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Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.
Antidepressant medication and interpersonal psychotherapy (IPT) are both recommended interventions in depression treatment guidelines based on literature reviews and meta-analyses. However, ‘conventional’ meta-analyses comparing their efficacy are limited by their reliance on reported study-level information and a narrow focus on depression outcome measures assessed at treatment completion. Individual participant data (IPD) meta-analysis, considered the gold standard in evidence synthesis, can improve the quality of the analyses when compared with conventional meta-analysis.
We describe the protocol for a systematic review and IPD meta-analysis comparing the efficacy of antidepressants and IPT for adult acute-phase depression across a range of outcome measures, including depressive symptom severity as well as functioning and well-being, at both post-treatment and follow-up (PROSPERO: CRD42020219891).
We will conduct a systematic literature search in PubMed, PsycINFO, Embase and the Cochrane Library to identify randomised clinical trials comparing antidepressants and IPT in the acute-phase treatment of adults with depression. We will invite the authors of these studies to share the participant-level data of their trials. One-stage IPD meta-analyses will be conducted using mixed-effects models to assess treatment effects at post-treatment and follow-up for all outcome measures that are assessed in at least two studies.
This will be the first IPD meta-analysis examining antidepressants versus IPT efficacy. This study has the potential to enhance our knowledge of depression treatment by comparing the short- and long-term effects of two widely used interventions across a range of outcome measures using state-of-the-art statistical techniques.
Surgical site infection (SSI) is a common postprocedure complication that may be prevented by adhering to established recommendations, including administration of preoperative antibiotic prophylaxis. Patients with a β-lactam allergy (BLA) label have an increased risk of SSI. We sought to evaluate the appropriateness of preoperative antibiotic prophylaxis in patients labeled with a BLA compared those without a BLA.
This was a single-center, retrospective, matched cohort study of adult patients who underwent a clean or clean-contaminated knee replacement, abdominal hysterectomy, colorectal surgery, or coronary artery bypass graft (CABG). Patients with a BLA label were matched to patients without a BLA label based on procedure, age, and body mass index (BMI). The primary end point was the rate of appropriate preoperative antibiotic prophylaxis, including antibiotic selection and timing prior to incision.
In total, 260 patients were included. Knee replacement (38%) was the most common procedure, followed by abdominal hysterectomy (25%), colorectal surgery (18%), and CABG (18%). Appropriate preoperative antibiotic prophylaxis was higher among patients without a BLA (76% vs 37%; P < .001). Among patients with a mild-to-moderate reaction or intolerance, 29 (53%) received antibiotics that would have been appropriate only if the patient had had a severe BLA. Patients with a BLA were more likely to have had an antibiotic omitted from the prophylactic regimen (44% vs 4%; P < .001).
Patients with a BLA were more likely to receive inappropriate preoperative antibiotic prophylaxis, attributed to misinterpretation of BLA labels and antibiotic omissions. Optimizing antibiotic prophylaxis among patients with BLAs remains an area of opportunity to prevent SSIs.
Typical enteropathogenic Escherichia coli (tEPEC) infection is a major cause of diarrhoea and contributor to mortality in children <5 years old in developing countries. Data were analysed from the Global Enteric Multicenter Study examining children <5 years old seeking care for moderate-to-severe diarrhoea (MSD) in Kenya. Stool specimens were tested for enteric pathogens, including by multiplex polymerase chain reaction for gene targets of tEPEC. Demographic, clinical and anthropometric data were collected at enrolment and ~60-days later; multivariable logistic regressions were constructed. Of 1778 MSD cases enrolled from 2008 to 2012, 135 (7.6%) children tested positive for tEPEC. In a case-to-case comparison among MSD cases, tEPEC was independently associated with presentation at enrolment with a loss of skin turgor (adjusted odds ratio (aOR) 2.08, 95% confidence interval (CI) 1.37–3.17), and convulsions (aOR 2.83, 95% CI 1.12–7.14). At follow-up, infants with tEPEC compared to those without were associated with being underweight (OR 2.2, 95% CI 1.3–3.6) and wasted (OR 2.5, 95% CI 1.3–4.6). Among MSD cases, tEPEC was associated with mortality (aOR 2.85, 95% CI 1.47–5.55). This study suggests that tEPEC contributes to morbidity and mortality in children. Interventions aimed at defining and reducing the burden of tEPEC and its sequelae should be urgently investigated, prioritised and implemented.
Gravitational waves from coalescing neutron stars encode information about nuclear matter at extreme densities, inaccessible by laboratory experiments. The late inspiral is influenced by the presence of tides, which depend on the neutron star equation of state. Neutron star mergers are expected to often produce rapidly rotating remnant neutron stars that emit gravitational waves. These will provide clues to the extremely hot post-merger environment. This signature of nuclear matter in gravitational waves contains most information in the 2–4 kHz frequency band, which is outside of the most sensitive band of current detectors. We present the design concept and science case for a Neutron Star Extreme Matter Observatory (NEMO): a gravitational-wave interferometer optimised to study nuclear physics with merging neutron stars. The concept uses high-circulating laser power, quantum squeezing, and a detector topology specifically designed to achieve the high-frequency sensitivity necessary to probe nuclear matter using gravitational waves. Above 1 kHz, the proposed strain sensitivity is comparable to full third-generation detectors at a fraction of the cost. Such sensitivity changes expected event rates for detection of post-merger remnants from approximately one per few decades with two A+ detectors to a few per year and potentially allow for the first gravitational-wave observations of supernovae, isolated neutron stars, and other exotica.
The radiocarbon (14C) calibration curve so far contains annually resolved data only for a short period of time. With accelerator mass spectrometry (AMS) matching the precision of decay counting, it is now possible to efficiently produce large datasets of annual resolution for calibration purposes using small amounts of wood. The radiocarbon intercomparison on single-year tree-ring samples presented here is the first to investigate specifically possible offsets between AMS laboratories at high precision. The results show that AMS laboratories are capable of measuring samples of Holocene age with an accuracy and precision that is comparable or even goes beyond what is possible with decay counting, even though they require a thousand times less wood. It also shows that not all AMS laboratories always produce results that are consistent with their stated uncertainties. The long-term benefits of studies of this kind are more accurate radiocarbon measurements with, in the future, better quantified uncertainties.
Tobacco smoking is a leading cause of preventable death and disease worldwide. Adults with mental ill-health smoke tobacco at substantially higher rates than other adults, with public health approaches effective in the population overall having less impact on those with mental ill-health. However, less is known about the tobacco smoking behaviours, attitudes and knowledge of young people with mental ill-health, despite this being the peak period of onset for both mental illness and cigarette smoking.
Young people attending a youth mental health centre (providing both primary and specialist care) in Melbourne, Australia were approached by youth peer researchers and asked to complete a survey about smoking behaviours, attitudes and knowledge. We examined smoking and associated attitudes in the sample overall, and as a function of the services accessed.
In total, 114 young people completed the survey, with 56.3% reporting lifetime cigarette smoking, 42.0% smoking in the last 12 months and 28.6% in the past week. Of current regular smokers, 75.0% acknowledged they should quit in the future; however, only 23.5% planned to do so in the next month, with 44.4% confident that they could quit. Participants lacked knowledge about interactions between tobacco smoking, mental and physical health.
Youth presenting for mental ill-health had high rates of cigarette smoking relative to population rates. Presentation at youth mental health services may represent a critical window for early intervention to reduce the lifetime impacts of cigarette smoking in mental ill-health. Interventions to support smoking cessation in this group are urgently needed.
Inner-city youth suffer a high burden of mental illness and seek health care on an episodic basis (McCreary, 2001).
These youth tend to receive limited support services due to a lack of continuity of care as they move from child to adult services. Other barriers include homelessness and substance use.
The Vancouver Inner City Youth Mental Health Program (ICYMHP) is a psychiatry led initiative to provide psychiatric services and further collaboration between inner-city youth agencies providing care to at risk youth.
To introduce and review a collaborative model of care between psychiatric services and community based organizations.
To review the demographics, presentations and outcomes of youth assessed through the ICYMHP.
A chart review of all clients assessed through the program from its inception (November 2007) to May 2009 (18 months).
Results from clients seen between November 2007 and June 2008 indicate an incidence of psychosis of 40% in men and 21% in women. Mood disorders were the primary diagnosis in 18% of men and 29% of women. Active substance misuse is high (71% of men, cannabis as drug of choice; 54% of women, methamphetamine as drug of choice). Length of stay at Covenant House nearly tripled for those under the care of the ICYMH versus the general shelter population, a positive outcome (21 days versus 9).
Inner-city homeless youth suffer from a high burden of mental illness. A collaborative model of care exists to improve health care quality and delivery to this population.
Lymphopenia is common in adults who have had a Fontan operation although its aetiology and clinical implications remain unknown. Previous work suggests an association between lymphopenia and both liver disease and splenomegaly. The objective of this study was to assess the prevalence of lymphopenia in adults with a Fontan circulation and evaluate its associations with risk factors and clinical outcomes. Using a retrospective cohort study design, we studied 73 adult Fontan patients (age 25.0 ± 8.4 years) who had a complete blood count and abdominal imaging performed. Patients with protein-losing enteropathy were excluded. Clinical data were extracted from hospital records. The mean white blood cell count was 6580 ± 220/ml with a mean lymphocyte count of 1223 ± 508/ml. Lymphopenia, defined as lymphocyte count <1000/ml, was present in 23 (32%) patients. Patients with lymphopenia had a lower total white blood cell count (5556 ± 2517 versus 7136 ± 1924/ml, p = 0.009) and a lower platelet count (162 ± 69 versus 208 ± 69 k/ml, p = 0.008). Lymphopenia was also associated with findings of portal hypertension, including splenomegaly (36 versus 14%, p = 0.04), varices (22 versus 6%, p = 0.04), and ascites (39 versus 14%, p = 0.02). Lymphopenia did not correlate with any cardiac imaging, haemodynamic or exercise testing variables. In conclusion, lymphopenia is common in adult Fontan patients and is associated with markers of portal hypertension. Larger studies are needed to better define the relationship between lymphopenia and clinical outcomes.
Mental disorders are increasingly common among adults in both the developed and developing world and are predicted by the WHO to be the leading cause of disease burden by 2030. Many common physical conditions are more common among people who also have a common mental disorder. This scoping review aims to examine the current literature about the prevention, identification and treatment of physical problems among people with pre-existing mental health disorders in primary care in Europe.
The scoping review framework comprised a five-stage process developed by Arksey & O’Malley (2005). The search process was guided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. Both quantitative and qualitative studies were included, with no restriction on study design.
The initial search identified 299 studies, with a further 28 added from the hand-search (total n = 327) of which 19 were considered relevant to the review research question and included for full analysis. Depression was the mental health condition most commonly studied (nine studies), followed by depression and anxiety (seven studies), with three studies examining any mental disorder. Eleven studies examined the effects of various interventions to address physical and mental comorbidity, with the most commonly studied intervention being collaborative care.
With just 19 studies meeting our criteria for inclusion, there is clearly a paucity of research in this area. Further research is essential in order to understand the pathophysiological mechanisms underlying the association between mental disorders and chronic conditions.
Implantation of bone-anchored hearing devices is performed to improve hearing in patients with chronic suppurative otitis media who cannot wear a conventional hearing aid. The surgical procedure can be safely performed in children aged over five years.
A 15-year-old patient with bilateral chronic suppurative otitis media and conductive hearing loss underwent the procedure to implant a bone-anchored hearing device but was found to have skull thickness of less than 2.5 mm and the procedure was abandoned. A computed tomography scan of the skull was undertaken and a three-dimensional template was reconstructed to identify appropriate thickness of the skull to implant the abutment during a second procedure.
Bone-anchored hearing devices can be implanted by prior imaging and using a template to identify the area of appropriate skull thickness to implant the abutment safely.
Advancements in computer technology have enabled three-dimensional (3D) reconstruction, data-stitching, and manipulation of 3D data obtained on X-ray imaging systems such as micro-computed tomography (μ-CT). Likewise, intuitive evaluation of these 3D datasets can be enhanced by recent advances in virtual reality (VR) hardware and software. Additionally, the generation, viewing, and manipulation of 3D X-ray diffraction datasets, such as pole figures employed for texture analysis, can also benefit from these advanced visualization techniques. We present newly-developed protocols for porting 3D data (as TIFF-stacks) into a Unity gaming software platform so that data may be toured, manipulated, and evaluated within a more-intuitive VR environment through the use of game-like controls and 3D headsets. We demonstrate this capability by rendering μ-CT data of a polymer dogbone test bar at various stages of in situ mechanical strain. An additional experiment is presented showing 3D XRD data collected on an aluminum test block with vias. These 3D XRD data for texture analysis (χ, ϕ, 2θ dimensions) enables the viewer to visually inspect 3D pole figures and detect the presence or absence of in-plane residual macrostrain. These two examples serve to illustrate the benefits of this new methodology for multidimensional analysis.
Laboratory identification of carbapenem-resistant Enterobacteriaceae (CRE) is a key step in controlling its spread. Our survey showed that most Veterans Affairs laboratories follow VA guidelines for initial CRE identification, whereas 55.0% use PCR to confirm carbapenemase production. Most respondents were knowledgeable about CRE guidelines. Barriers included staffing, training, and financial resources.
Adverse pregnancy outcomes including prematurity and low birth weight (LBW) have been associated with life-long chronic disease risk for the infant. Stress during pregnancy increases the risk of adverse pregnancy outcomes. Many studies have reported the incidence of adverse pregnancy outcomes in Indigenous populations and a smaller number of studies have measured rates of stress and depression in these populations. This study sought to examine the potential association between stress during pregnancy and the rate of adverse pregnancy outcomes in Australian Indigenous women residing in rural and remote communities in New South Wales. This study found a higher rate of post-traumatic stress disorder, depression and anxiety symptoms during pregnancy than the general population. There was also a higher incidence of prematurity and LBW deliveries. Unfortunately, missing post-traumatic stress disorder and depressive symptomatology data impeded the examination of associations of interest. This was largely due to the highly sensitive nature of the issues under investigation, and the need to ensure adequate levels of trust between Indigenous women and research staff before disclosure and recording of sensitive research data. We were unable to demonstrate a significant association between the level of stress and the incidence of adverse pregnancy outcomes at this stage. We recommend this longitudinal study continue until complete data sets are available. Future research in this area should ensure prioritization of building trust in participants and overestimating sample size to ensure no undue pressure is placed upon an already stressed participant.
This study investigated the characteristics of subjective memory complaints (SMCs) and their association with current and future cognitive functions.
A cohort of 209 community-dwelling individuals without dementia aged 47–90 years old was recruited for this 3-year study. Participants underwent neuropsychological and clinical assessments annually. Participants were divided into SMCs and non-memory complainers (NMCs) using a single question at baseline and a memory complaints questionnaire following baseline, to evaluate differential patterns of complaints. In addition, comprehensive assessment of memory complaints was undertaken to evaluate whether severity and consistency of complaints differentially predicted cognitive function.
SMC and NMC individuals were significantly different on various features of SMCs. Greater overall severity (but not consistency) of complaints was significantly associated with current and future cognitive functioning.
SMC individuals present distinctive features of memory complaints as compared to NMCs. Further, the severity of complaints was a significant predictor of future cognition. However, SMC did not significantly predict change over time in this sample. These findings warrant further research into the specific features of SMCs that may portend subsequent neuropathological and cognitive changes when screening individuals at increased future risk of dementia.
External auditory canal exostoses are known to occur in patients who engage in cold-water sports. Although the majority of patients with exostosis remain asymptomatic, larger lesions can cause wax impaction, conductive hearing loss and predispose to recurrent otitis externa.
A novel technique is described of using a piezo saw to excise exostoses that are symptomatic. The piezo saw is used to perform various procedures, but its use in removing exostoses has not been described in the literature.
Excision of exostoses of the ear canal using a piezo saw is a safe technique and patients have a speedy recovery. This paper describes a new technique for removing exostoses.
The adenovirus vaccine and benzathine penicillin G (BPG) have been used by the US military to prevent acute respiratory diseases (ARD) in trainees, though these interventions have had documented manufacturing problems. We fit Poisson regression and random forest models (RF) to 26 years of weekly ARD incidence data to explore the impact of the adenovirus vaccine and BPG prophylaxis on respiratory disease burden. Adenovirus vaccine availability was among the most important predictors of ARD in the RF, while BPG was the ninth most important. BPG was a significant protective factor against ARD (incidence rate ratio (IRR) = 0.68; 95% confidence interval (CI) 0.67–0.70), but less so than either the old or new adenovirus vaccine (IRR = 0.39, 95% CI 0.38–0.39 and IRR = 0.11, 95% CI 0.11–0.11), respectively. These results suggest that BPG is moderately predictive of, and significantly protective against ARD, though to a lesser extent than either the old or new adenovirus vaccine.
Childhood obesity rates are higher among Indigenous compared with non-Indigenous Australian children. It has been hypothesized that early-life influences beginning with the intrauterine environment predict the development of obesity in the offspring. The aim of this paper was to assess, in 227 mother–child dyads from the Gomeroi gaaynggal cohort, associations between prematurity, Gestation Related-Optimal Weight (GROW) centiles, maternal adiposity (percentage body fat, visceral fat area), maternal non-fasting plasma glucose levels (measured at mean gestational age of 23.1 weeks) and offspring BMI and adiposity (abdominal circumference, subscapular skinfold thickness) in early childhood (mean age 23.4 months). Maternal non-fasting plasma glucose concentrations were positively associated with infant birth weight (P=0.005) and GROW customized birth weight centiles (P=0.008). There was a significant association between maternal percentage body fat (P=0.02) and visceral fat area (P=0.00) with infant body weight in early childhood. Body mass index (BMI) in early childhood was significantly higher in offspring born preterm compared with those born at term (P=0.03). GROW customized birth weight centiles was significantly associated with body weight (P=0.01), BMI (P=0.007) and abdominal circumference (P=0.039) at early childhood. Our findings suggest that being born preterm, large for gestational age or exposed to an obesogenic intrauterine environment and higher maternal non-fasting plasma glucose concentrations are associated with increased obesity risk in early childhood. Future strategies should aim to reduce the prevalence of overweight/obesity in women of child-bearing age and emphasize the importance of optimal glycemia during pregnancy, particularly in Indigenous women.
Introduction: High fidelity in-situ simulation has been found to detect system deficiencies, equipment failures, and conditions predisposing to medical errors, also known as latent safety threats (LST). What is not well reported is whether these LSTs are effectively managed. As a part of an ongoing quality improvement project, multidisciplinary, in-situ simulations were conducted across emergency departments (ED) in the Edmonton zone with the aim to identify LST and subsequently manage them to improve patient care. Methods: In 2017 simulations were conducted at EDs in the Edmonton Zone (N=10). Following each simulation, a cross sectional, survey based assessment tool, was completed by participants to identify LST. These LST were shared with the site clinical nurse educator and/or site manager and a management plan made. Two to six months follow-up was made to track progress. For reporting, LST were grouped into themes, progress on LST were coded as either resolved, ongoing, or not managed. Results: A total of 112 LST were identified through 18 separate simulations. The most commonly identified LTS were: resuscitation resource required (n 23), lack of staff training (21), equipment not immediately available (20), IT resource required (8), medication not immediately available (6), staff requiring familiarization (5), medication resource required (5), IT issue (4), large equipment needed (4), small equipment needed (4), lack of staff resource (3), medication needed, (3), equipment malfunction (2), Environment cluttered (2), non-appropriate resource removed (2). Site follow-up identified a total of 52 LST that where resolved, and 60 LST that had ongoing work to manage them. No occurrences of LST not being managed were identified. Conclusion: Simulation was used to effectively identify LST. Creating a structured plan and follow up allowed many LST to be resolved and effectively managed. In 2018 simulation will reassess if LST remain.