Nanostructured Copper Selenide Coatings for Antifouling Applications.

The accumulation of microorganisms, plants, algae, or small animals on wet surfaces that have a mechanical function causes biofouling, which can result in structural or other functional deficiencies. The maritime shipping industry must constantly manage biofouling to optimize operational performance, which is a common and long-lasting problem. It can occur on any metal structure in contact with or submerged in ocean water, which represents additional costs in terms of repairs and maintenance. This study is focused on the production of antifouling coatings, made with nanoparticles of copper selenide (CuSe NPs) modified with gum arabic, within a water-base acrylic polymeric matrix. During the curing of the acrylic resin, the CuSe NPs remain embedded in the resin, but this does not prevent the release of ions. The coatings released copper and selenium ions for up to 80 days, and selenium was the element that was released the most. The adhesion of film coatings to metallic substrates showed good adhesion, scale 5B (ASTM D3359 standard). Antimicrobial activity tests show that the coatings have an inhibitory effect on Escherichia coli and Candida albicans. The effect is more noticeable when the coating is detached from the substrate and placed on a growing medium, compared to the coating on a substrate. Scanning electron microscopy (SEM) observations show that nanostructured CuSe coatings are made up of rod-shaped and spherical particles with an average particle size of 101.6 nm and 50 nm, respectively. The energy dispersive X-ray spectroscopy (EDS) studies showed that the ratio of selenium nanoparticles is greater than that of copper and that their distribution is homogeneous.

ThyroidPrint®: clinical utility for indeterminate thyroid cytology.

Molecular testing contributes to improving the diagnosis of indeterminate thyroid nodules (ITNs). ThyroidPrint® is a ten-gene classifier aimed to rule out malignancy in ITN. Post-validation studies are necessary to determine the real-world clinical benefit of ThyroidPrint® in patients with ITN. A single-center, prospective, noninterventional clinical utility study was performed, analyzing the impact of ThyroidPrint® in the physicians' clinical decisions for ITN. Demographics, nodule characteristics, benign call rates (BCRs), and surgical outcomes were measured. Histopathological data were collected from surgical biopsies of resected nodules. Of 1272 fine-needle aspirations, 109 (8.6%) were Bethesda III and 135 (10.6%) were Bethesda IV. Molecular testing was performed in 155 of 244 ITN (63.5%), of which 104 were classified as benign (BCR of 67.1%). After a median follow-up of 15 months, 103 of 104 (99.0%) patients with a benign ThyroidPrint® remained under surveillance and one patient underwent surgery which was a follicular adenoma. Surgery was performed in all 51 patients with a suspicious for malignancy as per ThyroidPrint® result and in 56 patients who did not undergo testing, with a rate of malignancy of 70.6% and 32.1%, respectively. A higher BCR was observed in follicular lesion of undetermined significance (87%) compared to atypia of undetermined significance (58%) (P < 0.05). False-positive cases included four benign follicular nodules and six follicular and four oncocytic adenomas. Our results show that, physicians chose active surveillance instead of diagnostic surgery in all patients with a benign ThyroidPrint® result, reducing the need for diagnostic surgery in 67% of patients with preoperative diagnosis of ITN.

Identifying the neurodevelopmental and psychiatric signatures of genomic disorders associated with intellectual disability: a machine learning approach.

BACKGROUND: Genomic conditions can be associated with developmental delay, intellectual disability, autism spectrum disorder, and physical and mental health symptoms. They are individually rare and highly variable in presentation, which limits the use of standard clinical guidelines for diagnosis and treatment. A simple screening tool to identify young people with genomic conditions associated with neurodevelopmental disorders (ND-GCs) who could benefit from further support would be of considerable value. We used machine learning approaches to address this question. METHOD: A total of 493 individuals were included: 389 with a ND-GC, mean age = 9.01, 66% male) and 104 siblings without known genomic conditions (controls, mean age = 10.23, 53% male). Primary carers completed assessments of behavioural, neurodevelopmental and psychiatric symptoms and physical health and development. Machine learning techniques (penalised logistic regression, random forests, support vector machines and artificial neural networks) were used to develop classifiers of ND-GC status and identified limited sets of variables that gave the best classification performance. Exploratory graph analysis was used to understand associations within the final variable set. RESULTS: All machine learning methods identified variable sets giving high classification accuracy (AUROC between 0.883 and 0.915). We identified a subset of 30 variables best discriminating between individuals with ND-GCs and controls which formed 5 dimensions: conduct, separation anxiety, situational anxiety, communication and motor development. LIMITATIONS: This study used cross-sectional data from a cohort study which was imbalanced with respect to ND-GC status. Our model requires validation in independent datasets and with longitudinal follow-up data for validation before clinical application. CONCLUSIONS: In this study, we developed models that identified a compact set of psychiatric and physical health measures that differentiate individuals with a ND-GC from controls and highlight higher-order structure within these measures. This work is a step towards developing a screening instrument to identify young people with ND-GCs who might benefit from further specialist assessment.

Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications.

Elucidating spatiotemporal changes in gene expression has been an essential goal in studies of health, development, and disease. In the emerging field of spatially resolved transcriptomics, gene expression profiles are acquired with the tissue architecture maintained, sometimes at cellular resolution. This has allowed for the development of spatial cell atlases, studies of cell-cell interactions, and in situ cell typing. In this review, we focus on padlock probe-based in situ sequencing, which is a targeted spatially resolved transcriptomic method. We summarize recent methodological and computational tool developments and discuss key applications. We also discuss compatibility with other methods and integration with multiomic platforms for future applications.

A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.

The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.

The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.

Histone 3 lysine27-to-methionine (H3-K27M) mutations most frequently occur in diffuse midline gliomas (DMGs) of the childhood pons but are also increasingly recognized in adults. Their potential heterogeneity at different ages and midline locations is vastly understudied. Here, through dissecting the single-cell transcriptomic, epigenomic and spatial architectures of a comprehensive cohort of patient H3-K27M DMGs, we delineate how age and anatomical location shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We show that stem-like oligodendroglial precursor-like cells, present across all clinico-anatomical groups, display varying levels of maturation dependent on location. We reveal a previously underappreciated relationship between mesenchymal cancer cell states and age, linked to age-dependent differences in the immune microenvironment. Further, we resolve the spatial organization of H3-K27M DMG cell populations and identify a mitotic oligodendroglial-lineage niche. Collectively, our study provides a powerful framework for rational modeling and therapeutic interventions.

Epidemiological characteristics of Omicron and Delta SARS-CoV-2 variant infection in Santiago, Chile.

The variant of concern (VOC) SARS-CoV-2 Omicron (B.1.1529) has been described as a highly contagious variant but less virulent than the current variant being monitored (VBM) Delta (B.1.617.2), causing fewer cases of hospitalizations, symptomatology, and deaths associated with COVID-19 disease. Although the epidemiological comparison of both variants has been previously reported in other countries, no report indicates their behavior and severity of infection in Chile. In this work, we report for the first time the effect of the Omicron and Delta variants in a cohort of 588 patients from the Hospital de Urgencia Asistencia pública (HUAP), a high-complexity health center in Santiago, Chile. This report is framed at the beginning of Chile's third wave of the COVID-19 pandemic, with a marked increase in the Omicron variant and a decrease in the circulating Delta variant. Our results indicated a similar proportion of patients with a complete vaccination schedule for both variants. However, the Delta variant was associated with a higher prevalence of hospitalization and more significant symptomatology associated with respiratory distress. On the other hand, our data suggest that vaccination is less effective in preventing infection by the Omicron variant. This antecedent, with a low severity but high contagiousness, suggests that the Omicron variant could even collapse the primary health care service due to the high demand for health care.

Impact of secondary salts, temperature, and pH on the colloidal stability of graphene oxide in water.

The stability of graphene oxide (GO) in water is extremely relevant because of its application as an adsorbent material, as well as for its fate and behavior in the environment. Zeta potential was used to study the effect of secondary salts (carbonate, sulfate, and phosphate), temperature (20 to 60 °C), and pH (5 to 9) on the stability of six different GOs produced from natural, synthetic, and amorphous graphite-with and without the use of attrition milling. Generally, GOs produced with attrition-milled graphites had lower ζ-potentials than their unmilled counterparts because of their smaller particle sizes and higher concentration of oxygen-containing functional groups. It was observed that GO produced from graphite and synthetic graphite had ζ-potential values lower than -30 mV, even at 30 °C. However, it was observed that all the GOs studied were unstable in the presence of carbonate and sulfate salts at concentrations between 170 and 1695 mg L-1, as they reached a ζ-potential of -4.1 mV. Density-functional theory electronic structure calculations suggested that the instability of GO in the presence of carbonate and sulfate was caused by the abstraction of a proton resulting in interaction energies E int of 28.3 and 168.9 kJ mol-1, respectively. Our results suggest that temperatures above 30 °C, as well as carbonate and sulfate salts at concentrations relevant to arid and semi-arid regions, could promote the formation of agglomerates of GO, thus limiting its use and mobility in water.

De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.

With the emergence of high throughput single cell techniques, the understanding of the molecular and cellular diversity of mammalian organs have rapidly increased. In order to understand the spatial organization of this diversity, single cell data is often integrated with spatial data to create probabilistic cell maps. However, targeted cell typing approaches relying on existing single cell data achieve incomplete and biased maps that could mask the true diversity present in a tissue slide. Here we applied a de novo technique to spatially resolve and characterize cellular diversity of in situ sequencing data during human heart development. We obtained and made accessible well defined spatial cell-type maps of fetal hearts from 4.5 to 9 post conception weeks, not biased by probabilistic cell typing approaches. With our analysis, we could characterize previously unreported molecular diversity within cardiomyocytes and epicardial cells and identified their characteristic expression signatures, comparing them with specific subpopulations found in single cell RNA sequencing datasets. We further characterized the differentiation trajectories of epicardial cells, identifying a clear spatial component on it. All in all, our study provides a novel technique for conducting de novo spatial-temporal analyses in developmental tissue samples and a useful resource for online exploration of cell-type differentiation during heart development at sub-cellular image resolution.

Spatial Resolution of Mycobacterium tuberculosis Bacteria and Their Surrounding Immune Environments Based on Selected Key Transcripts in Mouse Lungs.

Mycobacterium tuberculosis (Mtb) bacilli are the causative agent of tuberculosis (TB), a major killer of mankind. Although it is widely accepted that local interactions between Mtb and the immune system in the tuberculous granuloma determine whether the outcome of infection is controlled or disseminated, these have been poorly studied due to methodological constraints. We have recently used a spatial transcriptomic technique, in situ sequencing (ISS), to define the spatial distribution of immune transcripts in TB mouse lungs. To further contribute to the understanding of the immune microenvironments of Mtb and their local diversity, we here present two complementary automated bacteria-guided analysis pipelines. These position 33 ISS-identified immune transcripts in relation to single bacteria and bacteria clusters. The analysis was applied on new ISS data from lung sections of Mtb-infected C57BL/6 and C3HeB/FeJ mice. In lungs from C57BL/6 mice early and late post infection, transcripts that define inflammatory macrophages were enriched at subcellular distances to bacteria, indicating the activation of infected macrophages. In contrast, expression patterns associated to antigen presentation were enriched in non-infected cells at 12 weeks post infection. T-cell transcripts were evenly distributed in the tissue. In Mtb-infected C3HeB/FeJ mice, transcripts characterizing activated macrophages localized in apposition to small bacteria clusters, but not in organized granulomas. Despite differences in the susceptibility to Mtb, the transcript patterns found around small bacteria clusters of C3HeB/FeJ and C57BL/6 mice were similar. Altogether, the presented tools allow us to characterize in depth the immune cell populations and their activation that interact with Mtb in the infected lung.

Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue.

Highly multiplexed spatial mapping of transcripts within tissues allows for investigation of the transcriptomic and cellular diversity of mammalian organs previously unseen. Here we explore a direct RNA (dRNA) detection approach incorporating the use of padlock probes and rolling circle amplification in combination with hybridization-based in situ sequencing chemistry. We benchmark a High Sensitivity Library Preparation Kit from CARTANA that circumvents the reverse transcription needed for cDNA-based in situ sequencing (ISS) via direct RNA detection. We found a fivefold increase in transcript detection efficiency when compared to cDNA-based ISS and also validated its multiplexing capability by targeting a curated panel of 50 genes from previous publications on mouse brain sections, leading to additional data interpretation such as de novo cell clustering. With this increased efficiency, we also found to maintain specificity, multiplexing capabilities and ease of implementation. Overall, the dRNA chemistry shows significant improvements in target detection efficiency, closing the gap to other fluorescent in situ hybridization-based technologies and opens up possibilities to explore new biological questions previously not possible with cDNA-based ISS.

[Effectiveness of treatment with Pygeum africanum in patients with lower urinary tract symptoms and benign prostatic hyperplasia: a cross-sectional study in the real-world clinical practice in Spain (The PROFIT Study)]. / Efectividad del tratamiento con Pygeum africanum en pacientes con síntomas del tracto urinario inferior e hiperplasia benigna de próstata: estudio transversal en la práctica clínica real en España (Estudio PROFIT).

OBJECTIVES: To assess the effectivenessand tolerability of treatment with P africanum(P. africanum) in patients with lower urinary tractsymptoms (LUTS) associated with benign prostatichyperplasia (BPH) in routine clinical practice. MATERIAL AND METHODS: Cross-sectional observationalstudy in which 115 patients with LUTS/BPHtreated for 6 months with P. africanum (Tebetane® compuesto)in real-world clinical practice conditions wereincluded. The primary objective was to assess thequality of life (QoL) according to changes in the scoresof item 8 of the International Prostate Symptom Score(IPSS) questionnaire (a score ≥ 4 indicates a significantimpairment of QoL). Secondary objectives includedimprovement of urinary symptoms, urinary flow, satisfactionand compliance with treatment as well astolerability. Data were collected in a single scheduledvisit at 6 months of treatment with P. africanum andwere compared with data registered in the medicalrecords at the beginning of treatment. RESULTS: After 6 months of treatment withP. africanum, the percentage of patient with significantimpairment of QoL was 22.6% as compared with45.2% at the initiation of treatment (P 0,-001). Theoverall IPSS score showed a mean decreas of -4,-5points (median -4,0, interquartile range [IQR] -7,-0 to-2,0) and 69 patients (60%) showed a clinically significantimprovement (reduction of ≥ 4 points). Therewere significant decreases in IPSS subscales of storage(mean -1,-8; median -2,-0, IQR -3,-0 to 0 (P 0,-001)and voiding (mean -1,-9; median -2,-0, IQR -3,-0 to 0)(P 0,-001) symptoms. The degree of satisfaction and compliance with treatment was high with mean scores(median) of 6,9 (7,0) and 9,2 (10), respectively in the1-10 visual analogue scale. Treatment-related adverseeffects did not occur. CONCLUSIONS: Treatment with P. africanum during6 months improved significantly QoL and LUTS inpatients with BPH, with a high level of satisfaction andcompliance with treatment, without adverse events.

OBJETIVO: Evaluar la efectividad y latolerabilidad del tratamiento con Pygeum africanum (P.africanum) en pacientes con síntomas del tracto urinarioinferior (STUI) asociados a hiperplasia benigna depróstata (HBP) en la práctica clínica habitual.MATERIAL Y MÉTODOS: Estudio observacionaltransversal en el que se incluyeron 115 pacientes conSTUI/HBP tratados durante 6 meses con P. africanum (Tebetane® compuesto) en condiciones de prácticaclínica real. El objetivo primario fue evaluar la calidadde vida (CdV) en función del cambio en la pregunta 8del cuestionario de Puntuación Internacional de losSíntomas Prostáticos (IPSS) (puntuación ≥ 4 indicaafectación significativa de la CdV). Los objetivos secundariosincluyeron la mejoría de síntomas urinarios,flujo urinario, satisfacción y cumplimiento con eltratamiento, así como la tolerabilidad del mismo. Losdatos se recogieron en una única visita programada alos 6 meses de tratamiento con P. africanum y se compararoncon los registrados en la historia clínica alinicio del tratamiento. RESULTADOS: Tras 6 meses de tratamiento conP. africanum, el porcentaje de pacientes con afectaciónsignificativa de la CdV fue del 22,6% en comparacióncon un 45,2% al inicio del tratamiento (P 0,001).La puntuación global del IPSS disminuyó de mediaen -4,5 puntos (mediana -4,0, rango intercuartílico [RIQ] -7,0 a -2,0) y 69 pacientes (60%) mostraron unamejoría clínicamente significativa (disminución ≥ 4puntos). Se observaron disminuciones significativasen las subescalas del IPSS de los síntomas de llenado(media -1,8; mediana -2,0, RIQ -3,0 a 0) (P 0,001) yvaciado (media -1,9; mediana -2,0, RIQ -3,0 a 0) (P 0,001). El grado de satisfacción y cumplimiento con eltratamiento fue elevado con valores medios (mediana)de 6,9 (7,0) y 9,2 (10) respectivamente, en una escalaanalógica visual 1-10 cm. No se registraron efectosadversos relacionados con el tratamiento. CONCLUSION: El tratamiento con P. africanum(P. africanum) durante 6 meses mejoró significativamentela CdV y los STUI en pacientes con HBP, con unalto grado de satisfacción y cumplimiento con el tratamiento,sin registrarse reacciones adversas.

Efectividad del tratamiento con pygeum africanum en pacientes con síntomas del tracto urinario inferior e hiperplasia benigna de próstata: estudio transversal en la práctica clínica real en españa (estudio profit) / Effectiveness of treatment with Pygeum africanum in patients with lower urinary tract symptoms and benign prostatic hyperplasia: a cross-sectional study in the real-world clinical practice in Spain (The PROFIT Study)

OBJETIVO: Evaluar la efectividad y latolerabilidad del tratamiento con Pygeum africanum (P.africanum) en pacientes con síntomas del tracto urinario inferior (STUI) asociados a hiperplasia benigna depróstata (HBP) en la práctica clínica habitual.MATERIAL Y MÉTODOS: Estudio observacionaltransversal en el que se incluyeron 115 pacientes conSTUI/HBP tratados durante 6 meses con P. africanum (Tebetane® compuesto) en condiciones de prácticaclínica real. El objetivo primario fue evaluar la calidadde vida (CdV) en función del cambio en la pregunta 8del cuestionario de Puntuación Internacional de losSíntomas Prostáticos (IPSS) (puntuación ≥ 4 indicaafectación significativa de la CdV). Los objetivos secundarios incluyeron la mejoría de síntomas urinarios, flujo urinario, satisfacción y cumplimiento con eltratamiento, así como la tolerabilidad del mismo. Losdatos se recogieron en una única visita programada alos 6 meses de tratamiento con P. africanum y se compararon con los registrados en la historia clínica alinicio del tratamiento.RESULTADOS: Tras 6 meses de tratamiento conP. africanum, el porcentaje de pacientes con afectaciónsignificativa de la CdV fue del 22,6% en comparacióncon un 45,2% al inicio del tratamiento (P < 0,001).La puntuación global del IPSS disminuyó de mediaen -4,5 puntos (mediana -4,0, rango intercuartílico [RIQ] -7,0 a -2,0) y 69 pacientes (60%) mostraron unamejoría clínicamente significativa (disminución ≥ 4puntos). Se observaron disminuciones significativasen las subescalas del IPSS de los síntomas de llenado(media -1,8; mediana -2,0, RIQ -3,0 a 0) (P < 0,001) yvaciado (media -1,9; mediana -2,0, RIQ -3,0 a 0) (P <0,001). El grado de satisfacción y cumplimiento con eltratamiento fue elevado con valores medios (mediana)de 6,9 (7,0) y 9,2 (10) respectivamente, en una escalaanalógica visual 1-10 cm. No se registraron efectosadversos relacionados con el tratamiento.

OBJECTIVES: To assess the effectiveness and tolerability of treatment with P africanum(P. africanum) in patients with lower urinary tractsymptoms (LUTS) associated with benign prostatichyperplasia (BPH) in routine clinical practice.MATERIAL AND METHODS: Cross-sectional observational study in which 115 patients with LUTS/BPHtreated for 6 months with P. africanum (Tebetane® compuesto) in real-world clinical practice conditions wereincluded. The primary objective was to assess thequality of life (QoL) according to changes in the scoresof item 8 of the International Prostate Symptom Score(IPSS) questionnaire (a score ≥ 4 indicates a significantimpairment of QoL). Secondary objectives includedimprovement of urinary symptoms, urinary flow, satisfaction and compliance with treatment as well astolerability. Data were collected in a single scheduledvisit at 6 months of treatment with P. africanum andwere compared with data registered in the medicalrecords at the beginning of treatment.RESULTS: After 6 months of treatment withP. africanum, the percentage of patient with significant impairment of QoL was 22.6% as compared with45.2% at the initiation of treatment (P < 0,-001). Theoverall IPSS score showed a mean decreas of -4,-5points (median -4,0, interquartile range [IQR] -7,-0 to-2,0) and 69 patients (60%) showed a clinically significant improvement (reduction of ≥ 4 points). Therewere significant decreases in IPSS subscales of storage(mean -1,-8; median -2,-0, IQR -3,-0 to 0 (P < 0,-001)and voiding (mean -1,-9; median -2,-0, IQR -3,-0 to 0)(P < 0,-001) symptoms. The degree of satisfaction and compliance with treatment was high with mean scores(median) of 6,9 (7,0) and 9,2 (10), respectively in the1-10 visual analogue scale. Treatment-related adverseeffects did not occur.CONCLUSIONS: Treatment with P. africanum during 6 months improved significantly QoL and LUTS inpatients with BPH, with a high level of satisfaction

Evidence of autochthonous transmission of urinary schistosomiasis in Almeria (southeast Spain): An outbreak analysis.

BACKGROUND: Schistosomiasis is endemic in 78 countries belonging to tropical and subtropical areas. However, autochthonous transmission of urogenital schistosomiasis was reported in Corsica (France) in 2013. We present evidence of autochthonous transmission of urogenital schistosomiasis in Almería (Spain) in 2003. METHODS: Description of the outbreak in farmers and subsequent epidemiological studies aimed at searching for Bulinus snails and their genotypic characteristics. RESULTS: The outbreak affected 4 farmers out of a group of 5 people who repeatedly bathed that summer in an irrigation pool in the area. Two of them presented macroscopic hematuria with bilharziomas, showing the presence of Schistosoma eggs in bladder biopsies. Two others were asymptomatic but the serology for schistosomiasis was positive. In 2015, the presence of the vector Bulinus truncatus was demonstrated in Almería in water collections of appropriate characteristics. DNA sequencing proving that local B. truncatus species were base-to-base identical to B. truncatus from Senegal. CONCLUSIONS: We present a new outbreak of autochthonous transmission of urogenital schistosomiasis in Europe. Although no new cases of autochthonous transmission have been reported, some other cases may have occurred at that time or later on and be unnoticed as many cases of schistosomiasis are asymptomatic or present mild and unspecific symptoms.

Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps.

BACKGROUND: A range of spatially resolved transcriptomic methods has recently emerged as a way to spatially characterize the molecular and cellular diversity of a tissue. As a consequence, an increasing number of computational techniques are developed to facilitate data analysis. There is also a need for versatile user friendly tools that can be used for a de novo exploration of datasets. RESULTS: Here we present MATLAB-based Analysis toolbox for in situ sequencing (ISS) expression maps (Matisse). We demonstrate Matisse by characterizing the 2-dimensional spatial expression of 119 genes profiled in a mouse coronal section, exploring different levels of complexity. Additionally, in a comprehensive analysis, we further analyzed expression maps from a second technology, osmFISH, targeting a similar mouse brain region. CONCLUSION: Matisse proves to be a valuable tool for initial exploration of in situ sequencing datasets. The wide set of tools integrated allows for simple analysis, using the position of individual reads, up to more complex clustering and dimensional reduction approaches, taking cellular content into account. The toolbox can be used to analyze one or several samples at a time, even from different spatial technologies, and it includes different segmentation approaches that can be useful in the analysis of spatially resolved transcriptomic datasets.

Early versus deferred anti-SARS-CoV-2 convalescent plasma in patients admitted for COVID-19: A randomized phase II clinical trial.

BACKGROUND: Convalescent plasma (CP), despite limited evidence on its efficacy, is being widely used as a compassionate therapy for hospitalized patients with COVID-19. We aimed to evaluate the efficacy and safety of early CP therapy in COVID-19 progression. METHODS AND FINDINGS: The study was an open-label, single-center randomized clinical trial performed in an academic medical center in Santiago, Chile, from May 10, 2020, to July 18, 2020, with final follow-up until August 17, 2020. The trial included patients hospitalized within the first 7 days of COVID-19 symptom onset, presenting risk factors for illness progression and not on mechanical ventilation. The intervention consisted of immediate CP (early plasma group) versus no CP unless developing prespecified criteria of deterioration (deferred plasma group). Additional standard treatment was allowed in both arms. The primary outcome was a composite of mechanical ventilation, hospitalization for >14 days, or death. The key secondary outcomes included time to respiratory failure, days of mechanical ventilation, hospital length of stay, mortality at 30 days, and SARS-CoV-2 real-time PCR clearance rate. Of 58 randomized patients (mean age, 65.8 years; 50% male), 57 (98.3%) completed the trial. A total of 13 (43.3%) participants from the deferred group received plasma based on clinical aggravation. We failed to find benefit in the primary outcome (32.1% versus 33.3%, odds ratio [OR] 0.95, 95% CI 0.32-2.84, p > 0.999) in the early versus deferred CP group. The in-hospital mortality rate was 17.9% versus 6.7% (OR 3.04, 95% CI 0.54-17.17 p = 0.246), mechanical ventilation 17.9% versus 6.7% (OR 3.04, 95% CI 0.54-17.17, p = 0.246), and prolonged hospitalization 21.4% versus 30.0% (OR 0.64, 95% CI, 0.19-2.10, p = 0.554) in the early versus deferred CP group, respectively. The viral clearance rate on day 3 (26% versus 8%, p = 0.204) and day 7 (38% versus 19%, p = 0.374) did not differ between groups. Two patients experienced serious adverse events within 6 hours after plasma transfusion. The main limitation of this study is the lack of statistical power to detect a smaller but clinically relevant therapeutic effect of CP, as well as not having confirmed neutralizing antibodies in donor before plasma infusion. CONCLUSIONS: In the present study, we failed to find evidence of benefit in mortality, length of hospitalization, or mechanical ventilation requirement by immediate addition of CP therapy in the early stages of COVID-19 compared to its use only in case of patient deterioration. TRIAL REGISTRATION: NCT04375098.

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.

Visualization of the transcriptome in situ has proven to be a valuable tool in exploring single-cell RNA-sequencing data, providing an additional spatial dimension to investigate multiplexed gene expression, cell types, disease architecture or even data driven discoveries. In situ sequencing (ISS) method based on padlock probes and rolling circle amplification has been used to spatially resolve gene transcripts in tissue sections of various origins. Here, we describe the next iteration of ISS, HybISS, hybridization-based in situ sequencing. Modifications in probe design allows for a new barcoding system via sequence-by-hybridization chemistry for improved spatial detection of RNA transcripts. Due to the amplification of probes, amplicons can be visualized with standard epifluorescence microscopes for high-throughput efficiency and the new sequencing chemistry removes limitations bound by sequence-by-ligation chemistry of ISS. HybISS design allows for increased flexibility and multiplexing, increased signal-to-noise, all without compromising throughput efficiency of imaging large fields of view. Moreover, the current protocol is demonstrated to work on human brain tissue samples, a source that has proven to be difficult to work with image-based spatial analysis techniques. Overall, HybISS technology works as a targeted amplification detection method for improved spatial transcriptomic visualization, and importantly, with an ease of implementation.

A Thyroid Genetic Classifier Correctly Predicts Benign Nodules with Indeterminate Cytology: Two Independent, Multicenter, Prospective Validation Trials.

Background: Although most thyroid nodules with indeterminate cytology are benign, in most of the world, surgery remains as the most frequent diagnostic approach. We have previously reported a 10-gene thyroid genetic classifier, which accurately predicts benign thyroid nodules. The assay is a prototype diagnostic kit suitable for reference laboratory testing and could potentially avoid unnecessary diagnostic surgery in patients with indeterminate thyroid cytology. Methods: Classifier performance was tested in two independent, ethnically diverse, prospective multicenter trials (TGCT-1/Chile and TGCT-2/USA). A total of 4061 fine-needle aspirations were collected from 15 institutions, of which 897 (22%) were called indeterminate. The clinical site was blind to the classifier score and the clinical laboratory blind to the pathology report. A matched surgical pathology and valid classifier score was available for 270 samples. Results: Cohorts showed significant differences, including (i) clinical site patient source (academic, 43% and 97% for TGCT-1 and -2, respectively); (ii) ethnic diversity, with a greater proportion of the Hispanic population (40% vs. 3%) for TGCT-1 and a greater proportion of African American (11% vs. 0%) and Asian (10% vs. 1%) populations for TGCT-2; and (iii) tumor size (mean of 1.7 and 2.5 cm for TGCT-1 and -2, respectively). Overall, there were no differences in the histopathological profile between cohorts. Forty-one of 155 and 45 of 115 nodules were malignant (cancer prevalence of 26% and 39% for TGCT-1 and -2, respectively). The classifier predicted 37 of 41 and 41 of 45 malignant nodules, yielding a sensitivity of 90% [95% confidence interval; CI 77-97] and 91% [95% CI 79-98] for TGCT-1 and -2, respectively. One hundred one of 114 and 61 of 70 nodules were correctly predicted as benign, yielding a specificity of 89% [95% CI 82-94] and 87% [95% CI 77-94], respectively. The negative predictive values for TGCT-1 and TGCT-2 were 96% and 94%, respectively, whereas the positive predictive values were 74% and 82%, respectively. The overall accuracy for both cohorts was 89%. Conclusions: Clinical validation of the classifier demonstrates equivalent performance in two independent and ethnically diverse cohorts, accurately predicting benign thyroid nodules that can undergo surveillance as an alternative to diagnostic surgery.