esa-sceva/satcom-chunk-collection huggingface dataset:
## 2 Discovery of CRISPR/Cas Systems  
The first report of interspaced palindromic repeat sequences was made by [PERSON] _et al_. who detected five 29 bp repeats with 32 bp spacers near the _iap_ gene of _Escherichia coli_[11]. Further reports were made for _Mycobacterium tuberculosis_[12], _Haloferax_ spp. [13] and _Archaeoglobus fulgidus_[14,15]; however, they were not detected in eukaryotic or virus sequences [15]. [PERSON] and co-workers performed a comparative _in silico_ study of those repetitive elements to determine structure and sequence similarity, as well as their phylogenetic distribution [16] showing that CRISPR display ahigh degree of homology between phylogenetically distant species and a wide distribution in bacteria and archaea. To date CRISPR/Cas systems have been found in almost 50% of bacterial and 85% of archaeal genome sequences available [17].  
Terminology for these repeated elements was inconsistent and included interspaced short sequence repeats (SSR) [18], **sp**acer **n**terspersed **d**irect **r**epeats (SPIDR) [15] or **s**short **r**egularly **s**paced **r**epeats (SRSRs) [16]. For simplicity, the name CRISPR (**c**lustered **r**egularly **s**l  
A critical discovery came in 2005 with three independent studies showing that spacers matched sequences of extrachromosomal origin, including phages, prophages and plasmids [21, 22, 23]. Furthermore, there was a positive correlation between the presence of spacers matching a particular phage and phage resistance [22, 23]. In combination with detailed bioinformatics analyses of the Cas proteins, it was hypothesized that CRISPR/Cas systems provide an RNAi-like mechanism of resistance against invading genetic elements [21, 22, 23, 24, 25].  
The first direct evidence that CRISPR/Cas could protect bacteria from phages or plasmids was provided by two key studies. Firstly, [PERSON] _et al_. obtained phage resistant mutants following phage challenge of _Streptococcus thermophilus_. The phage resistant strains had incorporated new spacers matching to the viral genome while removal or addition of spacers matching to the phages resulted in phage sensitivity or resistance, respectively [26]. Subsequently, [PERSON] and [PERSON] showed that CRISPR/Cas systems can also prevent both conjugation and transformation of plasmids in _Staphylococcus epidermidis_[27]. Recently, it was shown that the _Streptococcus pneumoniae_ CRISPR/Cas can prevent natural transformation. Non-capsulated _S. pneumoniae_ with CRISPR programmed to target capsule genes were unable to be transformed into capsulated strains during infection in mice [28].
## 1 Introduction
### Topographic Influences  
Topography plays a significant role in the concentration of UFPs, influencing their distribution and concentration in the environment because of the complicated effects of truck size, loading condition, speed, and the uphill and downhill movement of trucks on UFP emissions. In complex terrains, higher UFP concentrations occur because of the increased fuel burning caused by trucks requiring more engine power to ascend steep inclines.  
As [PERSON] notes, mountainous regions with rugged terrains are prone to trap pollutants near the ground, leading to elevated concentrations [31]. A study by [PERSON] et al. found that UFP concentrations near diesel truck routes in hilly areas were significantly higher than in flat terrains [32].  
A literature review study by [PERSON], [PERSON], and [PERSON], for instance, found that particulate matter tends to accumulate in steep regions [33]. Truck traffic near steep terrains enhances the emission of UFPs. Understanding these interactions is crucial for developing effective strategies to mitigate UFP pollution. This includes designing urban environments that minimize the adverse effects of topography on air quality, as well as implementing targeted emission controls and green spaces to improve ventilation and reduce particle buildup.
## 2 Methods
### Monitoring Data Preparation  
#### 2.2.1 SAR Data  
In this paper, we aimed to comprehensively analyze the deformation law of the slopes of the deep excavation channels of the South-North Water-Diversion Project in China. For this purpose, we acquired a set of 11 views of high-resolution, programmed TerraSAR-X uplink images. The selected StripMap mode offers a coverage width of 35 km and a spatial resolution of 3 m, rendering it suitable for fine deformation monitoring in key areas. The coverage of the programmed TerraSAR-X images is shown in Figure 2, and the related parameter information is shown in Table 1. SRTM-DEM with a 30 m grid resolution was selected as the reference data for the topographic phase removal process.
## 3 Results and Discussion  
### Films Characterization  
#### 3.1.1 Optical Properties  
The optical properties of the developed films were evaluated since high transparency of the packaging is required in the visible region to provide consumers with a visual control of the commodity's condition [25]. The transmittance indicates how much light can get through the material [29] and film transparency has been reported as a suitable tool to get information about the particle size of the dispersed particles [30]. Transparency values at 600 nm (t600) of all the developed films are shown in Table 1. No significant differences were found in transparency values for all the formulations, maintaining a good transparency even for PE/PA/PB13 and indicating that the LDPE/PA/PB systems were miscible blends as it can be seen in Figure 1.  
The obtained results are in accordance with previous studies that confirm a high transparency of neat LDPE films that was not significantly reduced by the addition of thermoplastic starch-clay hybrids, indicating the homogeneous dispersion of particles of both additives inside the polymer matrix [30]. Following this line, [PERSON] et al. [31] studied the incorporation of a volatile and aromatic compound such as thymol in PLA matrices. The reported results confirmed that the incorporation of an aromatic additive at a concentration level lower than 10 wt % did not affect dramatically the transparency of PLA films.
which is assigned to trans 1,4 units [34] was also present. These results revealed a good dispersion and distribution of PB in the extruded films because of a physically stable blend.
## 2 Materials and Methods
### Patient and Image Characteristics  
The dataset was composed of 436 patients, each with a set of assigned features. For convenience, the features were categorized into three subsets: Clinical, Radiomic, and Radiological.  
The clinical features available at hospital admission were divided into (a) continuous: age at the time of the CT exam and respiratory rate in breaths/min, and (b) binary: Sex of the patient, obesity status, fever at the hospital admission, hypertension condition, and smoking history.  
One-hundred and seventy-nine radiomic features were supported by the segmentation software, the majority of which were described in [4], with the addition of visceral fat and abdominal mass.  
The six radiological features included the acquisition parameters (kVp, current, and slice thickness) extracted from the DICOM header and Boolean features (such as the bilaterality of the lung damage, the presence of GGO, lung consolidations, and crazy paving) assessed by expert radiologists and extracted from the structured medical report.  
Different models were built using each of the feature groups to compare performance in a single and/or combined fashion and evaluate the potential benefits in terms of prognostic value. The structure of the training and testing, reported below in this section, was the same in all subsets regardless of the input features; the models were named using the same name as the family given in the input features. The outcome investigated was the mortality observed in 78/436 patients.
## 6 Conclusions  
High-precision positioning and navigation have seen significant advancements, with the integration of new technologies aimed at enhancing accuracy and reliability. As these  
Figure 23: Horizontal position RMSE comparison with respect to the number of available satellites and a simulated outage duration.  
Figure 22: Horizontal dilution of precision (HDOP) for different algorithms.  
technologies mature, their applications in various domains continue to expand. This study proposes two algorithms for GNSS/INS integration, evaluated using a real-road trajectory to assess the performance enhancement of smartphone sensors. The developed MDDA method was applied to all visible satellites, leading to a 13% improvement in 2D position RMSE and a 43% improvement in 3D position RMSE compared to the solution based on the Google weighting matrix. The LC algorithm was employed to further reduce position RMSE. The combined MDDA-LC algorithm achieved reductions of 25% and 66.8% in 2D and 3D position RMSE, respectively. Meanwhile, the MDDA-TC algorithm demonstrated even greater improvements, exceeding 90% in 2D and 75% in 3D position RMSE compared to the baseline solution. Additionally, the smartphone's GNSS receiver faced novel constraints, limiting the solution to the most accessible channels rather than utilizing all detected satellites within view. Both the MDDA-LC and MDDA-TC algorithms exhibited equivalent enhancements in 2D and 3D position RMSE, demonstrating their effectiveness in improving positioning accuracy.  
[PERSON] proposed the algorithm, participated in performing the experiments, and wrote the manuscript; [PERSON] and [PERSON] reviewed the manuscript and provided important suggestions to improve the algorithm; [PERSON] revised the manuscript; [PERSON] participated in preparing the algorithm, the experimental work, and the analysis of the results and revised the manuscript. All authors have read and agreed to the published version of the manuscript.  
This research received no external funding.  
Not applicable.  
Data are contained within the article.  
The authors declare no conflicts of interest.
# A Digital Twin Architecture to Optimize Productivity within Controlled Environment Agriculture
## 3 Digital Twin Architecture
### Technologies  
The technologies for instantiating the framework into an architecture are selected. These are depicted in Figure 4 and illustrated next:  
* Greenhouse \(\longrightarrow\) two DHT11 sensors to, respectively, measure indoor and outdoor temperature and relative humidity, 12 V fan and exhaust fan, and a 12 V mini submersible pump.
* Controller \(\longrightarrow\) Arduino Uno.
* Gateway \(\longrightarrow\) Raspberry Pi 4: Communicates with the storage layer through wireless communication and with Arduino through serial communication.
* Storage \(\longrightarrow\) phpMyAdmin: Administrator tool that manages a MySQL server for the data stored in the cloud.
* Intelligence Layer \(\longrightarrow\) Visual Studio: Programmed in Python, it enables the communication with the cloud through MySQL and with the gateway through the MQTT communication protocol.  
Figure 3: Prototype automated greenhouse utilized as case study. In the figure, the different components are indicated with numbers.  
* Digital Twin 1\(\longrightarrow\) EnergyPlus (energypilus.net): Builds energy software able to predict the microclimate within the greenhouse due to the ability to simulate the behaviour of heating, cooling, ventilation, and lighting systems, amongst others. It can communicate with Python-based IDEs through the EnergyPlus API (nrel.github.io/EnergyPlus/api/python).
* Digital Twin 2\(\longrightarrow\) DSSAT (dssat.net): Agricultural decision support system that allows the simulation of growth, development, and yield as a function of \"soil-plant-atmosphere dynamics\" [32]. It can communicate with Python-based IDEs through TraDSSAT (github.com/julienmalard/traDSSAT).  
EnergyPlus and DSSAT were selected as simulation software for the DTs since their integration has the premises to achieve the optimization of the productivity. EnergyPlus enables the optimization of control strategies related to the control of the crop microclimate [33], whereas DSSAT enables the optimization of treatments related to the crop management [34].
# Noise-Free Security Assessment of Eviction Set Construction Algorithms with Randomized Caches
## 5 Analysis of Eviction Set Construction Algorithms
### Behavior Analysis of Eviction Set Construction
#### 5.2.2 Single Address Elimination Algorithm  
Figure 5 shows the success rate and the time required to construct an eviction set from the different sized candidate sets using the single address elimination algorithm. As shown in Figure 5a, the success rate increased when the size of the candidate set contained more than 10,000 addresses.  
Due to the quadratic complexity of the algorithm, the simulations took a long time to find an eviction set. As shown in Figure 5b, the execution time could grow up to 160 s per simulation, which resulted in the algorithm needing more than two days to simulate a candidate set with 20,000 addresses.
# Chainlet-Based Ear Recognition Using Image Multi-Banding and Support Vector Machine
## 4 Experimental Results
### Execution Time  
Ear recognition methods can normally be categorized into two main groups: statistical-based and learning-based algorithms. Statistical-based methods, comprising PCA, eigenfaces, 2D-MBPCA and the anchor chainlet technique, extract some statistics or features directly from the image and use these features to find the best match, whereas learning-based methods employ a range of information comprising image statistics, features and other data extracted from the image dataset to train classifiers, e.g., neural networks and support vector machines such as the proposed CERMB-SVM method. Learning-based techniques then use the trained classifiers to find the best match for an input query image. Subsequently, learning-based ear recognition methods are considerably more computationally costly than their statistical-based counterparts.  
Figure 8: Region of interest of the CMC curves for ‘neural network and SVM’ (purple), GoogLeNet (green), VGG-based ensembles (red) and 2D-CERMB-SVM (blue) for the USTB I dataset [20]. The ‘ResNet18 and SVM’ method produced identical results to 2D-CERMB-SVM.  
Figure 7: Region of interest of the CMC curves for ‘BSIF and SVM’ (purple), GoogLeNet (green), ‘ResNet18 and SVM’ (orange), VGG-based ensembles (red) and 2D-CERMB-SVM (blue) for the IITD II dataset [19].  
Figure 10: The number of features and total eigenvector energy versus the number of frames, where the intersection reveals the number of frames for maximum attainable performance, for the USTB I dataset [20].  
Figure 9: The number of features and total eigenvector energy against the number of frames, where the intersection shows the number of frames for maximum attainable performance, for the IITD II dataset [19].  
To give the reader a sense of the computational complexity of the proposed CERMB-SVM algorithm with respect to statistical based algorithms and the state-of-the-art learning-based methods, Single Image PCA, eigenfaces [4], 2D-MBPCA [17], the anchor chainlet, 'BSIF and SVM' [15], GoogLeNet [11], 'ResNet18 and SVM' [12], VGG-based Ensembles [23], 'neural network and SVM' based [14] and the proposed CERMB-SVM methods were implemented in MATLAB. The resulting techniques were then executed on a Windows 10 personal computer equipped with a 7 th generation Intel core i7 processor, an NVIDIA GTX 1080 graphics card and a 512 GB Toshiba NVMe solid-state drive (no other applications, updates or background programs were running during the computation). The average computation time for processing an query image using each technique (learning-based algorithms were previously trained and their training time has not been contained in their measurement) was calculated using 100 randomly chosen query images from each dataset. The resulting measurements are presented in Table 4.
# Applications of Digital Twin across Industries: A Review
## 10 Maritime and Shipping  
Anything or any activity related to the ocean, sea, ships, navigation of ships from one destination to another, seafarers, etc., is represented by the maritime industry which also includes the transportation of passengers and freight on both inland and international waters [147,148]. Globally, around 80% of trade by volume and 70% by value is carried by sea, according to the United Nations (UN) [149], making it the most important means of transport for goods. Similar to the aviation industry, the main application of DT in this industry focuses on increasing the reliability of the assets, improving maintenance, and reducing operational costs.  
Military Sealift Command, the leading organization for providing military transport ships to the United States Navy and Department of Defense, with the help of GE, is building a DT for their cargo ammunition vessels [150]. The data collected from marine equipment, such as variable frequency drives, propulsion motors, diesel engines, and generators, are used to check the real-time performance of the vessel against the calculated one, and any performance deviations which indicate potential failure in the engines or other critical infrastructure are reported and resolved before it ever happens, thus improving their assets' and missions' availability, efficiency, operations, and readiness. The DT also makes remote monitoring and diagnostics possible [150].  
In 2019, DNV GL, the creator of the aforementioned WindGEMINI, which is also the world's leading classification society and a recognized advisor for the maritime industry, implemented DT technology on one of the world's largest crane vessels. The vessel demands constant inspections due to its large lifting capability of 14,000 tons, which puts the vessel under high stress. The DT makes reporting, assessing problems, maintenance planning, and predictive analysis easier, which results in huge cost savings [151]. DNV GLbelieves that DT can bring significant benefits to everyone involved in the maritime industry, including ship owners, equipment manufacturers, authorities, universities, maritime academies, and consultancy services [152].  
The DT technology is not restricted to just vessels/ships, but it is finding its way to ports as well. The Port of Rotterdam [153] has sensors throughout its docks that gather real-time data of the environment around and water conditions, which includes air temperature, wind speed, humidity, turbidity, water salinity, flow, levels, tides, and currents. The port even has 'Digital Dolphins', smart quay walls, and sensor-equipped buoys. In addition, they have a physical container, Container 42, fitted with a sensor, which uses AI to optimize the time for the vessel to sail and several cargos to carry. They are planning to become the first digital port by 2030.
###### Abstract  
The initial surface reaction of gallium nitride (GaN) grown by atomic layer deposition (GaN-ALD) was investigated using density functional theory (DFT) calculations. Trimethylgallium (TMG) and ammonia (NH\({}_{3}\)) were used as gallium (Ga) and nitrogen (N) precursors, respectively. DFT calculations at the B3 LYP/6-311+G(2d,p) and 6-31G(d) levels were performed to compute relative energies and optimize chemical structures, respectively. TMG adsorption on Si\({}_{15}\)H\({}_{18}\)-(NH\({}_{2}\))\({}_{2}\) and Si\({}_{15}\)H\({}_{20}\)=(NH)\({}_{2}\) clusters was modeled, where -NH\({}_{2}\) and =NH surface species served as adsorption sites. The reaction mechanisms in the adsorption and nitridation steps were investigated. The results showed that TMG can adsorb on both surface adsorption sites. In the initial adsorption stage, TMG adsorbs onto =NH- and -NH\({}_{2}\)-terminated Si(100) surfaces with activation energies of 1.11 and 2.00 eV, respectively, indicating that the =NH site is more reactive. During subsequent NH3 adsorption, NH\({}_{3}\) adsorbs onto the residual TMG on the =NH- and -NH\({}_{2}\)-terminated surfaces with activation energies of approximately 2.00 \(\pm\) 0.02 eV. The reaction pathways indicate that NH\({}_{3}\) adsorbs via similar mechanisms on both surfaces, resulting in comparable nitridation kinetics. Furthermore, this study suggests that highly reactive NH\({}_{2}\)\({}^{-}\) species generated in the gas phase from ionized NH\({}_{3}\) may help reduce the process temperature in the GaN-ALD process.  
gallium nitride; thin film; atomic layer deposition; semiconductor; DFT +
Footnote †: journal: Applied Sciences
## 3 Current Status of Research
### Air-To-Air Optical Communications  
In 2013, Changchun University of Science and Technology conducted a dynamic optical communication link test between airplanes. In the test, a dual fixed-wing airplane carrying an optical communication terminal, flying at an altitude of 4.7 km and with a distance of more than 100 km between the airplanes, successfully established a link connection within 20 s. When the data transmission rate is 2.5 Gbps and 1.5 Gbps, the BER is lower than 6.2 \(\times\) 10\({}^{-5}\) and 10\({}^{-7}\), respectively, which meets the test objectives. This test realizes laser high-speed information transmission between multiple nodes and provides essential support for developing a laser communication networking system. However, the test was not conducted in a complex environment, and the UAV optical communication payload faced challenges from various unfavorable factors, such as the airborne platform and external space environment [12; 13].  
In 2014, General Atomics launched the Air-Based Laser Communications System Demonstration Project, which planned to install laser communication equipment on the MQ-9 UAV platform. After two years of ground testing, the program completed flight test validation in 2017. By 2020, the company had completed the communication part of the test. It established a low-interception-rate and low-detection-rate UAV communication link, which was realized at 1.064 \(\upmu\)m and 1.550 \(\upmu\)m optical wavelengths, respectively [14; 15].  
In 2014, [PERSON] from Xi'an University of Technology successfully developed a wireless laser communication integrated operational machine. The core structure of the working machine is a building block design based on FPGA. On the transmitter side, it utilizes OOK (on-off keying) modulation. The receiving end performs a ping-pong operation through two FIFOs (first-in-first-out queues). This design controls the speed of information processing and restores the clock signal. The signals are processed by oversampling eight times, allowing the clock signal to be recovered. Duplex communication is realized, capable of transmitting two videos and 150 voice signals simultaneously at a transmission rate of up to 10 Mb/s, demonstrating excellent utility [16].  
In 2019, a research team from the University of Southern California used orbital angular momentum with multiple input and multiple output techniques to enhance the performance of an optical communication link between a UAV and a ground base station. As shown in Figure 8, in the experiment, a dual-channel 40 Gb/s high-speed link was realized  
Figure 7: FSO/RF communication link system model.  
using an inverse modulation reflector on the UAV, and the BER was controlled within an acceptable range, with a communication distance of 100 m [17].