ResearchPad - research-laboratories https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Analytical performance of thrombospondin-1 and cathepsin D immunoassays part of a novel CE-IVD marked test as an aid in the diagnosis of prostate cancer]]> https://www.researchpad.co/article/elastic_article_15745 The Prostate Specific Antigen (PSA) test suffers from low specificity for the diagnosis of Prostate Cancer (PCa). We originally discovered two cancer-related proteins thrombospondin-1 (THBS1) and cathepsin D (CTSD) using a mass-spectrometry-based proteomics approach. The two serum proteins were shown to improve the diagnosis of high-grade PCa. Thus, we developed quantitative ELISAs for the determination of their concentration in human serum. Here we report their analytical performance in terms of limit of detection, specificity, precision, linearity and interferences, which were determined based on CLSI guidelines. Further, we investigated the influence of pre-analytical factors on concentration measurements. For this, blood from 4–6 donors was collected in different tubes and stored at room temperature for different times prior to centrifugation at different centrifugal forces and temperatures. Stability of THBS1 and CTSD under different storage temperatures was also evaluated. Our results show that the assays are specific, linear and sensitive enough to allow measurement of clinical samples. Precision in terms of repeatability and total within-laboratory coefficient of variation (CV) are 5.5% and 8.1% for THBS1 and 4.3% and 7.2% for CTSD, respectively. Relative laboratory-to-laboratory differences were -6.3% for THBS1 and -3% for CTSD. Both THBS1 and CTSD were stable in serum samples, with 80–120% recoveries of concentrations across donors, sample preparation and storage. In conclusion, the ELISAs as part of the novel commercial in vitro diagnostic test Proclarix are suitable for the use in clinical practice. THBS1 and CTSD can be accurately measured for their intended use independent of the lot and laboratory when conditions consistent with routine practice for PSA sampling and storage are used.

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<![CDATA[The perceived impact of isoniazid resistance on outcome of first-line rifampicin-throughout regimens is largely due to missed rifampicin resistance]]> https://www.researchpad.co/article/elastic_article_15716 Meta-analyses on impact of isoniazid-resistant tuberculosis informed the World Health Organization recommendation of a levofloxacin-strengthened rifampicin-based regimen.We estimated the effect of initial rifampicin resistance (Rr) and/or isoniazid resistance (Hr) on treatment failure or relapse. We also determined the frequency of missed initial and acquired Rr to estimate the impact of true Hr.MethodsRetrospective analysis of 7291 treatment episodes with known initial isoniazid and rifampicin status obtained from individual patient databases maintained by the Damien Foundation Bangladesh over 20 years. Drug susceptibility test results were confirmed by the programme’s designated supra-national tuberculosis laboratory. To detect missed Rr among isolates routinely classified as Hr, rpoB gene sequencing was done randomly and on a sample selected for suspected missed Rr.ResultsInitial Hr caused a large recurrence excess after the 8-month regimen for new cases (rifampicin for two months), but had little impact on rifampicin-throughout regimens: (6 months, new cases; 3.8%; OR 0.8, 95%CI:0.3,2.8; 8 months, retreatment cases: 7.3%, OR 1.8; 95%CI:1.3,2.6). Rr was missed in 7.6% of randomly selected "Hr" strains. Acquired Rr was frequent among recurrences on rifampicin-throughout regimens, particularly after the retreatment regimen (31.9%). It was higher in mono-Hr (29.3%; aOR 3.5, 95%CI:1.5,8.5) and poly-Hr (53.3%; aOR 10.2, 95%CI 4.4,23.7) than in susceptible tuberculosis, but virtually absent after the 8-month new case regimen. Comparing Bangladesh (low Rr prevalence) with a high Rr prevalence setting,true Hr corrected for missed Rr caused only 2–3 treatment failures per 1000 TB cases (of whom 27% were retreatments) in both.ConclusionsOur analysis reveals a non-negligible extent of misclassifying as isoniazid resistance of what is actually missed multidrug-resistant tuberculosis. Recommending for such cases a “strengthened” regimen containing a fluoroquinolone provokes a direct route to extensive resistance while offering little benefit against the minor role of true Hr tuberculosis in rifampicin-throughout first-line regimen. ]]> <![CDATA[Associations between demographic factors and the academic trajectories of medical students in Japan]]> https://www.researchpad.co/article/elastic_article_15714 Group-based trajectory modeling is a useful tool for categorizing students’ academic trajectories and their determinants. Using insights gained from the analyses, we can identify students at risk for poor academic performance and monitor them to provide support. To date, studies investigating the associations between demographic factors and academic performance trajectories among medical students are scarce. The study objective was to examine the associations between demographic factors and academic performance trajectories in medical students using group-based trajectory modeling.MethodsParticipants included all medical students admitted to Tokyo Medical and Dental University in Japan in 2013 and 2014 (n = 202). Academic performance was evaluated by biannual grade point average (GPA) scores in preclinical years. We used group-based trajectory modeling to categorize students into GPA trajectories. Multinomial logistic regression was used to examine the association between the odds of being in a certain GPA trajectory group and demographic factors such as high school type, high school geographical area, admission test type, high school graduation year, whether the student was a biology major, and sex.ResultsStudents’ GPA trajectories were classified into four trajectory groups as well as another group that consisted of students who withdrew or repeated years. We found that students whose high school geographical area was outside the National Capital Region were 7.2 times more likely to withdraw or repeat years in comparison with students whose school was inside the National Capital Region (OR: 7.21, 95% CI: 1.87, 27.76). In addition, admission test type, high school graduation year, and sex were associated with GPA trajectories.ConclusionsHigh school geographical area, admission test type, high school graduation year, and sex were associated with GPA trajectories. These findings provide important insights into identifying students at risk for poor academic performance and strategies for monitoring them to provide adequate and timely support. ]]> <![CDATA[A twenty-eight-year laboratory-based retrospective trend analysis of malaria in Dakar, Senegal]]> https://www.researchpad.co/article/elastic_article_14736 Health facility-based records offer a rich source of information to understand trends and changes in malaria cases over time. This study is aimed at determining the changes in malaria occurrence over the last 28 years, from 1989 to 2016 in Dakar, Senegal.MethodsLaboratory suspected and confirmed malaria records from 1989 to 2016 were reviewed from the laboratory registers of the Laboratory of Parasitology and Mycology of Aristide Le Dantec Hospital. Interrupted time series (ITS) analysis was used to estimate the changes by comparing malaria cases post-intervention (2006–2016) with that of the pre-intervention (1989–2005) period.ResultsA total of 5,876 laboratory confirmed malaria cases were reported out of 29,852 tested cases, with total slide positivity rate (SPR) of 19.7%. Malaria case counts exhibited a fluctuating trend with major peaks occurring in the years 1995 and 2003 with SPR of 42.3% and 42.5%, respectively. Overall, a remarkable decline in the total number of laboratory confirmed malaria cases was observed over the last 28 years. P. falciparum was almost the only reported species, accounting for 99.98% of cases. The highest SPR was observed in the age group of under five years during the pre-intervention period while this shifted to the age group of 6–15 years old for the subsequent years. Two major malaria peak seasons were observed: one in September during the pre-intervention period and the other in November for the post-intervention period. The ITS analysis showed a dramatic decline of 83.6% in SPR following the scale-up of interventions in 2006.ConclusionA remarkable decline in laboratory confirmed malaria cases in Dakar over 28 years was observed. The period of rapid decline in malaria SPR coincided with the scale-up in interventions beginning in 2006 with the introduction of ACTs, followed by the widespread introduction in 2008 of bed nets treated with insecticides. Robust surveillance data should be maintained in the context of malaria elimination efforts. ]]> <![CDATA[Evaluation of residue management practices on barley residue decomposition]]> https://www.researchpad.co/article/elastic_article_13875 Optimizing barley (hordeum vulgare L.) production in Idaho and other parts of the Pacific Northwest (PNW) should focus on farm resource management. The effect of post-harvest residue management on barley residue decomposition has not been adequately studied. Thus, the objective of this study was to determine the effect of residue placement (surface vs. incorporated), residue size (chopped vs. ground-sieved) and soil type (sand and sandy loam) on barley residue decomposition. A 50-day(d) laboratory incubation experiment was conducted at a temperature of 25°C at the Aberdeen Research and Extension Center, Aberdeen, Idaho, USA. Following the study, a Markov-Chain Monte Carlo (MCMC) modeling approach was applied to investigate the first-order decay kinetics of barley residue. An accelerated initial flush of residue carbon(C)-mineralization was measured for the sieved (Day 1) compared to chopped (Day 3 to 5) residues for both surface incorporated applications. The highest evolution of carbon dioxide (CO2)-C of 8.3 g kg-1 dry residue was observed on Day 1 from the incorporated-sieved application for both soils. The highest and lowest amount of cumulative CO2-C released and percentage residue decomposed over 50-d was observed for surface-chopped (107 g kg-1 dry residue and 27%, respectively) and incorporated-sieved (69 g kg-1 dry residue and 18%, respectively) residues, respectively. There were no significant differences in C-mineralization from barley residue based on soil type or its interactions with residue placement and size (p >0.05). The largest decay constant k of 0.0083 d-1 was calculated for surface-chopped residue where the predicted half-life was 80 d, which did not differ from surface sieved or incorporated chopped. In contrast, incorporated-sieved treatments only resulted in a k of 0.0054 d-1 and would need an additional 48 d to decompose 50% of the residue. Future residue decomposition studies under field conditions are warranted to verify the residue C-mineralization and its impact on residue management.

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<![CDATA[Comparison of triglyceride glucose index, and related parameters to predict insulin resistance in Korean adults: An analysis of the 2007-2010 Korean National Health and Nutrition Examination Survey]]> https://www.researchpad.co/article/5c990272d5eed0c484b97e62

The triglyceride glucose (TyG) index, a product of triglyceride and fasting glucose, is a reliable marker for insulin resistance (IR). Obesity is also known to be closely related with IR. Recently, the efficiency of TyG-related markers that combine obesity markers with TyG index has been studied; however, earlier studies were limited in number and the results were inconsistent. Therefore, in this study, we investigated the efficiency of several combinations of TyG index and obesity indices, namely, body mass index (BMI), waist circumference (WC), and waist-to-height ratio (WHtR), in reflecting IR. Data were obtained from the Korean National Health and Nutrition Examination Survey from 2007–2010. A total of 11,149 subjects (4,777 men and 6,372 women) were included. IR was defined as the homeostasis model assessment for IR (HOMA-IR) of above the 75th percentile for each gender. Logistic regression analysis was performed after adjusting for confounding factors, to compare and identify the associations of the 4 parameters (TyG index, TyG-BMI, TyG-WC, and TyG-WHtR) with IR. For each parameter, odds ratios (OR) and 95% confidence intervals (CIs) of quartiles 2–4 were calculated and compared with quartile 1 as a reference. A receiver operating characteristic (ROC) curve analysis was conducted to evaluate the ability of each parameter to predict IR. The adjusted ORs of quartile 4 in comparison with quartile 1 (95% CIs) for IR were 7.60 (6.52–8.87) for TyG index, 12.82 (10.89–15.10) for TyG-BMI, 16.29 (13.70–19.38) for TyG-WC, and 14.86 (12.53–17.62) for TyG-WHtR. The areas under the ROC curve for each parameter were 0.690 for TyG index, 0.748 for TyG-BMI, 0.731 for TyG-WC, and 0.733 for TyG-WHtR. In conclusion, TyG-BMI was found to be superior to other parameters for IR prediction. We propose TyG-BMI as an alternative marker for assessing IR in clinical settings.

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<![CDATA[Open notebook science can maximize impact for rare disease projects]]> https://www.researchpad.co/article/5c58d65dd5eed0c484031ce9

Transparency lies at the heart of the open lab notebook movement. Open notebook scientists publish laboratory experiments and findings in the public domain in real time, without restrictions or omissions. Research on rare diseases is especially amenable to the open notebook model because it can both increase scientific impact and serve as a mechanism to engage patient groups in the scientific process. Here, I outline and describe my own success with my open notebook project, LabScribbles, as well as other efforts included in the openlabnotebooks.org initiative.

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<![CDATA[Evaluation of direct costs associated with alveolar and cystic echinococcosis in Austria]]> https://www.researchpad.co/article/5c5ca2d2d5eed0c48441eb7a

Background

Cystic echinococcosis (CE) is a globally occurring zoonosis, whereas alveolar echinococcosis (AE) is endemic only in certain parts of the Northern Hemisphere. The socioeconomic impact of human echinococcosis has been shown to be considerable in highly endemic regions. However, detailed data on direct healthcare-related costs associated with CE and AE are scarce for high income countries. The aim of this study was to evaluate direct costs of human disease caused by CE and AE in Austria.

Methods

Clinical data from a registry maintained at a national reference center for echinococcosis at the Medical University of Vienna were obtained for the years 2012–2014. These data were used in conjunction with epidemiological data from Austria’s national disease reporting system and diagnostic reference laboratory for echinococcosis to assess nationwide costs attributable to CE and AE.

Results

In Austria, total modelled direct costs were 486,598€ (95%CI 341,825€ – 631,372€) per year for CE, and 683,824€ (95%CI 469,161€ - 898,486€) for AE. Median costs per patient with AE from diagnosis until the end of a 10-year follow-up period were 30,832€ (25th– 75th percentile: 23,197€ - 31,220€) and 62,777€ (25th– 75th percentile: 60,806€ - 67,867€) for inoperable and operable patients, respectively. Median costs per patients with CE from diagnosis until end of follow-up after 10 years were 16,253€ (25th– 75th percentile: 8,555€ - 24,832€) and 1,786€ (25th– 75th percentile: 736€ - 2,146€) for patients with active and inactive cyst stages, respectively. The first year after inclusion was the most cost-intense year in the observed period, with hospitalizations and albendazole therapy the main contributors to direct costs.

Conclusions

This study provides detailed information on direct healthcare-related costs associated with CE and AE in Austria, which may reflect trends for other high-income countries. Surgery and albendazole therapy, due to surprisingly high drug prices, were identified as important cost-drivers. These data will be important for cost-effectiveness analyses of possible prevention programs.

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<![CDATA[Intensive longitudinal modelling predicts diurnal activity of salivary alpha-amylase]]> https://www.researchpad.co/article/5c5217f6d5eed0c484795c77

Salivary alpha-amylase (sAA) activity has been widely used in psychological and medical research as a surrogate marker of sympathetic nervous system activation, though its utility remains controversial. The aim of this work was to compare alternative intensive longitudinal models of sAA data: (a) a traditional model, where sAA is a function of hour (hr) and hr squared (sAAj,t = f(hr, hr2), and (b) an autoregressive model, where values of sAA are a function of previous values (sAAj,t = f(sAA j,t-1, sAA j,t-2, , sAA j,t-p). Nineteen normal subjects (9 males and 10 females) participated in the experiments and measurements were performed every hr between 9:00 and 21:00 hr. Thus, a total of 13 measurements were obtained per participant. The Napierian logarithm of the enzymatic activity of sAA was analysed. Data showed that a second-order autoregressive (AR(2)) model was more parsimonious and fitted better than the traditional multilevel quadratic model. Therefore, sAA follows a process whereby, to forecast its value at any given time, sAA values one and two hr prior to that time (sAA j,t = f(SAAj,t-1, SAAj,t-2) are most predictive, thus indicating that sAA has its own inertia, with a “memory” of the two previous hr. These novel findings highlight the relevance of intensive longitudinal models in physiological data analysis and have considerable implications for physiological and biobehavioural research involving sAA measurements and other stress-related biomarkers.

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<![CDATA[Examining the ‘cosmetics placebo effect’]]> https://www.researchpad.co/article/5c40f772d5eed0c48438619f

Previous studies have found a positive effect of cosmetics on certain behavioral measures, such as the tip given to waitresses by male patrons. These studies have employed confederates who usually wear cosmetics. We therefore sought to examine whether the positive effect found in these studies could, in part, be explained by a change in behavior. In order to test the possibility of a ‘cosmetics placebo effect’, we employed a confederate to solicit donations from passersby. On some days our confederate would not have any cosmetics applied to her face (i.e., no cosmetics condition), on some days cosmetics were pretended to be applied to her face (i.e., placebo cosmetics condition), and on other days cosmetics were actually applied to her face (i.e., cosmetics condition). In line with previous research, we found that across conditions men donated significantly more than women to our female solicitor, providing support for the ‘showoff hypothesis’, in which male generosity serves as a mating tactic. When investigating men’s donations in more detail, we found that the highest percentage of donations came in the cosmetics condition, followed by the placebo cosmetics condition, and then by no cosmetics condition. The effect of condition on donation rates, however, was not statistically significant. Our study was limited to one solicitor and one dependent variable (i.e., percentage of people approached who donated) and therefore future research would benefit from using more confederates as well as examining other behavioral measures. Given the influence of cosmetics use on so many real-world outcomes, we believe that further exploration into a possible ‘cosmetics placebo effect’ would be valuable.

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<![CDATA[BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2]]> https://www.researchpad.co/article/5c2d2eb3d5eed0c484d9b2c0

The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org. The purpose of the BRCA Exchange is to provide the community with a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype. More than 20,000 variants have been aggregated, three times the number found in the next-largest public database at the project’s outset, of which approximately 7,250 have expert classifications. The data set is based on shared information from existing clinical databases—Breast Cancer Information Core (BIC), ClinVar, and the Leiden Open Variation Database (LOVD)—as well as population databases, all linked to a single point of access. The BRCA Challenge has brought together the existing international Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium expert panel, along with expert clinicians, diagnosticians, researchers, and database providers, all with a common goal of advancing our understanding of BRCA1 and BRCA2 variation. Ongoing work includes direct contact with national centers with access to BRCA1 and BRCA2 diagnostic data to encourage data sharing, development of methods suitable for extraction of genetic variation at the level of individual laboratory reports, and engagement with participant communities to enable a more comprehensive understanding of the clinical significance of genetic variation in BRCA1 and BRCA2.

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<![CDATA[Comparison between continuous and discrete doses for model based designs in cancer dose finding]]> https://www.researchpad.co/article/5c3fa5a0d5eed0c484ca69e5

Despite of an extensive statistical literature showing that discretizing continuous variables results in substantial loss of information, categorization of continuous variables has been a common practice in clinical research and in cancer dose finding (phase I) clinical trials. The objective of this study is to quantify the loss of information incurred by using a discrete set of doses to estimate the maximum tolerated dose (MTD) in phase I trials, instead of a continuous dose support. Escalation With Overdose Control and Continuous Reassessment Method were used because they are model-based designs where dose can be specified either as continuous or as a set of discrete levels. Five equally spaced sets of doses with different interval lengths and three sample sizes with sixteen scenarios were evaluated to compare the operating characteristics between continuous and discrete dose designs by Monte Carlo simulation. Loss of information was quantified by safety and efficiency measures. We conclude that if there is insufficient knowledge about the true MTD value, as commonly happens in phase I clinical trials, a continuous dose scheme minimizes information loss. If one is required to implement a design using discrete doses, then a scheme with 9 to 11 doses may yield similar results to the continuous dose scheme.

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<![CDATA[Assessment and verification of commercially available pressure cookers for laboratory sterilization]]> https://www.researchpad.co/article/5c1966d5d5eed0c484b53056

Laboratory science requires careful maintenance of sterile reagents and tools as well as the sterilization of waste prior to disposal. However, steam autoclaves typically used for this purpose may not be readily accessible to everyone in the scientific community, such as K-12 teachers, researchers in the field, students in under-funded laboratories, or persons in the developing world who lack funding and resources. This work examines the use of commercial electric pressure cookers as an alternative method for the sterilization of media, instruments, and waste. Four commonly available brands of pressure cooker were tested for their ability to sterilize microbiological media, a variety of metal instruments, and high-titer microbial cultures. All four pressure cookers were able to sterilize these starting materials as well as a range of microbial types, including Gram-positive bacteria, Gram-negative bacteria, filamentous fungi, unicellular fungi, and mixed environmental samples. Only the Instant Pot, however, was able to sterilize autoclave tester ampoules of Geobacillus stearothermophilus spores. These results suggest that, depending on the nature of the work undertaken, store-bought pressure cookers can be an appropriate substitute for commercial autoclaves. Their adoption may also help increase the accessibility of science to a broader range of investigators.

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<![CDATA[Checking facts and fighting back: Why journalists should defend their profession]]> https://www.researchpad.co/article/5c1813b5d5eed0c4847759e9

Bias accusations have eroded trust in journalism to impartially check facts. Traditionally journalists have avoided responding to such accusations, resulting in an imbalanced flow of arguments about the news media. This study tests what would happen if journalists spoke up more in defense of their profession, while simultaneously also testing effects of doing more fact checking. A five-day field experiment manipulated whether an online news portal included fact check stories and opinion pieces defending journalism. Fact checking was beneficial in terms of three democratically desirable outcomes–media trust, epistemic political efficacy, and future news use intent–only when defense of journalism stories were also present. No partisan differences were found in effects: Republicans, Democrats, and Independents were all affected alike. These results have important implications for journalistic practice as well as for theories and methods of news effects.

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<![CDATA[Laboratory challenges of Plasmodium species identification in Aceh Province, Indonesia, a malaria elimination setting with newly discovered P. knowlesi]]> https://www.researchpad.co/article/5c0ae437d5eed0c4845892c2

The discovery of the life-threatening zoonotic infection Plasmodium knowlesi has added to the challenges of prompt and accurate malaria diagnosis and surveillance. In this study from Aceh Province, Indonesia, a malaria elimination setting where P. knowlesi endemicity was not previously known, we report the laboratory investigation and difficulties encountered when using molecular detection methods for quality assurance of microscopically identified clinical cases. From 2014 to 2015, 20 (49%) P. falciparum, 16 (39%) P. vivax, 3 (7%) P. malariae, and 2 (5%) indeterminate species were identified by microscopy from four sentinel health facilities. At a provincial-level reference laboratory, loop-mediated isothermal amplification (LAMP), a field-friendly molecular method, was performed and confirmed Plasmodium in all samples though further species-identification was limited by the unavailability of non-falciparum species-specific testing with the platform used. At a national reference laboratory, several molecular methods including nested PCR (nPCR) targeting the 18 small sub-unit (18S) ribosomal RNA, nPCR targeting the cytochrome-b (cytb) gene, a P. knowlesi-specific nPCR, and finally sequencing, were necessary to ultimately classify the samples as: 19 (46%) P. knowlesi, 8 (20%) P. falciparum, 14 (34%) P. vivax. Microscopy was unable to identify or mis-classified up to 56% of confirmed cases, including all cases of P. knowlesi. With the nPCR methods targeting the four human-only species, P. knowlesi was missed (18S rRNA method) or showed cross-reactivity for P. vivax (cytb method). To facilitate diagnosis and management of potentially fatal P. knowlesi infection and surveillance for elimination of human-only malaria in Indonesia and other affected settings, new detection methods are needed for testing at the point-of-care and in local reference laboratories.

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<![CDATA[Cervical cancer screening in Sweden 2014-2016]]> https://www.researchpad.co/article/5c215143d5eed0c4843f9669

Background

To enable incremental optimization of screening, regular reporting of quality indicators is required.

Aim

To report key quality indicators and basic statistics about cervical screening in Sweden.

Methods

We collected individual level data on all cervical cytologies, histopathologies, human papillomavirus tests and all invitations for cervical screening in Sweden during 2013–2016.

Results

There were over 2,278,000 cervical samples collected in Sweden in 2014–2016. Organized samples (resulting from an invitation) constituted 69% of samples. The screening test coverage of all resident women aged 23–60 was 82%. The coverage has slowly increased for >10 years. There is large variability between counties (from 71% to 92%) over time. There were 25,725 women with high-grade lesions in cytology during 2013–2015. Only 96% of these women had a follow-up histopathology within a year. Cervical cancer incidence showed an increasing trend.

Conclusion

Key quality indicators such as population coverage and follow-up rates were stable or improving, but there was nevertheless an unexplained cervical cancer increase.

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<![CDATA[Distribution of HCV genotypes in Belgium from 2008 to 2015]]> https://www.researchpad.co/article/5c117b69d5eed0c484699195

Background

The knowledge of circulating HCV genotypes and subtypes in a country is crucial to guide antiviral therapy and to understand local epidemiology. Studies investigating circulating HCV genotypes and their trends have been conducted in Belgium. However they are outdated, lack nationwide representativeness or were not conducted in the general population.

Methods

In order to determine the distribution of different circulating HCV genotypes in Belgium, we conducted a multicentre study with all the 19 Belgian laboratories performing reimbursed HCV genotyping assays. Available genotype and subtype data were collected for the period from 2008 till 2015. Furthermore, a limited number of other variables were collected: some demographic characteristics from the patients and the laboratory technique used for the determination of the HCV genotype.

Results

For the study period, 11,033 unique records collected by the participating laboratories were used for further investigation.

HCV genotype 1 was the most prevalent (53.6%) genotype in Belgium, with G1a and G1b representing 19.7% and 31.6%, respectively. Genotype 3 was the next most prevalent (22.0%). Further, genotype 4, 2, and 5 were responsible for respectively 16.1%, 6.2%, and 1.9% of HCV infections. Genotype 6 and 7 comprise the remaining <1%. Throughout the years, a stable distribution was observed for most genotypes. Only for genotype 5, a decrease as a function of the year of analysis was observed, with respectively 3.6% for 2008, 2.3% for 2009 and 1.6% for the remaining years.

The overall M:F ratio was 1.59 and was mainly driven by the high M:F ratio of 3.03 for patients infected with genotype 3. Patients infected with genotype 3 are also younger (mean age 41.7 years) than patients infected with other genotypes (mean age above 50 years for all genotypes). The patients for whom a genotyping assay was performed in 2008 were younger than those from 2015.

Geographical distribution demonstrates that an important number of genotyped HCV patients live outside the Belgian metropolitan cities.

Conclusion

This national monitoring study allowed a clear and objective view of the circulating HCV genotypes in Belgium and will help health authorities in the establishment of cost effectiveness determinations before implementation of new treatment strategies.

This baseline characterization of the circulating genotypes is indispensable for a continuous surveillance, especially for the investigation of the possible impact of migration from endemic regions and prior to the increasing use of highly potent direct-acting antiviral (DAA) agents.

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<![CDATA[Importance of real-time RT-PCR to supplement the laboratory diagnosis in the measles elimination program in China]]> https://www.researchpad.co/article/5c0ae44dd5eed0c484589580

In addition to high vaccination coverage, timely and accurate laboratory confirmation of measles cases is critical to interrupt measles transmission. To evaluate the role of real-time reverse transcription-polymerase chain reaction (RT-PCR) in the diagnosis of measles cases, 46,363 suspected measles cases with rash and 395 suspected measles cases without rash were analyzed in this study; the cases were obtained from the Chinese measles surveillance system (MSS) during 2014–2017 and simultaneously detected by measles-specific IgM enzyme-linked immunosorbent assay (ELISA) and real-time RT-PCR. However, some IgM-negative measles cases were identified by real-time RT-PCR. The proportion of these IgM-negative and viral nucleic acid-positive measles cases was high among measles cases with measles vaccination history, cases without rash symptoms, and cases within 3 days of specimen collection after onset. The proportion of IgM-negative and viral nucleic acid-positive measles cases in the 0–3 day group was up to 14.4% for measles cases with rash and 40% for measles cases without rash. Moreover, the proportions of IgM-negative and nucleic acid-positive measles cases gradually increased with the increase in the measles vaccination dose. Therefore, integrated with IgM ELISA, real-time RT-PCR would greatly improve the accurate diagnosis of measles cases and avoid missing the measles cases, especially for measles cases during the first few days after onset when the patients were highly contagious and for measles cases with secondary vaccine failure. In conclusion, our study reconfirmed that IgM ELISA is the gold-standard detection assay for measles cases confirmation. However, real-time RT-PCR should be introduced and used to supplement the laboratory diagnosis, especially in the setting of pre-elimination and/or elimination wherever appropriate.

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<![CDATA[Backpack PCR: A point-of-collection diagnostic platform for the rapid detection of Brugia parasites in mosquitoes]]> https://www.researchpad.co/article/5bff05b5d5eed0c484a339d2

Background

Currently, molecular xenomonitoring efforts for lymphatic filariasis rely on PCR or real-time PCR-based detection of Brugia malayi, Brugia timori and Wuchereria bancrofti in mosquito vectors. Most commonly, extraction of DNA from mosquitoes is performed using silica column-based technologies. However, such extractions are both time consuming and costly, and the diagnostic testing which follows typically requires expensive thermal cyclers or real-time PCR instruments. These expenses present significant challenges for laboratories in many endemic areas. Accordingly, in such locations, there exists a need for inexpensive, equipment-minimizing diagnostic options that can be transported to the field and implemented in minimal resource settings. Here we present a novel diagnostic approach for molecular xenomonitoring of filarial parasites in mosquitoes that uses a rapid, NaOH-based DNA extraction methodology coupled with a portable, battery powered PCR platform and a test strip-based DNA detection assay. While the research reported here serves as a proof-of-concept for the backpack PCR methodology for the detection of filarial parasites in mosquitoes, the platform should be easily adaptable to the detection of W. bancrofti and other mosquito-transmitted pathogens.

Methodology/Principal findings

Through comparisons with standard silica column-based DNA extraction techniques, we evaluated the performance of a rapid, NaOH-based methodology for the extraction of total DNA from pools of parasite-spiked vector mosquitoes. We also compared our novel test strip-based detection assay to real-time PCR and conventional PCR coupled with gel electrophoresis, and demonstrated that this method provides sensitive and genus-specific detection of parasite DNA from extracted mosquito pools. Finally, by comparing laboratory-based thermal cycling with a field-friendly miniaturized PCR approach, we have demonstrated the potential for the point-of-collection-based use of this entire diagnostic platform that is compact enough to fit into a small backpack.

Conclusions/Significance

Because this point-of-collection diagnostic platform eliminates reliance on expensive and bulky instrumentation without compromising sensitivity or specificity of detection, it provides an alternative to cost-prohibitive column-dependent DNA extractions that are typically coupled to detection methodologies requiring advanced laboratory infrastructure. In doing so, this field-ready system should increase the feasibility of molecular xenomonitoring within B. malayi-endemic locations. Of greater importance, this backpack PCR system also provides the proof-of-concept framework for the development of a parallel assay for the detection of W. bancrofti.

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<![CDATA[Cryptococcal antigen positivity combined with the percentage of HIV-seropositive samples with CD4 counts <100 cells/μl identifies districts in South Africa with advanced burden of disease]]> https://www.researchpad.co/article/5b297b7d463d7e06147f8d6f

Introduction

Cryptococcal meningitis (CM) is an opportunistic fungal disease with a high mortality among HIV-positive patients with severe immunosuppression (CD4 count <100 cells/μl). Reflexed screening for cryptococcal antigen (CrAg) in remnant blood samples was initially piloted at selected CD4 testing laboratories of the National Health Laboratory Service (NHLS) prior to the implementation of a national screening programme using a lateral flow assay (LFA) (IMMY, Norman, OK, USA). The aim of this study was to assess CrAg positivity nationally, per province and district in combination with the percentage of CD4 samples tested with a CD4 count <100 cells/μl to identify areas with advanced HIV/CrAg disease burden.

Methods

CrAg and CD4 laboratory result data were extracted from the NHLS corporate data warehouse. Monthly test volumes were used to assess CrAg test volumes and coverage, while bubble charts were used to display the relationship between CD4 <100 cells/μl, CrAg positivity and number of positive CrAg samples by district. ArcGIS software was used to spatially report CrAg positivity.

Results

CrAg screening coverage was stable at around 96% after November 2016. Samples with a CD4 <100 cell/μl and CrAg positivity were also stable over the study period at 10% and ~5% respectively. The highest CrAg positivity was reported for the Kwa-Zulu Natal province (7.3%), which also had the lowest percentage of samples with a CD4 <100 cells/μl (7.2%). Uthungulu and Umkhanyakude districts had the highest CrAg positivity (9.3% and 8.9% respectively). Ethekwini and Johannesburg Metro districts contributed to 22% of the total number of CrAg-positive samples tested across South Africa for the period reported.

Conclusion

Existing CD4 testing services were used to rapidly scale up CrAg reflex testing in South Africa. Districts with advanced HIV and CrAg disease burden were identified that need further investigation of patient management interventions.

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