Ensuring sample quality for biomarker discovery studies - Use of ict tools to trace biosample life-cycle

The growing demand of personalized medicine marked the transition from an empirical medicine to a molecular one, aimed at predicting safer and more effective medical treatment for every patient, while minimizing adverse effects. This passage has emphasized the importance of biomarker discovery studies, and has led sample availability to assume a crucial role in biomedical research. Accordingly, a great interest in Biological Bank science has grown concomitantly. In biobanks, biological material and its accompanying data are collected, handled and stored in accordance with standard operating procedures (SOPs) and existing legislation. Sample quality is ensured by adherence to SOPs and sample whole life-cycle can be recorded by innovative tracking systems employing information technology (IT) tools for monitoring storage conditions and characterization of vast amount of data. All the above will ensure proper sample exchangeability among research facilities and will represent the starting point of all future personalized medicine-based clinical trials

Food Characterization of the Spotted Pimelodid Fish Pimelodus Maculatus From a Polluted Urban River in Argentina

On the present study, the nourishment and the digestive system of a population of the spotted pimelodid Pimelodus maculatus Lacepède 1803 from a polluted urban river in Argentina were analyzed (Reconquista River, Buenos Aires province). The specimens are characterized by having benthic habits and an omnivore diet. In their intestinal content, a diversity of components was identified. Such components were grouped into ten alimentary items, with dietary variations according to body size while the longitude of the intestine remained proportional to standard length. Microbiological analysis in the gills, stomach and intestine showed the occurrence of Staphylococcus aureus, Escherichia coli and Salmonella sp. Fungi and yeast were also detected. Bacterial accounts were very high both in the analyzed organs as well in water samples. The ecological and sanitary significance of the identified bacteria is discussed

A Tuberculin Skin Test Survey and the Annual Risk of Mycobacterium tuberculosis Infection in Gambian School Children.

BACKGROUND: A Tuberculin skin test (TST) survey was conducted to assess the prevalence of latent TB Infection (LTBI) and to estimate the annual risk of M. tuberculosis infection (ARTI) in Gambian school children. The results are expected to contribute to understanding of Tuberculosis epidemiology in The Gambia. METHODS: This was a nationwide, multi-cluster survey in children aged 6-11 years. Districts, 20 of 37, were selected by probability proportional to size and schools by simple random sampling. All TST were performed using the Mantoux method. Height and weight measurements were obtained for all participants. We calculated prevalence of LTBI using cut-off points of 10mm, the mirror and mixture modelling methods. RESULTS: TST readings were completed 13,386 children with median age of 9 years (interquartile range [IQR] 8-10 years). Mixture analysis yielded a cut-off point of 12 mm, and LTBI prevalence of 6.9% [95%CI 6.47-7.37] and the ARTI was 0.75% [95%CI 0.60-0.91]. LTBI was associated gender and urban residence (p <0.01). Nutritional status was not associated with non-reactive TST or sizes of TST indurations. ARTI did not differ significantly by age, gender, BCG vaccination or residence. CONCLUSIONS: This estimates for LTBI prevalence and ARTI were low but this survey provides updated data. Malnutrition did not affect estimates of LTBI and ARTI. Given the low ARTI in this survey and the overlapping distribution of indurations with mixture modelling, further surveys may require complementary tests such as interferon gamma release assays or novel diagnostic tools

Does insecticide resistance contribute to heterogeneities in malaria transmission in The Gambia?

BACKGROUND: Malaria hotspots, areas with consistently higher than average transmission, may become increasingly common as malaria declines. This phenomenon, currently observed in The Gambia, may be caused by several factors, including some related to the local vectors, whose contribution is poorly understood. METHODS: Using WHO susceptibility bioassays, insecticide resistance status was determined in vector populations sampled from six pairs of villages across The Gambia, each pair contained a low and high prevalence village. RESULTS: Three vector species were observed (23.5% Anopheles arabiensis, 31.2% Anopheles gambiae, 43.3% Anopheles coluzzii and 2.0% An. coluzzii × An. gambiae hybrids). Even at a fine scale, significant differences in species composition were detected within village pairs. Resistance to both DDT and deltamethrin was more common in An. gambiae, most markedly in the eastern part of The Gambia and partly attributable to differing frequencies of resistance mutations. The Vgsc-1014F target site mutation was strongly associated with both DDT (OR = 256.7, (95% CI 48.6-6374.3, p < 0.001) and deltamethrin survival (OR = 9.14, (95% CI 4.24-21.4, p < 0.001). A second target site mutation, Vgsc-1575Y, which co-occurs with Vgsc-1014F, and a metabolic marker of resistance, Gste2-114T, conferred additional survival benefits to both insecticides. DDT resistance occurred significantly more frequently in villages with high malaria prevalence (p = 0.025) though this did not apply to deltamethrin resistance. CONCLUSION: Whilst causality of relationships requires further investigation, variation in vector species and insecticide resistance in The Gambia is associated with malaria endemicity; with a notably higher prevalence of infection and insecticide resistance in the east of the country. In areas with heterogeneous malaria transmission, the role of the vector should be investigated to guide malaria control interventions

Ranking Malaria Risk Factors to Guide Malaria Control Efforts in African Highlands

INTRODUCTION: Malaria is re-emerging in most of the African highlands exposing the non immune population to deadly epidemics. A better understanding of the factors impacting transmission in the highlands is crucial to improve well targeted malaria control strategies. METHODS AND FINDINGS: A conceptual model of potential malaria risk factors in the highlands was built based on the available literature. Furthermore, the relative importance of these factors on malaria can be estimated through "classification and regression trees", an unexploited statistical method in the malaria field. This CART method was used to analyse the malaria risk factors in the Burundi highlands. The results showed that Anopheles density was the best predictor for high malaria prevalence. Then lower rainfall, no vector control, higher minimum temperature and houses near breeding sites were associated by order of importance to higher Anopheles density. CONCLUSIONS: In Burundi highlands monitoring Anopheles densities when rainfall is low may be able to predict epidemics. The conceptual model combined with the CART analysis is a decision support tool that could provide an important contribution toward the prevention and control of malaria by identifying major risk factors

AN ASSESSMENT OF SCOPE OPPORTUNITIES ASSOCIATED WITH EUROPEAN LOW-COST CARRIER USE OF NEXT GENERATION NARROW BODY AIRCRAFT ACROSS THE ATLANTIC

This research assesses the economies of scope opportunities that may arise through the use of next generation, long-range narrow body aircraft, namely the 737MAX-7, 737MAX-8, A321LR and A321XLR, by European Low-Cost Carriers (LCCs), who have hitherto been reluctant to consider transatlantic long-haul lowcost operations. A proof of concept approach was taken using actual 2021 aircraft schedules and 2018-2019 aircraft utilisation data and was compared with a selection of hypothesised schedules by European-based LCCs using new longer-range narrow body aircraft for long-haul transatlantic operations in addition to regular short-haul sectors with a particular focus on the winter season when average utilisation levels are generally lower than the busier European summer season. It was found that the superior capacity-range at maximum payload characteristics of the A321LR/XLR and 738MAX8 aircraft can potentially increase total aircraft utilisation rates during the quieter European winter season by adding a transatlantic sector to an aircraft’s typical daily European operations to as many as 791 different route combinations to the Americas, some of which may be attractive for winter sun seekers and/or cost conscious independent travellers. It was noted that this type of interworked aircraft solution has its wider advantages and disadvantages e.g. it may only be attractive for existing short-haul LCCs with intentions for a one-class configuration on long-haul sectors, or multiple classes but with much lower levels of service differentiation. Individual constraints and considerations will be different for each carrier, therefore future research should centre on testing the concept within the networks and planning frameworks for individual case airlines

Artemisinin-based combination therapy in pregnant women in Zambia: efficacy, safety and risk of recurrent malaria.

BACKGROUND: In Zambia, malaria is one of the leading causes of morbidity and mortality, especially among under five children and pregnant women. For the latter, the World Health Organization recommends the use of artemisinin-based combination therapy (ACT) in the second and third trimester of pregnancy. In a context of limited information on ACT, the safety and efficacy of three combinations, namely artemether-lumefantrine (AL), mefloquine-artesunate (MQAS) and dihydroartemisinin-piperaquine (DHAPQ) were assessed in pregnant women with malaria. METHODS: The trial was carried out between July 2010 and August 2013 in Nchelenge district, Luapula Province, an area of high transmission, as part of a multi-centre trial. Women in the second or third trimester of pregnancy and with malaria were recruited and randomized to one of the three study arms. Women were actively followed up for 63 days, and then at delivery and 1 year post-delivery. RESULTS: Nine hundred pregnant women were included, 300 per arm. PCR-adjusted treatment failure was 4.7% (12/258) (95% CI 2.7-8.0) for AL, 1.3% (3/235) (95% CI 0.4-3.7) for MQAS and 0.8% (2/236) (95% CI 0.2-3.0) for DHAPQ, with significant risk difference between AL and DHAPQ (p = 0.01) and between AL and MQAS (p = 0.03) treatments. Re-infections during follow up were more frequent in the AL (HR: 4.71; 95% CI 3.10-7.2; p < 0.01) and MQAS (HR: 1.59; 95% CI 1.02-2.46; p = 0.04) arms compared to the DHAPQ arm. PCR-adjusted treatment failure was significantly associated with women under 20 years [Hazard Ratio (HR) 5.35 (95% CI 1.07-26.73; p = 0.04)] and higher malaria parasite density [3.23 (95% CI 1.03-10.10; p = 0.04)], and still women under 20 years [1.78, (95% CI 1.26-2.52; p < 0.01)] had a significantly higher risk of re-infection. The three treatments were generally well tolerated. Dizziness, nausea, vomiting, headache and asthenia as adverse events (AEs) were more common in MQAS than in AL or DHAPQ (p < 0.001). Birth outcomes were not significantly different between treatment arms. CONCLUSION: As new infections can be prevented by a long acting partner drug to the artemisinins, DHAPQ should be preferred in places as Nchelenge district where transmission is intense while in areas of low transmission intensity AL or MQAS may be used

Deploying Machine Learning Models Using Progressive Web Applications: Implementation Using a Neural Network Prediction Model for Pneumonia Related Child Mortality in The Gambia.

BACKGROUND: Translating research outputs into practical tools for medical practitioners is a neglected area and could have a substantial impact. One of the barriers to implementing artificial intelligence (AI) and machine learning (ML) applications is their practical deployment in the field. Traditional web-based (i.e., server sided) applications are dependent on reliable internet connections, which may not be readily available in rural areas. Native mobile apps require device specific programming skills as well as contemporary hardware and software, with often rapid and unpredictable platform specific changes. This is a major challenge for using AI/ML tools in resource-limited settings. METHODS: An emerging technology, progressive web applications (PWAs), first introduced by Google in 2015, offers an opportunity to overcome the challenges of deploying bespoke AI/ML systems. The same PWA code can be implemented across all desktop platforms, iOS and Android phones and tablets. In addition to platform independence, a PWA can be designed to be primarily offline. RESULTS: We demonstrate how a neural network-based pneumonia mortality prediction triage tool was migrated from a typical academic framework (paper and web-based prototype) to a tool that can be used offline on any mobile phone-the most convenient deployment vehicle. After an initial online connection to download the software, the application runs entirely offline, reading data from cached memory, and running code via JavaScript. On mobile devices the application is installed as a native app, without the inconvenience of platform specific code through manufacturer code stores. DISCUSSION: We show that an ML application can be deployed as a platform independent offline PWA using a pneumonia-related child mortality prediction tool as an example. The aim of this tool was to assist clinical staff in triaging children for hospital admission, by predicting their risk of death. PWAs function seamlessly when their host devices lose internet connectivity, making them ideal for e-health apps that can help improve health and save lives in resource-limited settings in line with the UN Sustainable Development Goal 3 (SDG3)

Coverage and timing of children's vaccination: an evaluation of the expanded programme on immunisation in The Gambia.

OBJECTIVE: To evaluate the coverage and timeliness of the Expanded Programme on Immunisation (EPI) in The Gambia. METHODS: Vaccination data were obtained between January 2005 and December 2012 from the Farafenni Health and Demographic Surveillance System (FHDSS), the Basse Health and Demographic Surveillance System (BHDSS), the Kiang West Demographic surveillance system (KWDSS), a cluster survey in the more urban Western Health Region (WR) and a cross sectional study in four clinics in the semi-urban Greater Banjul area of WR. Kaplan-Meier survival function was used to estimate the proportion vaccinated by age and to assess timeliness to vaccination. FINDINGS: BCG vaccine uptake was over 95% in all regions. Coverage of DPT1 ranged from 93.2% in BHDSS to 99.8% in the WR. Coverage decreased with increasing number of DPT doses; DPT3 coverage ranged from 81.7% in BHDSS to 99.0% in WR. Measles vaccination coverage ranged from 83.3% in BHDSS to 97.0% in WR. DPT4 booster coverage was low and ranged from 43.9% in the WR to 82.8% in KWDSS. Across all regions, delaying on previous vaccinations increased the likelihood of being delayed for the subsequent vaccination. CONCLUSIONS: The Gambia health system achieves high vaccine coverage in the first year of life. However, there continues to be a delay to vaccination which may impact on the introduction of new vaccines. Examples of effectively functioning EPI programmes such as The Gambia one may well be important models for other low income countries struggling to achieve high routine vaccination coverage

HLA and cross-reactive antigen group matching for cadaver kidney allocation

Background. Allocation of cadaver kidneys by graded human leukocyte antigen (HLA) compatibility scoring arguably has had little effect on overall survival while prejudicing the transplant candidacy of African-American and other hard to match populations. Consequently, matching has been proposed of deduced amino acid residues of the individual HLA molecules shared by cross- reactive antigen groups (CREGs). We have examined the circumstances under which compatibility with either method impacted graft survival. Methods. Using Cox proportional hazards regression modeling, we studied the relationship between levels of conventional HLA mismatch and other donor and recipient factors on primary cadaver kidney survival between 1981 and 1995 at the University of Pittsburgh (n=1,780) and in the United Network for Organ Sharing (UNOS) Scientific Registry during 1991-1995 (n=31,291). The results were compared with those obtained by the matching of amino acid residues that identified CREG-compatible cases with as many as four (but not five and six) HLA mismatches. Results. With more than one HLA mismatch (>85% of patients in both series), most of the survival advantage of a zero mismatch was lost. None of the HLA loci were 'weak.' In the UNOS (but not Pittsburgh) category of one-HLA mismatch (n=1334), a subgroup of CREG-matched recipients (35.3%) had better graft survival than the remaining 64.7%, who were CREG-mismatched. There was no advantage of a CREG match in the two- to four-HLA incompatibility tiers. Better graft survival with tacrolimus was observed in both the Pittsburgh and UNOS series. Conclusions. Obligatory national sharing of cadaver kidneys is justifiable only for zero-HLA-mismatched kidneys. The potential value of CREG matching observed in the one-HLA-mismatched recipients of the UNOS (but not the Pittsburgh) experience deserves further study