Genomic Machine Learning Meta-regression: Insights on Associations of Study Features with Reported Model Performance

Background: Many studies have been conducted with the goal of correctly predicting diagnostic status of a disorder using the combination of genetic data and machine learning. The methods of these studies often differ drastically. It is often hard to judge which components of a study led to better results and whether better reported results represent a true improvement or an uncorrected bias inflating performance. Methods: In this systematic review, we extracted information about the methods used and other differentiating features in genomic machine learning models. We used the extracted features in mixed-effects linear regression models predicting model performance. We tested for univariate and multivariate associations as well as interactions between features. Results: In univariate models the number of hyperparameter optimizations reported and data leakage due to feature selection were significantly associated with an increase in reported model performance. In our multivariate model, the number of hyperparameter optimizations, data leakage due to feature selection, and training size were significantly associated with an increase in reported model performance. The interaction between number of hyperparameter optimizations and training size as well as the interaction between data leakage due to optimization and training size were significantly associated reported model performance. Conclusions: Our results suggest that methods susceptible to data leakage are prevalent among genomic machine learning research, which may result in inflated reported performance. The interactions of these features with training size suggest that if data leakage susceptible methods continue to be used, modelling efforts using larger data sets may result in unexpectedly lower results compared to smaller data sets. Best practice guidelines that promote the avoidance and recognition of data leakage may help the field advance and avoid biased results.

Analysis of COVID-19 news coverage by Televisión Española (TVE1)

This article analyzes the news coverage of the COVID-19 health crisis by Televisión Española (TVE1), to determine if this media reported the news with rigor and in accordance with journalism professional codes and best practice guidelines. For this purpose, content analysis was conducted on the universe of news stories (n=1,449) in the TVE1 daily newscast, starting with the first outbreak of the pandemic on the Iberian Peninsula on February 26, 2020, until the end of the first state of emergency on June 21, 2020. Our categories of analysis were: information sources, news frames, predominant topics, resources used for dramatic effects, and breaches of journalism ethics in reporting news. In general, TVE1 did not engage in sensationalized or dramatized news coverage, but instead attempted to transmit a message that was educational and instructional. Its policy was to provide information on measures adopted by authorities to help prevent the spread of the pandemic. Nevertheless, TVE’s benevolent attitude towards the government and its policies can be observed in its news reporting, revealing a lack of impartiality and editorial independence by this media. Despite the importance of specialized and expert information in times of a pandemic, eyewitness sources were those most used in reporting news, even in economic news framing. Furthermore, these latter sources were employed instead of expert ones, which were in fact the least used, and whose presence progressively declined during the analyzed period.

Language Matters: How Baker Library is Working Towards Conscious and Inclusive Description

Inclusive and conscious archival description can support consistency in researching and describing marginalized groups and can serve to provide context and a counter-narrative reflecting the perspective of the documented community. It can also help to address the power imbalances between creators and subjects of records. In this article, the authors describe efforts to prepare best practice guidelines for inclusive description and for revising descriptions to remediate outdated, problematic, or offensive language and meet modern standards. They also share how the project team is working together to create meaningful and enduring changes that both provide a better experience for staff and users and support Harvard Business School’s Action Plan for Racial Equality.

Evaluation and Treatment of Post-Extubation Dysphagia: The Importance of the Speech Pathologist in the Intensive Care Unit

Purpose: Post-extubation dysphagia is associated with negative health outcomes including pneumonia, prolonged hospital stay, in-hospital mortality, and inability to discharge home. The purpose of this review article is to summarize published research on screening, evaluating, and treating post-extubation dysphagia. Method: Review of published literature on post-extubation dysphagia to shape best practice guidelines for speech pathologists. Results: Current research on post-extubation dysphagia focuses heavily on screening and evaluation. There are limited data on targeted treatment methods for post-extubation dysphagia. Conclusions: Speech pathologists play a critical role in helping patients safely return to oral alimentation following prolonged endotracheal intubation. Speech pathologists should use the available research to shape best practice guidelines within their facility for who, when, and how to evaluate for dysphagia following extubation.

Intra-articular glucocorticoid injection site: best practice guidelines

The article presents modern recommendations for the use of systemic administration of glucocorticoids. It is indicated that there is a clear tendency to minimize the doses and timing of the appointment of systemic glucocorticoids in rheumatoid arthritis, and in seronegative spondyloarthropathies (ankylosing spondylitis, psoriatic arthritis), in accordance with both foreign and domestic recommendations, systemic therapy with glucocorticoids is not carried out. It is emphasized that at the present stage, the role of local administration of glucocorticoids will increase as an effective way to reduce the activity of arthritis in any nosologically form. The mechanisms of action of locally administered glucocorticoids leading to anti-inflammatory and analgesic effects are described. The comparative characteristics of locally administered glucocorticoids with different duration of action according to their effectiveness and safety are presented. Predictors of the effectiveness of local therapy with glucocorticoids are described. The data on the evaluation of the duration of the anti-inflammatory and analgesic effects of various local glucocorticoids, including in comparison with the intra-articular administration of hyaluronic acid preparations, which showed the advantages of betamethasone over triamcinolone acetate, are presented. The differences in the crystal structure of betamethasone and triamcinolone acetate are described. It is indicated that the 2.5-fold smaller size of betamethasone crystals compared to triamcinolone acetate crystals and the absence of betamethasone crystals makes it possible to use betamethasone in the treatment of inflammatory processes in periarticular tissues, as well as in crystalline arthritis (gout, pseudogout). The data on the safety of the use of intra-articular injection of glucocorticoids are presented. It is indicated that the registration in the Russian Federation of a new form of betamethasone in pre-filled syringes makes it even more possible to avoid infectious complications of this type of therapy. Rare cases of complications of local therapy with glucocorticoids are described.

Using Keeper Questionnaires to Capture Zoo-Housed Tiger (Panthera tigris) Personality: Considerations for Animal Management

Individual personalities affect animal experiences of zoo environments, impact on an animal’s coping ability and have potential implications for welfare. Keeper assessments have been identified as a quick and reliable way of capturing data on personality in a range of species and have practical application in improving animal welfare on an individual level. Despite widespread recognition of the importance of animal personality within a zoo environment, there is a paucity of research into tiger personality and the potential impact of this on tiger experiences within zoos. This research investigated the personality of 34 tigers (19 Amur and 15 Sumatran) across 14 facilities in the UK using keeper ratings and identified changes keepers made in animal husbandry to support tiger welfare. Reliability across keepers (n = 49) was established for nine adjectives and a principal component analysis identified three personality components: ‘anxious’, ‘quiet’ and ‘sociable’. When subspecies were combined, there was no relationship between tiger scores on the personality components and age or sex of tigers (p > 0.05). Subspecies of tiger was not related to scores on the ‘quiet’ or ‘sociable’ components (p > 0.05). Sumatran tigers scored more highly than Amur tigers on the ‘anxious’ component (mean ± SD, Sumatran: 3.0 ± 1.7, Amur: 1.8 ± 0.6, p < 0.05). Analysis within subspecies found that male Amur tigers were more sociable than females (mean ± SD, males: 5.5 ± 0.707; females: 4.15 ± 0.55). Amur tiger age was also negatively correlated with scores on the sociable personality component (R = −0.742, p < 0.05). No significant differences were seen in Sumatran tigers. Keepers reported a number of changes to husbandry routines based on their perceptions of their tigers’ personality/needs. However, there was no significant relationship between these changes and tiger personality scores (p > 0.05). Despite significant evolutionary differences between Amur and Sumatran tigers, there are no subspecies specific guidelines for zoo tigers. This research has highlighted the potential for these two subspecies to display personality differences and we advocate further research into this area. Specifically, we highlight a need to validate the relationship between tiger personality, management protocols and behavioural and physiological metrics of welfare. This will enable a fuller understanding of the impact of personality on zoo tiger experiences and will enable identification of evidence-based best practice guidelines.

Tutorial on Clinical Practice for Use of the Fiberoptic Endoscopic Evaluation of Swallowing Procedure With Adult Populations: Part 1

Purpose: Representatives of the American Board of Swallowing and Swallowing Disorders (AB-SSD) and American Speech-Language-Hearing Association (ASHA) Special Interest Group (SIG) 13: Swallowing and Swallowing Disorders (Dysphagia) developed this tutorial to identify and recommend best practice guidelines for speech-language pathologists who conduct and interpret fiberoptic endoscopic evaluation of swallowing (FEES) procedures in adults. This document also includes proposed training needs and methods for achieving competency. Expert opinion is provided regarding indications for performing the FEES exam, potential contraindications, adverse effects and safety, equipment and personal protection, the exam protocol, interpretation and documentation of findings, and training requirements to perform and interpret the exam. Conclusions: This tutorial by the AB-SSD and SIG 13 represents the first update about the FEES procedure since ASHA's position paper and technical report published in 2004. Creation of this document by members of the AB-SSD and SIG 13 is intended to guide professionals who are training for or practicing FEES in the adult population toward established best practices and the highest standards of care.