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Constructing discriminative representations of molecules lies at the core of a number of domains such as drug discovery, chemistry, and medicine. State-of-the-art methods employ graph neural networks and self-supervised learning (SSL) to learn unlabeled data for structural representations, which can then be fine-tuned for downstream tasks. Albeit powerful, these methods are pre-trained solely on molecular structures and thus often struggle with tasks involved in intricate biological processes. Here, it is proposed to assist the learning of molecular representation by using the perturbed high-content cell microscopy images at the phenotypic level. To incorporate the cross-modal pre-training, a unified framework is constructed to align them through multiple types of contrastive loss functions, which is proven effective in the formulated novel tasks to retrieve the molecules and corresponding images mutually. More importantly, the model can infer functional molecules according to cellular images generated by genetic perturbations. In parallel, the proposed model can transfer non-trivially to molecular property predictions, and has shown great improvement over clinical outcome predictions. These results suggest that such cross-modality learning can bridge molecules and phenotype to play important roles in drug discovery.
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Vaccines are the most effective and feasible way to control pathogen infection. Helminths have been reported to jeopardize the protective immunity mounted by several vaccines. However, there are no experimental data about the effect of helminth infection on the effectiveness of COVID-19 vaccines. Here, a mouse model of trichinosis, a common zoonotic disease worldwide, was used to investigate effects of Trichinella spiralis infection on the RBD protein vaccine of SARS-CoV-2 and the related immunological mechanism, as well as the impact of albendazole (ALB) deworming on the inhibitory effect of the parasite on the vaccination. The results indicated that both the enteric and muscular stages of T. spiralis infection inhibited the vaccine efficacy, evidenced by decreased levels of IgG, IgM, sIgA, and reduced serum neutralizing antibodies, along with suppressed splenic germinal center (GC) B cells in the vaccinated mice. Pre-exposure to trichinosis promoted Th2 and/or Treg immune responses in the immunized mice. Furthermore, ALB treatment could partially reverse the inhibitory effect of T. spiralis infection on the efficiency of the vaccination, accompanied by a restored proportion of splenic GC B cells. Therefore, given the widespread prevalence of helminth infections worldwide, deworming therapy needs to be considered when implementing COVID-19 vaccination strategies.
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Polyphenols have attracted extensive attention due to their rich functional activities, such as antioxidant, anti-inflammatory and anti-tumor. However, the low solubility and poor stability limit their bioavailability and functional activities. Plant-derived ferritin cages have a unique hollow cage structure that can embed polyphenols to improve their unfavorable properties. Therefore, it is essential to adequately elaborate and summarize plant-derived ferritin cages to maximize their potential benefits in nutritional interventions. This review focuses on the fundamental properties of plant-derived ferritin cages, including the preparation process, purification technology, identification methods, and structural and functional properties. The relevant research on ferritin cages in polyphenol delivery has been summarized, including the delivery of water/lipid soluble polyphenols, modification of ferritin cages, and the interaction between polyphenols and ferritin cages. The research progress, shortcomings and prospects of plant-derived ferritin cages in precise nutrition are introduced. In addition, the relevant research on ferritin in immune response and protein engineering is also discussed to provide the theoretical basis for applying plant-derived ferritin cages in many frontier fields.
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Ferritinas , Polifenóis , Ferritinas/química , Polifenóis/química , Humanos , Plantas/química , Disponibilidade Biológica , Antioxidantes/química , Antioxidantes/farmacologiaRESUMO
Sensitive substances have attracted wide attention due to their rich functional activities, such as antibiosis activities, antioxidant activities and prevent disease, etc. However, the low stability of sensitive substances limits their bioavailability and functional activities. Protein-based microcapsules can encapsulate sensitive substances to improve their adverse properties due to their good stability, strong emulsifying ability and wide source. Therefore, it is necessary to fully elaborate and summarize protein-based microcapsules to maximize their potential benefits in nutritional interventions. The focus of this review is to highlight the classification of protein-based microcapsules. In addition, the principles, advantages and disadvantages of preparation methods for protein-based microcapsules are summarized. Some novel preparation methods for protein-based microcapsules are also emphasized. Moreover, the mechanism of protein-based microcapsules that release sensitive substances in vitro is elucidated and summarized. Furthermore, the applications of protein-based microcapsules are outlined. Protein-based microcapsules can effectively encapsulate sensitive substances, which improve their bioavailability, and provide protective effects during storage and gastrointestinal digestion. In addition, microcapsules can improve the sensory quality of food and enhance its stability. The performance of protein-based microcapsules for delivering sensitive substances is influenced by factors such as protein type, the ratio between protein ratio and the other wall material, the preparation process, etc. Future research should focus on the new composite protein-based microcapsule delivery system, which can be applied to in vivo research and have synergistic effects and precise nutritional functions. In summary, protein-based microcapsules have broader research prospects in the functional foods and nutrition field.
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Cápsulas , Proteínas , Proteínas/química , Proteínas/administração & dosagem , Humanos , Disponibilidade Biológica , Sistemas de Liberação de Medicamentos/métodos , Portadores de Fármacos/química , AnimaisRESUMO
Ultrasound extraction (UE) enhanced with deep eutectic solvent (DES) was used to extract Lentinus edodes polysaccharides. Box-Behnken design (BBD) was applied to investigate the influences of water content (10-90 %), solid-liquid solvent (1 : 10-1 : 50 g/mL), time (4-12â min), temperature (40-80 °C) and ultrasonic power (100-500â W) on the yield of Lentinus edodes polysaccharides. The optimal extraction conditions were ultrasonic power of 300â W, extraction time of 8â min, water content of 80 %, a solid-liquid ratio of 1 : 30 g/mL and a temperature of 60 °C, respectively. The highest extraction yield of Lentinus edodes polysaccharide was 10.17 % under optimal conditions. The results of FT-IR, SEM, and monosaccharide composition confirmed that the extracts possessed the characteristics of polysaccharides. In addition, the polysaccharides obtained with the UE enhanced with DES method exhibited higher antioxidant activities than the polysaccharides extracted with the UE method and HWE method. This extraction method can further expand the production efficiency and structural diversity of Lentinus edodes polysaccharides and meet the supply and demand relationship. It can be foreseen that this method can be applied to the extraction of more active substances.
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Antioxidantes , Polissacarídeos , Cogumelos Shiitake , Antioxidantes/química , Antioxidantes/isolamento & purificação , Antioxidantes/farmacologia , Compostos de Bifenilo/antagonistas & inibidores , Compostos de Bifenilo/química , Solventes Eutéticos Profundos/química , Picratos/antagonistas & inibidores , Polissacarídeos/química , Polissacarídeos/isolamento & purificação , Polissacarídeos/farmacologia , Cogumelos Shiitake/química , Ondas UltrassônicasRESUMO
Rationale: Primordial follicles are limited in number and cannot be regenerated, dormant primordial follicles cannot be reversed once they enter a growth state. Therefore, the length of the female reproductive lifespan depends on the orderly progression and selective activation of primordial follicles, the mechanism of which remains unclear. Methods: We used human ovarian cortical biopsy specimens, granulosa cells from diminished ovarian reserve (DOR) patients, Hdac6-overexpressing transgenic mouse model, and RNA sequencing to analyze the crucial roles of histone deacetylase 6 (HDAC6) in fertility preservation and primordial follicle activation. Results: In the present study, we found that HDAC6 was highly expressed in most dormant primordial follicles. The HDAC6 expression was reduced accompanying reproductive senescence in human and mouse ovaries. Overexpression of Hdac6 delayed the rate of primordial follicle activation, thereby prolonging the mouse reproductive lifespan. Short-term inhibition of HDAC6 promoted primordial follicle activation and follicular development in humans and mice. Mechanism studies revealed that HDAC6 directly interacted with NGF, reducing acetylation modification of NGF and thereby accelerating its ubiquitination degradation. Consequently, the reduced NGF protein level maintained the dormancy of primordial follicles. Conclusions: The physiological significance of the high expression of HDAC6 in most primordial follicles is to reduce NGF expression and prevent primordial follicle activation to maintain female fertility. Reduced HDAC6 expression increases NGF expression in primordial follicles, activating their development and contributing to reproduction. Our study provides a clinical reference value for fertility preservation.
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Desacetilase 6 de Histona , Camundongos Transgênicos , Fator de Crescimento Neural , Folículo Ovariano , Ubiquitinação , Animais , Feminino , Humanos , Camundongos , Acetilação , Células da Granulosa/metabolismo , Desacetilase 6 de Histona/metabolismo , Desacetilase 6 de Histona/genética , Fator de Crescimento Neural/metabolismo , Folículo Ovariano/metabolismoRESUMO
Polycyclic aromatic hydrocarbons (PAHs), a widespread class of food pollutants, are commonly exposed to humans along with edible oil. The dietary exposure pattern of PAH4 was simulated to study the toxicity and oxidative stress of oil-based PAH4 on hepatocytes. The findings demonstrated that oil-based PAH4 induced cell viability and mitochondrial membrane potential decreased and promoted apoptosis and oxidative stress in a concentration-dependent manner. Benzo[a]pyrene had the strongest toxicity and HL-7702 cells were more sensitive to toxicity than HepG2 cells, due to differences in induced CYP1A enzyme activity. Oil-based PAH4 had greater cytotoxicity than PAH4, attributed to the synergistic effect of oil and PAH4. Furthermore, oil-based PAH4 induced oxidative stress in HepG2 and HL-7702 cells through the same AHR-Nrf2-KEAP1 pathway, which was elucidated by detecting genes and proteins expression. This study lays the foundation for elucidating the harm of dietary exposure to PAHs and reminds us that food composition may increase the harm of PAHs.
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Contaminação de Alimentos , Hidrocarbonetos Policíclicos Aromáticos , Humanos , Proteína 1 Associada a ECH Semelhante a Kelch/genética , Contaminação de Alimentos/análise , Fator 2 Relacionado a NF-E2/genética , Alimentos , Hidrocarbonetos Policíclicos Aromáticos/toxicidade , Hidrocarbonetos Policíclicos Aromáticos/análise , Estresse OxidativoRESUMO
While significant advances have been made in predicting static protein structures, the inherent dynamics of proteins, modulated by ligands, are crucial for understanding protein function and facilitating drug discovery. Traditional docking methods, frequently used in studying protein-ligand interactions, typically treat proteins as rigid. While molecular dynamics simulations can propose appropriate protein conformations, they're computationally demanding due to rare transitions between biologically relevant equilibrium states. In this study, we present DynamicBind, a deep learning method that employs equivariant geometric diffusion networks to construct a smooth energy landscape, promoting efficient transitions between different equilibrium states. DynamicBind accurately recovers ligand-specific conformations from unbound protein structures without the need for holo-structures or extensive sampling. Remarkably, it demonstrates state-of-the-art performance in docking and virtual screening benchmarks. Our experiments reveal that DynamicBind can accommodate a wide range of large protein conformational changes and identify cryptic pockets in unseen protein targets. As a result, DynamicBind shows potential in accelerating the development of small molecules for previously undruggable targets and expanding the horizons of computational drug discovery.
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Simulação de Dinâmica Molecular , Proteínas , Ligantes , Proteínas/metabolismo , Conformação Proteica , Descoberta de Drogas , Ligação Proteica , Simulação de Acoplamento MolecularRESUMO
Polycyclic aromatic hydrocarbons (PAHs) as a group of prevalent persistent organic pollutants in the environment are always found as mixtures. The combined toxicity of oil-based PAH4 seems seldom to be mentioned. To evaluate the combined toxicity of oil-based PAH4 mixtures on HL-7702 cells, the effects of single, binary, ternary, and quaternary mixtures on cell viability were examined, and the concentration addition model and combination index (CI)-isobologram model were selected to predict the toxicological interactions of the mixtures. The results showed that the PAH4 mixtures had a concentration-dependent effect on cell viability. The CI model was more suitable for elucidating the toxicity interactions of mixtures. In addition, the combined toxicity of BaA + BaP and BaA + Chr + BbF + BaP was antagonistic, BaA + Chr, BaA + BbF, Chr + BbF, and BaA + Chr + BbF was synergistic, and the remaining mixtures shifted from antagonistic to synergistic. Antagonistic effects were observed in all mixtures containing BaP, indicating that oil-based PAH4 mixtures containing BaP had a mitigating effect on cytotoxicity. Furthermore, BbF was identified as playing a key role in the synergistic effects in binary and ternary mixtures. This study provided a new acknowledgment to assess the interactions of PAH4 mixtures which is helpful for further study of the toxicity risks in the environment.
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Hidrocarbonetos Policíclicos Aromáticos , Hidrocarbonetos Policíclicos Aromáticos/toxicidade , Sobrevivência CelularRESUMO
Lipids are closely related to the generation of PAHs during food thermal processing. During heating, lipids mainly triglycerides undergo hydrolysis, oxidation and decomposition. The relationship between the various products and the formation of PAHs is still unclear. This paper investigated the effect of different lipid standards on PAH4 production, and explored their thermal stability and reaction products to delve into nature of the differences in PAH4 production. Fatty acids were more prone to generate PAH4 than glycerides. The higher the degree of esterification of glycerides, the higher its thermal stability and the lower the content of PAH4 generated, implying that hydrolysis of glycerides promoted the generation of PAH4. In addition, there was a positive correlation between unsaturation in lipids and the PAH4 production. After heat treatment, hydroperoxides, unsaturated fatty alcohols and aldehydes, alkenes and aromatic substances were abundant in oleic acid and linoleic acid which produced the most PAH4. Thermal decomposition of lipid hydroperoxides was the pathway for the generation of conjugated hydrocarbon radicals, alcohols, aldehydes, and alkenes. The intramolecular cyclization and Diels-Alder reaction acted as ring-forming reactions, with consequent dehydrogenation, decarboxylation, side-chain breaks and radical reorganization, ultimately facilitating the amplification of the aromatic rings and the formation of PAHs.
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Hidrocarbonetos Policíclicos Aromáticos , Triglicerídeos , Hidrocarbonetos , Alcenos , AldeídosRESUMO
The emulsifying performance of glycerophospholipids alone is inferior to proteins, etc., while the sphingomyelin (SM) and cholesterol (Chol) naturally existing in biological membranes could interact with glycerophospholipids to influence the polar lipid arrangement. Inspired by the natural membranes, the effect of SM and Chol on the physicochemical stability of soy phospholipid (SPL)-stabilized emulsions during storage or under environmental stresses was determined. The results indicated that the addition of SM and/or Chol could improve the storage stability of the emulsions and protective effect on lutein significantly (p < 0.05). Except for UV irradiation, the addition of Chol significantly improved the stability of the emulsions against acid, salt, and heat. The strong intermolecular hydrogen bonds and condensed assembly formed by SM and Chol contributed to the best stability of SPL + SM + Chol-stabilized emulsions. The results gave insight into improving the emulsifying properties of glycerophospholipids with SM and Chol.
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Fosfolipídeos , Esfingomielinas , Esfingomielinas/química , Fosfolipídeos/química , Luteína , Emulsões , Glicerofosfolipídeos , Colesterol/químicaRESUMO
Deer tendon, a deer processing byproduct, is an excellent protein source for the preparation of peptides for improving osteoporosis by its high protein content and high nutritional value. The optimal process of collagen acid extraction was implemented and the results showed that the acid concentration was 7%, the material-liquid ratio was 1:25, and the soaking time was 48 h. DTCHs could promote MC3T3-E1 cell proliferation and increase alkaline phosphatase activities in vitro. In addition, compared with the model group, the DTCHs treatment groups with an oral dosage of 350, 750, and 1500 mg/kg rat/day could significantly improve the shape, weight, bone mechanics, and alkaline phosphatase activities of tail-suspended mice. Bone microstructure and mineralization also recovered significantly in vivo. This result is expected to provide the structural and biological information for DTCHs-based functional foods.
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Cervos , Osteoporose , Animais , Camundongos , Ratos , Fosfatase Alcalina , Colágeno/farmacologia , Osteoporose/tratamento farmacológico , TendõesRESUMO
INTRODUCTION: The COVID-19 patients in the convalescent stage noticeably have pulmonary diffusing capacity impairment (PDCI). The pulmonary diffusing capacity is a frequently-used indicator of the COVID-19 survivors' prognosis of pulmonary function, but the current studies focusing on prediction of the pulmonary diffusing capacity of these people are limited. The aim of this study was to develop and validate a machine learning (ML) model for predicting PDCI in the COVID-19 patients using routinely available clinical data, thus assisting the clinical diagnosis. METHODS: Collected from a follow-up study from August to September 2021 of 221 hospitalized survivors of COVID-19 18 months after discharge from Wuhan, including the demographic characteristics and clinical examination, the data in this study were randomly separated into a training (80%) data set and a validation (20%) data set. Six popular machine learning models were developed to predict the pulmonary diffusing capacity of patients infected with COVID-19 in the recovery stage. The performance indicators of the model included area under the curve (AUC), Accuracy, Recall, Precision, Positive Predictive Value(PPV), Negative Predictive Value (NPV) and F1. The model with the optimum performance was defined as the optimal model, which was further employed in the interpretability analysis. The MAHAKIL method was utilized to balance the data and optimize the balance of sample distribution, while the RFECV method for feature selection was utilized to select combined features more favorable to machine learning. RESULTS: A total of 221 COVID-19 survivors were recruited in this study after discharge from hospitals in Wuhan. Of these participants, 117 (52.94%) were female, with a median age of 58.2 years (standard deviation (SD) = 12). After feature selection, 31 of the 37 clinical factors were finally selected for use in constructing the model. Among the six tested ML models, the best performance was accomplished in the XGBoost model, with an AUC of 0.755 and an accuracy of 78.01% after experimental verification. The SHAPELY Additive explanations (SHAP) summary analysis exhibited that hemoglobin (Hb), maximal voluntary ventilation (MVV), severity of illness, platelet (PLT), Uric Acid (UA) and blood urea nitrogen (BUN) were the top six most important factors affecting the XGBoost model decision-making. CONCLUSION: The XGBoost model reported here showed a good prognostic prediction ability for PDCI of COVID-19 survivors during the recovery period. Among the interpretation methods based on the importance of SHAP values, Hb and MVV contributed the most to the prediction of PDCI outcomes of COVID-19 survivors in the recovery period.
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COVID-19 , Capacidade de Difusão Pulmonar , Humanos , Feminino , Pessoa de Meia-Idade , Masculino , Seguimentos , Área Sob a Curva , Aprendizado de MáquinaRESUMO
Morchella sp. is a kind of precious medicinal and edible fungus with a unique flavor and is rich in various amino acids and organic germanium needed by the human body. Most notably, Morchella sp. polysaccharides have attracted widespread attention due to their significant bioactivity in recent years. At present, extensive studies have been carried out on the extraction methods, structural characterization and activity evaluation of Morchella sp. polysaccharides, which provides a good theoretical basis for its further development and application. However, the systematic summary of the related research of Morchella sp. polysaccharides has not been reported yet. Therefore, this review mainly focused on the isolation and purification methods, structural characterization, biological activities and structure-activity relationship of Morchella sp. polysaccharides. This work will help to have a better in-depth understanding of Morchella sp. polysaccharides and provide a scientific basis and direct reference for more scientific and rational applications.
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Ascomicetos , Polissacarídeos , Humanos , Polissacarídeos/química , Ascomicetos/química , Relação Estrutura-Atividade , Antioxidantes/farmacologiaRESUMO
BACKGROUND: Curcumin (Cur) is a natural pigment containing a diketone structure, which has attracted extensive attention due to its strong functional activities. However, the low solubility and poor stability of Cur limit its low bioavailability and multi-function. It is essential to develop effective measures to improve the unfavorable nature of Cur and maximize its potential benefits in nutritional intervention. SCOPE AND APPROACH: The focus of this review is to emphasize the construction of lipo-solubility delivery vehicles for Cur, including emulsion, nanoliposome and solid liposome. In addition, the potential benefits of vehicles-encapsulated Cur in the field of precise nutrition were summarized, including high targeting properties and multiple disease interventions. Further, the deficiencies and prospects of Cur encapsulated in vehicles for precise nutrition were discussed. KEY FINDINGS AND CONCLUSIONS: The well-designed lipo-solubility delivery vehicles for Cur can improve its stability in food processing and the digestion in vivo. To meet the nutritional requirements of special people for Cur-based products, the improvement of the bioavailability by using delivery vehicles will provide a theoretical basis for the precise nutrition of Cur in functional food.
Structural properties and bioavailability of curcumin were summarized.The practical problems and challenges in the utilization of curcumin were discussed.Various technologies for preparing lipo-solubility delivery vehicles for curcumin were described.The design of delivery vehicles for curcumin and intervention strategies in precise nutrition was reviewed.
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Recently, plant protein as a necessary nutrient source for human beings, a common ingredient of traditional processed food, and an important element of new functional food has gained prominence due to the increasing demand for healthy food. Walnut protein (WP) is obtained from walnut kernels and walnut oil-pressing waste and has better nutritional, functional, and essential amino acids in comparison with other vegetable and grain proteins. WP can be conveniently obtained by various extraction techniques, including alkali-soluble acid precipitation, salting-out, and ultrasonic-assisted extraction, among others. The functional properties of WP can be modified for desired purposes by using some novel methods, including free radical oxidation, enzymatic modification, high hydrostatic pressure, etc. Moreover, walnut peptides play an important biological role both in vitro and in vivo. The main activities of the walnut peptides are antihypertensive, antioxidant, learning improvement, and anticancer, among others. Furthermore, WP could be applied in the development of functional foods or dietary supplements, such as delivery systems and food additives, among others. This review summarizes recent knowledge on the nutritional, functional, and bioactive peptide aspects of WP and possible future products, providing a theoretical reference for the utilization and development of oil crop waste.
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Juglans , Humanos , Juglans/química , Nozes/química , Peptídeos/química , Proteínas de Plantas/metabolismo , Antioxidantes/químicaRESUMO
Polycyclic aromatic hydrocarbons (PAHs) are carcinogenic and lipophilic, which can be found in frying system. This review summarized the formation, migration and derivation for PAHs, hypothesized the possible mechanism for PAHs generation during frying and presented the research prospects. Some factors like high oil consumption, high temperature, long time and oil rich in unsaturated fatty acids promoted the formation of PAHs and the presence of antioxidants inhibited the PAHs formation. The effect of proteins and carbohydrates in foods on the formation of PAHs is inconclusive. The formed PAHs were migrated into food and air. Moreover, some PAHs transformed into more toxic PAHs-derivatives during frying. The generation of PAHs may be related to low-barrier free radical-mediated reaction and the unsaturated hydrocarbons may be precursors of PAHs during frying. In future, the isotope tracer technology and on-line detection may be applied to discover intermediates and provide clues for studying PAHs generation mechanisms.
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Hidrocarbonetos Policíclicos Aromáticos , Alimentos , CarcinógenosRESUMO
This study aimed to elucidate the effect of casein phosphopeptides (CPP) on the thermal stability and sensory quality of whey protein emulsions containing calcium beta-hydroxy-beta-methylbutyrate (WPEs-HMB-Ca). The interaction mechanism among CPP, HMBCa, and WP in the emulsions before and after autoclaving (121 °C, 15 min) was systematically investigated from macroscopic external and microscopic molecular perspectives. It was found that WPEs-HMB-Ca treated by autoclaving resulted in an increase in droplet size (d4,3 = 24.09 µm) due to aggregation/flocculation of proteins, along with a stronger odor with higher viscosity, compared to those without autoclaving. When CPP:HMB-Ca = 1:25 (w/w) in the emulsion, the droplets exhibited a more uniform and consistent state in the emulsion. In addition, CPP was able to inhibit the formation of complex spatial network structures of proteins during autoclaving by binding with Ca2+, thus improving the thermal stability and storage stability of WPEs-HMB-Ca. This work might provide theoretical guidance for developing functional milk drinks with good thermal stability and flavor.
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Cálcio , Caseínas , Proteínas do Soro do Leite , Caseínas/química , Emulsões/química , FosfopeptídeosRESUMO
Background: The study of the etiology of acute febrile illness (AFI) has historically been designed as a prevalence of pathogens detected from a case series. This strategy has an inherent unrealistic assumption that all pathogen detection allows for causal attribution, despite known asymptomatic carriage of the principal causes of acute febrile illness in most low- and middle-income countries (LMICs). We designed a semi-quantitative PCR in a modular format to detect bloodborne agents of acute febrile illness that encompassed common etiologies of AFI in the region, etiologies of recent epidemics, etiologies that require an immediate public health response and additional pathogens of unknown endemicity. We then designed a study that would delineate background levels of transmission in the community in the absence of symptoms to provide corrected estimates of attribution for the principal determinants of AFI. Methods: A case-control study of acute febrile illness in patients ten years or older seeking health care in Iquitos, Loreto, Peru, was planned. Upon enrollment, we will obtain blood, saliva, and mid-turbinate nasal swabs at enrollment with a follow-up visit on day 21-28 following enrollment to attain vital status and convalescent saliva and blood samples, as well as a questionnaire including clinical, socio-demographic, occupational, travel, and animal contact information for each participant. Whole blood samples are to be simultaneously tested for 32 pathogens using TaqMan array cards. Mid-turbinate samples will be tested for SARS-CoV-2, Influenza A and Influenza B. Conditional logistic regression models will be fitted treating case/control status as the outcome and with pathogen-specific sample positivity as predictors to attain estimates of attributable pathogen fractions for AFI. Discussion: The modular PCR platforms will allow for reporting of all primary results of respiratory samples within 72 hours and blood samples within one week, allowing for results to influence local medical practice and enable timely public health responses. The inclusion of controls will allow for a more accurate estimate of the importance of specific, prevalent pathogens as a cause of acute illness. Study Registration: Project 1791, Registro de Proyectos de Investigación en Salud Pública (PRISA), Instituto Nacional de Salud, Perú.
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BACKGROUND: The study of the etiology of acute febrile illness (AFI) has historically been designed as a prevalence of pathogens detected from a case series. This strategy has an inherent unrealistic assumption that all pathogen detection allows for causal attribution, despite known asymptomatic carriage of the principal causes of acute febrile illness in most low- and middle-income countries (LMICs). We designed a semi-quantitative PCR in a modular format to detect bloodborne agents of acute febrile illness that encompassed common etiologies of AFI in the region, etiologies of recent epidemics, etiologies that require an immediate public health response and additional pathogens of unknown endemicity. We then designed a study that would delineate background levels of transmission in the community in the absence of symptoms to provide corrected estimates of attribution for the principal determinants of AFI. METHODS: A case-control study of acute febrile illness in patients ten years or older seeking health care in Iquitos, Loreto, Peru, was planned. Upon enrollment, we will obtain blood, saliva, and mid-turbinate nasal swabs at enrollment with a follow-up visit on day 21-28 following enrollment to attain vital status and convalescent saliva and blood samples, as well as a questionnaire including clinical, socio-demographic, occupational, travel, and animal contact information for each participant. Whole blood samples are to be simultaneously tested for 32 pathogens using TaqMan array cards. Mid-turbinate samples will be tested for SARS-CoV-2, Influenza A and Influenza B. Conditional logistic regression models will be fitted treating case/control status as the outcome and with pathogen-specific sample positivity as predictors to attain estimates of attributable pathogen fractions for AFI. DISCUSSION: The modular PCR platforms will allow for reporting of all primary results of respiratory samples within 72 h and blood samples within one week, allowing for results to influence local medical practice and enable timely public health responses. The inclusion of controls will allow for a more accurate estimate of the importance of specific prevalent pathogens as a cause of acute illness. STUDY REGISTRATION: Project 1791, Registro de Proyectos de Investigación en Salud Pública (PRISA), Instituto Nacional de Salud, Perú.