Epidemiology of malaria in the provinces of Sarangani, South Cotabato and TawiTawi in Mindanao, The Philippines

The Philippines is targeting malaria elimination by 2020. To reach this goal, it is important to locate all residual foci of malaria and where possible, aggressively diagnose and treat every malaria infection. In low endemic provinces malaria transmission becomes focal in hard-to-reach areas where asymptomatic people do not actively seek treatment and thus, continue to perpetuate transmission. This study aimed (a) to estimate prevalence of Plasmodium species in three malaria-endemic provinces in Mindanao, (b) to measure malaria transmission intensity in these provinces using antibody markers of exposure to P. falciparum and P. vivax AMA-1 and MSP-119 antigens, (c) to determine polymorphisms in pfcrt, pfmdr1 and pvmdr1 genes, and (d) to discuss implications of these findings to malaria elimination in Mindanao. Cross-sectional surveys were conducted to a total of 2,628 consenting participants across all ages in the provinces of Sarangani, South Cotabato and Tawi-Tawi from 2010 to 2013. The RDT FalciVax™ was used for field diagnosis of malaria in Sarangani Province and South Cotabato Province for P. falciparum and P. vivax infection while microscopy was used in Tawi-Tawi Province for field diagnosis of malaria. Finger-prick blood spots on filter paper were collected from participants for PCR diagnosis, genotyping of pfcrt, pfmdr1 and pvmdr1 genes, and screening antibodies to P. falciparum and P. vivax AMA-1 and MSP-119 antigens using indirect ELISA. Blood spots were also collected from patients presenting with malaria symptoms from selected municipalities of Sarangani Province and South Cotabato Province as a pilot survey. Overall malaria prevalence by PCR was 3.7% in Sarangani Province, 10% in South Cotabato Province and 4.2% in Tawi-Tawi Province. P. falciparum prevalence by PCR was higher than P. vivax prevalence in Sarangani Province and Tawi-Tawi Province but the opposite was found in South Cotabato Province. There was one imported case of P. malariae in South Cotabato and there were no P. knowlesi and P. ovale infections found in the three provinces surveyed. There were disagreements in diagnosing P. falciparum and P. vivax using antigen detection, microscopy and PCR and these were attributed to sampling low parasite-density infections from small volume of peripheral blood spotted on filter paper. The pfcrt codons 72-76 haplotypes CVMNK (27.4%), CVIET (59.7%) and SVMNT (9.7%) were described in 62 P. falciparum isolates from Mindanao. The pfcrt mutant A144T and L160Y alleles were not found among P. falciparum isolates with pfcrt K76T mutant allele but lacked the pfcrt A220S mutation. The pfmdr1 86N- 184F-1034S-1042N-1246D haplotype, which was repeatedly associated with higher parasite survival following artemether-lumefantrine treatment, was found in seven P. falciparum isolates from Mindanao. Genotyped P. vivax isolates from Mindanao have the wild type pvmdr1 91N allele, which corresponded to pfmdr1 codon 86. The pvmdr1 Y976F mutant allele, which has been reported in chloroquine-resistant P. vivax in other countries, was found in 55.6% (5/9) P. vivax isolates successfully genotyped in this codon while the pvmdr1 1076L wild-type allele was found in three P. vivax isolates successfully genotyped in this codon. Combined seroprevalence to P. falciparum and P. vivax AMA-1 and MSP-119 antigens suggested that exposure to P. falciparum was higher than exposure to P. vivax in Sarangani Province and Tawi-Tawi Province. Overall seroprevalence to P. falciparum and P. vivax was 18.9% and 14.6% in Sarangani Province respectively. In Tawi-Tawi Province the overall seroprevalence to P. falciparum and P. vivax was 18.2% and 12.9% respectively. The opposite was observed in South Cotabato Province where overall seroprevalence to P. falciparum (3.4%) was lower than the overall seroprevalence to P. vivax. The seroconversion rates (λ) for P. falciparum and P. vivax malaria were estimated using simple reversible catalytic models. In Sarangani Province the SCR for P. falciparum (0.014, 95%CI 0.010-0.020) was lower than SCR for P. vivax (0.019, 95% CI 0.010-0.036). A model allowing two forces of infection was used to estimate SCR for P. falciparum in Tawi-Tawi. Results suggested that there was a change in P. falciparum transmission in Tawi-Tawi Province approximately 25 years before the survey was conducted. The estimated SCR for P. falciparum was 0.041 (95% CI 0.017-0.098) in Tawi-Tawi Province before 1987. The model suggested that SCR was reduced to 0.007 (95% CI 0.005-0.009) after 1987 to the time of survey. In South Cotabato the SCR for P. falciparum was very low (0.004, 95% CI 0.001-0.016). There was no SCR estimated for P. vivax in South Cotabato because seropositivity was equally distributed across age groups. Findings in this study were held back by sample size and low-density parasite infections in small number of infected humans. Nevertheless, this provided important baseline data for malaria epidemiology in Mindanao

Divergent selection for humoral immune responsiveness in chickens: distribution and effects of major histocompatibility complex types

International audienc

Adaptive approximate Bayesian computation for complex models

Approximate Bayesian computation (ABC) is a family of computational techniques in Bayesian statistics. These techniques allow to fi t a model to data without relying on the computation of the model likelihood. They instead require to simulate a large number of times the model to be fi tted. A number of re finements to the original rejection-based ABC scheme have been proposed, including the sequential improvement of posterior distributions. This technique allows to de- crease the number of model simulations required, but it still presents several shortcomings which are particu- larly problematic for costly to simulate complex models. We here provide a new algorithm to perform adaptive approximate Bayesian computation, which is shown to perform better on both a toy example and a complex social model.Comment: 14 pages, 5 figure

Clades and clans: a comparison study of two evolutionary models

The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under these two models provides valuable insights into macro-evolutionary processes, and is important in hypothesis testing and Bayesian analyses in phylogenetics. Here we show that these distributions are log-convex, which implies that very large clades or very small clades are more likely to occur under these two models. Moreover, we prove that there exists a critical value $\kappa(n)$ for each $n\geqslant 4$ such that for a given clade with size $k$, the probability that this clade is contained in a random tree with $n$ leaves generated under the YHK model is higher than that under the PDA model if $1<k<\kappa(n)$, and lower if $\kappa(n)<k<n$. Finally, we extend our results to binary unrooted trees, and obtain similar results for the distributions of clan sizes.Comment: 21page

Management of Small Renal Masses

We commend Dr Xing and colleagues for their interesting comparative analysis of treatment modalities for small renal masses in the July 2018 issue of Radiology (cf. Xing M, Kokabi N, Zhang D, Ludwig JM, Kim HS. Comparative effectiveness of thermal ablation, surgical resection, and active surveillance for T1a renal cell carcinoma: a Surveillance, Epidemiology, and End Results (SEER)–Medicare-linked population study. Radiology 2018;288[1]:81–90). This is clearly an important clinical question. The authors made use of propensity score–matched observational data from the Surveillance, Epidemiology, and End Results (SEER)–Medicare database adjusted for 17 variables to compare cancer-specific and overall survival with partial nephrectomy (PN), radical nephrectomy (RN), thermal ablation (TA), and active surveillance (AS)

A supervisory-based collaborative Obstacle-Guided Path Refinement algorithm for path planning in wide terrains

Robotic exploration of wide terrains, such as agricultural fields, could be challenging while considering the limited robot’s capabilities in terms of sensing and power. Thus, in this article, we proposed OGPR*, an Obstacle Guided Path Refinement algorithm for quickly planning collision-free paths utilizing the obstacles existing in the environment. To tackle the issue of exploring wide terrains, a supervisory-based collaboration between the quadcopter and a mobile robot is proposed. The quadcopter is responsible for streaming subsequently live two-dimensional images for the environment under discussion while planning safe paths for the ground the mobile robot is planning safe paths to manoeuvre. Numerical simulations proved the significant performance of the proposed OGBR* algorithm when compared to the state of the art algorithms exist in the literature

Qualitative exploration of the renal stone patients' experience and development of the renal stone-specific patient-reported outcome measure

OBJECTIVES: To investigate the experience of patients living with renal calculi via a qualitative methodology, aiming to develop and validate a disease-specific patient-reported outcome measure (PROM) for renal stones, the Cambridge Renal Stone PROM (CReSP). PATIENTS, SUBJECTS AND METHODS: Patients with radiologically confirmed renal calculi who had undergone a range of management options were invited to focus groups or semi-structured interviews to elicit patient input and generate the PROM content. The developed renal stone PROM underwent validity studies included Cronbach's α for internal consistency, Spearman's and Pearson's correlation coefficients for test-retest reliability. Discriminant validity was assessed by Pearson's correlation coefficients vs the EuroQol five-dimensional five-level questionnaire (EQ-5D-5L). Our project has Health and Social Care Research Ethics Committee approval. RESULTS: A total of 106 subjects participated in creating the newly developed PROM. In all, 36 patients were invited to 22 semi-structured interviews and four focus groups, until reaching saturation. Major issues reported, and themes selected for the renal stone PROM included pain, anxiety, limitations to social life and tiredness, urinary symptoms, dietary changes' impacts, and gastrointestinal tract symptoms. Reliability analysis for 30 patients to determine internal consistency using Cronbach's α with a mean (range) of 0.91 (0.90-0.93) within domains and Cronbach's α between domains was 0.92. Average inter-item Pearson's and Spearman's correlation within domains was performed, with a Pearson's correlation mean (range) of 0.77 (0.73-0.85) and Spearman's correlation mean (range) of 0.72 (0.63-0.77). The test-retest Pearson's correlation mean (range) was 0.85 (0.57-0.95). Validity assessment was performed for 20 patients vs 20 controls. Pearson's correlation with EQ-5D-5L was -0.74, showing the newly developed PROM successfully discriminated patients with kidney stones. Our final renal stone PROM consists of 14 questions that are rated on a Likert scale; the higher the score, the worse the effect on a patient's quality of life. CONCLUSIONS: Although pain was the most frequent symptom, other health-related and social well-being issues significantly impacted patients' lives. Our validated patient-derived CReSP is a new instrument, specifically tailored to measure renal stone disease health outcomes from the patient's point of view

Kilohertz QPOs in low-mass X-ray binaries as oscillation modes of tori around neutron stars - I

There have been many efforts to explain the dynamical mechanisms behind the phenomenology of quasi-periodic oscillations (QPOs) seen in the X-ray light curves of low-mass X-ray binaries. Up to now, none of the models can successfully explain all the frequencies observed in the power spectral density of the light curves. After performing several general-relativistic hydrodynamic simulations of non-self-gravitating axisymmetric thick tori with constant specific angular momentum oscillating around a neutron star such as the one associated with the low-mass X-ray binary 4U 1636 − 53, we find that the oscillation modes give rise to QPOs similar to those seen in the observational data. In particular, when matching pairs of kilohertz QPOs from the numerical simulations with those observed, certain combinations reproduce well the observations, provided we take a mass for the neutron star that is smaller than what is generally assumed. At the same time, we find that tori with constant specific angular momentum cannot match the entire range of frequencies observed for 4U 1636−53 due to physical constraints set on their size. Finally, we show that our results are consistent with the observed shifts in QPO frequency that could accompany state transitions of the accretion disc