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Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.
Studies in the sociopolitics of archaeology have shown patterns of inequality in publishing. Because this inequality affects the richness of perspectives on the past, the extent of unevenness requires continual documentation. This article explores gendered and institutionally based patterns of authorship in prominent archaeology journals, archaeology papers in general science journals, and Sapiens, a public-facing web magazine, from 2016 to 2021. We find that the representation of women is similar across these two types of journals, for authors both in the United States and abroad. Men still publish significantly more than women though the gap is narrowing due to the publication activity of recent PhDs. Using a large database of PhDs as a baseline for comparison, we find that women publish less in these venues than expected, resulting in an imbalance. Some archaeology programs have a larger presence in journal publishing than others, but this imbalance is not as pervasive as what has been observed in hiring practices. Archaeology journals exhibit healthier measures of diversity, compared to Science, in terms of the institutional affiliation of authors.
Pb–Zr–Ti–O (PZT) perovskites span a large solid-solution range and have found widespread use due to their piezoelectric and ferroelectric properties that also span a large range. Crystal structure analysis via Rietveld refinement facilitates materials analysis via the extraction of the structural parameters. These parameters, often obtained as a function of an additional dimension (e.g., pressure), can help to diagnose materials response within a use environment. Often referred to as “in-situ” studies, these experiments provide an abundance of data. Viewing structural changes due to applied pressure conditions can give much-needed insight into materials performance. However, challenges exist for viewing/presenting results when the details are inherently three-dimensional (3D) in nature. For PZT perovskites, the use of polyhedra (e.g., Zr/Ti–O6 octahedra) to view bonding/connectivity is beneficial; however, the visualization of the octahedra behavior with pressure dependence is less easily demonstrated due to the complexity of the added pressure dimension. We present a more intuitive visualization by projecting structural data into virtual reality (VR). We employ previously published structural data for Pb0.99(Zr0.95Ti0.05)0.98Nb0.02O3 as an exemplar for VR visualization of the PZT R3c crystal structure between ambient and 0.62 GPa pressure. This is accomplished via our in-house CAD2VR™ software platform and the new CrystalVR plugin. The use of the VR environment enables a more intuitive viewing experience, while enabling on-the-fly evaluation of crystal data, to form a detailed and comprehensive understanding of in-situ datasets. Discussion of methodology and tools for viewing are given, along with how recording results in video form can enable the viewing experience.
Childhood adversity and cannabis use are considered independent risk factors for psychosis, but whether different patterns of cannabis use may be acting as mediator between adversity and psychotic disorders has not yet been explored. The aim of this study is to examine whether cannabis use mediates the relationship between childhood adversity and psychosis.
Data were utilised on 881 first-episode psychosis patients and 1231 controls from the European network of national schizophrenia networks studying Gene–Environment Interactions (EU-GEI) study. Detailed history of cannabis use was collected with the Cannabis Experience Questionnaire. The Childhood Experience of Care and Abuse Questionnaire was used to assess exposure to household discord, sexual, physical or emotional abuse and bullying in two periods: early (0–11 years), and late (12–17 years). A path decomposition method was used to analyse whether the association between childhood adversity and psychosis was mediated by (1) lifetime cannabis use, (2) cannabis potency and (3) frequency of use.
The association between household discord and psychosis was partially mediated by lifetime use of cannabis (indirect effect coef. 0.078, s.e. 0.022, 17%), its potency (indirect effect coef. 0.059, s.e. 0.018, 14%) and by frequency (indirect effect coef. 0.117, s.e. 0.038, 29%). Similar findings were obtained when analyses were restricted to early exposure to household discord.
Harmful patterns of cannabis use mediated the association between specific childhood adversities, like household discord, with later psychosis. Children exposed to particularly challenging environments in their household could benefit from psychosocial interventions aimed at preventing cannabis misuse.
While cannabis use is a well-established risk factor for psychosis, little is known about any association between reasons for first using cannabis (RFUC) and later patterns of use and risk of psychosis.
We used data from 11 sites of the multicentre European Gene-Environment Interaction (EU-GEI) case–control study. 558 first-episode psychosis patients (FEPp) and 567 population controls who had used cannabis and reported their RFUC.
We ran logistic regressions to examine whether RFUC were associated with first-episode psychosis (FEP) case–control status. Path analysis then examined the relationship between RFUC, subsequent patterns of cannabis use, and case–control status.
Controls (86.1%) and FEPp (75.63%) were most likely to report ‘because of friends’ as their most common RFUC. However, 20.1% of FEPp compared to 5.8% of controls reported: ‘to feel better’ as their RFUC (χ2 = 50.97; p < 0.001). RFUC ‘to feel better’ was associated with being a FEPp (OR 1.74; 95% CI 1.03–2.95) while RFUC ‘with friends’ was associated with being a control (OR 0.56; 95% CI 0.37–0.83). The path model indicated an association between RFUC ‘to feel better’ with heavy cannabis use and with FEPp-control status.
Both FEPp and controls usually started using cannabis with their friends, but more patients than controls had begun to use ‘to feel better’. People who reported their reason for first using cannabis to ‘feel better’ were more likely to progress to heavy use and develop a psychotic disorder than those reporting ‘because of friends’.
Growing urban expansion can alter ecological processes within trophic networks. Predation on herbivores is known to vary with the size of the area covered by vegetation, successional stage, altitude and predator community structure; however there are gaps in understanding how this occurs in urban and suburban environments. The purpose of this study was to determine whether predation pressure on artificial models of caterpillars varied with the degree of urbanisation and type of substrate. Artificial caterpillars were placed on two types of substrates (leaf vs. stem) in two areas of the city (urban vs. suburban). Total predation was measured as the number of models with evidence of attack by predators, with the predation rate estimated on a weekly basis. Predation was affected by the degree of urbanisation, being higher in urban (x̄ = 9.88%; SD = 4.09%, n = 8) than suburban areas (x̄ = 5.75%, SD = 4.21%, n = 8). Attack marks were observed in 23.8% (n = 125) of artificial caterpillars. The weekly predation rate on leaves (x̄ = 9.63%, SD = 5.95%, n = 8) was higher than that on stems (x̄ = 6%, SD = 4.2%, n = 8). These results suggest that the incidence of predation might vary with the degree of urbanisation and by the type of substrate on which prey organisms are found.
Tungsten (W) films have many applications in the semiconducting industry for sensor technology. Deposition conditions can significantly impact the resulting W films in terms of the phases present (α-BCC or β-A12), microstructural grain orientation (texture), and residual strain. Tilt-A-Whirl methodology has been employed for the evaluation of a W film showing both texture and residual strain. Sin2(ψ) analysis of the film was performed to quantify the strongly tensile in-plane strain (+0.476%) with an estimated in-plane tensile stress of ~1.9 GPa. The 3D dataset was also evaluated qualitatively via 3D visualization. Visualization of 3D texture/strain data poses challenges due to peak broadening resulting from defocusing of the beam at high ψ tilt angles. To address this issue, principal component analysis (PCA) was employed to diagnose, model, and remove the broadening component from the diffraction data. Evaluation of the raw data and subsequent corrected data (after removal of defocusing effects) has been performed through projection of the data into a virtual 3D environment (via CAD2VR software) to qualitatively detect the impact of residual strain on the observed pole figure.
The Hierarchical Taxonomy of Psychopathology (HiTOP) has emerged out of the quantitative approach to psychiatric nosology. This approach identifies psychopathology constructs based on patterns of co-variation among signs and symptoms. The initial HiTOP model, which was published in 2017, is based on a large literature that spans decades of research. HiTOP is a living model that undergoes revision as new data become available. Here we discuss advantages and practical considerations of using this system in psychiatric practice and research. We especially highlight limitations of HiTOP and ongoing efforts to address them. We describe differences and similarities between HiTOP and existing diagnostic systems. Next, we review the types of evidence that informed development of HiTOP, including populations in which it has been studied and data on its validity. The paper also describes how HiTOP can facilitate research on genetic and environmental causes of psychopathology as well as the search for neurobiologic mechanisms and novel treatments. Furthermore, we consider implications for public health programs and prevention of mental disorders. We also review data on clinical utility and illustrate clinical application of HiTOP. Importantly, the model is based on measures and practices that are already used widely in clinical settings. HiTOP offers a way to organize and formalize these techniques. This model already can contribute to progress in psychiatry and complement traditional nosologies. Moreover, HiTOP seeks to facilitate research on linkages between phenotypes and biological processes, which may enable construction of a system that encompasses both biomarkers and precise clinical description.
Schizophrenia (SZ), bipolar disorder (BD) and depression (D) run in families. This susceptibility is partly due to hundreds or thousands of common genetic variants, each conferring a fractional risk. The cumulative effects of the associated variants can be summarised as a polygenic risk score (PRS). Using data from the EUropean Network of national schizophrenia networks studying Gene-Environment Interactions (EU-GEI) first episode case–control study, we aimed to test whether PRSs for three major psychiatric disorders (SZ, BD, D) and for intelligent quotient (IQ) as a neurodevelopmental proxy, can discriminate affective psychosis (AP) from schizophrenia-spectrum disorder (SSD).
Participants (842 cases, 1284 controls) from 16 European EU-GEI sites were successfully genotyped following standard quality control procedures. The sample was stratified based on genomic ancestry and analyses were done only on the subsample representing the European population (573 cases, 1005 controls). Using PRS for SZ, BD, D, and IQ built from the latest available summary statistics, we performed simple or multinomial logistic regression models adjusted for 10 principal components for the different clinical comparisons.
In case–control comparisons PRS-SZ, PRS-BD and PRS-D distributed differentially across psychotic subcategories. In case–case comparisons, both PRS-SZ [odds ratio (OR) = 0.7, 95% confidence interval (CI) 0.54–0.92] and PRS-D (OR = 1.31, 95% CI 1.06–1.61) differentiated AP from SSD; and within AP categories, only PRS-SZ differentiated BD from psychotic depression (OR = 2.14, 95% CI 1.23–3.74).
Combining PRS for severe psychiatric disorders in prediction models for psychosis phenotypes can increase discriminative ability and improve our understanding of these phenotypes. Our results point towards the potential usefulness of PRSs in specific populations such as high-risk or early psychosis phases.
No established risk prediction tool exists in United Kingdom and Irish Paediatric Cardiology practice for patients undergoing cardiac catheterisation. The Catheterisation RISk score for Paediatrics is used primarily in North American practice to assess risk prior to cardiac catheterisation. Validating the utility and transferability of such a tool in practice provides the opportunity to employ an already established risk assessment tool in everyday practice.
To ascertain whether the Catheterisation RISk score for Paediatrics assessment tool can accurately predict complications within United Kingdom and Irish congenital catheterisation practice.
Clinical and procedural data including National Institute for Cardiovascular Outcomes Research derived outcome data from 1500 patients across five large congenital cardiology centres in the United Kingdom and Ireland were retrospectively collected. Catheterisation RISk score for Paediatrics were then calculated for each case and compared with the observed procedural outcomes. Chi-square analysis was used to determine the relationship between observed and predicted events.
Ninety-eight (6.6%) patients in this study experienced a significant complication as qualified by National Institute for Cardiovascular Outcomes Research classification. 4% experienced a moderate complication, 2.3% experienced a major complication and 0.3% experienced a catastrophic complication resulting in death. Calculated Catheterisation RISk score for Paediatrics scores correlated well with all observed adverse events for paediatric patients across all CRISP categories. The association was also transferable to adult congenital heart disease patients in lower Catheterisation RISk score for Paediatrics categories (CRISP 1–3).
The Catheterisation RISk score for Paediatrics score accurately predicts significant complications in congenital catheterisation practice in the United Kingdom and Ireland. Our data validated the Catheterisation RISk score for Paediatrics assessment tool in five congenital centres using National Institute for Cardiovascular Outcomes Research-derived outcome data.
A history of childhood adversity is associated with psychotic disorder, with an increase in risk according to the number of exposures. However, it is not known why only some exposed individuals go on to develop psychosis. One possibility is pre-existing polygenic vulnerability. Here, we investigated, in the largest sample of first-episode psychosis (FEP) cases to date, whether childhood adversity and high polygenic risk scores for schizophrenia (SZ-PRS) combine synergistically to increase the risk of psychosis, over and above the effect of each alone.
We assigned a schizophrenia-polygenic risk score (SZ-PRS), calculated from the Psychiatric Genomics Consortium (PGC2), to all participants in a sample of 384 FEP patients and 690 controls from the case–control component of the EU-GEI study. Only participants of European ancestry were included in the study. A history of childhood adversity was collected using the Childhood Trauma Questionnaire (CTQ). Synergistic effects were estimated using the interaction contrast ratio (ICR) [odds ratio (OR)exposure and PRS − ORexposure − ORPRS + 1] with adjustment for potential confounders.
There was some evidence that the combined effect of childhood adversities and polygenic risk was greater than the sum of each alone, as indicated by an ICR greater than zero [i.e. ICR 1.28, 95% confidence interval (CI) −1.29 to 3.85]. Examining subtypes of childhood adversities, the strongest synergetic effect was observed for physical abuse (ICR 6.25, 95% CI −6.25 to 20.88).
Our findings suggest possible synergistic effects of genetic liability and childhood adversity experiences in the onset of FEP, but larger samples are needed to increase precision of estimates.
Residual strain in electrodeposited Li films may affect safety and performance in Li metal battery anodes, so it is important to understand how to detect residual strain in electrodeposited Li and the conditions under which it arises. To explore this Li films, electrodeposited onto Cu metal substrates, were prepared under an applied pressure of either 10 or 1000 kPa and subsequently tested for the presence or absence of residual strain via sin2(ψ) analysis. X-ray diffraction (XRD) analysis of Li films required preparation and examination within an inert environment; hence, a Be-dome sample holder was employed during XRD characterization. Results show that the Li film grown under 1000 kPa displayed a detectable presence of in-plane compressive strain (−0.066%), whereas the Li film grown under 10 kPa displayed no detectable in-plane strain. The underlying Cu substrate revealed an in-plane residual strain near zero. Texture analysis via pole figure determination was also performed for both Li and Cu and revealed a mild fiber texture for Li metal and a strong bi-axial texture of the Cu substrate. Experimental details concerning sample preparation, alignment, and analysis of the particularly air-sensitive Li films have also been detailed. This work shows that Li metal exhibits residual strain when electrodeposited under compressive stress and that XRD can be used to quantify that strain.
The ‘jumping to conclusions’ (JTC) bias is associated with both psychosis and general cognition but their relationship is unclear. In this study, we set out to clarify the relationship between the JTC bias, IQ, psychosis and polygenic liability to schizophrenia and IQ.
A total of 817 first episode psychosis patients and 1294 population-based controls completed assessments of general intelligence (IQ), and JTC, and provided blood or saliva samples from which we extracted DNA and computed polygenic risk scores for IQ and schizophrenia.
The estimated proportion of the total effect of case/control differences on JTC mediated by IQ was 79%. Schizophrenia polygenic risk score was non-significantly associated with a higher number of beads drawn (B = 0.47, 95% CI −0.21 to 1.16, p = 0.17); whereas IQ PRS (B = 0.51, 95% CI 0.25–0.76, p < 0.001) significantly predicted the number of beads drawn, and was thus associated with reduced JTC bias. The JTC was more strongly associated with the higher level of psychotic-like experiences (PLEs) in controls, including after controlling for IQ (B = −1.7, 95% CI −2.8 to −0.5, p = 0.006), but did not relate to delusions in patients.
Our findings suggest that the JTC reasoning bias in psychosis might not be a specific cognitive deficit but rather a manifestation or consequence, of general cognitive impairment. Whereas, in the general population, the JTC bias is related to PLEs, independent of IQ. The work has the potential to inform interventions targeting cognitive biases in early psychosis.
The objective of the Caribbean Strong Summit was to plan an intersectoral summit to address the equity of community health and resilience for disaster preparedness, response and recovery and develop a set of integrated and actionable recommendations for Puerto Rico and the Caribbean Region post Hurricanes Irma and Maria. A three-day meeting was convened with a wide range of community, organizational and private sector leaders along with representatives from Puerto Rico, the Caribbean, the Americas, and global experts to generate recommendations for enhanced resilience based upon lessons learned and evidence-based approaches. More than 500 participants from the region gave 104 presentations with recommendations for resilience. Over 150 recommendations were generated and ranked for importance and actionability by participants. A representative sample of these are presented along with five major themes for building health resilient communities in the Caribbean. This summit was successful in compiling a set of integrated recommendations from more than 19 diverse sectors and in defining five major thematic areas for future work to enhance resilience for all types of future disasters. A follow-up meeting should be planned to continue this discussion and to showcase work that has been accomplished in these areas. A complete set of the recommendations from the Caribbean Strong Summit and their analysis and compilation would be published and should serve as a foundational effort to enhance preparedness and resiliency towards future disasters in the Caribbean.
The powder-bed laser additive manufacturing (AM) process is widely used in the fabrication of three-dimensional metallic parts with intricate structures, where kinetically controlled diffusion and microstructure ripening can be hindered by fast melting and rapid solidification. Therefore, the microstructure and physical properties of parts made by this process will be significantly different from their counterparts produced by conventional methods. This work investigates the microstructure evolution for an AM fabricated AlSi10Mg part from its nonequilibrium state toward equilibrium state. Special attention is placed on silicon dissolution, precipitate formation, collapsing of a divorced eutectic cellular structure, and microstructure ripening in the thermal annealing process. These events alter the size, morphology, length scale, and distribution of the beta silicon phase in the primary aluminum, and changes associated with elastic properties and microhardness are reported. The relationship between residual stress and silicon dissolution due to changes in lattice spacing is also investigated and discussed.
X-ray fluorescence (XRF) has been employed as one of several orthogonal means of screening materials to prevent counterfeit and adulterated products from entering the product stream. We document the use of principal component analysis (PCA) of XRF data on compositionally similar and dissimilar stainless steels for the purpose of testing the feasibility of employing XRF spectra to parse and bin these alloys as the same or significantly different alloy materials. The results indicate that XRF spectra can separate and assign alloys via PCA, but that important corrections for detector drift and scaling must be performed in order to achieve valid results.