Crop type classification and spatial mapping in River Nile and Northern State, Sudan, using Sentinel-2 satellite data and field observation

Maintaining productive farmland necessitates precise crop mapping and identification. While satellite remote sensing makes it possible to generate such maps, there are still issues to resolve, such as how to choose input data and the best classifier algorithm, especially in areas with scarce field data. Accurate assessments of the land used for farming are a crucial part of national food supply and production accounting in many African countries, and to this end, remote sensing tools are being increasingly put to use. The aim of this study was to assess the potentiality of Sentinel-2 to distinguish and discriminate crop species in the study area and constraints on accurately mapping cropping patterns in the winter season in River Nile and Northern State, Sudan. The research utilized Sentinel-2 Normalized Different Vegetation Index (NDVI) at 10 m resolution, unsupervised and supervised classification method with ground sample and accuracy assessment. The results of the study found that the signatures of grain sorghum, wheat, okra, Vicia faba, alfalfa, corn, haricot, onion, potato, tomato, lupine, tree cover, and garlic have clear distinctions, permitting an overall accuracy of 87.38%, with trees cover, onion, wheat, potato, garlic, alfalfa, tomato, lupine and Vicia faba achieving more than 87% accuracy. Major mislabeling problems occurred primarily in irrigated areas for grain sorghum, okra, corn, and haricot, in wooded areas comprised of small parcels of land. The research found that high-resolution temporal images combined with ground data had potential and utility for mapping cropland at the field scale in the winter

Machado-Joseph disease in a Sudanese family links East Africa to Portuguese families and allows reestimation of ancestral age of the Machado lineage

Machado-Joseph disease (MJD/SCA3) is the most frequent dominant ataxia worldwide. It is caused by a (CAG)n expansion. MJD has two major ancestral backgrounds: the Machado lineage, found mainly in Portuguese families; and the Joseph lineage, present in all five continents, probably originating in Asia. MJD has been described in a few African and African-American families, but here we report the first diagnosed in Sudan to our knowledge. The proband presented with gait ataxia at age 24; followed by muscle cramps and spasticity, and dysarthria, by age 26; he was wheel-chair bound at 29 years of age. His brother had gait problems from age 20 years and, by age 21, lost the ability to run, showed dysarthria and muscle cramps. To assess the mutational origin of this family, we genotyped 30 SNPs and 7 STRs flanking the ATXN3_CAG repeat in three siblings and the non-transmitting father. We compared the MJD haplotype segregating in the family with our cohort of MJD families from diverse populations. Unlike all other known families of African origin, the Machado lineage was observed in Sudan, being shared with 86 Portuguese, 2 Spanish and 2 North-American families. The STR-based haplotype of Sudanese patients, however, was distinct, being four steps (2 STR mutations and 2 recombinations) away from the founder haplotype shared by 47 families, all of Portuguese extraction. Based on the phylogenetic network constructed with all MJD families of the Machado lineage, we estimated a common ancestry at 3211 ± 693 years ago. © 2023, The Author(s)

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Burnout among surgeons before and during the SARS-CoV-2 pandemic: an international survey

Background: SARS-CoV-2 pandemic has had many significant impacts within the surgical realm, and surgeons have been obligated to reconsider almost every aspect of daily clinical practice. Methods: This is a cross-sectional study reported in compliance with the CHERRIES guidelines and conducted through an online platform from June 14th to July 15th, 2020. The primary outcome was the burden of burnout during the pandemic indicated by the validated Shirom-Melamed Burnout Measure. Results: Nine hundred fifty-four surgeons completed the survey. The median length of practice was 10 years; 78.2% included were male with a median age of 37 years old, 39.5% were consultants, 68.9% were general surgeons, and 55.7% were affiliated with an academic institution. Overall, there was a significant increase in the mean burnout score during the pandemic; longer years of practice and older age were significantly associated with less burnout. There were significant reductions in the median number of outpatient visits, operated cases, on-call hours, emergency visits, and research work, so, 48.2% of respondents felt that the training resources were insufficient. The majority (81.3%) of respondents reported that their hospitals were included in the management of COVID-19, 66.5% felt their roles had been minimized; 41% were asked to assist in non-surgical medical practices, and 37.6% of respondents were included in COVID-19 management. Conclusions: There was a significant burnout among trainees. Almost all aspects of clinical and research activities were affected with a significant reduction in the volume of research, outpatient clinic visits, surgical procedures, on-call hours, and emergency cases hindering the training. Trial registration: The study was registered on clicaltrials.gov "NCT04433286" on 16/06/2020

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

Background Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide.Methods A multimethods analysis was performed as part of the GlobalSurg 3 study-a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital.Findings Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3.85 [95% CI 2.58-5.75]; p&lt;0.0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63.0% vs 82.7%; OR 0.35 [0.23-0.53]; p&lt;0.0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer.Interpretation Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised

The History of Gene Hunting in Hereditary Spinocerebellar Degeneration: Lessons From the Past and Future Perspectives

International audienceHereditary spinocerebellar degeneration (SCD) encompasses an expanding list of rare diseases with a broad clinical and genetic heterogeneity, complicating their diagnosis and management in daily clinical practice. Correct diagnosis is a pillar for precision medicine, a branch of medicine that promises to flourish with the progressive improvements in studying the human genome. Discovering the genes causing novel Mendelian phenotypes contributes to precision medicine by diagnosing subsets of patients with previously undiagnosed conditions, guiding the management of these patients and their families, and enabling the discovery of more causes of Mendelian diseases. This new knowledge provides insight into the biological processes involved in health and disease, including the more common complex disorders. This review discusses the evolution of the clinical and genetic approaches used to diagnose hereditary SCD and the potential of new tools for future discoveries

Identifier les gènes candidats prédisposant à la dégénérescence spinocérébelleuse héréditaire dans une cohorte de familles soudanaises

Les dégénérescences spinocérébelleuses héréditaires forme un groupe de troubles monogéniques qui partagent des mécanismes pathogènes communs et comprennent les paraplégies spastiques, l'ataxie cérébelleuse et l'ataxie spinocérébelleuse. Elles peuvent être pures ou complexe associant une neuropathie axonale ou des troubles cognitifs. Plus de 200 gènes et locus hérités via tous les modes de transmission mendéliens sont connus. L'hérédité autosomique récessive prédomine dans les communautés consanguines; cependant, une transmission autosomique dominante, de novo, et liée au chromosome X est parfois retrouvée. Le Soudan est composé de populations génétiquement diverses, mais il possède un des taux les plus élevés de consanguinité. Nous avons utilisé une combinaison de séquençage de nouvelle génération, de génotypage, d’analyse bioinformatique, et d'expérimentation fonctionnelle pour étudier 87 patients de 38 familles Soudanaises présentant ces maladies. Nous avons obtenu un diagnostic génétique dans 71-92% de ces familles, y compris sept familles dans lesquelles se transmettent des variants dans de nouveaux gènes candidats et trois familles associée à de nouveaux phénotypes dans des gènes connus. Ces résultats montrent l’hétérogénéité génétique de ces maladies et viennent compléter un peu plus leur nosologie avec des conséquences en diagnostic génétique en pratique médicale.Hereditary spinocerebellar degenerations are group of monogenic disorders that share common pathogenic mechanisms and include spastic paraplegia, cerebellar ataxia, and spinocerebellar ataxia. They can be pure or complicated with axonal neuropathy or mental impairment. More than 200 genes and loci inherited through all modes of Mendelian inheritance are known. Autosomal recessive inheritance predominates in consanguineous communities; however, autosomal dominant, de novo, and X-linked inheritance can also occur. Sudan is inhabited by genetically diverse populations, yet it has high rates of consanguinity. We used next-generation sequencing, genotyping, bioinformatics analysis, and functional experimentation to study 87 patients from 38 Sudanese families segregating multiple forms of these diseases. We reached a genetic diagnosis in 71-92% of these families, including seven families harboring variants in seven novel candidate genes and three families with novel phenotypes associated to known genes. These results highlight the heterogeneity of these diseases and add novel findings to their nosology which should have consequences in genetic diagnosis in clinical practice

B-type natriuretic peptide in hypertensive crises: Diagnostic use in hypertensive urgencies and emergencies

Background: It is not so easy to make a quick screening between hypertensive emergency (HE) and hypertensive urgency (HU), as it often requires sophisticated, complex and time consuming clinical, instrumental and diagnostic tests. Aim: To address the role of B-type natriuretic peptide (BNP) in hypertension and how to use it to differentiate HE from HU to alleviate possible complications. Methods: A total of 30 patients with rapid severe elevation of blood pressure (BP) admitted to the in-patient wards and critical care department, Cairo University, were included in a prospective, non-interventional study. On the basis of the clinical findings, patients were subdivided into two groups: Group I: 15 patients with HE with acute organ involvement and group II: 15 patients with HU without acute organ damage. Another 10 patients with chronic hypertension were taken as control group. BNP was measured in the blood at the time of admission based on the principle of competitive enzyme immunoassay. Results: There was no significant correlation between the patients’ age (58.5 ± 12) and BNP level (183.67 ± 216.3) (r = −0.17, p = 0.3) and also there was no significant difference in BNP blood level between males (223.35 ± 179.2) and females (131.77 ± 255.2) (p = 0.26) and it was significantly higher in HE patients (324.33 ± 233.16) than HU patients (43 ± 13.5) and control group (8.13 ± 5.8) with p-value of  0.05 in all). Receiver operator characteristic (ROC) curve was calculated for the use of BNP level as a diagnostic marker. The area under curve (AUC) for BNP as a diagnostic marker was 0.96. Conclusion: During hypertensive crises BNP blood level determination could have a role as a diagnostic tool for the screening of HE and its evaluation is very useful in patients admitted with acute and rapid elevation of BP to limit target organ damage