Estimating herbarium specimen digitization rates: Accounting for human experience

PREMISE

Herbaria are invaluable sources for understanding the natural world, and in recent years there has been a concerted effort to digitize these collections. To organize such efforts, a method for estimating the necessary labor is desired. This work analyzes digitization productivity reports of 105 participants from eight herbaria, deriving generalized labor estimates that account for human experience.

METHODS AND RESULTS

Individuals' rates of digitization were grouped based on cumulative time performing each task and then used to estimate a series of generalized labor projection models. In most cases, productivity was shown to improve with experience, suggesting longer technician retention can reduce labor requirements by 20%.

CONCLUSIONS

Using student labor is a common tactic for digitization efforts, and the resulting outreach exposes future professionals to natural history collections. However, overcoming the learning curve should be considered when estimating the labor necessary to digitize a collection.

Efficacy and safety of a sodium-glucose co-transporter-2 inhibitor versus placebo as an add-on therapy for people with type 2 diabetes inadequately treated with metformin and a dipeptidyl peptidase-4 inhibitor: a systematic review and meta-analysis of randomised controlled trials

AIMS

To conduct a systematic review and meta-analysis to assess the efficacy, safety and tolerability of sodium-glucose co-transporter-2 inhibitors vs placebo as add-on therapy after metformin and dipeptidyl peptidase-4 inhibitor dual therapy in type 2 diabetes.

METHODS

This systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PROSPERO registration number: CRD42018099398). A search was conducted via PubMed, www.clinicaltrials.gov and Cochrane Central Register of Controlled Trials of relevant randomised controlled trials up until 14 August 2020 that compared sodium-glucose co-transporter-2 inhibitors vs placebo as add-on therapy after metformin and dipeptidyl peptidase-4 inhibitor therapy. A random-effects model was used.

RESULTS

Six randomised controlled trials (1661 participants) met the inclusion criteria. Compared with placebo, sodium-glucose co-transporter-2 inhibitor treatment, as add-on to metformin and dipeptidyl peptidase-4 inhibitor therapy, was associated with a significant reduction in HbA_1c level [mean difference -8 mmol/mol, 95% CI -10, -6 (-0.7%, 95% CI -0.9, -0.6); P < 0.00001], in fasting plasma glucose level [mean difference -1.70 mmol/l, 95% CI -1.91, -1.49; P < 0.00001], in weight (mean difference -1.76 kg, 95% CI -2.04, -1.48; P < 0.00001) and in blood pressure (systolic blood pressure: mean difference -3.6 mmHg, 95% CI -4.8, -2.4; P < 0.00001; diastolic blood pressure: mean difference -1.5 mmHg; 95% CI -2.4, -0.6; P = 0.002). Genital mycotic infections (odds ratio 7.37, 95% CI 3.06, 17.76; P < 0.00001) were more common with sodium-glucose co-transporter-2 inhibitors, but there was no significant statistical difference in urinary tract infections (odds ratio 1.16, 95% CI 0.63, 2.13; P = 0.64), in hypoglycaemia (odds ratio 1.36, 95% CI 0.61, 3.04; P = 0.45), or in discontinuation rates due to adverse events (odds ratio 1.52, 95% CI 0.78, 2.97; P = 0.22) between the two groups.

CONCLUSIONS

In comparison with placebo, add-on therapy with a sodium-glucose co-transporter-2 inhibitor is significantly more efficacious in lowering HbA_1c , fasting plasma glucose and weight in people with type 2 diabetes following inadequate glycaemic control with metformin and a dipeptidyl peptidase-4 inhibitor. The rate of discontinuation due to adverse events was similar despite higher risk of genital mycotic infections.

What factors influence organisational readiness for change? Implementation of the Australian clinical pathway for the screening, assessment and management of anxiety and depression in adult cancer patients (ADAPT CP)

AIMS

Translation of evidence-based psycho-oncology interventions into routine care can significantly improve patient outcomes, yet effective implementation remains challenging due to numerous real-world barriers. A key factor that may influence implementation is organisational readiness for change. This mixed method study sought to identify factors associated with organisational readiness for implementing the Australian clinical pathway for the screening, assessment and management of anxiety and depression in adult cancer patients (ADAPT CP).

METHODS

We collected data from multidisciplinary staff across six Australian cancer services who were preparing to implement the ADAPT CP. Services were categorised as having 'high' versus 'mid-range' organisational readiness based on a median split on the Organizational Readiness for Implementing Change (ORIC) questionnaire (score range = 12-60). Qualitative data from the semi-structured interviews based on the Promoting Action Research in Health Services (PARiHS) framework were analysed thematically and compared for services with high- versus mid-range organisational readiness.

RESULTS

Three services with high- (mean ORIC range, 52.25-56.88), and three with mid-range (range, 38.75-46.39) organisational readiness scores were identified. Staff at services reporting higher readiness described a more collaborative and proactive service culture, strong communication processes and greater role flexibility. They also reported greater confidence in overcoming anticipated barriers and clearer strategies for addressing issues.

CONCLUSIONS

Levels of organisational readiness were related to distinct qualitative themes. Targeting these issues in services where readiness is mid-range or low prior to full-scale roll-out may improve staff levels of confidence and efficacy in implementing psycho-oncology-focused interventions.

Post-tuberculosis lung health: perspectives from the First International Symposium

ALTHOUGH CURABLE, TB frequently leaves the individual with chronic physical and psycho-social impairment, but these consequences have been largely neglected. The 1^st International Post-Tuberculosis Symposium (Stellenbosch, South Africa) was held to discuss priorities and gaps in addressing this issue. A barrier to progress has been the varied terminology and nomenclature, so the Delphi process was used to achieve consensus on definitions. Lack of sufficient evidence hampered definitive recommendations in most domains, including prevention and treatment of post-TB lung disease (PTLD), but the discussions clarified the research needed. A consensus was reached on a toolkit for future PTLD measurement and on PTLD patterns to be considered. The importance of extra-pulmonary consequences and progressive impairment throughout the life-course was identified, including TB recurrence and increased mortality. Patient advocates emphasised the need to address the psychological and social impacts post TB and called for clinical guidance. More generally, there is an urgent need for increased awareness and research into post-TB complications.

Enabling automated herbarium sheet image post-processing using neural network models for color reference chart detection

PREMISE

Large-scale efforts to digitize herbaria have resulted in more than 18 million publicly available Plantae images on sites such as iDigBio. The automation of image post-processing will lead to time savings in the digitization of biological specimens, as well as improvements in data quality. Here, new and modified neural network methodologies were developed to automatically detect color reference charts (CRC), enabling the future automation of various post-processing tasks.

METHODS AND RESULTS

We used 1000 herbarium specimen images from 52 herbaria to test our novel neural network model, ColorNet, which was developed to identify CRCs smaller than 4 cm2, resulting in a 30% increase in accuracy over the performance of other state-of-the-art models such as Faster R-CNN. For larger CRCs, we propose modifications to Faster R-CNN to increase inference speed.

CONCLUSIONS

Our proposed neural networks detect a range of CRCs, which may enable the automation of post-processing tasks found in herbarium digitization workflows, such as image orientation or white balance correction.

The Mortality After Release from Incarceration Consortium (MARIC): Protocol for a multi-national, individual participant data meta-analysis

INTRODUCTION

More than 30 million adults are released from incarceration globally each year. Many experience complex physical and mental health problems, and are at markedly increased risk of preventable mortality. Despite this, evidence regarding the global epidemiology of mortality following release from incarceration is insufficient to inform the development of targeted, evidence-based responses. Many previous studies have suffered from inadequate power and poor precision, and even large studies have limited capacity to disaggregate data by specific causes of death, sub-populations or time since release to answer questions of clinical and public health relevance.

OBJECTIVES

To comprehensively document the incidence, timing, causes and risk factors for mortality in adults released from prison.

METHODS

We created the Mortality After Release from Incarceration Consortium (MARIC), a multi-disciplinary collaboration representing 29 cohorts of adults who have experienced incarceration from 11 countries. Findings across cohorts will be analysed using a two-step, individual participant data meta-analysis methodology.

RESULTS

The combined sample includes 1,337,993 individuals (89% male), with 75,795 deaths recorded over 9,191,393 person-years of follow-up.

CONCLUSIONS

The consortium represents an important advancement in the field, bringing international attention to this problem. It will provide internationally relevant evidence to guide policymakers and clinicians in reducing preventable deaths in this marginalized population.

KEY WORDS

Mortality; incarceration; prison; release; individual participant data meta-analysis; consortium; cohort.

Randomised controlled trial of internet-delivered cognitive behaviour therapy for clinical depression and/or anxiety in cancer survivors (iCanADAPT Early)

PURPOSE

To evaluate internet-delivered cognitive behavioural therapy (iCBT) on clinical depression and/or anxiety, distress, fear of cancer recurrence, and quality of life in cancer survivors.

METHODS

Random assignation of 114 participants to iCBT or treatment-as-usual (TAU). The clinician-supervised iCBT program (iCanADAPT Early) consisted of eight lessons over 16 weeks. Self-report questionnaires occurred at baseline, midpoint, and posttreatment for both groups with 3-month follow-up for iCBT participants. A mixed modelling approach to compare groups occurred.

RESULTS

iCBT was superior to TAU on all outcome measures at posttreatment. Compared with TAU, the iCBT group showed a significant decrease over time in anxiety and depression symptoms (primary outcome, Hospital Anxiety and Depression Scale, Hedges g = 1.51). Additionally the iCBT group had significantly lower general distress (Kessler-10, g = 1.56), fear of cancer recurrence (Fear of Cancer Recurrence Inventory, g = 0.39), and significantly higher quality of life (Functional Assessment of Cancer Therapy-General, g = 0.74) at posttreatment compared with the TAU group. High adherence and satisfaction were found for iCBT with low clinician time.

CONCLUSION

Clinician-supervised iCBT has significant benefits for cancer survivors with clinical depression and anxiety disorders.

The personality disorder patient pathway: Service user and clinical perspectives

AIMS

There have been recent policy developments and research into care provision for service users with personality disorder. However, few studies have focused on service user and staff perspectives on how services could be improved.

METHODS

A qualitative study was undertaken in the UK between 2016 and 2017. We conducted six focus groups with clinicians in mental health services with experience of working with people with personality disorder. Using an online survey, we asked current and past service users with personality disorder to describe their experiences of mental health services and make recommendations for improvements. A thematic analysis was conducted.

RESULTS

Forty-five clinicians participated in the focus group and 131 service users contributed to the online survey. The main areas of concern identified by both staff and patients were the diagnosis of personality disorder, the absence of a coherent care pathway, access to psychological treatment and staff training.

CONCLUSIONS

The care pathway for individuals with personality disorder is unclear to clinicians and service users, and elements of the pathway are disjointed and not working as effectively as they could. Guidelines recommended by National Institute for Health and Care Excellence are not being followed. Specialist psychological interventions should be available to ensure consistent and stable care provision. © 2019 John Wiley & Sons, Ltd.

A born-digital field-to-database solution for collections-based research using collNotes and collBook

PREMISE

The digitization of natural history collections includes transcribing specimen label data into standardized formats. Born-digital specimen data initially gathered in digital formats do not need to be transcribed, enabling their efficient integration into digitized collections. Modernizing field collection methods for born-digital workflows requires the development of new tools and processes.

METHODS AND RESULTS

collNotes, a mobile application, was developed for Android and iOS to supplement traditional field journals. Designed for efficiency in the field, collNotes avoids redundant data entries and does not require cellular service. collBook, a companion desktop application, refines field notes into database-ready formats and produces specimen labels.

CONCLUSIONS

collNotes and collBook can be used in combination as a field-to-database solution for gathering born-digital voucher specimen data for plants and fungi. Both programs are open source and use common file types simplifying either program's integration into existing workflows.

Markers in time and space: A review of the last decade of plant phylogeographic approaches

Plant studies comprise a relatively small proportion of the phylogeographic literature, likely as a consequence of the fundamental challenges posed by the complex genomic structures and life history strategies of these organisms. Comparative plastomics (i.e., comparisons of mutation rates within and among regions of the chloroplast genome) across plant lineages has led to an increased understanding of which markers are likely to provide the most information at low taxonomic levels. However, the extent to which the results of such work have influenced the literature has not been fully assessed, nor has the extent to which plant phylogeographers explicitly analyse markers in time and space, both of which are integral components of the field. Here, we reviewed more than 400 publications from the last decade of plant phylogeography to specifically address the following questions: (i) What is the phylogenetic breadth of studies to date? (ii) What molecular markers have been used, and why were they chosen? (iii) What kinds of markers are most frequently used and in what combinations? (iv) How frequently are divergence time estimation and ecological niche modelling used in plant phylogeography? Our results indicate that chloroplast DNA sequence data remain the primary tool of choice, followed distantly by nuclear DNA sequences and microsatellites. Less than half (42%) of all studies use divergence time estimation, while even fewer use ecological niche modelling (14%). We discuss the implications of our findings, as well as the need for community standards on data reporting.