Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome from Paired Samples Improves the Power of Comprehensive COVID-19 Host-Viral Characterization

Previous transcriptome profiling studies showed significantly upregulated genes and altered biological pathways in acute COVID-19. However, changes in the transcriptional signatures during a defined time frame are not yet examined and described. The aims of this study included viral metagenomics and evaluation of the total expression in time-matched and tissue-matched paired COVID-19 samples with the analysis of the host splicing profile to reveal potential therapeutic targets. Prospective analysis of paired nasopharyngeal swabs (NPS) and blood (BL) samples from 18 COVID-19 patients with acute and resolved infection performed using Kallisto, Suppa2, Centrifuge, EdgeR, PantherDB, and L1000CDS2 tools. In NPS, we discovered 6 genes with changed splicing and 40 differentially expressed genes (DEG) that yielded 88 altered pathways. Blood samples yielded 15 alternatively spliced genes. Although the unpaired DEG analysis failed, pairing identified 78 genes and 242 altered pathways with meaningful clinical interpretation and new candidate drug combinations with up to 65% overlap. Metagenomics analyses showed SARS-CoV-2 dominance during and after the acute infection, with a significant reduction in NPS (0.008 vs. 0.002, p = 0.019). Even though both NPS and BL give meaningful insights into expression changes, this is the first demonstration of how the power of blood analysis is vastly maximized by pairing. The obtained results essentially showed that pairing is a determinant between a failed and a comprehensive study. Finally, the bioinformatics results prove to be a comprehensive tool for full-action insights, drug development, and infectious disease research when designed properly.
Trends in Outcomes of Major Intracerebral Haemorrhage in a National Cohort of Very Preterm Born Infants in Switzerland

Background: Major brain lesions, such as grade 3 intraventricular haemorrhage (G3-IVH) and periventricular haemorrhagic infarction (PVHI) are among the main predictors for poor neurodevelopment in preterm infants. In the last decades advancements in neonatal care have led to a general decrease in adverse outcomes. Aim: To assess trends of mortality and neurodevelopmental impairment (NDI) in a recent Swiss cohort of very preterm infants with grade 3 intraventricular haemorrhage (G3-IVH) and periventricular haemorrhagic infarction (PVHI). Methods: In this retrospective population-based cohort study, rates of mortality, and NDI at 2 years corrected age were reported in infants born at 24–29 weeks gestational age (GA) in Switzerland in 2002–2014, with G3-IVH and/or PVHI. Results: Out of 4956 eligible infants, 462 (9%) developed G3-IVH (n = 172) or PVHI (n = 290). The average mortality rates for the two pathologies were 33% (56/172) and 60% (175/290), respectively. In 2002–2014, no change in rates of mortality (G3-IVH, p = 0.845; PVHI, p = 0.386) or NDI in survivors (G3-IVH, p = 0.756; PVHI, p = 0.588) were observed, while mean GA decreased (G3-IVH, p = 0.020; PVHI, p = 0.004). Multivariable regression analysis showed a strong association of G3-IVH and PVHI for both mortality and NDI. Death occurred after withdrawal of care in 81% of cases. Conclusion: In 2002–2014, rates of mortality and NDI in very preterm born infants with major brain lesions did not change. The significant decrease in mean GA and changing hospital policies over this time span may factor into the interpretation of these results.
Al-Kitab Journal for Pure Sciences

: In the era of data-driven applications and resource-constrained devices, the need for lightweight algorithms has become increasingly important. Lightweight algorithms refer to computational techniques that strike a balance between efficiency and resource utilization, making them well-suited for low-power devices, embedded systems, and scenarios with limited computational capabilities. For the new encryption method PRESENT
A Federated Byzantine Agreement Model to Operate Offline Electric Vehicle Supply Equipment

Providing equitable and resilient electric vehicle supply equipment (EVSE) to remote locations with limited access to the Internet infrastructure is one of the paradoxes in the decarbonization plan. In this paper, we develop an electric vehicle (EV) charging management system comprised of offline EVSEs based on a Federated Byzantine Agreement (FBA) system. To enable offline peer-to-peer (P2P) authentication between the user’s device (UD) and EVSE stations, we use a distributed certificate management based on Shamir’s algorithm and blind signing approach using the ring signature. We introduce extended FBA for charge point operator (FBA-CPO) systems and include explicit operational functions to ensure the ledger dissemination and scalability of the network. We specifically employ a pre-authorized mechanism for deferral vouchers using a pre-signed and weighted signing method. In the FBA-CPO network, each charger records all transactions on a local ledger and publicly publishes ledgers through random UD nodes. Under a generalization of the property of the federated quorum system, the proposed approach could provide a reliable network centrality with or without offline EVSEs. Eventually, we examined the performance of the proposed model using a system of real devices and their digital twins. Results show the FBA-CPO satisfies all functional and cross-cutting requirements for a consistent transnational mechanism.
Uppsalas biotekniska industriella system : En ekonomisk-geografisk studie av interaktion, kunskapsspridning och arbetsmarknadsrörlighet

The main purpose of the thesis is to study industrial transformation and growth within a local cluster of biotech activities in Uppsala, Sweden. A combination of theoretical approaches is used to address questions of why certain regions become more competitive: the cluster approach, innovation systems theory, and the technological systems approach. First, the industrial system is mapped in order to identify important local actors and structures. Secondly, by using interviews, a questionnaire, and a longitudinal database, key relations are studied from a spatial point of view. Four different fields of interaction are studied: business and market interaction; interaction with investors; collaborative and overall social interaction; and labor market interaction. The importance of the local milieu varies depending on the types of interaction in focus. Business interaction is predominantly global. Relations with investors are mainly regional and focused to the broader Stockholm region. The local milieu in Uppsala is more significant with respect to formal cooperation and collaboration, especially between local academy and industry actors, as well as informal interaction and social networks. The local milieu also seems to be important for knowledge transfer on the labor market. The creation of innovations and competitiveness is not just an outcome of buyer-supplier linkages, but is also a result of both formal and informal interaction occurring between industry and actors in the institutional and environmental setting, where knowledge, skills and information can be traded and/or transferred. Thus, the presence of knowledge intensive local actors and the quality of the relations is an important factor for the creation of industrial transformation and growth.
Design of TID-Tolerant ADCs in Multivoltage Domain Based on Body Effect

Total ionizing dose (TID) irradiation induces parameter drift and increases the leakage current in high-voltage analog-to-digital converters (ADCs) fabricated with thick-gate-oxide metal-oxide-semiconductor field-effect transistors (MOSFETs). In serious cases, these changes can affect the conversion performance of ADCs chips. In this study, the functional failures of high-voltage ADCs in multivoltage-domain circuits were examined after TID irradiation using simulation studies and experimental measurements. Accordingly, a circuit- and layout-based strategy was proposed to improve radiation tolerance. The reinforced circuit was fabricated by applying the characteristics of multivoltage domains and a combination of the body effect and TID effect. A charge pump unit was added to reduce TID irradiation. Furthermore, layout reinforcement was performed based on a commercial process by adopting an enclosed gate and isolation ring. The integral nonlinearity (INL) of the unreinforced device drifted by −18.11 least significant bit (LSB) after 30-krad (Si) irradiation. However, the INL of the reinforced device drifted by only 0.51 and 1.68 LSB after 30- and 100-krad (Si) irradiation, respectively. Hence, the total dose resistance of the reinforced device was more than ten times that of the unreinforced device. Consequently, a multivoltage-domain radiation-tolerant ADC with a TID tolerance of 100 krad (Si) could be generated.
Assimilation de données de télédétection pour le suivi des surfaces continentales : Mise en oeuvre sur un site expérimental

Le travail realise dans le cadre de cette these porte sur l'assimilation de donnees de teledetection pour le suivi des surfaces continentales. Les variables analysees sont l'etat hydrique du sol et la biomasse de la vegetation, sur la jachere du site experimental SMOSREX, de 2001 a 2004, au sud-ouest de Toulouse. Quatre methodes d'assimilation (EKF, EnKF, 1D-VAR et T-VAR) ont ete mises en œuvre dans le modele ISBA-A-gs de Meteo-France, et comparees. La methode 1D-VAR est la plus performante, aussi bien pour la qualite des analyses qu'en temps de calcul. Cette methode a ete appliquee a l'assimilation simultanee des observations de l'humidite de la surface et de l'indice foliaire, ainsi qu'aux mesures de teledetection realisees sur le site. L'assimilation ameliore la simulation de controle, a condition d'introduire un point de fletrissement dynamique (cela est particulierement utile pendant les periodes de forte secheresse). Les effets d'une incertitude sur les precipitations sont evalues.
Occupational Stress Affects Well-Being and Job Performance of Doctors: A Case Study in the Covid-19 Epidemic Context

Objective: The goal of the study is to demonstrate the impact of work stress on the well-being and performance of doctors in the context of the Covid-19 epidemic. Method: In this study, quota sampling based on the criteria such as gender, age, education background, working place is used to collect data. The survey areas are major cities in Vietnam, including Ho Chi Minh City, Da Nang City, and Can Tho City. After the data screening step, the study collects 252 observations. The study applies structural equation modeling to analyze the data. Results: The result has shown factors constituting doctors’ occupational stress include work overload, pressure from superiors, time pressure, income pressure, working conditions, and workplace relationships. Stress at work negatively affects doctors' well-being and performance. Besides, the study has pointed out a positive relationship between perceived happiness and doctors’ performance. Conclusions: Hospital administrators need to control the causes of work pressure to improve the feeling of happiness and performance. The causes include work overload, pressure from superiors, time pressure, income pressure, working conditions, and workplace relationships. In particular, work overload needs to be paid the most attention.
Trait Association and their Contribution in Yield Improvement in Spring Wheat (Triticum aestivum L)

The present investigation was conducted at the Breeder Seed Production Unit, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur, M.P., India during November to April, (Rabi season), 2021 to 2022 analyse grain yield and its attributing traits of wheat by correlation and path coefficient analysis. The twenty genotypes were in randomized complete block design with three replications. The results indicated that the biological yield per plant had highly significant correlation followed by harvest index with a moderate positive value and is significant with the grain yield per plant. Similarly the analysis of direct and indirect effects shows that the plant height, flag leaf length, flag leaf width, days to 50% flowering, grains per spike, biological yield per plant, and harvest index had positive direct effect on grain yield per plant. Hence it may be considered that traits namely, plant height, flag leaf length, flag leaf width, days to 50% flowering, grains per spike, biological yield per plant, and harvest index may be utilized for yield improvement breeding strategies in wheat. However, biological yield and harvest index will be given prime importance during selection of traits, due to their significant association and having a direct or indirect effect in crop yield improvement.
Image-to-Patient Registration in Computer-Assisted Surgery of Head and Neck: State-of-the-Art, Perspectives, and Challenges

Today, image-guided systems play a significant role in improving the outcome of diagnostic and therapeutic interventions. They provide crucial anatomical information during the procedure to decrease the size and the extent of the approach, to reduce intraoperative complications, and to increase accuracy, repeatability, and safety. Image-to-patient registration is the first step in image-guided procedures. It establishes a correspondence between the patient’s preoperative imaging and the intraoperative data. When it comes to the head-and-neck region, the presence of many sensitive structures such as the central nervous system or the neurosensory organs requires a millimetric precision. This review allows evaluating the characteristics and the performances of different registration methods in the head-and-neck region used in the operation room from the perspectives of accuracy, invasiveness, and processing times. Our work led to the conclusion that invasive marker-based methods are still considered as the gold standard of image-to-patient registration. The surface-based methods are recommended for faster procedures and applied on the surface tissues especially around the eyes. In the near future, computer vision technology is expected to enhance these systems by reducing human errors and cognitive load in the operating room.
The economic impact of water supply disruption from the Selangor River, Malaysia

The insidious economic impact of water disruption has received less attention compared to palpable climate disasters, but climate change and water security concerns call for investigation on cost consequences of property values and business losses in an already fragile water supply-demand balance in many developing countries. The economic impact of frequent water supply disruptions from the Selangor River in Malaysia due to technical issues, water pollution, and climate-related problems was estimated using the stock flow measure to assess property at risk, and survey to estimate business loss. The findings revealed that commercial, residential, and industrial property valued at RM459,041 million in 2020 in the State of Selangor and parts of Kuala Lumpur, were at risk due to frequent water supply disruptions. A survey of small and medium enterprises from the manufacturing, construction, and services sectors revealed that 46% of the respondents were affected with losses amounting to RM2,053 million. The total economic impact of water supply disruption in 2020, combining both property value at risk and business loss, is amounted to RM461,094 million, which accounted for 34% of Malaysia's GDP. A number of recommendations are made to prevent the widespread occurrence of water disruptions.
Relationships between Community Festival Participation, Social Capital, and Subjective Well-Being in a Cross-Cultural Context

This study explores the relationships among social capital, community festival participation, and subjective well-being (SWB). It examines the mediating role of festival participation between social capital and SWB. The dataset Social Well-being Survey in Asia from the Philippines and Thailand was collected using nationwide surveys in 2016. The total number of respondents was 1057 in the Philippines and 982 in Thailand. The results affirm several determinants related to SWB, which is composed of happiness and overall life satisfaction. The models show significant relationships among festival participation, social capital, and SWB. The results indicate strong associations among social capital with family and relatives, festival participation, and SWB. The interaction effects between the two countries are included. Structural and cognitive social capital with kinship groups were important determinants in facilitating festival participation, and positively associated with SWB. Moreover, the results identify the mediating effect of festival participation between social capital with family and relatives and SWB. The results can provide similarities and differences in the relationships among social capital and kinship groups, community festival participation, and SWB between the Philippines and Thailand. This study offers important empirical evidence of a cross-cultural study in the context of the Philippines and Thailand.
Potential Diagnostic Utility of microRNAs in Gastrointestinal Cancers

Abstract Early detection of gastrointestinal cancers is beneficial for patient survival and prognosis. MiRNAs have been shown to be potential cancer biomarkers that can be used to diagnose cancers. MiRNAs are single-stranded, small non-coding RNAs that are involved in the post-transcriptional regulation of the expression of different oncogenes. Cancer tissues contain miRNAs that play a special role in the etiology of cancer development or limiting cancer suppression. Dysregulation of miRNAs occurs in a variety of malignancies, including gastrointestinal cancers. MiRNAs are stable and protected against degradation by RNase, which enables their detection in tissues and biological fluids. The results of many studies suggest that miRNAs have a relatively higher diagnostic efficiency in distinguishing cancer patients from healthy people. The researchers have identified many miRNA signature in the blood for the detection of gastrointestinal cancers. This review focuses on the role and potential utility of miRNAs in the early detection, prognosis and evaluation of the treatment effectiveness of gastrointestinal cancers.
Effect of Switching to Once-Weekly Semaglutide on Non-Alcoholic Fatty Liver Disease: The SWITCH-SEMA 1 Subanalysis

Non-alcoholic fatty liver disease (NAFLD) is an important common comorbidity in individuals with type 2 diabetes (T2DM). Although some glucagon-like peptide-1 receptor agonists (GLP-1RAs) have beneficial effects on NAFLD, the efficacy of once-weekly semaglutide has not been established. This was a subanalysis of the SWITCH-SEMA 1 study, a multicenter, prospective, randomized, parallel-group trial comparing switching from liraglutide or dulaglutide to once-weekly semaglutide in subjects with T2DM (SWITCH) versus continuing current GLP-1RAs (Continue) for 24 weeks. This subanalysis consisted of participants who were suspected to have NAFLD [fatty liver index (FLI) ≥ 30]. In total, 58 participants met the criteria of this subanalysis. There were no statistical differences in baseline characteristics between the SWITCH (n = 31) and Continue groups (n = 27). FLI significantly improved during treatment in the SWITCH group (68.6 to 62.7) but not in the Continue group (71.1 to 72.3) (p < 0.01). The improvement of FLI in the SWITCH group was greater in switching from dulaglutide to semaglutide and significantly correlated with older age (p = 0.016) and lower baseline FLI (p < 0.01). The multiple linear regression analysis revealed that the switch from dulaglutide was associated with an improvement in FLI (p = 0.041). Switching from conventional GLP-1RAs to once-weekly semaglutide might be beneficial for individuals with NAFLD complicated with T2DM.
Investigation of Egg Weight, Ovarian Follicles Morphology and Growth Differentiation Factor 9 mRNA Expression in Potchefstroom Koekoek Chicken Breed

The growth differentiation factor 9 ( GDF9 ) gene plays a vital role in the growth and maturation of ovarian follicles in laying hens. However, its messenger ribonucleic acid (mRNA) expression levels in preovulatory ovarian follicles of indigenous chickens remain poorly understood. The study aimed to identify the association between egg weight and egg quality traits, ovarian follicles morphology, and mRNA expression levels of the GDF9 gene in pre-ovulatory ovarian follicles of the South African Potchefstroom Koekoek chicken breed. The correlation results showed that egg weight (EW) had a positively high significant correlation ( p< 0.01) with egg width (EWD), yolk weight (YW), shell surface area (SSA), albumen weight (AW), albumen ratio (AR) and egg volume (EV), and a positive significant correlation ( p< 0.05) with egg length (EL). The Student’s T-test results revealed that the numbers of large yellow follicles were significantly lower ( p< 0.05) than those of small yellow follicles. ANOVA findings showed that there was a significant difference ( p< 0.05) in the average weight of the large yellow follicles. The quantitative Reverse Transcription Polymerase Chain Reaction (RT-qPCR) findings indicated that there were significant differences ( p< 0.05) in the mRNA expression levels of the GDF9 gene in preovulatory ovarian follicles of the Potchefstroom Koekoek chicken breed. The mRNA expression was more abundant in F1 and F4 than in other ovarian follicles.
Machine Learning-Assisted Analysis of Electrochemical Biosensors

Machine learning (ML) is effective at handling multiparameter and nonlinear problems owing to its self-learning ability. ML is used in biosensors to predict the species or concentration of an analyte. In this work, the ML-assisted classification of electrochemical biosensor measurement data are presented to predict KCl and glucose concentrations. Experiments were carried out to obtain capacitance response for KCl concentrations of 10–100 mM using the electrochemical impedance spectroscopy technique. The amperometric method was used to obtain the current response for various glucose concentrations ranging from 0.01 to 5 mM. The multiple ML-based classifiers were used for the training and testing of impedimetric and amperometric datasets using MATLAB. The confusion matrices were obtained for different ML-classifiers and their performance was evaluated based on accuracy, precision, recall, and training time. The receiver operating characteristics were also examined to determine the efficiency of prediction. The neural network models were found to be the best-performing ML-based classifiers with the highest accuracy and precision for both impedimetric and amperometric datasets.
Siloed discourses: a year-long study of twitter engagement on the use of CRISPR in food and agriculture

Gene editing technologies are emerging as powerful tools for agricultural development, spurring both hopes and concerns in society. To understand emerging discourses and coalitions around the role of CRISPR gene editing in food and agriculture we map the main actors and themes emerging from English-speaking Twitter networks over the course of one year (2021). Scientific actors are the most active and best networked in the debate. They promote a positive image of CRISPR gene editing and actively work to strengthen their network. A smaller but equally distinct group comprises civil society actors, who voice skepticism towards the technology and sometimes questions scientists’ claims, but without eliciting responses from the scientists. We conclude that emerging discourse coalitions forming around the topic of CRISPR in food and agriculture on Twitter are siloed, with limited interaction between contrasting perspectives.