A systematic and thematic analysis of the top 100 cited articles on mRNA vaccine indexed in Scopus database.

The success of mRNA vaccines against SARS-CoV-2 implies that this technology can be applied to target any pathogen. However, the scientific production and research trends using the bibliometric method are still unknown. The top 100 most cited articles on mRNA vaccine research were obtained from the Scopus database from 1995 to 2021. Bibliometrix, an R-Package, and VOSviewer 1.6.11 were used for data analysis. There is a rapid growth in scientific outputs with a gradual increase in 2021. The United States produced 45 (45%) of the articles, followed by Germany with 15 (15%) and Israel with 10 (10%). The New England Journal of Medicine published the most papers in this field 13 (13%), followed by Nature 6(6%). Barney S. Graham was the most productive author among the top 100 most cited mRNA vaccine articles. University of Pennsylvania Perelman School of Medicine, US, was the top ranking institution, having 37 (37%). The visualization map clearly and spontaneously displayed the current state and research hot spots of mRNA research from a specific perspective. The most frequent keywords were COVID-19, vaccine, mRNA vaccine, mRNA, SARS-CoV-2, and immunogenicity, among others. A systematic review of the articles provided evidence that out of 100 articles, approximately 25 (25%) were focused on vaccine production and evaluation, followed by 26 (26%) in mRNA vaccine safety and efficacy, 23 (23%) were into mRNA vaccination, 23 (23%) considered risk factors associated with mRNA vaccination, while 8 (8%) of the articles covered the issue of mRNA vaccine delivery. In addition, 42% of the articles focused on COVID-19, 17% on cancer, 8% on influenza virus, 4% on COVID-19 and kidney disease, 3% COVID-19 and myocarditis, and 3% on rabies virus, among others. The findings of this systematic and thematic analysis provided the knowledge basis for further research on mRNA vaccines globally.

A Comparison Between Working and Nonworking Donkeys Welfare Issues in Nyala City, South Darfur, Sudan.

In impoverished nations, donkeys help people make a living. The welfare of donkeys in Sudan is neglected compared with developed countries. However, there is no information available about donkey welfare in Nyala. This study aimed to assess the welfare of donkeys in Nyala. Donkeys were divided into two groups (n = 50), working and nonworking. The donkeys' physical, emotional, and clinical parameters and an owner's interview were assessed. There were significant differences in body condition scores: 37% and 47% of working and nonworking donkeys, respectively, had ideal body condition scores, while 13% of working donkeys were emaciated. Of the working and nonworking 33% and 19% had hoof problems, respectively. Fifteen percent of working donkeys had ocular discharge, and 25% had wounds. In working donkeys, 7% and 5% depressive and aggressive behavioral responses, respectively, were observed. Furthermore, there were significant differences in tools used for hitting donkeys, with 33% and 17% of owners using a stick and whip, respectively, for hitting working donkeys. Eighty-two percent of owners feed their donkeys one to three times daily (50% working and 32% nonworking donkeys), and free access feeding was only observed in 18% of nonworking donkeys. There were no significant differences (P > .06) in emotional parameters. We conclude that working donkeys suffer from multiple welfare problems more than nonworking donkeys in Nyala. More awareness, veterinary services, and research are needed to improve donkey care in Nyala.

Natural adaptation and human selection of northeast African sheep genomes.

African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ∼54× for 130 samples (Ethiopia, Libya) and ∼20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.

Genomic signatures for drylands adaptation at gene-rich regions in African zebu cattle.

BACKGROUND: Indigenous Sudanese cattle are mainly indicine/zebu (humped) type. They thrive in the harshest dryland environments characterised by high temperatures, long seasonal dry periods, nutritional shortages, and vector disease challenges. Here, we sequenced 60 indigenous Sudanese cattle from six indigenous breeds and analysed the data using three genomic scan approaches to unravel cattle adaptation to the African dryland region. RESULTS: We identified a set of gene-rich selective sweep regions, detected mostly on chromosomes 5, 7 and 19, shared across African and Gir zebu. These include genes involved in immune response, body size and conformation, and heat stress response. We also identified selective sweep regions unique to Sudanese zebu. Of these, a 250 kb selective sweep on chromosome 16 spans seven genes, including PLCH2, PEX10, PRKCZ, and SKI, which are involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. CONCLUSIONS: Our results suggest that environmental adaptation may involve recent and ancient selection at gene-rich regions, which might be under a common regulatory genetic control, in zebu cattle.

Artificial Intelligence and Machine Learning in Cancer Research: A Systematic and Thematic Analysis of the Top 100 Cited Articles Indexed in Scopus Database.

INTRODUCTION: Cancer is a major public health problem and a global leading cause of death where the screening, diagnosis, prediction, survival estimation, and treatment of cancer and control measures are still a major challenge. The rise of Artificial Intelligence (AI) and Machine Learning (ML) techniques and their applications in various fields have brought immense value in providing insights into advancement in support of cancer control. METHODS: A systematic and thematic analysis was performed on the Scopus database to identify the top 100 cited articles in cancer research. Data were analyzed using RStudio and VOSviewer.Var1.6.6. RESULTS: The top 100 articles in AI and ML in cancer received a 33 920 citation score with a range of 108 to 5758 times. Doi Kunio from the USA was the most cited author with total number of citations (TNC = 663). Out of 43 contributed countries, 30% of the top 100 cited articles originated from the USA, and 10% originated from China. Among the 57 peer-reviewed journals, the "Expert Systems with Application" published 8% of the total articles. The results were presented in highlight technological advancement through AI and ML via the widespread use of Artificial Neural Network (ANNs), Deep Learning or machine learning techniques, Mammography-based Model, Convolutional Neural Networks (SC-CNN), and text mining techniques in the prediction, diagnosis, and prevention of various types of cancers towards cancer control. CONCLUSIONS: This bibliometric study provides detailed overview of the most cited empirical evidence in AI and ML adoption in cancer research that could efficiently help in designing future research. The innovations guarantee greater speed by using AI and ML in the detection and control of cancer to improve patient experience.

Global scientific research progress in mycetoma: a bibliometric analysis.

BACKGROUND: Mycetoma is a neglected tropical disease that attracts little attention in regard to research and publications and hence this study was undertaken to determine the trends and global scientific research output in mycetoma-related fields. METHODS: Mycetoma data were retrieved from the Web of Science (WoS) and Scopus databases. The MeSH Browser was used to extract relevant keywords. Biblioshiny software (R-studio cloud), VOSviewer v. 1.6.6 and SPSS software were used for data management. RESULTS: Research trends on mycetoma increased globally from 1999 to 2020. The results were 404 documents (4444 citations) in WoS and 513 documents (5709 citations) in Scopus, and the average number of citations per article was 11 in WoS and 11.13 in Scopus. There was a significant association between the total number of citations and the total citations per year in both WoS (r=0.833, p<0.0001) and Scopus (r=0.926, p<0.0001). Sudan, India, the Netherlands and Mexico were the top-ranking productive countries for mycetoma publications in WoS, while India, the USA and Mexico were the top-ranking countries in Scopus. Articles on mycetoma were mainly published in PLoS Neglected Tropical Diseases, the International Journal of Dermatology and the Journal of Clinical Microbiology. A. H. Fahal from the Mycetoma Research Centre, University of Khartoum, Sudan, had the highest number of citations in mycetoma research during 1999-2020, followed by W. W. J. van de Sande from the Erasmus Medical Centre, University of Rotterdam, the Netherlands, during 2003-2020. CONCLUSION: The analysis provides insight into a global overview of Mycetoma research. In addition, the analysis holds a better understanding of the development trends that have emerged in Mycetoma over the past 21 years, which can also offer a scientific reference for future research.

Addressing Africa's pandemic puzzle: Perspectives on COVID-19 transmission and mortality in sub-Saharan Africa.

To date, SARS-CoV-2 (the virus that causes COVID-19) has spread to almost every region of the world, infecting millions and resulting in the deaths of hundreds of thousands of people. Although it was predicted that Africa would suffer a massive loss of life due to this pandemic, the number of COVID-19 cases has been relatively low across the continent. Researchers have speculated that several factors may be responsible for this outcome in Africa, including the extensive experience that countries have with infectious diseases and the young median age of their populations. However, it is still important for African countries to adopt aggressive and bold approaches against COVID-19, in case the nature of the pandemic changes. This short review will summarize the status of the outbreak in Africa and propose possible reasons for current trends, as well as discuss interventions aimed at preventing a rapid increase in the number of COVID-19 cases in the future.

Association of genotype III of dengue virus serotype 3 with disease outbreak in Eastern Sudan, 2019.

BACKGROUND: Dengue fever (DF) is an arthropod-borne disease caused by dengue virus (DENV). DENV is a member of the genus Flavivirus in the family Flaviviridae. Recently, DENV has been reported as an important emerging infectious viral pathogen in Sudan. Multiple outbreaks and sporadic cases of DF have been frequently reported in the eastern region of Sudan. The present study was conducted to confirm DENV outbreak in Kassala State, eastern Sudan, 2019, and to provide some information on the molecular characterization of the DENV isolate associated with the disease outbreak. METHODS: A hundred serum samples were collected during the outbreak from residents of Kassala State, Sudan, 2019. ELISA was used to detect DENV non structural protein NS1 (DENV-NS1) in acute phase sera sampled during the disease outbreak. RT-PCR assays were used to amplify a fragment of the capsid/pre-membrane region (CprM) of the viral polyprotein gene. The PCR products of the amplified CprM region of the viral polyprotein gene were purified and partial sequences were generated and used to confirm the specificity of DENV sequences and to identify the virus serotype. Phylogenetic tree was constructed to determine the genotype of DENV associated with the outbreak. RESULTS: Using DENV-NS1 ELISA assay, DENV infection was confirmed in 23% sampled sera. The detection of DENV RNA was made possible using group-specific RT-PCR assay. The virus was serotyped as DENV serotype 3 (DENV-3) using DENV serotype-specific RT-PCR assay. Phylogenetic analysis of the partial CprM sequences of the viral polyprotein gene indicates that the virus belonged to genotype III of DENV-3. CONCLUSION: The scientific data presented in this investigation confirmed that genotype III of DENV-3 was associated with the disease outbreak in eastern Sudan, 2019. The study represents the first report on molecular characterization of DENV-3 in Sudan.

Genome Diversity and Signatures of Selection for Production and Performance Traits in Dromedary Camels.

Dromedary camels (Camelus dromedarius) are single-humped animals found throughout the deserts of Africa, the Arabian Peninsula, and the southwest of Asia. This well-adapted species is mainly used for milk and meat production, although some specific types exhibit superior running performance and are used in racing competitions. However, neither performance nor production camels are bred under intensive genomic selection programs with specific aims to improve these traits. In this study, the full genome sequence data of six camels from the Arabian Peninsula and the genotyping-by-sequencing data of 44 camels (29 packing and 15 racing) from Sudan were analyzed to assess their genome diversities, relationships, and candidate signatures of positive selection. Genome ADMIXTURE and principle component analyses indicate clear geographic separation between the Sudanese and the Arabian Peninsula camels, but with no population-specific genetic distinction within populations. Camel samples from the Arabian Peninsula show higher mean heterozygosity (0.560 ± 0.003) than those from Sudan (0.347 ± 0.003). Analyses of signatures of selection, using pooled heterozygosity (Hp) approach, in the Sudanese camels revealed 176, 189, and 308 candidate regions under positive selection in the combined and packing and racing camel populations, respectively. These regions host genes that might be associated with adaptation to arid environment, dairy traits, energy homeostasis, and chondrogenesis. Eight regions show high genetic differentiation, based on Fst analysis, between the Sudanese packing and racing camel types. Genes associated with chondrogenesis, energy balance, and urinary system development were found within these regions. Our results advocate for further detailed investigation of the genome of the dromedary camel to identify and characterize genes and variants associated with their valuable phenotypic traits. The results of which may support the development of breeding programs to improve the production and performance traits of this unique domesticated species.

Polyphenolic composition, enzyme inhibitory effects ex-vivo and in-vivo studies on two Brassicaceae of north-central Italy.

In this study, three different extracts (soxhlet, microwave and decoction) from two species of broccoli: Brassica oleracea L. convar. Italica botrytis (L.) Alef. var. cymosa Duch. (Broccolo Fiolaro) and Brassica oleracea acephala L. convar. acephala (DC.) Alef. var. sabellica L. (Cavolo Nero), which are commonly spread in north-central Italy, were tested for their enzyme inhibitory effects. Enzyme inhibitory effects were investigated against cholinesterases, tyrosinase, α-amylase and α-glucosidase. The soxhlet extracts had the highest inhibitory AChE effects with 1.08 mgGALAE/g (in Cavolo Nero) and 0.90 mgGALAE/g (in Broccolo Fiolaro). The significant tyrosinase inhibitory effect was observed in the soxhlet extract of Cavolo Nero with 11.93 mgKAE/g. In addition, we evaluated the antioxidant activity of Broccolo Fiolaro and Cavolo Nero on lipopolysaccharide (LPS)-stimulated bladder, kidney and liver specimens, ex vivo. We observed a significant reduction of both nitrite and malondialdehyde (MDA) following treatment that indicates a significant inhibitory effect on oxidative/nitrosative stress and lipoperoxidation, respectively. Additionally, the blunting effect induced by extracts on LPS-induced lactate dehydrogenase (LDH) activity further support a protective effect by both Broccolo Fiolaro and Cavolo Nero in bladder, kidney and liver. HPLC analysis revealed that catechin, epicatechin, vanillic and 3-hydroxy benzoic acids were the major components. The phenolic components may contribute to the observed enzyme inhibitory effects. in vivo tests also demonstrated that the extracts decreased the biochemical parameters in diabetic rats. Particularly, we observed the reduction of plasma glucose levels, urea and total cholesterol following oral administration, with the higher inhibitory effects exerted by Broccolo Fiolaro compared to Cavolo Nero. Overall, our results could provide new insights on the use of these Broccoli species not only as foods but also as functional and nutraceutical supplements.

Gum Arabic extracts protect against hepatic oxidative stress in alloxan induced diabetes in rats.

Gum Arabic (GA) from Acacia seyal and Acacia senegal is a branched-chain polysaccharide which has strong antioxidant properties, and has been used to reduce the experimental toxicity. Yet, the effects of GA on oxidative stress in type I diabetic rats have not been reported. The aim of the study was to investigate the effects of GA on oxidative stress in Alloxan induced diabetes in rats. The rats were divided into 3 groups (n=20 of each): control group, diabetic group injected with allaoxan, and diabetic group given 15% GA in drinking water for 8 weeks. Oxidative damage to liver tissue was evaluated by measurement of key hepatic enzymes, lipid peroxidation, antioxidant enzymes and expression of oxidative stress genes. Activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) were significantly (P<0.05) increased in GA group compared to diabetic and control groups. Treatment of GA decreased liver malondialdehyde (MDA), and increased glutathione (GSH). In addition, GA was significantly (P<0.05) reduced the activities of key liver enzymes, including alanine transaminase (ALT) and aspartate transaminase (AST). SOD, GPx and heat shock protein 70 (HSP70) mRNA were significantly increased in GA group compared to control and diabetic groups. Liver of all diabetic rats showed marked degeneration whereas slight degeneration was observed in GA treated rats compared to control. The results suggest that GA may protect liver by modulating the expression of oxidative stress genes, and thus can improve antioxidant status.

Association of lipoprotein lipase gene with coronary heart disease in Sudanese population.

Cardiovascular disease is stabilizing in high-income countries and has continued to rise in low-to-middle-income countries. Association of lipid profile with lipoprotein lipase gene was studied in case and control subject. The family history, hypertension, diabetes mellitus, smoking and alcohol consumption were the most risk factors for early-onset of coronary heart disease (CHD). Sudanese patients had significantly (P<0.05) lower TC and LDL-C levels compared to controls. Allele frequency of LPL D9N, N291S and S447X carrier genotype was 4.2%, 30.7% and 7.1%, respectively. We conclude that lipoprotein lipase polymorphism was not associated with the incidence of CHD in Sudan.

Molecular Characterization of Sudanese and Southern Sudanese Chicken Breeds Using mtDNA D-Loop.

The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only. Median joining networks analysis showed that haplotype LBB49 has the highest frequency. The hierarchal analysis of molecular variance (AMOVA) showed that genetic variation within the population was 88.6% and the differentiation among the population was 11.4%. When the populations was redefined into two geographical zones, rich and poor Savanna, the results were fractioned into three genetic variations: between individuals within population 95.5%, between populations within the group 0.75%, and genetic variation between groups 3.75%. The pair wise F st showed high genetic difference between Betwil populations and the rest with F st ranging from 0.1492 to 0.2447. We found that there is large number of gene exchanges within the Sudanese indigenous chicken (Nm = 4.622).

Construction, characterization and expression of full length cDNA clone of sheep YAP1 gene.

RT-PCR, 5'RACE, 3'RACE were used to clone sheep full length cDNA sequence of YAP1 (Yes-associated protein 1), eukaryotic expression plasmid and a mutant that cannot be phosphorylated at Ser42 was successfully constructed. The amino acid sequence analysis revealed that sheep YAP1 gene encoded water-soluble protein and its relative molecular weight and isoelectric point was 44,079.0 Da and 4.91, respectively. Sub-cellular localization of YAP1 was in the nucleus, it is hydrophilic non-transmembrane and non-secreted protein. YAP1 protein contained 33 phosphorylation sites, seven glycosylation sites and two WW domains. The secondary structure of YAP1 was mainly composed of random coil, while the tertiary structure of domain area showed a forniciform helix structure. YAP1 gene was expressed in different tissues, the highest expression was in kidney and the lowest was in hypothalamus. The CDS of sheep YAP1was amplified by RT-PCR from healthy sheep longissimus dorsi muscle, cloned into pMD19-T simple vector by T/A ligation. YAP1 coding region was further sub-cloned into pEGFP-C1 vector by T4 Ligase to construct a eukaryotic expression plasmid and then make the eukaryotic expression vector as the template to construct the phosphorylation site mutant. PCR, restriction enzyme and sequencing were used to confirm the recombinant plasmid. The sheep full-length YAP1 cDNA sequence is 1712 in length encoding 403 amino acids. It was confirmed that the sheep YAP1 CDS was correctly inserted into eukaryotic expression vector and serine had been mutated to alanine by PCR, restriction digestion and sequencing. The result showed that the recombinant plasmid pEGFP-C1-YAP1 and pEGFP-C1-YAP1 S42A was constructed correctly, this will help for further studies on the YAP1 protein expression and its biological activities.

Genome array of hair follicle genes in lambskin with different patterns.

Hu sheep lambskin comes from a specific breed of sheep of China. Hu sheep are considered a protected breed by the Chinese government. The hair follicles of these sheep have three types of waves, large, medium, and small. There are only few histological reports of Hu sheep lambskin, and there are no modern molecular or biological studies, so the molecular mechanisms underlying the formation of hair follicles with different patterns are not currently known. The aim of this article was to study the molecular mechanism of the formation of these types of hair follicles in Hu sheep. Histological and microscopic analysis indicated that the number of follicles with small waves was not significantly higher than the number of follicles with large waves (P>0.05). The diameters of primary and secondary small-wave follicles were significantly smaller than those of large-wave follicles (P<0.05; P<0.01). The ratio between the number primary follicles and the number of secondary follicles was significantly higher among small-wave follicles than among large-wave follicles (P<0.05). Differentially expressed genes in the skin tissue were screened using an Agilent gene chip and RT-PCR. Differential expression analysis revealed 3 groups of large waves and small waves; 1067, 2071, and 3879 differentially expressed genes; and 137 genes common to all 3 groups. Differentially expressed genes were classified using gene ontology. They were found to be mainly involved in cell differentiation, proliferation, apoptosis, growth, immune response, and ion transport. RT-PCR results of 4 differentially expressed genes were consistent with gene chip results. Combined with related literature, our results suggest that BMP7, MMP2, SNAI1, SFXN1, CDKNIC, MT3, and POU1F1 may have important effects on the formation of large-wave and small-wave hair follicles. This study may enrich knowledge of hair follicle development, and may identify the genes responsible for the formation of hair follicles with different patterns.

The Prevalence of Multi-Drug Resistance-1 Gene of Plasmodium Falciparum Malaria in Gezira State-Central Sudan

Abstract:Malaria parasite resistance to chloroquine poses a severe and increasing health problem in tropical countries. Implementing molecular markers for monitoring the drug resistance may be essential to overcome the problem. The aim of the present study is to investigate the prevalence of multi-drug resistance of p. falciparum parasite in malaria patients. Blood samples for DNA extraction were collected from the positive malaria patients. The prevalence of mutations in P. falciparum multi-drug resistant gene-1 (pfmdr-1) was detected by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) methods. Approximately; 74.1 of study populations are adults and 25.9 are children. Regression analysis shows a decrease in malaria incidence with increasing age. The prevalence of malaria is higher in males (58.6) compared to females (41.4). There were no statistical differences between malaria incidence and the socioeconomic level within the study population. The frequency of homozygous N/86 and Y/86 alleles were 51.7 and 37.9; respectively; and the heterozygous N/Y86 allele was 10.3.In conclusion the frequency of Pfmdr-1 N/Y86 allele among P. falciparum multi-drug resistant isolates support the hypothesis that Pfmdr-1 N/Y86 allele could be used as predictive marker to monitor multi-drug susceptibility in epidemiological surveys

Genetic differentiation and phylogeny relationships of functional ApoVLDL-II gene in red jungle fowl and domestic chicken populations.

A total of 243 individuals from Red Jungle Fowl (Gallus gallus spadiceus), Rugao, Anka, Wenchang and Silikes chicken populations were used for polymorphism analysis in functional apoVLDL-II gene by Restriction fragment length polymorphism and single strand conformation polymorphism markers. The results show that Anka population has highest gene diversity and Shannon information index, while Red jungle fowl shows highest effective number of allele. In addition, the higher coefficient of genetic differentiation (Gst) across all loci in apoVLDL-II was indicating that high variation is proportioned among populations. As expected total gene diversity (Ht) has upper estimate compared with within population genetic diversity (Hs) across all loci. The mean Gst value across all loci was (0.194) indicating about 19.4% of total genetic variation could be explained by breeds differences, while the remaining 80.6% was accounted for differences among individuals. The average apoVLDL-II gene flow across all loci in five chicken populations was 1.189. The estimates of genetic identity and distance confirm that these genes are significantly different between genetically fat and lean population, because fat type breed Anka shows highest distance with the other Silikes and Rugao whish are genetically lean. In addition, Wenchang and Red jungle fowl were found more closely and genetically related than the other breeds with 49.4% bootstrapping percentages, then they were related to Silikes by 100% bootstrapping percentages followed by Rugao and finally all of them are related with exotic fat breed Anka.