Distributed Spatial Data Sharing: a new era in sharing spatial data

The advancements in information and communications technology, including the widespread adoption of GPS-based sensors, improvements in computational data processing, and satellite imagery, have resulted in new data sources, stakeholders, and methods of producing, using, and sharing spatial data. Daily, vast amounts of data are produced by individuals interacting with digital content and through automated and semi-automated sensors deployed across the environment. A growing portion of this information contains geographic information directly or indirectly embedded within it. The widespread use of automated smart sensors and an increased variety of georeferenced media resulted in new individual data collectors. This raises a new set of social concerns around individual geopricacy and data ownership. These changes require new approaches to managing, sharing, and processing geographic data. With the appearance of distributed data-sharing technologies, some of these challenges may be addressed. This can be achieved by moving from centralized control and ownership of the data to a more distributed system. In such a system, the individuals are responsible for gathering and controlling access and storing data. Stepping into the new area of distributed spatial data sharing needs preparations, including developing tools and algorithms to work with spatial data in this new environment efficiently. Peer-to-peer (P2P) networks have become very popular for storing and sharing information in a decentralized approach. However, these networks lack the methods to process spatio-temporal queries. During the first chapter of this research, we propose a new spatio-temporal multi-level tree structure, Distributed Spatio-Temporal Tree (DSTree), which aims to address this problem. DSTree is capable of performing a range of spatio-temporal queries. We also propose a framework that uses blockchain to share a DSTree on the distributed network, and each user can replicate, query, or update it. Next, we proposed a dynamic k-anonymity algorithm to address geoprivacy concerns in distributed platforms. Individual dynamic control of geoprivacy is one of the primary purposes of the proposed framework introduced in this research. Sharing data within and between organizations can be enhanced by greater trust and transparency offered by distributed or decentralized technologies. Rather than depending on a central authority to manage geographic data, a decentralized framework would provide a fine-grained and transparent sharing capability. Users can also control the precision of shared spatial data with others. They are not limited to third-party algorithms to decide their privacy level and are also not limited to the binary levels of location sharing. As mentioned earlier, individuals and communities can benefit from distributed spatial data sharing. During the last chapter of this work, we develop an image-sharing platform, aka harvester safety application, for the Kakisa indigenous community in northern Canada. During this project, we investigate the potential of using a Distributed Spatial Data sharing (DSDS) infrastructure for small-scale data-sharing needs in indigenous communities. We explored the potential use case and challenges and proposed a DSDS architecture to allow users in small communities to share and query their data using DSDS. Looking at the current availability of distributed tools, the sustainable development of such applications needs accessible technology. We need easy-to-use tools to use distributed technologies on community-scale SDS. In conclusion, distributed technology is in its early stages and requires easy-to-use tools/methods and algorithms to handle, share and query geographic information. Once developed, it will be possible to contrast DSDS against other data systems and thereby evaluate the practical benefit of such systems. A distributed data-sharing platform needs a standard framework to share data between different entities. Just like the first decades of the appearance of the web, these tools need regulations and standards. Such can benefit individuals and small communities in the current chaotic spatial data-sharing environment controlled by the central bodies

Molecular analysis of the clavulanic acid regulatory gene isolated from an Iranian strain of Streptomyces clavuligerus, PTCC 1709

Objective: The clavulanic acid regulatory gene (claR) is in the clavulanic acid biosynthetic gene cluster that encodes ClaR. This protein is a putative regulator of the late steps of clavulanic acid biosynthesis. The aim of this research is the molecular cloning of claR, isolated from the Iranian strain of Streptomyces clavuligerus (S. clavuligerus). Materials and Methods: In this experimental study, two different strains of S. clavuligerus were used (PTCC 1705 and DSM 738), of which there is no claR sequence record for strain PTCC 1705 in all three main gene banks. The specific designed primers were subjected to a few base modifications for introduction of the recognition sites of BamHI and ClaI. The claR gene was amplified by polymerase chain reaction (PCR) using DNA isolated from S. clavuligerus PTCC 1705. Nested-PCR, restriction fragment length polymorphism (PCR-RFLP), and sequencing were used for molecular analysis of the claR gene. The confirmed claR was subjected to double digestion with BamHI and ClaI. The cut claR was ligated into a pBluescript (pBs) vector and transformed into E. coli. Results: The entire sequence of the isolated claR (Iranian strain) was identified. The presence of the recombinant vector in the transformed colonies was confirmed by the colony-PCR procedure. The correct structure of the recombinant vector, isolated from the transformed E. coli, was confirmed using gel electrophoresis, PCR, and double digestion with restriction enzymes. Conclusion: The constructed recombinant cassette, named pZSclaR, can be regarded as an appropriate tool for site directed mutagenesis and sub-cloning. At this time, claR has been cloned accompanied with its precisely selected promoter so it could be used in expression vectors. Hence the ClaR is known as a putative regulatory protein. The overproduced protein could also be used for other related investigations, such as a mobility shift assa

Landform classification using a sub-pixel spatial attraction model to increase spatial resolution of digital elevation model (DEM)

The purpose of the present study is preparing a landform classification by using digital elevation model (DEM) which has a high spatial resolution. To reach the mentioned aim, a sub-pixel spatial attraction model was used as a novel method for preparing DEM with a high spatial resolution in the north of Darab, Fars province, Iran. The sub-pixel attraction models convert the pixel into sub-pixels based on the neighboring pixels fraction values, which can only be attracted by a central pixel. Based on this approach, a mere maximum of eight neighboring pixels can be selected for calculating of the attraction value. In the mentioned model, other pixels are supposed to be far from the central pixel to receive any attraction. In the present study by using a sub-pixel attraction model, the spatial resolution of a DEM was increased. The design of the algorithm is accomplished by using a DEM with a spatial resolution of 30 m (the Advanced Space borne Thermal Emission and Reflection Radiometer; (ASTER)) and a 90 m (the Shuttle Radar Topography Mission; (SRTM)). In the attraction model, scale factors of (S = 2, S = 3, and S = 4) with two neighboring methods of touching (T = 1) and quadrant (T = 2) are applied to the DEMs by using MATLAB software. The algorithm is evaluated by taking the best advantages of 487 sample points, which are measured by surveyors. The spatial attraction model with scale factor of (S = 2) gives better results compared to those scale factors which are greater than 2. Besides, the touching neighborhood method is turned to be more accurate than the quadrant method. In fact, dividing each pixel into more than two sub-pixels decreases the accuracy of the resulted DEM. On the other hand, in these cases DEM, is itself in charge of increasing the value of root-mean-square error (RMSE) and shows that attraction models could not be used for S which is greater than 2. Thus considering results, the proposed model is highly capable of increasing the spatial resolution of DEM (the new DEM with high spatial resolution). In the next step, in order to prepare the geomorphology map using topographic position index (TPI), the DEM with scale factor of (S = 2) was used, touching neighborhood serves as input. The landform classes were extracted by using TPI with the new DEM; consequently, the attraction model extraction showed details of landforms that make them more separable than the landform map prepared by utilizing the 90 m spatial resolution DEM. Moreover, the results showed that the landform of the 90 m spatial resolution DEM (S = 2, T = 2) and ASTER DEM 30 m were similar to each other, these results indicate a high accuracy of the proposed attraction model. Keywords: Landform, TPI, DEM, Sub-pixel, Spatial resolutio

Exon 10 CFTR gene mutation in male infertility

Background: About 10% of infertilities with obstructive azoospermia are congenital and caused by CF gene mutations. M469I mutation was observed for the first time in Taiwanese patients. This mutation not only causes CF, but also may be the origin of infertility too.Objective: In this study, we aimed in designing a rapid, reliable RFLP-PCR procedure for detection of M469I mutation. The correlation and association between M469I mutation with infertility was investigated in this study.Materials and Methods: one hundred ten patients (90 non obstructive and 20 obstructive) and 60 normal individuals were considered in this study. M469I mutation was detected using RFLP-PCR. This technique was completely designed for M469I genotyping, for the first time in our study. Amplification of the region surrounding the mutation in exon 10 of CFTR gene was then performed. RFLP analysis was carried out using the NdeI restriction enzyme.Results: All genomic DNA samples were genotyped successfully. M469I mutation was observed only in patients group. Therefore, genotype containing mutant allele (GT) has been detected only in the patients group. There was no significant correlation between GT and TT genotypes with infertility (p=0.437).Conclusion: The M469I mutation has only been observed in Exon 10 CFTR gene of infertile patients, not in the control group. This mutation causes congenital bilateral absence of vaz deferens and finally infertility. This indicates a strong association between the M469I mutation and male infertility. Therefore, this is a CF-causing CFTR mutation that could be considered as a cause of infertilit

‌RNA secondary structure and qRT-PCR analyses pertained to expressed anti-CD25 CAR in NK-92 cell line

Background and Objectives: Tumor-infiltrating regulatory T (TI-Treg) cells perform the significant function in cancer immune escape. In this study, the third generation CAR construct was designed against human CD25 antigen, the significant cell surface biomarker of TI-Tregs. Methods: Initially, the construct of anti-CD25 CAR was designed. Using RNAfold web server, the RNA secondary structure was evaluated. Also, utilizing lentiviral vectors, NK-92 cell line was transduced. Afterward, the expression level of anti-CD25 CAR RNA was assessed by qRT-PCR in NK-92 cells transduced with CAR and mock transfer vectors and also untreated cells. Results: The RNA secondary structure was stable. Also, the expression level of anti-CD25 CAR RNA in transduced NK-92 cells by pCDH-513B-1-anti-CD25 CAR transfer vector was significantly higher than transduced NK-92 cells by mock transfer vector and untreated cells (p˂0.0001). Conclusion: The present study on anti-CD25 CAR RNA showed that this type of CAR transcripts were stable and expressed at high level. In fact, this type of CAR can be further studied in the future as a tool to remove the cancer immune escape in all types of solid and liquid cancers

Analysis of HER2 gene amplification using Differential PCR in breast cancer patients of Isfahan Province

Background: Amplification of HER2 is seen in 20-30% of breast cancer cases. Measurement of HER2 gene amplification appears to be of vital importance in planning the treatment schedule for patients with breast carcinoma. The aim of our study was to evaluate HER2 amplification status in malignant and benign breast tumors by differential PCR (dPCR). Materials and Methods: The genomic DNA was extracted using the phenol/chloroform extraction procedure from 76 different breast tissues. Differential PCR was performed using the DNA samples isolated from fresh and paraffin- embedded breast cancer tissues. The relative copy number ratio of target gene (HER2) to control gene ( INF-γ ) was measured. dPCR products were then separated by electrophoresis using 2% agarose gel. The intensity of HER2 and INFγ bands were determined for each sample by ImageJ software. Results: According to the ratio between the band intensity of HER2 to INFγ in tumour and also normal samples, 7% and 26% rates of HER2 amplification were observed in benign and malignant samples respectively. The ratio showed a 2-5 fold increase in HER2 gene copy number for tissues with HER2 amplification whereas, a one-fold increase was found in other samples. Conclusion: Differential PCR provides a relatively rapid and inexpensive technique to assess the HER2 gene amplification, especially alongside immunohistochemistry as a routine assessing method