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"Inverse distance weighted interpolation"
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Alpha-1 antitrypsin PiZ gene frequency and PiZZ genotype numbers worldwide: an update
by
Blanco, Ignacio
,
Bueno, Patricia
,
Casas-Maldonado, Francisco
in
alpha 1-Antitrypsin - genetics
,
alpha 1-Antitrypsin Deficiency - diagnosis
,
alpha 1-Antitrypsin Deficiency - enzymology
2017
In alpha-1 antitrypsin deficiency (AATD), the Z allele is present in 98% of cases with severe disease, and knowledge of the frequency of this allele is essential from a public health perspective. However, there is a remarkable lack of epidemiological data on AATD worldwide, and many of the data currently used are outdated. Therefore, the objective of this study was to update the knowledge of the frequency of the Z allele to achieve accurate estimates of the prevalence and number of Pi*ZZ genotypes worldwide based on studies performed according to the following criteria: 1) samples representative of the general population, 2) AAT phenotyping characterized by adequate methods, and 3) measurements performed using a coefficient of variation calculated from the sample size and 95% confidence intervals. Studies fulfilling these criteria were used to develop maps with an inverse distance weighted (IDW)-interpolation method, providing numerical and graphical information of Pi*Z distribution worldwide. A total of 224 cohorts from 65 countries were included in the study. With the data provided by these cohorts, a total of 253,404 Pi*ZZ were estimated worldwide: 119,594 in Europe, 91,490 in America and Caribbean, 3,824 in Africa, 32,154 in Asia, 4,126 in Australia, and 2,216 in New Zealand. In addition, the IDW-interpolation maps predicted Pi*Z frequencies throughout the world even in some areas that lack real data. In conclusion, the inclusion of new well-designed studies and the exclusion of the low-quality ones have significantly improved the reliability of results, which may be useful to plan strategies for future research and diagnosis and to rationalize the therapeutic resources available.
Journal Article
Estimated Prevalence and Number of PiMZ Genotypes of Alpha-1 Antitrypsin in Seventy-Four Countries Worldwide
by
Bueno, Patricia
,
Miravitlles, Marc
,
Blanco, Ignacio
in
alpha 1-Antitrypsin - genetics
,
alpha 1-Antitrypsin Deficiency - diagnosis
,
alpha 1-Antitrypsin Deficiency - epidemiology
2021
The α-1 antitrypsin (AAT) protease inhibitor PiMZ is a moderately deficient genotype, until recently considered of little or negligible risk. However, a growing number of studies show that MZ carriers have an increased risk of developing lung and liver diseases, if exposed to smoking or other airborne or industrial pollutants, and hepatotoxic substances.
We used the epidemiological studies performed to determine the frequencies of PiM and PiZ worldwide, based on the following criteria: 1) samples representative of the general population; 2) AAT phenotyping or genotyping characterized by adequate methods, including isoelectric focusing and polymerase chain reaction; and 3) studies with reliable results assessed with a coefficient of variation calculated from the sample size and 95% confidence intervals, to measure the precision of the results in terms of dispersion of the data around the mean.
The present review reveals an impressive number of MZs of more than 35 million in 74 countries of the world with available data. Seventy-five percent of them are people of Caucasian European heritage, mostly living in Europe, America, Australia and New Zealand. Twenty percent of the remaining MZs live in Asia, with the highest concentrations in the Middle East, Eastern¸ Southern, and South-eastern regions of the Asian continent. The remaining five percent are Africans residing in Western and Eastern Africa.
Considering the high rate of smoking, the outdoor and the indoor air pollution from solid fuels used in cooking and heating, and the exposure to industrial dusts and chemicals in many of these countries, these figures are very worrying, and hence the importance of adequately assessing MZ subjects, recommending them rigorous preventive measures based on the adoption of healthy lifestyles, including avoidance of smoking and alcohol.
Journal Article
Alpha-1 antitrypsin PiSZ genotype: estimated prevalence and number of SZ subjects worldwide
by
Blanco, Ignacio
,
Bueno, Patricia
,
Casas-Maldonado, Francisco
in
alpha 1-Antitrypsin - genetics
,
alpha 1-Antitrypsin Deficiency - diagnosis
,
alpha 1-Antitrypsin Deficiency - enzymology
2017
The alpha-1 antitrypsin (AAT) haplotype Pi*S, when inherited along with the Pi*Z haplotype to form a Pi*SZ genotype, can be associated with pulmonary emphysema in regular smokers, and less frequently with liver disease, panniculitis, and systemic vasculitis in a small percentage of people, but this connection is less well established. Since the detection of cases can allow the application of preventive measures in patients and relatives with this congenital disorder, the objective of this study was to update the prevalence of the SZ genotype to achieve accurate estimates of the number of Pi*SZ subjects worldwide, based on studies performed according to the following criteria: 1) samples representative of the general population, 2) AAT phenotyping characterized by adequate methods, and 3) selection of studies with reliable results assessed with a coefficient of variation calculated from the sample size and 95% confidence intervals. Studies fulfilling these criteria were used to develop tables and maps with an inverse distance-weighted (IDW) interpolation method, to provide numerical and geographical information of the Pi*SZ distribution worldwide. A total of 262 cohorts from 71 countries were included in the analysis. With the data provided by these cohorts, a total of 1,490,816 Pi*SZ were estimated: 708,792 in Europe; 582,984 in America and Caribbean; 85,925 in Africa; 77,940 in Asia; and 35,176 in Australia and New Zealand. Remarkably, the IDW interpolation maps predicted the Pi*SZ prevalence throughout the entire world even in areas lacking real data. These results may be useful to plan strategies for future research, diagnosis, and management of affected individuals.
Journal Article
Research on Non-Destructive Testing of Log Knot Resistance Based on Improved Inverse-Distance-Weighted Interpolation Algorithm
2024
The objective of this paper is to propose a non-destructive resistance detection imaging algorithm for log knots based on improved inverse-distance-weighted interpolation algorithm, i.e., the eccentric circle-based inverse-distance-weighted (ECIDW) method, to predict the size, shape, and position of internal knots of logs; evaluate its precision and accuracy; and both lay a theoretical foundation and provide a scientific basis for predicting and assessing knots in standing trees. Six sample logs with natural knots were selected for this study. Resistance measurements were performed on the log cross-sections using a digital bridge, and resistance tomography was conducted using the improved ECIDW algorithm, which combines the azimuth search method with the eccentric circle search method. The results indicated that both the conventional inverse-distance-weighted (IDW) algorithm and the ECIDW algorithm accurately predicted the positions of the knots. However, neither algorithm was able to predict the shape of the knots with high precision, leading to some discrepancies between the predicted and actual knot shapes. The relative error (Dt1) between the knot areas measured by the IDW algorithm and the actual knot areas ranged from 18.97% to 88.34%. The relative error (Dt2) for the knot areas predicted by the ECIDW algorithm ranged from 1.82% to 74.16%. The average prediction accuracy for the knot areas using the IDW algorithm was 51.58%, compared to 72.90% using the ECIDW algorithm. This indicates that the ECIDW algorithm has higher accuracy in predicting knot areas compared to the conventional IDW algorithm. The ECIDW algorithm proposed in this paper provides a more reasonable and accurate prediction and evaluation of knots inside logs. Compared to the conventional IDW algorithm, the ECIDW algorithm demonstrates greater precision and accuracy in predicting the shape and size of knots. While the resistance method shows significant potential for predicting internal knots in logs and standing trees, further improvements to the algorithm were needed to enhance the imaging effects and the precision and accuracy of knot area and shape predictions.
Journal Article
Ancestry inference using principal component analysis and spatial analysis: a distance-based analysis to account for population substructure
by
Byun, Jinyoung
,
Seldin, Michael F.
,
Amos, Christopher I.
in
Analysis
,
Ancestry inference
,
Animal Genetics and Genomics
2017
Background
Accurate inference of genetic ancestry is of fundamental interest to many biomedical, forensic, and anthropological research areas. Genetic ancestry memberships may relate to genetic disease risks. In a genome association study, failing to account for differences in genetic ancestry between cases and controls may also lead to false-positive results. Although a number of strategies for inferring and taking into account the confounding effects of genetic ancestry are available, applying them to large studies (tens thousands samples) is challenging. The goal of this study is to develop an approach for inferring genetic ancestry of samples with unknown ancestry among closely related populations and to provide accurate estimates of ancestry for application to large-scale studies.
Methods
In this study we developed a novel distance-based approach, Ancestry Inference using Principal component analysis and Spatial analysis (AIPS) that incorporates an Inverse Distance Weighted (IDW) interpolation method from spatial analysis to assign individuals to population memberships.
Results
We demonstrate the benefits of AIPS in analyzing population substructure, specifically related to the four most commonly used tools EIGENSTRAT, STRUCTURE, fastSTRUCTURE, and ADMIXTURE using genotype data from various intra-European panels and European-Americans. While the aforementioned commonly used tools performed poorly in inferring ancestry from a large number of subpopulations, AIPS accurately distinguished variations between and within subpopulations.
Conclusions
Our results show that AIPS can be applied to large-scale data sets to discriminate the modest variability among intra-continental populations as well as for characterizing inter-continental variation. The method we developed will protect against spurious associations when mapping the genetic basis of a disease. Our approach is more accurate and computationally efficient method for inferring genetic ancestry in the large-scale genetic studies.
Journal Article
Automatic Road Marking Extraction and Vectorization from Vehicle-Borne Laser Scanning Data
by
Wu, Hangbin
,
Yao, Lianbi
,
Qin, Changcai
in
Adaptive algorithms
,
adaptive threshold segmentation
,
Algorithms
2021
Automatic driving technology is becoming one of the main areas of development for future intelligent transportation systems. The high-precision map, which is an important supplement of the on-board sensors during shielding or limited observation distance, provides a priori information for high-precision positioning and path planning in automatic driving. The position and semantic information of the road markings, such as absolute coordinates of the solid lines and dashed lines, are the basic components of the high-precision map. In this paper, we study the automatic extraction and vectorization of road markings. Firstly, scan lines are extracted from the vehicle-borne laser point cloud data, and the pavement is extracted from scan lines according to the geometric mutation at the road boundary. On this basis, the pavement point clouds are transformed into raster images with a certain resolution by using the method of inverse distance weighted interpolation. An adaptive threshold segmentation algorithm is used to convert raster images into binary images. Followed by the adaptive threshold segmentation is the Euclidean clustering method, which is used to extract road markings point clouds from the binary image. Solid lines are detected by feature attribute filtering. All of the solid lines and guidelines in the sample data are correctly identified. The deep learning network framework PointNet++ is used for semantic recognition of the remaining road markings, including dashed lines, guidelines and arrows. Finally, the vectorization of the identified solid lines and dashed lines is carried out based on a line segmentation self-growth algorithm. The vectorization of the identified guidelines is carried out according to an alpha shape algorithm. Point cloud data from four experimental areas are used for road marking extraction and identification. The F-scores of the identification of dashed lines, guidelines, straight arrows and right turn arrows are 0.97, 0.66, 0.84 and 1, respectively.
Journal Article
Improvement of the Estimation of the Vertical Crustal Motion Rate at GNSS Campaign Stations Based on the Information of GNSS Reference Stations
2024
With the enrichment of GNSS data and the improvement in data processing accuracy, GNSS technology has been widely applied in fields such as crustal deformation. The Crustal Movement Observation Network of China (CMONOC) has provided decades of Global Navigation Satellite System (GNSS) data and related data products for crustal deformation research on the Chinese mainland. The coordinate time series of continuously observed reference stations contain abundant information on crustal movements. In contrast, the coordinate time series of periodically observed campaign stations have limited data, making it difficult to separate or remove instantaneous non-tectonic movements from the time series, as performed with reference stations, to obtain a stable and reliable crustal movement velocity field. To address this issue, this paper proposes a method to improve the estimation of crustal movement velocity at campaign stations using the information of neighboring reference stations. This method constructs a Delaunay triangulation of reference stations and fits the periodic movement of each campaign station using an inverse distance weighted interpolation algorithm based on the reference station information. The crustal movement velocity of the campaign stations is then estimated after removing the periodic movement. This method was verified by its application to the estimation of the vertical motion rate at some reference and campaign stations in Yunnan Province. The results show that the accuracy of vertical motion rate estimation for virtual and real campaign stations improved by an average of 24.4% and 9.6%, respectively, demonstrating the effectiveness of the improved method, which can be applied to estimate crustal movement velocity at campaign stations in other areas.
Journal Article
A Decision Tree Approach for Spatially Interpolating Missing Land Cover Data and Classifying Satellite Images
by
Holloway, Jacinta
,
Helmstedt, Kate J.
,
Schmidt, Michael
in
Algorithms
,
artificial intelligence
,
Australia
2019
Sustainable Development Goals (SDGs) are a set of priorities the United Nations and World Bank have set for countries to reach in order to improve quality of life and environment globally by 2030. Free satellite images have been identified as a key resource that can be used to produce official statistics and analysis to measure progress towards SDGs, especially those that are concerned with the physical environment, such as forest, water, and crops. Satellite images can often be unusable due to missing data from cloud cover, particularly in tropical areas where the deforestation rates are high. There are existing methods for filling in image gaps; however, these are often computationally expensive in image classification or not effective at pixel scale. To address this, we use two machine learning methods—gradient boosted machine and random forest algorithms—to classify the observed and simulated ‘missing’ pixels in satellite images as either grassland or woodland. We also predict a continuous biophysical variable, Foliage Projective Cover (FPC), which was derived from satellite images, and perform accurate binary classification and prediction using only the latitude and longitude of the pixels. We compare the performance of these methods against each other and inverse distance weighted interpolation, which is a well-established spatial interpolation method. We find both of the machine learning methods, particularly random forest, perform fast and accurate classifications of both observed and missing pixels, with up to 0.90 accuracy for the binary classification of pixels as grassland or woodland. The results show that the random forest method is more accurate than inverse distance weighted interpolation and gradient boosted machine for prediction of FPC for observed and missing data. Based on the case study results from a sub-tropical site in Australia, we show that our approach provides an efficient alternative for interpolating images and performing land cover classifications.
Journal Article
Changes in per capita wheat production in China in the context of climate change and population growth
by
Sun, Haowei
,
Wang, Li
,
Ma, Jinghan
in
Agricultural production
,
Agriculture
,
Biomedical and Life Sciences
2023
To address challenges associated with climate change, population growth and decline in international trade linked to the COVID-19 pandemic, determining whether national crop production can meet populations’ requirements and contribute to socio-economic resilience is crucial. Three crop models and three global climate models were used in conjunction with predicted population changes. Compared with wheat production in 2000–2010, total production and per capita wheat production were significantly (P < 0.05) increase in 2020–2030, 2030–2040 and 2040–2050, respectively, under RCP4.5 and RCP8.5 due to climate change in China. However, when considering population and climate changes, the predicted per capita production values were 125.3 ± 0.3, 127.1 ± 2.3 and 128.8 ± 2.7 kg during the 2020–2030, 2030–2040, 2040–2050 periods under RCP4.5, or 126.2 ± 0.7, 128.7 ± 2.5, and 131.0 ± 4.1 kg, respectively, under RCP8.5. These values do not significantly differ (P > 0.05) from the baseline level (127.9 ± 1.3 kg). The average per capita production in Loess Plateau and Gansu-Xinjiang subregions declined. In contrast, per capita production in the Huanghuai, Southwestern China, and Middle-Lower Yangtze Valleys subregions increased. The results suggest that climate change will increase total wheat production in China, but population change will partly offset the benefits to the grain market. In addition, domestic grain trade will be influenced by both climate and population changes. Wheat supply capacity will decline in the main supply areas. Further research is required to address effects of the changes on more crops and in more countries to obtain deeper understanding of the implications of climate change and population growth for global food production and assist formulation of robust policies to enhance food security.
Journal Article
Mapping in a radon-prone area in Adamawa region, Cameroon, by measurement of radon activity concentration in soil
2023
The radon-prone area of the Adamawa region in Cameroon is characterized by high natural radiation background resulting from the high concentrations of radium-226, thorium-232, and indoor radon. To produce a radon-risk map, radon measurements in soil were carried out in the city of Ngaoundere. The radon activity concentration in soil gas ranged from 256 to 166 kBq m−3 with a mean of 80 kBq m−3 and a standard deviation of 38 kBq m−3. The area is mostly classified as high risk (80%) according to the Swedish classification, and 20% as medium risk. A low-risk area was not observed. Granite-like geology sites were characterized by higher radon concentration. A ratio of about 295:1 was obtained for soil radon gas to indoor radon concentrations, with a positive correlation (R = 0.40), and a transfer factor of 3 per mil. These results demonstrate that in situ measurements of radon concentration in soil can provide accurate information on the level of indoor radon concentrations. Geostatistical and deterministic interpolation techniques have been used to obtain a radon map by comparing the suitability of ordinary kriging and inverse-distance-weighted (IDW) interpolation methods. It turned out that there is not much difference in the prediction errors of the two techniques (Root Mean Square Error = 34.4 for ordinary kriging and 34.3 for IDW). It is concluded that both methods give acceptable results. In situ measurements and geostatistical analysis allow assessment of expected indoor radon exposure in a given area at reduced costs and time required. However, for the investigated area, more research is needed to produce reliable radon-risk maps.
Journal Article