bluuebunny/crossref_metadata_2025_split huggingface dataset:
Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees
Authors: Smith Martin R 
Published: June 2020

Abstract

Motivation
The Robinson–Foulds (RF) metric is widely used by biologists, linguists and chemists to quantify similarity between pairs of phylogenetic trees. The measure tallies the number of bipartition splits that occur in both trees—but this conservative approach ignores potential similarities between almost-identical splits, with undesirable consequences. ‘Generalized’ RF metrics address this shortcoming by pairing splits in one tree with similar splits in the other. Each pair is assigned a similarity score, the sum of which enumerates the similarity between two trees. The challenge lies in quantifying split similarity: existing definitions lack a principled statistical underpinning, resulting in misleading tree distances that are difficult to interpret. Here, I propose probabilistic measures of split similarity, which allow tree similarity to be measured in natural units (bits).

Results
My new information-theoretic metrics outperform alternative measures of tree similarity when evaluated against a broad suite of criteria, even though they do not account for the non-independence of splits within a single tree. Mutual clustering information exhibits none of the undesirable properties that characterize other tree comparison metrics, and should be preferred to the RF metric.

Availability and implementation
The methods discussed in this article are implemented in the R package ‘TreeDist’, archived at https://dx.doi.org/10.5281/zenodo.3528123.

Supplementary information
Supplementary data are available at Bioinformatics online.
Community development ‘yet-to-come’ during and post the COVID-19 pandemic: from Derrida to Zuboff
Authors: Westoby Peter , Harris Verne 
Published: June 2020

AbstractThe contours of this article, written as a dialogue between two authors, one in Australia (Westoby) and one in South Africa (Harris), outline a Derridean deconstruction of community development ‘yet-to-come’ during and post coronavirus disease 2019. Reflecting on our two countries’ experiences, drawing on theorists such as Zuboff (surveillance capitalism), Freire (critical literacy), Foucault (biopower), Escobar (pluriversality) and Berardi (semio-capitalism), we argue for transformational critical digital literacy work that enables greater community awareness of the consequences of digital lives and also transformative praxis. Riffing off many experiences that readers will be familiar with (lockdown, social distancing, tracing apps, virtual meetings and so on), the dialogue also suggests a soulful community development yet-to-come, foregrounding embodied lives, slowness, place, relationality and connection.
Investigating Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Surface and Air Contamination in an Acute Healthcare Setting During the Peak of the Coronavirus Disease 2019 (COVID-19) Pandemic in London
Authors: Zhou Jie , Otter Jonathan A , Price James R , Cimpeanu Cristina , Meno Garcia Danel , Kinross James , Boshier Piers R , Mason Sam , Bolt Frances , Holmes Alison H , Barclay Wendy S 
Published: June 2020

Abstract

Background
We evaluated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface and air contamination during the coronavirus disease 2019 (COVID-19) pandemic in London.

Methods
Prospective, cross-sectional, observational study in a multisite London hospital. Air and surface samples were collected from 7 clinical areas occupied by patients with COVID-19 and a public area of the hospital. Three or four 1.0-m3 air samples were collected in each area using an active air sampler. Surface samples were collected by swabbing items in the immediate vicinity of each air sample. SARS-CoV-2 was detected using reverse-transcription quantitative polymerase chain reaction (PCR) and viral culture; the limit of detection for culturing SARS-CoV-2 from surfaces was determined.

Results
Viral RNA was detected on 114 of 218 (52.3%) surfaces and in 14 of 31 (38.7%) air samples, but no virus was cultured. Viral RNA was more likely to be found in areas immediately occupied by COVID-19 patients than in other areas (67 of 105 [63.8%] vs 29 of 64 [45.3%]; odds ratio, 0.5; 95% confidence interval, 0.2–0.9; P = .025, χ2 test). The high PCR cycle threshold value for all samples (&gt;30) indicated that the virus would not be culturable.

Conclusions
Our findings of extensive viral RNA contamination of surfaces and air across a range of acute healthcare settings in the absence of cultured virus underlines the potential risk from environmental contamination in managing COVID-19 and the need for effective use of personal protective equipment, physical distancing, and hand/surface hygiene.
Prevalence of Potential Drug–Drug Interactions in Patients of the Swiss HIV Cohort Study in the Era of HIV Integrase Inhibitors
Authors: Deutschmann Elisabeth , Bucher Heiner C , Jaeckel Steffen , Gibbons Sara , McAllister Katie , Scherrer Alexandra U , Braun Dominique L , Cavassini Matthias , Hachfeld Anna , Calmy Alexandra , Battegay Manuel , Cipriani Michela , Elzi Luigia , Young James , Lopez-Centeno Beatriz , Berenguer Juan , Khoo Saye , Moffa Giusi , Marzolini Catia ,   Swiss HIV Cohort Study
Published: June 2020

Abstract

Background
Prevalence of potential drug–drug interactions (PDDIs) between antiretroviral drugs (ARVs) and co-medications was high in 2008 in a Swiss HIV Cohort Study (SHCS) survey. We reassessed the prevalence of PDDIs in the era of human immunodeficiency virus (HIV) integrase inhibitors (INIs), characterized by more favorable interaction profiles.

Methods
The prevalence of PDDIs in treated HIV-positive individuals was assessed for the period 01–12/2018 by linkage of the Liverpool HIV drug interactions and SHCS databases. PDDIs were categorized as harmful (red flagged), of potential clinical relevance (amber flagged), or of weak clinical significance (yellow flagged).

Results
In 9298 included individuals, median age was 51 years (IQR, 43–58), and 72% were males. Individuals received unboosted INIs (40%), boosted ARVs (30%), and nonnucleoside reverse transcriptase inhibitor (NNRTIs) (32%)–based regimens. In the entire cohort, 68% received ≥1 co-medication, 14% had polypharmacy (≥5 co-medications) and 29% had ≥1 PDDI. Among individuals with co-medication, the prevalence of combined amber and yellow PDDIs was 43% (33% amber—mostly with cardiovascular drugs—and 20% yellow-flagged PDDIs) compared to 59% in 2008. Two percent had red-flagged PDDIs (mostly with corticosteroids), the same as in the 2008 survey. Compared with 2008, fewer individuals received boosted ARVs (−24%) and NNRTIs (−13%) but the use of co-medications was higher.

Conclusions
Prevalence of PDDIs was lower with more widespread use of INIs in 2018 than in 2008. Continued use of boosted regimens and increasing needs for co-medications in this aging population impeded lower rates of PDDIs.
Effect of wearable sensor-based Otago Exercise Program biofeedback in older adults with moderate to high risk of falling
Authors: Martins A C , Francisco D , Guia D 
Published: June 2020

Abstract
Introduction Falls remain a major public health issue. The ageing process is characterized by a progressive decrease in muscle strength, reaction time, postural control and changes in sensory systems. Wearable sensor-based biofeedback systems used in physiotherapy, particularly incorporated in exercise programs, are promising strategies to enhance the learning of strength and balance exercises and improve self-efficacy.
Objectives To evaluate the effect of the wearable sensor-based Otago Exercise Program (OTAGO) biofeedback in older adults with moderate to high risk.
Methodology Sixty participants (84.35 years) were distributed to the experimental group (26) and a control group (34). The EG underwent the OTAGO incorporated in a technological system using pressure and inertial sensors and biofeedback in real-time, administered by a physiotherapist for 5 weeks, with a frequency of 2 times a week. The CG kept doing their regular activities. Outcome measures included handgrip strength (HG), Time Up and Go (TUG), 30 seconds Sit to Stand, 10 meters Walking Speed (10m WS), 4 Stage Balance Test “Modified”, Step test and Questionnaire of Self-efficacy for exercise.
Results At baseline, significant differences were observed regarding the 10m WS (p &lt; 0.001), TUG (p = 0.036) and HG (p = 0.001). Relatively to 4SBTM, in post-intervention was seen significant difference (p = 0.008) and in EG there was also substantial results (p &lt; 0.001). The same happens in SEE (p = 0.013 and p = 0.020, respectively). A significant increase was found in EG so that the post-intervention 10m WS was statistically higher compared with the CG (EG: 0.42±0.29; CG: 1.10±0.51; p = 0.003). In the CG worst results were observed in some of the functional tests.
Conclusion Biofeedback in real-time facilitates the self-learning of the exercise program, and it is a useful tool for training strength, balance and self-efficacy for exercise, contributing to reducing the risk of falls.
Impact of adverse effects to oral antidiabetics on adherence and quality of life in patients with type 2 diabetes
Authors: Almeida C , Rocha C , Cruz R 
Published: June 2020

Abstract
Introduction Diabetes is a metabolic disorder with many comorbidities, microvascular and macrovascular complications. In Portugal the prevalence was 13,3% which corresponds to 1 million Portuguese diagnosed, but the forecasts are for a big increase. The various therapeutic options currently available have been shown to be effective in controlling glycaemia and HbA1 levels. Adherence with this therapeutic is essential for optimization and control of chronic conditions. However, they present side effects that may compromise adherence to therapy and the quality of life of the patients.
Objectives The objective of this study is to evaluate the impact of the adverse effects of oral antidiabetic medicines on patient’s quality of life and adherence to therapy.
Methodology We developed a cross-sectional study in a sample of 65 patients with type 2 diabetes recruited in several Portuguese pharmacies. Data collected through a questionnaire previously validated with MAT Scale and EQ-5D-3L questionnaire.
Results In total, 36 men (55,4%) and 29 women (44,6%) participated in the study, the mean age was 65 years. 73,8 % take oral medication and 92,30% of people have high adherence. The adverse events with more impact in the patients’ perception are "Discomfort in the genital area", "Dry mouth" and gastrointestinal events such as "Abdominal distention", "Flatulence" and "Constipation". The number of adverse events have a negative impact on patients’ quality of life (rs=-0,479; p≤0,01). The satisfaction with the therapeutic regime is significantly associated with adherence (rs = 0,348; p≤0,01)and their quality of life (rs = 0,316; p=0,01).
Conclusion We concluded that the adverse events have a negative impact on adherence and quality of life. The presence of adverse events, the type of medication and the therapeutic regimen are factors that negatively influence the patients’ quality of life, especially in the polymedicated elderly people.
Development of a Virtual Game with Android Operating System for the Rehabilitation of Chewing and Swallowing in the Elderly
Authors: Lins C , Silva T , Albuquerque L , Moreira R , Coriolano M , Rodrigues M 
Published: June 2020

Abstract
Introduction With the aging, the orofacial structures may suffer changes related to disorganization of the stomatognathic system, with a reduction in the strength and resistance of the tongue reflecting delays in the handling of the boluses in the mouth and the elevation of the hyolaryngeal complex; it may result in changes in swallowing (presbifagia or dysphagia). Changes in swallowing may be adjuvants for the illness of the elderly with great socioeconomic impact due to the high costs that bring to the public health with prolonged hospitalizations.
Objectives Before it an app was created with a board game for android operating system with the possibility of training in the functions of chewing and swallowing in elderly using biofeedback.
Methodology A hardware was built capable of capturing, conditioning and transmitting the electrical signal of the masseter and supra-hyoid muscles, with surface electrodes, using an interface system scan with four channels for a mobile device with Android operating system via Bluetooth. The electrical signal is received by software through a biogame, which originally held the calibration of the data, being the value range of the strength of the bite ranging from zero to 255 µV. The participant will receive the information to chew and swallow through the simulation of a “virtual farm” with the displacement of a tractor irrigating the earth which will create a plantation. The chewing cycle was standardized in 10 insect chewing’s, five for each side, ending with the swallowing.
Results At the end of the game a report stating: date of the examination, consistency of the food chosen, testing time, masticatory cycles completed and incomplete, maximum and average power of bite and muscle activity of the swallowing of each side.
Conclusion The application with game developed is a promising resource for training of the masticatory muscles and the swallowing of the elderly.
Hearing Screening in Preschool Children of a Rural Community in Portugal - A 10-year Experience
Authors: Fonseca S , Reis C , Monteiro L , Monteiro C , Serrano M 
Published: June 2020

Abstract
Introduction Preschool hearing screening programmes would identify later onset or progressive hearing losses and conductive hearing loss, due to the high prevalence of otitis media with effusion in childhood. Hearing loss associated with otitis media with effusion can have a great impact on reading, writing, central auditory processing and balance.
Objectives The present study aims at characterising the audiological alterations found in preschool children screened in a rural community in Portugal, and the correlation between audiological findings and otoscopy.
Methodology This is an observational study using the results obtained in a ten year audiological and otological screening of preschool children. Otoscopy, Tympanometry and Audiometry (1, 2 and 4 KHz presented at 40 and 20 dB intensity) were performed at the first stage of the screening and the results were classified as “pass” or “refer”. Every non-normal result of any category would imply a second stage consisting of observation by an ENT specialist at the site and the establishing of a follow-up plan. Written Informed Consent was obtained from the parents prior to initiating the study.
Results 595 children aged 5 and 6 years were screened between 2007 and 2017, of whom 192 (32.3%) required referral to the second stage. The most frequent alteration was found in the tympanogram. The tympanograms showed a significant correlation with the otoscopy performed by the ENT doctor, mainly type B tympanograms. The pass/refer audiometry also showed a statistically significant correlation with the medical otoscopy, although weak in all frequencies studied.
Conclusion It’s extremely important to perform a hearing screening in the age range of 5-6 years (with a high predisposition to middle ear problems), with the main objective of identifying and referring for treatment children who present alterations in order to reduce the consequences of the hearing impairment.
Cybersecurity risk analysis in healthcare institutions
Authors: Nunes P , Antunes M , Silva C 
Published: June 2020

Abstract
Introduction The growing digitization of businesses and its increasing dependence on Internet infrastructure has boosted the concerns related to data privacy and confidentiality. Healthcare institutions have been challenged with specific issues, namely the sensitivity of data, the specificity of networked equipment and the average information technology skills held by of healthcare professionals in Portugal.
Objectives To understand the relationship level established by healthcare professionals with the information security by assessing attitudes and behaviours in cybersecurity; to identify risks and actions that may be taken to enhance the healthcare professional’s cybersecurity awareness.
Methodology The study consists in translating, adjusting and applying two previously validated and published Likert-type response scales to assess health professionals' cybersecurity attitudes and behaviours in the Portuguese health environment. This is an observational, quantitative, cross-sectional and descriptive study in cybersecurity attitudes and behaviours in a healthcare institution in Portugal.
Results The sample was composed by 56 professionals, 71% women and 29% men, divided in four professional groups, where a mean (±SD) of 31.59 (±14.211) points was achieved for the cybersecurity risky behaviour (RScB) scale and 66.41 (±6,26) points for the cybersecurity and cybercrime in business attitudes scale (ATC-IB).
Conclusions There was no-significant statistical differences between the sociodemographic factors and the scores obtained on both scales. However, the points of the scales for the different domains evidences a statistical difference between ages, genders and professional groups by items, which are therefore important points for the development of future studies. The results showed a relationship between acquired behaviours and the attitudes of involvement with work and organizational commitment, establishing a bridge for the quantification in awareness.
Big data and machine learning in health
Authors: Carvalho D , Cruz R 
Published: June 2020

Abstract
Introduction Big data is defined as the amount of data that once organized and analysed, can make a value, make decisions, make predictions and discover patterns in order to reduce costs, avoid risks and optimize services. Machine Learning (ML) is a field of artificial intelligence and is characterized as a method of machine learning, which uses algorithms that learn from data analysis, allowing computers to find patterns, draw conclusions and make predictions. These tools can be used in different areas of human knowledge, particularly in the health sector which are generated daily a huge amount of information, allowing the creation of algorithms that learn and gain understanding to assist in various clinical practices.
Objectives The purpose of this paper is to analyse the benefits of Big Data and Machine Learning in providing overall health care.
Methodology We conducted a review of the scientific literature published in the electronic databases PubMed/MEDLINE and Google Scholar, according to specific criteria, using keywords: Big Data”, “Machine Learning".
Results In the field of oncology (skin cancer, breast, lung, leukaemia) ML and Big Data have contributed to early diagnosis of different pathologies and their evolution, as well as optimizing therapies. In ophthalmology (diabetic retinopathy and congenital cataract) has shown high efficacy in rapid diagnosis and appropriate treatment crucial to prevent the progress of the disease. The tested algorithms achieved very favourable results in cases of Parkinson’s and cardiovascular diseases. In the pharmaceutical industry these computer and digital tools have contributed to the optimization of clinical trials, genome sequencing of tumours to then identify and develop specific drugs to fight it.
Conclusion Advances of MIL and Big data are notorious and development opportunities are immense and can come to revolutionize tasks such as diagnosis, treatment and health care in general.
Influence of prenatal exposure to dexamethasone on neurodevelopmental behaviour
Authors: Cruz A , Henriques C , Ferreira A , Galvão S , Neves C , Gaspar R , Ambrósio A , Gomes C , Baptista F 
Published: June 2020

Abstract
Introduction Early life stress, such as prenatal exposure to exogenous glucocorticoids (GC), can have a negative impact on brain development. Dexamethasone (DEX) is a synthetic GC used in preterm pregnancies to promote lung maturation. However, prenatal exposure to DEX induces an anxious-like behaviour in male and female offspring at adulthood. Notably, only males respond positively to therapeutics with a proposed anxiolytic.
Objectives Since the influence of prenatal DEX on neurodevelopmental behaviour remains to be elucidated and could help explain this difference in drug efficacy, we aim to clarify the effects of this GC on neurodevelopment during infancy, comparing male and female offspring neurodevelopment at this early age.
Methodology To obtain an animal model of chronic anxiety, Wistar pregnant dams were injected subcutaneously with DEX (1mg/kg) on gestational days 18 and 19. The vestibular system development, locomotion, upper limbs strength, discriminatory ability, auditory response and eye opening day were assessed in male and female offspring between P5 and P17. Animal procedures were approved by the Animal Welfare Committee and done in agreement with the law.
Results Male and female offspring prenatally exposed to DEX had a better performance in the tests assessing the vestibular system development and discriminatory ability, especially at P5 and P6. Additionally, DEX anticipated the day of eye opening and had a positive impact in the upper limb strength of the offspring of both sexes. However, the locomotor ability and auditory response were impaired comparing with controls.
Conclusion Exposure to DEX improves limb strength, balance, spatial orientation and anticipates eye opening. These results may suggest that prenatal DEX exposure promotes offspring development and maturation in both males and females. Prenatal DEX did not differently affect male and female neurodevelopment at early age. It remains to clarify the underlying motives that induce a dimorphic gender response to anxiolytic therapy in adulthood.
Assessing fitness to drive: Knowledge and practices from medical doctors and psychologists
Authors: Ferreira I , Gonçalves S , Almiro P 
Published: June 2020

Abstract
Introduction Medical and psychological assessment of fitness to drive is a professional activity performed in a large number of candidates and drivers to validate a driving license. Medical doctors and psychologists are responsible to assess medical and psychological abilities for driving, respectively. Despite the legal framework for assessing fitness to drive on each country, the knowledge and practices among professionals may vary.
Objectives To examine the knowledge and practices of Portuguese medical doctors and psychologists concerning the assessment of fitness to drive.
Methodology Two online questionnaires, one version for medical doctors and another for psychologists, were designed to measure self-reported knowledge and practices towards assessment of fitness to drive. The questionnaires were disseminated by e-mail to a non-probability sample, responding 273 participants, including 128 medical doctors and 145 psychologists.
Results In the sample of medical doctors, 49% recognized themselves as not qualified to do a medical assessment of fitness to drive, 40% reported lack of knowledge about the related legislation and the majority (83%) feel that would benefit from further education in this area. Concerning psychologists, 52.4% judged themselves as not qualified for psychological assessment for driving, 49.7% recognized lack of knowledge about the legislation and 70% would like to do training in this area. Both groups pointed lack of knowledge about several parameters such as mandatory assessments and periods, professional responsibilities and assessment methods.
Conclusion Medical doctors and psychologists highlighted lack of knowledge and confidence to practice assessments of fitness to drive. Academic education and training needs are pointed in order to improve the professional practices in those assessments with potential impact on road safety and public health.