Updated single cell reference atlas for the starlet anemone Nematostella vectensis.

BACKGROUND: The recent combination of genomics and single cell transcriptomics has allowed to assess a variety of non-conventional model organisms in much more depth. Single cell transcriptomes can uncover hidden cellular complexity and cell lineage relationships within organisms. The recent developmental cell atlases of the sea anemone Nematostella vectensis, a representative of the basally branching Cnidaria, has provided new insights into the development of all cell types (Steger et al Cell Rep 40(12):111370, 2022; Sebé-Pedrós et al. Cell 173(6):1520-1534.e20). However, the mapping of the single cell reads still suffers from relatively poor gene annotations and a draft genome consisting of many scaffolds. RESULTS: Here we present a new wildtype resource of the developmental single cell atlas, by re-mapping of sequence data first published in Steger et al. (2022) and Cole et al. (Nat Commun 14(1):1747, 2023), to the new chromosome-level genome assembly and corresponding gene models in Zimmermann et al. (Nat Commun 14, 8270 (2023). https://doi.org/10.1038/s41467-023-44080-7 ). We expand the pre-existing dataset through the incorporation of additional sequence data derived from the capture and sequencing of cell suspensions from four additional samples: 24 h gastrula, 2d planula, an inter-parietal region of the bodywall from a young unsexed animal, and another adult mesentery from a mature male animal. CONCLUSION: Our analyses of the full cell-state inventory provide transcriptomic signatures for 127 distinct cell states, of which 47 correspond to neuroglandular subtypes. We also identify two distinct putatively immune-related transcriptomic profiles that segregate between the inner and outer cell layers. Furthermore, the new gene annotation Nv2 has markedly improved the mapping on the single cell transcriptome data and will therefore be of great value for the community and anyone using the dataset.

Implementation of REDCap mobile app in an oral HIV clinical study.

BACKGROUND: In Peru, HIV cases are highly concentrated among men who have sex with men (MSM). Despite the availability of anti-retroviral therapy, people living with HIV (PWH) have higher levels of oral diseases. Alcohol use disorder (AUD) is significantly present among PWH. Our overarching goal was to generate foundational evidence on the association of AUD and oral health in MSM with HIV and enhance research capacity for future intersectional research on AUD, oral health and HIV. Our specific aim was to implement an on-site electronic data collection system through the use of a REDCap Mobile App in a low-middle income country (LMIC) setting. METHODS: Five validated surveys were utilized to gather data on demographics, medical history, HIV status, alcohol use, HIV stigma, perceived oral health status, and dietary supplement use. These surveys were developed in REDCap and deployed with the REDCap Mobile App, which was installed on ten iPads across two medical HIV clinics in Lima, Peru. REDCap app as well as the protocol for data collection were calibrated with feedback from trial participants and clinical research staff to improve clinical efficiency and participant experience. RESULTS: The mean age of participants (n = 398) was 35.94 ± 9.13y, of which 98.5% identified as male, and 85.7% identified as homosexual. 78.1% of participants binge drank, and 12.3% reported being heavy drinkers. After pilot testing, significant modifications to the structure and layout of the surveys were performed to improve efficiency and flow. The app was successfully deployed to replace cumbersome paper records and collected data was directly stored in a REDCap database. CONCLUSIONS: The REDCap Mobile App was successfully used due to its ability to: (a) capture and store data offline, (b) timely translate between multiple languages on the mobile app interface, and (c) provide user-friendly interface with low associated costs and ample support. TRIAL REGISTRATION: 1R56DE029639-01.

Topological structures and syntenic conservation in sea anemone genomes.

There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these genome features. Here we report chromosome-level genome assemblies of two related anthozoans, the sea anemones Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. We find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages; yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.

Validación de intervención psicoeducativa para mejorar el afrontamiento y adaptación de familiares en la UCI / Psychoeducational Intervention Validation to Improve Relatives in the ICU Coping and Adaptation / Validação de uma intervenção psicoeducativa para melhorar o enfrentamento e adaptação de familiares na UTI

Introducción: la hospitalización de una paciente afecta directamente el estado de salud de sus familiares, por lo tanto, se requiere de una intervención psicoeducativa que reduzca el efecto ocasionado en las familias para favorecer el afrontamiento y la adaptación. Objetivo: determinar los componentes con mayor consenso entre profesionales expertos para validar una intervención psicoeducativa que mejore el afrontamiento y la adaptación en familiares de pacientes hospitalizados en la Unidad de Cuidados Intensivos (UCI). Método: estudio cuantitativo y descriptivo realizado con la técnica Delphi, por medio de una única ronda entre profesionales de la salud con experiencia mayor a 2 años en atención a pacientes críticos o investigación en esta área. Resultados: se obtuvieron 14 ítems distribuidos de la siguiente manera: matriz de componentes (3 ítems) y protocolo de la intervención (11 ítems). El 7,14 % de los ítems logró un consenso total, el 85,7 % aceptable y solo el 7,14 % de los ítems no alcanzó un consenso. Conclusiones: los componentes, actividades y acciones propuestas en la intervención psicoeducativa a través de la matriz de componentes como el protocolo de intervención, según el consenso de expertos, es pertinente, congruente, factible y genera impacto, lo cual permite mejorar el afrontamiento y adaptación de familiares de pacientes hospitalizados en UCI. La intervención requiere ser validada por medio de una prueba piloto y un estudio cuasi-experimental que permita medir el impacto de estos resultados.

Introduction: A patient's hospitalization directly affects the health status of their relatives, therefore, a psychoeducational intervention is required to reduce the effect on families, favoring coping and adaptation. Objective: Determine the components with the highest consensus among experts to operationalize psychoeducational intervention that improves coping and adaptation in relatives of hospitalized patients in Intensive Care Units (ICU). Methodology: Primary quantitative and descriptive study, carried out using the Delphi technique, through a single round among health professionals with more than 2 years of experience in critical patient care or research in this area. Results: 14 items were obtained, distributed as follows: component matrix (3 items) and intervention protocol (11 items). 7.14 % of the items reached a total consensus, 85.7 % acceptable and only 7.14 % of the items did not reach a consensus. Conclusions: The components, activities and actions proposed in the psychoeducational intervention through the matrix of components, such as the intervention protocol, according to the consensus of experts proves to be pertinent, congruent, feasible, and generates impact. This allows to improve coping and adaptation of hospitalized patients in ICU's relatives. The intervention needs to be validated by means of a pilot test and a quasi-experimental study that allow measuring the impact of these results.

Introdução: A hospitalização de um paciente afeta diretamente o estado de saúde de seus familiares, portanto, é necessária uma intervenção psicoeducacional que reduza o efeito causado nas famílias, favorecendo o enfrentamento e a adaptação. Objetivo: Determinar os componentes de maior consenso entre os especialistas para operacionalizar a intervenção psicoeducacional que melhora o enfrentamento e a adaptação em familiares de pacientes internados em UTI. Metodologia: Estudo primário, quantitativo e descritivo, realizado pela técnica Delphi, por meio de rodada única, entre profissionais de saúde com mais de 2 anos de familia na assistência ao paciente crítico ou em pesquisa na área. Resultados: foram obtidos 14 itens, assim distribuídos: matriz de componentes (3 itens) e protocolo de intervenção (11 itens). 7,14 % dos itens alcançaram consenso total, 85,7 % aceitáveis e apenas 7,14 % dos itens não alcançaram consenso. Conclusões: Os componentes, atividades e ações propostas na intervenção psicoeducacional através da matriz de componentes como o protocolo de intervenção, segundo o consenso dos especialistas é pertinente, congruente, factível e gera impacto, o que permite melhorar o enfrentamento e adaptação dos familiares de pacientes internados em UTI. A intervenção familia ser validada por meio de um teste piloto e um estudo quase-experimental que permita mensurar o impacto desses resultados.

Phylogenomic Analysis of the Plastid Genome of the Peruvian Purple Maize Zea mays subsp. mays cv. 'INIA 601'.

Peru is an important center of diversity for maize; its different cultivars have been adapted to distinct altitudes and water availability and possess an array of kernel colors (red, blue, and purple), which are highly appreciated by local populations. Specifically, Peruvian purple maize is a collection of native landraces selected and maintained by indigenous cultures due to its intense purple color in the seed, bract, and cob. This color is produced by anthocyanin pigments, which have gained interest due to their potential use in the food, agriculture, and pharmaceutical industry. It is generally accepted that the Peruvian purple maize originated from a single ancestral landrace 'Kculli', but it is not well understood. To study the origin of the Peruvian purple maize, we assembled the plastid genomes of the new cultivar 'INIA 601' with a high concentration of anthocyanins, comparing them with 27 cultivars/landraces of South America, 9 Z. mays subsp. parviglumis, and 5 partial genomes of Z. mays subsp. mexicana. Using these genomes, plus four other maize genomes and two outgroups from the NCBI database, we reconstructed the phylogenetic relationship of Z. mays. Our results suggest a polyphyletic origin of purple maize in South America and agree with a complex scenario of domestication with recurrent gene flow from wild relatives. Additionally, we identify 18 plastid positions that can be used as high-confidence genetic markers for further studies. Altogether, these plastid genomes constitute a valuable resource to study the evolution and domestication of Z. mays in South America.

Monitoring PHB production in Synechocystis sp. with hyperspectral images.

Microalgae wastewater treatment systems have the potential for producing added-value products. More specifically, cyanobacteria are able to accumulate polyhydroxybutyrates (PHBs), which can be extracted and used for bioplastics production. Nonetheless, PHB production requires proper culture conditions and continue monitoring, challenging the state-of-the-art technologies. The aim of this study was to investigate the application of hyperspectral technologies to monitor cyanobacteria population growth and PHB production. We have established a ground-breaking measurement method able to discern spectral reflectance changes from light emitted to cyanobacteria in different phases. All in all, enabling to distinguish between cyanobacteria growth phase and PHB accumulation phase. Furthermore, first tests of classification algorithms used for machine learning and image recognition technologies had been applied to automatically recognize the different cyanobacteria species from a complex microbial community containing cyanobacteria and microalgae cultivated in pilot-scale photobioreactors (PBRs). We have defined three main indicators for monitoring PHB production: (i) cyanobacteria specific-strain density, (ii) differentiate between growth and PHB-accumulation and (iii) chlorosis progression. The results presented in this study represent an interesting alternative for traditional measurements in cyanobacteria PHB production and its application in pilot-scale PBRs. Although not directly determining the amount of PHB production, they would give insights on the undergoing processes.

Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence.

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.

Gene Co-expression Network Analysis.

Gene co-expression analysis is a data analysis technique that helps identify groups of genes with similar expression patterns across several different conditions. By means of these techniques, different groups have been able to assign putative metabolic pathways and functions to understudied genes and to identify novel metabolic regulation networks for different metabolites. Some groups have even used network comparative studies to understand the evolution of these networks from green algae to land plants. In this chapter, we will go over the basic definitions required to understand network topology and gene module identification. Additionally, we offer the reader a walk-through a standard analysis pipeline as implemented in the package WGCNA that takes as input raw fastq files and obtains co-expressed gene clusters and representative gene expression patterns from each module for downstream applications.

Archean continental crust formed by magma hybridization and voluminous partial melting.

Archean (4.0-2.5 Ga) tonalite-trondhjemite-granodiorite (TTG) terranes represent fragments of Earth's first continents that formed via high-grade metamorphism and partial melting of hydrated basaltic crust. While a range of geodynamic regimes can explain the production of TTG magmas, the processes by which they separated from their source and acquired distinctive geochemical signatures remain uncertain. This limits our understanding of how the continental crust internally differentiates, which in turn controls its potential for long-term stabilization as cratonic nuclei. Here, we show via petrological modeling that hydrous Archean mafic crust metamorphosed in a non-plate tectonic regime produces individual pulses of magma with major-, minor-, and trace-element signatures resembling-but not always matching-natural Archean TTGs. Critically, magma hybridization due to co-mingling and accumulation of multiple melt fractions during ascent through the overlying crust eliminates geochemical discrepancies identified when assuming that TTGs formed via crystallization of discrete melt pulses. We posit that much Archean continental crust is made of hybrid magmas that represent up to ~ 40 vol% of partial melts produced along thermal gradients of 50-100 °C/kbar, characteristic of overthickened mafic Archean crust at the head of a mantle plume, crustal overturns, or lithospheric peels.

A Survey of Alzheimer's Disease Early Diagnosis Methods for Cognitive Assessment.

Dementia is a syndrome that is characterised by the decline of different cognitive abilities. A high rate of deaths and high cost for detection, treatments, and patients care count amongst its consequences. Although there is no cure for dementia, a timely diagnosis helps in obtaining necessary support, appropriate medication, and maintenance, as far as possible, of engagement in intellectual, social, and physical activities. The early detection of Alzheimer Disease (AD) is considered to be of high importance for improving the quality of life of patients and their families. In particular, Virtual Reality (VR) is an expanding tool that can be used in order to assess cognitive abilities while navigating through a Virtual Environment (VE). The paper summarises common AD screening and diagnosis techniques focusing on the latest approaches that are based on Virtual Environments, behaviour analysis, and emotions recognition, aiming to provide more reliable and non-invasive diagnostics at home or in a clinical environment. Furthermore, different AD diagnosis evaluation methods and metrics are presented and discussed together with an overview of the different datasets.

Fulminant myocarditis due to the influenza B virus in adults: Report of two cases and literature review / Miocarditis fulminante en adultos por el virus de la influenza B: reporte de dos casos y revisión de la literatura

La miocarditis es una enfermedad inflamatoria del miocardio. Las infecciones virales son la causa más común, aunque también puede deberse a reacciones de hipersensibilidad y de etiología autoinmunitaria, entre otras. El espectro clínico de la enfermedad es variado y comprende desde un curso asintomático, seguido de dolor torácico, arritmias y falla cardiaca aguda, hasta un cuadro fulminante. El término 'fulminante' se refiere al desarrollo de un shock cardiogénico con necesidad de soporte vasopresor e inotrópico o dispositivos de asistencia circulatoria, ya sea oxigenación por membrana extracorpórea o balón de contrapulsación intraaórtico. Cerca del 10 % de los casos de falla cardiaca por miocarditis corresponde a miocarditis fulminante. La miocarditis por influenza se considera una condición infrecuente; no obstante, su incidencia ha aumentado desde el 2009 a raíz de la pandemia de influenza por el virus AH1N1. Por su parte, la miocarditis por influenza de tipo B sigue siendo una condición infrecuente. Se describen aquí dos casos confirmados de miocarditis fulminante por el virus de la influenza B atendidos en un centro cardiovascular, que requirieron dispositivos de asistencia circulatoria mecánica.

Myocarditis is an inflammatory disease of the myocardium. Viral infections are the most common cause, although it can also be due to hypersensitivity reactions and autoimmune etiology, among other causes. The clinical spectrum of the disease is varied, from an asymptomatic course, followed by chest pain, arrhythmias, and acute heart failure, to a fulminant episode. The term fulminant refers to the development of cardiogenic shock with a need for vasopressor support and inotropic or assisted circulation devices either extracorporeal membrane oxygenation (ECMO) or intra-aortic counterpulsation balloon. About 10% of cases of heart failure due to myocarditis correspond to fulminant myocarditis. Influenza myocarditis has been considered an infrequent condition. However, its incidence has increased since 2009 as a result of the AH1N1 pandemic; otherwise, myocarditis due to the Influenza type B virus remains an infrequent entity. We describe the experience in a cardiovascular center of two confirmed cases of fulminant myocarditis due to influenza B that required circulatory assistance devices.

Data Stream Mining Applied to Maximum Wind Forecasting in the Canary Islands.

The Canary Islands are a well known tourist destination with generally stable and clement weather conditions. However, occasionally extreme weather conditions occur, which although very unusual, may cause severe damage to the local economy. The ViMetRi-MAC EU funded project has among its goals, managing climate-change-associated risks. The Spanish National Meteorology Agency (AEMET) has a network of weather stations across the eight Canary Islands. Using data from those stations, we propose a novel methodology for the prediction of maximum wind speed in order to trigger an early alert for extreme weather conditions. The methodology proposed has the added value of using an innovative kind of machine learning that is based on the data stream mining paradigm. This type of machine learning system relies on two important features: models are learned incrementally and adaptively. That means the learner tunes the models gradually and endlessly as new observations are received and also modifies it when there is concept drift (statistical instability), in the modeled phenomenon. The results presented seem to prove that this data stream mining approach is a good fit for this kind of problem, clearly improving the results obtained with the accumulative non-adaptive version of the methodology.

Wild Origins of Macadamia Domestication Identified Through Intraspecific Chloroplast Genome Sequencing.

Identifying the geographic origins of crops is important for the conservation and utilization of novel genetic variation. Even so, the origins of many food crops remain elusive. The tree nut crop macadamia has a remarkable domestication history, from subtropical rain forests in Australia through Hawaii to global cultivation all within the last century. The industry is based primarily on Macadamia integrifolia and M. integrifolia-M. tetraphylla hybrid cultivars with Hawaiian cultivars the main contributors to world production. Sequence data from the chloroplast genome assembled using a genome skimming strategy was used to determine population structure among remnant populations of the main progenitor species, M. integrifolia. Phylogenetic analysis of a 506 bp chloroplast SNP alignment from 64 wild and cultivated accessions identified phylogeographic structure and deep divergences between clades providing evidence for historical barriers to seed dispersal. High levels of variation were detected among wild accessions. Most Hawaiian cultivars, however, shared a single chlorotype that was also present at two wild sites at Mooloo and Mt Bauple from the northernmost distribution of the species in south-east Queensland. Our results provide evidence for a maternal genetic bottleneck during early macadamia domestication, and pinpoint the likely source of seed used to develop the Hawaiian cultivars. The extensive variability and structuring of M. integrifolia chloroplast genomic variation detected in this study suggests much unexploited genetic diversity is available for improvement of this recently domesticated crop.

Immune reconstitution inflammatory syndrome associated with secondary syphilis: dermatologic, neurologic and ophthalmologic compromise in an HIV patient.

The presentation of syphilis as a manifestation of immune reconstitution inflammatory syndrome in patients with human immunodeficiency virus (HIV) infection is rare and can be associated with the varied clinical expression of unusual syphilitic manifestations. We report a case of immune reconstitution syndrome with dermatologic, ophthalmologic and neurologic compromise of secondary syphilis in a patient with HIV infection.

Identificación de variante anatómica en la ablación exitosa de aleteo auricular típico luego de cirugía valvular: utilidad de la ecografía intracardiaca / Identification of an anatomical variant in the successful ablation of a typical atrial flutter after valve surgery: Usefulness of intracardiac echocardiography

Resumen Se hizo ablación tridimensional de aleteo auricular, dependiente del istmo cavotricuspídeo, en un paciente con cirugía previa de válvula tricúspide. El uso de ecocardiografía intracardiaca permitió identificar una estructura sacular en el aspecto septal del istmo. Después de la ablación en este punto, el aleteo terminó y se confirmó bloqueo bidireccional. Este reporte sugiere, además, que el miocardio auricular ligado al anillo valvular, sirve como vía de conducción crítica del aleteo auricular.

Abstract A three-dimensional ablation of an atrial flutter, dependent on the cavo-tricuspid isthmus, was performed on a patient with previous tricuspid valve surgery. The use of intracardiac echocardiography enabled a saccular structure to be identified in the septal aspect of the isthmus. After the ablation in this point, the flutter stopped and a two-directional block was confirmed. This report suggests, furthermore, that the atrial myocardium together with the valvular ring, serves as a critical conduction pathway of the atrial flutter.