Community-developed checklists for publishing images and image analyses.

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images and image-analysis results, there are currently no unified guidelines for best practices. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here, we present community-developed checklists for preparing light microscopy images and describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data.

Recognising the importance and impact of Imaging Scientists: Global guidelines for establishing career paths within core facilities.

In the dynamic landscape of scientific research, imaging core facilities are vital hubs propelling collaboration and innovation at the technology development and dissemination frontier. Here, we present a collaborative effort led by Global BioImaging (GBI), introducing international recommendations geared towards elevating the careers of Imaging Scientists in core facilities. Despite the critical role of Imaging Scientists in modern research ecosystems, challenges persist in recognising their value, aligning performance metrics and providing avenues for career progression and job security. The challenges encompass a mismatch between classic academic career paths and service-oriented roles, resulting in a lack of understanding regarding the value and impact of Imaging Scientists and core facilities and how to evaluate them properly. They further include challenges around sustainability, dedicated training opportunities and the recruitment and retention of talent. Structured across these interrelated sections, the recommendations within this publication aim to propose globally applicable solutions to navigate these challenges. These recommendations apply equally to colleagues working in other core facilities and research institutions through which access to technologies is facilitated and supported. This publication emphasises the pivotal role of Imaging Scientists in advancing research programs and presents a blueprint for fostering their career progression within institutions all around the world.

Ultrasound clinical references of the healthy toenail unit.

The toenail unit, commonly called the nail, is one of the most frequently examined and treated structures in clinical podiatry. Ultrasound is a standard clinical technique because it is a noninvasive, painless, and rapid diagnostic tool. The main objective of this study was to obtain morphometric data of the healthy toenail unit by ultrasound for clinical application. The nails of 76 participants (152 hallux nails; 38 men, 38 women, average age 26.83 ± 12.20) were examined using a VINNO E35 ultrasound system and an X6-16L linear probe with a frequency of 18 MHz. Five ultrasound measures of the healthy toenail unit were obtained, of which only the distance from the center of the distal phalange to the nail plate varied with age, sex, weight, and foot (p-values ≤ 0.050). The other four parameters were less influenced by the variables analyzed, except sex, which influenced nearly all (p-values ≤ 0.050). In one of these variables, indications of significance were observed (p-values = 0.060), with greater distances in the men than in the women, except for nail plate curvature, which showed a higher value. The other variables studied did not influence the parameters analyzed. High-frequency ultrasound can be used to examine the healthy toenail unit and define anthropometric reference measurements that can be used for more accurate and comparative diagnosis.

Targeting Trypanothione Metabolism in Trypanosomatids.

Infectious diseases caused by trypanosomatids, including African trypanosomiasis (sleeping sickness), Chagas disease, and different forms of leishmaniasis, are Neglected Tropical Diseases affecting millions of people worldwide, mainly in vulnerable territories of tropical and subtropical areas. In general, current treatments against these diseases are old-fashioned, showing adverse effects and loss of efficacy due to misuse or overuse, thus leading to the emergence of resistance. For these reasons, searching for new antitrypanosomatid drugs has become an urgent necessity, and different metabolic pathways have been studied as potential drug targets against these parasites. Considering that trypanosomatids possess a unique redox pathway based on the trypanothione molecule absent in the mammalian host, the key enzymes involved in trypanothione metabolism, trypanothione reductase and trypanothione synthetase, have been studied in detail as druggable targets. In this review, we summarize some of the recent findings on the molecules inhibiting these two essential enzymes for Trypanosoma and Leishmania viability.

Genotypes and morphologies of bovine papillomaviruses in Costa Rica.

Bovine papillomaviruses (BPVs) infect the basal layer of the epithelium of bovines, where they persist asymptomatically or produce benign fibroepithelial hyperplasia in the skin or mucosa. The aim of the present study was to describe the genotypes of bovine papillomas at the macroscopic and microscopic level. A descriptive study was carried out using non-probabilistic convenience sampling. Ninety-nine papillomas from 63 animals were collected on 32 farms, as well as information about age, gender, breed, and productive use of the bovines. The location, type, and degree of epithelial invasion of the papillomas were recorded. The samples were subjected to molecular and histopathological analysis. Papillomas were found most frequently on dairy farms (75.0%), in females (95.0%), in cattle of the Holstein breed (45.0%), and in animals over 24 months of age (50.0%). Most of the positive animals had from 1 to 15 papillomas (31.6%) and only one type of papilloma (79.4%). Cauliflower-like papillomas were found in 48.5% of the cases, while atypical papillomas were found in 11.1% of the cases. Cauliflower-like papillomas were found mainly on the udder (14.4%), head (10.0%), and neck (10.0%) and were associated with five BPV genotypes (BPV1, BPV2, BPV6, BPV7, and BPV10), while BPV2 and BPV6 were found to be associated with all types of papillomas (cauliflower, flat, pedunculated, and atypical). The presence of BPV11 in flat papillomas and BPV6 in atypical papillomas is reported here for the first time. Morphology and histopathological findings did not allow differentiation of the BPV genotypes.

HIV Pre-Exposure Prophylaxis in the Emergency Department: A Systematic Review.

STUDY OBJECTIVE: Many emergency departments (EDs) have identified the importance of HIV prevention and have implemented steps to screen and offer preexposure prophylaxis (PrEP). The objective of this study was to systematically review existing literature that identifies PrEP eligibility in the ED and summarize outcomes along the PrEP cascade of care (awareness, interest, linkage to treatment, initiation, and retention) for patients in ED. METHODS: Four databases captured all PrEP-related studies in EDs from January 1, 2013 to January 27, 2022. Data were extracted on study characteristics and outcomes, and study quality was assessed using a modified quality assessment tool by the Effective Public Health Practice Project. RESULTS: Of the 218 articles, 16 were subjected to full-text review, and 7 met inclusion criteria. Although most studies identified patients who were PrEP eligible using criteria adapted from the 2017 Centers for Disease Control and Prevention PrEP guidelines, the number and time frame for each criterion varied. Six studies reported outcomes on the PrEP cascade of care, showing a relatively high prevalence of awareness and interest but a very low prevalence of linkage and uptake. No studies documented retention in PrEP treatment. CONCLUSION: Although up to a third of patients in ED assessed in the current study were PrEP eligible, less than half of PrEP-eligible participants had prior knowledge of PrEP, and very few who expressed interest in the ED were ultimately linked to PrEP treatment or initiated PrEP. Future research is necessary to identify strategies to increase PrEP education, interest, and linkage to care from the ED.

Chemical traits of cerebral amyloid angiopathy in familial British-, Danish-, and non-Alzheimer's dementias.

Familial British dementia (FBD) and familial Danish dementia (FDD) are autosomal dominant forms of dementia caused by mutations in the integral membrane protein 2B (ITM2B, also known as BRI2) gene. Secretase processing of mutant BRI2 leads to secretion and deposition of BRI2-derived amyloidogenic peptides, ABri and ADan that resemble APP/ß-amyloid (Aß) pathology, which is characteristic of Alzheimer's disease (AD). Amyloid pathology in FBD/FDD manifests itself predominantly in the microvasculature by ABri/ADan containing cerebral amyloid angiopathy (CAA). While ABri and ADan peptide sequences differ only in a few C-terminal amino acids, CAA in FDD is characterized by co-aggregation of ADan with Aß, while in contrast no Aß deposition is observed in FBD. The fact that FDD patients display an earlier and more severe disease onset than FBD suggests a potential role of ADan and Aß co-aggregation that promotes a more rapid disease progression in FDD compared to FBD. It is therefore critical to delineate the chemical signatures of amyloid aggregation in these two vascular dementias. This in turn will increase the knowledge on the pathophysiology of these diseases and the pathogenic role of heterogenous amyloid peptide interactions and deposition, respectively. Herein, we used matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) in combination with hyperspectral, confocal microscopy based on luminescent conjugated oligothiophene probes (LCO) to delineate the structural traits and associated amyloid peptide patterns of single CAA in postmortem brain tissue of patients with FBD, FDD as well as sporadic CAA without AD (CAA+) that show pronounced CAA without parenchymal plaques. The results show that CAA in both FBD and FDD consist of N-terminally truncated- and pyroglutamate-modified amyloid peptide species (ADan and ABri), but that ADan peptides in FDD are also extensively C-terminally truncated as compared to ABri in FBD, which contributes to hydrophobicity of ADan species. Further, CAA in FDD showed co-deposition with Aß x-42 and Aß x-40 species. CAA+ vessels were structurally more mature than FDD/FBD CAA and contained significant amounts of pyroglutamated Aß. When compared with FDD, Aß in CAA+ showed more C-terminal and less N-terminally truncations. In FDD, ADan showed spatial co-localization with Aß3pE-40 and Aß3-40 but not with Aßx-42 species. This suggests an increased aggregation propensity of Aß in FDD that promotes co-aggregation of both Aß and ADan. Further, CAA maturity appears to be mainly governed by Aß content based on the significantly higher 500/580 patterns observed in CAA+ than in FDD and FBD, respectively. Together this is the first study of its kind on comprehensive delineation of Bri2 and APP-derived amyloid peptides in single vascular plaques in both FDD/FBD and sporadic CAA that provides new insight in non-AD-related vascular amyloid pathology. Cover Image for this issue: https://doi.org/10.1111/jnc.15424.

Meta-analysis of the antifungal activities of three essential oils as alternative therapies in dermatophytosis infections.

AIMS: This work examines the available scientific evidence about the efficiency of essential oils (EO) as an alternative therapy to traditional treatment of fungal infections, including onychomycosis, assessing the effect of the three EO most frequently studied for their antifungal activity (thyme, cinnamon and tea tree EO) against three causative agents of fungal diseases in humans: Trichophyton rubrum, Trichophyton mentagrophytes complex and Candida albicans. METHODS AND RESULTS: The PRISMA statement protocol was followed to conduct a bibliographical search and 54 articles that met all the inclusion criteria were retrieved. Differences were observed in the MIC and MFC values depending on the micro-organism strain and the EO used. The lowest MIC were observed with Cinnamomum zeylanicum EO (0.013-1120 µl ml-1 ) against the three micro-organisms. For MFC, the lowest value was found for Thymus vulgaris EO (4.2 µl ml-1 ) against Trichophyton rubrum. CONCLUSIONS: The antifungal effects of EO could be a very promising solution to overcome the therapeutic shortcomings of antimycotic medication. More experiments are needed to examine the properties of these oils to devise effective and nonaggressive therapies for treatment of dermatophytosis. SIGNIFICANCE AND IMPACT OF STUDY: The results indicate that EO remain good candidates for future treatments and could provide a solution for failed medications and/or adverse reactions to current pharmacological treatments.

Validation of an RF Image System for Real-Time Tracking Neurosurgical Tools.

A radio frequency (RF)-based system for surgical navigation is presented. Surgical navigation technologies are widely used nowadays for aiding the surgical team with many interventions. However, the currently available options still pose considerable limitations, such as line-of-sight occlusion prevention or restricted materials and equipment allowance. In this work, we suggest a different approach based on a microwave broadband antenna system. We combine techniques from microwave medical imaging, which can overcome the current limitations in surgical navigation technologies, and we propose methods to develop RF-based systems for real-time tracking neurosurgical tools. The design of the RF system to perform the measurements is shown and discussed, and two methods (Multiply and Sum and Delay Multiply and Sum) for building the medical images are analyzed. From these measurements, a surgical tool's position tracking system is developed and experimentally assessed in an emulated surgical scenario. The reported results are coherent with other approaches found in the literature, while overcoming their main practical limitations. The discussion of the results discloses some hints on the validity of the system, the optimal configurations depending on the requirements, and the possibilities for future enhancements.

Regulation of ovule initiation by gibberellins and brassinosteroids in tomato and Arabidopsis: two plant species, two molecular mechanisms.

Ovule primordia formation is a complex developmental process with a strong impact on the production of seeds. In Arabidopsis this process is controlled by a gene network, including components of the signalling pathways of auxin, brassinosteroids (BRs) and cytokinins. Recently, we have shown that gibberellins (GAs) also play an important role in ovule primordia initiation, inhibiting ovule formation in both Arabidopsis and tomato. Here we reveal that BRs also participate in the control of ovule initiation in tomato, by promoting an increase on ovule primordia formation. Moreover, molecular and genetic analyses of the co-regulation by GAs and BRs of the control of ovule initiation indicate that two different mechanisms occur in tomato and Arabidopsis. In tomato, GAs act downstream of BRs. BRs regulate ovule number through the downregulation of GA biosynthesis, which provokes stabilization of DELLA proteins that will finally promote ovule primordia initiation. In contrast, in Arabidopsis both GAs and BRs regulate ovule number independently of the activity levels of the other hormone. Taken together, our data strongly suggest that different molecular mechanisms could operate in different plant species to regulate identical developmental processes even, as for ovule primordia initiation, if the same set of hormones trigger similar responses, adding a new level of complexity.

QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy.

A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.

The effects of time valuation in cancer optimal therapies: a study of chronic myeloid leukemia.

BACKGROUND: The mathematical design of optimal therapies to fight cancer is an important research field in today's Biomathematics and Biomedicine given its relevance to formulate patient-specific treatments. Until now, however, cancer optimal therapies have considered that malignancy exclusively depends on the drug concentration and the number of cancer cells, ignoring that the faster the cancer grows the worse the cancer is, and that early drug doses are more prejudicial. Here, we analyze how optimal therapies are affected when the time evolution of treated cancer is envisaged as an additional element determining malignancy, analyzing in detail the implications for imatinib-treated Chronic Myeloid Leukemia. METHODS: Taking as reference a mathematical model describing Chronic Myeloid Leukemia dynamics, we design an optimal therapy problem by modifying the usual malignancy objective function, unaware of any temporal dimension of cancer malignance. In particular, we introduce a time valuation factor capturing the increase of malignancy associated to the quick development of the disease and the persistent negative effects of initial drug doses. After assigning values to the parameters involved, we solve and simulate the model with and without the new time valuation factor, comparing the results for the drug doses and the evolution of the disease. RESULTS: Our computational simulations unequivocally show that the consideration of a time valuation factor capturing the higher malignancy associated with early growth of cancer and drug administration allows more efficient therapies to be designed. More specifically, when this time valuation factor is incorporated into the objective function, the optimal drug doses are lower, and do not involve medically relevant increases in the number of cancer cells or in the disease duration. CONCLUSIONS: In the light of our simulations and as biomedical evidence strongly suggests, the existence of a time valuation factor affecting malignancy in treated cancer cannot be ignored when designing cancer optimal therapies. Indeed, the consideration of a time valuation factor modulating malignancy results in significant gains of efficiency in the optimal therapy with relevant implications from the biomedical perspective, specially when designing patient-specific treatments.

Boiling and Pressure Cooking Impact on IgE Reactivity of Soybean Allergens.

BACKGROUND: Soybean is one of the 8 foods that causes the most significant rate of food allergies in the USA and Europe. Thermal processing may impact on the allergenic potential of certain foods. We aimed to investigate modifications of the IgE-binding properties of soybean proteins due to processing methods that have been previously found to impact on the allergenicity of legumes such as peanut. METHODS: Soybean seeds were subjected to different thermal processing treatments. To evaluate their impact on the IgE-binding capacity of soybean proteins, individual sera from 25 patients sensitized to soybean were used in in vitro immunoassays. Detection of specific soybean allergens in untreated and treated samples was carried out with specific monoclonal and polyclonal antibodies. In vivo studies of skin prick testing (SPT) were also performed. RESULTS: The IgE reactivity of soybean was resistant to boiling up to 30 min, and this treatment had a higher impact when applied for 60 min. Treatment that combined heat and pressure produced a fragmentation of proteins in both soluble and insoluble fractions that went along with a decreased capacity to bind IgE and reduced the SPT wheal size. However, allergens such as 7S globulins survived this treatment. CONCLUSIONS: Thermal-processing methods able to attenuate the capacity of soybean proteins to bind IgE may contribute to the improvement of food safety and could constitute a potential strategy for the induction of tolerance to soybean.

Outbreak of acute hepatitis A in the health area served by the Hospital Universitario Virgen de la Victoria (HUVV): a change in epidemiology.

In 2016, an outbreak of hepatitis A was identified in the Malaga province among patients with specific epidemiological characteristics, which were predominantly males. This is a report of 51 subjects with acute hepatitis A and a mean age of 35.7 years, 90% were male and 55% of cases were men who had had sex with other men within the last two months. Half of them required hospitalization for significant coagulopathy at diagnosis and no cases progressed to fulminant failure or encephalopathy. Four patients had ascites at the time of diagnosis. This outbreak adds to those reported in the United Kingdom and the Netherlands with a similar number of cases and epidemiology. These studies highlight the importance of epidemiological surveillance, the need for vaccination in this particular at risk population and the need for informative campaigns in order to prevent this disease.

Full-length antibodies versus single-chain antibody fragments for a selective impedimetric lectin-based glycoprofiling of prostate specific antigen.

The main aim of the research was to design a functional impedimetric biosensor able to glycoprofile prostate specific antigen (PSA), a biomarker for prostate cancer (PCa), with high specificity using lectins as glycan recognising proteins. Traditionally, full-length antibody is immobilised on the biosensor interface for specific capture of PSA with subsequent glycoprofiling of PSA by addition of lectins. Since full-length antibodies contain glycans in the Fc domain, particular attention has to be paid to suppress direct binding of lectins to immobilised full-length antibodies, which would compromise accurate glycoprofiling. This issue is addressed here using a recombinant single-chain antibody fragments (scAb), which do not contain any carbohydrate moiety. Surface plasmon resonance was applied to prove negligible interaction of lectins with immobilised scAb fragments, while substantial binding of lectins to full length antibodies was observed. Eight different biosensor designs were tested for their ability to detect PSA. The biosensor device based on scAb fragments covalently immobilised on the gold electrode surface, patterned by a mixed SAM using standard amine coupling chemistry, proved to be the most sensitive. The scAb fragment-based biosensor exhibited sensitivity of 15.9 ± 0.8% decade-1 (R2 = 0.991 with an average RSD of 4.9%), while the full antibody-based biosensor offered sensitivity towards PSA of 4.2 ± 0.1% decade-1 (R2 = 0.999 with an average RSD of 4.8%). Moreover, the selectivity of the scAb-based biosensor was tested using a kallikrein 2 protein, a protein structurally similar to PSA, and the results indicated high selectivity for PSA detection.

Essential genetic interactors of SIR2 required for spatial sequestration and asymmetrical inheritance of protein aggregates.

Sir2 is a central regulator of yeast aging and its deficiency increases daughter cell inheritance of stress- and aging-induced misfolded proteins deposited in aggregates and inclusion bodies. Here, by quantifying traits predicted to affect aggregate inheritance in a passive manner, we found that a passive diffusion model cannot explain Sir2-dependent failures in mother-biased segregation of either the small aggregates formed by the misfolded Huntingtin, Htt103Q, disease protein or heat-induced Hsp104-associated aggregates. Instead, we found that the genetic interaction network of SIR2 comprises specific essential genes required for mother-biased segregation including those encoding components of the actin cytoskeleton, the actin-associated myosin V motor protein Myo2, and the actin organization protein calmodulin, Cmd1. Co-staining with Hsp104-GFP demonstrated that misfolded Htt103Q is sequestered into small aggregates, akin to stress foci formed upon heat stress, that fail to coalesce into inclusion bodies. Importantly, these Htt103Q foci, as well as the ATPase-defective Hsp104Y662A-associated structures previously shown to be stable stress foci, co-localized with Cmd1 and Myo2-enriched structures and super-resolution 3-D microscopy demonstrated that they are associated with actin cables. Moreover, we found that Hsp42 is required for formation of heat-induced Hsp104Y662A foci but not Htt103Q foci suggesting that the routes employed for foci formation are not identical. In addition to genes involved in actin-dependent processes, SIR2-interactors required for asymmetrical inheritance of Htt103Q and heat-induced aggregates encode essential sec genes involved in ER-to-Golgi trafficking/ER homeostasis.

Immunoproteomic tools are used to identify masked allergens: Ole e 12, an allergenic isoflavone reductase from olive (Olea europaea) pollen.

Proteins performing important biochemical activities in the olive tree (Olea europaea) pollen have been identified as allergens. One novel 37-kDa protein seems to be associated to the IgE-binding profile of a group of patients suffering allergy to peach and olive pollen. Three previously described olive pollen allergens exhibit very similar molecular mass. Our objective was to identify this allergen by using immunoproteomic approaches. After 2D-electrophoresis and mass spectrometry, peptide sequences from several IgE-binding spots, allowed identifying this new allergen, as well as cloning and DNA sequencing of the corresponding gene. The allergen, named Ole e 12, is a polymorphic isoflavone reductase-like protein of 308 amino acids showing 80% and 74% identity with birch and pear allergens, Bet v 6 and Pyr c 5, respectively. A prevalence of 33% in the selected population is in contrast to 4%-10% in groups of subjects suffering from pollinosis. Recombinant allergen was produced in Escherichia coli, and deeply characterised. Immunoblotting and ELISA detection as well as inhibition experiments were performed with polyclonal antisera and allergic patients' sera. The recombinant allergen retains the IgE reactivity of its natural counterpart. Close structural and immunological relationships between members of this protein family were supported by their IgG recognition in vegetable species. In summary, Ole e 12 is a minor olive pollen allergen, which gains relevance in patients allergic to peach with olive pollinosis. Proteomic approaches used to analyse this allergen provide useful tools to identify hidden allergens, relevant for several allergic populations and thus complete allergenic panels.