Natural peat has been found to possess sorption properties in relation to petroleum products. The sorbent capacity of peat can be observed from the first minutes of contact with motor oil and diesel fuel, and significantly depends on their viscosity. For the evaluation of thermal properties of peat saturated with petroleum products, experimental studies have been conducted on determination of moisture and ash content of as-fired fuel. It is shown that adsorbed oil increases the moisture and ash content of peat in comparison with the initial sample. Therefore, when intended for energy use, peat saturated with petroleum products is to be subjected to additional drying. Simulation of net calorific value has been performed based on the calorific values of peat and petroleum products with different ratios of petroleum product content in peat and for a saturated peat sample. The obtained results are compared with those of experiments conducted in a calorimetric bomb and recalculated for net calorific value. A satisfactory discrepancy is obtained, which amounts to about 12%. Options have been considered providing for combustion of saturated peat as fuel (burnt per se and combined with a solid fuel) and processing it to produce liquid, gaseous and solid fuels. Peat can be used to solve environmental problems of elimination of emergency spills of crude oil and petroleum products and as an additional resource in solving the problem of finding affordable energy.

Segmentasi Citra Mri Menggunakan Deteksi Tepi Untuk Identifikasi Kanker Payudara

2017 ◽  
Vol 15 (2) ◽  
pp. 17 ◽  
Author(s):  
Ervina Varijki ◽  
Bambang Krismono Triwijoyo
Keyword(s):  
Breast Cancer ◽  
Edge Detection ◽  
Object Segmentation ◽  
Computation Time ◽  
Input Image ◽  
Boundary Line ◽  
Cancer Breast ◽  
Average Computation Time ◽  
Breast Cancer Mri ◽  
Image Format

One type of cancer that is capable identified using MRI technology is breast cancer. Breast cancer is still the leading cause of death world. therefore early detection of this disease is needed. In identifying breast cancer, a doctor or radiologist analyzing the results of magnetic resonance image that is stored in the format of the Digital Imaging Communication In Medicine (DICOM). It takes skill and experience sufficient for diagnosis is appropriate, andaccurate, so it is necessary to create a digital image processing applications by utilizing the process of object segmentation and edge detection to assist the physician or radiologist in identifying breast cancer. MRI image segmentation using edge detection to identification of breast cancer using a method stages gryascale change the image format, then the binary image thresholding and edge detection process using the latest Robert operator. Of the20 tested the input image to produce images with the appearance of the boundary line of each region or object that is visible and there are no edges are cut off, with the average computation time less than one minute.

Judgments of Moral Responsibility in Tissue Donation Cases

2020 ◽  
Author(s):  
James R. Beebe
Keyword(s):  
Moral Responsibility ◽  
Significant Role ◽  
Primary Factor ◽  
Tissue Donation ◽  
Potential Donor ◽  
Sperm Donor ◽  
Perceived Burden ◽  
Related Individuals ◽  
Unique Ability

If a person requires a tissue donation in order to survive, many philosophers argue that whatever moral responsibility a biological relative may have to donate to the person in need will be grounded at least partially, if not entirely, in the biological relations the potential donor bears to the recipient. Such views tend to ignore the role played by a potential donor’s unique ability to help the person in need and the perceived burden of the donation type in underwriting such judgments. If, for example, a sperm donor is judged to have a significant moral responsibility to donate tissue to a child conceived with his sperm, we argue that such judgments will largely be grounded in the presumed unique ability of the sperm donor to help the child due to the compatibility of his tissues with those of the recipient. In this paper, we report the results of two main studies and three supplementary studies designed to investigate the comparative roles that biological relatedness, unique ability to help, and donation burden play in generating judgments of moral responsibility in tissue donation cases. We found that the primary factor driving individuals’ judgments about the moral responsibility of a potential donor to donate tissue to someone in need was the degree to which a donor was in a unique ability to help. We observed no significant role for biological relatedness as such. Biologically related individuals were deemed to have a significant moral responsibility to donate tissue only when they are one of a small number of people who have a relatively unique capacity to help. We also found that people are less inclined to think individuals have a moral responsibility to donate tissue when the donation is more costly to make. We bring these results into dialogue with contemporary disputes concerning the ethics of tissue donation.

Judgments of moral responsibility in tissue donation cases

2020 ◽  
Author(s):  
James R. Beebe
Keyword(s):  
Moral Responsibility ◽  
Tissue Donation ◽  
Potential Donor ◽  
Sperm Donor ◽  
Biological Relationship ◽  
Related Individuals ◽  
Unique Ability

If a person requires an organ or tissue donation to survive, many philosophers argue that whatever moral responsibility a biological relative may have to donate to the person in need will be grounded at least partially, if not entirely, in biological relations the potential donor bears to the recipient. We contend that such views ignore the role that a potential donor’s unique ability to help the person in need plays in underwriting such judgments. If, for example, a sperm donor is judged to have a significant moral responsibility to donate tissue to a child conceived with his sperm, we think this will not be due to the fact that the donor stands in a close biological relationship to the recipient. Rather, we think such judgments will largely be grounded in the presumed unique ability of the sperm donor to help the child due to the compatibility of his tissues and organs with those of the recipient. In this paper, we report the results of two studies designed to investigate the comparative roles that biological relatedness and unique ability play in generating judgments of moral responsibility in tissue donation cases. We found that biologically related individuals are deemed to have a significant moral responsibility to donate tissue only when they are one of a small number of people who have the capacity to help.

Layout Overlay Techniques to Improve Failure Analysis

1998 ◽  
Author(s):  
Christian Burmer ◽  
Siegfried Görlich ◽  
Siegfried Pauthner
Keyword(s):  
Failure Analysis ◽  
Focused Ion Beam ◽  
New Technologies ◽  
Ion Beam ◽  
Image Correlation ◽  
Microelectronic Devices ◽  
Overlay Technique ◽  
Correlation Techniques ◽  
Navigation Software ◽  
Image Format

Abstract New layout overlay technique has been developed based on standard image correlation techniques to support failure analysis in modern microelectronic devices, which are critical to analyze because they are realized in new technologies using sub-ìm design rules, chemical mechanical polishing techniques (CMP) and autorouted design techniques. As the new technique is realized as an extension of a standard CAD-navigation software and as it makes use of standard image format "TIFF" for data input, which is available at all modern equipments for failure analysis, these technique can be applied to all modern failure analysis methods. Here examples are given for three areas of application: circuit modification using Focused Ion Beam (FIB), support of preparation for backside inspection and fault localization using emission microscopy.

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