Miracle-dz/UniFAR-FTUs huggingface dataset:
Regional neurodegeneration correlates with sleep-wake dysfunction after stroke.

Sleep-wake disruption is a key modifiable risk factor and sequela of stroke. The pathogenesis of post-stroke sleep dysfunction is unclear. It is not known whether post-stroke sleep pathology is due to focal infarction to sleep-wake hubs, or to accelerated post-stroke neurodegeneration in subcortical structures after stroke. We characterise the first prospective post-stroke regional brain volumetric and whole-brain, fibre-specific, white matter markers of objectively measured sleep-wake dysfunction. We hypothesised that excessively long sleep (≥8 hr) duration and poor sleep efficiency (<80%) measured using the Sensewear Armband 3-months post-stroke (n=112) would be associated with reduced regional brain volumes of a priori selected sleep-wake regions of interest when compared to healthy controls with optimal sleep characteristics (n=35). We utilised a novel technique known as whole brain fixel-based analysis to investigate the fibre-specific white-matter differences in participants with long sleep duration. Stroke participants with long sleep (n=24) duration exhibited reduced regional volumes of the ipsilesional thalamus and contralesional amygdala when compared to controls. Poor sleep efficiency after stroke (n=29) was associated with reduced ipsilesional thalamus, contralesional hippocampus, and contralesional amygdala volumes. Whole-brain fixel-based analyses revealed widespread macrostructural degeneration to the cortico-ponto-cerebellar tract in stroke participants with long sleep, with fibre reductions of up to 40%. Neurodegeneration to subcortical structures, which appear to be vulnerable to accelerated brain volume loss after stroke, may drive sleep-wake deficiencies post-stroke, independent of lesion characteristics and confounding comorbidities. We discuss these findings in the context of the clinicopathological implications of sleep-related neurodegeneration and attempt to corroborate previous mechanistic-neuroanatomical findings.
Validity of a nonspeech dynamic assessment of the alphabetic principle in preschool and school-aged children

Abstract Learning to read and spell is an important but difficult achievement for children who have complex communication needs. Given that assessment is a vital part of any intervention program, one major barrier is the lack of reliable and valid assessments for this population. This study evaluated the reliability and validity of Dynamic Assessment of the Alphabetic Principle (DAAP), which does not require spoken responses. For this study, 27 preschool and school-aged children with typical development completed the DAAP and other standard measures of phonemic awareness and early literacy. Results indicated the DAAP had high internal consistency and strong correlations among its subtests, indicating high reliability. Moreover, performance on the DAAP had high correlations with standard measures of phonemic awareness and early literacy, providing evidence of its validity. Consequently, the DAAP represents one approach to fill the important need for assessments of early literacy that do not require speech responses.
How Many Ways Can You Say That? Determining Linguistic Variation in Clinical Documents

Introduction Linguistic variation is a main contributing factor to the challenges for enabling computers to understand human language. Because language as a communication medium is meant to be expressive to convey complex concepts and thoughts, variations for stating the same or very similar information will inevitably continue to be an integrated part of language. However, computationally determining linguistic variation is surprisingly challenging as humans readily perform this task quite easily. For any section of text, multiple thoughts are typically expressed in the form of phrases that make up lexical subsections of sentences. Determining the different ways of conveying the same thought requires identifying the phrases that correspond to those thoughts. This is challenging because phrases are not easily implied from syntactic structure alone and sometimes do not conform to syntactic groupings at all.
Longitudinal associations between dietary quality and Alzheimer’s disease genetic risk on cognitive performance among African American adults

Abstract Poor diet quality (DQ) is associated with poor cognition and increased neurodegeneration, including Alzheimer’s disease (AD). We are interested in the role of DQ on cognitive functioning (by sex and increasing genetic risk for AD), in a sample of African American (AA) middle-aged adults. We analysed a sub-group of participants (about 55 % women; mean follow-up time of about 4·7 years) from the Healthy Aging in Neighborhoods of Diversity across the Life Span study with a genetic risk score for AD (hAlzScore). The Healthy Eating Index-2010, Dietary Approaches to Stop Hypertension and the mean adequacy ratio computed at baseline (2004–2009) and follow-up visits (2009–2013) were used to assess initial DQ and change over time. Linear mixed-effects regression models were utilised, adjusting for select covariates, selection bias and multiple testing. DQ change (ΔDQ) was associated with California Verbal Learning Test-List A – overall (0·15 (se 0·06), P = 0·008) and in women (0·21 (se 0·08), P = 0·006), at highest AD risk, indicating protective effects over time. Greater AD risk was longitudinally associated with poorer Clock Command Test scores in men. Poor DQ was positively and cross-sectionally associated with Trails B scores, but in women only. Better-quality diet was associated with a slower decline in verbal memory among AA women, with greater AD risk. Insufficient clinical evidence and/or mixed findings dictate that more studies are needed to investigate brain morphology and volume changes in relation to DQ in an at-risk population for AD, over time.
Cognitive Correlates of Digital Clock Drawing Metrics in Older Adults with and without Mild Cognitive Impairment.

BACKGROUND A digital version of the clock drawing test (dCDT) provides new latency and graphomotor behavioral measurements. These variables have yet to be validated with external neuropsychological domains in non-demented adults. OBJECTIVE The current investigation reports on cognitive constructs associated with selected dCDT latency and graphomotor variables and compares performances between individuals with mild cognitive impairment (MCI) and non-MCI peers. METHODS 202 non-demented older adults (age 68.79 ± 6.18, 46% female, education years 16.02 ± 2.70) completed the dCDT and a comprehensive neuropsychological protocol. dCDT variables of interest included: total completion time (TCT), pre-first hand latency (PFHL), post-clock face latency (PCFL), and clock face area (CFA). We also explored variables of percent time drawing (i.e., 'ink time') versus percent time not drawing (i.e., 'think time'). Neuropsychological domains of interest included processing speed, working memory, language, and declarative memory. RESULTS Adjusting for age and premorbid cognitive reserve metrics, command TCT positively correlated with multiple cognitive domains; PFHL and PCFL negatively associated with worse performance on working memory and processing speed tests. For Copy, TCT, PCFL, and PFHL negatively correlated with processing speed, and CFA negatively correlated with language. Between-group analyses show MCI participants generated slower command TCT, produced smaller CFA, and required more command 'think' (% Think) than 'ink' (% Ink) time. CONCLUSION Command dCDT variables of interest were primarily processing speed and working memory dependent. MCI participants showed dCDT differences relative to non-MCI peers, suggesting the dCDT may assist with classification. Results document cognitive construct validation to digital metrics of clock drawing.
Many inpatients may not be physically prepared for community ambulation on discharge from a publicly funded rehabilitation centre: a cross-sectional cohort study

Abstract Purpose We assessed the ability of patients discharging home from inpatient rehabilitation to meet criteria for community ambulation. Methods Cross-sectional observational study design. Participants were assessed, within 48-hours of discharge on their ability to: ascend/descend three steps, walk at a speed of 0.44 m/s, ascend/descend a slope, ascend/descend a kerb, and walk 315 m continuously. Demographic data were collected from medical records. Multiple logistic regression determined factors predictive of meeting criteria. Results Of 200 participants (mean 73 years, 66% women, mixed diagnosis), 64 (32%) met all criteria. The least commonly met criteria were walking 315 m continuously (37%) and ascending/descending steps (70%). Participants who were female (OR: 0.27, 95%CI: 0.12–0.61), with a high comorbidity index (OR: 0.71, 95%CI: 0.56–0.91) or a traumatic orthopaedic diagnosis (OR: 0.22, 95%CI: 0.05–0.96) were less likely to meet all criteria. Participants with a higher admission functional independence walk item score (OR: 1.37, 95%CI: 1.05–1.78) or higher ambulatory self-confidence (OR: 1.02, 95%CI: 1.01–1.04) were more likely to meet all criteria. Conclusions Approximately, one-third of inpatients discharged home from a publicly funded rehabilitation centre met the community ambulation criteria, suggesting many may not be physically prepared to participate in their community. Implications for Rehabilitation Only about one in three inpatients discharging home from a publicly funded rehabilitation centre met physical criteria for community ambulation. Patients discharging home from inpatient rehabilitation have most difficulty walking long distances (≥315 m) compared to other criteria required for community ambulation (i.e., walking at a speed of 0.44 m/s, stepping up/down a kerb, ascending/descending a slope and ascending/descending three steps) and rehabilitation during this phase may require an increased focus on improving walking endurance/physical activity. Women with a high co-morbidity index, traumatic orthopaedic diagnosis, low self-confidence with ambulation on discharge and who require more assistance with walking on admission are least likely to meet the physical criteria for community ambulation at discharge, and therefore may require additional rehabilitation or supports.
Exploring the EQ-5D Dimension of Pain/Discomfort in Dermatology Outpatients from a Multicentre Study in 13 European Countries

Pain and discomfort are important symptoms in dermatology. The aim of this cross-sectional, multicentre study was to describe the prevalence of pain/discomfort and its associations in patients with several dermatological conditions across 13 European countries. The outcome was the prevalence of pain/discomfort according to a question of the EQ-5D questionnaire. Data collected from November 2011 to February 2013 were complete for 3,509 consecutive outpatients. Moderate or extreme pain/discomfort was reported by 55.5% of patients and 31.5% of controls with no skin conditions. The highest proportions were reported by patients with hidradenitis suppurativa (92.9%), leg ulcer (81.4%), prurigo (80%) and lichen planus (75.6%). Pain/discomfort was associated with older age, low educational level, clinical severity, flare on scalp or hands, itch, depression, anxiety, low quality of life, and thoughts of suicide. It is important to enquire specifically about pain/discomfort during clinical consultations and to address it when planning a patient’s care.
Neural Stochastic Differential Equations with Bayesian Jumps for Marked Temporal Point Process

Many real-world systems evolve according to continuous dynamics and get interrupted by stochastic events i.e. systems that both ﬂow (often described by a differential equation) and jump. If the equation of the continuous motion is unknown, the stochastic event generation process can be modeled as samples generated from a marked temporal point process , in the form of event sequences with non-uniform time intervals. Additionally, each event is marked with the type of the event and a real-valued noisy measurement. The noisy measurements themselves are the realizations of a stochastic process with an unknown stochastic differential equation (SDE). We present a framework that simultaneously models the intensity function of the temporal point process and learn stochastic process governing the distribution of the observed noisy measurements. Similar to the underlying system of interest, the latent dynamics of our framework evolves continuously according to ordinary differential equations (ODEs) while, the jumps at the observations are controlled by Gated Recurrent Units (GRUs) through a Bayesian update, which accounts for the observation noise. We present preliminary data ﬁtting results on a real-world medical dataset.
A Multi-View Deep Neural Network Model for Chemical-Disease Relation Extraction From Imbalanced Datasets

Understanding the chemical-disease relations (CDR) is a crucial task in various biomedical domains. Manual mining of these information from biomedical literature is costly and time-consuming. To address these issues, various researches have been carried out to design an efficient automatic tool. In this paper, we propose a multi-view based deep neural network model for CDR task. Typically, multiple representations (or views) of the datasets are not available for this task. So, we train multiple conceptually different deep neural network models on the dataset to generate different abstract features, treated as different views. A novel loss function, “Penalized LF”, is defined to address the problem of imbalance dataset. The proposed loss function is generic in nature. The model is designed as a combination of Convolution Neural Network (CNN) and Bidirectional Long Short Term Memory (Bi-LSTM) network along with a Multi-Layer Perceptron (MLP). To show the efficacy of our proposed model, we have compared it with six baseline models and other state-of-the-art techniques, on “chemicals-and-disease-DFE” dataset, a free text dataset created by Li et al. from BioCreative V Chemical Disease Relation dataset. Results show that the proposed model attains highest $F1-score$ for individual classes, proving its efficiency in handling class imbalance problem in the dataset. To further demonstrate the efficacy of the proposed model, we have presented results on BioCreative V dataset and two Protein-Protein Interaction Identification (PPI) datasets, viz., AiMed and BioInfer. All these results are also compared with the state-of-the-art models.
The Reliability of Balance, Gait, and Muscle Strength Test for the Elderly with Dementia: A Systematic Review

PURPOSE: To summarize the evaluation tools of balance [Berg Balance Scale (BBS), timed up and Go (TUG), forward reaching test (FRT)], gait [6 m walking Test (6MWT)], and strength [Chair Stand Test (CST)] for patients with dementia. METHODS: The following databases were searched: Pub MED, Cochrane, Sciences Direct, and Web of Sciences. The inclusion criteria were as follows: 1) repeated measurement design, 2) subjects with dementia, 3) use of testing tools such as the BBS, TUG, FRT, 6MWT, and CST, 4) report the reliability. One reviewer performed the quality assessment of diagnostic accuracy study and two evaluators performed data extraction independently. RESULTS: Six articles and one letter were included. The interrater reliability of 6MWT, TUG, and CST, were acceptable (ICC>.90). However, FRT had unacceptable reliability. In test-retest reliability, only BBS has acceptable reliability (ICC>.90). Others had various reliabilities. The
Systematic Review Looking at the Use of Technology to Measure Free-Living Symptom and Activity Outcomes in Parkinson’s Disease in the Home or a Home-like Environment

Background: The emergence of new technologies measuring outcomes in Parkinson’s disease (PD) to complement the existing clinical rating scales has introduced the possibility of measurement occurring in patients’ own homes whilst they freely live and carry out normal day-to-day activities. Objective: This systematic review seeks to provide an overview of what technology is being used to test which outcomes in PD from free-living participant activity in the setting of the home environment. Additionally, this review seeks to form an impression of the nature of validation and clinimetric testing carried out on the technological device(s) being used. Methods: Five databases (Medline, Embase, PsycInfo, Cochrane and Web of Science) were systematically searched for papers dating from 2000. Study eligibility criteria included: adults with a PD diagnosis; the use of technology; the setting of a home or home-like environment; outcomes measuring any motor and non-motor aspect relevant to PD, as well as activities of daily living; unrestricted/unscripted activities undertaken by participants. Results: 65 studies were selected for data extraction. There were wide varieties of participant sample sizes (<10 up to hundreds) and study durations (<2 weeks up to a year). The metrics evaluated by technology, largely using inertial measurement units in wearable devices, included gait, tremor, physical activity, bradykinesia, dyskinesia and motor fluctuations, posture, falls, typing, sleep and activities of daily living. Conclusions: Home-based free-living testing in PD is being conducted by multiple groups with diverse approaches, focussing mainly on motor symptoms and sleep.
Moral distress: A concept clarification

Background Over the past few decades, moral distress has been examined in the nursing literature. It is thought to occur when an individual has made a moral decision but is unable to act on it, often attributable to constraints, internal or external. Varying definitions can be found throughout the healthcare literature. This lack of cohesion has led to complications for study of the phenomenon, along with its effects to nursing practice, education and targeted policy development. Objectives The aim of this analysis was to uncover unique definitions of moral distress as found in the nursing literature and to examine the relationship between these definitions. Research Design and Context Morse’s method of concept clarification was applied given the large body of literature which includes definitions, descriptions and measurements of the concept in research. The steps include (a) conducting a literature review; (b) analysing the literature; and (c) identifying, describing, comparing, and contrasting attributes, antecedents and consequences of each category. Findings Each of the 18 included studies described constraints in their definition of moral distress, whether implied or explicitly stated. External constraints are widely described as obstacles outside of the individual, whether institutional, systemic or situational, while internal constraints are located within the individuals themselves and are described as personal limitations, failings or weakness of will. Conclusion Upon reviewing these definitions, we determined that the term ‘internal constraints’ is problematic due to the emphasis of responsibility on the individual experiencing moral distress. We propose an alteration to ‘internal characteristics’ that will assume less responsibility of change from the individual to place a heavier onus on systemic and institutional constraints.
Determinants of diet in pregnancy: development of an explanatory model and application to cross-sectional data from a social-epidemiological birth cohort study

Diet in pregnancy is crucial for maternal and child health and pregnancy has been described as a good time for initiating behaviour change. Evidence from developed countries, however, suggests that dietary intake in pregnant women is inadequate despite food (theoretically) being abundant. There is currently little knowledge on dietary intakes of pregnant women in Germany. A need for furthering theoretical knowledge in the field of nutrition research has also been identified. This dissertation thus aimed to assess the determinants of diet in pregnancy in developed contexts and their interaction with each other. Based on an initial scoping of the theoretical and empirical literature, a conceptual framework was developed. Pregnancy-related, socio-demographic, individual behavioural and biological responses and environmental determinants were identified as key drivers of diet in pregnancy. Framework ‘fit’ was improved based on findings from a systematic review and application to cross-sectional data from the BaBi birth cohort study. The initial framework could not be refined into a definitive explanatory model as the evidence on the role of pregnancy-related and environmental factors is inconclusive at this stage and the interaction of the different determinants could not be fully disentangled. Nevertheless, this dissertation showed that the determinants of diet in pregnancy are very complex and in stark contrast to the notion of pregnancy as a time of ‘heightened awareness’ where behaviour change can easily be implemented. Both a social and behavioural gradient of diet in pregnancy were identified, i.e. women who are less affluent or exhibit health risk behaviours are less likely to exhibit adequate diets in pregnancy. Younger women were also identified as an at-risk group. Recommendations were made to realise adequate diet in pregnancy for all women. Among these were the improvement of dietary guidelines and communication thereof in Germany and the development of policies to act on the complex determinants of diet. As the field of research advances, clearer and more detailed policy recommendations can be drawn.
(How Fast) Does Export Quality Really Converge?

In this paper, we demonstrate why rapid unconditional convergence in export quality can be reconciled with a stable distribution of incomes across countries, despite the well-documented relationship between income levels and export quality: while export quality within products converges, quality improvements across export goods are systematically biased towards products typically exported by higher-income countries. Notably, those countries benefit from exporting more complex goods which are better aligned to their human and physical capital endowments. We illustrate that those cross-product quality dynamics in favor of high-income countries outweigh within-product quality convergence by creating bilateral quality estimates for 122 countries and 2,700 manufacturing goods during the ‘globalization decade’ before the global financial crisis.
A theoretical and empirical assessment of stomatal optimization modeling.

Optimal stomatal control models have shown great potential in predicting stomatal behavior and improving carbon cycle modeling. Basic stomatal optimality theory posits that stomatal regulation maximizes the carbon gain relative to a penalty of stomatal opening. All models take a similar approach to calculate instantaneous carbon gain from stomatal opening (the gain function). Where the models diverge is in how they calculate the corresponding penalty (the penalty function). In this review, we compare and evaluate ten different optimization models in how they quantify the penalty and how well they predict stomatal responses to the environment. We evaluate models in two ways. First, we compare their penalty functions against seven criteria that ensure a unique and qualitatively realistic solution. Second, we quantitatively test model against multiple leaf gas-exchange datasets. The optimization models with better predictive skills have penalty functions that meet our seven criteria and use fitting parameters that are both few in number and physiology-based. The most skilled models are those with a penalty function based on stress-induced hydraulic failure. We conclude by proposing a new model that has a hydraulics-based penalty function which meets all seven criteria and demonstrates a highly predictive skill against our test datasets.