Methods for Analyzing High Dimensional Data with Applications to the Wearable and Microbiome Data Analysis

Modern studies in medicine, epidemiology, pharmacy and other fields generate high dimensional data. We developed statistical analysis methods for two types of such data: activity and microbiome data. Specifically, reliable measures of the frequency, duration and intensity of physical activity provided by wearable technology were used in the analysis of activity data. Accelerometry-derived measures of physical activity were compared with established predictors of 5-year all-cause mortality in older adults, aged between 50 and 85 years from the 2003- 2006 National Health and Nutritional Examination Survey, in terms of individual, relative, and combined predictive performance. A total of 33 predictors of 5-year all-cause mortality, including 20 measures of objective physical activity, were compared using single-predictor and multiple logistic regression. The results show that objective accelerometry-derived physical activity measures outperform traditional predictors of 5-year mortality in single predictor models, and offer some improvement in multiple predictor models beyond what age and other traditional predictors provide. This highlights the importance of wearable technology for providing reproducible, unbiased, and prognostic biomarkers of health. In microbiome data, we concentrated on pre-processing steps, where both the sparsity of counts and the large number of observed taxa were considered. The current approach is to remove taxa that appear in small counts in a few samples, which is known as filtering. We present the package PERFect which performs a permutation filtering approach designed to address two problems in microbiome data processing: (1) define and quantify loss due to filtering by implementing thresholds; and (2) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering. The package employs an unbalanced binary search algorithm that greatly reduces computational time for these permutations. The effectiveness of the proposed approach on downstream microbiome data analysis is illustrated on two microbiome quality control datasets. Our filtering method reduces: (1) the magnitude of differences in alpha diversity for samples containing the same bacteria processed at different labs and (2) the dissimilarity between samples (beta diversity) that contain the same microbiome potentially alleviating technical variability

An Economic Analysis of Hazard Analysis Critical Control Point-Based Risk Management Programme in the New Zealand Meat Industry

The replacement of the Meat Act 1981 by the Animal Products Act 1999 opened a new era for food safety management in New Zealand. Administering food legislation is now the sole responsibility of the New Zealand Food Safety Authority instead of being shared between the Ministry of Agriculture and Forestry and the Ministry of Health as previously. At the core of the legislative change is the requirement for Risk Management Programmes (RMP). Every single animal primary processing business is required to have an RMP for each type of product. An RMP is required to embrace the principles of Hazard Analysis and Critical Control Point (HACCP). While there have been some studies considering the implementation of HACCP in food businesses worldwide, there has not been any study focusing on HACCP adoption in New Zealand. The mandating of RMP has also made the implementation process more complex. On the other hand, it also brings new experience in terms of food safety management. This thesis examines the implementation process of HACCP/RMP in New Zealand. It also explores the interaction between food safety management and international competitiveness through an economic analysis of the impacts of the program on a New Zealand food processing industry. The meat industry was chosen as a case study as it is one of the first industries that had to comply with the first deadline of the implementation (July 2003). Also, being a significant export-oriented industry of New Zealand, the meat industry provides an ideal case for the purpose of this study. The thesis consists of four parts. Part I presents an introduction to the study including a review of international and national food safety issues, the relationship between food safety and trade and international competitiveness, and the HACCP economic literature. This background helps to shape the research objectives and methodology as described in Chapter 3. Chapter 4 discusses the design of the survey to collect plant experience regarding the implementation of HACCP/RMP in New Zealand. Part II analyses the experiences within the New Zealand meat industry regarding the implementation of HACCP/RMP. It discusses plant motivations to adopt the program and the implementation issues they are facing. Plant observations on the costs and benefits of the implementation are reported. Further, data gathered from the survey are used in a non-parametric analysis of the influences of the plant characteristics on the HACCP/RMP implementation process. The analysis provides implications for HACCP/RMP policy design. Part III presents the modelling techniques to quantify the costs and benefits of HACCP/RMP implementation. In Chapter 8, a quality-adjusted cost function is used to estimate the change in variable cost of production due to HACCP/RMP. It shows that this type of cost can make up a significant proportion of the total implementation cost. In Chapter 9, an export model is employed to analyse the impact of HACCP/RMP on meat industry export performance. The results show that the programme can bring a positive impact on exports. However, the magnitude of the impact depends on the status of existing food safety management before HACCP/RMP implementation. In Chapter 10, the Global Trade Analysis Project (GTAP) model is used to simulate the scenarios where market accesses to significant export destinations are lost when HACCP/RMP is not adopted. The estimated costs of these losses signal the potential benefits of HACCP/RMP. The research results show that HACCP/RMP can deliver a net benefit to the New Zealand meat industry. The thesis concludes with implications for policy design and future research directions. It signifies that the research findings, in addition to reporting an investigation into HACCP/RMP implementation process in New Zealand, provide an important foundation for future research on food safety and international competitiveness

Management and monitoring of air and water pollution by using GIS technology: Research article

The need for a green clean living environment is increasing today, with the boom of the socioeconomic development, educational level. However, the environmental pollution becomes an alerted global issue due to the large amount of wastes discharged making this need to be not easily met at the moment. Greenhouse gas emission mainly from energy, transport and agricultural land use is causing climate change because of their long atmospheric lifetime and trapping the heat in the atmosphere. Harmful effects and damages caused by environment pollution and climate change are unpredictable. It was reported that every year millions of people die because of fine particles when exposing to air pollution and other millions die from water-born diseases. Management and monitoring of air and water pollution by using GIS technology is an effective method. The measured data can be obtained continuously, quickly and accurately at stations in any regions even with complex terrain. This helps reduce the required number of employees, manage automatically and continuously a large number of data.Ngày nay nhu cầu về một môi trường sống xanh, sạch đang gia tăng, với sự bùng nổ của phát triển kinh tế - xã hội và trình độ dân trí. Tuy nhiên, ô nhiễm môi trường đang trở thành một vấn đề cảnh báo toàn cầu do số lượng lớn các chất thải được xả ra môi trường làm cho nhu cầu này không dễ dàng được đáp ứng tại thời điểm này. Phát thải khí nhà kính chủ yếu là từ sử dụng năng lượng, giao thông vận tải và đất nông nghiệp đang gây ra biến đổi khí hậu vì thời gian tồn tại của cúng dài và giữ nhiệt trong khí quyển. Các ảnh hưởng xấu và thiệt hại gây ra bởi ô nhiễm môi trường và biến đổi khí hậu là không thể đoán trước. Thông tin báo cáo chỉ ra rằng mỗi năm có hàng triệu người chết vì hít các hạt bụi mịn khi tiếp xúc với ô nhiễm không khí; và hàng triệu người khác chết vì bệnh do nước sinh ra. Quản lý và giám sát ô nhiễm không khí và nước bằng cách sử dụng công nghệ GIS là một phương pháp hiệu quả. Các dữ liệu đo có thể được lấy liên tục, nhanh chóng và chính xác tại các trạm ở bất kể khu vực nào, ngay cả nơi có địa hình phức tạp. Điều này giúp làm giảm số lượng lao động cần thiết, quản lý tự động và liên tục một số lượng lớn dữ liệu

CONTROL OF A PENDULUM USING HEDGE ALGEBRAS CONTAINING ACTUATOR SATURATION

In this study, the control problem of a pendulum using hedge-algebras-based fuzzy controller (HAC) containing actuator saturation is presented. In HAC, linguistic values of linguistic terms are obtained through semantically quantifying mappings (SQMs) based on several fuzzy parameters of each linguistic variable without using any fuzzy set and inherent order relationships between linguistic values are always ensured. Hence, the design of a HAC leads to determining parameters of SQMs. Numerical results of HAC are compared with those of an analogical conventional fuzzy controller (FC) in order to show advantages of the proposed method.In this study, the control problem of a pendulum using hedge-algebras-based fuzzy controller (HAC) containing actuator saturation is presented. In HAC, linguistic values of linguistic terms are obtained through semantically quantifying mappings (SQMs) based on several fuzzy parameters of each linguistic variable without using any fuzzy set and inherent order relationships between linguistic values are always ensured. Hence, the design of a HAC leads to determining parameters of SQMs. Numerical results of HAC are compared with those of an analogical conventional fuzzy controller (FC) in order to show advantages of the proposed method

The Predictive Performance of Objective Measures of Physical Activity Derived From Accelerometry Data For 5-Year All-Cause Mortality in Older Adults: National Health and Nutritional Examination Survey 2003-2006

Background: Declining physical activity (PA) is a hallmark of aging. Wearable technology provides reliable measures of the frequency, duration, intensity, and timing of PA. Accelerometry-derived measures of PA are compared to established predictors of 5-year all-cause mortality in older adults in terms of individual, relative, and combined predictive performance. Methods: Participants between 50 and 85 years old from the 2003-2006 National Health and Nutritional Examination Survey (NHANES, n = 2978) wore a hip-worn accelerometer in the free-living environment for up to 7 days. A total of 33 predictors of 5-year all-cause mortality (number of events = 297), including 20 measures of objective PA, were compared using univariate and multivariate logistic regression. Results: In univariate logistic regression, the total activity count was the best predictor of 5-year mortality (AUC = 0.771) followed by age (AUC = 0.758). Overall, 9 of the top 10 predictors were objective PA measures (AUC from 0.771 to 0.692). In multivariate regression, the 10-fold cross-validated AUC was 0.798 for the model without objective PA variables (9 predictors) and 0.838 for the forward selection model with objective PA variables (13 predictors). The Net Reclassification Index (NRI) was substantially improved by adding objective PA variables (p \u3c .001). Conclusions: Objective accelerometry-derived PA measures outperform traditional predictors of five-year mortality, including age. This highlights the importance of wearable technology for providing reproducible, unbiased, and prognostic biomarkers of health

The Influence of the Self-focusing Effect on the Optical Force Acting on Dielectric Particle Embedded in Kerr Medium

The influence of the self-focusing effect arised from Kerr effect on the optical force acting on the dielecric particle embedded in the Kerr medium, which is irradiated by the Gaussian beam, is proposed to concern. The expressions of the optical forces with the nonlinear refractive index and nonlinear focal length are derived. Using them, the distribution of the optical forces in the trapping region of the optical tweezer is simulated and discussed for same distinguished case of the Kerr medium with different nonlinear coefficients. The results show that the stabe region of the optical tweezer depends on the nonlinear coefficient of refractive index. Moreover, the stable region could be brokendown with a critical value of the nonlinear coefficient of refractive index of the surrounding medium irradiated by Gaussian laser pulse described by given parameters as  intensity, duration and radius of beam waist.

Imaging Biomarkers and Prevalence of Complex Aortic Plaque in Cryptogenic Stroke: A Systematic Review

Atherosclerosis; Imaging; StrokeAterosclerosis; Imágenes; IctusAterosclerosi; Imatges; IctusBackground Complex aortic plaque (CAP) is a potential embolic source in patients with cryptogenic stroke (CS). We review CAP imaging criteria for transesophageal echocardiogram (TEE), computed tomography angiography (CTA), and magnetic resonance imaging and calculate CAP prevalence in patients with acute CS. Methods and Results PubMed and EMBASE databases were searched up to December 2022 in accordance with the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guideline. Two independent reviewers extracted data on study design, imaging techniques, CAP criteria, and prevalence. The Cochrane Collaboration tool and Guideline for Reporting Reliability and Agreement Studies were used to assess risk of bias and reporting completeness, respectively. From 2293 studies, 45 were reviewed for CAP imaging biomarker criteria in patients with acute CS (N=37 TEE; N=9 CTA; N=6 magnetic resonance imaging). Most studies (74%) used ≥4 mm plaque thickness as the imaging criterion for CAP although ≥1 mm (N=1, CTA), ≥5 mm (N=5, TEE), and ≥6 mm (N=2, CTA) were also reported. Additional features included mobility, ulceration, thrombus, protrusions, and assessment of plaque composition. From 23 prospective studies, CAP was detected in 960 of 2778 patients with CS (0.32 [95% CI, 0.24–0.41], I2=94%). By modality, prevalence estimates were 0.29 (95% CI, 0.20–0.40; I2=95%) for TEE; 0.23 (95% CI, 0.15–0.34; I2=87%) for CTA and 0.22 (95% CI, 0.06–0.54; I2=92%) for magnetic resonance imaging. Conclusions TEE was commonly used to assess CAP in patients with CS. The most common CAP imaging biomarker was ≥4 mm plaque thickness. CAP was observed in one‐third of patients with acute CS. However, high study heterogeneity suggests a need for reproducible imaging methods.The work is supported by the National Heart, Lung, and Blood Institute (R01 HL147355, Z.F.), American Heart Association Career Development Awards (938082 to J.W.S.; 23CDA1053561 to J.W.), Vice Provost for University Research Foundation (J.W.S.), and Institute of Translational Medicine and Therapeutics (J.W.S.)

Stress and sleep quality in medical students: a cross-sectional study from Vietnam

BackgroundThe COVID-19 pandemic has resulted in significant global social and economic disruptions, as well as changes in personal attitude and behavior. The purpose of this research is to assess the sleep quality and stress levels of medical students.MethodData was collected from medical students over the course of a month in 2021. A total of 4,677 students at the University of Medicine Pham Ngoc Thach were invited to complete an anonymous web-based survey, which included the Pittsburgh Sleep Quality Questionnaire Index (PSQI) for measuring sleep quality and the COVID-19 Student Stress Questionnaire (CSSQ) for evaluating stress.ResultsA total of 1,502 students participated in our survey. More than half of the participants exhibited poor quality of sleep as indicated by their PSQI score. Many students reported going to bed after midnight and spending time on their smartphones. Among the students surveyed, 21.84% experienced low levels of stress (CSSQ ≤6), 63.38% had mild stress (7 ≤ CSSQ score ≤ 14), 14.78% reported high levels of stress (CSSQ >14).ConclusionThis study showed a high prevalence of poor sleep quality in the surveyed students, which could be attributed to changes in their behavior following the COVID-19 outbreak. Mild stress was also frequently observed, and it may be related to sleep disorders in this population. These important findings provide valuable insights for making recommendations, including lifestyle modifications to improve sleep quality

Will REDD+ safeguards mitigate corruption? Qualitative evidence from Southeast Asia

High levels of faith and finance are being invested in REDD+ as a promising global climate change mitigation policy. Since its inception in 2007, corruption has been viewed as a potential impediment to the achievement of REDD+ goals, partly motivating ‘safeguards’ rolled out as part of national REDD+ readiness activities. We compare corruption mitigation measures adopted as part of REDD+ safeguards, drawing on qualitative case evidence from three Southeast Asian countries that have recently piloted the scheme: Indonesia, the Philippines, and Vietnam. We find that while REDD+ safeguards adopt a conventional principal-agent approach to tackling corruption in the schemes, our case evidence confirms our theoretical expectation that REDD+ corruption risks are perceived to arise not only from principal-agent type problems: they are also linked to embedded pro-corruption social norms. This implies that REDD+ safeguards are likely to be at best partially effective against corruption, and at worst will not mitigate corruption at all