True grit? Comparative anatomy and evolution of gizzards in fishes.

Gut morphology frequently reflects the food organisms digest. Gizzards are organs of the gut found in archosaurs and fishes that mechanically reduce food to aid digestion. Gizzards are thought to compensate for edentulism and/or provide an advantage when consuming small, tough food items (e.g., phytoplankton and algae). It is unknown how widespread gizzards are in fishes and how similar these structures are among different lineages. Here, we investigate the distribution of gizzards across bony fishes to (1) survey different fishes for gizzard presence, (2) compare the histological structure of gizzards in three species, (3) estimate how often gizzards have evolved in fishes, and (4) explore whether anatomical and ecological traits like edentulism and microphagy predict gizzard presence. According to our analyses, gizzards are rare across bony fishes, evolving only six times in a broad taxonomic sampling of 51 species, and gizzard presence is not clearly correlated with factors like gut length or dentition. We find that gizzard morphology varies among the lineages where one is present, both macroscopically (presence of a crop) and microscopically (varying tissue types). We conclude that gizzards likely aid in the mechanical reduction of food in fishes that have lost an oral dentition in their evolutionary past; however, the relative scarcity of gizzards suggests they are just one of many possible solutions for processing tough, nutrient-poor food items. Gizzards have long been present in the evolutionary history of fishes, can be found in a wide variety of marine and freshwater clades, and likely have been overlooked in many taxa.

Motor skill competence and moderate- and vigorous-intensity physical activity: a linear and non-linear cross-sectional analysis of eight pooled trials.

BACKGROUND: Few studies have examined the relationship between motor skill competence and device-measured physical activity in large samples and none have used non-linear modelling. This study assessed the linear and non-linear associations between motor skill competence and physical activity in children using pooled data from eight studies. METHODS: Cross-sectional ActiGraph accelerometer and motor skills competence data from 988 children (50.8% boys) aged 3-11 years were included. Total, object control and locomotor skill competence were assessed using the Test of Gross Motor Skill Development. Linear mixed models were fitted to examine linear associations between motor skill competence and physical activity. Then, restricted cubic splines models were used to assess potential non-linear relationships. Interactions by sex and age were assessed. RESULTS: There was evidence of positive linear associations between total skill, and object control and locomotor skills, with moderate- and vigorous-intensity physical activity; however, the associations with total skill competence and object control better fitted a non-linear model. Non-linear models indicated associations were positive but relatively weak in the low to mid ranges of TGMD/object control scores but at high ranges (~ > 70 out of 100/ and ~ 35 out of 50) the association strength increased for both moderate- and vigorous-intensity physical activity. There were sex interactions for locomotor skills only, specifically for vigorous activity with boys having a stronger positive association than girls. CONCLUSIONS: There appears to be a threshold for object control skill proficiency that children need to reach to enhance their physical activity levels which provides support for a motor skill "proficiency barrier". This provides a tangible benchmark for children to achieve in motor competence programs.

Liver Injury in People With HIV on Antituberculosis and/or Antiretroviral Therapy-Assessing Causality Using the Updated Roussel Uclaf Causality Assessment Method.

PURPOSE: We compared performance of the Roussel Uclaf Causality Assessment Method (RUCAM) with multidisciplinary expert panel review in identifying a drug-induced liver injury (DILI) due to antituberculosis therapy (ATT) and/or antiretroviral therapy (ART). METHODS: Cases were drawn from a prospective registry of hospitalised adults with suspected DILI due to ATT and/or ART in Cape Town, South Africa. Participants had to fulfil American Thoracic Society criteria for ATT interruption (alanine transaminase [ALT] ≥5 times upper limit of normal [ULN]/ALT ≥3 times [ULN] and symptomatic). Causality assessment by expert panel review served as reference standard. The panel ranked potentially implicated drugs as certain, probable, possible or unlikely causes guided by World Health Organization Uppsala Monitoring Centre criteria. The RUCAM was performed for each potentially implicated drug. We calculated sensitivity and specificity of the RUCAM in identifying a probable/certain drug cause for liver injury. RESULTS: We included 48 participants. All were people with HIV (PWH). Twenty-seven were on concomitant ART and ATT, with a median of six potentially hepatotoxic drugs per case. Sensitivity and specificity of the RUCAM in identifying a probable/certain drug cause of liver injury compared with expert panel review was 7% and 100% respectively. Implicated drugs (times ranked probable/certain by panel) were isoniazid (18/0), pyrazinamide (17/0), rifampicin (15/1), efavirenz (6/4) and lopinavir/ritonavir (1/0). CONCLUSIONS: PWH with liver injury received multiple potentially implicated drugs, which may increase liver injury risk and complicate causality assessment. Compared with expert panel review, the RUCAM had low sensitivity in detecting probable or certain drug causes of liver injury.

Maternal mind-mindedness and infant oxytocin are interrelated and negatively associated with postnatal depression.

Previous studies show that maternal mind-mindedness positively impacts children's social development. In the current studies, we examine the relation between mind-mindedness during parent-child interaction, oxytocin (OT), and postnatal depression in a sample of mothers (N = 62, ages 23-44) and their infant (ages 3-9 months). In Study 1, infant salivary OT was positively correlated with mothers' appropriate mind-related comments, and negatively correlated (at trend level) with maternal depression scores. Mothers experiencing symptoms of depression used fewer appropriate mind-related comments than controls. Study 2 was a double-blind, placebo-controlled, experimental study, in which the same women who participated in Study 1 were administered nasal OT. This did not significantly influence levels of mind-mindedness. Study 2 warrants a larger trial to investigate the effect of OT on mind-mindedness further. Study 1 is the first to demonstrate an association between maternal mind-mindedness and variation in children's OT levels. Since both OT and mind-mindedness have been repeatedly implicated in processes of maternal-infant attachment, this association highlights the centrality of mothers' caregiving representations in facilitating the parent-child relationship and children's early development.

The moment of tooth: rate, fate and pattern of Pacific lingcod dentition revealed by pulse-chase.

Tooth replacement rates of polyphyodont cartilaginous and bony fishes are hard to determine because of a lack of obvious patterning and maintaining specimens long enough to observe replacement. Pulse-chase is a fluorescent technique that differentially colours developing mineralized tissue. We present in situ tooth replacement rate and position data for the oral and pharyngeal detentions of Ophiodon elongatus (Pacific lingcod). We assessed over 10 000 teeth, in 20 fish, and found a daily replacement rate of about two teeth (3.6% of the dentition). The average tooth is in the dental battery for 27 days. The replacement was higher in the lower pharyngeal jaw (LPJ). We found no difference between replacement rates of feeding and non-feeding fish, suggesting feeding was not a driver of tooth replacement. Lingcod teeth have both a size and location fate; smaller teeth at one spot will not grow into larger teeth, even if a large tooth nearby is lost. We also found increased rates of replacement at the posterior of the LPJ relative to the anterior. We propose that lingcod teeth do not migrate in the jaw as they develop; their teeth are fated in size and location, erupting in their functional position.

Open Agile text mining for bioinformatics: the PubAnnotation ecosystem.

MOTIVATION: Most currently available text mining tools share two characteristics that make them less than optimal for use by biomedical researchers: they require extensive specialist skills in natural language processing and they were built on the assumption that they should optimize global performance metrics on representative datasets. This is a problem because most end-users are not natural language processing specialists and because biomedical researchers often care less about global metrics like F-measure or representative datasets than they do about more granular metrics such as precision and recall on their own specialized datasets. Thus, there are fundamental mismatches between the assumptions of much text mining work and the preferences of potential end-users. RESULTS: This article introduces the concept of Agile text mining, and presents the PubAnnotation ecosystem as an example implementation. The system approaches the problems from two perspectives: it allows the reformulation of text mining by biomedical researchers from the task of assembling a complete system to the task of retrieving warehoused annotations, and it makes it possible to do very targeted customization of the pre-existing system to address specific end-user requirements. Two use cases are presented: assisted curation of the GlycoEpitope database, and assessing coverage in the literature of pre-eclampsia-associated genes. AVAILABILITY AND IMPLEMENTATION: The three tools that make up the ecosystem, PubAnnotation, PubDictionaries and TextAE are publicly available as web services, and also as open source projects. The dictionaries and the annotation datasets associated with the use cases are all publicly available through PubDictionaries and PubAnnotation, respectively.

Fitness variation among host species and the paradox of ineffective rhizobia.

Legumes can preferentially select beneficial rhizobial symbionts and sanction ineffective strains that fail to fix nitrogen. Yet paradoxically, rhizobial populations vary from highly beneficial to ineffective in natural and agricultural soils. Classic models of symbiosis focus on the single dimension of symbiont cost-benefit to sympatric hosts, but fail to explain the widespread persistence of ineffective rhizobia. Here, we test a novel framework predicting that spatio-temporal and community dynamics can maintain ineffective strains in rhizobial populations. We used clonal and multistrain inoculations and quantitative culturing to investigate the relative fitness of four focal Bradyrhizobium strains varying from effective to ineffective on Acmispon strigosus. We found that an ineffective Bradyrhizobium strain can be sanctioned by its native A. strigosus host across the host's range, forming fewer and smaller nodules compared to beneficial strains. But the same ineffective Bradyrhizobium strain exhibits a nearly opposite pattern on the broadly sympatric host Acmispon wrangelianus, forming large nodules in both clonal and multistrain inoculations. These data suggest that community-level effects could favour the persistence of ineffective rhizobia and contribute to variation in symbiotic nitrogen fixation.

A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support.

BACKGROUND: Probabilistic assessments of clinical care are essential for quality care. Yet, machine learning, which supports this care process has been limited to categorical results. To maximize its usefulness, it is important to find novel approaches that calibrate the ML output with a likelihood scale. Current state-of-the-art calibration methods are generally accurate and applicable to many ML models, but improved granularity and accuracy of such methods would increase the information available for clinical decision making. This novel non-parametric Bayesian approach is demonstrated on a variety of data sets, including simulated classifier outputs, biomedical data sets from the University of California, Irvine (UCI) Machine Learning Repository, and a clinical data set built to determine suicide risk from the language of emergency department patients. RESULTS: The method is first demonstrated on support-vector machine (SVM) models, which generally produce well-behaved, well understood scores. The method produces calibrations that are comparable to the state-of-the-art Bayesian Binning in Quantiles (BBQ) method when the SVM models are able to effectively separate cases and controls. However, as the SVM models' ability to discriminate classes decreases, our approach yields more granular and dynamic calibrated probabilities comparing to the BBQ method. Improvements in granularity and range are even more dramatic when the discrimination between the classes is artificially degraded by replacing the SVM model with an ad hoc k-means classifier. CONCLUSIONS: The method allows both clinicians and patients to have a more nuanced view of the output of an ML model, allowing better decision making. The method is demonstrated on simulated data, various biomedical data sets and a clinical data set, to which diverse ML methods are applied. Trivially extending the method to (non-ML) clinical scores is also discussed.

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.

BACKGROUND: Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction from the scientific literature. In order to better understand the nature of the phenomenon of coreference in biomedical publications and to increase performance on the task, we annotated the Colorado Richly Annotated Full Text (CRAFT) corpus with coreference relations. RESULTS: The corpus was manually annotated with coreference relations, including identity and appositives for all coreferring base noun phrases. The OntoNotes annotation guidelines, with minor adaptations, were used. Interannotator agreement ranges from 0.480 (entity-based CEAF) to 0.858 (Class-B3), depending on the metric that is used to assess it. The resulting corpus adds nearly 30,000 annotations to the previous release of the CRAFT corpus. Differences from related projects include a much broader definition of markables, connection to extensive annotation of several domain-relevant semantic classes, and connection to complete syntactic annotation. Tool performance was benchmarked on the data. A publicly available out-of-the-box, general-domain coreference resolution system achieved an F-measure of 0.14 (B3), while a simple domain-adapted rule-based system achieved an F-measure of 0.42. An ensemble of the two reached F of 0.46. Following the IDENTITY chains in the data would add 106,263 additional named entities in the full 97-paper corpus, for an increase of 76% percent in the semantic classes of the eight ontologies that have been annotated in earlier versions of the CRAFT corpus. CONCLUSIONS: The project produced a large data set for further investigation of coreference and coreference resolution in the scientific literature. The work raised issues in the phenomenon of reference in this domain and genre, and the paper proposes that many mentions that would be considered generic in the general domain are not generic in the biomedical domain due to their referents to specific classes in domain-specific ontologies. The comparison of the performance of a publicly available and well-understood coreference resolution system with a domain-adapted system produced results that are consistent with the notion that the requirements for successful coreference resolution in this genre are quite different from those of the general domain, and also suggest that the baseline performance difference is quite large.

Effects of a 'school-based' physical activity intervention on adiposity in adolescents from economically disadvantaged communities: secondary outcomes of the 'Physical Activity 4 Everyone' RCT.

BACKGROUND/OBJECTIVES: Obesity prevention during adolescence is a health priority. The 'Physical Activity 4 Everyone' (PA4E1) study tested a multi-component physical activity intervention in 10 secondary schools from socio-economically disadvantaged communities. This paper aimed to report the secondary outcomes of the study; to determine whether the intervention impacted on adiposity outcomes (weight, body mass index (BMI), BMI z-score), and whether any effect was moderated by sex, baseline BMI and baseline physical activity level, at 12 and 24 months. SUBJECTS/METHODS: A cluster randomised controlled trial was conducted in New South Wales, Australia. The school-based intervention included seven physical activity strategies targeting the following: curriculum (strategies to maximise physical activity in physical education, student physical activity plans, an enhanced school sport programme); school environment (physical activity during school breaks, modification of school policy); and parents and the community (parent engagement, links with community physical activity providers). Students' weight (kg), BMI and BMI z-score, were collected at baseline (Grade 7), 12 and 24 months. Linear Mixed Models were used to assess between-group mean difference from baseline to 12 and 24 months. Exploratory sub-analyses were undertaken according to three moderators of energy balance. RESULTS: A total of 1150 students (mean age=12 years) provided outcome data at baseline, 1051 (91%) at 12 months and 985 (86%) at 24 months. At 12 months, there were group-by-time effects for weight (mean difference=-0.90 kg (95% confidence interval (CI)=-1.50, -0.30), P<0.01) and BMI (-0.28 kg m-2 (-0.50, -0.06), P=0.01) in favour of the intervention group, but not for BMI z-score (-0.05 (-0.11; 0.01), P=0.13). These findings were consistent for weight (-0.62 kg (-1.21, 0.03), P=0.01) and BMI (-0.28 kg m-2 (-0.49, -0.06), P=0.01) at 24 months, with group-by-time effects also found for BMI z-score (-0.08 (-0.14; -0.02), P=0.02) favouring the intervention group. CONCLUSION: The PA4E1 school-based intervention achieved moderate reductions in adiposity among adolescents from socio-economically disadvantaged communities. Multi-component interventions that increase adolescents' engagement in moderate-to-vigorous physical activity (MVPA) may assist in preventing unhealthy weight gain.

The interaction between artemether-lumefantrine and lopinavir/ritonavir-based antiretroviral therapy in HIV-1 infected patients.

BACKGROUND: Artemether-lumefantrine is currently the most widely recommended treatment of uncomplicated malaria. Lopinavir-based antiretroviral therapy is the commonly recommended second-line HIV treatment. Artemether and lumefantrine are metabolised by cytochrome P450 isoenzyme CYP3A4, which lopinavir/ritonavir inhibits, potentially causing clinically important drug-drug interactions. METHODS: An adaptive, parallel-design safety and pharmacokinetic study was conducted in HIV-infected (malaria-negative) patients: antiretroviral-naïve and those stable on lopinavir/ritonavir-based antiretrovirals. Both groups received the recommended six-dose artemether-lumefantrine treatment. The primary outcome was day-7 lumefantrine concentrations, as these correlate with antimalarial efficacy. Adverse events were solicited throughout the study, recording the onset, duration, severity, and relationship to artemether-lumefantrine. RESULTS: We enrolled 34 patients. Median day-7 lumefantrine concentrations were almost 10-fold higher in the lopinavir than the antiretroviral-naïve group [3170 versus 336 ng/mL; p = 0.0001], with AUC(0-inf) and Cmax increased five-fold [2478 versus 445 µg.h/mL; p = 0.0001], and three-fold [28.2 versus 8.8 µg/mL; p < 0.0001], respectively. Lumefantrine Cmax, and AUC(0-inf) increased significantly with mg/kg dose in the lopinavir, but not the antiretroviral-naïve group. While artemether exposure was similar between groups, Cmax and AUC(0-8h) of its active metabolite dihydroartemisinin were initially two-fold higher in the lopinavir group [p = 0.004 and p = 0.0013, respectively]. However, this difference was no longer apparent after the last artemether-lumefantrine dose. Within 21 days of starting artemether-lumefantrine there were similar numbers of treatment emergent adverse events (42 vs. 35) and adverse reactions (12 vs. 15, p = 0.21) in the lopinavir and antiretroviral-naïve groups, respectively. There were no serious adverse events and no difference in electrocardiographic QTcF- and PR-intervals, at the predicted lumefantrine Tmax. CONCLUSION: Despite substantially higher lumefantrine exposure, intensive monitoring in our relatively small study raised no safety concerns in HIV-infected patients stable on lopinavir-based antiretroviral therapy given the recommended artemether-lumefantrine dosage. Increased day-7 lumefantrine concentrations have been shown previously to reduce the risk of malaria treatment failure, but further evidence in adult patients co-infected with malaria and HIV is needed to assess the artemether-lumefantrine risk : benefit profile in this vulnerable population fully. Our antiretroviral-naïve patients confirmed previous findings that lumefantrine absorption is almost saturated at currently recommended doses, but this dose-limited absorption was overcome in the lopinavir group. TRIAL REGISTRATION: Clinical Trial Registration number NCT00869700. Registered on clinicaltrials.gov 25 March 2009.

Clinical evaluation of the IONA test: a non-invasive prenatal screening test for trisomies 21, 18 and 13.

OBJECTIVE: To evaluate the clinical accuracy of the IONA® test for aneuploidy screening. METHODS: This was a multicenter blinded study in which plasma samples from pregnant women at increased risk of trisomy 21 underwent cell-free DNA analysis utilizing the IONA test. For each sample, the IONA software generated a likelihood ratio and a maternal age-adjusted probability risk score for trisomies 21, 18 and 13. All results from the IONA test were compared against accepted diagnostic karyotyping. RESULTS: A total of 442 maternal samples were obtained, of which 437 had test results available for analysis and assessment of clinical accuracy. The IONA test had a detection rate of 100% for trisomies 21 (n = 43; 95% CI, 87.98-100%), 18 (n = 10; 95% CI, 58.72-100%) and 13 (n = 5; 95% CI, 35.88-100%) with cut-offs applied to likelihood ratio (cut-off > 1 considered high risk for trisomy) and probability risk score incorporating adjustment for maternal age (cut-off ≥ 1/150 considered high risk for trisomy). The false-positive rate (FPR) was 0% for trisomies 18 and 13 with both analysis outputs. For trisomy 21, a FPR of 0.3% was observed for the likelihood ratio, but became 0% with adjustment for maternal age. CONCLUSION: This study indicates that the IONA test is suitable for trisomy screening in a high-risk screening population. The result-interpretation feature of the IONA software should facilitate wider implementation, particularly in local laboratories, and should be a useful addition to the current screening methods for trisomies 21, 18 and 13.

Diagnosis of fetal submicroscopic chromosomal abnormalities in failed array CGH samples: copy number by sequencing as an alternative to microarrays for invasive fetal testing.

OBJECTIVES: Array comparative genomic hybridization (CGH) has become the technology of choice for high-resolution prenatal whole genome analysis. Limitations of microarrays are mainly related to the analog nature of the analysis, and poor-quality DNA can result in failed quality metrics with these platforms. We examined a cohort of abnormal fetuses with failed array CGH results using a next-generation sequencing algorithm, CNV-Seq. We assessed the ability of the platform to handle suboptimal prenatal samples and generate interpretable molecular karyotypes. METHODS: Nine samples obtained from abnormal fetuses and one from a normal control fetus were sequenced using an Illumina GAIIx. A segmentation algorithm for sequencing data was used to determine regional copy number data on the sequencing datasets. RESULTS: Phred quality scores were satisfactory for analysis of all samples. CNV-Seq identified both large- and small-scale abnormalities in the cohort, and normal results were obtained for fetuses for which microarray data were previously uninterpretable. No variants of uncertain significance were detected. Analysis of the digital sequencing datasets offered some advantages over array CGH output. CONCLUSIONS: Using next-generation sequencing for the detection of genomic copy number variants may be advantageous for poor-quality, invasively-acquired prenatal samples. CNV-Seq could become a potential alternative to array CGH in this setting.

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters.

BACKGROUND: Ontological concepts are useful for many different biomedical tasks. Concepts are difficult to recognize in text due to a disconnect between what is captured in an ontology and how the concepts are expressed in text. There are many recognizers for specific ontologies, but a general approach for concept recognition is an open problem. RESULTS: Three dictionary-based systems (MetaMap, NCBO Annotator, and ConceptMapper) are evaluated on eight biomedical ontologies in the Colorado Richly Annotated Full-Text (CRAFT) Corpus. Over 1,000 parameter combinations are examined, and best-performing parameters for each system-ontology pair are presented. CONCLUSIONS: Baselines for concept recognition by three systems on eight biomedical ontologies are established (F-measures range from 0.14-0.83). Out of the three systems we tested, ConceptMapper is generally the best-performing system; it produces the highest F-measure of seven out of eight ontologies. Default parameters are not ideal for most systems on most ontologies; by changing parameters F-measure can be increased by up to 0.4. Not only are best performing parameters presented, but suggestions for choosing the best parameters based on ontology characteristics are presented.

Mining the pharmacogenomics literature--a survey of the state of the art.

This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011. Pharmacogenomics (or pharmacogenetics) is the field that studies how human genetic variation impacts drug response. Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years. This survey covers efforts dealing with the automatic recognition of relevant named entities (e.g. genes, gene variants and proteins, diseases and other pathological phenomena, drugs and other chemicals relevant for medical treatment), as well as various forms of relations between them. A wide range of text genres is considered, such as scientific publications (abstracts, as well as full texts), patent texts and clinical narratives. We also discuss infrastructure and resources needed for advanced text analytics, e.g. document corpora annotated with corresponding semantic metadata (gold standards and training data), biomedical terminologies and ontologies providing domain-specific background knowledge at different levels of formality and specificity, software architectures for building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensive ways to disseminate and interact with the typically huge amounts of semiformal knowledge structures extracted by text mining tools. Finally, we consider some of the novel applications that have already been developed in the field of pharmacogenomic text mining and point out perspectives for future research.

Chapter 16: text mining for translational bioinformatics.

Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

Dental Dynamics: A Fast New Tool for Quantifying Tooth and Jaw Biomechanics in 3D Slicer.

Teeth reveal how organisms interact with their environment. Biologists have long looked at the diverse form and function of teeth to study the evolution of feeding, fighting, and development. The exponential rise in the quantity and accessibility of computed tomography (CT) data has enabled morphologists to study teeth at finer resolutions and larger macroevolutionary scales. Measuring tooth function is no easy task, in fact, much of our mechanical understanding is derived from dental shape. Categorical descriptors of tooth shape such as morphological homodonty and heterodonty, overlook nuances in function by reducing tooth diversity for comparative analysis. The functional homodonty method quantitatively assesses the functional diversity of whole dentitions from tooth shape. This method uses tooth surface area and position to calculate the transmission of stress and estimates a threshold for functionally homodont teeth through bootstrapping and clustering techniques. However, some vertebrates have hundreds or thousands of teeth and measuring the shape and function of every individual tooth can be a painstaking task. Here, we present Dental Dynamics, a module for 3D Slicer that allows for the fast and precise quantification of dentitions and jaws. The tool automates the calculation of several tooth traits classically used to describe form and function (i.e., aspect ratio, mechanical advantage, force, etc.). To demonstrate the usefulness of our module we used Dental Dynamics to quantify 780 teeth across 20 salamanders that exhibit diverse ecologies. We coupled these data with the functional homodonty method to investigate the hypothesis that arboreal Aneides salamanders have novel tooth functions. Dental Dynamics provides a new and fast way to measure teeth and increases the accessibility of the functional homodonty method. We hope Dental Dynamics will encourage further theoretical and methodological development for quantifying and studying teeth.

Los dientes revelan cómo los organismos interactúan con su entorno. Los biólogos llevan mucho tiempo observando las diversas formas y funciones de los dientes para estudiar la evolución de la alimentación, la lucha y el desarrollo. El aumento exponencial en la cantidad y accesibilidad de los datos de la tomografía computarizada (CT) ha permitido a los morfólogos estudiar los dientes con resoluciones más finas y escalas macroevolutivas más grandes. Medir la función dental no es una tarea fácil; de hecho, gran parte de nuestro conocimiento mecánico se deriva de la forma dental. Los descriptores categóricos de la forma de los dientes, como la homodoncia y la heterodoncia morfológicas, pasan por alto los matices funcionales al reducir la diversidad de los dientes para el análisis comparativo. El método de la homodoncia funcional cuantitativamente evalúa la diversidad funcional de denticiones enteras a partir de la forma del diente. Sin embargo, algunos vertebrados tienen cientos o miles de dientes y medir la forma y función de cada uno de los dientes individuales puede ser una tarea minuciosa. Aquí te presentamos Dental Dynamics, un módulo para 3D Slicer que permite la cuantificación rápida y precisa de denticíon y mandíbulas. La herramienta automatiza el cálculo de varios rasgos dentales utilizados clásicamente para describir forma y función (es decir, relación de aspecto, ventaja mecánica, fuerza, etc.). Para demostrar la utilidad de nuestros módulos utilizamos Dental Dynamics para cuantificar 780 dientes en 20 salamandras que exhiben ecologías diversas. Combinamos estos datos con el método de homodoncia funcional para investigar la hipótesis de que las salamandras arbóreas Aneides tienen nuevas funciones dentales. Dinámica Dental proporciona una forma nueva y rápida de medir los dientes y aumenta la accesibilidad de los método funcionales de homodoncia. Esperamos que Dental Dynamics fomente más conocimientos teóricos y desarrollo metodológico para la cuantificación y estudio de los dientes.

Correction: Emerging pollutants in the Esmeraldas watershed in Ecuador: discharge and attenuation of emerging organic pollutants along the San Pedro-Guayllabamba-Esmeraldas rivers.

Correction for 'Emerging pollutants in the Esmeraldas watershed in Ecuador: discharge and attenuation of emerging organic pollutants along the San Pedro-Guayllabamba-Esmeraldas rivers' by A. Voloshenko-Rossin et al., Environ. Sci.: Processes Impacts, 2015, 17, 41-53, https://doi.org/10.1039/C4EM00394B.

Signal of harm in morphine use in adults with acute pulmonary oedema: A rapid systematic review.

BACKGROUND: Heart failure affects nearly 65 million people globally, resulting in recurrent hospital admissions and substantial healthcare expenditure. The use of morphine in the management of acute pulmonary oedema remains controversial, with conflicting guidance and significant variation in practice. Synthesised evidence is needed to inform standard treatment guidelines and clinical practice. OBJECTIVE: To determine whether morphine should be used in the treatment of acute pulmonary oedema (APE) in adults. METHODS: A rapid review of systematic reviews of randomised controlled trials or observational studies, and then randomised controlled trials, was conducted searching three electronic databases (PubMed, Embase, Cochrane Library) and one clinical trial registry on 12 February 2022. We used a prespecified protocol following Cochrane rapid review methods and aligned to the National Standard Treatment Guidelines and Essential Medicines List methodology. We first considered relevant high-quality systematic reviews of randomised controlled trials or observational studies, then (if required) randomised controlled trials to inform time-sensitive or urgent evidence requests, clinical practice, policy, or standard treatment guidelines. RESULTS: We identified four systematic reviews of observational studies. The two most relevant, up-to-date, and highest-quality reviews were used to inform evidence for critical outcomes. Morphine may increase in-hospital mortality (odds ratio (OR) 1.78; 95% confidence interval (CI) 1.01 - 3.13; low certainty of evidence; six observational studies, n=151 735 participants), resulting in 15 more per 1 000 hospital deaths, ranging from 0 to 40 more hospital deaths. Morphine may result in a large increase in invasive mechanical ventilation (OR 2.72; 95% CI 1.09 - 6.80; low certainty of evidence; four observational studies, n=167 847 participants), resulting in 45 more per 1 000 ventilations, ranging from 2 more to 136 more. Adverse events and hospital length of stay were not measured across reviews or trials. CONCLUSION: Based on the most recent, relevant and best-available quality evidence, morphine use in adults with APE may increase in-hospital and all-cause mortality and may result in a large increase in the need for invasive mechanical ventilation compared to not using morphine. Recommending against the use of morphine in pulmonary oedema may improve patient outcomes. Disinvesting in morphine for this indication may result in cost savings, noting the possible accrued benefits of fewer patients requiring invasive ventilation and management of morphine-related side-effects.

Randomized evaluation of an online single-session intervention for minority stress in LGBTQ+ adolescents.

Background: LGBTQ+ youth face myriad adverse health outcomes due to minority stress, creating a need for accessible, mechanism-targeted interventions to mitigate these minority stress-related risk factors. We tested the effectiveness and acceptability of Project RISE, an online single-session intervention designed to ameliorate internalized stigma and improve other outcomes among LGBTQ+ youth. We hypothesized that youth assigned to RISE (versus a control) would report significantly reduced internalized stigma and increased identity pride at post-intervention and at two-week follow-up and would find RISE acceptable. Methods: We recruited adolescents nationally through Instagram advertisements in May 2022 (N = 538; M age = 15.06, SD age = 0.97). Participants were randomly assigned to RISE or an information-only control and completed questionnaires pre-intervention, immediately post-intervention, and two weeks post-intervention. Inclusion criteria included endorsing: (1) LGBTQ+ identity, (2) age 13-16, (3) English fluency (4) Internet access, and (5) subjective negative impact of LGBTQ+ stigma. Results: Relative to participants in the control condition, participants who completed RISE reported significant decreases in internalized stigma (d = -0.49) and increases in identity pride (d = 0.25) from pre- to immediately post-intervention, along with decreased internalized stigma (d = -0.26) from baseline to two-week follow-up. Participants rated both RISE and the information-only control as highly, equivalently acceptable. Conclusions: RISE appears to be an acceptable and useful online SSI for LGBTQ+ adolescents, with potential to reduce internalized stigma in both the short- and longer-term. Future directions include evaluating effects of Project RISE over longer follow-ups and in conjunction with other mental health supports.