NeuroSCAN: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks.

Volume electron microscopy (vEM) datasets such as those generated for connectome studies allow nanoscale quantifications and comparisons of the cell biological features underpinning circuit architectures. Quantifications of cell biological relationships in the connectome result in rich multidimensional datasets that benefit from data science approaches, including dimensionality reduction and integrated graphical representations of neuronal relationships. We developed NeuroSCAN, an online open-source platform that bridges sophisticated graph analytics from data science approaches with the underlying cell biological features in the connectome. We analyze a series of published C. elegans brain neuropils and demonstrate how these integrated representations of neuronal relationships facilitate comparisons across connectomes, catalyzing new insights on the structure-function relationships of the circuits and their changes during development. NeuroSCAN is designed for intuitive examination and comparisons across connectomes, enabling synthesis of knowledge from high-level abstractions of neuronal relationships derived from data science techniques to the detailed identification of the cell biological features underpinning these abstractions.

Analysis of the Mechanical Properties of Structural Ceramics Made from Aggregate Washing Sludge and Manganese Mining Waste.

The construction sector is presently among the most resource-intensive industries, driving a substantial body of research dedicated to the development of more sustainable materials to address these demands. A particularly promising approach within the framework of the circular economy is the repurposing of waste as a principal raw material for the creation of new construction products. Within this context, the primary aim of this study is to engineer ceramic materials for brick production using 100% waste-derived inputs, specifically aggregate washing sludge and manganese mining by-products. To evaluate the potential of these sustainable ceramic materials, an extensive investigation was conducted, encompassing both physical and mechanical testing, as well as a thorough characterisation of the waste inputs. For this purpose, a series of ceramic specimens were fabricated with varying proportions of mining residues and aggregate washing sludge, adhering to the conventional protocols employed in the manufacture of ceramic bricks. The results demonstrate that these sustainable ceramics exhibit a linear shrinkage reduction of up to 5% compared to traditional clay-based ceramics. Furthermore, they show water absorption levels-whether via capillarity, cold water, or hot water absorption-that are up to twice those observed in conventional clay ceramics, while maintaining comparable density values. This increased absorption, however, correlates with a reduction in mechanical strength at higher concentrations of manganese waste, yet the material continues to meet the minimum strength requirements as specified by industry standards for such products. In conclusion, this research introduces a novel, sustainable ceramic material that not only reduces economic and environmental costs but also adheres to the required performance criteria for construction applications.

Lab-on-a-lollipop (LoL) platform for preventing food-induced toxicity: all-in-one system for saliva sampling and electrochemical detection of vanillin.

Saliva has emerged as a primary biofluid for non-invasive disease diagnostics. Saliva collection involves using kits where individuals stimulate saliva production via a chewing device like a straw, then deposit the saliva into a designated collection tube. This process may pose discomfort to patients due to the necessity of producing large volumes of saliva and transferring it to the collection vessel. This work has developed a saliva collection and analysis device where the patient operates it like a lollipop, stimulating saliva production. The lollipop-mimic device contains yarn-based microfluidic channels that sample saliva and transfer it to the sensing zone embedded in the stem of the device. We have embedded electrochemical sensors in the lollipop platform to measure vanillin levels in saliva. Vanillin is the most common food flavoring additive and is added to most desserts such as ice cream, cakes, and cookies. Overconsumption of vanillin can cause side effects such as muscle weakness, and damage to the liver, kidneys, stomach, and lungs. We detected vanillin using direct oxidation at a laser-induced graphene (LIG) electrode. We showed a dynamic range of 2.5 µM to 30 µM, covering the physiologically relevant concentration of vanillin in saliva. The lab-on-a-lollipop platform requires only 200 µL of saliva and less than 2 minutes to fill the channels and complete the measurement. This work introduces the first sensor-embedded lollipop-mimic saliva collection and measurement system.

An ANXA11 P93S variant dysregulates TDP-43 and causes corticobasal syndrome.

INTRODUCTION: Variants of uncertain significance (VUS) surged with affordable genetic testing, posing challenges for determining pathogenicity. We examine the pathogenicity of a novel VUS P93S in Annexin A11 (ANXA11) - an amyotrophic lateral sclerosis/frontotemporal dementia-associated gene - in a corticobasal syndrome kindred. Established ANXA11 mutations cause ANXA11 aggregation, altered lysosomal-RNA granule co-trafficking, and transactive response DNA binding protein of 43 kDa (TDP-43) mis-localization. METHODS: We described the clinical presentation and explored the phenotypic diversity of ANXA11 variants. P93S's effect on ANXA11 function and TDP-43 biology was characterized in induced pluripotent stem cell-derived neurons alongside multiomic neuronal and microglial profiling. RESULTS: ANXA11 mutations were linked to corticobasal syndrome cases. P93S led to decreased lysosome colocalization, neuritic RNA, and nuclear TDP-43 with cryptic exon expression. Multiomic microglial signatures implicated immune dysregulation and interferon signaling pathways. DISCUSSION: This study establishes ANXA11 P93S pathogenicity, broadens the phenotypic spectrum of ANXA11 mutations, underscores neuronal and microglial dysfunction in ANXA11 pathophysiology, and demonstrates the potential of cellular models to determine variant pathogenicity. HIGHLIGHTS: ANXA11 P93S is a pathogenic variant. Corticobasal syndrome is part of the ANXA11 phenotypic spectrum. Hybridization chain reaction fluorescence in situ hybridization (HCR FISH) is a new tool for the detection of cryptic exons due to TDP-43-related loss of splicing regulation. Microglial ANXA11 and related immune pathways are important drivers of disease. Cellular models are powerful tools for adjudicating variants of uncertain significance.

Isolation and sequencing of Orthoflavivirus ilheusense from mosquitoes collected in the Brazilian cerrado, West-Central region, Brazil.

The Orthoflavivirus ilheusense (ILHV) is an arbovirus that was first isolated in Brazil in 1944 during an epidemiologic investigation of yellow fever. Is a member of the Flaviviridae family and it belongs to the antigenic complex of the Ntaya virus group. Psorophora ferox is the primary vector of ILHV and this study presents the isolation and phylogenetic analysis of ILHV in a pool of Ps. ferox collected in the state of Goiás in 2021. Viral isolation tests were performed on Vero cells and C6/36 clones. The indirect immunofluorescence test (IFI) was used to confirm the positivity of the sample. The positive sample underwent RT-qPCR, sequencing, and phylogenetic analysis. This is the first report of ILHV circulation in this municipality and presented close relationship between this isolate and another ILHV isolate collected in the city of Belém (PA).

Exploring regenerative coupling in phononic crystals for room temperature quantum optomechanics.

Quantum technologies play a pivotal role in driving transformative advancements across diverse fields, surpassing classical approaches and empowering us to address complex challenges more effectively; however, the need for ultra-low temperatures limits the use of these technologies to particular fields. This work comes to alleviate this problem. We present a way of phononic bandgap engineering using FEM by which the radiative mechanical energy dissipation of a nanomechanical oscillator can be significantly suppressed through coupling with a complementary oscillating mode of a defect of the surrounding phononic crystal (PnC). Applied to an optomechanically coupled nanobeam resonator in the megahertz regime, we find a mechanical quality factor improvement of up to four orders of magnitude compared to conventional PnC designs. As this method is based on geometrical optimization of the PnC and frequency matching of the resonator and defect mode, it is applicable to a wide range of resonator types and frequency ranges. Taking advantage of the, hereinafter referred to as, "regenerative coupling" in phononic crystals, the presented device is capable of reaching f × Q products exceeding 10E16 Hz with only two rows of PnC shield. Thus, stable quantum states with mechanical decoherence times up to 700 µs at room temperature can be obtained, offering new opportunities for the optimization of mechanical resonator performance and advancing the room temperature quantum field across diverse applications.

Acromegaly Type 1: A Representative Patient.

A 46-year-old woman was troubled by a 3-year history of constant headaches and arthralgias. She was treated with paracetamol with no symptom resolution. An abnormal fasting glucose level prompted endocrine evaluation. On physical examination, she casually mentioned that her wedding ring no longer fit, and she also confirmed an increase in shoe size. There were no characteristic facial features for acromegaly and there was no evidence of acral enlargement. Biochemical evaluation, including insulin-like growth factor type 1 (IGF-1) measurement and oral glucose loading with growth hormone (GH) measurement confirmed excess GH production and a diagnosis of acromegaly. Pituitary magnetic resonance imaging showed a central pituitary microadenoma. After transsphenoidal surgical resection, tissue immunohistochemistry revealed a densely granulated somatotroph adenoma. Currently, the patient is asymptomatic with biochemical disease control, normal fasting glucose levels, and no pituitary hormone deficiencies. This patient is illustrative of a type 1 acromegaly with mild clinical manifestations. Clinicians should be aware of acromegaly subtypes to avoid delay in diagnosis and to individualize therapy.

An overview of log likelihood ratio cost in forensic science - Where is it used and what values can we expect?

There is increasing support for reporting evidential strength as a likelihood ratio (LR) and increasing interest in (semi-)automated LR systems. The log-likelihood ratio cost (Cllr) is a popular metric for such systems, penalizing misleading LRs further from 1 more. Cllr = 0 indicates perfection while Cllr = 1 indicates an uninformative system. However, beyond this, what constitutes a "good" Cllr is unclear. Aiming to provide handles on when a Cllr is "good", we studied 136 publications on (semi-)automated LR systems. Results show Cllr use heavily depends on the field, e.g., being absent in DNA analysis. Despite more publications on automated LR systems over time, the proportion reporting Cllr remains stable. Noticeably, Cllr values lack clear patterns and depend on the area, analysis and dataset. As LR systems become more prevalent, comparing them becomes crucial. This is hampered by different studies using different datasets. We advocate using public benchmark datasets to advance the field.

Antagonism between neuropeptides and monoamines in a distributed circuit for pathogen avoidance.

Pathogenic infection elicits behaviors that promote recovery and survival of the host. After exposure to the pathogenic bacterium Pseudomonas aeruginosa PA14, the nematode Caenorhabditis elegans modifies its sensory preferences to avoid the pathogen. Here, we identify antagonistic neuromodulators that shape this acquired avoidance behavior. Using an unbiased cell-directed neuropeptide screen, we show that AVK neurons upregulate and release RF/RYamide FLP-1 neuropeptides during infection to drive pathogen avoidance. Manipulations that increase or decrease AVK activity accelerate or delay pathogen avoidance, respectively, implicating AVK in the dynamics of avoidance behavior. FLP-1 neuropeptides drive pathogen avoidance through the G protein-coupled receptor DMSR-7, as well as other receptors. DMSR-7 in turn acts in multiple neurons, including tyraminergic/octopaminergic neurons that receive convergent avoidance signals from the cytokine DAF-7/transforming growth factor ß. Neuromodulators shape pathogen avoidance through multiple mechanisms and targets, in agreement with the distributed neuromodulatory connectome of C. elegans.

Local and dynamic regulation of neuronal glycolysis in vivo.

Energy metabolism supports neuronal function. While it is well established that changes in energy metabolism underpin brain plasticity and function, less is known about how individual neurons modulate their metabolic states to meet varying energy demands. This is because most approaches used to examine metabolism in living organisms lack the resolution to visualize energy metabolism within individual circuits, cells, or subcellular regions. Here, we adapted a biosensor for glycolysis, HYlight, for use in Caenorhabditis elegans to image dynamic changes in glycolysis within individual neurons and in vivo. We determined that neurons cell-autonomously perform glycolysis and modulate glycolytic states upon energy stress. By examining glycolysis in specific neurons, we documented a neuronal energy landscape comprising three general observations: 1) glycolytic states in neurons are diverse across individual cell types; 2) for a given condition, glycolytic states within individual neurons are reproducible across animals; and 3) for varying conditions of energy stress, glycolytic states are plastic and adapt to energy demands. Through genetic analyses, we uncovered roles for regulatory enzymes and mitochondrial localization in the cellular and subcellular dynamic regulation of glycolysis. Our study demonstrates the use of a single-cell glycolytic biosensor to examine how energy metabolism is distributed across cells and coupled to dynamic states of neuronal function and uncovers unique relationships between neuronal identities and metabolic landscapes in vivo.

Understanding neural circuit function through synaptic engineering.

Synapses are a key component of neural circuits, facilitating rapid and specific signalling between neurons. Synaptic engineering - the synthetic insertion of new synaptic connections into in vivo neural circuits - is an emerging approach for neural circuit interrogation. This approach is especially powerful for establishing causality in neural circuit structure-function relationships, for emulating synaptic plasticity and for exploring novel patterns of circuit connectivity. Contrary to other approaches for neural circuit manipulation, synaptic engineering targets specific connections between neurons and functions autonomously with no user-controlled external activation. Synaptic engineering has been successfully implemented in several systems and in different forms, including electrical synapses constructed from ectopically expressed connexin gap junction proteins, synthetic optical synapses composed of presynaptic photon-emitting luciferase coupled with postsynaptic light-gated channels, and artificial neuropeptide signalling pathways. This Perspective describes these different methods and how they have been applied, and examines how the field may advance.

Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD.

Functional loss of TDP-43, an RNA binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to the inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote the degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43-depleted human iPSC-derived neurons in vitro, and de novo peptides were found in cerebrospinal fluid (CSF) samples from patients with ALS or FTD. Using coordinated transcriptomic and proteomic studies of TDP-43-depleted human iPSC-derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43-depleted human iPSC-derived neurons were predictive of cryptic exons expressed in postmortem brain tissue from patients with TDP-43 proteinopathy. These cryptic exons produced transcript variants that generated de novo proteins. We found that the inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Last, we showed that 18 de novo peptides across 13 genes were present in CSF samples from patients with ALS/FTD spectrum disorders. The demonstration of cryptic exon translation suggests new mechanisms for ALS/FTD pathophysiology downstream of TDP-43 dysfunction and may provide a potential strategy to assay TDP-43 function in patient CSF.

Dinâmica espaço-temporal da febre amarela no Brasil / Spatio-temporal dynamics of yellow fever in Brazil

Introdução: No século XXI, o Brasil registrou os maiores surtos da história da febre amarela (FA) silvestre no país, colocando-o na primeira posição em produção de casos nas Américas e na segunda posição no mundo. As reemergências do vírus na região extra-amazônica (não endêmica) causaram profundos impactos à saúde pública e à biodiversidade. A despeito dos esforços de vigilância, a dinâmica do ciclo silvestre de transmissão tem desafiado as autoridades de saúde, à medida que o vírus se aproxima cada vez mais dos grandes centros urbanos, infestados por Aedes aegypti, numa diversidade de contextos epidemiológicos, ambientais e socioeconômicos. Assim, esses estudos propõem-se a ampliar a compreensão sobre o potencial impacto da FA nas populações humanas e sobre a dinâmica de transmissão do vírus, sobretudo dos fatores que desencadeiam as reemergências na região extraamazônica, no sentido de direcionar esforços e recursos para a prevenção de surtos e óbitos pela doença e para a resposta às emergências em saúde pública. Objetivos: Descrever a dinâmica espaço-temporal de ocorrência da FA no Brasil. Os objetivos específicos foram (i) produzir estimativas atualizadas da carga de febre amarela, (ii) identificar fatores contextuais associados à sazonalidade da FA, relacionados à exposição ao risco de infecção, e (iii) descrever os padrões temporais de ocorrência da FA e identificar variáveis que permitam predizer alterações no perfil de transmissão do vírus amarílico. Métodos: Foram realizados três estudos ecológicos. No Objetivo 1, foram ajustados modelos lineares generalizados (GLM) para os dados de ocorrência de FA em função de variáveis ambientais, de adequabilidade de habitat e de diversidade de PNH. No Objetivo 2, foi utilizado um algoritmo de aprendizagem de máquina (Random Forests) para classificar os municípios a partir de dados de distribuição de primatas não-humanos (PNH), de demografia e de sazonalidade das atividades agrícolas (plantio e colheita). No Objetivo 3, modelos lineares generalizados autorregressivos de média móvel (GLARMA) foram utilizados para investigar a associação entre a FA e variáveis climáticas e meteorológicas, com especial interesse nos índices relacionados ao fenômeno El Niño. Resultados: No Objetivo 1, as estimativas de carga global da FA colocam o Brasil na quarta posição em número de óbitos potenciais pela doença em função da elevada força de infecção estimada para a região amazônica. No Objetivo 2, a sazonalidade do plantio e colheita de algumas culturas foram associadas à ocorrência de casos humanos de FA, abrindo caminho para a priorização de ações em áreas e períodos específicos. No Objetivo 3, a ocorrência de FA em humanos e PNH foram associadas a variáveis de temperatura, precipitação, velocidade do vento e índices do El Niño, com diferentes deslocamentos no tempo (lags) e conjuntos de variáveis distintos entre os biomas. Conclusões: Os estudos apresentados incorporam novos conhecimentos sobre os impactos e os fatores preditores da FA e fornecem subsídios para o aprimoramento das estratégias e políticas públicas de vigilância em saúde, para o planejamento e direcionamento das ações e dos recursos disponíveis e para a avaliação das intervenções em saúde.

Introduction: In the 21st century, Brazil recorded the largest outbreaks of sylvatic yellow fever (YF) in the country's history, ranking it first in case production in the Americas and second in the world. The re-emergences of the virus in the extra-Amazon region (non-endemic) have caused profound impacts on public health and biodiversity. Despite surveillance efforts, the dynamics of the sylvatic transmission cycle have challenged health authorities, as the virus moves ever closer to large urban centers, infested by Aedes aegypti, in a variety of epidemiological, environmental, and socio-economic contexts. These studies aim to broaden the understanding of the potential impact of YF on human populations and of the dynamics of virus transmission, especially the factors that trigger re-emergences in the extra-Amazon region, in order to direct efforts and resources towards preventing outbreaks and deaths from the disease and responding to public health emergencies. Objectives: To describe the spatiotemporal dynamics of YF occurrence in Brazil. The specific objectives were (i) to produce upto- date estimates of the YF burden, (ii) to identify contextual factors associated with the seasonality of YF, related to exposure to the risk of infection, and (iii) to describe the temporal patterns of YF occurrence and identify variables that make it possible to predict changes in the transmission profile of the virus. Methods: Three ecological studies were carried out. In Objective 1, generalized linear models (GLM) were fitted to data on the occurrence of YF as a function of environmental variables, habitat suitability and NHP diversity. In Objective 2, a machine learning algorithm (Random Forests) was used to classify municipalities based on data on the distribution of non-human primates (NHP), demographics and the seasonality of agricultural activities (planting and harvesting). In Objective 3, generalized linear autoregressive moving average (GLARMA) models were used to investigate the association between YF and climatic and meteorological variables, with special interest in indices related to the El Niño phenomenon. Results: In Objective 1, estimates of the global burden of YF place Brazil in fourth position in terms of the number of potential deaths from the disease due to the high force of infection estimated for the Amazon region. In Objective 2, the seasonality of planting and harvesting some crops was associated with the occurrence of human cases of YF, paving the way for prioritizing actions in specific areas and periods. In Objective 3, the occurrence of YF in humans and NHP was associated with variables such as temperature, rainfall, wind speed and El Niño indices, with different lags and different sets of variables among biomes. Conclusions: The studies presented incorporate new knowledge on the impacts and predictors of YF and provide input for improving public health surveillance strategies and policies, for planning and targeting actions and available resources, and for evaluating health interventions

The American Society of Pain and Neuroscience (ASPN) Guidelines for Radiofrequency Ablative Procedures in Patients with Implanted Devices.

Radiofrequency ablation (RFA) is a treatment modality used in interventional pain management to treat several conditions including chronic neck or back pain, sacroiliac joint pain, major joint pain, and pain from sites that can be isolated to a sensory nerve amenable to RFA. The goals of such procedures are to reduce pain, improve function, delay need for surgical intervention, and reduce pain medication consumption. As applications for RFA expand through novel techniques and nerve targets, there is concern with how RFA may impact patients with implanted medical devices. Specifically, the electrical currents used in RFA produce electromagnetic interference, which can result in unintentional energy transfer to implanted devices. This may also interfere with device function or cause damage to the device itself. As the number of patients with implanted devices increases, it is imperative to establish guidelines for the management of implanted devices during RFA procedures. This review aims to establish guidelines to assist physicians in the preoperative, intraoperative, and postoperative management of implanted devices in patients undergoing procedures using radiofrequency energy. Here, we provide physicians with background knowledge and a summary of current evidence to allow safe utilization of RFA treatment in patients with implanted devices such as cardiac implantable electronic devices, spinal cord stimulators, intrathecal pumps, and deep brain stimulators. While these guidelines are intended to be comprehensive, each patient should be assessed on an individual basis to optimize outcomes.

Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy.

Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing image acquisition, applying additional dose, or introducing more optics into the imaging path. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks, making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations to show that applying the trained 'de-aberration' networks outperforms alternative methods, and subsequently apply the networks to diverse datasets captured with confocal, light-sheet, multi-photon, and super-resolution microscopy. In all cases, the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation, including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in C. elegans embryos.

An ANXA11 P93S variant dysregulates TDP-43 and causes corticobasal syndrome.

As genetic testing has become more accessible and affordable, variants of uncertain significance (VUS) are increasingly identified, and determining whether these variants play causal roles in disease is a major challenge. The known disease-associated Annexin A11 (ANXA11) mutations result in ANXA11 aggregation, alterations in lysosomal-RNA granule co-trafficking, and TDP-43 mis-localization and present as amyotrophic lateral sclerosis or frontotemporal dementia. We identified a novel VUS in ANXA11 (P93S) in a kindred with corticobasal syndrome and unique radiographic features that segregated with disease. We then queried neurodegenerative disorder clinic databases to identify the phenotypic spread of ANXA11 mutations. Multi-modal computational analysis of this variant was performed and the effect of this VUS on ANXA11 function and TDP-43 biology was characterized in iPSC-derived neurons. Single-cell sequencing and proteomic analysis of iPSC-derived neurons and microglia were used to determine the multiomic signature of this VUS. Mutations in ANXA11 were found in association with clinically diagnosed corticobasal syndrome, thereby establishing corticobasal syndrome as part of ANXA11 clinical spectrum. In iPSC-derived neurons expressing mutant ANXA11, we found decreased colocalization of lysosomes and decreased neuritic RNA as well as decreased nuclear TDP-43 and increased formation of cryptic exons compared to controls. Multiomic assessment of the P93S variant in iPSC-derived neurons and microglia indicates that the pathogenic omic signature in neurons is modest compared to microglia. Additionally, omic studies reveal that immune dysregulation and interferon signaling pathways in microglia are central to disease. Collectively, these findings identify a new pathogenic variant in ANXA11, expand the range of clinical syndromes caused by ANXA11 mutations, and implicate both neuronal and microglia dysfunction in ANXA11 pathophysiology. This work illustrates the potential for iPSC-derived cellular models to revolutionize the variant annotation process and provides a generalizable approach to determining causality of novel variants across genes.

[Septic shock originating from a pulmonary focus caused by Pasteurella multocida. Report of one case]. / Shock séptico de foco respiratorio por Pasteurella multocida en un paciente inmunocompetente. Caso Clínico.

Pasteurella multocida is a gram-negative coccobacillus bacterium found as a commensal in the oropharynx of domestic animals such as cats and dogs and some farm animals. Soft tissue infections and occasionally bacteremia in immunocompromised patients with direct contact with animals are described. We report a 61 year old male with a history of scratches and close contact with domestic cats, with a septic shock originating from a pulmonary focus, requiring mechanical ventilation and vasopressors. Blood cultures disclosed the presence of Pasteurella multocida. He responded successfully to antimicrobials.

A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline.

Here, we present a standardized, "off-the-shelf" proteomics pipeline working in a single 96-well plate to achieve deep coverage of cellular proteomes with high throughput and scalability. This integrated pipeline streamlines a fully automated sample preparation platform, a data-independent acquisition (DIA) coupled with high-field asymmetric waveform ion mobility spectrometer (FAIMS) interface, and an optimized library-free DIA database search strategy. Our systematic evaluation of FAIMS-DIA showing single compensation voltage (CV) at -35 V not only yields the deepest proteome coverage but also best correlates with DIA without FAIMS. Our in-depth comparison of direct-DIA database search engines shows that Spectronaut outperforms others, providing the highest quantifiable proteins. Next, we apply three common DIA strategies in characterizing human induced pluripotent stem cell (iPSC)-derived neurons and show single-shot mass spectrometry (MS) using single-CV (-35 V)-FAIMS-DIA results in >9,000 quantifiable proteins with <10% missing values, as well as superior reproducibility and accuracy compared with other existing DIA methods.

Case report: Urbanized non-human primates as sentinels for human zoonotic diseases: a case of acute fatal toxoplasmosis in a free-ranging marmoset in coinfection with yellow fever virus.

Free-ranging non-human primates (NHP) can live in anthropized areas or urban environments in close contact with human populations. This condition can enable the emergence and transmission of high-impact zoonotic pathogens. For the first time, we detected a coinfection of the yellow fever (YF) virus with Toxoplasma gondii in a free-ranging NHP in a highly urbanized area of a metropolis in Brazil. Specifically, we observed this coinfection in a black-tufted marmoset found dead and taken for a necropsy by the local health surveillance service. After conducting an epidemiological investigation, characterizing the pathological features, and performing molecular assays, we confirmed that the marmoset developed an acute fatal infection caused by T. gondii in coinfection with a new YF virus South American-1 sub-lineage. As a result, we have raised concerns about the public health implications of these findings and discussed the importance of diagnosis and surveillance of zoonotic agents in urbanized NHPs. As competent hosts of zoonotic diseases such as YF and environmental sentinels for toxoplasmosis, NHPs play a crucial role in the One Health framework to predict and prevent the emergence of dangerous human pathogens.