Systematizing FAIR research data management in biomedical research projects: a data life cycle approach

Biomedical researchers are facing data management challenges brought by a new generation of data driven by the advent of translational medicine research. These challenges are further complicated by the recent calls for data re-use and long-term stewardship spearheaded by the FAIR principles initiative. As a result, there is an increasingly wide-spread recognition that advancing biomedical science is becoming dependent on the application of data science to manage and utilize highly diverse and complex data in ways that give it context, meaning, and longevity beyond its initial purpose. However, current methods and practices in biomedical informatics remain to adopt a traditional linear view of the informatics process (collect, store and analyse); focusing primarily on the challenges in data integration and analysis, which are challenges only pertaining to a part of the overall life cycle of research data. The aim of this research is to facilitate the adoption and integration of data management practices into the research life cycle of biomedical projects, thus improving their capabilities into solving data management-related challenges that they face throughout the course of their research work. To achieve this aim, this thesis takes a data life cycle approach to define and develop a systematic methodology and framework towards the systematization of FAIR data management in biomedical research projects. The overarching contribution of this research is the provision of a data-state life cycle model for research data management in Biomedical Translational Research Projects. This model provides insight into the dynamics between 1) the purpose of a research-driven data use case, 2) the data requirements that renders data in a state fit for purpose, 3) the data management functions that prepare and act upon data and 4) the resulting state of data that is _t to serve the use case. This insight led to the development of a FAIR data management framework, which is another contribution of this thesis. This framework provides data managers the groundwork, including the data models, resources and capabilities, needed to build a FAIR data management environment to manage data during the operational stages of a biomedical research project. An exemplary implementation of this architecture (PlatformTM) was developed and validated by real-world research datasets produced by collaborative research programs funded by the Innovative Medicine Initiative (IMI) BioVacSafe 1 , eTRIKS 2 and FAIRplus 3.Open Acces

Image multiplexing using residue number system coding over MIMO-OFDM communication system

Image transmission over Orthogonal Frequency-Division Multiplexing (OFDM) communication system is prone to distortion and noise due to the encountered High-Peak-to-Average-Power-Ratio (PAPR) generated from the OFDM block. This paper studies the utilization of Residue Number System (RNS) as a coding scheme for digital image transmission over Multiple-Input-Multiple-Output (MIMO) – OFDM transceiver communication system. The use of the independent parallel feature of RNS, as well as the reduced signal amplitude to convert the input signal to parallel smaller residue signals, enable to reduce the signal PAPR, decreasing the signal distortion and the Bit Error Rate (BER). Consequently, improving the received Signal-to-Noise Ratio (SNR) and enhancing the received image quality. The performance analyzed though BER, and PAPR. Moreover, image quality measurement is achieved through evaluating the Mean Squared Error (MSE), Peak Signal to Noise Ratio (PSNR), and the correlation values between the initial and retrieved images. Simulation results had shown the performance of transmission/reception model with and without RNS coding implementation.

Olmesartan modulates proliferating cell nuclear antigen expression and improves dextran sulfate - induced ulcerative colitis in rats

Background: Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by sudden attacks of remissions and exacerbations with increased incidence of cancer colon. The present study aims to determine the possible ameliorative mechanisms of Olmesartan in UC induced experimentally in rat.Methods: Adult albino rats were randomly grouped into control, UC model non treated group: Rats received dextran sodium (DSS) orally for 21 days with intra-colic administration of acetic acid (AA) for 3 consecutive days for induction of UC model, Olmesartan (1, 5, 10mg/kg/orally) and UC + Olmesartan in different doses (1 mg, 5 mg and 10 mg/kg/day orally).Results: DSS orally and AA intra-rectal produced sever colitis manifested by significant weight loss, watery and bloody diarrhea. Significant increase in serum and colonic tissue levels of tumor necrosis factor alpha and interleukine-1β. Pro-apoptotic Bax protein, myeloperoxidase (MPO) and expression of PCNA significantly increased in colonic tissue. Lipid peroxidation (MDA) significantly elevated while reduced glutathione (GSH) was depleted in UC non-treated group compared with normal control group. Treatment with Olmesartan (5 mg, 10 mg/kg/day, orally) ameliorated mucosal ulceration and improved inflammatory signs as confirmed by immunohistochemical and histopathological examination. Also, Olmesartan significantly attenuates overexpression of PCNA in colonic mucosa.Conclusions: Our results point out that Olmesartan had ameliorative effects on UC by its anti-inflammatory, antioxidant and anti-apoptotic effects and attenuates PCNA expression which is the main cause of dysplasia and colorectal cancer. Olmesartan may be a promising therapeutic drug for treating UC and protection of colorectal carcinoma. 

Wound Surface Area and Colony Count of Various Modes of Phototherapy

Background: The degree of tissue damage caused by related inflammatory and immunological sequelae poses a major therapeutic treatment problem in burn wounds. Chronic wounds frequently have a significant bioburden and pathogens that are resistant to antibiotics. This review article discusses present research on phototherapy, which is believed to be useful in managing wound bioburden and promoting healing.Objective: To evaluate the wound healing efficacy of polarized light therapy (BLT) against low-level laser therapy (GaAs laser) in order to determine which is more efficient and successful at speeding burn healing.Subject and methods: The current study enrolled thirty patients having partial thickness thermal burn on the forearm (dermal burn). They were selected from Burn Unit at Legislation Association Hospital for Burns & Oncology. They were randomly assigned into two equal groups: Group (A) that included fifteen patients who received the BLT with mean age of 28.8 ± 2.51 years old and group (B) that enrolled fifteen patients who received LLLT with mean age of 29.6 ± 2.79 years old. Both groups also received traditional physical therapy and conservative treatment for the burn site three times weekly for four weeks.Results: Group A and B showed a significant reduction in colony count and wound surface area after treatment in comparison to that before treatment (p > 0.001). In group A, the colony count and wound surface area decreased by 38.63% and 55.1% respectively, but in group B, by 15.6% and 37.92% respectively.Conclusion: Both polarized light therapy and low-level laser therapy had a therapeutic efficiency on wound healing, but BLT is more efficient and more successful in the acceleration of the burned wounds healing

Corrected qt interval in normal egyptian neonates: Comparison to corrected qt interval of other ethnic groups

Long QT syndromes (LQTs) is a familial cardiovascular disorder characterized by abnormal cardiac repolarization and sudden death from ventricular fibrillation Possible acquisition of standardized neonatal screening method to identify children with (LQTs) has led to interest in establishing normal values for neonatal QT intervals.Aim of the workto compare corrected QT interval in normal Egyptian neonates to published values of other ethnic groups.Subjects and methodsThis cross sectional study was conducted on neonates following up in Children’s Hospital Ain Shams University, with post natal ages ranging from 8 to 28days (mean 13.91±3.97days). They were subjected to: history taking, clinical examination, Echocardiography and 12 lead ECG assessment of corrected QT interval using Bazetts formula Results: Cut off point of LQTc was >0.44s, while that of short QTc was< 0.29s significant increase in mean QTc values and LQTc %was found in upper Egypt than Delta (p 0.026, 0.01). Eighty five percent of neonates had normal QTc (0.300–0.450s), 9% had LQTc (>0.45s) and 6% had short QTc (<0.300s) significant increase in short QTc was found in PT than FT while significant increase in LQTc was found in FT (P=0.020, 0.019).ConclusionCut off point was >0.44s for LQTc and < 0.29s for short QTc in studied Egyptian neonates A higher percentage of patients with LQTc was found in Upper Egypt than Delta, and in FT than PT. Higher percentage of SQTc was found in PT than FT. Further studies are needed to confirm our results

Impact of Nutritional Educational Program on the Nutritional Habits and Status among Older Adults at Qena City, Egypt

Background: The age-related changes of the gastrointestinal tract, availability of the food and the functional ability affect the nutritional intake among elderly people. Most of the diseases originate from malnutrition especially among the vulnerable group as older adults. Therefore, the aim of this study is to improve older adults' nutritional habits. The study followed a quesi experimental research design and was carried out in the Elderly Club at Qena City. Sample; One hundred and six older adults who fulfilled the inclusion criteria participated in this study and assigned randomly into fifty-three intervention group and fifty-three control group. Two tools were used to collect the data; Tool I Structured Interview Form and tool II Mini-Nutritional Assessment Scale. The results of this study revealed that there are no statistically significant differences of frequency of usual food consumed per week between pre-test and Posttest among the intervention or control group (P > 0.05). There are significance differences between pre-test and Posttest of food preparation method and the substances used in cooking among only the intervention group. It was concluded from the current study that the intervention improved the nutritional habits. Based on the study results, it will be useful implement the nutritional educational program at all older organizations which provide services to older adults such as elderly homes, elderly clubs, and hospitals in Egypt

Techno-economic Feasibility of Renewable Energy Based Stand-alone Energy System for a Green House: Case Study

As the negative impacts of fossil fuel consumption for power generation become increasingly globally evident—particularly the effects of greenhouse gas (GHG) emissions on climate change—so too does the conversely positive potential of renewable energies to reduce the rate of damaging environmental impacts as energy demand grows. In addition to the clear environmental advantage, stand-alone renewable energy power generation options offer energy security and stability in regions where socio-political issues or geographic location might otherwise pose access limitations on fuel and/or electric grid power, particularly in remote communities. This paper discusses the techno-economic considerations for renewable energy power systems in residential community applications. A case study for a residential house in New Cairo in Egypt compares two different renewable energy systems that meet typical electrical demand for this region. Economic assessment—in terms of system net present cost (NPC) and levelized cost of electricity (LCOE)—provide measures for system performance comparison and optimization. The LCOE for system-I and system-II are found to be $0.359/kWh and$0.373/kWh, respectively

Analysis of gene expression data from non-small celllung carcinoma cell lines reveals distinct sub-classesfrom those identified at the phenotype level

Microarray data from cell lines of Non-Small Cell Lung Carcinoma (NSCLC) can be used to look for differences in gene expression between the cell lines derived from different tumour samples, and to investigate if these differences can be used to cluster the cell lines into distinct groups. Dividing the cell lines into classes can help to improve diagnosis and the development of screens for new drug candidates. The micro-array data is first subjected to quality control analysis and then subsequently normalised using three alternate methods to reduce the chances of differences being artefacts resulting from the normalisation process. The final clustering into sub-classes was carried out in a conservative manner such that subclasses were consistent across all three normalisation methods. If there is structure in the cell line population it was expected that this would agree with histological classifications, but this was not found to be the case. To check the biological consistency of the sub-classes the set of most strongly differentially expressed genes was be identified for each pair of clusters to check if the genes that most strongly define sub-classes have biological functions consistent with NSCLC

The International Natural Product Sciences Taskforce (INPST) and the power of Twitter networking exemplified through #INPST hashtag analysis

Background: The development of digital technologies and the evolution of open innovation approaches have enabled the creation of diverse virtual organizations and enterprises coordinating their activities primarily online. The open innovation platform titled "International Natural Product Sciences Taskforce" (INPST) was established in 2018, to bring together in collaborative environment individuals and organizations interested in natural product scientific research, and to empower their interactions by using digital communication tools. Methods: In this work, we present a general overview of INPST activities and showcase the specific use of Twitter as a powerful networking tool that was used to host a one-week "2021 INPST Twitter Networking Event" (spanning from 31st May 2021 to 6th June 2021) based on the application of the Twitter hashtag #INPST. Results and Conclusion: The use of this hashtag during the networking event period was analyzed with Symplur Signals (https://www.symplur.com/), revealing a total of 6,036 tweets, shared by 686 users, which generated a total of 65,004,773 impressions (views of the respective tweets). This networking event's achieved high visibility and participation rate showcases a convincing example of how this social media platform can be used as a highly effective tool to host virtual Twitter-based international biomedical research events