Fission chamber data acquisition system for neutron flux measurements on the Mega-Amp Spherical Tokamak Upgrade

Neutron flux measurements are important in fusion devices for both safety requirements and physics studies. A new system has been built for the Mega-Amp Spherical Tokamak Upgrade (MAST Upgrade) that provides neutron count, DC, and Campbell mode measurements for a 1 µs period at 1 MHz. The acquisition system uses a Red Pitaya board to sample current from two fission chambers mounted on the side of the MAST-U vessel. The system-on-chip design of the Zynq-7020 on the Red Pitaya also allows a web server implementation using Flask for data retrieval and diagnostic configuration over the MAST Upgrade network.

Multidimensional, High Precision Measurements of Beam Single Spin Asymmetries in Semi-inclusive π^{+} Electroproduction off Protons in the Valence Region

High precision measurements of the polarized electron beam-spin asymmetry in semi-inclusive deep inelastic scattering (SIDIS) from the proton have been performed using a 10.6 GeV incident electron beam and the CLAS12 spectrometer at Jefferson Lab. We report here a high precision multidimensional study of single π^{+} SIDIS data over a large kinematic range in Bjorken x, fractional energy, and transverse momentum of the hadron as well as photon virtualities Q^{2} ranging from 1-7  GeV^{2}. In particular, the structure function ratio F_{LU}^{sinϕ}/F_{UU} has been determined, where F_{LU}^{sinϕ} is a twist-3 quantity that can reveal novel aspects of emergent hadron mass and quark-gluon correlations within the nucleon. The data's impact on the evolving understanding of the underlying reaction mechanisms and their kinematic variation is explored using theoretical models for the different contributing transverse momentum dependent parton distribution functions.

Evolution of 18F-FDG-PET/CT findings in patients following COVID-19 pneumonia: An Initial Investigation

The aim of this study was to assess the temporal evolution of pulmonary ¹⁸F-FDG uptake in patients with coronavirus disease 2019 (COVID-19) and post–COVID-19 lung disease (PCLD). Methods: Using our hospital’s clinical electronic records, we retrospectively identified 23 acute COVID-19, 18 PCLD, and 9 completely recovered ¹⁸F-FDG PET/CT patients during the 2 peaks of the U.K. pandemic. Pulmonary ¹⁸F-FDG uptake was measured as a lung target-to-background ratio (TBR_lung = SUV_max/SUV_min) and compared with temporal stage. Results: In acute COVID-19, less than 3 wk after infection, TBR_lung was strongly correlated with time after infection (r_s = 0.81, P < 0.001) and was significantly higher in the late stage than in the early stage (P = 0.001). In PCLD, TBR_lung was lower in patients treated with high-dose steroids (P = 0.003) and in asymptomatic patients (P < 0.001). Conclusion: Pulmonary ¹⁸F-FDG uptake in COVID-19 increases with time after infection. In PCLD, pulmonary ¹⁸F-FDG uptake rises despite viral clearance, suggesting ongoing inflammation. There was lower pulmonary ¹⁸F-FDG uptake in PCLD patients treated with steroids.

Observation of Beam Spin Asymmetries in the Process ep→e^{'}π^{+}π^{-}X with CLAS12

The observation of beam spin asymmetries in two-pion production in semi-inclusive deep inelastic scattering off an unpolarized proton target is reported. The data presented here were taken in the fall of 2018 with the CLAS12 spectrometer using a 10.6 GeV longitudinally spin-polarized electron beam delivered by CEBAF at JLab. The measured asymmetries provide the first opportunity to extract the parton distribution function e(x), which provides information about the interaction between gluons and quarks, in a collinear framework that offers cleaner access than previous measurements. The asymmetries also constitute the first ever signal sensitive to the helicity-dependent two-pion fragmentation function G_{1}^{⊥}. A clear sign change is observed around the ρ mass that appears in model calculations and is indicative of the dependence of the produced pions on the helicity of the fragmenting quark.

Genotype and defects in microtubule-based motility correlate with clinical severity in KIF1A-associated neurological disorder

KIF1A-associated neurological disorder (KAND) encompasses a group of rare neurodegenerative conditions caused by variants in KIF1A,a gene that encodes an anterograde neuronal microtubule (MT) motor protein. Here we characterize the natural history of KAND in 117 individuals using a combination of caregiver or self-reported medical history, a standardized measure of adaptive behavior, clinical records, and neuropathology. We developed a heuristic severity score using a weighted sum of common symptoms to assess disease severity. Focusing on 100 individuals, we compared the average clinical severity score for each variant with in silico predictions of deleteriousness and location in the protein. We found increased severity is strongly associated with variants occurring in protein regions involved with ATP and MT binding: the P loop, switch I, and switch II. For a subset of variants, we generated recombinant proteins, which we used to assess transport in vivo by assessing neurite tip accumulation and to assess MT binding, motor velocity, and processivity using total internal reflection fluorescence microscopy. We find all modeled variants result in defects in protein transport, and we describe three classes of protein dysfunction: reduced MT binding, reduced velocity and processivity, and increased non-motile rigor MT binding. The rigor phenotype is consistently associated with the most severe clinical phenotype, while reduced MT binding is associated with milder clinical phenotypes. Our findings suggest the clinical phenotypic heterogeneity in KAND likely reflects and parallels diverse molecular phenotypes. We propose a different way to describe KAND subtypes to better capture the breadth of disease severity.

A mathematical-descriptor of tumor-mesoscopic-structure from computed-tomography images annotates prognostic- and molecular-phenotypes of epithelial ovarian cancer

The five-year survival rate of epithelial ovarian cancer (EOC) is approximately 35-40% despite maximal treatment efforts, highlighting a need for stratification biomarkers for personalized treatment. Here we extract 657 quantitative mathematical descriptors from the preoperative CT images of 364 EOC patients at their initial presentation. Using machine learning, we derive a non-invasive summary-statistic of the primary ovarian tumor based on 4 descriptors, which we name "Radiomic Prognostic Vector" (RPV). RPV reliably identifies the 5% of patients with median overall survival less than 2 years, significantly improves established prognostic methods, and is validated in two independent, multi-center cohorts. Furthermore, genetic, transcriptomic and proteomic analysis from two independent datasets elucidate that stromal phenotype and DNA damage response pathways are activated in RPV-stratified tumors. RPV and its associated analysis platform could be exploited to guide personalized therapy of EOC and is potentially transferrable to other cancer types.

Discovery of pre-therapy 2-deoxy-2-18F-fluoro-D-glucose positron emission tomography-based radiomics classifiers of survival outcome in non-small-cell lung cancer patients

PURPOSE

The aim of this multi-center study was to discover and validate radiomics classifiers as image-derived biomarkers for risk stratification of non-small-cell lung cancer (NSCLC).

PATIENTS AND METHODS

Pre-therapy PET scans from a total of 358 Stage I-III NSCLC patients scheduled for radiotherapy/chemo-radiotherapy acquired between October 2008 and December 2013 were included in this seven-institution study. A semi-automatic threshold method was used to segment the primary tumors. Radiomics predictive classifiers were derived from a training set of 133 scans using TexLAB v2. Least absolute shrinkage and selection operator (LASSO) regression analysis was used for data dimension reduction and radiomics feature vector (FV) discovery. Multivariable analysis was performed to establish the relationship between FV, stage and overall survival (OS). Performance of the optimal FV was tested in an independent validation set of 204 patients, and a further independent set of 21 (TESTI) patients.

RESULTS

Of 358 patients, 249 died within the follow-up period [median 22 (range 0-85) months]. From each primary tumor, 665 three-dimensional radiomics features from each of seven gray levels were extracted. The most predictive feature vector discovered (FVX) was independent of known prognostic factors, such as stage and tumor volume, and of interest to multi-center studies, invariant to the type of PET/CT manufacturer. Using the median cut-off, FVX predicted a 14-month survival difference in the validation cohort (N = 204, p = 0.00465; HR = 1.61, 95% CI 1.16-2.24). In the TESTI cohort, a smaller cohort that presented with unusually poor survival of stage I cancers, FVX correctly indicated a lack of survival difference (N = 21, p = 0.501). In contrast to the radiomics classifier, clinically routine PET variables including SUVmax, SUVmean and SUVpeak lacked any prognostic information.

CONCLUSION

PET-based radiomics classifiers derived from routine pre-treatment imaging possess intrinsic prognostic information for risk stratification of NSCLC patients to radiotherapy/chemo-radiotherapy.

Clinical translation of [18F]ICMT-11 for measuring chemotherapy-induced caspase 3/7 activation in breast and lung cancer

BACKGROUND

Effective anticancer therapy is thought to involve induction of tumour cell death through apoptosis and/or necrosis. [18F]ICMT-11, an isatin sulfonamide caspase-3/7-specific radiotracer, has been developed for PET imaging and shown to have favourable dosimetry, safety, and biodistribution. We report the translation of [18F]ICMT-11 PET to measure chemotherapy-induced caspase-3/7 activation in breast and lung cancer patients receiving first-line therapy.

RESULTS

Breast tumour SUVmax of [18F]ICMT-11 was low at baseline and unchanged following therapy. Measurement of M30/M60 cytokeratin-18 cleavage products showed that therapy was predominantly not apoptosis in nature. While increases in caspase-3 staining on breast histology were seen, post-treatment caspase-3 positivity values were only approximately 1%; this low level of caspase-3 could have limited sensitive detection by [18F]ICMT-11-PET. Fourteen out of 15 breast cancer patients responded to first-line chemotherapy (complete or partial response); one patient had stable disease. Four patients showed increases in regions of high tumour [18F]ICMT-11 intensity on voxel-wise analysis of tumour data (classed as PADS); response was not exclusive to patients with this phenotype. In patients with lung cancer, multi-parametric [18F]ICMT-11 PET and MRI (diffusion-weighted- and dynamic contrast enhanced-MRI) showed that PET changes were concordant with cell death in the absence of significant perfusion changes.

CONCLUSION

This study highlights the potential use of [18F]ICMT-11 PET as a promising candidate for non-invasive imaging of caspase3/7 activation, and the difficulties encountered in assessing early-treatment responses. We summarize that tumour response could occur in the absence of predominant chemotherapy-induced caspase-3/7 activation measured non-invasively across entire tumour lesions in patients with breast and lung cancer.

Association of water quality with soil-transmitted helminthiasis and diarrhea in Nueva Santa Rosa, Guatemala, 2010

Improved water quality reduces diarrhea, but the impact of improved water quality on Ascaris and Trichuris, soil-transmitted helminths (STH) conveyed by the fecal-oral route, is less well described. To assess water quality associations with diarrhea and STH, we conducted a cross-sectional survey in households of south-eastern Guatemala. Diarrhea was self-reported in the past week and month. STH was diagnosed by stool testing using a fecal parasite concentrator method. We explored associations between Escherichia coli-positive source water (water quality) and disease outcomes using survey logistic regression models. Overall, 732 persons lived in 167 households where water was tested. Of these, 79.4% (581/732) had E. coli-positive water, 7.9% (58/732) had diarrhea within the week, 14.1% (103/732) had diarrhea within the month, and 6.6% (36/545) tested positive for Ascaris or Trichuris, including 1% (6/536) who also reported diarrhea. Univariable analysis found a statistically significant association between water quality and STH (odds ratio [OR] = 5.1, 95% confidence interval [CI] = 1.1-24.5) but no association between water quality and diarrhea. Waterborne transmission and effects of water treatment on STH prevalence should be investigated further. If a causal relationship is found, practices such as household water treatment including filtration might be useful adjuncts to sanitation, hygiene, and deworming in STH control programs.

Resilience theory incorporated into urban wastewater systems management. State of the art

Government bodies, utilities, practitioners, and researchers have growing interest in the incorporation of resilience into wastewater management. Since resilience is a multidisciplinary term, it is important to review what has been achieved in the wastewater sector, and describe the future research directions for the forthcoming years. This work presents a critical review of studies that deal with resilience in the wastewater treatment sector, with a special focus on understanding how they addressed the key elements for assessing resilience, such as stressors, system properties, metrics and interventions to increase resilience. The results showed that only 17 peer-reviewed papers and 6 relevant reports, a small subset of the work in wastewater research, directly addressed resilience. The lack of consensus in the definition of resilience, and the elements of a resilience assessment, is hindering the implementation of resilience in wastewater management. To date, no framework for resilience assessment is complete, comprehensive or directly applicable to practitioners; current examples are lacking key elements (e.g. a comprehensive study of stressors, properties and metrics, examples of cases study, ability to benchmark interventions or connectivity with broader frameworks). Furthermore, resilience is seen as an additional cost or extra effort, instead of a means to overcome project uncertainty that could unlock new opportunities for investment.

Cardiology-cardiothoracic subspeciality training in South Africa: a position paper of the South Africa Heart Association

Over the past decades, South Africa has undergone rapid demographic changes, which have led to marked increases in specific cardiac disease categories, such as rheumatic heart disease (now predominantly presenting in young adults with advanced and symptomatic disease) and coronary artery disease (with rapidly increasing prevalence in middle age). The lack of screening facilities, delayed diagnosis and inadequate care at primary, secondary and tertiary levels have led to a large burden of patients with heart failure. This leads to suffering of the patients and substantial costs to society and the healthcare system.

In this position paper, the South African Heart Association (SA Heart) National Council members have summarised the current state of cardiology, cardiothoracic surgery and paediatric cardiology reigning in South Africa. Our report demonstrates that there has been minimal change in the number of successfully qualified specialists over the last decade and, therefore, a de facto decline per capita. We summarise the major gaps in training and possible interventions to transform the healthcare system, dealing with the colliding epidemic of communicable disease and the rapidly expanding epidemic of non-communicable disease, including cardiac disease.

Response to sunitinib (Sutent) in chemotherapy refractory clear cell ovarian cancer

•Case describes a response to sunitinib in clear cell ovarian cancer.•Discussion of unique molecular characteristics of clear cell ovarian cancers•Practical points regarding dosing and toxicity when using sunitinib discussed.

The relationship between motor proficiency and mental health outcomes in young adults: A test of the Environmental Stress Hypothesis

Growing evidence has highlighted the importance of motor proficiency in relation to psychosocial outcomes including self-perceived competence in various domains, perceived social support, and emotional areas such as anxiety and depression. The Environmental Stress Hypothesis-elaborated (Cairney, Rigoli, & Piek, 2013) is a proposed theoretical framework for understanding these relationships and recent studies have begun examining parts of this model using child and adolescent populations. However, the extent to which the relationships between these areas exist, persist or change during early adulthood is currently unclear. The current study aimed to investigate the Environmental Stress Hypothesis in a sample of 95 young adults aged 18-30years and examined the mediating role of physical self-worth and perceived social support in the relationship between motor proficiency and internalising symptoms. The McCarron Assessment of Neuromuscular Development (McCarron, 1997) was used to assess motor proficiency, the Depression Anxiety Stress Scale (Lovibond & Lovibond, 1995) provided a measure of internalising symptoms, and the Physical Self Perceptions Profile (Fox & Corbin, 1989) and the Multidimensional Scale of Perceived Social Support (Zimet, Dahlem, Zimet, & Farley, 1988) were used to investigate the possible mediating role of physical self-worth and perceived social support respectively. Potential confounding variables such as age, gender and BMI were also considered in the analysis. Structural Equation Modelling revealed that perceived social support mediated the relationship between motor proficiency and internalising symptoms, whereas, the mediating role of physical self-worth was non-significant. The current results provide support for part of the model pathways as described in the Environmental Stress Hypothesis and suggest an important relationship between motor proficiency and psychosocial outcomes in young adults. Specifically, the results support previous literature regarding the significant role of perceived social support for mental well-being and suggest that an intervention that considers social support may also indirectly influence mental health outcomes in young adults who experience movement difficulties.

Fundamental problems with the cooperative breeding hypothesis. A reply to Burkart & van Schaik

The cooperative breeding hypothesis (CBH) states that cooperative breeding, a social system in which group members help to rear offspring that are not their own, has important socio‐cognitive consequences. Thornton & McAuliffe (2015; henceforth T&M) critiqued this idea on both conceptual and empirical grounds, arguing that there is no reason to predict that cooperative breeding should favour the evolution of enhanced social cognition or larger brains, nor any clear evidence that it does. In response to this critique, Burkart & van Schaik (2016 henceforth B&vS) attempt to clarify the causal logic of the CBH, revisit the data and raise the possibility that the hypothesis may only apply to primates. They concede that cooperative breeding is unlikely to generate selection pressures for enhanced socio‐cognitive abilities, but argue instead that the CBH operates purely through cooperative breeding reducing social or energetic constraints. Here, we argue that this revised hypothesis is also untenable because: (1) it cannot explain why resources so released would be allocated to cognitive traits per se rather than any other fitness‐related traits, (2) key assumptions are inconsistent with available evidence and (3) ambiguity regarding the predictions leaves it unclear what evidence would be required to falsify it. Ultimately, the absence of any compelling evidence that cooperative breeding is associated with elevated cognitive ability or large brains (indeed data suggest the opposite is true in non‐human primates) also casts doubt on the capacity of the CBH to explain variation in cognitive traits.

Population Density, Poor Sanitation, and Enteric Infections in Nueva Santa Rosa, Guatemala

Poor sanitation could pose greater risk for enteric pathogen transmission at higher human population densities because of greater potential for pathogens to infect new hosts through environmentally mediated and person-to-person transmission. We hypothesized that incidence and prevalence of diarrhea, enteric protozoans, and soil-transmitted helminth infections would be higher in high-population-density areas compared with low-population-density areas, and that poor sanitation would pose greater risk for these enteric infections at high density compared with low density. We tested our hypotheses using 6 years of clinic-based diarrhea surveillance (2007–2013) including 4,360 geolocated diarrhea cases tested for 13 pathogens and a 2010 cross-sectional survey that measured environmental exposures from 204 households (920 people) and tested 701 stool specimens for enteric parasites. We found that population density was not a key determinant of enteric infection nor a strong effect modifier of risk posed by poor household sanitation in this setting.