Geospatial Analytics for COVID-19 Active Case Detection

Ever since the COVID-19 pandemic started in Wuhan,China,much research work has been focusing on the clinical aspect of SARS-CoV-2.Researchers have been leveraging on various Artificial Intelligence techniques as an alternative to medical approach in understanding the virus.Limited studies have,however,reported on COVID-19 transmission pattern analysis,and using geography features for prediction of potential outbreak sites.Predicting the next most probable outbreak site is crucial,particularly for optimizing the planning of medical personnel and supply resources.To tackle the challenge,this work proposed distance-based similarity measures to predict the next most probable outbreak site together with its magnitude,when would the outbreak likely to happen and the duration of the outbreak.The work began with preprocessing of 1365 patient records from six districts in the most populated state named Selangor in Malaysia.The dataset was then aggregated with population density information and human elicited geography features that might promote the transmission of COVID-19.Empirical findings indicated that the proposed unified decision-making approach outperformed individual distance metric in predicting the total cases,next outbreak location,and the time interval between start dates of two similar sites.Such findings provided valuable insights for policymakers to perform Active Case Detection.

Assessment of Contributions of Community Tuberculosis Intervention to Tuberculosis Case Detection and Treatment Outcome in Two States in Nigeria

Background: Nigeria, one of the high burden Tuberculosis countries, has developed various intervention strategies to ensuring universal access to quality-assured tuberculosis diagnosis and treatment. However, low case detection and unsuccessful treatment outcome still remains a serious challenge in most states. Community Tuberculosis care was born against this background in 2010 as a complementing front to combat the challenges, bringing directly observed treatment short-course strategy beyond the clinic settings to the door steps of patients. This study evaluates the contributions of the intervention to Tuberculosis case detection and treatment outcomes in two states in Nigeria. Materials and Method: A retrospective study with multistage sampling technique was employed to review 23,241 presumptive Tuberculosis cases enrolled for management between 2014-2017. Chi-square (χ2) test was used for test of association between the independent variables and the main outcomes of the study, with statistical significance set at p-value of 5%. Results: The annual percentage increase for both states was 24.7%, 189.8% and 114.5% in the study group as against 5.2%, 44.6% and 65.6% in control group. Overall, 23.8% were bacteriologically positive (either AFB or Gene-Xpert MTB/Rif) and 1.4% were clinically evaluated to be positive, while 74.8% were bacteriologically negative. Of the total 5861 cases treated, successful treatment rate of the patients in the study group was 88.6% as compared to 76.1% in the control group. The relationship between the referral system from communities where the intervention program was implemented and the case detection/treatment outcome was statistically significant (OR 95% CI = 3.15, 2.95 - 3.35). Conclusion: The community level Tuberculosis intervention led to significantly better case detection and treatment outcome when compared to the conventional approach (p ≤ 0.05). Therefore, full community engagement should be advocated as a major strategy for End Tuberculosis planed by WHO since the patients are found in the community and not in the health facilities.

Establishing a standard method for analysing case detection delay in leprosy using a Bayesian modelling approach

Background Leprosy is an infectious disease caused by Mycobacterium leprae and remains a source of preventable disability if left undetected.Case detection delay is an important epidemiological indicator for progress in interrupting transmission and preventing disability in a community.However,no standard method exists to effectively analyse and interpret this type of data.In this study,we aim to evaluate the characteristics of leprosy case detection delay data and select an appropriate model for the variability of detection delays based on the best fitting distribution type.Methods Two sets of leprosy case detection delay data were evaluated:a cohort of 181 patients from the post exposure prophylaxis for leprosy(PEP4LEP)study in high endemic districts of Ethiopia,Mozambique,and Tanzania;and self-reported delays from 87 individuals in 8 low endemic countries collected as part of a systematic literature review.Bayesian models were fit to each dataset to assess which probability distribution(log-normal,gamma or Weibull)best describes variation in observed case detection delays using leave-one-out cross-validation,and to estimate the effects of individual factors.Results For both datasets,detection delays were best described with a log-normal distribution combined with covariates age,sex and leprosy subtype[expected log predictive density(ELPD)for the joint model:-1123.9].Patients with multibacillary(MB)leprosy experienced longer delays compared to paucibacillary(PB)leprosy,with a relative difference of 1.57[95%Bayesian credible interval(BCI):1.14-2.15].Those in the PEP4LEP cohort had 1.51(95%BCI:1.08-2.13)times longer case detection delay compared to the self-reported patient delays in the systematic review.Conclusions The log-normal model presented here could be used to compare leprosy case detection delay datasets,including PEP4LEP where the primary outcome measure is reduction in case detection delay.We recommend the application of this modelling approach to test different probability distributions and covariate effects in studies with similar outcomes in the field of leprosy and other skin-NTDs.

Evaluating active leprosy case identifcation methods in six districts of Nepal

Background Nepal has achieved and sustained the elimination of leprosy as a public health problem since 2009,but 17 districts and 3 provinces with 41%(10,907,128)of Nepal’s population have yet to eliminate the disease.Pediatric cases and grade-2 disabilities(G2D)indicate recent transmission and late diagnosis,respectively,which necessitate active and early case detection.This operational research was performed to identify approaches best suited for early case detection,determine community-based leprosy epidemiology,and identify hidden leprosy cases early and respond with prompt treatment.Methods Active case detection was undertaken in two Nepali provinces with the greatest burden of leprosy,Madhesh Province(40%national cases)and Lumbini Province(18%)and at-risk prison populations in Madhesh,Lumbini and Bagmati provinces.Case detection was performed by(1)house-to-house visits among vulnerable populations(n=26,469);(2)contact examination and tracing(n=7608);in Madhesh and Lumbini Provinces and,(3)screening prison populations(n=4428)in Madhesh,Lumbini and Bagmati Provinces of Nepal.Per case direct medical and nonmedical costs for each approach were calculated.Results New case detection rates were highest for contact tracing(250),followed by house-to-house visits(102)and prison screening(45)per 100,000 population screened.However,the cost per case identifed was cheapest for house-to-house visits[Nepalese rupee(NPR)76,500/case],followed by contact tracing(NPR 90,286/case)and prison screening(NPR 298,300/case).House-to-house and contact tracing case paucibacillary/multibacillary(PB:MB)ratios were 59:41 and 68:32;female/male ratios 63:37 and 57:43;pediatric cases 11%in both approaches;and grade-2 disabilities(G2D)11%and 5%,respectively.Developing leprosy was not signifcantly diferent among household and neighbor contacts[odds ratios(OR)=1.4,95%confdence interval(CI):0.24-5.85]and for contacts of MB versus PB cases(OR=0.7,95%CI 0.26-2.0).Attack rates were not signifcantly diferent among household contacts of MB cases(0.32%,95%CI 0.07-0.94%)and PB cases(0.13%,95%CI 0.03-0.73)(χ^(2)=0.07,df=1,P=0.9)and neighbor contacts of MB cases(0.23%,0.1-0.46)and PB cases(0.48%,0.19-0.98)(χ^(2)=0.8,df=1,P=0.7).BCG vaccination with scar presence had a signifcant protective efect against leprosy(OR=0.42,0.22-0.81).Conclusions The most efective case identifcation approach here is contact tracing,followed by house-to-house visits in vulnerable populations and screening in prisons,although house-to-house visits are cheaper.The fndings suggest that hidden cases,recent transmission,and late diagnosis in the community exist and highlight the importance of early case detection.

Detection and Analysis of Multidrug Resistance in 100 Cases of Acute Leukemia.

Bone marrow specimens from 100 cases of acute leukemia (AL) diagnosed by MIC were detected with

Characteristics of rifampicin-resistant tuberculosis detection in China,2015–2019

Background The very high burden of rifampicin resistance tuberculosis(RR-TB)and the very low detection of RR-TB cases are a major challenge that China has been facing.This study analyzed the characteristics of RR-TB detection in China after the change of RR-TB detection strategy since 2015,aiming to provide reference and evidence for the development of more precise national drug resistance tuberculosis prevention and control policy.Methods We extracted data related to rifampicin resistance screening from the national Tuberculosis Information Management System(TBIMS)from 2015 to 2019,and used descriptive research methods to analyze the screening rate of presumptive RR-TB,the number and duration of RR-TB patients detected and drug resistance testing methods in each year.Chi-square test was used to compare the differences in component ratio or rate between years,and Kruskal Wallis test was used to compare the differences in median days for detection of RR-TB patients in each year.Results A total of 68,200 RR-TB cases were detected during 2015–2019,of which 48.1%were new cases.The number and detection rate of RR-TB cases increased year by year,from 10019 and 14.3%in 2015 to 18623 and 28.7%in 2019,respectively.Of the bacteriologically confirmed TB cases,81.9%were tested for RR in 2019,a considerable increase from 29.5%in 2015.In 2019,only 41.0%of RR-TB cases had fluoroquinolones(FQs)susceptibility testing performed,and this proportion has been declining year by year since 2016.The proportion of application of rapid molecular tools increased from 24.0%in 2015 to 67.1%in 2019,and the median days to obtain RR results was significantly shortened.In 2019,76.0%of RR-TB cases were diagnosed as presumptive RR-TB in county-level hospitals.Conclusions After China modified the RR-TB detection strategy,the screening rate of RR and the number of RR-TB cases increased significantly.The RR testing methods now predominantly utilize rapid molecular tools.However,comprehensive measures should be implemented to close the gap in the detection of RR-TB cases.It is imperative to take FQs susceptibility testing seriously and effectively strengthen the laboratory capacity of county-level hospitals.

A case of pulmonary arteriovenous fistula detected by contrast transthoracic echocardiography combined with CTA

Pulmonary arteriovenous fistula （PAVF） is a kind of malformation resulting in the abnormal vessels between pulmonary artery and pulmonary vein. Part of pulmonary arterial blood flows into pulmonary veins through the fistula and then arrives at left atrium, inducing the right-to-left shunt. Moreover, the emboli and bacteria can also flow directly through the PAVF into systemic circulation, which can cause thromboembolic diseases such as stroke.

Measurement-While-Milling(MWM):An innovative approach for increasing the casing milling efficiency in deep drilling operations

Deep boreholes are secured by steel tubes(casings)which are run in the hole and cemented in place.In most cases,these casings are considered a permanent installation.However,sometimes they have to be removed in order to repair or abandon the well.As the casing is cemented in place,it cannot be pulled,but needs to be milled to small chips which are flushed out of the borehole by the drilling mud.One of the main challenges in casing milling operations is continuous and complete chip removal.If the metal chips are too long,chip nests will grow around the milling string.As a result,this will restrict the annulus flow area and affect the chip removal in boreholes.The obvious solution in such condition is to do round tripping and clean the chip nest which is associated with the risk of injuries,as well as,increasing the none-productive time.In the worst case,the poor cleaning and circulation of chips can even end up with the milling string stucking problem in boreholes,consequently long-time fishing job.According to the available literatures,hardly any study for identifying the chip shapes and accordingly adapting the operation parameters to the casing milling process environment downhole to keep milling within desired generated chip shapes and sizes could be found.This paper presents an encouraging idea to monitor the milling process in real time by utilizing the acoustic emission signals(vibration modes)accompanied with the milling process to identify the desired chip shape and size range.Initial laboratory tests have been carried out to investigate and study the acoustic emission signals accompanying the casing milling process to identify the chip shapes and sizes.The preliminary test results show very good correlation and agreement between the chip length formed during those specific tests and the observed burst events in the measured signals.The study results have demonstrated the functionality of the new concept,and thus confirmed that it is a very promising idea towards developing a practical real time downhole monitoring system for milling operations.Adapting the milling operation parameters downhole in real time to keep the milling process within the desired generated chip shapes and sizes will offer better cleaning and removal of the chips and will prevent the development of chip nest around the drill string and its consequences such as round tripping,risk of drilling crew injury,none-productive time and even milling string stucking problems.

Study on factors affecting TB/HIV co-infection in four counties of China

The factors affecting case detection of tuber-culosis(TB)/human immunodeficiency virus(HIV)co-infection cases were explored in order to provide evidence-based formulation of a TB/HIV co-infection control strategy in China.Four counties with different modes of HIV transmission and varying cooperation mechanisms between TB and HIV institutions were selected.HIV test among TB patients and TB examination among people living with HIV/acquired immunodeficiency syndrome(AIDS)were conducted.Patients also completed ques-tionnaires on potential factors affecting TB/HIV co-infection.The results showed that 19(1.7%)were HIV-positive among 1089 cases of people living with active TB who received HIV testing.Conversely,there were 126(10%)cases of active TB among 1255 cases of people living with HIV/AIDS.Among the newly discovered 145 cases of TB/HIV co-infection,AIDS institutions found 86.9%of these co-infections and 14.1%came from TB institutes.In different registration categories,there were 31(21.4%)cases of smear positive TB,104(71.7%)cases of smear negative TB,and extrapulmonary cases accounted for 10(6.9%).Gender,occupation,marital status,ethnic group,education,HIV transmission route,CD4 level,and type of TB susceptible symptoms had significant effects on whether HIV/AIDS patients were co-infected with TB disease(P<0.01).Sex,age,ethnic group,occupation,and type of tuberculosis had no significant influence on whether TB patients had HIV infection.AIDS institutions couldfind more TB/HIV co-infection patients in compar-ison with TB institutions,particularly in patients with smear negative pulmonary tuberculosis and extrapulmon-ary tuberculosis.Therefore,a cooperation mechanism should be built up between TB and HIV control systems,and routine TB checks should be conducted for HIV/AIDS patients.In areas where sex or drug use is the major transmission mode of HIV infection,antiretroviral therapy should be expanded,treatment adherence should be improved and patients’immunity level should be increased in order to decrease TB incidence.Cough and expectora-tion of more than two weeks,bloody sputum,and recurrent fevers could be revealing symptoms in TB screening of HIV/AIDS patients.

Integrating innovations:a qualitative analysis of referral non-completion among rapid diagnostic test-positive patients in Uganda’s human African trypanosomiasis elimination programme

Background:The recent development of rapid diagnostic tests(RDTs)for human African trypanosomiasis(HAT)enables elimination programmes to decentralise serological screening services to frontline health facilities.However,patients must still undertake multiple onwards referral steps to either be confirmed or discounted as cases.Accurate surveillance thus relies not only on the performance of diagnostic technologies but also on referral support structures and patient decisions.This study explored why some RDT-positive suspects failed to complete the diagnostic referral process in West Nile,Uganda.Methods:Between August 2013 and June 2015,85%(295/346)people who screened RDT-positive were examined by microscopy at least once;10 cases were detected.We interviewed 20 RDT-positive suspects who had not completed referral(16 who had not presented for their first microscopy examination,and 4 who had not returned for a second to dismiss them as cases after receiving discordant[RDT-positive,but microscopy-negative results]).Interviews were analysed thematically to examine experiences of each step of the referral process.Results:Poor provider communication about HAT RDT results helped explain non-completion of referrals in our sample.Most patients were unaware they were tested for HAT until receiving results,and some did not know they had screened positive.While HAT testing and treatment is free,anticipated costs for transportation and ancillary health services fees deterred many.Most expected a positive RDT result would lead to HAT treatment.RDT results that failed to provide a definitive diagnosis without further testing led some to question the expertise of health workers.For the four individuals who missed their second examination,complying with repeat referral requests was less attractive when no alternative diagnostic advice or treatment was given.Conclusions:An RDT-based surveillance strategy that relies on referral through all levels of the health system is inevitably subject to its limitations.In Uganda,a key structural weakness was poor provider communication about the possibility of discordant HAT test results,which is the most common outcome for serological RDT suspects in a HAT elimination programme.Patient misunderstanding of referral rationale risks harming trust in the whole system and should be addressed in elimination programmes.

Evaluating the yield of systematic screening for tuberculosis among three priority groups in Ho Chi Minh City,Viet Nam

Background: In order to end tuberculosis(TB),it is necessary to expand coverage of TB care services,including systematic screening initiatives.However,more evidence is needed for groups among whom systematic screening is only conditionally recommended by the World Health Organization.This study evaluated concurrent screening in multiple target groups using community health workers(CHW).Methods:: In our two-year intervention study lasting from October 2017 to September 2019,CHWs in six districts of Ho Chi Minh City,Viet Nam verbally screened three urban priority groups:(1)household TB contacts;(2)close TB contacts;and(3)residents of urban priority areas without clear documented exposure to TB including hotspots,boarding homes and urban slums.Eligible persons were referred for further screening with chest radiography and follow-on testing with the Xpert MTB/RIF assay.Symptomatic individuals with normal or without radiography results were tested on smear microscopy.We described the TB care cascade and characteristics for each priority group,and calculated yield and number needed to screen.Subsequently,we fitted a mixed-effect logistic regression to identify the association of these target groups and secondary patient covariates with TB treatment initiation.Results: We verbally screened 321020 people including 24232 household contacts,3182 social and close contacts and 293606 residents of urban priority areas.This resulted in 1138 persons treated for TB,of whom 85 were household contacts,39 were close contacts and 1014 belonged to urban priority area residents.The yield of active TB in these groups was 351,1226 and 345 per 100000,respectively,corresponding to numbers needed to screen of 285,82 and 290.The fitted model showed that close contacts[adjusted odds ratio(aOR)=2.07;95%CI:1.38–3.11;P<0.001]and urban priority area residents(aOR=2.18;95%CI:1.69–2.79;P<0.001)had a greater risk of active TB than household contacts.Conclusions: The study detected a large number of unreached persons with TB,but most of them were not among persons in contact with an index patient.Therefore,while programs should continue to optimize screening in contacts,to close the detection gap in high TB burden settings such as Viet Nam,coverage must be expanded to persons without documented exposure such as residents in hotspots,boarding homes and urban slums.