Federated Learning for Medical Applications: A Taxonomy, Current Trends, Challenges, and Future Research Directions

With the advent of the IoT, AI, ML, and DL algorithms, the landscape of data-driven medical applications has emerged as a promising avenue for designing robust and scalable diagnostic and prognostic models from medical data. This has gained a lot of attention from both academia and industry, leading to significant improvements in healthcare quality. However, the adoption of AI-driven medical applications still faces tough challenges, including meeting security, privacy, and quality of service (QoS) standards. Recent developments in \ac{FL} have made it possible to train complex machine-learned models in a distributed manner and have become an active research domain, particularly processing the medical data at the edge of the network in a decentralized way to preserve privacy and address security concerns. To this end, in this paper, we explore the present and future of FL technology in medical applications where data sharing is a significant challenge. We delve into the current research trends and their outcomes, unravelling the complexities of designing reliable and scalable \ac{FL} models. Our paper outlines the fundamental statistical issues in FL, tackles device-related problems, addresses security challenges, and navigates the complexity of privacy concerns, all while highlighting its transformative potential in the medical field. Our study primarily focuses on medical applications of \ac{FL}, particularly in the context of global cancer diagnosis. We highlight the potential of FL to enable computer-aided diagnosis tools that address this challenge with greater effectiveness than traditional data-driven methods. We hope that this comprehensive review will serve as a checkpoint for the field, summarizing the current state-of-the-art and identifying open problems and future research directions.Comment: Accepted at IEEE Internet of Things Journa

Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars

Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources

Community engagement in Cutaneous Leishmaniasis research in Brazil, Ethiopia, and Sri Lanka: A decolonial approach for global health.

Cutaneous leishmaniasis (CL) is a parasitic skin disease endemic in at least 88 countries where it presents an urgent, albeit often "neglected" public health problem. In this paper, we discuss our model of decolonial community engagement in the ECLIPSE global health research program, which aims to improve physical and mental health outcomes for people with CL. The ECLIPSE program has four interlinked phases and underpinning each of these phases is sustained and robust community engagement and involvement that guides and informs all activities in ECLIPSE. Our decolonial approach implies that the model for community engagement will be different in Brazil, Ethiopia and Sri Lanka. Indeed, we adopt a critical anthropological approach to engaging with community members and it is precisely this approach we evaluate in this paper. The data and material we draw on were collected through qualitative research methods during community engagement activities. We established 13 Community Advisory Groups (CAGs): in Brazil ( = 4), Ethiopia ( = 6), and Sri Lanka ( = 3). We identified four overarching themes during a thematic analysis of the data set: (1) Establishing community advisory groups, (2) CAG membership and community representation, (3) Culturally appropriate and context-bespoke engagement, and (4) Relationships between researchers and community members. During our first period of ECLIPSE community engagement, we have debunked myths (for instance about communities being "disempowered"), critiqued our own practices (changing approaches in bringing together CAG members) and celebrated successes (notably fruitful online engagement during a challenging COVID-19 pandemic context). Our evaluation revealed a gap between the exemplary community engagement frameworks available in the literature and the messy, everyday reality of working in communities. In the ECLIPSE program, we have translated ideal(istic) principles espoused by such community engagement guidance into the practical realities of "doing engagement" in low-resourced communities. Our community engagement was underpinned by such ideal principles, but adapted to local sociocultural contexts, working within certain funding and regulatory constraints imposed on researchers. We conclude with a set of lessons learned and recommendations for the conduct of decolonial community engagement in global health research. [Abstract copyright: Copyright © 2022 Polidano, Parton, Agampodi, Agampodi, Haileselassie, Lalani, Mota, Price, Rodrigues, Tafere, Trad, Zerihun and Dikomitis.

Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources

Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet’s genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Al-susceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet. RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop

Early Use of Adjunctive Therapies for Pediatric Acute Respiratory Distress Syndrome:A PARDIE Study

Rationale: Few data exist to guide early adjunctive therapy use in pediatric acute respiratory distress syndrome (PARDS). Objectives: To describe contemporary use of adjunctive therapies for early PARDS as a framework for future investigations. Methods: This was a preplanned substudy of a prospective, international, cross-sectional observational study of children with PARDS from 100 centers over 10 study weeks. Measurements and Main Results: We investigated six adjunctive therapies for PARDS: continuous neuromuscular blockade, corticosteroids, inhaled nitric oxide (iNO), prone positioning, high-frequency oscillatory ventilation (HFOV), and extracorporeal membrane oxygenation. Almost half (45%) of children with PARDS received at least one therapy. Variability was noted in the median starting oxygenation index of each therapy; corticosteroids started at the lowest oxygenation index (13.0; interquartile range, 7.6–22.0) and HFOV at the highest (25.7; interquartile range, 16.7–37.3). Continuous neuromuscular blockade was the most common, used in 31%, followed by iNO (13%), corticosteroids (10%), prone positioning (10%), HFOV (9%), and extracorporeal membrane oxygenation (3%). Steroids, iNO, and HFOV were associated with comorbidities. Prone positioning and HFOV were more common in middle-income countries and less frequently used in North America. The use of multiple ancillary therapies increased over the first 3 days of PARDS, but there was not an easily identifiable pattern of combination or order of use. Conclusions: The contemporary description of prevalence, combinations of therapies, and oxygenation threshold for which the therapies are applied is important for design of future studies. Region of the world, income, and comorbidities influence adjunctive therapy use and are important variables to include in PARDS investigations

Predicting Mortality in Children With Pediatric Acute Respiratory Distress Syndrome:A Pediatric Acute Respiratory Distress Syndrome Incidence and Epidemiology Study

OBJECTIVES: Pediatric acute respiratory distress syndrome is heterogeneous, with a paucity of risk stratification tools to assist with trial design. We aimed to develop and validate mortality prediction models for patients with pediatric acute respiratory distress syndrome. DESIGN: Leveraging additional data collection from a preplanned ancillary study (Version 1) of the multinational Pediatric Acute Respiratory Distress syndrome Incidence and Epidemiology study, we identified predictors of mortality. Separate models were built for the entire Version 1 cohort, for the cohort excluding neurologic deaths, for intubated subjects, and for intubated subjects excluding neurologic deaths. Models were externally validated in a cohort of intubated pediatric acute respiratory distress syndrome patients from the Children's Hospital of Philadelphia. SETTING: The derivation cohort represented 100 centers worldwide; the validation cohort was from Children's Hospital of Philadelphia. PATIENTS: There were 624 and 640 subjects in the derivation and validation cohorts, respectively. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The model for the full cohort included immunocompromised status, Pediatric Logistic Organ Dysfunction 2 score, day 0 vasopressor-inotrope score and fluid balance, and PaO2/FIO2 6 hours after pediatric acute respiratory distress syndrome onset. This model had good discrimination (area under the receiver operating characteristic curve 0.82), calibration, and internal validation. Models excluding neurologic deaths, for intubated subjects, and for intubated subjects excluding neurologic deaths also demonstrated good discrimination (all area under the receiver operating characteristic curve ≥ 0.84) and calibration. In the validation cohort, models for intubated pediatric acute respiratory distress syndrome (including and excluding neurologic deaths) had excellent discrimination (both area under the receiver operating characteristic curve ≥ 0.85), but poor calibration. After revision, the model for all intubated subjects remained miscalibrated, whereas the model excluding neurologic deaths showed perfect calibration. Mortality models also stratified ventilator-free days at 28 days in both derivation and validation cohorts. CONCLUSIONS: We describe predictive models for mortality in pediatric acute respiratory distress syndrome using readily available variables from day 0 of pediatric acute respiratory distress syndrome which outperform severity of illness scores and which demonstrate utility for composite outcomes such as ventilator-free days. Models can assist with risk stratification for clinical trials

Community engagement in cutaneous leishmaniasis research in Brazil, Ethiopia, and Sri Lanka : a Decolonial approach for global health

Cutaneous leishmaniasis (CL) is a parasitic skin disease endemic in at least 88 countries where it presents an urgent, albeit often “neglected” public health problem. In this paper, we discuss ourmodel of decolonial community engagement in the ECLIPSE global health research program, which aims to improve physical and mental health outcomes for people with CL. The ECLIPSE program has four interlinked phases and underpinning each of these phases is sustained and robust community engagement and involvement that guides and informs all activities in ECLIPSE. Our decolonial approach implies that the model for community engagement will be different in Brazil, Ethiopia and Sri Lanka. Indeed, we adopt a critical anthropological approach to engaging with community members and it is precisely this approach we evaluate in this paper. The data andmaterial we draw on were collected through qualitative research methods during community engagement activities. We established 13 Community Advisory Groups (CAGs): in Brazil (n = 4), Ethiopia (n = 6), and Sri Lanka (n = 3). We identified four overarching themes during a thematic analysis of the data set: (1) Establishing community advisory groups, (2) CAG membership and community representation, (3) Culturally appropriate and context-bespoke engagement, and (4) Relationships between researchers and community members. During our first period of ECLIPSE community engagement, we have debunked myths (for instance about communities being “disempowered”), critiqued our own practices (changing approaches in bringing together CAG members) and celebrated successes (notably fruitful online engagement during a challenging COVID-19 pandemic context). Our evaluation revealed a gap between the exemplary community engagement frameworks available in the literature and the messy, everyday reality of working in communities. In the ECLIPSE program, we have translated ideal(istic) principles espoused by such community engagement guidance into the practical realities of “doing engagement” in low-resourced communities. Our community engagement was underpinned by such ideal principles, but adapted to local sociocultural contexts, working within certain funding and regulatory constraints imposed on researchers. We conclude with a set of lessons learned and recommendations for the conduct of decolonial community engagement in global health research.peer-reviewe

Risk factors of visceral leishmaniasis: a case control study in north-western Ethiopia

Background Visceral leishmaniasis (VL, also called “kala-azar”), is a life threatening neglected tropical infectious disease which mainly affects the poorest of the poor. VL is prevalent in Ethiopia particularly in the northwest of the country. Understanding the risk factors of VL infection helps in its prevention and control. The aim of the present study was to identify the factors associated with VL. Methods A case–control study was carried out during the period of January-July 2013 in northwest Ethiopia. Cases and controls were diagnosed using clinical presentation, the rk39 rapid diagnostic test and Direct Agglutination Test (DAT). A total of 283 (84.8% males versus 15.2% females) participants were interviewed. 90 cases and 193 controls were involved, matched by age, sex and geographical location with a ratio of 1:2 (case: controls). Univariate and backward multivariate conditional logistic regression were used to identify risk factors of VL. Results Elevated odds of VL was associated with goat ownership (OR = 6.4; 95%: confidence interval [Cl]: 1.5-28.4), living in houses with cracked wall (OR = 6.4; 95% Cl: 1.6-25.6), increased family size (OR = 1.3; 95% Cl: 1.0-1.8) and the number of days spent in the farm field (OR = 1.1; 95% Cl: 1.0-1.2). However, daily individual activities around the home and farm fields, mainly sleeping on a bed (OR = 0.2; 95%: Cl 0.03-0.9), sleeping outside the house under a bed net (OR = 0.1; 95% Cl: 0.02-0.36)] and smoking plant parts in the house during the night time (OR = 0.1; 95% Cl: 0.01-0.6) were associated with decreased odds of being VL case. Conclusion Our findings showed that use of bed net and smoke could be helpful for the prevention of VL in the area particularly among individuals who spend most of their time in the farm. VL control effort could be focused on improving housing conditions, such as sealing cracks and crevices inside and outside houses. Further research is warranted to elucidate the role of goats in the transmission of L. donovani, assess the impact of bed nets and the role of the traditional practice of smoking plants

Access to Water Source, Latrine Facilities and Other Risk Factors of Active Trachoma in Ankober, Ethiopia

Objective: This study aims to determine the prevalence and correlates of active trachoma in Ankober, Ethiopia. Methods: A cross-sectional community-based study was conducted during July 2007. A total of 507 children (ages 1–9 years), from 232 households were included in the study. All children were examined for trachoma by ophthalmic nurses using the WHO simplified clinical grading system. Interviews and observations were used to assess risk factors. Logistic regression procedures were used to determine associations between potential risk factors and signs of active trachoma. Results: Overall, the prevalence of active trachoma was found to be 53.9 % (95%CI 49.6%–58.2%). Presence of fly-eye (fly contact with the eyelid margin during eye examination) (Odds Ratio (OR) = 4.03 95 % CI 1.40–11.59), absence of facial cleanliness (OR = 7.59; 95%CI 4.60–12.52), an illiterate mother (OR = 5.88; 95%CI 2.10–15.95), lack of access to piped water (OR = 2.19; 95%CI 1.14–6.08), and lack of access to latrine facilities (OR = 4.36; 95%CI 1.49–12.74) were statistically significantly associated with increased risk of active trachoma. Conclusion: Active trachoma among children 1–9 years of age in Ankober is highly prevalent and significantly associated with a number of risk factors including access to water and latrine facilities. Trachoma prevention programs that include improved access to water and sanitation, active fly control, and hygiene education are recommended to lower the burde