Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling complex cell regulation in the zebrafish circadian clock

The interdisciplinary "systems biology" approach of combining traditional biological investigations with tools from the mathematical and computer sciences has enabled novel insights into many highly complex and dynamic biological systems. The use of models has, for instance, revealed much about the intricate feedback mechanisms and acute importance of gene regulatory networks, and one such network of special note is our internal time keeper, or circadian clock. The circadian clock plays a pivotal role in modulating critical physiological processes, and has also been implicated, either directly or indirectly, in a whole range of pathological states. This research project investigates how the underlying dynamics of the circadian clock in the zebrafish model organism may be captured by a mathematical model, considering in particular the entrainment effect due to external cues such as light. Simulated data is contrasted with experimental results from different light regime experiments to validate the model and guide its refinement. Furthermore, various statistical methods are implemented to process the raw data and support its analysis. Extending the initial deterministic approach to take into account stochastic effects and additive population level effects emerges as a powerful means of representing the circadian signal decay in prolonged darkness, as well as light initiated re-synchronization as a strong component of entrainment. Consequently, it emerges that stochastic effects may be considered an essential feature of the circadian clock in zebrafish. A further cornerstone of the project is the implementation of an integrated simulation environment, including a Sequential Monte Carlo parameter estimation function, which succeeds in predicting a range of previously determined and also novel suitable parameter values. However, considerable difficulties in obtaining parameter values that satisfy the entire range of important target values simultaneously highlights the inherent complexity of accurately simulating the circadian clock.
Fuzzy Neural Network Model for Weather Forecasting of Airport

For a multifactor weather prediction problem,this paper constructs a new model of fuzzy neural network based on rough set.This model applies the rough set theory to reduce factors of weather and extract rules,the model of fuzzy neural network is built by these rules,and the initial parameters' value of fuzzy neural networks is decided by the statistical parameters of rules and the result of discretization and the networks is trained by BP methods.The application example showi that this model is superior to the traditional one on fitting precision and training rate.
Development of an innovative in vivo model of PJI treated with DAIR

Introduction Prosthetic Joint Infection (PJI) are catastrophic complications of joint replacement. Debridement, implant retention, and antibiotic therapy (DAIR) is the usual strategy in acute infections but fails in 45% of MRSA infections. We describe the development of a model of infected arthroplasty in rabbits, treated with debridement and a course of vancomycin with clinically relevant dosage. Materials and methods A total of 15 rabbits were assigned to three groups: vancomycin pharmacokinetics (A), infection (B), and DAIR (C). All groups received a tibial arthroplasty using a Ti-6Al-4V implant. Groups B and C were infected per-operatively with a 5.5 log10 MRSA inoculum. After 1 week, groups C infected knees were surgically debrided. Groups A and C received 1 week of vancomycin. Pharmacokinetic profiles were obtained in group A following 1st and 5th injections. Animals were euthanized 2 weeks after the arthroplasty. Implants and tissue samples were processed for bacterial counts and histology. Results Average vancomycin AUC0–12 h were 213.0 mg*h/L (1st injection) and 207.8 mg*h/L (5th injection), reaching clinical targets. All inoculated animals were infected. CFUs were reproducible in groups B. A sharp decrease in CFU was observed in groups C. Serum markers and leukocytes counts increased significantly in infected groups. Conclusion We developed a reproducible rabbit model of PJI treated with DAIR, using vancomycin at clinically relevant concentrations.
Stereotactic partial breast irradiation in primary breast cancer: A comprehensive review of the current status and future directions

In selected low-risk breast cancer patients, accelerated partial breast irradiation (APBI) may represent an alternative option to the whole breast irradiation to reduce the volume of irradiated breast and total treatment duration. In the last few years, preliminary data from clinical trials showed that stereotactic partial breast radiotherapy may have the advantage to be less invasive compared to other APBI techniques, with preliminary good results in terms of local toxicity and cosmesis: the use of magnetic resonance, fiducial markers in the tumor bed, and new breast devices support both a precise definition of the target and radiation planning. Systematic review registration https://www.crd. york.ac. uk/prospero/display_record. php? ID=CRD42021257856, identifier CRD42021257856.
Low‐Level and Surface Wind Jets Near Sea Ice Edge in the Beaufort Sea in Late Autumn

Low‐level wind jets (LLJs) and strong surface winds are frequently observed near the sea ice edge in the presence of strong thermal contrast between open water and sea ice. Two LLJ cases near the sea ice edge in the Beaufort Sea are examined using dropsonde observations made from Seasonal Ice Zone Reconnaissance Survey flights. Ensembles of Polar Weather Research and Forecast simulations with and without sea ice demonstrate the contribution of the surface thermal contrast to the boundary layer structure, the LLJ, and surface ice edge jets. Because the surface temperature contrast only influences the lower most hundreds of meters in the atmospheric boundary layer, its contribution to the temperature gradient and wind speed at the level of the LLJ is limited. The sea ice does strengthen the LLJ by extending the LLJ northward over sea ice and increasing the maximum LLJ wind speeds by up to 13% and as much as 29% further north at a lower altitude. However, the primary reason for the observed strong winds in these two cases are the synoptic interactions between anticyclones and approaching cyclones. The effect of the surface thermal contrast on surface winds is controlled by a separate mechanism. The cold and stable boundary layer over sea ice prevents the momentum transport from the LLJ to the surface. This leads to weaker surface winds over sea ice and confines the strong surface winds close to the sea ice edge. This mechanism contributes to the frequent occurrence of the surface “ice edge jets. ”
Sparse representation based classification for face recognition

Building a computer as intelligent as or more intelligent th an human is the ultimate goal of machine learning. To explore this powerful ability in compu ter vision, it inspires numerous interesting and useful research areas and applications. Fa ce recognition (FR), as one of the most challenging problems in machine learning and computer vision, provides a good test bed to show how intelligent a machine can be. Moreover, it shows h uge potential for commercial and surveillance, such as access control, computer-human inte raction and anti-terrorist. FR remains a hot research topic though it has been studied for more than t hree decades. One important reason is that there is still large gap between human and mach ine to recognize the identity of a face image due to extreme illumination, expression and pose variation, disguise, and occlusion et al. Recently, sparse representation based classification (SRC ) has been introduced and applied to FR in dealing with some challenge scenarios. Different fr om the traditional classifiers, which represent the query image by each individual class, SRC cons iders the query image as a sparse linear combination of training samples of all subjects. The optimization of the sparse coefficients lets every training sample compete against the other s o win its representation share of the query image. This is a good discriminating process. The a dvantages of SRC lead to some encouraging and impressive FR results. Although SRC shows i ts merit in handling the query image with sparse corruption (e.g., occlusion or disguise), t h re are still many problems remained to be addressed. In this thesis, we propose several algorith ms for FR to tackle the limitations
THE DISCUSSION ON METADATA OF GEO-SPATIAL DATA

Abstrcat The content of Geo-spatial data is complicated and its quantity is enormous. It is practical and feasible method to set up the Geo-spatial metadata for managing and sharing the data. This paper discusses the concept, status quo of research and the management of Geo-spatial metadata, and finally builds a frame of metadata management system. 
THE INTEGRATED APPROACH TO SUSTAINABLE DEVELOPMENT: THE CASE OF ENERGY EFFICIENCY AND SOLID WASTE MANAGEMENT

The purpose of this article is to explore the possibilities and develop proposals for the integrated solution of some of the problems of sustainable development related to waste processing and improving the energy efficiency of the economy. This purpose was achieved by solving the following objectives: 1) analysis of the problem of energy efficiency and how to solve it; 2) study of the problem of waste management and approaches to its solution; 3) development of proposals for the implementation of energy-efficient waste treatment. The leading methods used in the article were the following: a review of the literature, statistical analysis, expert assessments, systems, technological and institutional analysis, economic modeling. As a result of the study, it was proved that the problems of energy efficiency of the economy and waste management should not be solved in isolation, but in a comprehensive manner. The key idea of the study was that waste may be an unconventional (alternative) energy source. The existing technological solutions for their implementation require significant investments, changes in regulation, as well as transformation of the behavior of the population. Modernization of waste management often comes down to the modernization of landfill management. This is not effective enough (from environmental, economic, energy efficiency positions). The development of new institutional rules and innovative technologies is required. The authors propose to use waste as an energy resource using the technology of thermal catalytic depolymerization. In addition to the beneficial environmental effect, the proposed technology has high energy efficiency.
Influence of soil-structure interaction on the dynamic response of continuous and integral bridge subjected to moving loads

ABSTRACT In this paper, the effects of high-speed moving train loads over a non-prismatic continuous and integral bridge are investigated, in which the dynamic soil-structure interaction (SSI) analysis is comprehensively considered. Initially, a complete-pile model and an equivalent spring model of the continuous bridge are analyzed and compared. Two complex cases of track loading for the complete-pile model Case-I (C-I): one train moving on the single track, and Case-II (C-II): two trains moving on both the tracks entering at same instant but in opposite direction), under the CRH3 train loading, are studied. The variations in dynamic responses of the bridge for these cases confirm the influence of soil-structure interaction. C-II represents higher vertical displacement and acceleration bridge response compared to the C-I for both, continuous and integral bridge. It is proposed to analyze a detailed 3D model under critical loading condition for acquiring an accurate vertical dynamic response of bridge structure.
Radio Frequency Integrated Circuits and Systems

Focusing on the core topics of radio frequency integrated circuits (RFICs) and system design, this textbook provides the in-depth coverage and detailed mathematical analyses needed to gain a thorough understanding of the subject. Throughout, theory is linked to practice with real-world application examples; practical design guidance is also offered, covering the pros and cons of various topologies, and preparing students for future work in industry. Written for graduate courses on RFICs, this uniquely intuitive and practical book will also be of value to practising RFIC and system designers. Key topics covered include RF components, signals and systems, two-ports, noise, distortion, low-noise amplifiers, mixers, oscillators, power amplifiers, and transceiver architectures. Lecture slides and a solutions manual for instructors are provided online to complete the course package.
Assessing the effectiveness of management measures in the Ria Formosa coastal lagoon, Portugal

The Ria Formosa is an important transitional and coastal lagoon on the south coast of Portugal that provides valuable ecosystem services. The lagoon is a protected area under national and international conventions. There is a great potential for Blue Growth sectors, such as aquaculture and coastal tourism, but these rely on good water quality. European environmental legislation, such as the Water Framework Directive, requires member states, such as Portugal to implement management measures if a surface water body is not of good ecological status. This work addresses the effectiveness of management measures, such as wastewater treatment plant implementation and dredging, on the water quality of the Ria Formosa coastal lagoon system. This is an important social-ecological issue, since management measures can be very expensive. The ecological status of Ria Formosa was evaluated, according to the physico-chemical and biological quality elements of the Water Framework Directive. The main indicators were the physico-chemical quality elements of nutrient and oxygen condition, and the biological quality element chlorophyll a, as a proxy for phytoplankton biomass, under the Water Framework Directive. The data for these quality elements from the Ria Formosa were analyzed for consistency with the classification for the Water Framework Directive water bodies. The data after the implementation of management measures was compared with historical data to evaluate if these measures had been effective. The relation between nutrient pressures, meteorological and hydrological conditions was addressed, especially rainfall and runoff. Results showed a decrease in nutrient concentration after the management interventions, despite the increase of population and intensifying agriculture in the catchment. The Ecological Status is spatially variable with an overall moderate status, indicating the need for further management measures. There is a significant reduction in nutrient pressure on the lagoon during drought years. This indicates that climate change may alter the structure and function of the lagoon in the future.
Spatial Analysis of Forest–Tundra Ecotones Reveals the Influence of Topography and Vegetation on Alpine Treeline Patterns in the Subarctic

The response of vegetation to recent climate change is a central theme in contemporary biogeography. A tenet of this research is that forests will advance upslope and northward as climate warms, replacing tundra communities. There has been considerable variation, however, in the pace and extent of recent change, particularly in alpine regions. The objectives of this study were to determine how and why tree spatial patterns vary across different topographic features, and to use spatial patterns to infer the mechanisms governing treeline dynamics in an alpine region of subarctic Canada. We mapped trees across different elevations, slope aspects, and slope angles in two QuickBird satellite images, and in field plots established within the bounds of each image. We then quantified the degree of clustering among trees using Ripley’s K(t) statistic. We also classified each image into vegetation classes and used class-level landscape metrics to quantify the degree of treeline abruptness in different topographic settings. We found that clustering of stems was more common on south than north aspects, likely due to the high occurrence of overwinter damage on the former. Treelines were also more abrupt on south aspects, likely because high tall shrub abundance on these slopes inhibits tree seedling establishment. We conclude that the spatial patterns of subarctic alpine treelines are strongly influenced by both physical and biological factors that vary strongly with slope aspect. The response of treelines to future climate change will likely be highly variable at the landscape scale, despite experiencing similar climatic conditions. Key Words: forest–tundra ecotone, FragStats, landscape metrics, QuickBird, spatial pattern analysis, Yukon.
SERIOUS GAMES TO IMPROVE STUDENT LEARNING IN ENGINEERING CLASSES

A serious game can be defined as a world where the students play simulated events using characters that interact with them, and, in turn, make them learn a concept much more thoroughly than what is possible in a classroom or in a lab session. This paper describes a project where a university joined with a private company to teach the concept of the design process by using a serious game and provides details about the design and development of the game. The research model integrates organizational, engineering education and educational learning literature to research how game play interacts with learning styles, gender and race of the participants, thereby having the potential to act as facilitators to the learning process. The targeted student groups for this experiment were freshmen engineering students at two universities. This paper describes a project where the concept of an engineering design process was taught using two engineering design learning modules, and evaluated using a control/experimental set up. In the control class, the students were exposed to a lecture about the engineering design process, an active learning exercise (Title: Statistics Applied to Data Analysis), and a pasta tower building activity. In the experimental set up, the students were exposed to a lecture about the engineering design process, a design simulation exercise (Serious game titled 'Engineering Heights: The Design Process in Action'), and a pasta tower building activity. External evaluators used the same instruments and focus groups to collect both quantitative and qualitative assessment data for both sections. All the students in the experimental group who worked with the game achieved better learning outcomes, had higher performance scores in the pasta tower design challenge, and higher perceived concentration levels. In focus group sessions, students commented that the serious game helped them understand the effects of different shapes and structures when presented with the practical challenge of designing and building pasta towers.
Palynofacies Analyses of Fox Bay Formation (Devonian), Falkland Islands

The Falkland Islands are an archipelago consisting two main islands (West and East) that show contrasts in their sedimentary history. The palynofacies analysis was applied as tool for reconstructing the history of sedimentary organic matter deposition during the Devonian. The material derives from the Fox Bay Formation that crops out in the East and West Falklands. Spore Color Indices (SCI) and Total Organic Carbon (TOC) also were conducted. Seven kerogen categories were identified: amorphous organic matter (AOM), opaque phytoclasts, Spongiophyton, acritarchs, prasinophycean algae and spores. In general, the samples are carbonized, in particular the AOM that is most abundant, and are distinguished into two subgroups: amorphous organic matter (AOM) and amorphous organic matter carbonized (AOMc). Four palynofacies associations were identified: Palynofacies A, which is composed of prasinophycean algae and acritarchs, Palynofacies B of spores and AOMc, Palynofacies C of phytoclasts and Spongiophyton; and Palynofacies D only of AOM. The results confirm a differentiation between the West and East islands. In fact, this reflects the abundance of AOM and AOMc, respectively. In West Falkland the sedimentary organic matter is not completely carbonized indicated by a lower abundance of AOMc as a result of a lesser thermal influence caused probably by movement of the Hornby Mountains Fault.
Extracellular electrophysiology with close-packed recording sites: Spike sorting and characterization

Advances in recording technologies now allow us to record populations of neurons simultaneously, data necessary to understand the network dynamics of the brain. Extracellular probes are fabricated with ever greater numbers of recording sites to capture the activity of increasing numbers of neurons. However, the utility of this extracellular data is limited by an initial analysis step, spike sorting, that extracts the activity patterns of individual neurons from the extracellular traces. Commonly used spike sorting methods require manual processing that limits their scalability, and errors can bias downstream analyses. Leveraging the replication of the activity from a single neuron on nearby recording sites, we designed a spike sorting method consisting of three primary
Small shift detection based on MCUSUM-ICA-PCA

In order to detect the process influenced by gradual small shifts and extract the non-Gaussian information,a new multivariate statistical process monitoring method was proposed,which extended the conventional cumulative sum(CUSUM) to MCUSUM and combined it with independent component analysis(ICA) and principal component analysis(PCA) to form MCUSUM-ICA-PCA.A two-step information extraction strategy was proposed to extract the full information(including non-Gaussian and Gaussian),then three statistics and their corresponding statistical limits were built.A case study of the Tennessee Eastman(TE) process shows that the proposed method is efficient,the process monitoring performance is evidently improved,and it also enhances the reliability and stability of the TE process.
SMS-Based Mobile Learning

Students today combine study and work and expect significant cost and time savings from the use of information and communication technologies, including mobile communication. A strong interest in implementing mobile technologies in learning has emerged. Experiments with one of the most popular technologies—text messaging—have been reported in the literature (e.g., Stone & Briggs, 2002; Finn, 2004) with some including the development of blended learning models (Stone, Briggs, & Smith, 2002). An early definition of mobile learning (m-learning) as “learning through mobile computational devices” can be found in Quinn (2000). Later, frameworks and research models were developed, providing guidelines for implementing suitable pedagogical approaches and for building services and applications relevant to a variety of mobile platforms and contextual settings (Garner, Francis, & Wales, 2002; Seng & Lin, 2004; Berth; 2005; Brown, 2005). SMS (short message service, or text messaging) is an extremely popular and still growing 2G mobile data service, especially with young adults (Finn, 2004; Prensky, 2005; MMA, 2006; Grinter & Eldridge, 2003), which makes it suitable as a learning technology. This short article presents and illustrates the concepts of SMS-enabled m-learning, describing a series of SMS learning scenarios derived from the literature. The defining features of the scenarios are identified and discussed, including future trends.