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[This corrects the article DOI: 10.1371/journal.pone.0265513.].

The colonial green microalga Botryococcus braunii is well known for producing liquid hydrocarbons that can be utilized as biofuel feedstocks. B. braunii is taxonomically classified as a single species made up of three chemical races, A, B, and L, that are mainly distinguished by the hydrocarbons produced. We previously reported a B race draft nuclear genome, and here we report the draft nuclear genomes for the A and L races. A comparative genomic study of the three B. braunii races and 14 other algal species within Chlorophyta revealed significant differences in the genomes of each race of B. braunii. Phylogenomically, there was a clear divergence of the three races with the A race diverging earlier than both the B and L races, and the B and L races diverging from a later common ancestor not shared by the A race. DNA repeat content analysis suggested the B race had more repeat content than the A or L races. Orthogroup analysis revealed the B. braunii races displayed more gene orthogroup diversity than three closely related Chlamydomonas species, with nearly 24-36% of all genes in each B. braunii race being specific to each race. This analysis suggests the three races are distinct species based on sufficient differences in their respective genomes. We propose reclassification of the three chemical races to the following species names: Botryococcus alkenealis (A race), Botryococcus braunii (B race), and Botryococcus lycopadienor (L race).

The development of high molecular weight (HMW) genomic DNA (gDNA) extraction protocols for non-model species is essential to fully exploit long-read sequencing technologies in order to generate genome assemblies that can help answer complex questions about these organisms. Obtaining enough high-quality HMW gDNA can be challenging for these species, especially for tissues rich in polysaccharides such as biomass from species within the Botryococcus genus. The existing protocols based on column-based DNA extraction and biochemical lysis kits can be inefficient and may not be useful due to variations in biomass polysaccharide content. We developed an optimized protocol for the efficient extraction of HMW gDNA from Botryococcus biomass for use in long-read sequencing technologies. The protocol utilized an initial wash step with sorbitol to remove polysaccharides and yielded HMW gDNA concentrations up to 220 ng/μL with high purity. We then demonstrated the suitability of the HMW gDNA isolated from this protocol for long-read sequencing on the Oxford Nanopore PromethION platform for three Botryococcus species. Our protocol can be used as a standard for efficient HMW gDNA extraction in microalgae rich in polysaccharides and may be adapted for other challenging species.

Linear regression of optical coherence tomography measurements of peripapillary retinal nerve fiber layer thickness is often used to detect glaucoma progression and forecast future disease course. However, current measurement frequencies suggest that clinicians often apply linear regression to a relatively small number of measurements (e.g., less than a handful). In this study, we estimate the accuracy of linear regression in predicting the next reliable measurement of average retinal nerve fiber layer thickness using Zeiss Cirrus optical coherence tomography measurements of average retinal nerve fiber layer thickness from a sample of 6,471 eyes with glaucoma or glaucoma-suspect status. Linear regression is compared to two null models: no glaucoma worsening, and worsening due to aging. Linear regression on the first M ≥ 2 measurements was significantly worse at predicting a reliable M+1st measurement for 2 ≤ M ≤ 6. This range was reduced to 2 ≤ M ≤ 5 when retinal nerve fiber layer thickness measurements were first "corrected" for scan quality. Simulations based on measurement frequencies in our sample-on average 393 ± 190 days between consecutive measurements-show that linear regression outperforms both null models when M ≥ 5 and the goal is to forecast moderate (75th percentile) worsening, and when M ≥ 3 for rapid (90th percentile) worsening. If linear regression is used to assess disease trajectory with a small number of measurements over short time periods (e.g., 1-2 years), as is often the case in clinical practice, the number of optical coherence tomography examinations needs to be increased.

BackgroundMalignant bowel obstruction is experienced by 15% of people with advanced cancer, preventing them from eating and drinking and causing pain, nausea and vomiting. Surgery is not always appropriate. Management options include tube or stent drainage of intestinal contents and symptom control using medication. Published literature describing palliative interventions uses a broad range of outcome measures, few of which are patient-relevant. This hinders evidence synthesis, and fails to consider the perspectives of people undergoing treatment.AimsTo develop a Core Outcome Set for the assessment of inoperable malignant bowel obstruction with clinician, patient and caregiver involvement, using COMET methodology (Core Outcome Measures in Effectiveness Trials).MethodsA systematic review of clinical trials and observational studies, a rapid review of the qualitative literature and in-depth patient and clinician interviews were conducted to identify a comprehensive list of outcomes. Outcomes were compared and consolidated by the study Steering Group and Patient and Public Involvement contributors, and presented to an international clinical Expert Panel for review. Outcomes from the finalised list were rated for importance in a three-round international Delphi process: results of two survey rounds were circulated to respondents, and two separate consensus meetings were conducted with clinicians and with patients and caregivers via virtual conferencing, using live polling to reach agreement on a Core Outcome Set.Results130 unique outcomes were identified. Following the independent Expert Panel review, 82 outcomes were taken into round 1 of the Delphi survey; 24 outcomes reached criteria for critical importance across all stakeholder groups and none reached criteria for dropping. All outcomes rated critically important were taken forward for re-rating in round 2 and all other outcomes dropped. In round 2, all outcomes were voted critically important by at least one stakeholder group. Round 2 outcomes were presented again at online consensus meetings, categorised as high ranking (n = 9), middle ranking (n = 7) or low ranking (n = 8). Stakeholders reached agreement on 16 core outcomes across four key domains: Symptom control, Life impact, Treatment outcomes, and Communication and patient preferences.ConclusionUse of this Core Outcome Set can help to address current challenges in making sense of the evidence around treatment for inoperable malignant bowel obstruction to date, and underpin a more robust future approach. Clearer communication and an honest understanding between all stakeholders will help to provide a basis for responsible decision-making in this distressing situation in clinical practice.

PurposeThis study aimed to measure stakeholder satisfaction with our usual delivery format, which previously relied on a blend of didactic lectures and clinical skills sessions compared to a revised format, which had more emphasis on online learning. We hypothesised that the online flipped classroom (OFC) would facilitate delivery of content in the wake of the pandemic, and result in improved levels of student satisfaction and knowledge gain.DesignNon randomised intervention study. Group 1 = Traditional delivery (TD) and Group 2 = OFC group.MethodsA validated course evaluation questionnaire (CEQ) compared perspectives of teaching faculty (n = 5) and students with the traditional delivery (TD) of the 4th year ophthalmology clinical attachment and an OFC approach (TD n = 129 v OFC n = 114).ResultsThe OFC group (n = 114; response rate = 24.6%) reported significantly reduced satisfaction with staff motivation of students and provision of feedback, compared to TD (n = 129; response rate = 17.8%). OFC students also felt it was harder to determine what standard of work was expected and found the course less beneficial at helping develop problem-solving skills. Students were dissatisfied with the level of choice afforded by the OFC, specifically how they would learn and assessment options. No significant difference in exam score was observed between the TD and OFC groups. For faculty (n = 5), there was no evidence of a difference between OFC and TD.ConclusionsStudents indicated a preference for the TD compared to the OFC approach. However, both delivery approaches led to comparable student performances as determined by MCQ examination.

We present four experiments investigating adaptation to a regional grammatical structure through reading exposure, using both the needs + past participle construction (e.g., The car needs washed) and the double modal construction (e.g. You might could go there). In each experiment, participants read two stories containing informal dialogue. Half of the participants were exposed to one of the regional constructions and half were not. Those readers exposed to the regional constructions adapted, gradually reading the novel constructions faster over 9 to 15 exemplars. The degree to which the exposed group learned the construction was tested in two ways. In the first two experiments, learning was measured by comparing reading times to acceptable and unacceptable variants of the novel constructions. Readers did not learn either the verb tense rule for the needs construction (Experiment 1) or a simple ordering rule for double modal constructions (Experiment 2). Similarly, in Experiments 3 and 4, metalinguistic judgments used to test learning revealed that participants had failed to acquire the regional grammar of either novel construction. These experiments suggest that the adaptation effects reflect learning some general properties of the experimental stimuli, not learning the syntactic constructions themselves.

The western corn rootworm (WCR) Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae) remains one of the economically most important pests of maize (Zea mays) due to its adaptive capabilities to pest management options. This includes the ability to develop resistance to some of the commercial pesticidal proteins originating from different strains of Bacillus thuringiensis. Although urgently needed, the discovery of new, environmentally safe agents with new modes of action is a challenge. In this study we report the discovery of a new family of binary pesticidal proteins isolated from several Chryseobacterium species. These novel binary proteins, referred to as GDI0005A and GDI0006A, produced as recombinant proteins, prevent growth and increase mortality of WCR larvae, as does the bacteria. These effects were found both in susceptible and resistant WCR colonies to Cry3Bb1 and Cry34Ab1/Cry35Ab1 (reassigned Gpp34Ab1/Tpp35Ab1). This suggests GDI0005A and GDI0006A may not share the same binding sites as those commercially deployed proteins and thereby possess a new mode of action. This paves the way towards the development of novel biological or biotechnological management solutions urgently needed against rootworms.

The colonial green microalga Botryococcus braunii is well known for producing liquid hydrocarbons that can be utilized as biofuel feedstocks. B. braunii is taxonomically classified as a single species made up of three chemical races, A, B, and L, that are mainly distinguished by the hydrocarbons produced. We previously reported a B race draft nuclear genome, and here we report the draft nuclear genomes for the A and L races. A comparative genomic study of the three B. braunii races and 14 other algal species within Chlorophyta revealed significant differences in the genomes of each race of B. braunii. Phylogenomically, there was a clear divergence of the three races with the A race diverging earlier than both the B and L races, and the B and L races diverging from a later common ancestor not shared by the A race. DNA repeat content analysis suggested the B race had more repeat content than the A or L races. Orthogroup analysis revealed the B. braunii races displayed more gene orthogroup diversity than three closely related Chlamydomonas species, with nearly 24-36% of all genes in each B. braunii race being specific to each race. This analysis suggests the three races are distinct species based on sufficient differences in their respective genomes. We propose reclassification of the three chemical races to the following species names: Botryococcus alkenealis (A race), Botryococcus braunii (B race), and Botryococcus lycopadienor (L race). [ABSTRACT FROM AUTHOR]

The development of high molecular weight (HMW) genomic DNA (gDNA) extraction protocols for non-model species is essential to fully exploit long-read sequencing technologies in order to generate genome assemblies that can help answer complex questions about these organisms. Obtaining enough high-quality HMW gDNA can be challenging for these species, especially for tissues rich in polysaccharides such as biomass from species within the Botryococcus genus. The existing protocols based on column-based DNA extraction and biochemical lysis kits can be inefficient and may not be useful due to variations in biomass polysaccharide content. We developed an optimized protocol for the efficient extraction of HMW gDNA from Botryococcus biomass for use in long-read sequencing technologies. The protocol utilized an initial wash step with sorbitol to remove polysaccharides and yielded HMW gDNA concentrations up to 220 ng/μL with high purity. We then demonstrated the suitability of the HMW gDNA isolated from this protocol for long-read sequencing on the Oxford Nanopore PromethION platform for three Botryococcus species. Our protocol can be used as a standard for efficient HMW gDNA extraction in microalgae rich in polysaccharides and may be adapted for other challenging species. [ABSTRACT FROM AUTHOR]

Purpose: This study aimed to measure student satisfaction with a revised ophthalmology delivery format, which due to the pandemic had previously relied on a remote online flipped classroom (OFC) format compared to a blended learning format. This educational strategy combined online learning with in-person seminars and practical patient centred sessions. Our previous investigations demonstrated a significant lack of student satisfaction with a curriculum solely reliant on a remote OFC, as such we hypothesised that a blended learning approach would result in improved levels of student satisfaction and knowledge gain. Methods: Non-randomised intervention study of two groups; group 1 = OFC group and group 2 = BL group, compared perspectives of 4th year ophthalmology students using a validated course evaluation questionnaire (CEQ). Results: A total of 59 students from the BL group (n = 257; response rate = 23.0%) and 28 from the OFC group agreed to participate in the study (n = 114; response rate = 24.6%). Participants in the BL group felt it was easier to determine the standard of work that was expected (77.42% v 60.71%) and demonstrated significantly increased satisfaction with staff motivation of students (95.16% v 64.29%, p <0.001) and provision of feedback (74.19% v 46.43%, p = 0.004), compared to the OFC group. Furthermore, students in the BL group also felt the course significantly improved their analytical skills (64.52% v 42.85%, p = 0.023) and ability to work as part of team (69.36% v 25%, p <0.001) as well as reporting reduced dissatisfaction with the level of choice afforded in terms of how they would learn (33.88% v 60.71%, p = 0.31) and the how they were assessed (59.68% v 89.28%, p = 0.004). No evidence of a statistical difference in exam score was observed. Conclusions: The COVID-19 pandemic necessitated an unavoidable pivot to online and distance learning, to meet the challenges presented by government mandates and social distancing requirements. Since many of these directives have been reversed, it is important to evaluate the effectiveness and learner perceptions' of the online and distance learning interventions. In this study we demonstrated a significant student preference for BL compared to the OFC approach, with comparable student performances determined by MCQ examinations. Our findings suggest a preference for reintroducing in-person and patient engagement activities in post-pandemic health professions education. [ABSTRACT FROM AUTHOR]

PurposeStroke is a leading cause of death and disability worldwide. Despite the prevalence and associated burden of post-stroke cognitive impairment, there is uncertainty regarding optimum interventions to improve cognitive function in people post-stroke. The aim of this study is to explore the perspectives of key stakeholders on the design and development of a multidisciplinary intervention to rehabilitate cognitive deficits in people post-stroke.Materials and methodsAudio-recorded, semi-structured interviews were employed with people post-stroke, caregivers, healthcare professionals and academics. All transcribed interviews were exported to NVivo software and analysed using reflexive thematic analysis.ResultsThirty interviews were conducted across stakeholder groups including people post-stroke (n = 10), caregivers (n = 5), healthcare professionals (n = 14) and academics (n = 1). Four themes relevant to the design and development of the intervention were identified (i) engagement in the intervention must be meaningful, (ii) the point of readiness to engage, (iii) a familiar but flexible setting is key (iv) pragmatics of intervention delivery.ConclusionsThese findings present new perspectives across stakeholder groups on the design and delivery of an intervention to rehabilitate cognitive deficits in people post-stroke. Taken together with existing quantitative evidence, these findings will inform the development of a feasibility trial, examining patient and process outcomes, to rehabilitate cognitive deficits post-stroke.

ObjectivesAffective communication in outpatient care is important, especially in the palliative phase. Appropriate responses by healthcare providers to emotional cues or concerns let patients express their feelings and enhance information recall and patient satisfaction. Patients with limited health literacy experience more barriers in health-related communication and information, which makes recognizing their cues and concerns even more relevant. This study explores emotional cues/concerns expressed by patients with limited health literacy and evaluates healthcare providers' responses to these utterances.MethodsVerona Coding Definitions of Emotional Sequences (VR-CoDES), a consensus-based system for coding patients' expression of emotional distress in medical consultations, was used in this exploratory observational study to analyse affective communication in video-recorded outpatient consultations. Consultations of 18 (10 female, 8 male) COPD or lung cancer patients (aged 70.3±6.8) with limited health literacy were recorded and analysed. Eight healthcare providers in four hospitals participated in the study.Results101 cues and 11 concerns were observed, making 6.2 (SD = 4.2) cues or concerns per consultation. Healthcare provider responses were explicit in 56% and left scope for further disclosures in 58% of the cases. Patients with limited health literacy seem to express more cues or concerns than other patient populations. Healthcare providers responded roughly equally often in five different ways, but they shied away from further exploring the emotion disclosed in the cue/concern. Future research should elaborate on these exploratory observations, especially regarding why HCPs often only leave limited space for further disclosure of emotions in palliative care.

Since the early 2000s, unconventional natural gas development (UNGD) has rapidly grown throughout Pennsylvania. UNGD extracts natural gas using a relatively new method known as hydraulic fracturing (HF). Here we addressed the association of HF with asthma Hospitalization Admission Rates (HAR) using publicly available data. Using public county-level data from the Pennsylvania Department of Health (PA-DOH) and the Pennsylvania Department of Environmental Protection for the years 2001-2014, we constructed regression models to study the previously observed association between asthma exacerbation and HF. After considering multicollinearity, county-level demographics and area-level covariables were included to account for known asthma risk factors. We found a significant positive association between the asthma HAR and annual well density for all the counties in the state (3% increase in HAR attributable to HF, p

BackgroundThere is encouraging evidence that interdisciplinary teams of Health and Social Care Professionals (HSCPs) can enhance patient care in the Emergency Department (ED), especially for older adults with complex needs. However, no formal process evaluations of implementations of ED-based HSCP interventions are available. The study aimed to evaluate the development and delivery of a HSCP team intervention for older adults in the ED of a large Irish teaching hospital.MethodsUsing the Medical Research Council (MRC) Framework for process evaluations, we investigated implementation and delivery, mechanisms of impact, and contextual influences on implementation by analysing the HSCP team's activity notes and participant recruitment logs, and by carrying out six interviews and four focus groups with 26 participants (HSCP team members, ED doctors and nurses, hospital staff). Qualitative insights were analysed thematically.ResultsThe implementation process had three phases (pre-implementation, piloting, and delivery), with the first two described as pivotal to optimise care procedures and build positive stakeholders' involvement. The team's motivation and proactive communication were key to promote acceptability and integration in the ED (Theme 1); also, their specialised skills and interdisciplinary approach enhanced patient and staff's ED experience (Theme 2). The investment and collaboration of multiple stakeholders were described as essential contextual enablers of implementation (Theme 4). Delivering the intervention within a randomised controlled trial fostered credibility but caused frustration among patients and staff (Theme 3).DiscussionThis process evaluation is the first to provide in-depth and practical insights on the complexities of developing and delivering an ED-based HSCP team intervention for older adults. Our findings highlight the importance of establishing a team of HSCPs with a strong interdisciplinary ethos to ensure buy-in and integration in the ED processes. Also, actively involving relevant stakeholders is key to facilitate implementation.Trial registrationClinicalTrials.gov, NCT03739515; registered on 12th November 2018.

Linear regression of optical coherence tomography measurements of peripapillary retinal nerve fiber layer thickness is often used to detect glaucoma progression and forecast future disease course. However, current measurement frequencies suggest that clinicians often apply linear regression to a relatively small number of measurements (e.g., less than a handful). In this study, we estimate the accuracy of linear regression in predicting the next reliable measurement of average retinal nerve fiber layer thickness using Zeiss Cirrus optical coherence tomography measurements of average retinal nerve fiber layer thickness from a sample of 6,471 eyes with glaucoma or glaucoma-suspect status. Linear regression is compared to two null models: no glaucoma worsening, and worsening due to aging. Linear regression on the first M ≥ 2 measurements was significantly worse at predicting a reliable M+1st measurement for 2 ≤ M ≤ 6. This range was reduced to 2 ≤ M ≤ 5 when retinal nerve fiber layer thickness measurements were first "corrected" for scan quality. Simulations based on measurement frequencies in our sample—on average 393 ± 190 days between consecutive measurements—show that linear regression outperforms both null models when M ≥ 5 and the goal is to forecast moderate (75th percentile) worsening, and when M ≥ 3 for rapid (90th percentile) worsening. If linear regression is used to assess disease trajectory with a small number of measurements over short time periods (e.g., 1–2 years), as is often the case in clinical practice, the number of optical coherence tomography examinations needs to be increased. [ABSTRACT FROM AUTHOR]

Wood is a habitat for a variety of organisms, including saprophytic fungi and bacteria, playing an important role in wood decomposition. Wood inhabiting fungi release a diversity of volatiles used as signaling compounds to attract or repel other organisms. Here, we show that volatiles of Schizophyllum commune are active against wood-decay fungi and bacteria found in its mycosphere. We identified sesquiterpenes as the biologically active compounds, that inhibit fungal growth and modify bacterial motility. The low number of cultivable wood inhabiting bacteria prompted us to analyze the microbial community in the mycosphere of S. commune using a culture-independent approach. Most bacteria belong to Actinobacteria and Proteobacteria, including Pseudomonadaceae, Sphingomonadaceae, Erwiniaceae, Yersiniaceae and Mariprofundacea as the dominating families. In the fungal community, the phyla of ascomycetes and basidiomycetes were well represented. We propose that fungal volatiles might have an important function in the wood mycosphere and could meditate interactions between microorganisms across domains and within the fungal kingdom.

ObjectiveTo assess whether machine learning algorithms (MLA) can predict eyes that will undergo rapid glaucoma progression based on an initial visual field (VF) test.DesignRetrospective analysis of longitudinal data.Subjects175,786 VFs (22,925 initial VFs) from 14,217 patients who completed ≥5 reliable VFs at academic glaucoma centers were included.MethodsSummary measures and reliability metrics from the initial VF and age were used to train MLA designed to predict the likelihood of rapid progression. Additionally, the neural network model was trained with point-wise threshold data in addition to summary measures, reliability metrics and age. 80% of eyes were used for a training set and 20% were used as a test set. MLA test set performance was assessed using the area under the receiver operating curve (AUC). Performance of models trained on initial VF data alone was compared to performance of models trained on data from the first two VFs.Main outcome measuresAccuracy in predicting future rapid progression defined as MD worsening more than 1 dB/year.Results1,968 eyes (8.6%) underwent rapid progression. The support vector machine model (AUC 0.72 [95% CI 0.70-0.75]) most accurately predicted rapid progression when trained on initial VF data. Artificial neural network, random forest, logistic regression and naïve Bayes classifiers produced AUC of 0.72, 0.70, 0.69, 0.68 respectively. Models trained on data from the first two VFs performed no better than top models trained on the initial VF alone. Based on the odds ratio (OR) from logistic regression and variable importance plots from the random forest model, older age (OR: 1.41 per 10 year increment [95% CI: 1.34 to 1.08]) and higher pattern standard deviation (OR: 1.31 per 5-dB increment [95% CI: 1.18 to 1.46]) were the variables in the initial VF most strongly associated with rapid progression.ConclusionsMLA can be used to predict eyes at risk for rapid progression with modest accuracy based on an initial VF test. Incorporating additional clinical data to the current model may offer opportunities to predict patients most likely to rapidly progress with even greater accuracy.

The epithelial tissues of the distal lung are continuously exposed to inhaled air, and are of research interest in studying respiratory exposure to both hazardous and therapeutic materials. Pharmaco-toxicological research depends on the development of sophisticated models of the alveolar epithelium, which better represent the different cell types present in the native lung and interactions between them. We developed an air-liquid interface (ALI) model of the alveolar epithelium which incorporates cell lines which bear features of type I (hAELVi) and type II (NCI-H441) epithelial cells. We compared morphology of single cells and the structure of cell layers of the two lines using light and electron microscopy. Working both in monotypic cultures and cocultures, we measured barrier function by trans-epithelial electrical resistance (TEER), and demonstrated that barrier properties can be maintained for 30 days. We created a mathematical model of TEER development over time based on these data in order to make inferences about the interactions occurring in these culture systems. We assessed expression of a panel of relevant genes that play important roles in barrier function and differentiation. The coculture model was observed to form a stable barrier akin to that seen in hAELVi, while expressing surfactant protein C, and having a profile of expression of claudins and aquaporins appropriate for the distal lung. We described cavities which arise within stratified cell layers in NCI-H441 and cocultured cells, and present evidence that these cavities represent an aberrant apical surface. In summary, our results support the coculture of these two cell lines to produce a model which better represents the breadth of functions seen in native alveolar epithelium.

Artificial reefs act as high-rugosity habitats and are often deployed to enhance fishing; however, the effects of man-made features on fish communities can be unpredictable and are poorly understood in deeper waters. In this study, we used a submersible to describe a deep-water artificial reef complex (93-245 m) off of Ewa Beach, Oahu, Hawaii, USA, and evaluated possible conservation and/or fisheries-related contributions. Sixty-eight species were recorded, with larger features supporting greater diversity of species. Species composition changed strongly with depth and a faunal break was detected from 113-137 m. While the features supported diverse fish communities, they were not similar to those on natural substrates, and were numerically dominated by only two species, Lutjanis kasmira and Chromis verater. Depth-generalist and endemic species were present at levels comparable to natural substrates, but were less abundant and species-rich than at biogenic Leptoseris reefs at similar depths. While the non-native L. kasmira was highly abundant, its presence and abundance were not associated with discernable changes in the fish community, and was not present deeper than 120 m. Finally, five species of commercially- and recreationally-important 'Deep 7' fisheries species were also observed, but the artificial reef complex was mostly too shallow to provide meaningful benefits.

BACKGROUND:Retention in opioid substitution (OST) treatment is associated with substantial reductions in all cause and overdose mortality. This systematic review aims to identify both protective factors supporting retention in OST, and risk factors for treatment dropout. METHODS:A systematic search was performed using MEDLINE, Embase, PsycInfo, CINAHL and Web of Science (January 2001 to October 2019). Randomised controlled trials (RCTs) and observational cohort studies reporting on retention rates and factors associated with retention in OST were included. Factors associated with treatment retention and dropout were explored according to the Maudsley Addiction Profile. A narrative synthesis is provided. RESULTS:67 studies were included in this review (4 RCTs and 63 observational cohort studies; N = 294,592), all assessing factors associated with retention in OST or treatment dropout. The median retention rate across observational studies was approximately 57% at 12 months, which fell to 38.4% at three years. Studies included were heterogeneous in nature with respect to treatment setting, type of OST, risk factor assessment, ascertainment of outcome and duration of follow-up. While the presence of such methodological heterogeneity makes it difficult to synthesise results, there is limited evidence to support the influence of a number of factors on retention, including age, substance use, OST drug dose, legal issues, and attitudes to OST. CONCLUSIONS:Younger age, substance use particularly cocaine and heroin use, lower doses of methadone, criminal activity/incarceration, and negative attitudes to MMT appear to be associated with reduced retention in OST. A consensus definition of retention is required to allow for comparability across future studies.

BackgroundCommunication and shared decision-making (SDM) are essential to patient-centered care. Hospital-based palliative care with patients with limited health literacy (LHL) poses particular demands on communication. In this context, patients' emotions and vulnerable condition impact their skills to obtain, understand, process and apply information about health and healthcare even more. If healthcare providers (HCPs) meet these demands, it could enhance communication. In this study, HCPs were interviewed and asked for their strategies, barriers and suggestions for improvement regarding communication and SDM with LHL patients in hospital-based palliative care.MethodsA qualitative interview study was conducted in 2018 in four Dutch hospitals with 17 HCPs-11 physicians and 6 nurses. Transcripts were analyzed using thematic analysis.ResultsIn general HCPs recognized limited literacy as a concept, however, they did not recognize limited health literacy. Regarding SDM some HCPs were strong advocates, others did not believe in SDM as a concept and perceived it as unfeasible. Furthermore, five themes, acting as either strategies, barriers or suggestions for improvement emerged from the interviews: 1) time management; 2) HCPs' communication skills; 3) information tailoring; 4) characteristics of patients and significant others; 5) the content of the medical information.ConclusionsAccording to HCPs, more time to communicate with their patients could resolve the most prominent barriers emerged from this study. Further research should investigate the organizational possibilities for this and the actual effectiveness of additional time on effective communication and SDM. Additionally, more awareness for the concept of LHL is needed as a precondition for recognizing LHL. Furthermore, future research should be directed towards opportunities for tailoring communication, and the extent to which limited knowledge and complex information affect communication and SDM. This study provides first insights into perspectives of HCPs, indicating directions for research on communication, SDM and LHL in hospital-based palliative care.

The number of cancer-related emergency presentations and admissions has been steadily increasing in the UK. Drivers of this phenomenon are complex, multifactorial and interlinked. The main objective of this study was to understand the complexity of emergency hospital use in cancer patients. We conducted semi-structured interviews with 42 senior clinicians (20 doctors, 22 nurses) with diverse expertise and experience in caring for acutely ill cancer patients in the secondary care setting. Data analysis included thematic analysis and purposive text analysis to develop Causal Loop Diagrams. Our Causal Loop Diagrams represent an integrated understanding of the complex factors (13) influencing emergency hospital use in cancer patients. Eight factors formed five reinforcing feedback loops and therefore were high-leverage influences: Ability of patients and carers to self-care and cope; Effective and timely management of ambulatory care sensitive conditions by primary and community care; Sufficient and effective social care for patients and carers; Avoidable emergency hospital use; Bed capacity; Patients accessing timely appropriate specialist inpatient or ambulatory care; Prompt and effective management and prevention of acute episode; Timely and safe discharge with appropriate support. The loops show that reduction of avoidable hospital use helps relieve hospital bed pressure; improved bed capacity then has a decisive, positive influence on patient pathway and thus outcome and experience in the hospital; in turn, better in-hospital care and discharge help patients and carers self-care and cope better back home with better support from community-based health and social care services, which then reduces their future emergency hospital use. To optimise acute and emergency cancer care, it is also essential that patients, carers and other clinicians caring for cancer patients have prompt access to senior cancer specialists for advice, assessment, clinical decision and other support. The findings provide a useful framework and focus for service planners aiming to optimise care.

The triggering and development of Rheumatoid Arthritis (RA) is conditioned by environmental and genetic factors. Despite the identification of more than one hundred genetic variants associated with the disease, not all the cases can be explained. Here, we performed Whole Exome Sequencing in 9 multiplex families (N = 30) to identify rare variants susceptible to play a role in the disease pathogenesis. We pre-selected 77 genes which carried rare variants with a complete segregation with RA in the studied families. Follow-up linkage and association analyses with pVAAST highlighted significant RA association of 43 genes (p-value < 0.05 after 106 permutations) and pinpointed their most likely causal variant. We re-sequenced the 10 most significant likely causal variants (p-value ≤ 3.78*10-3 after 106 permutations) in the extended pedigrees and 9 additional multiplex families (N = 110). Only one SNV in SUPT20H: c.73A>T (p.Lys25*), presented a complete segregation with RA in an extended pedigree with early-onset cases. In summary, we identified in this study a new variant associated with RA in SUPT20H gene. This gene belongs to several biological pathways like macro-autophagy and monocyte/macrophage differentiation, which contribute to RA pathogenesis. In addition, these results showed that analyzing rare variants using a family-based approach is a strategy that allows to identify RA risk loci, even with a small dataset.

One of the most popular techniques in zebrafish research is microinjection. This is a rapid and efficient way to genetically manipulate early developing embryos, and to introduce microbes, chemical compounds, nanoparticles or tracers at larval stages. Here we demonstrate the development of a machine learning software that allows for microinjection at a trained target site in zebrafish eggs at unprecedented speed. The software is based on the open-source deep-learning library Inception v3. In a first step, the software distinguishes wells containing embryos at one-cell stage from wells to be skipped with an accuracy of 93%. A second step was developed to pinpoint the injection site. Deep learning allows to predict this location on average within 42 μm to manually annotated sites. Using a Graphics Processing Unit (GPU), both steps together take less than 100 milliseconds. We first tested our system by injecting a morpholino into the middle of the yolk and found that the automated injection efficiency is as efficient as manual injection (~ 80%). Next, we tested both CRISPR/Cas9 and DNA construct injections into the zygote and obtained a comparable efficiency to that of an experienced experimentalist. Combined with a higher throughput, this results in a higher yield. Hence, the automated injection of CRISPR/Cas9 will allow high-throughput applications to knock out and knock in relevant genes to study their mechanisms or pathways of interest in diverse areas of biomedical research.

BackgroundDedicated Health and Social Care Professional (HSCP) teams have been proposed for emergency departments (EDs) in an effort to improve patient and process outcomes. This systematic review synthesises the totality of evidence relating to the impact of early assessment and intervention by HSCP teams on quality, safety and effectiveness of care in the ED.MethodsA systematic literature search was conducted in April 2019 to identify experimental studies examining the effectiveness of ED-based HSCP teams providing services to adults aged ≥ 18 years old and including two or more of the following disciplines: occupational therapist, physiotherapist, medical social worker, clinical pharmacist, or speech and language therapist. Data extraction and quality appraisal of each study were conducted independently by two reviewers.ResultsSix studies were included in the review (n = 273,886), all describing interdisciplinary Care Coordination Teams (CCTs) caring for adults aged ≥ 65 years old. CCT care was associated with on average 2% reduced rates of hospital admissions (three studies), improved referrals to community services for falls (one study), increased satisfaction (two studies) with the safety of discharge (patients and staff), and with the distribution of workload (staff), improved health-related quality of care (one study). No statistically significant differences between intervention and control groups emerged in terms of rates of ED re-visits, ranging between 0.2% and 3% (two studies); hospital length of stay (one hour difference noted in one study) or mortality rates (0.5% difference in one study). Increased rates of unplanned hospitalisations following the intervention (13.9% difference) were reported in one study. The methodological quality of the studies was mixed.DiscussionWe found limited and heterogeneous evidence on the impact of HSCP teams in the ED, suggesting a reduction in hospital admissions as well as improved patient and staff satisfaction. More robust investigations including cost-effectiveness evaluations are needed.

BackgroundAtrial fibrillation (AF) is the most common type of cardiac arrhythmia and is associated with increased risk of stroke and congestive heart failure. Lead-I electrocardiogram (ECG) devices are handheld instruments that can detect AF at a single-time point.PurposeTo assess the diagnostic test accuracy, clinical impact and cost effectiveness of single-time point lead-I ECG devices compared with manual pulse palpation (MPP) followed by a 12-lead ECG for the detection of AF in symptomatic primary care patients with an irregular pulse.MethodsElectronic databases (MEDLINE, MEDLINE Epub Ahead of Print and MEDLINE In-Process, EMBASE, PubMed and Cochrane Databases of Systematic Reviews, Cochrane Central Database of Controlled Trials, Database of Abstracts of Reviews of Effects, Health Technology Assessment Database) were searched to March 2018. Two reviewers screened the search results, extracted data and assessed study quality. Summary estimates of diagnostic accuracy were calculated using bivariate models. Cost-effectiveness was evaluated using an economic model consisting of a decision tree and two cohort Markov models.ResultsDiagnostic accuracy The diagnostic accuracy (13 publications reporting on nine studies) and clinical impact (24 publications reporting on 19 studies) results are derived from an asymptomatic population (used as a proxy for people with signs or symptoms of AF). The summary sensitivity of lead-I ECG devices was 93.9% (95% confidence interval [CI]: 86.2% to 97.4%) and summary specificity was 96.5% (95% CI: 90.4% to 98.8%). Cost effectiveness The de novo economic model yielded incremental cost effectiveness ratios (ICERs) per quality adjusted life year (QALY) gained. The results of the pairwise analysis show that all lead-I ECG devices generate ICERs per QALY gained below the £20,000-£30,000 threshold. Kardia Mobile is the most cost effective option in a full incremental analysis. Lead-I ECG tests may identify more AF cases than the standard diagnostic pathway. This comes at a higher cost but with greater patient benefit in terms of mortality and quality of life.LimitationsNo published data evaluating the diagnostic accuracy, clinical impact or cost effectiveness of lead-I ECG devices for the target population are available.ConclusionsThe use of single-time point lead-I ECG devices in primary care for the detection of AF in people with signs or symptoms of AF and an irregular pulse appears to be a cost effective use of NHS resources compared with MPP followed by a 12-lead ECG, given the assumptions used in the base case model.RegistrationThe protocol for this review is registered on PROSPERO as CRD42018090375.

Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling. Here, we generated 42 human whole-exome sequencing data sets from fresh-frozen (FF) and FFPE samples. These samples include normal and tumor tissues from two different organs (liver and colon), that we extracted with three different FFPE extraction kits (QIAamp DNA FFPE Tissue kit and GeneRead DNA FFPE kit from Qiagen, Maxwell™ RSC DNA FFPE Kit from Promega). We determined the rate of concordance of called variants between matched FF and FFPE samples on all common variants (representing at least 86% of the total number of variants for SNVs). The concordance rate is very high between all matched FF / FFPE pairs, with equivalent values for the three kits we analyzed. On the other hand, when looking at the difference between the total number of variants in FF and FFPE, we find a significant variation for the three different FFPE DNA extraction kits. Coverage analysis shows that FFPE samples have less good indicators than FF samples, yet the coverage quality remains above accepted thresholds. We detect limited but statistically significant variations in coverage indicator values between the three FFPE extraction kits. Globally, the GeneRead and QIAamp kits have better variant calling and coverage indicators than the Maxwell kit on the samples used in this study, although this kit performs better on some indicators and has advantages in terms of practical usage. Taken together, our results confirm the potential of FFPE samples analysis for clinical genomic studies, but also indicate that the choice of a FFPE DNA extraction kit should be done with careful testing and analysis beforehand in order to maximize the accuracy of the results.

OBJECTIVE:Over 12% of women in the United States have reduced fertility and/or fecundity. Environmental factors, such as temperature, and socioeconomic factors have been implicated in reducing female fecundity. The purpose of this study is to investigate the effect of environmental factors coupled with socioeconomic factors on birth rate at the country-level. We use birth rate as a proxy for female fecundity. This will enable us to identify the most important factors affecting female fecundity. METHODS:Using country-specific data from 182 countries, we constructed a regression model of the effects of environmental and socioeconomic factors on birth rate at the country-level. Our model assesses the role of temperature, Gross Domestic Product (GDP) per capita, fine air particulate matter (PM 2.5), and prevalence of male and female Body Mass Index (BMI) > = 25 (age-standardized) on birth rate per country. Because many of these factors are inter-dependent, we include all possible two-way interaction terms to assess the role of individual factors and interactions between multiple factors in the model. RESULTS:In the full regression model, we found that GDP per capita along with 5 interaction terms were significant after adjusting for multiple testing. Female BMI was only nominally significant. GDP per capita was independently associated with birth rate (adjusted p-value = 25 age-standardized in males and females were also significant when interacting with air pollution or GDP on female fecundity (birth rate). Temperature did not affect birth rate either independently or as an interaction unless BMI was removed from the model. CONCLUSION:A country's economic wealth was the most significant factor in predicting birth rate in a statistical model that includes environmental and socioeconomic variables. This is important for future studies investigating environmental factors involved in increasing or decreasing female fecundity.

Calcium is an important second messenger in plants that is released into the cytosol early after recognition of various environmental stimuli. Decoding of such calcium signals by calcium sensors is the key for the plant to react appropriately to each stimulus. Several members of Calmodulin-like proteins (CMLs) act as calcium sensors and some are known to mediate both abiotic and biotic stress responses. Here, we study the role of the Arabidopsis thaliana CML9 in different stress responses. CML9 was reported earlier as defense regulator against Pseudomonas syringae. In contrast to salicylic acid-mediated defense against biotrophic pathogens such as P. syringae, defenses against herbivores and necrotrophic fungi are mediated by jasmonates. We demonstrate that CML9 is induced upon wounding and feeding of the insect herbivore Spodoptera littoralis. However, neither different CML9 loss-of-function mutant lines nor overexpression lines were impaired upon insect feeding. No difference in herbivore-induced phytohormone elevation was detected in cml9 lines. The defense against the spider mite Tetranychus urticae was also unaffected. In addition, cml9 mutant lines showed a wild type-like reaction to the necrotrophic fungus Alternaria brassicicola. Thus, our data suggest that CML9 might be a regulator involved only in the defense against biotrophic pathogens, independent of jasmonates. In addition, our data challenge the involvement of CML9 in plant drought stress response. Taken together, we suggest that CML9 is a specialized rather than a general regulator of stress responses in Arabidopsis.

Changes in microbial community composition in the lung of patients suffering from moderate to severe COPD have been well documented. However, knowledge about specific microbiome structures in the human lung associated with CT defined abnormalities is limited.Bacterial community composition derived from brush samples from lungs of 16 patients suffering from different CT defined subtypes of COPD and 9 healthy subjects was analyzed using a cultivation independent barcoding approach applying 454-pyrosequencing of 16S rRNA gene fragment amplicons.We could show that bacterial community composition in patients with changes in CT (either airway or emphysema type changes, designated as severe subtypes) was different from community composition in lungs of patients without visible changes in CT as well as from healthy subjects (designated as mild COPD subtype and control group) (PC1, Padj = 0.002). Higher abundance of Prevotella in samples from patients with mild COPD subtype and from controls and of Streptococcus in the severe subtype cases mainly contributed to the separation of bacterial communities of subjects. No significant effects of treatment with inhaled glucocorticoids on bacterial community composition were detected within COPD cases with and without abnormalities in CT in PCoA. Co-occurrence analysis suggests the presence of networks of co-occurring bacteria. Four communities of positively correlated bacteria were revealed. The microbial communities can clearly be distinguished by their associations with the CT defined disease phenotype.Our findings indicate that CT detectable structural changes in the lung of COPD patients, which we termed severe subtypes, are associated with alterations in bacterial communities, which may induce further changes in the interaction between microbes and host cells. This might result in a changed interplay with the host immune system.

Canonical Hedgehog (Hh) signaling in vertebrate cells occurs following Smoothened activation/translocation into the primary cilia (Pc), followed by a GLI transcriptional response. Nonetheless, GLI activation can occur independently of the canonical Hh pathway. Using a murine model of liver injury, we previously identified the importance of canonical Hh signaling within the Pc+ liver progenitor cell (LPC) population and noted that SMO-independent, GLI-mediated signals were important in multiple Pc-ve GLI2+ intrahepatic populations. This study extends these observations to human liver tissue, and analyses the effect of GLI inhibition on LPC viability/gene expression. Human donor and cirrhotic liver tissue specimens were evaluated for SHH, GLI2 and Pc expression using immunofluorescence and qRT-PCR. Changes to viability and gene expression in LPCs in vitro were assessed following GLI inhibition. Identification of Pc (as a marker of canonical Hh signaling) in human cirrhosis was predominantly confined to the ductular reaction and LPCs. In contrast, GLI2 was expressed in multiple cell populations including Pc-ve endothelium, hepatocytes, and leukocytes. HSCs/myofibroblasts (>99%) expressed GLI2, with only 1.92% displaying Pc. In vitro GLI signals maintained proliferation/viability within LPCs and GLI inhibition affected the expression of genes related to stemness, hepatocyte/biliary differentiation and Hh/Wnt signaling. At least two mechanisms of GLI signaling (Pc/SMO-dependent and Pc/SMO-independent) mediate chronic liver disease pathogenesis. This may have significant ramifications for the choice of Hh inhibitor (anti-SMO or anti-GLI) suitable for clinical trials. We also postulate GLI delivers a pro-survival signal to LPCs whilst maintaining stemness.

Parallel transmission (pTx) technology, despite its great potential to mitigate the transmit field inhomogeneity problem in magnetic resonance imaging at ultra-high field (UHF), suffers from a cumbersome calibration procedure, thereby making the approach problematic for routine use. The purpose of this work is to demonstrate on two different 7T systems respectively equipped with 8-transmit-channel RF coils from two different suppliers (Rapid-Biomed and Nova Medical), the benefit of so-called universal pulses (UP), optimized to produce uniform excitations in the brain in a population of adults and making unnecessary the calibration procedures mentioned above. Non-selective and slice-selective UPs were designed to return homogeneous excitation profiles throughout the brain simultaneously on a group of ten subjects, which then were subsequently tested on ten additional volunteers in magnetization prepared rapid gradient echo (MPRAGE) and multi-slice gradient echo (2D GRE) protocols. The results were additionally compared experimentally with the standard non-pTx circularly-polarized (CP) mode, and in simulation with subject-specific tailored excitations. For both pulse types and both coils, the UP mode returned a better signal and contrast homogeneity than the CP mode. Retrospective analysis of the flip angle (FA) suggests that the FA deviation from the nominal FA on average over a healthy adult population does not exceed 11% with the calibration-free parallel-transmit pulses whereas it goes beyond 25% with the CP mode. As a result the universal pulses designed in this work confirm their relevance in 3D and 2D protocols with commercially available equipment. Plug-and-play pTx implementations henceforth become accessible to exploit with more flexibility the potential of UHF for brain imaging.

The increasing prevalence of social media means that we often encounter written language characterized by both stylistic variation and outright errors. How does the personality of the reader modulate reactions to non-standard text? Experimental participants read 'email responses' to an ad for a housemate that either contained no errors or had been altered to include either typos (e.g., teh) or homophonous grammar errors (grammos, e.g., to/too, it's/its). Participants completed a 10-item evaluation scale for each message, which measured their impressions of the writer. In addition participants completed a Big Five personality assessment and answered demographic and language attitude questions. Both typos and grammos had a negative impact on the evaluation scale. This negative impact was not modulated by age, education, electronic communication frequency, or pleasure reading time. In contrast, personality traits did modulate assessments, and did so in distinct ways for grammos and typos.

The free-living soil nematode Caenorhabditis elegans adapts its development to the availability of food. When food is scarce and population density is high, worms enter a developmentally arrested non-feeding diapause stage specialized for long-term survival called the dauer larva. When food becomes available, they exit from the dauer stage, resume growth and reproduction. It has been postulated that compound(s) present in food, referred to as the "food signal", promote exit from the dauer stage. In this study, we have identified NAD+ as a component of bacterial extract that promotes dauer exit. NAD+, when dissolved in alkaline medium, causes opening of the mouth and ingestion of food. We also show that to initiate exit from the dauer stage in response to NAD+ worms require production of serotonin. Thus, C. elegans can use redox cofactors produced by dietary organisms to sense food.

Visual survey by divers using open-circuit (OC) SCUBA is the most widely used approach to survey coral reef fishes. Therefore, it is important to quantify sources of bias in OC surveys, such as the possibility that avoidance of OC divers by fishes can lead to undercounting in areas where targeted species have come to associate divers with a risk of being speared. One potential way to reduce diver avoidance is to utilize closed circuit rebreathers (CCRs), which do not produce the noise and bubbles that are a major source of disturbance associated with OC diving. For this study, we conducted 66 paired OC and CCR fish surveys in the Main Hawaiian Islands at locations with relatively high, moderate, and light fishing pressure. We found no significant differences in biomass estimates between OC and CCR surveys when data were pooled across all sites, however there were differences at the most heavily fished location, Oahu. There, biomass estimates from OC divers were significantly lower for several targeted fish groups, including surgeonfishes, targeted wrasses, and snappers, as well as for all targeted fishes combined, with mean OC biomass between 32 and 68% of mean CCR biomass. There were no clear differences between OC and CCR biomass estimates for these groups at sites with moderate or low fishing pressure, or at any location for other targeted fish groups, including groupers, parrotfishes, and goatfishes. Bias associated with avoidance of OC divers at heavily fished locations could be substantially reduced, or at least calibrated for, by utilization of CCR. In addition to being affected by fishing pressure, the extent to which avoidance of OC divers is problematic for visual surveys varies greatly among taxa, and is likely to be highly influenced by the survey methodology and dimensions used.

The reciprocal interaction between the immune system and sleep regulation has been widely acknowledged but the cellular mechanisms that underpin this interaction are not completely understood. In the present study, we investigated the role of macrophages in sleep loss- and cold exposure-induced sleep and body temperature responses. Macrophage apoptosis was induced in mice by systemic injection of clodronate-containing liposomes (CCL). We report that CCL treatment induced an immediate and transient increase in non-rapid-eye movement sleep (NREMS) and fever accompanied by decrease in rapid-eye movement sleep, motor activity and NREMS delta power. Chronically macrophage-depleted mice had attenuated NREMS rebound after sleep deprivation compared to normal mice. Cold-induced increase in wakefulness and decrease in NREMS, rapid-eye movement sleep and body temperature were significantly enhanced in macrophage-depleted mice indicating increased cold sensitivity. These findings provide further evidence for the reciprocal interaction among the immune system, sleep and metabolism, and identify macrophages as one of the key cellular elements in this interplay.