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Music is a tool physical education (PE) teachers can use to help motivate students to greater physical activity (PA) rates during class activities. Music research in the PE context has found music to increase PA rates in the junior high school context (Brewer et al., 2016), that music increases the enjoyment of the PE experience for students (Barney et al., 2016) and can serve as a distraction during certain workouts (Higginson et al., 2019). This study aimed to examine the effects of music on physical activity rates (steps taken and time in activity) via pedometers of junior high school students in basketball gameplay. For this study, 270 junior high school students (157 males and 113 females) from eight intact seventh-, eighth-, and ninth-grade classes participated. The male and female participants attended different schools. Generally, it was found that the female participants were more active than their male counterparts when music was playing. These results and others illustrate music's effect on junior high school student PA rates., Introduction Music can be a powerful tool for increasing a person's physical activity. For example, college students' who listened to their personal music devices perceived that they worked harder and [...]

DNA collections are a valuable type of Natural Science collection, enabling the validation of past research, serving as a source for new genomic studies and supporting ex situ conservation. The DiSSCo Flanders DNA collection working group, aiming to advance and "unlock" their DNA collections, identified the need for: 1) actively sharing best practices regarding the management of DNA collections; and 2) providing guidance on how to bring theory into practice. By combining best practice examples from within the working group with available literature and brainstorming ideas, the working group co-created two outputs, referred to as: the "Challenges" and the "Key". The Challenges are a list of obstacles to DNA collection management, which shape the structure of the linked Key and can also be used to spark discussion amongst stakeholders. The Key is a tool that guides users through the maturation process of their DNA collection in a standardised way. It stimulates holistic growth, breaks down the needed work into manageable steps and helps to decide priorities during the process. Furthermore, the Key facilitates communication with both internal stakeholders and external DNA collection managers. The Key distinguishes itself from other self-assessment tools in several ways: it includes (re)investigation of the collection’s purpose and context; it is specialised for DNA collections; it delivers concrete goals linked to relevant information and shared experience; and it is inclusive, targeting all Natural Science DNA collections, regardless of their context or size.

Study objective: Hypertrophic cardiomyopathy (HCM) is the most common genetic myocardial disorder increasingly characterized by concomitant metabolic syndrome. Cardiac rehabilitation (CR) has been shown to improve metabolic parameters in populations with heart failure and myocardial infarction. However, there is a paucity of data on the impact of CR in the HCM population with metabolic syndrome. We designed the REHAB-HCM study to explore the feasibility, safety, and efficacy of CR in HCM patients with metabolic syndrome. Design: Prospective observation cohort study. Setting: A multi-disciplinary HCM clinic and Multidisciplinary Exercise-based Cardiac Rehabilitation program. Participants: Patients aged 18–80 years old diagnosed with HCM and metabolic syndrome, defined by the American Heart Association and American College of Cardiology guidelines, and the National Cholesterol Education Adult Treatment Panel III (NCEP-ATP III) criteria. Intervention: A structured 3-month CR program with 6 months extended follow-up of physical activity levels. Main outcome measures: Feasibility (e.g., attendance), safety (e.g., major adverse events and exercise-related harms), and efficacy pertaining to long term improvements in physical activity levels, metabolic health, cardiorespiratory fitness, quality of life, and systemic and cellular markers of inflammation. Conclusion: This prospective cohort study will address an important knowledge gap by evaluating the effect of an organized CR program in HCM patients and metabolic syndrome. It is anticipated that exercise and CR will be feasible and beneficial for this complex patient population without significant exercise-related harms.

Summary: We present a protocol to achieve a higher depth of long-read sequencing of region(s) of interest in potato cyst nematodes without amplification using a Cas9-based Nanopore enrichment approach. We describe steps for designing high-fidelity guide RNAs to be used with Cas9 nuclease, extracting high-molecular-weight DNA from the nematodes, and dephosphorylating genomic DNA ends. We then detail procedures for using Cas9-guide RNA complex to make targeted cleavage of the region of interest followed by a Nanopore library preparation.For complete details on the use and execution of this protocol, please refer to Sonawala et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Background Using reports of randomised trials of smoking cessation interventions as a test case, this study aimed to develop and evaluate machine learning (ML) algorithms for extracting information from study reports and predicting outcomes as part of the Human Behaviour-Change Project. It is the first of two linked papers, with the second paper reporting on further development of a prediction system. Methods Researchers manually annotated 70 items of information (‘entities’) in 512 reports of randomised trials of smoking cessation interventions covering intervention content and delivery, population, setting, outcome and study methodology using the Behaviour Change Intervention Ontology. These entities were used to train ML algorithms to extract the information automatically. The information extraction ML algorithm involved a named-entity recognition system using the ‘FLAIR’ framework. The manually annotated intervention, population, setting and study entities were used to develop a deep-learning algorithm using multiple layers of long-short-term-memory (LSTM) components to predict smoking cessation outcomes. Results The F1 evaluation score, derived from the false positive and false negative rates (range 0–1), for the information extraction algorithm averaged 0.42 across different types of entity (SD=0.22, range 0.05–0.88) compared with an average human annotator’s score of 0.75 (SD=0.15, range 0.38–1.00). The algorithm for assigning entities to study arms (e.g., intervention or control) was not successful. This initial ML outcome prediction algorithm did not outperform prediction based just on the mean outcome value or a linear regression model. Conclusions While some success was achieved in using ML to extract information from reports of randomised trials of smoking cessation interventions, we identified major challenges that could be addressed by greater standardisation in the way that studies are reported. Outcome prediction from smoking cessation studies may benefit from development of novel algorithms, e.g., using ontological information to inform ML (as reported in the linked paper 1 ).

Summary: Background: Survival among people with HIV (PWH) has vastly improved globally over the last few decades but remains lower than among the general population. We aimed to estimate time trends of survival among PWH and their families from 1995 to 2021. Methods: We conducted a registry-based, nationwide, population-based, matched cohort study. We included all Danish-born PWH from 1995 to 2021 who had been on antiretroviral therapy for 90 days, did not report intravenous drug use, and were not co-infected with hepatitis C (n = 4168). We matched population controls from the general population 10:1 to PWH by date of birth and sex (n = 41,680). For family cohorts, we identified siblings, mothers, and fathers of PWH and population controls. From Kaplan–Meier tables with age as time scale, we estimated survival from age 25. We compared PWH with population controls and families of PWH with families of population controls to calculate mortality rate ratios adjusted for sex, age, comorbidities, and education (aMRR). Findings: The median age of death among PWH increased from 27.5 years in 1995–1997 to 73.9 years (2010–2014), but thereafter survival increased only marginally. From 2015 to 2021, mortality was increased among PWH (aMRR 1.87 (95% CI: 1.65–2.11)) and siblings (aMRR: 1.25 (95% CI: 1.07–1.47)), mothers (aMRR: 1.30 (95% CI: 1.17–1.43)), and fathers (aMRR: 1.15 (95% CI: 1.03–1.29)) of PWH compared to their respective control cohorts. Mortality among siblings of PWH who reported heterosexual route of HIV transmission (aMRR: 1.51 (95% CI: 1.16–1.96)) was higher than for siblings of PWH who reported men who have sex with men as route of HIV transmission (aMRR 1.19 (95% CI: 0.98–1.46)). Interpretation: Survival among PWH improved substantially until 2010, after which it increased only marginally. This may partly be due to social and behavioural factors as PWH families also had higher mortality. Funding: Preben and Anna Simonsen’s Foundation and Independent Research Fund Denmark.

Plant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode. To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematode Heterodera schachtii at three key life-stages. We define 717 effector gene loci: 269 "known" high-confidence homologs of plant-parasitic nematode effectors, and 448 "novel" effectors with high gland cell expression. In doing so we define the most comprehensive "effectorome" of a plant-parasitic nematode to date. Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection.

Abstract Pulmonary arterial hypertension affects females more frequently than males, and there are known sex‐related differences in the lungs. However, normal sex‐related differences in pulmonary vascular structure remain incompletely described. We aimed to contrast computed tomography‐derived pulmonary vascular volume and its distribution within the lungs of healthy adult females and males. From the CanCOLD Study, we retrospectively identified healthy never‐smokers. We analyzed full‐inspiration computed tomography images, using vessel and airway segmentation to generate pulmonary vessel volume, vessel counts, and airway counts. Vessels were classified by cross‐sectional area >10, 5–10, and 10 mm2 (14 ± 8 vs. 27 ± 9 mL), vessel volume 5–10 mm2 (35 ± 11 vs. 55 ± 10 mL), and vessel volume 10 mm2 (11 ± 4 vs. 16 ± 4%, p

Singularly perturbed systems are a class of mathematical systems that are not well approximated by their limits and can be used to model plants with multiple fast and slow states. Multiple-timescale systems are very common in engineering applications, but adaptive control can be sensitive to timescale effects. Recently a method called [K]control of Adaptive Multiple-timescale Systems (KAMS) has shown improved performance and increased robustness for singularly perturbed systems, but it has only been studied on systems using adaptive control for the slow states. This article extends KAMS to the general case when adaptive control is used to stabilize both the slow and fast states simultaneously. This causes complex interactions between the fast state reference model and the manifold to which the fast states converge. It is proven that under certain conditions the system still converges to the reference model despite these complex interactions. This method is demonstrated on a nonlinear, nonstandard, numerical example.

Plant-parasitic nematodes are a major threat to crop production in all agricultural systems. The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages. Analysis of the hologenome of the plant-nematode infection site identified metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that a highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is required for full pathogenicity. Knockout of either plant-encoded or now nematode-encoded steps in the pathway significantly reduces parasitic success. Our experiments establish a reference for cyst nematodes, further our understanding of the evolution of plant-parasitism by nematodes, and show that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find nematode susceptibility genes. The approach identifies genome-editing-amenable targets for future development of nematode-resistant crops.

Reviewing complex interventions is challenging because they include many elements that can interact dynamically in a nonlinear manner. A systems perspective offers a way of thinking to help understand complex issues, but its application in evidence synthesis is not established. The aim of this project was to understand how and why systems perspectives have been applied in evidence synthesis. A methodological mapping review was conducted to identify papers using a systems perspective in evidence synthesis. A search was conducted in seven bibliographic databases and three search engines. A total of 101 papers (representing 98 reviews) met the eligibility criteria. Two categories of reviews were identified: (1) reviews using a "systems lens" to frame the topic, generate hypotheses, select studies, and guide the analysis and interpretation of findings (n = 76) and (2) reviews using systems methods to develop a systems model (n = 22). Several methods (e.g., systems dynamic modeling, soft systems approach) were identified, and they were used to identify, rank and select elements, analyze interactions, develop models, and forecast needs. The main reasons for using a systems perspective were to address complexity, view the problem as a whole, and understand the interrelationships between the elements. Several challenges for capturing the true nature and complexity of a problem were raised when performing these methods. This review is a useful starting point when designing evidence synthesis of complex interventions. It identifies different opportunities for applying a systems perspective in evidence synthesis, and highlights both commonplace and less familiar methods.

Here I offer a challenge to some of the theoretical truisms that have developed concerning gift exchange, which has been a topic of scholarly debate for almost a century. Much discussion has focussed on how giving creates obligations and increases the power of the giver. Taking the case of the Lelet of New Ireland, Papua New Guinea, 1 examine how people use magic to usurp the agency of the giver, thus forcing them to give through 'coercive exchange'. Magic, I argue, has the capacity to upend how obligation is understood to operate. People give, not because of the customary social obligation, but because magic has been used to extract their wealth. Keywords: agency, exchange, gift giving, magic, Papua New Guinea., INTRODUCTION Gift exchange has been a key feature of anthropological discourse for almost a century, ever since Mauss (1969 [1925]) published The Gift, a work which has acquired many of [...]

Abstract The current study tested whether the reported lower wellbeing of parents after preterm birth, relative to term birth, is a continuation of a pre-existing difference before pregnancy. Parents from Germany (the German Socio-Economic Panel Study, N = 10,649) and the United Kingdom (British Household Panel Study and Understanding Society, N = 11,012) reported their new-born’s birthweight and gestational age, subsequently categorised as very preterm or very low birthweight (VP/VLBW,

Abstract Consumer purchase data (CPD) is a promising instrument to assess the impact of purchases on health, but is limited by the need for manual scanning, a lack of access to data from multiple retailers, and limited information on product data and health outcomes. Here we describe the My Purchases cohort, a web-app enabled, prospective collection of CPD, covering several large retail chains in Denmark, that enables linkage to health outcomes. The cohort included 459 participants as of July 03, 2023. Up to eight years of CPD have been collected, with 2,225,010 products purchased, comprising 223,440 unique products. We matched 88.5% of all products by product name or item number to one generic food database and three product databases. Combined, the databases enable analysis of key exposures such as nutrients, ingredients, or additives. We found that increasing the number of retailers that provide CPD for each consumer improved the stability of individual CPD profiles and when we compared kilojoule information from generic and specific product matches, we found a median modified relative difference of 0.23. Combined with extensive product databases and health outcomes, CPD could provide the basis for extensive investigations of how what we buy affects our health.

Abstract Background Plant-parasitic nematodes compromise the agriculture of a wide variety of the most common crops worldwide. Obtaining information on the fundamental biology of these organisms and how they infect the plant has been restricted by the ability to visualize intact nematodes using small molecule stains, antibodies, or in situ hybridization. Consequently, there is limited information available about the internal composition of the nematodes or the biology of the effector molecules they use to reprogram their host plant. Results We present the Sperling prep - a whole mount method for nematode preparation that enables staining with small molecules, antibodies, or in situ hybridization chain reaction. This method does not require specialized apparatus and utilizes typical laboratory equipment and materials. By dissociating the strong cuticle and interior muscle layers, we enabled entry of the small molecule stains into the tissue. After permeabilization, small molecule stains can be used to visualize the nuclei with the DNA stain DAPI and the internal structures of the digestive tract and longitudinal musculature with the filamentous actin stain phalloidin. The permeabilization even allows entry of larger antibodies, albeit with lower efficiency. Finally, this method works exceptionally well with in situ HCR. Using this method, we have visualized effector transcripts specific to the dorsal gland and the subventral grand of the sugar beet cyst nematode, Heterodera schachtii, multiplexed in the same nematode. Conclusion We were able to visualize the internal structures of the nematode as well as key effector transcripts that are used during plant infection and parasitism. Therefore, this method provides an important toolkit for studying the biology of plant-parasitic nematodes.

Purpose The Health, Food, Purchases and Lifestyle (SMIL) cohort is a prospective open Danish cohort that collects electronic consumer purchase data, which can be linked to Danish nationwide administrative health and social registries. This paper provides an overview of the cohort’s baseline characteristics and marginal differences in the monetary percentage spent on food groups by sex, age and hour of the day.Participants As of 31 December 2022, the cohort included 11 214 users of a smartphone-based receipt collection application who consented to share their unique identification number for linkage to registries in Denmark. In 2022, the composition of the cohort was as follows: 62% were men while 24% were aged 45–55. The cohort had a median of 63 (IQR 26–116) unique shopping trips. The cohort included participants with a range of health statuses. Notably, 21% of participants had a history of cardiovascular disease and 8% had diabetes before donating receipts.Findings to date The feasibility of translating consumer purchase data to operationalisable food groups and merging with registers has been demonstrated. We further demonstrated differences in marginal distributions which revealed disparities in the amount of money spent on various food groups by sex and age, as well as systematic variations by the hour of the day. For example, men under 30 spent 8.2% of their total reported expenditure on sugary drinks, while women under 30 spent 6.5%, men over 30 spent 4.3% and women over 30 spent 3.9%.Future plans The SMIL cohort is characterised by its dynamic, continuously updated database, offering an opportunity to explore the relationship between diet and disease without the limitations of self-reported data. Currently encompassing data from 2018 to 2022, data collection is set to continue. We expect data collection to continue for many years and we are taking several initiatives to increase the cohort.

ABSTRACT Many pathogenic Gram-negative bacteria use repeats-in-toxin adhesins for colonization and biofilm formation. In the cholera agent Vibrio cholerae, flagellar-regulated hemagglutinin A (FrhA) enables these functions. Using bioinformatic analysis, a sugar-binding domain was identified in FrhA adjacent to a domain of unknown function. AlphaFold2 indicated the boundaries of both domains to be slightly shorter than previously predicted and assisted in the recognition of the unknown domain as a split immunoglobulin-like fold that can assist in projecting the sugar-binding domain toward its target. The AlphaFold2-predicted structure is in excellent agreement with the molecular envelope obtained from small-angle X-ray scattering analysis of a recombinant construct spanning the sugar-binding and unknown domains. This two-domain construct was probed by glycan micro-array screening and showed binding to mammalian fucosylated glycans, some of which are characteristic erythrocyte markers and intestinal cell epitopes. Isothermal titration calorimetry further showed the construct-bound l-fucose with a Kd of 21 µM. Strikingly, this recombinant protein construct bound and lysed erythrocytes in a concentration-dependent manner, and its hemolytic activity was blocked by the addition of l-fucose. A protein ortholog construct from Aeromonas veronii was also produced and showed a similar glycan-binding pattern, binding affinity, erythrocyte-binding, and hemolytic activities. As demonstrated here with Hep-2 cells, fucose-based inhibitors of this sugar-binding domain can potentially be developed to block colonization by V. cholerae and other pathogenic bacteria that share this adhesin domain.IMPORTANCEThe bacterium, Vibrio cholerae, which causes cholera, uses an adhesion protein to stick to human cells and begin the infection process. One part of this adhesin protein binds to a particular sugar, fucose, on the surface of the target cells. This binding can lead to colonization and killing of the cells by the bacteria. Adding l-fucose to the bacteria before they bind to the human cells can prevent attachment and has promise as a preventative drug to protect against cholera.

Background and aims Hypertension is a leading risk factor for cardiovascular disease. Electronic health records (EHRs) are routinely collected throughout a person’s care, recording all aspects of health status, including current and past conditions, prescriptions and test results. EHRs can be used for epidemiological research. However, there are nuances in the way conditions are recorded using clinical coding; it is important to understand the methods which have been applied to define exposures, covariates and outcomes to enable interpretation of study findings. This study aimed to identify codelists used to define hypertension in studies that use EHRs and generate recommended codelists to support reproducibility and consistency.Eligibility criteria Studies included populations with hypertension defined within an EHR between January 2010 and August 2023 and were systematically identified using MEDLINE and Embase. A summary of the most frequently used sources and codes is described. Due to an absence of Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) codelists in the literature, a recommended SNOMED CT codelist was developed to aid consistency and standardisation of hypertension research using EHRs.Findings 375 manuscripts met the study criteria and were eligible for inclusion, and 112 (29.9%) reported codelists. The International Classification of Diseases (ICD) was the most frequently used clinical terminology, 59 manuscripts provided ICD 9 codelists (53%) and 58 included ICD 10 codelists (52%). Informed by commonly used ICD and Read codes, usage recommendations were made. We derived SNOMED CT codelists informed by National Institute for Health and Care Excellence guidelines for hypertension management. It is recommended that these codelists be used to identify hypertension in EHRs using SNOMED CT codes.Conclusions Less than one-third of hypertension studies using EHRs included their codelists. Transparent methodology for codelist creation is essential for replication and will aid interpretation of study findings. We created SNOMED CT codelists to support and standardise hypertension definitions in EHR studies.

Plant-parasitic nematodes are a continuing threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics: forward genetics is largely restricted to studies of natural variation in populations and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate the progress of research on plant-parasitic nematodes, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic tool kit in plant-parasitic nematodes. We characterize the gonads of male Heterodera schachtii and Meloidogyne hapla in the context of spermatogenesis. We test and optimize various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult, but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of H. schachtii juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, will expedite the development of genetic modification tools for plant-parasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security.

Purpose –This study conducted a comparative analysis between hotels located in Brazil and England on human resource practices and employee motivation, using the cultural dimensions developed by Hofstede (1980) and the conservation of resources theory. Design/Methodology/Approach – Questionnaires were completed by 154 hotels, 96 and 58 dyads of human resources managers and frontline employees from Brazil and England, respectively, corresponding to a total of 308 respondents. Importance-performance analysis was used to examine the data collected through independent t-tests. Findings – The results showed that Brazilian managers considered training as the most important human resources practice, while information sharing had the best performance in their hotels. English managers ranked employment security with the highest importance and performance ratings. Brazilian frontline employees ranked intrinsic motivation with the highest importance and performance ratings, while English frontline employees ranked extrinsic motivation with the highest importance and performance ratings. Originality of the research – This research extended previous studies using the conservation of resources theory and also developed competitive strategies targeted to specific cultures. Another contribution was the comparative study between hotel employees (managers and frontline) from two countries (Brazil and England), applying the importance-performance analysis

IntroductionServices to treat problematic alcohol use (PAU) should be highly accessible to optimize treatment engagement. We conducted a scoping review to map characteristics of services for the treatment of PAU that have been reported in the literature to be barriers to or facilitators of access to treatment from the perspective of individuals with PAU.MethodsA protocol was developed a priori, registered, and published. We searched MEDLINE®, Embase, the Cochrane Library, and additional grey literature sources from 2010 to April 2022 to identify primary qualitative research and surveys of adults with current or past PAU requiring treatment that were designed to identify modifiable characteristics of PAU treatment services (including psychosocial and pharmacologic interventions) that were perceived to be barriers to or facilitators of access to treatment. Studies of concurrent PAU and other substance use disorders were excluded. Study selection was performed by multiple review team members. Emergent barriers were coded and mapped to the accessibility dimensions of the Levesque framework of healthcare access, then descriptively summarized.ResultsOne-hundred-and-nine included studies reported an extensive array of unique service-level barriers that could act alone or together to prevent treatment accessibility. These included but were not limited to lack of an obvious entry point, complexity of the care pathway, high financial cost, unacceptably long wait times, lack of geographically accessible treatment, inconvenient appointment hours, poor cultural/demographic sensitivity, lack of anonymity/privacy, lack of services to treat concurrent PAU and mental health problems.DiscussionBarriers generally aligned with recent reviews of the substance use disorder literature. Ranking of barriers may be explored in a future discrete choice experiment of PAU service users. The rich qualitative findings of this review may support the design of new or modification of existing services for people with PAU to improve accessibility.Systematic Review RegistrationOpen Science Framework doi: 10.17605/OSF.IO/S849R.

Background Using reports of randomised trials of smoking cessation interventions as a test case, this study aimed to develop and evaluate machine learning (ML) algorithms for extracting information from study reports and predicting outcomes as part of the Human Behaviour-Change Project. It is the first of two linked papers, with the second paper reporting on further development of a prediction system. Methods Researchers manually annotated 70 items of information (‘entities’) in 512 reports of randomised trials of smoking cessation interventions covering intervention content and delivery, population, setting, outcome and study methodology using the Behaviour Change Intervention Ontology. These entities were used to train ML algorithms to extract the information automatically. The information extraction ML algorithm involved a named-entity recognition system using the ‘FLAIR’ framework. The manually annotated intervention, population, setting and study entities were used to develop a deep-learning algorithm using multiple layers of long-short-term-memory (LSTM) components to predict smoking cessation outcomes. Results The F1 evaluation score, derived from the false positive and false negative rates (range 0-1), for the information extraction algorithm averaged 0.42 across different types of entity (SD=0.22, range 0.05-0.88) compared with an average human annotator’s score of 0.75 (SD=0.15, range 0.38-1.00). The algorithm for assigning entities to study arms (e.g., intervention or control) was not successful. This initial ML outcome prediction algorithm did not outperform prediction based just on the mean outcome value or a linear regression model. Conclusions While some success was achieved in using ML to extract information from reports of randomised trials of smoking cessation interventions, we identified major challenges that could be addressed by greater standardisation in the way that studies are reported. Outcome prediction from smoking cessation studies may benefit from development of novel algorithms, e.g., using ontological information to inform ML (as reported in the linked paper (1)).

Abstract Background Cyst nematodes are one of the major groups of plant-parasitic nematode, responsible for considerable crop losses worldwide. Improving genetic resources, and therefore resistant cultivars, is an ongoing focus of many pest management strategies. One of the major bottlenecks in identifying the plant genes that impact the infection, and thus the yield, is phenotyping. The current available screening method is slow, has unidimensional quantification of infection limiting the range of scorable parameters, and does not account for phenotypic variation of the host. The ever-evolving field of computer vision may be the solution for both the above-mentioned issues. To utilise these tools, a specialised imaging platform is required to take consistent images of nematode infection in quick succession. Results Here, we describe an open-source, easy to adopt, imaging hardware and trait analysis software method based on a pre-existing nematode infection screening method in axenic culture. A cost-effective, easy-to-build and -use, 3D-printed imaging device was developed to acquire images of the root system of Arabidopsis thaliana infected with the cyst nematode Heterodera schachtii, replacing costly microscopy equipment. Coupling the output of this device to simple analysis scripts allowed the measurement of some key traits such as nematode number and size from collected images, in a semi-automated manner. Additionally, we used this combined solution to quantify an additional trait, root area before infection, and showed both the confounding relationship of this trait on nematode infection and a method to account for it. Conclusion Taken together, this manuscript provides a low-cost and open-source method for nematode phenotyping that includes the biologically relevant nematode size as a scorable parameter, and a method to account for phenotypic variation of the host. Together these tools highlight great potential in aiding our understanding of nematode parasitism.