scholarly journals Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes

2020 ◽  
Vol 37 (12) ◽  
pp. 3684-3698 ◽  
Author(s):  
Ruidong Li ◽  
Han Qu ◽  
Jinfeng Chen ◽  
Shibo Wang ◽  
John M Chater ◽  
...  
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Genomic Data ◽  
Cost Effective ◽  
R Package ◽  
Chromosome Length ◽  
Sequencing Data ◽  
Experimental Phasing ◽  
Wide Range ◽  
Haplotype Data

Abstract Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.

scholarly journals Impresión 3D como Herramienta Didáctica para la Enseñanza de Algunos Conceptos de Ingeniería y Diseño

Ingeniería ◽  
2018 ◽  
Vol 23 (1) ◽  
pp. 70 ◽  
Author(s):  
Edwin Blasnilo Rua Ramirez ◽  
Fernando Jimenez Diaz ◽  
German Andres Gutierrez Arias ◽  
Nelson Iván Villamizar
Keyword(s):  
Teaching And Learning ◽  
Mechanical Engineering ◽  
Large Scale ◽  
Low Cost ◽  
Cost Effective ◽  
3D Printer ◽  
Course Grades ◽  
Wide Range ◽  
Technical Specifications ◽  
Future Work

Context: 3D printing can be used for a wide range of tasks such as the design and testing of prototypes and finished products in a shorter time. In mechanical engineering, prototype designs are continuously generated in academic class activities and final coursework projects by students and teachers. However, students show limitations while understanding the abstract concepts represented with such designs.Method: Firstly, a large scale 3D printer with improved technical specifications compared to traditional market options and similar price, was fabricated. By means of free software and hardware tools and easy-to-obtain alternative manufacturing materials, it was possible to decrease its manufacturing and operating costs. Then a set of study cases utilising the 3D printer in three different subject classes were designed and tested with two cohorts of students of Mechanical Engineering programme.Results: It was feasible to fabricate a cost-effective and practical 3D printer for constructing prototypes and pieces that benefit teaching and learning concepts in engineering and design areas. The experiments carried out in three subjects of engineering courses with second-year students, showed a similar trend of improving the average course grades, as it was observed in two cohorts in different terms.Conclusions: This type of low cost 3D printer obtained academic advantages as a didactic tool for the learning process in engineering and design subjects. Future work will consider applying this tool to other courses and subjects to further evaluate its convenience and effectivity.

scholarly journals Inference of Chromosome-length Haplotypes using Genomic Data of Three to Five Single Gametes

2018 ◽  
Author(s):  
Ruidong Li ◽  
Han Qu ◽  
Jinfeng Chen ◽  
Shibo Wang ◽  
John M. Chater ◽  
...  
Keyword(s):  
Cost Efficiency ◽  
Human Disease ◽  
Large Scale ◽  
Genomic Data ◽  
Cost Effective ◽  
Chromosome Length ◽  
Recombination Activity ◽  
Innovative Method ◽  
Human Reproductive ◽  
The Relationship

AbstractKnowledge of chromosome-length haplotypes will not only advance our understanding of the relationship between DNA and phenotypes, but also promote a variety of genetic applications. Here we present Hapi, an innovative method for chromosomal haplotype inference using only 3 to 5 gametes. Hapi outperformed all existing haploid-based phasing methods in terms of accuracy, reliability, and cost efficiency in both simulated and real gamete datasets. This highly cost-effective phasing method will make large-scale haplotype studies feasible to facilitate human disease studies and plant/animal breeding. In addition, Hapi can detect meiotic crossovers in gametes, which has promise in the diagnosis of abnormal recombination activity in human reproductive cells.

Teaching application of watercolor light color technique

2020 ◽  
pp. 002072092093683
Author(s):  
Yin Shi
Keyword(s):  
Art Education ◽  
Large Scale ◽  
Low Cost ◽  
Art Curriculum ◽  
Repeated Practice ◽  
Wide Range ◽  
Light Color ◽  
Teaching Application ◽  
Design Drawing

As a branch of watercolor painting, watercolor light color has been widely used in different fields. In the field of design, designers use the convenience, quickness, transparency and brilliance of watercolor to draw a design drawing. In the field of art creation, watercolor is usually the best choice for painters to go out to sketch and create large-scale drawings. In the field of art education, watercolor tools are easy to carry, low-cost and easy to operate, which can facilitate students’ repeated practice and outside Sketching is helpful to cultivate students’ sense of color and observation ability. Therefore, as a branch of art curriculum, watercolor light color has a wide range of uses and great practicability, which is worth exploring and studying.

Development of All-Plastic Microvalve Array for Multiplexed Immunoassay

2014 ◽  
Author(s):  
Shancy Augustine ◽  
Pan Gu ◽  
Xiangjun Zheng ◽  
Toshikazu Nishida ◽  
Z. Hugh Fan
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Simultaneous Detection ◽  
Cost Effective ◽  
Negative Control ◽  
Sensitive Material ◽  
Detection Scheme ◽  
Power Battery ◽  
Multiple Analytes ◽  
Multiplexed Immunoassay

There is a need for low-cost immunoassays that measure the presence and concentration of multiple harmful agents in one device. Currently, comparable immunoassays employ a one-analyte-per-test format that is time consuming and not cost effective for the requirement of detecting multiple analytes in a single sample. For instance, if a spectrum of harmful agents, including E. coli O157, cholera toxin, and Salmonella typhimurium, should be simultaneously monitored in foods and drinking water, then a one-analyte-per-test would be inefficient. This work demonstrates a platform capable of simultaneous detection of multiple analytes in a single, low-cost, microvalve array-enabled multiplexed immunoassay. This multiplexed immunoassay platform is demonstrated in a prototype COC (cyclic olefin copolymer) device with a 2×3 array in which 6 analytes can be detected simultaneously. In order to contain and regulate the flow of reagents in the multichannel device, an array of microfluidic valves actuated by a thermally expandable material and microfabricated resistors have been developed to direct the flow to the necessary assay sites. The microvalve-based immunoassay is shown to be reliable, easy to operate, and compatible with large-scale integration. The all-plastic microvalves use paraffin wax as the thermally sensitive material which drastically reduces power consumption by latching upon closing so that pulsed power is required only to close and latch the microvalve until it is necessary to re-open the valve. The multiplexed detection scheme has been demonstrated by using three proteins, C reactive protein (CRP) and transferrin, both of which are biomarkers associated with traumatic brain injury (TBI) as well as bovine serum albumin (BSA) as the negative control. Since there are no external bulky pneumatic accessories required to operate/latch the microvalves in the device, this compact, thermally actuated and latching microvalve-enabled multiplexed immunoassay has the potential to realize a portable, low power, battery operated microfluidic device for biological assays.

scholarly journals A Novel Adaptive Pixels Segmentation Algorithm for Pavement Crack Detection

2021 ◽  
Author(s):  
Nima Safaei ◽  
Omar Smadi ◽  
Babak Safaei ◽  
Arezoo Masoud
Keyword(s):  
Crack Detection ◽  
Low Cost ◽  
Local Level ◽  
Cost Effective ◽  
Segmentation Algorithm ◽  
Pavement Maintenance ◽  
Detection Systems ◽  
Wide Range ◽  
Cost Efficient ◽  
Pavement Crack Detection

<p>Cracks considerably reduce the life span of pavement surfaces. Currently, there is a need for the development of robust automated distress evaluation systems that comprise a low-cost crack detection method for performing fast and cost-effective roadway health monitoring practices. Most of the current methods are costly and have labor-intensive learning processes, so they are not suitable for small local-level projects with limited resources or are only usable for specific pavement types.</p> <p>This paper proposes a new method that uses an improved version of the weighted neighborhood pixels segmentation algorithm to detect cracks in 2-D pavement images. This method uses the Gaussian cumulative density function as the adaptive threshold to overcome the drawback of fixed thresholds in noisy environments. The proposed algorithm was tested on 300 images containing a wide range of noise representative of different noise conditions. This method proved to be time and cost-efficient as it took less than 3.15 seconds per 320 × 480 pixels image for a Xeon (R) 3.70 GHz CPU processor to determine the detection results. This makes the model a perfect choice for county-level pavement maintenance projects requiring cost-effective pavement crack detection systems. The validation results were promising for the detection of low to severe-level cracks (Accuracy = 97.3%, Precision = 79.21%, Recall= 89.18% and F<sub>1</sub> score = 83.9%).</p>

scholarly journals Optimizing smartphone-based canopy hemispherical photography

2021 ◽  
Author(s):  
Gastón Mauro Díaz
Keyword(s):  
Large Scale ◽  
Forest Canopy ◽  
Accuracy Assessment ◽  
Low Cost ◽  
R Package ◽  
Coefficient Of Determination ◽  
Native Forest ◽  
Hemispherical Photography ◽  
Area Index ◽  
Plant Area Index

1) Hemispherical photography (HP) is a long-standing tool for forest canopy characterization. Currently, there are low-cost fisheye lenses to convert smartphones into high-portable HP equipment; however, they cannot be used whenever since HP is sensitive to illumination conditions. To obtain sound results outside diffuse light conditions, a deep-learning-based system needs to be developed. A ready-to-use alternative is the multiscale color-based binarization algorithm, but it can provide moderate-quality results only for open forests. To overcome this limitation, I propose coupling it with the model-based local thresholding algorithm. I call this coupling the MBCB approach. 2) Methods presented here are part of the R package CAnopy IMage ANalysis (caiman), which I am developing. The accuracy assessment of the new MBCB approach was done with data from a pine plantation and a broadleaf native forest. 3) The coefficient of determination (R^2) was greater than 0.7, and the root mean square error (RMSE) lower than 20 %, both for plant area index calculation. 4) Results suggest that the new MBCB approach allows the calculation of unbiased canopy metrics from smartphone-based HP acquired in sunlight conditions, even for closed canopies. This facilitates large-scale and opportunistic sampling with hemispherical photography.

scholarly journals Process Design Kit and Design Automation for Flexible Hybrid Electronics

2019 ◽  
Vol 16 (3) ◽  
pp. 117-123
Author(s):  
Tsung-Ching Huang ◽  
Ting Lei ◽  
Leilai Shao ◽  
Sridhar Sivapurapu ◽  
Madhavan Swaminathan ◽  
...  
Keyword(s):  
Process Design ◽  
Design Automation ◽  
High Performance ◽  
Large Scale ◽  
Low Cost ◽  
Thin Film Transistor ◽  
Solution Process ◽  
Oxide Semiconductor ◽  
Wearable Electronics ◽  
Wide Range

Abstract High-performance low-cost flexible hybrid electronics (FHE) are desirable for applications such as internet of things and wearable electronics. Carbon nanotube (CNT) thin-film transistor (TFT) is a promising candidate for high-performance FHE because of its high carrier mobility, superior mechanical flexibility, and material compatibility with low-cost printing and solution processes. Flexible sensors and peripheral CNT-TFT circuits, such as decoders, drivers, and sense amplifiers, can be printed and hybrid-integrated with thinned (&lt;50 μm) silicon chips on soft, thin, and flexible substrates for a wide range of applications, from flexible displays to wearable medical devices. Here, we report (1) a process design kit (PDK) to enable FHE design automation for large-scale FHE circuits and (2) solution process-proven intellectual property blocks for TFT circuits design, including Pseudo-Complementary Metal-Oxide-Semiconductor (Pseudo-CMOS) flexible digital logic and analog amplifiers. The FHE-PDK is fully compatible with popular silicon design tools for design and simulation of hybrid-integrated flexible circuits.

Performance of rapid diagnostic tests for HCV infection in serum or plasma

2021 ◽  
Author(s):  
Stéphane Chevaliez ◽  
Françoise Roudot-Thoraval ◽  
Christophe Hézode ◽  
Jean-Michel Pawlotsky ◽  
Richard Njouom
Keyword(s):  
Hepatitis C ◽  
Diagnostic Tests ◽  
Large Scale ◽  
Low Cost ◽  
Antibody Test ◽  
Cost Effective ◽  
Rapid Diagnostic Tests ◽  
Treatment Programs ◽  
Clinical Sensitivity ◽  
Cost Treatment

Aim: HCV diagnosis will become the bottleneck in eliminating hepatitis C. Simple, accurate and cost-effective testing strategies are urgently needed to improve hepatitis C screening and diagnosis. Materials & methods: Performance of seven rapid diagnostic tests (RDT) have been assessed in a large series (n = 498) of serum or plasma specimens collected in France and in Cameroon. Results: Specificity varied from 96.1 to 100%. The clinical sensitivity, compared with immunoassays as the reference, was high for all seven RDT (97.2–100%). The Multisure HCV antibody assay and OraQuick HCV rapid antibody test reached sensitivity ≥99%. Conclusion: A number of RDT may be suitable for WHO prequalification and may be implemented in the framework of large-scale low-cost treatment programs to achieve the WHO viral hepatitis objectives by 2030.

scholarly journals Effect of Protocatechuic Acid on Euglena gracilis Growth and Accumulation of Metabolites

2020 ◽  
Vol 12 (21) ◽  
pp. 9158
Author(s):  
Xiaomiao Tan ◽  
Jiangyu Zhu ◽  
Minato Wakisaka
Keyword(s):  
Euglena Gracilis ◽  
Large Scale ◽  
Protocatechuic Acid ◽  
Biomass Yield ◽  
Growth Promotion ◽  
Low Cost ◽  
Cost Effective ◽  
Control Group ◽  
Biological Functions ◽  
First Time

The development of efficient, environmentally friendly, low-cost approaches used to boost the growth of microalgae is urgently required to meet the increasing demands for food supplements, cosmetics, and biofuels. In this study, the growth promotion effects of protocatechuic acid (PCA) in the freshwater microalga Euglena gracilis were confirmed for the first time. PCA is a simple phenolic compound derived from natural plants and has a range of biological functions. The highest biomass yield, 3.1-fold higher than that of the control, used at 1.3 g·L−1, was obtained at 800 mg·L−1 of PCA. The yields of the metabolites chlorophyll a, carotenoids, and paramylon in the presence of PCA at 800 mg·L−1 were 3.1, 3.3, and 1.7 times higher than those of the control group, respectively. The highest paramylon yield was achieved at a lower dosage of PCA (100 mg·L−1), which is considered to be feasible for economic paramylon production. The growth and biosynthesis of metabolites stimulated by phytochemicals such as PCA could be an efficient and cost-effective strategy to enhance the productivity of microalgae in large-scale cultivations.

scholarly journals One year later: Highlighting the challenges and opportunities in disseminating a breathing-retraining digital behaviour change intervention

2020 ◽  
Vol 6 ◽  
pp. 205520762093644
Author(s):  
Ben Ainsworth ◽  
Anne Bruton ◽  
Mike Thomas ◽  
Lucy Yardley
Keyword(s):  
Behaviour Change ◽  
Large Scale ◽  
Digital Health ◽  
Low Cost ◽  
Controlled Trial ◽  
Cost Effective ◽  
Challenges And Opportunities ◽  
Breathing Retraining ◽  
One Year ◽  
Randomised Controlled

Digital behaviour change interventions can provide effective and cost-effective treatments for a range of health conditions. However, after rigorous evaluation, there still remain challenges to disseminating and implementing evidence-based interventions that can hinder their effectiveness ‘in the real world’. We conducted a large-scale randomised controlled trial of self-guided breathing retraining, which we then disseminated freely as a digital intervention. Here we share our experience of this process after one year, highlighting the opportunities that digital health interventions can offer alongside the challenges that must be addressed in order to harness their effectiveness. Whilst such treatments can support many individuals at extremely low cost, careful dissemination strategies should be proactively planned in order to ensure such opportunities are maximised and interventions remain up to date in a fast-moving digital landscape.

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