Time-Domain Fluorescence Diffuse Optical Tomography: Algorithms and Applications

Fluorescence diffuse optical tomography provides non-invasive, in vivo imaging of molecular targets in small animals. While standard fluorescence microscopy is limited to shallow depths and small fields of view, tomographic methods allows recovery of the distribution of fluorescent probes throughout the small animal body. In this thesis, we present novel reconstruction algorithms for the tomographic separation of optical parameters using time-domain (TD) measurements. These technique are validated using simulations and with experimental phantom and mouse imaging studies. We outline the contributions of each chapter of the thesis below. First, we explore the TD fluorescence tomography reconstruction problem for single and multiple fluorophores with discrete lifetimes. We focus on late arriving photons and compare a direct inversion approach with a two-step, asymptotic approach operating on the same TD data. We show that for lifetime multiplexing, the two methods produce fundamentally different kinds of solutions. The direct inversion is computationally inefficient and results in poor separation but has overall higher resolution while the asymptotic approach provides better separation, relative quantitation of lifetime components and localization but has overall lower resolution. We verify these results with simulation and experimental phantoms. Second, we introduce novel high resolution lifetime multiplexing algorithms which combine asymptotic methods for separation of fluorophores with the high resolving power of early photon tomography. We show the effectiveness of such methods to achieve high resolution reconstructions of multiple fluorophores in simulations with complex-shaped phantoms, a digital mouse atlas and also experimentally in fluorescent tube phantoms. Third, we compare the performance of tomographic spectral and lifetime multiplexing. We show that both of these techniques involve a two-step procedure, consisting of a diffuse propagation step and a basis-function mixing step. However, in these two techniques, the order of the two steps is switched, which leads to a fundamental difference in imaging performance. As an illustration of this difference, we show that the relative concentrations of three colocalized fluorophores in a diffuse medium can accurately be retrieved with lifetime methods but cannot be retrieved with spectral methods. Fourth, we address the long standing challenge in diffuse optical tomography (DOT) of cross-talk between absorption and scattering. We extend the ideas developed from lifetime multiplexing algorithms by using a constrained optimization approach for separation of absorption and scattering in DOT. Using custom designed phantoms, we demonstrate a novel technique allows better separation of absorption and scattering inclusions compared to existing algorithms for CW and TD diffuse optical tomography. Finally, we show experimental validation of the lifetime multiplexing algorithms developed in this thesis using three experimental models. First, we show the reconstruction of overlapping complex shapes in a dish phantom. Second, we demonstrate the localization accuracy of lifetime based methods using fluorescent pellets embedded in a sacrificed mouse. Third, we show using planar imaging and tomography, the in vivo recovery of multiple anatomically targeted near-infrared fluorophores. In summary, we have presented novel reconstruction algorithms and experimental methods that extend the capability of time-domain fluorescence diffuse optical tomography systems. The methods developed in this thesis should also have applicability for general multi-parameter image reconstruction problems.Engineering and Applied Science

Cost-effective priorities for the expansion of global terrestrial protected areas: Setting 2 post-2020 global and national targets

Biodiversity loss is a social and ecological emergency, and calls have been made for the global expansion of protected areas (PAs) to tackle this crisis. It is unclear, however, where best to locate new PAs to protect biodiversity cost-effectively. To answer this question, we conducted a spatial meta-analysis by overlaying seven global biodiversity templates to identify Conservation Priority Zones (CPZs). These are then combined with Low Human Impact Areas (LIAs) to identify Cost-Effective Zones for PA designation (CEZs). CEZs cover around 38% of global terrestrial area, of which only 24% is currently covered by existing PAs. To protect more CEZs, we propose three scenarios with conservative, moderate and ambitious targets, which aim to protect 19%, 26% and 43% of global terrestrial area, respectively. These three targets are set for each Convention on Biological Diversity (CBD) party with spatially-explicit CEZs identified, providing valuable decision support for the post-2020 global biodiversity framework

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

โอกาสและความท้าทายของความร่วมมือทางการท่องเที่ยวระหว่างประเทศไทยและสาธารณรัฐประชาชนจีน และอิทธิพลต่อการพัฒนาการท่องเที่ยวอย่างยั่งยืน

Master of Business Administration (Hospitality and Tourism Management (International Program)), 2023The current study aimed to explore the opportunities of tourism cooperation between China and Thailand; the challenges of tourism cooperation between China and Thailand and how the tourism cooperation makes sustainable development in tourism industry. The qualitative method is adopted in this study and interview are conducted. Fifteen participants from the government, travel agency, other tourism companies (offices in Thailand/China) would be recruited. The research questions are answered the themes which are resources maximization (resources exchange, knowledge sharing, shared market), tourism economic recession (disruption of tourism, low inflow tourists, low spending power), and providing better service (high quality of management, meet the demand of tourists, high performance of tourist experience).The findings of this study show that there are opportunities for resource optimization, service improvement, and sustainable development in China-Thailand tourism cooperation. The study highlights the need to address the challenges of tourism recession, tourism disruptions, low tourist inflows and low spending power to ensure the sustainable development of the tourism industry. In addition, with high-quality management, meeting customer needs, and efficient tourist experience to provide better services, so as to achieve sustainable development of the tourism industry.ภาคการเดินทางและการท่องเที่ยวมีความสําคัญในประเทศจีน ตั้งแต่เริ่มการปฏิรูป และเปิดประเทศเมื่อหลายสิบปีก่อน ปริมาณการท่องเที่ยวได้เพิ่มขึ้นอย่างมาก ทั้งการเพิ่มขึ้นของ ชนชั้นกลางที่ร่ํารวยขึ้นใหม่และการที่รัฐบาลจีนคลายข้อจํากัดด้านเสรีภาพในการเคลื่อนไหวของ ประชาชน ต่างก็มีส่วนทําให้อุตสาหกรรมการท่องเที่ยวของประเทศเพิ่มขึ้น การศึกษามี วัตถุประสงค์เพื่อสํารวจโอกาสของความร่วมมือด้านการท่องเที่ยวระหว่างจีนและไทย สํารวจความท้าทายของความร่วมมือด้านการท่องเที่ยวระหว่างจีนและไทย และสํารวจผลประโยชน์สําหรับการ พัฒนาอย่างยั่งยืนในอุตสาหกรรมการท่องเที่ยว การศึกษาใช้วิธีการเชิงคุณภาพด้วยการสัมภาษณ์ ผู้ปฏิบัติงานด้านการท่องเที่ยวและเจ้าหน้าที่ของรัฐที่สําคัญ การศึกษาในปัจจุบันได้ตั้งคําถามการ วิจัยสามข้อและสร้างหัวข้อที่จะตอบตามลําดับ คําถามวิจัยข้อแรกเกี่ยวกับ “โอกาสของความร่วมมือ ด้านการท่องเที่ยวระหว่างจีนและไทยคืออะไร” และใช้หัวข้อของการใช้ทรัพยากรให้เกิดประโยชน์ สูงสุดเพื่อตอบคําถามนี้ หมายความว่าโอกาสของความร่วมมือด้านการท่องเที่ยวระหว่างจีนและ ไทยคือการใช้ทรัพยากรที่มีอยู่ในอุตสาหกรรมการท่องเที่ยวให้เกิดประโยชน์สูงสุด คําถามการวิจัย ที่สองคือ “อะไรคือความท้าทายของความร่วมมือด้านการท่องเที่ยวระหว่างจีนและไทย” และหัวข้อ ที่ใช้ในการตอบคือภาวะถดถอยของเศรษฐกิจการท่องเที่ยว นัยว่าความร่วมมือด้านการท่องเที่ยว ระหว่างจีนและไทยอาจได้รับผลกระทบและท้าทายจากภาวะเศรษฐกิจการท่องเที่ยวที่ถดถอย สุดท้าย คําถามวิจัยข้อที่สามคือ “ความร่วมมือด้านการท่องเที่ยวทําให้เกิดการพัฒนาที่ยั่งยืนใน อุตสาหกรรมการท่องเที่ยวได้อย่างไร” และหัวข้อที่ใช้ในการตอบคําถามวิจัยนี้คือการให้บริการที่ดี ขึ้น หมายความว่าความร่วมมือด้านการท่องเที่ยวทําให้ผู้ให้บริการทั้งไทยและจีนสามารถให้บริการ ได้ดียิ่งขึ้น และเกิดการพัฒนาที่ยั่งยืนในอุตสาหกรรมการท่องเที่ยว การศึกษาได้ระบุถึงโอกาส ความท้าทาย และผลลัพธ์ของความร่วมมือด้านการท่องเที่ยวระหว่างจีนและไทย โอกาสในการ ร่วมมือด้านการท่องเที่ยวอยู่ที่การใช้ทรัพยากรให้เกิดประโยชน์สูงสุด เช่น การแบ่งปันความรู้ ตลาดแบ่งปัน และการแลกเปลี่ยนทรัพยากร สิ่งนี้ทําให้อุตสาหกรรมการท่องเที่ยวสามารถขยาย ไปสู่ตลาดที่ใหญ่ขึ้น ลดความเสี่ยงของการขาดทุ

Understanding and controlling microbial biofilm formation by surface engineering and novel biofilm inhibitors

Microbial biofilms cause serious problems including biocorrosion and biofouling in industrial environments as well persistent infections in clinical settings. As one of the key intrinsic mechanisms, biofilms aggravate the wide spread of antimicrobial resistance. Despite the significant problems caused by biofilms, biofilm formation is still poorly understood and effective control of biofilms remains challenging. In this work, several interdisciplinary approaches were developed and characterized to better understand the fundamentals of biofilm formation and to improve biofilm control. Self-assembled monolayers (SAMs) were applied to obtain well-defined surfaces with tunable inertness to microbial adhesion and biofilm formation by changing the functional groups of SAMs. By applying this useful platform, micro-patterns of surface chemistry were obtained to study microbe-surface interactions at the molecular and cellular levels. D-mannitol-terminated SAM was found to have unprecedented inertness to biofilm formation (up to 26 days). In addition, the data of patterned biofilm formation suggest that a critical distance may exist, beyond which bacteria cannot interact appropriately between clusters in biofilm formation. In addition to the fundamental study, several approaches were also explored to better control biofilms. First, brominated furanones (BFs) and cationic antimicrobial peptides (AMPs) were investigated as novel biofilm inhibitors. Several new BFs were found to have potent inhibitory effects on biofilm formation at the concentrations noninhibitory to planktonic growth of Gram-negative bacteria. The data led to identification of important structural elements of BFs for biofilm control. Hexameric, octameric, and dendrimeric peptides with Trp/Arg repeats also exhibited strong inhibitory effects on biofilm formation. Octameric peptide was also found to be a possible biofilm dispersion agent. It removed and killed up to 95.4% of E. coli biofilm cells from a stainless steel surface at 200 μM. Furthermore, a biocompatible nanofibrous scaffold containing ionic silver was demonstrated to resist biofilm formation for 14 days with controlled release of silver ions. These data provide new insights for understanding biofilm formation and developing biofilm control with enhanced prolonged efficacy

STA-GAN: A Spatio-Temporal Attention Generative Adversarial Network for Missing Value Imputation in Satellite Data

Satellite data is of high importance for ocean environment monitoring and protection. However, due to the missing values in satellite data, caused by various force majeure factors such as cloud cover, bad weather and sensor failure, the quality of satellite data is reduced greatly, which hinders the applications of satellite data in practice. Therefore, a variety of methods have been proposed to conduct missing data imputation for satellite data to improve its quality. However, these methods cannot well learn the short-term temporal dependence and dynamic spatial dependence in satellite data, resulting in bad imputation performance when the data missing rate is large. To address this issue, we propose the Spatio-Temporal Attention Generative Adversarial Network (STA-GAN) for missing value imputation in satellite data. First, we develop the Spatio-Temporal Attention (STA) mechanism based on Graph Attention Network (GAT) to learn features for capturing both short-term temporal dependence and dynamic spatial dependence in satellite data. Then, the learned features from STA are fused to enrich the spatio-temporal information for training the generator and discriminator of STA-GAN. Finally, we use the generated imputation data by the trained generator of STA-GAN to fill the missing values in satellite data. Experimental results on real datasets show that STA-GAN largely outperforms the baseline data imputation methods, especially for filling satellite data with large missing rates

Combined effects of earthworms and biochar on PAHs-contaminated soil remediation: A review

International audienceEarthworm remove PAHs from soil by bioaccumulation and stimulating microbial degradation. • Biochar can adsorb PAHs and promote microbial degradation in soil. • Earthworm improve the adsorption process of biochar by bioturbation. • Biochar reduce the vermiaccumulation and improve the decomposition of PAHs by earthworm. Polycyclic aromatic hydrocarbons (PAHs) in soil pose a threat to the health of humans and other organisms due to their persistence. The remediation method of combined application of biochar and earthworms has received growing attention owing to its effectiveness in PAHs removal. However, the earthworm-biochar interaction and its influence on PAHs in soil has not been systematically reviewed. This review focuses on the effectiveness of combined application of earthworms and biochar in the remediation of PAHs-contaminated soils and the underlying mechanisms, including adsorption, bioaccumulation, and biodegradation. Earthworm-biochar interaction activates the functional microorganisms in soil and the PAHs-degrading microorganisms in earthworm guts, promoting PAHs biodegradation. This review provides a theoretical support for the combined application of biochar and earthworms in the remediation of PAHs-contaminated soils, points out the limitations of this remediation method, and finally shows the prospects for future research

Eco-civilisation provides new opportunities for rewilding in China

Ecological civilisation has become China’s national strategy to promote harmonious coexistence between man and nature. China is a country that contains vast amounts of wilderness, while facing the threats from reduction and degradation of wilderness areas. As ecological civilisation provides new opportunities for rewilding, this chapter analyses how to incorporate rewilding into the core actions of ecological civilisation, including the National Territory Spatial Planning System (NTSPS), national parks and protected areas, and ecological protection and restoration projects of Mountains-Rivers-Forests-Farmlands-Lakes-Grasslands (MRFFLG). Rewilding and ecological civilisation are both developing concepts, and integrated thinking on these two concepts will promote related research and practice

Assessing Changes of Habitat Quality for Shorebirds in Stopover Sites: a Case Study in Yellow River Delta, China

The population of shorebirds in the East Asian-Australasian Flyway (EAAF) has severely declined over the past several decades. One reason for this condition is low survival in stopover sites in the Yellow Sea Ecoregion (YSE) due to habitat degradation. Here, we focused on shorebird habitat quality in the Yellow River Delta (YRD), which is a representative shorebird stopover site in the YSE on the EAAF. We used the InVEST model to assess the past and future shorebird habitat quality changes by considering the effects of anthropogenic threats. The entire duration of the study was 1999-2016, and the modeling was done on 2000 and 2015 data. Our results indicate that the abundance of 11 shorebird species had significant downward trends (70-97% reduction) during 1999-2015. Tidal flats in the nature reserve had higher habitat quality than that in the northwestern (NW) and eastern (E) parts of the YRD because major mariculture occurred in NW and E. The mean habitat qualities in NW and E decreased by 27 and 31% during 2000-2015, respectively. The optimal habitat in the YRD declined from 1433km(2) in 2000 to 1154km(2) in 2015. The habitat quality decreased significantly in E and Dongying Port parts during 2015-2020