Digital Commons Network^™

Growth Outcomes Of Pseudomonas Aeruginosa Inhibitor Of Vertebrate Lysozyme Knockouts In Conditions Mimicking The Cystic Fibrosis Lung Environment, Amani Gaddy

Master of Science in Chemical Sciences Theses

Pseudomonas aeruginosa (PA) is a Gram-negative bacterium, often found in cystic fibrosis (CF) patients and can lead to the decline of lung functioning and premature death in 80% of infected patients when microcolonies form within the mucin of the lung. Due to its major capacity for antibiotic resistance, an alternative strategy towards defending against the bacterial invasion of PA is by the antibacterial activity of our own innate immune system with use of elements such as lysozyme. Pseudomonas aeruginosa inhibitor of vertebrate lysozyme class 1 (Ivyp1) is a periplasmic protein produced by gram-negative bacteria that inhibits the enzymatic activity of …

Advanced Analytical Method Development: From Highly-Enrolled Classroom To Data-Intensive Proteomics, Laxmi Sinduri Vuppala

USF Tampa Graduate Theses and Dissertations

In analytical chemistry, method development is key to identifying, separating, and quantifying chemical components of interest systems. The chemical aspects are fundamental to understanding the subject of any analytical system, whether in academic research, industry, or government. These methodologies serve as a bridge between the classroom, where students are taught to be curious and enlightened, and research, where one strives to contribute. The Ph.D. dissertation integrates advanced methodologies in basic and applied research and advanced instrumentation, but the core criteria for validation remain the same. As part of chemical education curriculum development, a large cohort of undergraduates performed two gas …

Drivers Of Spatiotemporal Eukaryote Plankton Distribution In A Trans-Basin Water Transfer Canal In China, Yuying Li, Faisal Hayat Khan, Jiamin Wu, Yun Zhang, Yeqing Jiang, Xiaonuo Chen, Yinlei Yao, Yangdong Pan, Xuemei Han

Environmental Science and Management Faculty Publications and Presentations

Planktonic eukaryotes are important components of aquatic ecosystems, and analyses of the whole eukaryotic planktonic community composition and function have far-reaching significance for water resource management. We aimed to understand the spatiotemporal variation and drivers of eukaryotic plankton distribution in the Middle Route Project of the South-to-North Water Diversion in Henan Province, China. Specifically, we examined planktonic assemblages and water quality at five stations along the canal and another one located before the dam in March, June, September, and December 2019. High-throughput sequencing revealed that the eukaryotic plankton community was primarily composed of 53 phyla, 200 genera, and 277 species, …

Nmr Analyses Of Flavored E-Cigarette Liquids Before And After Aerosolization, Paul Joseph Kerber

Dissertations and Theses

Electronic cigarettes (e-cigarettes) are the most commonly used tobacco products among adolescents with ~11 and ~3% of high school and middle school students reporting past 30 day use in 2021 according to the Centers for Disease Control and Prevention (CDC), respectively. Furthermore, greater than ~80% of high school and middle school e-cigarette consumers use flavored e-liquids. Consumers can be exposed to variable toxicant levels upon e-liquid aerosolization, depending on the composition of the e-liquid, type of e-cigarette, e-cigarette settings, and other customizations.

E-liquids are typically composed of a carrier solvent (propylene glycol (PG) and glycerol (GL)), flavorants, and nicotine. PG …

Toward A Standard Formal Semantic Representation Of The Model Card Report, Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu, Cui Tao

Faculty, Staff and Student Publications

BACKGROUND: Model card reports aim to provide informative and transparent description of machine learning models to stakeholders. This report document is of interest to the National Institutes of Health's Bridge2AI initiative to address the FAIR challenges with artificial intelligence-based machine learning models for biomedical research. We present our early undertaking in developing an ontology for capturing the conceptual-level information embedded in model card reports.

RESULTS: Sourcing from existing ontologies and developing the core framework, we generated the Model Card Report Ontology. Our development efforts yielded an OWL2-based artifact that represents and formalizes model card report information. The current release of …

Toward A Standard Formal Semantic Representation Of The Model Card Report, Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu, Cui Tao

Faculty, Staff and Student Publications

BACKGROUND: Model card reports aim to provide informative and transparent description of machine learning models to stakeholders. This report document is of interest to the National Institutes of Health's Bridge2AI initiative to address the FAIR challenges with artificial intelligence-based machine learning models for biomedical research. We present our early undertaking in developing an ontology for capturing the conceptual-level information embedded in model card reports.

RESULTS: Sourcing from existing ontologies and developing the core framework, we generated the Model Card Report Ontology. Our development efforts yielded an OWL2-based artifact that represents and formalizes model card report information. The current release of …

Impact Of Oil And A Tropical Cyclone On An Omnivore And Herbivore Population In Salt Marshes Of Louisiana, Hannah K. Gordon

LSU Master's Theses

Terrestrial arthropods are the ideal ecological indicators for the health of a salt marsh. Salt marshes are under extreme continuous stressors including climate change, land loss, oil spills, and tropical cyclones. Such stressors impact trophic and species level interactions, food resources, dispersal and population size of insects. In the present study, we collected terrestrial arthropods from eleven sites around Barataria Bay, five sites were oiled and five sites were unoiled, to determine the impact of the redistribution of oil from the Deepwater Horizon oil spill. Site C6 was excluded from the oiled and unoiled data because it was in close …

Prediction Of Cultivation Areas For The Commercial And An Early Flowering Wild Accession Of Salvia Hispanica L. In The United States, Mohammad Hassani, Thomas Piechota, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Salvia hispanica L., commonly known as chia, is a plant-based alternative to seafood and is rich in heart-healthy omega-3 fatty acid, protein, fiber, and antioxidants. In the Northern Hemisphere, chia flowering is triggered by the fall equinox (12-h light and dark, early October) and the seeds mature after approximately three months. Chia is sensitive to frost and end of season moisture which limits its cultivation to small areas in regions with temperate climate. The U.S. chia import has increased considerably over the years; however, chia is not widely cultivated in the United States. This study used the historical U.S. temperature …

Using Dietary Additives To Improve Palatability Of Diets Containing Single‐Cell Protein From Methanotrophic Bacteria In Yellowtail Kingfish (Seriola Lalandi) Diets, Luke Pilmer, Lindsey Woolley, Alan J. Lymbery, Michael Salini, Gavin Partridge

Fisheries Research Articles

Single-cell protein (SCP) derived from methanotrophic bacteria has significant potential as a fishmeal alternative in aquafeeds. However, SCP has known palatability issues, to overcome these issues tuna hydrolysate and garlic powder were tested as palatability enhancers against basal diets without these additives. This study tested the inclusion of SCP at four dietary levels of 0%, 10%, 20% and 30%, representing 0%, 25%, 50% and 75% fishmeal replacement in juvenile yellowtail kingfish (Seriola lalandi) (YTK) diets. YTK were fed these diets in triplicate over 35 days. Compared with the control diet, fish fed the SCP10% diet ate less feed, …

Characterization Of Mumian And Host Rock In Al-Amerat Cave, Oman., Sara Alqamshouai

Honors Theses

Mumian is a sticky black-brown material found in the Mumian cave in Wadi Al Mayh, Al Amerat, Oman. Mumian has been used for centuries as traditional medicine by the local Omani people. Though commonly ingested orally to resolve a variety of common ailments, very little is known about the Mumian material in terms of its chemical composition. The principle aim of this study is to characterize the Mumian and the host rock in terms of the mineralogy and chemical characteristics using a variety of analytic instruments, including XRD, NMR, FT-IR, XRF, and UV- VIS. A secondary goal of this study …

Circadiomics: Circadian Omic Web Portal, Muntaha Samad, Forest Agostinelli, Tomoki Sato, Kohei Shimaji, Pierre Baldi

Faculty Publications

Circadian rhythms are a foundational aspect of biology. These rhythms are found at the molecular level in every cell of every living organism and they play a fundamental role in homeostasis and a variety of physiological processes. As a result, biomedical research of circadian rhythms continues to expand at a rapid pace. To support this research, CircadiOmics (http://circadiomics.igb.uci.edu/) is the largest annotated repository and analytic web server for high-throughput omic (e.g. transcriptomic, metabolomic, proteomic) circadian time series experimental data. CircadiOmics contains over 290 experiments and over 100 million individual measurements, across >20 unique tissues/organs, and 11 different species. Users are …

A Gis Suitability Model Evaluating Habitat Characteristics Influencing Beaver (Castor Canadensis) Lodge Site Selection And Lodge Occupancy In Central Adirondacks, New York, Amanda K. Jacobs

Theses - ALL

The North American beaver (Castor canadensis) represents a quintessential example of an "ecosystem engineer." Yet the species' landscape-scale impacts on hydrology, geomorphology, and ecosystem ecology are not uniformly distributed through landscapes or time. Understanding beaver lodge site selection and lodge fidelity through time can help to predict where the greatest effects of beaver activity may occur. In this research project, I seek to understand the relationships between beaver habitat suitability, the habitat variables that currently define suitable areas, and lodge occupancy over time. Using Geographic Information Systems (GIS) to model habitat suitability, I use hydrologic, vegetative, and physiographic variables to …

Microhabitat And Patch Selection Detection From Gps Tracking Collars Of Semi-Free Ranging Mashona Cattle Within A Semi-Arid Environment, C. Gwatirisa, B. T. Mudereri, T. Chitata, C. Mukanga, M. M. Ngwenya, J. V. Muzvondiwa, R. Mugandani, M. Sungirai

All Peer-Reviewed Publications

Over the last 30 years, the global positioning system (GPS) tracking collars have significantly enhanced livestock grazing behavior studies. Practices designed to understand and improve livestock grazing distribution can now be accurately and cost-effectively monitored with GPS tracking. The behavior and spatiotemporal microhabitat selection of Mashona cattle relative to the season in a semi-free-range grazing system was evaluated using a low‐cost GPS herd activity monitoring (GPSHAM) collar. The GPSHAM automatically logged the position of the lead cow at 20-second intervals over a 7–hour daily grazing period. Additionally, the GPS data was complemented by visually observing the lead cow during daylight …

Effects Of Nutrient Enrichment On Mangrove And Saltmarsh Habitats, Elena A. Flores

Theses and Dissertations

Nutrient over-enrichment is a global threat to coastal and marine environments. Yet, system-specific attributes of estuarine and coastal ecosystems may result in large differences in their sensitivity and susceptibility to such threat. In tropical latitudes, plant species adapted to low-nutrient habitats generally have nutrient-conservation mechanisms that acquire, use, and internally recycle nutrients efficiently. Thus, a major challenge for managers and decision makers is to develop a predictive and holistic understanding of how nutrient loading alters ecosystem functions and therefore ecosystem services. The objective of the present research is to document short and long-term effects of persistent nutrient …

Harnessing Confidence For Report Aggregation In Crowdsourcing Environments, Hadeel Alhosaini, Xianzhi Wang, Lina Yao, Zhong Yang, Farookh Hussain, Ee-Peng Lim

Research Collection School Of Computing and Information Systems

Crowdsourcing is an effective means of accomplishing human intelligence tasks by leveraging the collective wisdom of crowds. Given reports of various accuracy degrees from workers, it is important to make wise use of these reports to derive accurate task results. Intuitively, a task result derived from a sufficient number of reports bears lower uncertainty, and higher uncertainty otherwise. Existing report aggregation research, however, has largely neglected the above uncertainty issue. In this regard, we propose a novel report aggregation framework that defines and incorporates a new confidence measure to quantify the uncertainty associated with tasks and workers, thereby enhancing result …

Institute For Global Health And Development : Issue 4 - July - Sept 2022, Institute For Global Health And Development

IGHD Newsletters

• Research Highlights
• Key Publications
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• Reflections from IGHD’s Associate Faculty
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Genomic Prediction Accuracy Of Stripe Rust In Six Spring Wheat Populations By Modeling Genotype By Environment Interaction, Kassa Semagn, Muhammad Iqbal, Diego Jarquin, Harpinder Randhawa, Reem Aboukhaddour, Reka Howard, Izabela Ciechanowska, Momna Farzand, Raman Dhariwal, Colin W. Hiebert, Amidou N’Diaye, Curtis Pozniak, Dean Spaner

Department of Statistics: Faculty Publications

Some previous studies have assessed the predictive ability of genome-wide selection on stripe (yellow) rust resistance in wheat, but the effect of genotype by environment interaction (GEI) in prediction accuracies has not been well studied in diverse genetic backgrounds. Here, we compared the predictive ability of a model based on phenotypic data only (M1), the main effect of phenotype and molecular markers (M2), and a model that incorporated GEI (M3) using three cross-validations (CV1, CV2, and CV0) scenarios of interest to breeders in six spring wheat populations. Each population was evaluated at three to eight field nurseries and genotyped with …

Phytochemical, Antibacterial, Antifungal, And Hemagglutination Screening Of Quercus Agrifolia Nee Root Extracts, Abdul Wahab, Arshad Farid, Muhammad Muzammal

Makara Journal of Science

In the current study, the roots of Quercus agrifolia Nee were subjected to phytochemical analysis to determine the presence of various compound groups. To explore the effect of Quercus agrifolia Nee roots, we evaluated four solvent extracts, namely, crude ethanolic extract (CEE), n-hexane, chloroform (CHCl₃), and ethyl acetate (EtOAc), for their antibacterial, antifungal, and hemagglutination activities. Agar well diffusion and agar tube dilution methods were used to determine the antibacterial and antifungal effects, respectively, and hemagglutination activity was measured against human erythrocyte blood groups. The qualitative phytochemical analysis of the solvent extracts of Quercus agrifolia Nee roots …

Silver Nanoparticles’ Biosynthesis And Characterization With The Extract Of Jatropha Curcas Leaf: Analysis Of Corrosion Inhibition Activity, Talabi Henry Kayode, Talabi Justina Yetunde, Adewuyi Benjamin Omotayo

Makara Journal of Science

The plant-mediated nanoparticles synthesis process is gaining popularity because of its effective cost, eco-friendliness, and nontoxic nature. The current study presents the silver nanoparticles (AgNPs) which synthesized with AgNO₃ as precursor salt and Jatropha curcas leaf extract. J. curcas leaf extract has phytochemicals that could reduce the precursor metal salt to nanoparticles and act as a capping agent surround the nanoparticles to enhance its stability. Phytochemical screening on J. curcas leaf extract showed that alkaloids, saponins, tannins, flavanoids, steroids, philobatannins, phenols, and cardiac glycosides are contained in the sample. The biosynthesized nanoparticles were investigated by UV-visible (UV-vis) spectroscopy, X-ray …

Jatropha Tanjorensis A Flora Of Southeast Nigeria: Isolation And Characterization Of Naringenin And Validation Of Bio-Enhanced Synergistical Activity Of Α- Tocopherol Toward Clinical Isolates Of Resistant Bacterial, Ikechukwu Kingsley Ijoma, Vincent Ishmael Egbulefu Ajiwe

Makara Journal of Science

Jatropha tanjorensis is among the rich floras of Southeast Nigeria and used by ethnic people to treat infections and manage health conditions. Ethnomedicine has long been employed in the treatment of ailments caused by bacterial pathogens. Studies showed that the incorporation of synthetic α-tocopherol to an antibacterial agent improves its activity. However, knowledge about the antibacterial-enhanced activity of plant-based α-tocopherols, especially those isolated from Jatropha tanjorensis, is limited because of the different bioactivities of synthetic and natural α-tocopherols. To determine the phytochemicals in J. tanjorensis, we carried out the structural elucidation of its leaf extracts. Naringenin and α-tocopherol …

Effects Of Feed Moisture Content, Soybean Ratio And Barrel Temperature On Physical And Functional Properties Of Extruded Maize-Soybean Flour Blends, Robert Mugabi, Stellah Byakika, Ivan Muzira Mukisa

Tanzania Journal of Science

The effects moisture content, temperature and soybean ratio on expanded product characteristics of extruded maize-soybean blends were studied. Response surface methodology was used to study the effects of extrusion conditions on extrudate properties taking barrel temperature (BT), feed moisture content (FM) and soybean flour ratio (SR) as factors. Expansion ratio (ER), water absorption index (WAI), water solubility index (WSI), hardness and colour (b* - (+) yellowness) of the extrudates were determined. BT and FM had significant effects on ER (p < 0.05). At low FM levels, ER increased with BT. It was observed that both FM and BT significantly affected WAI and WSI. WAI increased as FM increased. Increasing FM to 20% resulted in a decrease in WSI, beyond which an increase was observed. Hardness increased significantly as feed moisture content increased. High SR content significantly increased the extrudate hardness. FM had no significant effect on colour. Colour increased as the SR and BT increased. Significant regression models explained the effects of SR, FM, and BT on all response variables. All of the response variables' R2, were higher than 0.89. Keywords: Maize, Soybean, moisture content, extrusion

Critical P, K And S Concentrations In Soil And Shoot Samples For Optimal Tedera Productivity And Nodulation, Daniel Real, Richard G. Bennett, Nazanin K. Nazeri, David M. Weaver

Grain and Other Field Crops Research Articles

Tedera is a forage legume that can provide out-of-season green feed in Mediterranean climates. To date, growers have had no comprehensive soil nutrition guidelines to optimise tedera production. We undertook field and glasshouse studies to understand tedera’s macronutrient requirements. Three field experiments were sown with tedera cv. Lanza® at Cunderdin, Dandaragan and Three Springs in Western Australia. These experiments evaluated seven levels of phosphorus (P) (0–30 kg ha−1) and potassium (K) (0–80 kg ha−1) and two combined treatments with P and K. Glasshouse pot experiments were conducted using tedera cultivars Lanza® and Palma and lucerne cultivar SARDI Grazer. Ten concentrations …

Development Of Enhanced Food Packaging Systems Based On Blends Of Bio-Based And Biodegradable Polymers Exhibiting Antimicrobial Properties, Aishat Agboluaje

Theses and Dissertations

Food packaging is one of the important aspects of food processing, which contributes greatly to decreasing post-harvest food losses. While ensuring that foods are adequately packaged, it is also important to consider the impact of these food packaging materials on the environment. Accordingly, this research work was aimed at investigating the potential of bio-based and biodegradable blends of polyvinyl alcohol (PVA) and chitosan loaded with antimicrobial agents such as turmeric, clove, and cinnamon for use in food packaging applications. The methodology involved creating PVA/chitosan films with varying compositions via solvent casting method and selecting the best composition exhibiting the highest …

Polychlorinated Organic Contaminants In Baleen From North Pacific Ocean Whales, Briana R. Coulter

All HCAS Student Capstones, Theses, and Dissertations

Persistent organic pollutants (POP) have been detected and analyzed in various baleen whale tissues (blubber, muscles, liver, etc.) This study concentrated on detecting 7 polychlorinated biphenyls (PCB) and 14 organochlorine pesticides from baleen, a baleen whale tissue never before analyzed for POPs. These data were used to investigate temporal and geographic trends by sampling at every 1 cm interval along the length of the baleen plate. Four species of baleen whales stranded in the North Pacific Ocean were included in this study: gray (n=2), humpback (n=2), minke (n=1), and blue (n=1) whales. Organic contaminant concentrations were analyzed with respect to …

Association Between The Dietary Inflammatory Index And Gastric Disease Risk: Findings From A Korean Population-Based Cohort Study, Sundara Raj Sreeja, Trong-Dat Le, Bang Wool Eom, Seung Hyun Oh, Nitin Shivappa Mbbs, Mph, Ph.D., James R. Hébert Scd, Mi Kyung Kim

Faculty Publications

Evidence suggests that diets with high pro-inflammatory potential may play a substantial role in the origin of gastric inflammation. This study aimed to examine the association between the energy-adjusted dietary inflammatory index (E-DIITM) and gastric diseases at baseline and after a mean follow-up of 7.4 years in a Korean population. A total of 144,196 participants from the Korean Genome and Epidemiology Study_Health Examination (KoGES_HEXA) cohort were included. E-DII scores were computed using a validated semi-quantitative food frequency questionnaire. Multivariate logistic regression and Cox proportional hazards regression were used to assess the association between the E-DII and gastric disease risk. In …

Biomass Residues Improve Soil Chemical And Biological Properties Reestablishing Native Species In An Exposed Subsoil In Brazilian Cerrado, Thaís Soto Boni, Engil Isadora Pujol Pereira, Adriana Avelino Santos, Ana Maria Rodrigues Cassiolato, Kátia Luciene Maltoni

School of Earth, Environmental, & Marine Sciences Faculty Publications

Revegetation of exposed sub-soil, while a desirable strategy in the recovery processes, often fails due to extreme soil chemical properties, such as low organic matter and pH levels inhospitable to biological activities such as nutrients cycling and plant establishment. This is the case for approximately 800 ha of the Cerrado biome in Brazil, where erecting the embankment of a hydroelectric dam in the 1960’s stripped vegetation, soil, and subsoil layers thereby distorting the soil properties. This work evaluates the effectiveness of restoration management (RM) treatments, to restore the soil quality, including biological activity and chemical attributes. In a factorial scheme, …

Nitrogen Fixation Rates In Forested Mountain Streams: Are Sediment Microbes More Important Than Previously Thought?, Erica A. H. Bakker, Carmella Vizza, Clay Arango, Sarah S. Roley

Biology Faculty Scholarship

1. Biological nitrogen (N) fixation, the microbial conversion of N₂ gas to ammonia, makes N available to food webs. Low-N streams often have a high relative abundance of N-fixing taxa, suggesting that N fixation is an important N source in these systems. Despite this potential, stream N fixation has not been well-characterised, particularly compared to lakes and marine environments. One unknown is the relative contributions of various N-fixing organisms, particularly heterotrophic microbes.
2. In low-N streams in the Cascade Mountains (Washington, USA), three groups of N-fixers predominate: cyanobacteria (Nostoc paramelioides) colonies that house a midge symbiont (Cricotopus spp.), …

Adolescent Health Risk Behaviors, Adverse Experiences, And Self-Reported Hunger: Analysis Of 10 States From The 2019 Youth Risk Behavior Surveys, Kathryn L. Krupsky, Sarah Silwa, Hilary Seligman, Andrea D. Brown, Angela D. Liese Ph.D., Zewditu Demissie, Ellen Barnidge

Faculty Publications

We examined associations between adolescent self-reported hunger, health risk behaviors, and adverse experiences during the 2018–2019 school year. Youth Risk Behavior Survey data were pooled from 10 states. Prevalence ratios were calculated, and we assessed effect measure modification by sex. The prevalence of self-reported hunger was 13%. Self-reported hunger was associated with a higher prevalence of every health risk behavior/adverse experience analyzed, even after adjusting for sex, grade, and race/ethnicity. Sex did not modify associations. Findings underscore needs for longitudinal research with more robust measures of adolescent food insecurity to clarify the temporality of relationships.

‘Bunkering Down’: How One Community Is Tightening Social-Ecological Network Structures In The Face Of Global Change, Michele L. Barnes, Lorien Jasny, Andrew Bauman, Jon Ben, Ramiro Berardo, Örjan Bodin, Josh Eli Cinner, David A. Feary, Angela M. Guerrero, Fraser A. Januchowski-Hartley, John T. Kuange, Jacqueline D. Lau, Peng Wang, Jessica Zamborain-Mason

Marine & Environmental Sciences Faculty Articles

1. Complex networks of relationships among and between people and nature (social-ecological networks) play an important role in sustainability; yet, we have limited empirical understanding of their temporal dynamics.
2. We empirically examine the evolution of a social-ecological network in a common-pool resource system faced with escalating social and environmental change over the past two decades.
3. We first draw on quantitative and qualitative data collected between 2002 and 2018 in a Papua New Guinean reef fishing community to provide contextual evidence regarding the extent of social and environmental change being experienced. We then develop a temporal multilevel exponential random graph model using …

Marine Ranching Version 3.0: History, Status And Prospects, Hongsheng Yang, Dewen Ding

Bulletin of Chinese Academy of Sciences (Chinese Version)

Since the 1930s, the construction of marine ranching has successively experienced the version 1.0 (traditional marine ranching) of farming-ranching and engineering, and the version 2.0 (marine ecological ranching) of ecologization and informatization, and now it is about to enter the version 3.0 (global aquatic ecological ranching) of digitalization and systematization, which covers seawater and fresh water. Marine ranching version 3.0 must adhere to the modern aquatic ecological ranching development concept of "ecology, precision, intelligence, integration", characterized by synchronous protection and utilization, expansion of scene and space, breakthrough in core technology, and innovation in development patterns. After establishing the whole industrial …