Numerical groundwater flow modeling under future climate change in the Central Rift Valley Lakes Basin; Ethiopia

\ua9 2024 The AuthorsStudy area: Katar and Meki subbasins, Rift Valley Lakes Basin, Ethiopia.Study focus: This research was carried out to characterized the recharge mechanism and quantify the steady-state groundwater balance and its sensitivity to future climate change. A groundwater simulation model was constructed and calibrated using a hydro-geo spatial dataset. Three regional climate models were used to assess the potential impact of changes in future precipitation on the recharge rate and groundwater balance components.New Hydrogeological Insight: Groundwater potential assessment depends on accurate estimation of the recharge rate. Precipitation contributed 11.95% and 11.96% to groundwater recharge in the Katar and Meki subbasins, respectively. The steady-state numerical groundwater model was calibrated and the model performed in the ranges of R2: 0.95–0.99; RMSE: 16.17–25.18; and MAE: 12.69–24.55, demonstrating \u27excellent\u27 model performance. In particular, the model exhibited high sensitivity to changes in the recharge rate and horizontal hydraulic conductivity. Future change in precipitation caused a reduction in groundwater potential in the range of 6.24–40.32% by the 2040 s and 2070 s, respectively, in the Katar subbasin. Likewise, the Meki Subbasin will experience a reduction in groundwater potential in the range of 0.29–37.17% by the 2040 s and 2070 s, respectively. These results emphasize how crucial it is for future water resource development initiatives to take into account climate variability for sustainable groundwater development

Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region

The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the -lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with -lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance

Cellular and Cytokine Responses in the Granulomas of Asymptomatic Cattle naturally infected with Mycobacterium bovis in Ethiopia

Cells (CD3+ T cell and CD68+ macrophages), cytokines (IFN-γ+ and TNF-α+) and effector molecule (iNOS+) responses were evaluated in the lymph nodes and tissue of cattle naturally infected with Detailed post mortem and immunohistochemical examinations of lesions were performed on 16 cows positive for single intradermal cervical comparative tuberculin (SICCT) test which were identified from dairy farms located around the Addis Ababa City. The severity of the gross lesion was significantly higher (p=0.003) in culture positive (n=12) cows than in culture negative (n=4). Immunohistochemical techniques showed that in culture positive cows, the mean immunolabeling fraction of CD3+ T cells decreased as the stage of granuloma increased from stage I to stage IV (p<0.001). In contrast, the immunolabelling fraction of CD68+ macrophages, IFN-γ+, TNF-α+ and iNOS+ increased from stage I to stage IV (p< 0.001). In culture negative cows, early stages showed a significantly higher fraction of CD68+ macrophages (p=0.03) and iNOS+ (p=0.007) when compared to culture positive cows. Similarly, at advanced granuloma stages, culture negative cows demonstrated significantly higher mean proportions of CD3+ T cells (p< 0.001) compared to culture positive cows. Thus, this study demonstrates that following natural infection of cows with , as the stage of granuloma increases from stage I to stage IV, the immunolabelling fraction of CD3+ cells decreases while the immunolabeling fraction of CD68+ macrophages, IFN-γ+, TNF-α+ and iNOS+ increases. [Abstract copyright: Copyright © 2020 Tulu et al.

Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii

<p>Abstract</p> <p>Background</p> <p>Recent advances in the field of metabolic engineering have been expedited by the availability of genome sequences and metabolic modelling approaches. The complete sequencing of the <it>C. reinhardtii</it> genome has made this unicellular alga a good candidate for metabolic engineering studies; however, the annotation of the relevant genes has not been validated and the much-needed metabolic ORFeome is currently unavailable. We describe our efforts on the functional annotation of the ORF models released by the Joint Genome Institute (JGI), prediction of their subcellular localizations, and experimental verification of their structural annotation at the genome scale.</p> <p>Results</p> <p>We assigned enzymatic functions to the translated JGI ORF models of <it>C. reinhardtii</it> by reciprocal BLAST searches of the putative proteome against the UniProt and AraCyc enzyme databases. The best match for each translated ORF was identified and the EC numbers were transferred onto the ORF models. Enzymatic functional assignment was extended to the paralogs of the ORFs by clustering ORFs using BLASTCLUST.</p> <p>In total, we assigned 911 enzymatic functions, including 886 EC numbers, to 1,427 transcripts. We further annotated the enzymatic ORFs by prediction of their subcellular localization. The majority of the ORFs are predicted to be compartmentalized in the cytosol and chloroplast. We verified the structure of the metabolism-related ORF models by reverse transcription-PCR of the functionally annotated ORFs. Following amplification and cloning, we carried out 454FLX and Sanger sequencing of the ORFs. Based on alignment of the 454FLX reads to the ORF predicted sequences, we obtained more than 90% coverage for more than 80% of the ORFs. In total, 1,087 ORF models were verified by 454 and Sanger sequencing methods. We obtained expression evidence for 98% of the metabolic ORFs in the algal cells grown under constant light in the presence of acetate.</p> <p>Conclusions</p> <p>We functionally annotated approximately 1,400 JGI predicted metabolic ORFs that can facilitate the reconstruction and refinement of a genome-scale metabolic network. The unveiling of the metabolic potential of this organism, along with structural verification of the relevant ORFs, facilitates the selection of metabolic engineering targets with applications in bioenergy and biopharmaceuticals. The ORF clones are a resource for downstream studies.</p

Trends in measles incidence and measles vaccination coverage in Nigeria, 2008-2018

INTRODUCTION: All WHO regions have set measles elimination objective for 2020. To address the specific needs of achieving measles elimination, Nigeria is using a strategy focusing on improving vaccination coverage with the first routine dose of (monovalent) measles (MCV1) at 9 months, providing measles vaccine through supplemental immunization activities (children 9-59 months), and intensified measles case-based surveillance system. METHODS: We reviewed measles immunization coverage from population-based surveys conducted in 2010, 2013 and 2017-18. Additionally, we analyzed measles case-based surveillance reports from 2008-2018 to determine annual, regional and age-specific incidence rates. FINDINGS: Survey results indicated low MCV1 coverage (54.0% in 2018); with lower coverage in the North (mean 45.5%). Of the 153,097 confirmed cases reported over the studied period, 85.5% (130,871) were from the North. Moreover, 70.8% (108,310) of the confirmed cases were unvaccinated. Annual measles incidence varied from a high of 320.39 per 1,000,000 population in 2013 to a low of 9.80 per 1,000,000 in 2009. The incidence rate is higher among the 9-11 months (524.0 per million) and 12-59 months (376.0 per million). Between 2008 and 2018, the incidence rate had showed geographical variation, with higher incidence in the North (70.6 per million) compare to the South (17.8 per million). CONCLUSION: The aim of this study was to provide a descriptive analysis of measles vaccine coverage and incidence in Nigeria from 2008 to 2018 to assess country progress towards measles elimination. Although the total numbers of confirmed measles cases had decreased over the time period, measles routine coverage remains sub-optimal, and the incidence rates are critically high. The high burden of measles in the North highlight the need for region-specific interventions. The measles program relies heavily on polio resources. As the polio program winds down, strong commitments will be required to achieve elimination goals

Cellular and Cytokine Responses in the Granulomas of Asymptomatic Cattle naturally infected with

Cells (CD3+ T cell and CD68+ macrophages), cytokines (IFN-γ+ and TNF-α+) and effector molecule (iNOS+) responses were evaluated in the lymph nodes and tissue of cattle naturally infected with Detailed post mortem and immunohistochemical examinations of lesions were performed on 16 cows positive for single intradermal cervical comparative tuberculin (SICCT) test which were identified from dairy farms located around the Addis Ababa City. The severity of the gross lesion was significantly higher (p=0.003) in culture positive (n=12) cows than in culture negative (n=4). Immunohistochemical techniques showed that in culture positive cows, the mean immunolabeling fraction of CD3+ T cells decreased as the stage of granuloma increased from stage I to stage IV (

Type 1 diabetes in Africa:an immunogenetic study in the Amhara of North-West Ethiopia

Aims/hypothesis We aimed to characterise the immunogenic background of insulin-dependent diabetes in a resource-poor rural African community. The study was initiated because reports of low autoantibody prevalence and phenotypic differences from European-origin cases with type 1 diabetes have raised doubts as to the role of autoimmunity in this and similar populations. Methods A study of consecutive, unselected cases of recently diagnosed, insulin-dependent diabetes (n = 236, ≤35 years) and control participants (n = 200) was carried out in the ethnic Amhara of rural North-West Ethiopia. We assessed their demographic and socioeconomic characteristics, and measured non-fasting C-peptide, diabetes-associated autoantibodies and HLA-DRB1 alleles. Leveraging genome-wide genotyping, we performed both a principal component analysis and, given the relatively modest sample size, a provisional genome-wide association study. Type 1 diabetes genetic risk scores were calculated to compare their genetic background with known European type 1 diabetes determinants. Results Patients presented with stunted growth and low BMI, and were insulin sensitive; only 15.3% had diabetes onset at ≤15 years. C-peptide levels were low but not absent. With clinical diabetes onset at ≤15, 16–25 and 26–35 years, 86.1%, 59.7% and 50.0% were autoantibody positive, respectively. Most had autoantibodies to GAD (GADA) as a single antibody; the prevalence of positivity for autoantibodies to IA-2 (IA-2A) and ZnT8 (ZnT8A) was low in all age groups. Principal component analysis showed that the Amhara genomes were distinct from modern European and other African genomes. HLA-DRB1*03:01 (p = 0.0014) and HLA-DRB1*04 (p = 0.0001) were positively associated with this form of diabetes, while HLA-DRB1*15 was protective (p &lt; 0.0001). The mean type 1 diabetes genetic risk score (derived from European data) was higher in patients than control participants (p = 1.60 × 10−7 ). Interestingly, despite the modest sample size, autoantibody-positive patients revealed evidence of association with SNPs in the well-characterised MHC region, already known to explain half of type 1 diabetes heritability in Europeans. Conclusions/interpretation The majority of patients with insulin-dependent diabetes in rural North-West Ethiopia have the immunogenetic characteristics of autoimmune type 1 diabetes. Phenotypic differences between type 1 diabetes in rural NorthWest Ethiopia and the industrialised world remain unexplained

AfriSenti: A Twitter Sentiment Analysis Benchmark for African Languages

Africa is home to over 2,000 languages from more than six language families and has the highest linguistic diversity among all continents. These include 75 languages with at least one million speakers each. Yet, there is little NLP research conducted on African languages. Crucial to enabling such research is the availability of high-quality annotated datasets. In this paper, we introduce AfriSenti, a sentiment analysis benchmark that contains a total of >110,000 tweets in 14 African languages (Amharic, Algerian Arabic, Hausa, Igbo, Kinyarwanda, Moroccan Arabic, Mozambican Portuguese, Nigerian Pidgin, Oromo, Swahili, Tigrinya, Twi, Xitsonga, and Yorùbá) from four language families. The tweets were annotated by native speakers and used in the AfriSenti-SemEval shared task 1. We describe the data collection methodology, annotation process, and the challenges we dealt with when curating each dataset. We further report baseline experiments conducted on the different datasets and discuss their usefulness

High-Resolution Geospatial Mapping of Zero-Dose and Underimmunized Children Following Nigeria's 2021 Multiple Indicator Cluster Survey/National Immunization Coverage Survey

BACKGROUND: “Zero-dose” children are those who are without any routine vaccination or are lacking the first dose of the diphtheria, tetanus, and pertussis–containing vaccine. Based on global estimates from the World Health Organization/United Nations Children’s Fund in 2022, Nigeria has the highest number of zero-dose children, with >2.3 million unvaccinated. METHODS: We used data from the 2021 Nigeria Multiple Indicator Cluster Survey/National Immunization Coverage Survey to identify zero-dose and underimmunized children. Geospatial modeling techniques were employed to determine the prevalence of zero-dose children and predict risk areas with underimmunized children at a high resolution (1 × 1 km). RESULTS: Zero-dose and underimmunized children are more prevalent in socially deprived groups. Univariate and multivariate bayesian analyses showed positive correlations between the prevalence of zero-dose and underimmunized children and factors such as stunting, contraceptive prevalence, and literacy. The prevalence of zero-dose and underimmunized children varies significantly by region and ethnicity, with higher rates observed in the country's northern parts. Significant heterogeneity in the distribution of undervaccinated children was observed. CONCLUSIONS: Nigeria needs to enhance its immunization system and coverage. Geospatial modeling can help deliver vaccines effectively to underserved communities. By adopting this approach, countries can ensure equitable vaccine access and contribute to global vaccination objectives