Determination of the Stage Composition of Plasmodium Infections from Bulk Gene Expression Data.

Malaria symptoms are caused by the development of the parasites within the blood of an infected host. Bulk RNA sequencing (RNA-seq) of infected blood can reveal interactions between parasites and the host immune system during an infection, but because multiple developmental stages with distinct transcriptional profiles are concurrently present in infected blood, it is necessary to correct such analyses for differences in cell composition among samples. Gene expression deconvolution is a statistical approach that has been developed for inferring the cell composition of complex tissues characterized by bulk RNA-seq using gene expression profiles from reference cell types. Here, we describe the evaluation of a species-agnostic reference data set that can be used for efficient and accurate gene expression deconvolution of bulk RNA-seq data generated from any Plasmodium species and for correct gene expression analyses for biases caused by differences in stage composition among samples. IMPORTANCE Differences in cell type proportions among samples can introduce artifacts in gene expression analyses and mask genuine differences in gene regulation. Gene expression deconvolution allows estimation of the proportion of each cell type present in one sample directly from bulk RNA sequencing data, but this approach requires a reference data set with the signature profile of each cell type. Here, we evaluate the suitability of a rodent malaria parasite gene expression data set for estimating the proportions of each parasite developmental stage present in bulk RNA sequencing data generated from blood-stage infections with the human parasites Plasmodium falciparum and Plasmodium vivax. These analyses provide a species-agnostic approach for reliably estimating stage proportions in infected human blood and correcting subsequent gene expression analyses for these variations.

Neonatal outcomes in twin pregnancies with the first twin in breech presentation according to the mode of delivery: A cohort study from Dakar Senegal.

The objectives of this study were to compare perinatal outcomes in twin pregnancies where the first twin was in the breech presentation. To do so, we performed a 10-year retrospective cohort study in a single university center. All patients with a twin pregnancy with the first twin in breech presentation, a gestational age greater than or equal to 34 weeks' gestation, and a birth weight <= 1500 g were included. The main outcome measures were 5-minute Apgar score <7 and perinatal mortality. We included 353 pairs of twins which complied with the inclusion criteria. One hundred and fifty (150) patients delivered vaginally while 203 pairs of twins were delivered by caesarean section. Patients who delivered abdominally were similar to those who delivered vaginally with regard to age, parity, and gestational age. Six twins A delivered vaginally and 2 delivered by caesarean section had an Apgar score < 7 (p = 0.76) whereas 12 twins B delivered vaginally and 2 delivered abdominally had an Apgar score <7 (p = 0.001). Perinatal mortality did not differ significantly between twins delivered abdominally and those delivered vaginally. There was no evidence that vaginal delivery was risky with regards to depressed Apgar scores for Twin A and neonatal mortality for breech first twins that weighed at least 1500 g. However, Twin B delivered vaginally were more likely to present with a low 5-minute Apgar score. Along with the literature, the findings of this study do not currently allow to define a consensual obstetric attitude towards management of breech first twin deliveries. Until more prospective multicenter randomized controlled studies shed light on this problem, the skills, experience and judgment of the obstetrician will play a major role in the decision-making process.

Single-genome sequencing reveals within-host evolution of human malaria parasites.

Population genomics of bulk malaria infections is unable to examine intrahost evolution; therefore, most work has focused on the role of recombination in generating genetic variation. We used single-cell sequencing protocol for low-parasitaemia infections to generate 406 near-complete single Plasmodium vivax genomes from 11 patients sampled during sequential febrile episodes. Parasite genomes contain hundreds of de novo mutations, showing strong signatures of selection, which are enriched in the ApiAP2 family of transcription factors, known targets of adaptation. Comparing 315 P. falciparum single-cell genomes from 15 patients with our P. vivax data, we find broad complementary patterns of de novo mutation at the gene and pathway level, revealing the importance of within-host evolution during malaria infections.

Knowledge, attitudes and practices (KAP) to assess the impact of school children's awareness of malaria using the MOSKI KIT® tool: study case of some Dakar schools in Senegal.

BACKGROUND: MOSKI KIT® is a fun tool designed to interest children for prevention and management of malaria. This study was carried out with the objective to assess the short- and long-term impacts of this tool on the knowledge, attitudes, and practices of school children, and on the transmission of the knowledge received at the household level as well. METHOD: The study took place in elementary schools in the city centre (with relatively low endemicity) and in the Niayes area (at high risk of anopheline and malaria) in the Dakar region of Senegal. The various schools chosen for this study were divided into an intervention group and a control group. The intervention schools were also divided into two subgroups, a full package subgroup and another partial package. During this study three surveys were conducted, the first one before exposure to the MOSKI KIT®, the second one a week later and the third a year later. For the control schools only one survey was conducted and at the same time than the third for the intervention schools. Two household surveys (a week and a year after exposure) were also conducted for the intervention schools against one for the control schools. RESULTS: Before sensitization, the proportion of school children with a grade above or equal to the average was 50% for the complete package subgroup (CPS) and 53% for the partial package subgroup (PPS). A week later, these proportions were 69% and 71%, respectively for the complete and PPSs. A year later, they were 99.4% for the CPS, 98.1% for the PPS and 99.5% for the control group; The number of children who spoke to their parents about malaria was greater in intervention schools than that of control schools. They were 46.63% and 32.58%, respectively in intervention and control schools. CONCLUSION: The MOSKI KIT, has enabled an increase of the knowledge of school children about malaria in the short term and favoured its retention in the long term. However, its impact was not felt on their attitudes and practices.

Single-cell genome sequencing of protozoan parasites.

Despite considerable genetic variation within hosts, most parasite genome sequencing studies focus on bulk samples composed of millions of cells. Analysis of bulk samples is biased toward the dominant genotype, concealing cell-to-cell variation and rare variants. To tackle this, single-cell sequencing approaches have been developed and tailored to specific host-parasite systems. These are allowing the genetic diversity and kinship in complex parasite populations to be deciphered and for de novo genetic variation to be captured. Here, we outline the methodologies being used for single-cell sequencing of parasitic protozoans, such as Plasmodium and Leishmania spp., and how these tools are being applied to understand parasite biology.

Co-transmission of Related Malaria Parasite Lineages Shapes Within-Host Parasite Diversity.

In high-transmission regions, we expect parasite lineages within complex malaria infections to be unrelated due to parasite inoculations from different mosquitoes. This project was designed to test this prediction. We generated 485 single-cell genome sequences from fifteen P. falciparum malaria patients from Chikhwawa, Malawi-an area of intense transmission. Patients harbored up to seventeen unique parasite lineages. Surprisingly, parasite lineages within infections tend to be closely related, suggesting that superinfection by repeated mosquito bites is rarer than co-transmission of parasites from a single mosquito. Both closely and distantly related parasites comprise an infection, suggesting sequential transmission of complex infections between multiple hosts. We identified tetrads and reconstructed parental haplotypes, which revealed the inbred ancestry of infections and non-Mendelian inheritance. Our analysis suggests strong barriers to secondary infection and outbreeding amongst malaria parasites from a high transmission setting, providing unexpected insights into the biology and transmission of malaria.

Application of non-Gaussian water diffusional kurtosis imaging in the assessment of uterine tumors: A preliminary study.

OBJECTIVES: To evaluate the interobserver reliability and value of diffusional kurtosis imaging (DKI) in the assessment of uterine tumors compared with those of conventional diffusion-weighted imaging (DWI). METHODS: This retrospective study was approved by our institutional review board, which waived the requirement for informed consent. Fifty-eight women (mean age: 55.0 ± 13.6 years; range: 30-89 years) with suspected malignant uterine tumors underwent 3-T magnetic resonance imaging using DKI and DWI. Twelve had coexisting leiomyoma. Two observers analyzed region-of-interest measurements of diffusivity (D), kurtosis (K), and the apparent diffusion coefficient (ADC) of uterine lesions and healthy adjacent tissues. Interobserver agreement was evaluated using the intra-class correlation coefficient (ICC). The mean values were compared using one-way analysis of variance with a post-hoc Tukey's honestly significant difference test. The diagnostic accuracy of D and ADC in differentiating malignant tumors from benign leiomyomas was analyzed using receiver operating characteristic (ROC) analysis. RESULTS: The ICCs between the two observers in evaluating D, K, and the ADC of the malignant tumors were higher than 0.84, suggesting excellent interobserver agreements. The mean D (×10-3 mm2/s) of uterine cancers (1.05 ± 0.41 and 1.09 ± 0.40 for observers 1 and 2, respectively) were significantly lower than those of leiomyoma (1.40 ± 0.37 and 1.56 ± 0.33, respectively; P < 0.05), healthy myometrium (1.72 ± 0.27 and 1.69 ± 0.30, respectively; P < 0.001), and healthy endometrium (1.53 ± 0.35 and 1.42 ± 0.37, respectively; P < 0.005). There was no significant difference in the area under the ROC curve between D and ADC. The mean K of uterine cancers (0.88 ± 0.28 and 0.90 ± 0.23, respectively) were higher than those of myometrium (0.72 ± 0.10 and 0.73 ± 0.10, respectively; P < 0.001), healthy endometrium (0.65 ± 0.13 and 0.60 ± 0.18, respectively; P < 0.001), and leiomyoma (0.76 ± 0.14 and 0.77 ± 0.16, respectively; not significant, P > 0.1). CONCLUSIONS: Interobserver agreements in evaluating D, K, and ADC were moderate to excellent. D performed equally to conventional DWI in differentiating between benign and malignant uterine lesions. The mean K of malignant uterine lesions was significantly higher than that of non-tumorous myometrium or endometrium.

Evidence for parasite-mediated selection during short-lasting toxic algal blooms.

Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellate Alexandrium minutum and two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily reduction in relative A. minutum abundances, demonstrating strong parasite-mediated selection. There was genetic variability in infectivity in both parasite species, and in resistance in the host. We found no evidence for coevolution in one estuary; however, in the other estuary, we found high genetic diversity in the two parasite species, fluctuations in infectivity and suggestion that the two parasites are well adapted to their host, as in 'Red Queen' dynamics. Thus, coevolution is possible over the short time span of a bloom, but geographically variable, and may feedback on community dynamics.

Single-breath-hold thin-slice gadoxetic acid-enhanced hepatobiliary MR imaging using a newly developed three-dimensional fast spoiled gradient-echo sequence.

PURPOSE: To prospectively evaluate the efficacy of a new three-dimensional gradient-echo sequence (Turbo LAVA) that uses undersampled k-space acquisition combined with a two-dimensional parallel imaging technique for hepatobiliary MRI. MATERIALS AND METHODS: Sixty patients underwent T1-weighted gadoxetic acid-enhanced hepatobiliary axial MRI during a single breath-hold using both Turbo LAVA (thickness/interval=1.6/0.8mm) and conventional three-dimensional gradient-echo (4/2mm; LAVA) sequences at 3T. Axial 4-mm-thick reformation was performed from Turbo LAVA images. Portal vein-to-liver contrast (PLC), bile duct-to-liver contrast (BLC), and lesion-to-liver contrast (LLC) were compared. Two radiologists independently assessed image quality using a five-point scale. Sagittal 4-mm-thick multiplanar reconstructions (MPR) were performed from both sequences and assessed together with directly obtained 4-mm-thick sagittal LAVA images in terms of sharpness. The paired t-test was used to compare PLC, BLC, and LLC. The Wilcoxon signed rank test was used to compare five-point scales. RESULTS: The mean PLC (P<0.001), BLC (P<0.001), and LLC (P<0.005) were significantly higher for Turbo LAVA than for LAVA; the scores for image noise and sharpness were inferior (P=0.000 and 0.005) and superior (0.005 and 0.157) for Turbo LAVA. There were no significant differences in the scores for bile duct visualization, artifacts, fat suppression quality, overall quality, and focal lesion conspicuity. For sagittal images, MPR Turbo LAVA showed significantly better sharpness than MPR LAVA but showed significantly worse sharpness compared with directly obtained LAVA. CONCLUSION: High-spatial-resolution single-breath-hold hepatobiliary MRI using Turbo LAVA was feasible. Diagnostic-quality MPR images can be obtained using this sequence.