Plasmodium falciparum pfhrp2 and pfhrp3 Gene Deletions in Malaria-Hyperendemic Region, South Sudan.

Pfhrp2 and pfhrp3 gene deletions threaten the use of Plasmodium falciparum malaria rapid diagnostic tests globally. In South Sudan, deletion frequencies were 15.6% for pfhrp2, 20.0% for pfhrp3, and 7.5% for double deletions. Deletions were approximately twice as prevalent in monoclonal infections than in polyclonal infections.

Seasonal malaria chemoprevention in a context of high presumed sulfadoxine-pyrimethamine resistance: malaria morbidity and molecular drug resistance profiles in South Sudan.

BACKGROUND: Seasonal malaria chemoprevention (SMC) using sulfadoxine-pyrimethamine plus amodiaquine (SP-AQ), is a community-based malaria preventive strategy commonly used in the Sahel region of sub-Saharan Africa. However, to date it has not been implemented in East Africa due to high SP resistance levels. This paper is a report on the implementation of SMC outside of the Sahel in an environment with a high level of presumed SP-resistance: five cycles of SMC using SPAQ were administered to children 3-59 months during a period of high malaria transmission (July-December 2019) in 21 villages in South Sudan. METHODS: A population-based SMC coverage survey was combined with a longitudinal time series analysis of health facility and community health data measured after each SMC cycle. SMC campaign effectiveness was assessed by Poisson model. SPAQ molecular resistance markers were additionally analysed from dried blood spots from malaria confirmed patients. RESULTS: Incidence of uncomplicated malaria was reduced from 6.6 per 100 to an average of 3.2 per 100 after SMC administration (mean reduction: 53%) and incidence of severe malaria showed a reduction from 21 per 10,000 before SMC campaign to a mean of 3.3 per 10,000 after each cycle (mean reduction: 84%) in the target group when compared to before the SMC campaign. The most prevalent molecular haplotype associated with SP resistance was the IRNGE haplotype (quintuple mutant, with 51I/59R/108N mutation in pfdhfr + 437G/540E in pfdhps). In contrast, there was a low frequency of AQ resistance markers and haplotypes resistant to both drugs combined (< 2%). CONCLUSIONS: The SMC campaign was effective and could be used as an additional preventive tool in seasonal malaria settings outside of the Sahel, especially in areas where access to health care is unstable. Malaria case load reduction was observed despite the high level of resistance to SP.

Characterization of autochthonal yeasts isolated from Spanish soft raw ewe milk protected designation of origin cheeses for technological application.

The yeasts involved in the ripening process of artisanal soft raw ewe milk Protected Designation of Origin (PDO) Torta del Casar and Queso de la Serena cheeses produced in Extremadura, Spain, were isolated throughout their ripening process, strain typed, and characterized for some important technological properties. A total of 508 yeast isolates were obtained and identified by inter-single sequence repeat anchored PCR amplification analysis and subsequent sequencing of the internal transcribed spacer ITS1/ITS2 5.8S rRNA. A total of 19 yeast species representing 8 genera were identified. Debaryomyces hansenii, Pichia kudriavzevii, Kluyveromyces lactis, and Yarrowia lipolytica were the predominant species. We selected 157 isolates, by genotyping and origin, for technological characterization. The evaluation of yeast isolates' growth under stress conditions of cheese ripening showed that 87 presented better performance. Among them, 71 isolates were not able to catabolize tyrosine to produce a brown pigment. Principal component analysis of the biochemical features of these isolates showed that 9 strains stood out, 3 K. lactis strains (2287, 2725, and 1507), 2 Pichia jadinii (1731 and 433), 2 Yarrowia alimentaria (1204 and 2150), Y. lipolytica 2495 and P. kudriavzevii 373. These strains displayed strong extracellular proteolytic activity on skim milk agar as well as an adequate enzymatic profile (strong aminopeptidase and weak protease activity), suggesting their great potential for cheese proteolysis. Extracellular lipolytic activity was mainly restricted to Yarrowia spp. isolates and weakly present in P. kudriavzevii 373 and K. lactis 2725, although enzymatic characterization by API-ZYM (bioMérieux SA) evidenced that all may contribute, at least in part, to the lipolysis process. Moreover, these strains were able to assimilate lactose, galactose, and glucose at NaCl concentrations higher than that usually found in cheese. However, lactate and citrate assimilation were limited to Y. lipolytica 2495, P. kudriavzevii 373, and P. jadinii 433, and may contribute to the alkalinizing process relevant to biochemical processes that take place in the last stages of ripening. By contrast, K. lactis strains showed acidifying capacity and ß-galactosidase activity and may take part in the initial stages of ripening, together with lactic acid bacteria. Thus, considering the technological characteristics studied, the 9 selected strains presented biochemical features well suited to their potential use as adjunct cultures, alone or in combination with autochthonous starter bacteria in the cheesemaking process, to overcome the heterogeneity of these PDO cheeses, preserving their unique sensory characteristics.

Application of ultrasound for quality control of Torta del Casar cheese ripening.

This work aimed to establish the ultrasound parameters that can be useful to classify the defects in the soft cheese Torta del Casar during ripening. During ripening by ultrasound, 1 standard and 3 defective cheese batches (anomalous microbial population, inadequate pressing curd, and excessive pressing curd) were evaluated. Ultrasound parameters related to velocity, attenuation, and frequency were calculated and correlated with the physicochemical and rheological properties of the cheeses. Ultrasound data were considered variables in linear discriminant analysis to attempt cheese classification at different periods of the ripening process. Defective soft cheeses could be discriminated from standard ones with good accuracy, mainly at the final stages of ripening. The differentiation of cheese samples from 2 of the defective cheese batches (anomalous microbial population and inadequate pressing curd) from the standard was mainly attributed to different values of the attenuation-related parameters, whereas for samples from the other defective batch (excessive pressing curd), some parameters related to velocity and frequency were responsible for such discrimination.

Gene expression of Aspergillus flavus strains on a cheese model system to control aflatoxin production.

The expression of genes associated with aflatoxin biosynthesis by different Aspergillus flavus strains growing on a cheese model system has not been studied. To control aflatoxin biosynthesis, it would be useful to understand the changes in gene expression during cheesemaking and relate those changes to toxin production. The objective of this study was to evaluate the effects of pH, water activity, and temperature on the expression of 2 regulatory genes (aflR and aflS) and 1 structural gene (aflP) involved in aflatoxin biosynthesis, using 3 aflatoxigenic A. flavus strains growing on a cheese-based medium and reverse-transcription real-time PCR. The gene expression patterns were influenced by A. flavus strain and environmental conditions. The structural gene aflP and the regulatory genes aflR and aflS showed similar expression patterns in each A. flavus strain, but we also observed inter-strain differences. We observed the highest expression levels at 6 and 9 d of incubation by A. flavus strains CQ8 and CQ103, and saw a decrease in the days following. Strain CQ7 showed the lowest expression of these genes. We observed the highest expression levels of these genes at pH 5.5, water activity 0.95, and 20 to 25°C; strain CQ103 showed a different pattern for the aflS gene, with maximum expression at pH 6.0 on d 6 of incubation. For the 3 strains, we found a strong correlation between the relative expression of the aflR and aflS genes and the concentration of aflatoxins under conditions that simulated cheese ripening. Control strategies to avoid aflatoxin contamination during cheesemaking could use the detection of regulatory gene expression.

The role of nuclear mechanics in cell deformation under creeping flows.

Despite the relevant regulatory role that nuclear deformation plays in cell behaviour, a thorough understanding of how fluid flow modulates the deformation of the cell nucleus in non-confined environments is lacking. In this work, we investigated the dynamics of cell deformation under different creeping flows as a general simulation tool for predicting nuclear stresses and strains. Using this solid-fluid modelling interaction framework, we assessed the stress and strain levels that the cell nucleus experiences as a function of different microenvironmental conditions, such as physical constraints, fluid flows, cytosol properties, and nucleus properties and size. Therefore, the simulation methodology proposed here allows the design of deformability-based experiments involving fluid flow, such as real-time deformability cytometry and dynamic cell culture in bioreactors or microfluidic devices.

Bacterial communities of fresh goat meat packaged in modified atmosphere.

The objective of this work was to study the growth and development of fortuitous flora and food pathogens in fresh goat meat packaged under modified atmospheres containing two different concentrations of CO2. Meat samples were stored at 10 °C under two different modified-atmosphere packing (MAP) conditions: treatment A had 45% CO2 + 20% O2 + 35% N2 and treatment B had 20% CO2 + 55% O2 + 25% N2. During 14 days of storage, counts of each bacterial group and dominant species identification by 16S rRNA gene sequencing were performed to determine the microbial diversity present. The MAP condition used for treatment A was a more effective gas mixture for increasing the shelf life of fresh goat meat, significantly reducing the total number of viable bacteria and enterobacteria counts. Members of the Enterobacteriaceae family were the most common contaminants, although Hafnia alvei was dominant in treatment A and Serratia proteamaculans in treatment B. Identification studies at the species level showed that different microorganisms develop under different storage conditions, reflecting the importance of gas composition in the modified atmosphere on the bacterial community. This work provides new insights into the microbial changes of goat meat storage under different MAP conditions, which will be beneficial for the meat industry.

The growth and aflatoxin production of Aspergillus flavus strains on a cheese model system are influenced by physicochemical factors.

Traditional cheeses may be contaminated by aflatoxin-producing Aspergillus flavus during the ripening process, which has not been sufficiently taken into account. The objectives of this study were to evaluate the influence of water activity (aw), pH, and temperature on the lag phases, growth, and aflatoxin production of 3 A. flavus strains (CQ7, CQ8, and CG103) on a cheese-based medium. The results showed that the behavior of A. flavus strains was influenced by pH, aw, and temperature conditions. The CQ7 strain showed the maximum growth at pH 5.5, 0.99 aw, and 25°C, whereas for CQ8 and CQ103 strains, no differences were obtained at pH 5.5 and 6.0. In general, low pH, aw, and temperature values increased the latency times and decreased the growth rate and colony diameter, although aw and temperature were the most limiting factors. Maximum aflatoxin production on the cheese-based medium occurred at pH 5.0, 0.95 aw, and 25 or 30°C, depending on the strain. This study shows the effect of pH, aw, and temperature factors on growth and aflatoxin production of 3 aflatoxigenic A. flavus strains on a cheese-based medium. The findings may help to design control strategies during the cheesemaking process and storage, to prevent and avoid aflatoxin contamination by aflatoxigenic molds.

An Evaluation of Surgical Functional Reconstruction of the Foot Using Kinetic and Kinematic Systems: A Case Report.

Most pedobarographic studies of microsurgical foot reconstruction have been retrospective. In the present study, we report the results from a prospective pedobarographic study of a patient after microsurgical reconstruction of her foot with a latissimus dorsi flap and a cutaneous paddle, with a 42-month follow-up period. We describe the foot reconstruction plan and the pedobarographic measurements and analyzed its functional outcome. The goal of the present study was to demonstrate that pedobarography could have a role in the treatment of foot reconstruction from a quantitative perspective. The pedobarographic measurements were recorded after the initial coverage surgery and 2 subsequent foot remodeling procedures. A total of 4 pedobarographic measurements and 2 gait analyses were recorded and compared for both the noninvolved foot and the injured foot. Furthermore, the progress of the reconstructed foot was critically evaluated using this method. Both static and dynamic patterns were compared at subsequent follow-up visits after the foot reconstruction. The values and progression of the foot shape, peak foot pressure (kPa), average foot pressure (kPa), total contact surface (cm2), loading time (%), and step time (ms) were recorded. Initially, the pressure distribution of the reconstructed foot showed higher peak values at nonanatomic locations, revealing a greater ulceration risk. Over time, we found an improvement in the shape and values of these factors in the involved foot. To homogenize the pressure distribution and correct the imbalance between the 2 feet, patient-specific insoles were designed and fabricated. In our patient, pedobarography provided an objective, repeatable, and recordable method for the evaluation of the reconstructed foot. Pedobarography can therefore provide valuable insights into the prevention of pressure ulcers and optimization of rehabilitation.

Association between severity of symptoms and minimum mental health treatment duration in humanitarian contexts: a retrospective observational study.

Background: Understanding and optimising mental health and psychosocial support (MHPSS) interventions in humanitarian crises is crucial, particularly for the most prevalent mental health conditions in conflict settings: anxiety, depression, and post-traumatic stress disorder. However, research on what is the most appropriate length of psychological intervention is lacking in this setting. We aimed to establish which factors are most closely related to improvement and to determine the required number of consultations needed to achieve this improvement. Methods: We retrospectively analysed records from 9028 patients allocated to treatment for anxiety, depression, and post-traumatic symptoms from the MHPSS programme in Borno State, Nigeria, from January 2018 to December 2019. Patient characteristics, severity (Clinical Global Impression of Severity Scale, CGI-S scale), and clinical improvement were assessed by an attending counsellor (CGI-I scale) and by the patient (Mental Health Global State, MHGS scale). Improvement was defined as scores 1, 2, and 3 in the Clinical Global Impression of Improvement (CGI-I) scale, and as a decrease of at least 4 points in the MHGS scale. We investigated the associations between the category of symptoms, the severity of illness, and improvement of symptoms using multivariable logistic regression. We used Kaplan-Meier (KM) curves to assess the number of consultations (i.e., time of treatment) needed to achieve improvement of symptoms, by symptom category and symptom severity. Findings: The patients included were referred to treatment for anxiety (n = 3462), depression (n = 3970), or post-traumatic symptoms (n = 1596). Median age was 31 years (range 16-103), and 84.3% were female. Patients categorised as severe were less likely to present improvement according to the CGI-I scale (OR 0.11, 95% CI 0.05-0.25), while none of the other categories of symptoms showed significant results. Overall, three or more consultations were associated with improvement in both scales (OR 3.55, 95% CI 1.47-8.57 for CGI-I; and OR 3.04, 95% CI 2.36-3.90 for MHGS). KM curves for the category of symptoms showed that around 90% of patients with anxiety, depression, or post-traumatic symptoms, as well as those with mild or moderate severity, presented improvement after three consultations, compared with six consultations for those with severe symptoms. Interpretation: Classification by severity among patients with anxiety, depression, or post-traumatic symptoms could predict the probability of improvement, whereas classification by symptoms could not. Our study highlights the importance of classifying patient severity in MHPSS programmes to plan and implement the appropriate duration of care. A major limitation was the number of patients lost to follow up after the first consultation and excluded from the logistic regression and KM analysis. Funding: The study was funded and staffed entirely by Médicos Sin Fronteras (Médecins Sans Frontières), Spain.

Impact of Simulated Human Gastrointestinal Digestion on the Functional Properties of Dietary Fibres Obtained from Broccoli Leaves, Grape Stems, Pomegranate and Tomato Peels.

This study aimed to analyse the impact of a simulated human digestion process on the composition and functional properties of dietary fibres derived from pomegranate-peel, tomato-peel, broccoli-stem and grape-stem by-products. For this purpose, a computer-controlled simulated digestion system consisting of three bioreactors (simulating the stomach, small intestine and colon) was utilised. Non-extractable phenols associated with dietary fibre and their influence on antioxidant capacity and antiproliferative activity were investigated throughout the simulated digestive phases. Additionally, the modifications in oligosaccharide composition, the microbiological population and short-chain fatty acids produced within the digestion media were examined. The type and composition of each dietary fibre significantly influenced its functional properties and behaviour during intestinal transit. Notably, the dietary fibre from the pomegranate peel retained its high phenol content throughout colon digestion, potentially enhancing intestinal health due to its strong antioxidant activity. Similarly, the dietary fibre from broccoli stems and pomegranate peel demonstrated anti-proliferative effects in both the small and the large intestines, prompting significant modifications in colonic microbiology. Moreover, these fibre types promoted the growth of bifidobacteria over lactic acid bacteria. Thus, these results suggest that the dietary fibre from pomegranate peel seems to be a promising functional food ingredient for improving human health.

An agent-based method to estimate 3D cell migration trajectories from 2D measurements: Quantifying and comparing T vs CAR-T 3D cell migration.

BACKGROUND AND OBJECTIVE: Immune cell migration is one of the key features that enable immune cells to find invading pathogens, control tissue damage, and eliminate primary developing tumors. Chimeric antigen receptor (CAR) T-cell therapy is a novel strategy in the battle against various cancers. It has been successful in treating hematological tumors, yet it still faces many challenges in the case of solid tumors. In this work, we evaluate the three-dimensional (3D) migration capacity of T and CAR-T cells within dense collagen-based hydrogels. Quantifying three-dimensional (3D) cell migration requires microscopy techniques that may not be readily accessible. Thus, we introduce a straightforward mathematical model designed to infer 3D trajectories of cells from two-dimensional (2D) cell trajectories. METHODS: We develop a 3D agent-based model (ABM) that simulates the temporal changes in the direction of migration with an inverse transform sampling method. Then, we propose an optimization procedure to accurately orient cell migration over time to reproduce cell migration from 2D experimental cell trajectories. With this model, we simulate cell migration assays of T and CAR-T cells in microfluidic devices conducted under hydrogels with different concentrations of type I collagen and validate our 3D cell migration predictions with light-sheet microscopy. RESULTS: Our findings indicate that CAR-T cell migration is more sensitive to collagen concentration increases than T cells, resulting in a more pronounced reduction in their invasiveness. Moreover, our computational model reveals significant differences in 3D movement patterns between T and CAR-T cells. T cells exhibit migratory behavior in 3D whereas that CAR-T cells predominantly move within the XY plane, with limited movement in the Z direction. However, upon the introduction of a CXCL12 chemical gradient, CAR-T cells present migration patterns that closely resemble those of T cells. CONCLUSIONS: This framework demonstrates that 2D projections of 3D trajectories may not accurately represent real migration patterns. Moreover, it offers a tool to estimate 3D migration patterns from 2D experimental data, which can be easily obtained with automatic quantification algorithms. This approach helps reduce the need for sophisticated and expensive microscopy equipment required in laboratories, as well as the computational burden involved in producing and analyzing 3D experimental data.

Role of the microbial population on the flavor of the soft-bodied cheese Torta del Casar.

The purpose of this work was to investigate the influence of the spontaneous microbial population on the flavor of Torta del Casar cheese. A total of 16 batches of cheeses with different microbial qualities were used. Their physicochemical and microbial characteristics were evaluated during ripening and then related with the volatile compounds, taste, and flavor properties of the finished cheeses. Acids were the most abundant volatile compounds, followed by alcohols and carbonyls. The amount of acetic acid and several alcohols were linked to cheeses with higher counts of lactic acid bacteria (LAB), whereas Enterobacteriaceae counts were associated with semivolatile fatty acids. The gram-positive catalase-positive cocci counts were correlated with esters and methyl ketones. Although the role of the LAB in the flavor development of Torta del Casar is the most relevant, other microbial groups are necessary to impart the flavor of the cheese and to minimize the possible off-flavor derived from excessive concentrations of LAB metabolites, such as acetic acid.

Proteolytic effect of Cynara cardunculus rennet for use in the elaboration of 'Torta del Casar' cheese.

The purpose of this work was to analyse the influence of rennet from different Cynara cardunculus plants, selected for its clotting and proteolytic activity on caseins, on the characteristics of manufactured 'Torta del Casar' cheeses. After classifying the cardoon according to proteolytic activity into five groups of greater or lesser activity, 16 batches of cheeses were made with rennet derived from different wild cardoon plants. We observed a major development of the proteolysis during ripening leading to the generation of non-protein nitrogen compounds. Especially noteworthy was the relationship of amino acid nitrogen (AN) generation with rennet clotting activity after 24 h of maceration, and the fact that the production of biogenic amines was not related to the proteolytic activity of the rennet. The activities of the rennet observed 'in vitro' were also developed 'in vivo' in the cheeses, with the different rennets used affecting the final sensory characteristics of cheeses. The rennet with high clotting activity after 24 h of maceration was positively correlated with the creaminess, viscosity, and acceptability of the cheese. However, the high proteolytic activity rennet negatively influenced the acidity, bitterness, and creaminess parameters. Therefore the most appropriate cardoons for making this cheese are those with higher clotting activities and moderate proteolytic activities especially on ß-casein. The use of controlled and characterised cardoons in the manufacturing process of Torta del Casar is fundamental to obtaining the homogeneous product demanded by the Torta del Casar Registry of the Protected Designation of Origin.

Antimicrobial Properties of Essential Oils Obtained from Autochthonous Aromatic Plants.

The aim of this work was to determine the antimicrobial activity of the essential oils of six plants widely distributed in the Dehesa of Extremadura, such as Calendula officinalis, Cistus ladanifer, Cistus salviifolius, Cistus multiflorus, Lavandula stoechas, and Rosmarinus officinalis. The content of total phenolic compounds (TPC) and the antimicrobial activity of the essential oils against pathogenic and spoilage bacteria and yeasts as well as aflatoxin-producing molds were determined. A great variability was observed in the composition of the essential oils obtained from the six aromatic plants. The Cistus ladanifer essential oil had the highest content of total phenols (287.32 ppm), followed by the Cistus salviifolius essential oil; and the Rosmarinus officinalis essential oil showed the lowest amount of these compounds. The essential oils showed inhibitory effects on the tested bacteria and also yeasts, showing a maximum inhibition diameter of 11.50 mm for Salmonella choleraesuis and Kregervanrija fluxuum in the case of Cistus ladanifer and a maximum diameter of 9 mm for Bacillus cereus and 9.50 mm for Priceomyces carsonii in the case of Cistus salviifolius. The results stated that antibacterial and antiyeast activity is influenced by the concentration and the plant material used for essential oil preparation. In molds, aflatoxin production was inhibited by all the essential oils, especially the essential oils of Cistus ladanifer and Cistus salviifolius. Therefore, it can be concluded that the essential oils of native plants have significant antimicrobial properties against pathogenic and spoilage microorganisms, so they could be studied for their use in the industry as they are cheap, available, and non-toxic plants that favor the sustainability of the environment of the Dehesa of Extremeña.

Antifungal Effect of Autochthonous Aromatic Plant Extracts on Two Mycotoxigenic Strains of Aspergillus flavus.

This study identified the compounds obtained from four native Dehesa plants, which were holm oak, elm, blackberry and white rockrose, and evaluated their ability to inhibit the growth and production of aflatoxins B1 and B2 of two strains of mycotoxigenic Aspergillus flavus. For this purpose, phenolic compounds present in the leaves and flowers of the plants were extracted and identified, and subsequently, the effect on the growth of A. flavus, aflatoxin production and the expression of a gene related to its synthesis were studied. Cistus albidus was the plant with the highest concentration of phenolic compounds, followed by Quercus ilex. Phenolic acids and flavonoids were mainly identified, and there was great variability among plant extracts in terms of the type and quantity of compounds. Concentrated and diluted extracts were used for each individual plant. The influence on mold growth was not very significant for any of the extracts. However, those obtained from plants of the genus Quercus ilex, followed by Ulmus sp., were very useful for inhibiting the production of aflatoxin B1 and B2 produced by the two strains of A. flavus. Expression studies of the gene involved in the aflatoxin synthesis pathway did not prove to be effective. The results indicated that using these new natural antifungal compounds from the Dehesa for aflatoxin production inhibition would be desirable, promoting respect for the environment by avoiding the use of chemical fungicides. However, further studies are needed to determine whether the specific phenolic compounds responsible for the antifungal activity of Quercus ilex and Ulmus sp. produce the antifungal activity in pure form, as well as to verify the action mechanism of these compounds.

Bioactive Components and Biological Activities of Crocus sativus L. Byproducts: A Comprehensive Review.

The production of saffron spice results in numerous byproducts, as only 15 g of spice can be produced from 1 kg of flowers, indicating that over 90% of the saffron flower material is eventually discarded as waste. In view of this, the paper reviews current knowledge on the natural active components in saffron byproducts and their biological activities, aiming to lay a theoretical and scientific foundation for the further utilization. Saffron byproducts contain a variety of phytochemical components, such as flavonoids, anthocyanins, carotenoids, phenolic acids, monoterpenoids, alkaloids, glycosides, and saponins. The activities of saffron byproducts and their mechanisms are also discussed in detail here.

Screening for K13-Propeller Mutations Associated with Artemisinin Resistance in Plasmodium falciparum in Yambio County (Western Equatoria State, South Sudan).

Artemisinin-combined treatments are the recommended first-line treatment of Plasmodium falciparum malaria, but they are being threatened by emerging artemisinin resistance. Mutations in pfk13 are the principal molecular marker for artemisinin resistance. This study characterizes the presence of mutations in pfk13 in P. falciparum in Western Equatoria State, South Sudan. We analyzed 468 samples from patients with symptomatic malaria and found 15 mutations (8 nonsynonymous and 7 synonymous). Each mutation appeared only once, and none were validated or candidate markers of artemisinin resistance. However, some mutations were in the same or following position of validated and candidate resistance markers, suggesting instability of the gene that could lead to resistance. The R561L nonsynonymous mutation was found in the same position as the R561H validated mutation. Moreover, the A578S mutation, which is widespread in Africa, was also reported in this study. We found a high diversity of other pfk13 mutations in low frequency. Therefore, routine molecular surveillance of resistance markers is highly recommended to promptly detect the emergence of resistance-related mutations and to limit their spread.

A hybrid physics-based and data-driven framework for cellular biological systems: Application to the morphogenesis of organoids.

How cells orchestrate their cellular functions remains a crucial question to unravel how they organize in different patterns. We present a framework based on artificial intelligence to advance the understanding of how cell functions are coordinated spatially and temporally in biological systems. It consists of a hybrid physics-based model that integrates both mechanical interactions and cell functions with a data-driven model that regulates the cellular decision-making process through a deep learning algorithm trained on image data metrics. To illustrate our approach, we used data from 3D cultures of murine pancreatic ductal adenocarcinoma cells (PDAC) grown in Matrigel as tumor organoids. Our approach allowed us to find the underlying principles through which cells activate different cell processes to self-organize in different patterns according to the specific microenvironmental conditions. The framework proposed here expands the tools for simulating biological systems at the cellular level, providing a novel perspective to unravel morphogenetic patterns.

Tumour growth: An approach to calibrate parameters of a multiphase porous media model based on in vitro observations of Neuroblastoma spheroid growth in a hydrogel microenvironment.

To unravel processes that lead to the growth of solid tumours, it is necessary to link knowledge of cancer biology with the physical properties of the tumour and its interaction with the surrounding microenvironment. Our understanding of the underlying mechanisms is however still imprecise. We therefore developed computational physics-based models, which incorporate the interaction of the tumour with its surroundings based on the theory of porous media. However, the experimental validation of such models represents a challenge to its clinical use as a prognostic tool. This study combines a physics-based model with in vitro experiments based on microfluidic devices used to mimic a three-dimensional tumour microenvironment. By conducting a global sensitivity analysis, we identify the most influential input parameters and infer their posterior distribution based on Bayesian calibration. The resulting probability density is in agreement with the scattering of the experimental data and thus validates the proposed workflow. This study demonstrates the huge challenges associated with determining precise parameters with usually only limited data for such complex processes and models, but also demonstrates in general how to indirectly characterise the mechanical properties of neuroblastoma spheroids that cannot feasibly be measured experimentally.