DateLife: leveraging databases and analytical tools to reveal the dated Tree of Life.

Chronograms -phylogenies with branch lengths proportional to time- represent key data on timing of evolutionary events for the study of natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www .datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as sec- ondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8 and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.

Three decades after the publication of the Lamendin method for adult age-at-death estimation: Methodological evolution of the procedure and interpretations.

More than three decades have passed since the publication of Lamendin et al.'s proposal in 1992. Over this time, numerous investigations have been conducted to assess the applicability of the technique in different populations with acceptable results in terms of estimation errors. The proposal by Lamendin and colleagues remains relevant today, and has made a significant contribution to adult age-at-death estimation due to its simplicity, repeatability, replicability, and high performance. Indeed, significant progress towards systematizing and strengthening the procedure has been reported in the published literature. One noteworthy advancement is the development of an international database that supports the use of Bayesian statistics for age-at-death estimation. This resource plays a crucial role in standardizing the methodology and improving the reliability for obtaining more reliable results on a global scale. The aim of this study is to investigate the historical evolution of the technique, to assess the accuracy of the results obtained by different analytic procedures, and to explore its impact in forensic applications through a systematic analysis of the specialized literature on this field. The current state of research indicates that this type of methodological research is an ongoing process, far from being completed. Many questions and challenges that require further attention to address effectively these issues remain unanswered, such as the development of non-linear regressions and probabilistic approaches, the deepening of procedures that improve global approximations, and the intensification of research focused on achieving more accurate estimations among individuals over 70 years-old. However, studies generally agree that the Lamendin technique works well for individuals between the ages of 30-60 years. It is still in force today, although the method has been significantly perfected. Despite the degree of research development in this area, further efforts are needed to improve the understanding and performance of these kinds of procedures. This will ultimately lead to an improvement in the accuracy and reliability of forensic investigation results worldwide.

Respiratory virus detection among healthcare professionals in Brazil: work-related contact and episode recurrence during the COVID-19 pandemic.

OBJECTIVES: Since the beginning of the COVID-19 pandemic, changes in the circulation of respiratory viruses have been observed after measures to control the spread of SARS-CoV-2 were implemented. In this sense, we aimed to understand the circulation of the respiratory virus and its impact in a controlled healthy population of healthcare professional (HCP) volunteers in phase III of the clinical trial of the ChadOx nCoV1 conducted in São Paulo, Brazil. STUDY DESIGN: This was a nested observational cohort study within a clinical trial. METHODS: We performed RT-qPCR to detect SARS-CoV-2, influenza virus A and B (IVA and IVB), respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (hMPV), human coronaviruses (hCoVs: HKU-1, NL63, OC43, and 229-E), parainfluenza virus (PiV) I-IV, and q-PCR for adenovirus in nasopharyngeal and oropharyngeal samples obtained from HCP enrolled in the clinical trial to assess respiratory viruses infection among vaccinated and non-vaccinated. RESULTS: From July 2020 to January 2022, 876 samples were included from 737 volunteers (median age: 33 years, 62.9% female). New episodes were registered for 119 individuals. We observed an overall positivity of 37.7% for SARS-CoV-2 and 16.4% for other respiratory viruses; HRV was the second most detected virus (8%), followed by RSV (2.4%). Fully vaccinated individuals accounted for 53.3% of collected samples, and 52.9% presented at least one respiratory virus infection, with SARS-CoV-2 being the most predominant etiologic agent (62.3%). Influenza and hMPV were not detected among the tested samples. Among the subjects that presented more than one episode, SARS-CoV-2 and HRV infections were related to direct contact with patients (P < 0.002). CONCLUSIONS: Data show high infection rates among HCPs even under mask policies and contact precautions, highlighting the need for improvement in infection control measures in this population regardless of the vaccination program.

Surfactant-driven optimization of iron-based nanoparticle synthesis: a study on magnetic hyperthermia and endothelial cell uptake.

This work examines the effect of changing the ratio of different surfactants in single-core iron-based nanoparticles with respect to their specific absorption rate in the context of magnetic hyperthermia and cellular uptake by human umbilical vein endothelial cells (HUVEC). Three types of magnetic nanoparticles were synthesized by separately adding oleic acid or oleylamine or a mixture of both (oleic acid/oleylamine) as surfactants. A carefully controlled thermal decomposition synthesis process led to monodispersed nanoparticles with a narrow size distribution. Spherical-shaped nanoparticles were mainly obtained for those synthesized with oleic acid, while the shape changed upon adding oleylamine. The combined use of oleic acid and oleylamine as surfactants in single-core iron-based nanoparticles resulted in a substantial saturation magnetization, reaching up to 140 A m2 kg-1 at room temperature. The interplay between these surfactants played a crucial role in achieving this high magnetic saturation. By modifying the surface of the magnetic nanoparticles using a mixture of two surfactants, the magnetic fluid hyperthermia heating rate was significantly improved compared to using a single surfactant type. This improvement can be attributed to the larger effective anisotropy achieved through the modification with both (oleic acid/oleylamine). The mixture of surfactants enhances the control of interparticle distance and influences the strength of dipolar interactions, ultimately leading to enhanced heating efficiency. Functionalization of the oleic acid-coated nanoparticles with trimethoxysilane results in the formation of a core-shell structure Fe@Fe3O4, showing exchange bias (EB) associated with the exchange anisotropy between the shell and the core. The biomedical relevance of our synthesized Fe@Fe3O4 nanoparticles was demonstrated by their efficient uptake by human umbilical vein endothelial cells (HUVECs) in a concentration-dependent manner. This remarkable cellular uptake highlights the potential of these nanoparticles in biomedical applications.

Post-COVID-19 Brain [18F] FDG-PET Findings: A Retrospective Single-Center Study in the United States.

BACKGROUND AND PURPOSE: The pathophysiology of neurologic manifestations of postacute sequelae of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) infection is not clearly understood. Our aim was to investigate brain metabolic activity on [18F] FDG-PET/CT scans in patients with a history of coronavirus disease 2019 (COVID-19) infection before imaging. MATERIALS AND METHODS: This retrospective study included 45 patients who underwent [18F] FDG-PET/CT imaging for any reason and had, at least once, tested positive for COVID-19 at any time before imaging. Fifteen patients had available [18F] FDG-PET scans obtained under identical conditions before the infection. A group of 52 patients with melanoma or multiple myeloma who underwent [18F] FDG-PET/CT were used as controls. Whole-brain 2-sample t test analysis was performed using SPM software to identify clusters of hypo- and hypermetabolism and compare brain metabolic activity between patients with COVID-19 and controls. Paired sample t test comparison was also performed for 15 patients, and correlations between metabolic values of clusters and clinical data were measured. RESULTS: Compared with the control group, patients with a history of COVID-19 infection exhibited focal areas of hypometabolism in the bilateral frontal, parietal, occipital, and posterior temporal lobes and cerebellum (P = .05 uncorrected at the voxel level, family-wise error-corrected at the cluster level) that peaked during the first 2 months, improved to near-complete recovery around 6 months, and disappeared at 12 months. Hypermetabolism involving the brainstem, cerebellum, limbic structures, frontal cortex, and periventricular white matter was observed only at 2-6 months after infection. Older age, neurologic symptoms, and worse disease severity scores positively correlated with the metabolic changes. CONCLUSIONS: This study demonstrates a profile of time-dependent brain PET hypo- and hypermetabolism in patients with confirmed SARS-CoV-2 infection.

Why don't we share data and code? Perceived barriers and benefits to public archiving practices.

The biological sciences community is increasingly recognizing the value of open, reproducible and transparent research practices for science and society at large. Despite this recognition, many researchers fail to share their data and code publicly. This pattern may arise from knowledge barriers about how to archive data and code, concerns about its reuse, and misaligned career incentives. Here, we define, categorize and discuss barriers to data and code sharing that are relevant to many research fields. We explore how real and perceived barriers might be overcome or reframed in the light of the benefits relative to costs. By elucidating these barriers and the contexts in which they arise, we can take steps to mitigate them and align our actions with the goals of open science, both as individual scientists and as a scientific community.

The Clash of Two Epidemics: the Relationship Between Opioids and Glucose Metabolism.

PURPOSE OF REVIEW: We are currently in the midst of a global opioid epidemic. Opioids affect many physiological processes, but one side effect that is not often taken into consideration is the opioid-induced alteration in blood glucose levels. RECENT FINDINGS: This review shows that the vast majority of studies report that opioid stimulation increases blood glucose levels. In addition, plasma levels of the endogenous opioid ß-endorphin rise in response to low blood glucose. In contrast, in hyperglycaemic baseline conditions such as in patients with type 2 diabetes mellitus (T2DM), opioid stimulation lowers blood glucose levels. Furthermore, obesity itself alters sensitivity to opioids, changes opioid receptor expression and increases plasma ß-endorphin levels. Thus, opioid stimulation can have various side effects on glycaemia that should be taken into consideration upon prescribing opioid-based medication, and more research is needed to unravel the interaction between obesity, glycaemia and opioid use.

Activation of nucleus accumbens µ-opioid receptors enhances the response to a glycaemic challenge.

Opioids are known to affect blood glucose levels but their exact role in the physiological control of glucose metabolism remains unclear. Although there are numerous studies investigating the peripheral effects of opioid stimulation, little is known about how central opioids control blood glucose and which brain areas are involved. One brain area possibly involved is the nucleus accumbens because, as well as being a key site for opioid effects on food intake, it has also been implicated in the control of blood glucose levels. Within the nucleus accumbens, µ-opioid receptors are most abundantly expressed. Therefore, in the present study, we investigated the role of µ-opioid receptors in the nucleus accumbens in the control of glucose metabolism. We show that infusion of the µ-opioid receptor agonist [d-Ala2 , N-MePhe4 , Gly-ol]-enkephalin (DAMGO) in the nucleus accumbens by itself does not affect blood glucose levels, but it enhances the glycaemic response after both an insulin tolerance test, as well as a glucose tolerance test. These findings indicate that the nucleus accumbens plays a role in the central effects of opioids on glucose metabolism, and highlight the possibility of nucleus accumbens µ-opioid receptors as a therapeutic target for enhancing the counter-regulatory response.

Dosage adjustment recommendations of drugs in non-nephrology units with kidney disease / Recomendaciones de ajuste posológico de fármacos para enfermedad renal en unidades no nefrológicas

Purpose: Kidney disease (KD) is defined as an abnormality of the kidney in the structure or function with implications for the health, which can occur abruptly, and either resolve or become chronic. This status use to require medication dosage adjustment. Inappropriate prescribing is a common drug-related problem. The aim of this study is to evaluate the acceptance rate through pharmaceutical interventions with implementation of a daily cross-validation procedure in electronic prescription in patients with KD, susceptible to suffer a drug-related problem (DRP). Methods: A nine month-prospective study, in renal insufficiency inpatients (serum creatinine >1.7 mg/dl) treated with drugs that require dosage adjustment.Results: 539 patients with renal failure were identified, 135 of them needed any adjust in their prescription. We performed 179 dosage recommendations, 104 of which were accepted. Most of the recommendations were done in patients with G4 renal damage. Dose modification was the adjustment most widely required. 25 active ingredients were analyzed and the drugs with higher number of interventions were spironolactone, ranitidine, meropenem and allopurinol. General Internal Medicine was the unit with most interventions and acceptance rate. Conclusions: Pharmaceutical intervention stands out as a strategy to improve the population’s pharmacotherapeutic quality taking into account the integration of assisted electronic prescription systems to facilitate a fast and immediate intervention in decision-making in these situations. (AU)

Objetivos: Evaluar la tasa de aceptación de las intervenciones farmacéuticas con la implementación de un procedimiento diario de validación cruzada en prescripción electrónica de pacientes con IR susceptibles de sufrir un problema relacionado con la medicación (PRM). Material y método: Se trata de un estudio prospectivo de nueve meses de duración realizado en un hospital general universitario de 400 camas en pacientes con insuficiencia renal (creatinina sérica >1,7mg/dl) tratados con medicamentos que pueden requerir un ajuste posológico. La variable principal fue la tasa de aceptaación de las intervenciones farmacéuticas.Resultados: Se identificaron 539 pacientes con insuficiencia renal durante el período de estudio, 135 de ellos necesitaron algún ajuste en su prescripción. Se realizaron 179 recomendaciones farmacéuticas, 104 de las cuales fueron aceptadas. La mayoría de las recomendaciones se realizaron en pacientes con insuficiencia renal G4. Se analizaron 25 principios activos y los fármacos con mayor número de intervenciones fueron: espironolactona, ranitidina, meropenem y alopurinol. El servicio con más intervenciones y tasa de aceptación fue Medicina Interna. (AU)

Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life.

BACKGROUND: Phylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and non-specialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. RESULTS: Physcraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. The program can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). CONCLUSION: The Physcraper workflow showcases the benefits of doing open science for phylogenetics, encouraging researchers to strive for better scientific sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and usage are available at https://physcraper.readthedocs.io.

MRI features of intra-axial histiocytic brain mass lesions.

AIM: To describe MRI features, including diffusion-weighted imaging (DWI), magnetic resonance spectroscopy (MRS), and perfusion-weighted imaging (PWI), of intra-axial tumour-like presentations of four different subtypes of histiocytosis. MATERIAL AND METHODS: The brain MRI findings of 23 patients with histologically proven histiocytosis were reviewed retrospectively (11 Langerhans cell histiocytosis [LCH], eight Erdheim-Chester disease [ECD], one overlap form LCH/ECD, two Rosai-Dorfman disease [RDD], and one haemophagocytic lymphohistiocytosis [HLH]) with single or multiple enhancing intraparenchymal brain lesions. RESULTS: Histiocytic brain mass lesions show some similar MRI features including Supra and/or infratentorial and/or paraventricular subcortical well-delineated masses, linear ependymal enhancement along the ventricles and brain stem lesions. Masses always present with mixed hyper- and hypointense signal on T2-weighted imaging (WI). Their enhancement is often homogeneous. Apparent diffusion coefficient (ADC) values are often normal or elevated. CONCLUSION: The presence of multiple periventricular and subcortical enhancing lesions with mixed signal intensity on T2WI and normal or high ADC values should lead radiologists to consider the diagnosis of histiocytic lesions and search for associated systemic lesions.

Genomic imbalances in craniofacial microsomia.

The aim of this study was to perform 22q11.2 deletion screening and chromosomal microarray analysis (CMA) in individuals clinically diagnosed with craniofacial microsomia (CFM) and review previously published cases of CFM with genomic imbalances. It included 54 individuals who were evaluated by a clinical geneticist. Copy number variants (CNVs) in the 22q11.2 region were investigated by multiplex ligation-dependent probe amplification (MLPA) for all individuals. The CMA was performed only for individuals with additional major features. MLPA revealed pathogenic CNVs at the 22q11 region in 3/54 (5.6%) individuals. CMA revealed pathogenic CNVs in 4/17 (23.5%) individuals, including the three CNVs at the 22q11 region also detected by MLPA, and CNVs classified as variants of unknown significance (VOUS) in 4/17 (23.5%) individuals. Pathogenic alterations were found at the 2p12, 5p15, 13q13, and 22q11 regions. VOUS were found at 3q29, 5q22.2, 5q22.1, and 9p22 regions. All individuals with pathogenic alterations presented additional major features, including congenital heart disease (CHD). The literature review revealed pathogenic CNVs in 17/193 (8.8%) individuals and most of them also presented additional major features, such as CHD, renal anomalies, or developmental delay. In conclusion, CNVs should be investigated in patients with CFM and additional major features.

Phylotastic: Improving Access to Tree-of-Life Knowledge With Flexible, on-the-Fly Delivery of Trees.

A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts, including research, education, and public policy. Yet, accessing the tree of life typically requires special knowledge, complex software, or long periods of training. The Phylotastic project aims make it as easy to get a phylogeny of species as it is to get driving directions from mapping software. In prior work, we presented a design for an open system to validate and manage taxon names, find phylogeny resources, extract subtrees matching a user's taxon list, scale trees to time, and integrate related resources such as species images. Here, we report the implementation of a set of tools that together represent a robust, accessible system for on-the-fly delivery of phylogenetic knowledge. This set of tools includes a web portal to execute several customizable workflows to obtain species phylogenies (scaled by geologic time and decorated with thumbnail images); more than 30 underlying web services (accessible via a common registry); and code toolkits in R and Python (allowing others to develop custom applications using Phylotastic services). The Phylotastic system, accessible via http://www.phylotastic.org, provides a unique resource to access the current state of phylogenetic knowledge, useful for a variety of cases in which a tree extracted quickly from online resources (as distinct from a tree custom-made from character data) is sufficient, as it is for many casual uses of trees identified here.

Production of Fe nanoparticles from γ-Fe2O3 by high-pressure hydrogen reduction.

In this work, the reduction of iron oxide γ-Fe2O3 nanoparticles by hydrogen at high pressures is studied. Increasing the hydrogen pressure enables reduction of γ-Fe2O3 to α-Fe at significantly lower temperatures. At low pressures, a temperature of 390 °C is necessary whereas at 530 bar complete reduction can be realized at temperatures as low as 210 °C. This leads to significant improvement in the final particle morphology, maintaining high surface-to-volume ratio of the nanoparticles with an average size of 47 ± 5 nm which is close to that of the precursor γ-Fe2O3. Neck formation, coalescence and growth during reduction can be significantly suppressed. Investigations of magnetic properties show that saturation magnetization of the reduced α-Fe nanoparticles decreases with particle size from 209 A m2 kg-1 at 390 °C reduction temperature to 204 A m2 kg-1 at 210 °C. Coercivity for the fine iron particles reaches 0.076 T which exceeds the theoretical anisotropy field. This is attributed to nano-scale surface effects.

PET/TC en tumores uterinos. Avanzando por buen camino / PET/CT in uterine tumors. Progressing on the right direction

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Thirty clues to the exceptional diversification of flowering plants.

BACKGROUND AND AIMS: As angiosperms became one of the megadiverse groups of macroscopic eukaryotes, they forged modern ecosystems and promoted the evolution of extant terrestrial biota. Unequal distribution of species among lineages suggests that diversification, the process that ultimately determines species richness, acted differentially through angiosperm evolution. METHODS: We investigate how angiosperms became megadiverse by identifying the phylogenetic and temporal placement of exceptional radiations, by combining the most densely fossil-calibrated molecular clock phylogeny with a Bayesian model that identifies diversification shifts among evolutionary lineages and through time. We evaluate the effect of the prior number of expected shifts in the phylogenetic tree. KEY RESULTS: Major diversification increases took place over 100 Ma, from the Early Cretaceous to the end of the Paleogene, and are distributed across the angiosperm phylogeny. The long-term diversification trajectory of angiosperms shows moderate rate variation, but is underlain by increasing speciation and extinction, and results from temporally overlapping, independent radiations and depletions in component lineages. CONCLUSIONS: The identified deep time diversification shifts are clues to the identification of ultimate drivers of angiosperm megadiversity, which probably involve multivariate interactions among intrinsic traits and extrinsic forces. An enhanced understanding of angiosperm diversification will involve a more precise phylogenetic location of diversification shifts, and integration of fossil information.

Results of a surgical cricothyrotomy workshop with a pig trachea model. / Resultados de un taller de cricotiroidotomía quirúrgica con un modelo de tráquea de cerdo.

BACKGROUND: The latest Difficult Airway Society (DAS) guidelines recommend that all anaesthesiologists should to be trained in the performing of a surgical cricothyrotomy (CtQ). The aim of this study was to analyse the learning results of a CtQ workshop by assessing the success rate and time to perform CtQ on a porcine tracheal model. MATERIAL AND METHODS: A workshop was designed in which each student completed a questionnaire with demographic data and theoretical knowledge about surgical approaches of airway. During the following hour, a review was presented theoretical aspects of CtQ. The model was shown and a CtQ was performed using a classical technique. Afterwards, in groups of 3-4 students with an instructor, each one of the students performed 6 CtQ. A record was made on whether the ventilation was correct, the time to perform CtQ, and the ease of performing the CtQ by the students and instructors. Finally, students completed a questionnaire on the theoretical aspects. Students and instructors performed a workshop debriefing. A statistical analysis was performed, considering a P-value <0.05 as statistically significant. RESULTS: A total of 8 workshop sessions were held with a total of 91 students. At first attempt, 86% of students performed a CtQ with successful ventilation, and 92% at the sixth attempt (P<.0001). Time taken was 163 [107-211] seconds at first attempt, and 70 [55-85] seconds at the sixth (P<.0001). At the end of workshop, students had improved their theoretical knowledge (P<.0001) and perception of the ease of the technique. CONCLUSION: Workshop performance improved theoretical knowledge and competence in surgical cricothyrotomy.