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Near the northern border of Sumatra, the right-lateral strike–slip Sumatran fault zone splits into two branches and extends into the offshore, as revealed by seismic sounding surveys. However, due to its strike–slip faulting characteristics, the Sumatran fault zone's activity is rarely believed to cause tsunami hazards in this region. According to two reprocessed reflection seismic profiles, the extended Sumatran fault zone is strongly associated with chaotic facies, indicating that large submarine landslides have been triggered. Coastal steep slopes and new subsurface characteristics of submarine landslide deposits were mapped using recently acquired high-resolution shallow bathymetry data. Slope stability analysis revealed some targets with steep morphology to be close to failure. In an extreme hypothetical case, an earthquake of Mw 7 or more occurred, and the strong ground shaking triggered a submarine landslide off the northern shore of Sumatra. Based on a simulation of tsunami wave propagation in shallow water, the results of this study indicate that a potential tsunami hazard from several submarine landslide sources triggered by the strike–slip fault system can generate a tsunami as high as 4–8 m at several locations along the northern coast of Aceh. The landslide tsunami hazard assessment and early warning systems in this study area can be improved on the basis of this proposed scenario.

Abstract Background Important regulation occurs at the level of transcription in Plasmodium falciparum and growing evidence suggests that these apicomplexan parasites have complex regulatory networks. Recent studies implicate long noncoding RNAs (lncRNAs) as transcriptional regulators in P. falciparum. However, due to limited research and the lack of necessary experimental tools, our understanding of their role in the malaria-causing parasite remains largely unelucidated. In this work, we address one of these limitations, the lack of an updated and improved lncRNA annotation in P. falciparum. Results We generated long-read RNA sequencing data and integrated information extracted and curated from multiple sources to manually annotate lncRNAs. We identified 1119 novel lncRNAs and validated and refined 1250 existing annotations. Utilising the collated datasets, we generated evidence-based ranking scores for each annotation and characterised the distinct genomic contexts and features of P. falciparum lncRNAs. Certain features indicated subsets with potential biological significance such as 25 lncRNAs containing multiple introns, 335 lncRNAs lacking mutations in piggyBac mutagenic studies and lncRNAs associated with specific biologic processes including two new types of lncRNAs found proximal to var genes. Conclusions The insights and the annotation presented in this study will serve as valuable tools for researchers seeking to understand the role of lncRNAs in parasite biology through both bioinformatics and experimental approaches.

In a recent clinical trial for oral administration of cipargamin in individuals with malaria, there was an emergence of recrudescent parasites with a G358S mutation in PfATP4. In this work, the authors investigate the effect of this mutation on the function of the ATPase, on parasite growth and susceptibility to antimalarial drugs.

ABSTRACT The repeated emergence of antimalarial drug resistance in Plasmodium falciparum, including to the current frontline antimalarial artemisinin, is a perennial problem for malaria control. Next-generation sequencing has greatly accelerated the identification of polymorphisms in resistance-associated genes but has also highlighted the need for more sensitive and accurate laboratory tools to profile current and future antimalarials and to quantify the impact of drug resistance acquisition on parasite fitness. The interplay of fitness and drug response is of fundamental importance in understanding why particular genetic backgrounds are better at driving the evolution of drug resistance in natural populations, but the impact of parasite fitness landscapes on the epidemiology of drug resistance has typically been laborious to accurately quantify in the lab, with assays being limited in accuracy and throughput. Here we present a scalable method to profile fitness and drug response of genetically distinct P. falciparum strains with well-described sensitivities to several antimalarials. We leverage CRISPR/Cas9 genome-editing and barcode sequencing to track unique barcodes integrated into a nonessential gene (pfrh3). We validate this approach in multiplex competitive growth assays of three strains with distinct geographical origins. Furthermore, we demonstrate that this method can be a powerful approach for tracking artemisinin response as it can identify an artemisinin resistant strain within a mix of multiple parasite lines, suggesting an approach for scaling the laborious ring-stage survival assay across libraries of barcoded parasite lines. Overall, we present a novel high-throughput method for multiplexed competitive growth assays to evaluate parasite fitness and drug response. IMPORTANCE The complex interplay between antimalarial resistance and parasite fitness has important implications for understanding the development and spread of drug resistance alleles and the impact of genetic background on transmission. One limitation with current methodologies to measure parasite fitness is the ability to scale this beyond simple head-to-head competition experiments between a wildtype control line and test line, with a need for a scalable approach that allows tracking of parasite growth in complex mixtures. In our study, we have used CRISPR editing to insert unique DNA barcodes into a safe-harbor genomic locus to tag multiple parasite strains and use next-generation sequencing to read out strain dynamics. We observe inherent fitness differences between the strains, as well as sensitive modulation of responses to challenge with clinically relevant antimalarials, including artemisinin.

CRISPR editing has enabled the rapid creation of fluorescent Plasmodium transgenic lines, facilitating a deeper understanding of parasite biology. The impact of genetic perturbations such as gene disruption or the introduction of drug resistance alleles on parasite fitness is typically quantified in competitive growth assays between the query line and a wild type reference. Although fluorescent reporter lines offer a facile and frequently used method to measure relative growth, this approach is limited by the strain background of the existing reporter, which may not match the growth characteristics of the query strains, particularly if these are slower-growing field isolates. Here, we demonstrate an efficient CRISPR-based approach to generate fluorescently labelled parasite lines using mNeonGreen derived from the LanYFP protein in Branchiostoma lanceolatum, which is one of the brightest monomeric green fluorescent proteins identified. Using a positive-selection approach by insertion of an in-frame blasticidin S deaminase marker, we generated a Dd2 reporter line expressing mNeonGreen under the control of the pfpare (P. falciparum Prodrug Activation and Resistance Esterase) locus. We selected the pfpare locus as an integration site because it is highly conserved across P. falciparum strains, expressed throughout the intraerythrocytic cycle, not essential, and offers the potential for negative selection to further enrich for integrants. The mNeonGreen@pare line demonstrates strong fluorescence with a negligible fitness defect. In addition, the construct developed can serve as a tool to fluorescently tag other P. falciparum strains for in vitro experimentation.

Imidazolopiperazines (IZPs) are a class of compounds under clinical development for malaria, but their mechanism of action is unclear. Here, the authors show that IZPs inhibit the parasite’s secretory pathway, affecting protein trafficking and export.

Early detection of malignant thyroid nodules leading to patient-specific treatments can reduce morbidity and mortality rates. Currently, thyroid specialists use medical images to diagnose then follow the treatment protocols, which have limitations due to unreliable human false-positive diagnostic rates. With the emergence of deep learning, advances in computer-aided diagnosis techniques have yielded promising earlier detection and prediction accuracy; however, clinicians’ adoption is far lacking. The present study adopts Xception neural network as the base structure and designs a practical framework, which comprises three adaptable multi-channel architectures that were positively evaluated using real-world data sets. The proposed architectures outperform existing statistical and machine learning techniques and reached a diagnostic accuracy rate of 0.989 with ultrasound images and 0.975 with computed tomography scans through the single input dual-channel architecture. Moreover, the patient-specific design was implemented for thyroid cancer detection and has obtained an accuracy of 0.95 for double inputs dual-channel architecture and 0.94 for four-channel architecture. Our evaluation suggests that ultrasound images and computed tomography (CT) scans yield comparable diagnostic results through computer-aided diagnosis applications. With ultrasound images obtained slightly higher results, CT, on the other hand, can achieve the patient-specific diagnostic design. Besides, with the proposed framework, clinicians can select the best fitting architecture when making decisions regarding a thyroid cancer diagnosis. The proposed framework also incorporates interpretable results as evidence, which potentially improves clinicians’ trust and hence their adoption of the computer-aided diagnosis techniques proposed with increased efficiency and accuracy.

Vehicular ad-hoc networks (VANETs) aim to provide efficient safety and infotainment services. Wireless Access in Vehicular Environments (WAVE), which is a standard designed specifically for VANETs, stipulates seven 10-MHz channels: one control channel (CCH) for safety message transmission and six service channels (SCHs) for service message transmission. However, providing reliable broadcasting of safety messages on the CCH and efficient coordination of vehicles for service message transmission across the multiple SCHs in highly dynamic VANET environment is a nontrivial problem. In this paper, we propose a coordinated, adaptive, and reliable multichannel medium-access control scheme for the VANETs (VCAR-MAC). In VCAR-MAC, a novel time-division multiple access (TDMA)-based scheme that considers real-world environmental conditions is proposed to identify every vehicle quickly so that a time slot on the CCH can be allocated efficiently for reliable safety message transmission. On the SCHs, VCAR-MAC provides a multi-SCH coordination scheme, which adaptively adjusts the SCH reservation period in order to fully utilize the channel bandwidth. Furthermore, a dynamic contention window (CW) mechanism is proposed, in which the initial CW size is adaptively optimized to maximize the number of successful SCH reservations, thereby maximizing the service message throughput. It has been proven via the mathematical analysis and simulation experiment that VCAR-MAC can significantly improve throughput and reduce delay for both safety and service messages.

ABSTRACT Plasmodium parasites rely heavily on glycolysis for ATP production and for precursors for essential anabolic pathways, such as the methylerythritol phosphate (MEP) pathway. Here, we show that mutations in the Plasmodium falciparum glycolytic enzyme, phosphofructokinase (PfPFK9), are associated with in vitro resistance to a primary sulfonamide glycoside (PS-3). Flux through the upper glycolysis pathway was significantly reduced in PS-3-resistant parasites, which was associated with reduced ATP levels but increased flux into the pentose phosphate pathway. PS-3 may directly or indirectly target enzymes in these pathways, as PS-3-treated parasites had elevated levels of glycolytic and tricarboxylic acid (TCA) cycle intermediates. PS-3 resistance also led to reduced MEP pathway intermediates, and PS-3-resistant parasites were hypersensitive to the MEP pathway inhibitor, fosmidomycin. Overall, this study suggests that PS-3 disrupts core pathways in central carbon metabolism, which is compensated for by mutations in PfPFK9, highlighting a novel metabolic drug resistance mechanism in P. falciparum. IMPORTANCE Malaria, caused by Plasmodium parasites, continues to be a devastating global health issue, causing 405,000 deaths and 228 million cases in 2018. Understanding key metabolic processes in malaria parasites is critical to the development of new drugs to combat this major infectious disease. The Plasmodium glycolytic pathway is essential to the malaria parasite, providing energy for growth and replication and supplying important biomolecules for other essential Plasmodium anabolic pathways. Despite this overreliance on glycolysis, no current drugs target glycolysis, and there is a paucity of information on critical glycolysis targets. Our work addresses this unmet need, providing new mechanistic insights into this key pathway.

The emergence of artemisinin (ART) resistance in Plasmodium falciparum intra-erythrocytic parasites has led to increasing treatment failure rates with first-line ART-based combination therapies in Southeast Asia. Decreased parasite susceptibility is caused by K13 mutations, which are associated clinically with delayed parasite clearance in patients and in vitro with an enhanced ability of ring-stage parasites to survive brief exposure to the active ART metabolite dihydroartemisinin. Herein, we describe a panel of K13-specific monoclonal antibodies and gene-edited parasite lines co-expressing epitope-tagged versions of K13 in trans. By applying an analytical quantitative imaging pipeline, we localize K13 to the parasite endoplasmic reticulum, Rab-positive vesicles, and sites adjacent to cytostomes. These latter structures form at the parasite plasma membrane and traffic hemoglobin to the digestive vacuole wherein artemisinin-activating heme moieties are released. We also provide evidence of K13 partially localizing near the parasite mitochondria upon treatment with dihydroartemisinin. Immunoprecipitation data generated with K13-specific monoclonal antibodies identify multiple putative K13-associated proteins, including endoplasmic reticulum-resident molecules, mitochondrial proteins, and Rab GTPases, in both K13 mutant and wild-type isogenic lines. We also find that mutant K13-mediated resistance is reversed upon co-expression of wild-type or mutant K13. These data help define the biological properties of K13 and its role in mediating P. falciparum resistance to ART treatment.