bluuebunny/crossref_metadata_2025_split huggingface dataset:
Publication Rate of Presentations at a National Physical Medicine and Rehabilitation Scientific Conference From 2009 to 2018
Authors: Rhee Jess , Bateman Emma A. , Winston Paul , Dow Heather , Loh Eldon , Viana Ricardo 
Published: September 2021

Abstract
Conferences are important platforms for sharing research, but full-text publication is necessary for broader dissemination and impact. Few studies have examined the abstract-to-publication rate for physical medicine and rehabilitation. This study aimed to determine the abstract-to-publication rate of research abstracts presented from 2009–2018 at the Canadian Association of Physical Medicine and Rehabilitation annual scientific meetings. Using the official book of abstracts from 2009 to 2018, year of conference, abstract title, author names, and the affiliation/level of training of the first author were extracted. Systematic searches of abstract key words, authors’ names, and the abstract title were performed using PubMed and Google Scholar to determine whether an abstract proceeded to full-text publication; if so, the date and journal of publication were extracted. Of the 524 total abstracts presented at the Canadian Association of Physical Medicine and Rehabilitation from 2009 to 2018, 187 went on to full-text publication for an abstract-to-publication rate of 35.8%. The mean time to full-text publication was 23.4 ± 8.63 mos. The abstract-to-publication rate was 18.6% for medical students, 28.7% for residents, 41.1% for physical medicine and rehabilitation consultants, and 49.4% for nonphysician presenters. This study highlights that low abstract-to-publication rates for novel research presented at the Canadian Association of Physical Medicine and Rehabilitation disproportionately affects trainees. Further research is needed to identify and remedy barriers to publication.
Bounce-Back
Authors: Roberts Pamela , Aronow Harriet , Ouellette Debra , Sandhu Meenu , DiVita Margaret 
Published: September 2021

Objective
The aim of the study was to identify demographic, medical, and functional risk factors for discharge to an acute hospital before completion of an inpatient rehabilitation program and 7- and 30-day readmissions after completion of an inpatient rehabilitation program.

Design
This cohort study included 138,063 fee-for-service Medicare beneficiaries with a primary diagnosis of new onset stroke discharged from an inpatient rehabilitation facility from June 2009 to December 2011. Multivariate models examined readmission outcomes and included data from 6 mos before onset of the stroke to 30 days after discharge from the inpatient rehabilitation facility.

Results
In the acute discharge model (n = 9870), comorbidities and complications added risk, and the longer the stroke onset to admission to inpatient rehabilitation facility, the more likely discharge to the acute hospital. In the 7-day (n = 4755) and 30-day (n = 9861) readmission models, patients who were more complex with comorbidities, were black, or had managed care Medicare were more likely to have a readmission. Functional status played a role in all three models.

Conclusions
Results suggest that certain demographic, medical, and functional characteristics are associated differentially with rehospitalization after completion inpatient rehabilitation. The strongest model was the discharge to the acute hospital model with concordance statistic (c-statistic) of 0.87.
Targeting the stress response in pediatric pain: current evidence for psychosocial intervention and avenues for future investigation
Authors: Nelson Sarah , Borsook David , Bosquet Enlow Michelle 
Published: September 2021

Abstract
Nonpharmacological treatments for chronic pain in youth have been identified as first-line treatments over and above medication. Therapies such as cognitive-behavioral therapy and mindfulness-based stress reduction have shown good efficacy in reducing the psychological correlates (eg, anxiety, depression, and stress) and social or behavioral sequelae (eg, limited physical activity and lack of school engagement) associated with pediatric chronic pain. However, minimal research has examined the physiological mechanism(s) of action for these interventions. A recent review (Cunningham, et al., 2019) emphasized the need for objective (ie, physiological) assessment of treatment response in pediatric pain populations. The current review adds to this literature by identifying the physiological stress response as a particular target of interest in interventions for pediatric pain. Research indicates that youth with chronic pain report high rates of psychological stress, posttraumatic stress symptoms, and exposure to adverse childhood experiences (abuse/neglect, etc). In addition, a host of research has shown strong parallels between the neurobiology of pain processing and the neurobiology of stress exposure in both youth and adults. Interventions such as narrative or exposure therapy (eg, trauma-focused cognitive-behavioral therapy) and mindfulness-based or meditation-based therapies have shown particular promise in alleviating the neurobiological impact that stress and pain can have on the body, including reduction in allostatic load and altered connectivity in multiple brain regions. However, no study to date has specifically looked at these factors in the context of pediatric pain treatment. Future research should further explore these constructs to optimize prevention in and treatment of these vulnerable populations.
Tenofovir-diphosphate in peripheral blood mononuclear cells during low, medium and high adherence to emtricitabine/ tenofovir alafenamide vs. emtricitabine/ tenofovir disoproxil fumarate
Authors: Yager Jenna L. , Brooks Kristina M. , Castillo-Mancilla Jose R. , Nemkov Cricket , Morrow Mary , Peterson Skyler , Ibrahim Mustafa , Bushman Lane , Kiser Jennifer J. , MaWhinney Samantha , Anderson Peter L. 
Published: September 2021

Objective:
Tenofovir alafenamide (TAF) preferentially loads peripheral blood mononuclear cells (PBMCs), resulting in higher PBMC tenofovir-diphosphate (TFV-DP) vs. tenofovir disoproxil fumarate (TDF). No studies have yet compared TFV-DP in PBMC from lower than daily dosing between prodrugs, which has potential implications for event-driven preexposure prophylaxis and pharmacologic forgiveness.

Design:
Two separate randomized, directly observed therapy (DOT) crossover studies (DOT-DBS and TAF-DBS) were conducted to mimic low, medium and high adherence.

Methods:
HIV-negative adults were randomized to two 12-week DOT regimens of 33, 67 or 100% of daily dosing with emtricitabine (F)/TAF 200 mg/25 mg (TAF-DBS) or F/TDF 200 mg/300 mg (DOT-DBS), separated by a 12-week washout. PBMC steady-state concentrations (Css) of TFV-DP and FTC-TP were estimated using nonlinear mixed models and compared between F/TAF and F/TDF.

Results:
Thirty-five participants contributed to 33% (n = 23), 67% (n = 23) and 100% (n = 23) of daily F/TAF regimens. Forty-four contributed to 33% (n = 15), 67% (n = 16) and 100% (n = 32) of daily F/TDF regimens. PBMC TFV-DP Css were 7.3 [95% confidence interval (95% CI): 6.4–8.2], 7.1 (5.9–8.2) and 6.7- (4.4–8.9) fold higher (P < 0.0001) following F/TAF vs. F/TDF; 593 vs. 81.7, 407 vs. 57.4, and 215 vs. 32.3 fmol/106 cells, respectively. TFV-DP was 2.6 (2.1–3.1) fold higher with 33% F/TAF vs. 100% F/TDF. Estimated half-lives (95% CI) of TFV-DP in PBMC were 2.9 (1.5–5.5) days for F/TAF and 2.1 (1.5–2.9) days for F/TDF. FTC-TP was similar in both studies (P = 0.119).

Conclusion:
F/TAF produced 6.7 to 7.3-fold higher TFV-DP in PBMC vs. F/TDF across adherence levels, supporting increased potency and pharmacologic forgiveness with F/TAF in the PBMC compartment.
Single nucleotide polymorphisms in PNPLA3, ADAR-1 and IFIH1 are associated with advanced liver fibrosis in patients co-infected with HIV-1//hepatitis C virus
Authors: Franco Sandra , Horneros Judith , Soldevila Laura , Ouchi Dan , Galván-Femenía Iván , de Cid Rafael , Tenesa Montserrat , Bechini Jordi , Perez Ricardo , Llibre Josep M. , Clotet Bonaventura , Tural Cristina , Martínez Miguel Angel 
Published: September 2021

Objective:
Nonalcoholic fatty liver disease (NAFLD), insulin resistance and liver fibrosis are prevalent in individuals co-infected with HIV type 1 (HIV-1)/hepatitis C virus (HCV), even after HCV eradication. Our aim was to evaluate single nucleotide polymorphisms (SNPs) associated with advanced liver fibrosis in HIV-1/HCV co-infected patients.

Design/methods:
In a cohort of 102 participants, we genotyped 16 SNPs in 10 genes previously associated with NAFLD and the innate immune response and correlated the genotypes with liver fibrosis and fat accumulation.

Results:
Multinomial logistic regression analysis identified three metabolic parameters that were significantly associated with advanced liver fibrosis (stage F3–F4): albumin [odds ratio (OR) 0.80, 95% confidence interval (CI) 0.69–0.91, P = 0.001], percentage of visceral fat area (PVFA) (OR 1.06, 95% CI 1.01–1.12, P = 0.03) and BMI (OR 1.47, 95% CI 1.22–1.77, P < 0.0001). After adjustment for sex, albumin, PVFA and BMI, we found that three SNPs were significantly associated with advanced fibrosis, one each in PNPLA3/rs738409 (P = 0.016), ADAR-1/rs1127313 (P = 0.029) and IFIH1/rs1990760 (P = 0.033).

Conclusion:
Our results indicate that genotyping for these SNPs can be a useful predictive tool for liver fibrosis progression and liver fat accumulation in patients co-infected with HIV-1/HCV.
Phylogenetic signal in the vocalizations of vocal learning and vocal non-learning birds
Authors: Arato Jozsef , Fitch W. Tecumseh 
Published: September 2021

Some animal vocalizations develop reliably in the absence of relevant experience, but an intriguing subset of animal vocalizations is learned: they require acoustic models during ontogeny in order to develop, and the learner's vocal output reflects those models. To what extent do such learned vocalizations reflect phylogeny? We compared the degree to which phylogenetic signal is present in vocal signals from a wide taxonomic range of birds, including both vocal learners (songbirds) and vocal non-learners. We used publically available molecular phylogenies and developed methods to analyse spectral and temporal features in a carefully curated collection of high-quality recordings of bird songs and bird calls, to yield acoustic distance measures. Our methods were initially developed using pairs of closely related North American and European bird species, and then applied to a non-overlapping random stratified sample of European birds. We found strong similarity in acoustic and genetic distances, which manifested itself as a significant phylogenetic signal, in both samples. In songbirds, both learned song and (mostly) unlearned calls allowed reconstruction of phylogenetic trees nearly isomorphic to the phylogenetic trees derived from genetic analysis. We conclude that phylogeny and inheritance constrain vocal structure to a surprising degree, even in learned birdsong.This article is part of the theme issue ‘Vocal learning in animals and humans’.
Global cultural evolutionary model of humpback whale song
Authors: Zandberg Lies , Lachlan Robert F. , Lamoni Luca , Garland Ellen C. 
Published: September 2021

Humpback whale song is an extraordinary example of vocal cultural behaviour. In northern populations, the complex songs show long-lasting traditions that slowly evolve, while in the South Pacific, periodic revolutions occur when songs are adopted from neighbouring populations and rapidly spread. In this species, vocal learning cannot be studied in the laboratory, learning is instead inferred from the songs' complexity and patterns of transmission. Here, we used individual-based cultural evolutionary simulations of the entire Southern and Northern Hemisphere humpback whale populations to formalize this process of inference. We modelled processes of song mutation and patterns of contact among populations and compared our model with patterns of song theme sharing measured in South Pacific populations. Low levels of mutation in combination with rare population interactions were sufficient to closely fit the pattern of diversity in the South Pacific, including the distinctive pattern of west-to-east revolutions. Interestingly, the same learning parameters that gave rise to revolutions in the Southern Hemisphere simulations gave rise to evolutionary patterns of cultural evolution in the Northern Hemisphere populations. Our study demonstrates how cultural evolutionary approaches can be used to make inferences about the learning processes underlying cultural transmission and how they might generate emergent population-level processes.
This article is part of the theme issue ‘Vocal learning in animals and humans’.
Vocal production learning in mammals revisited
Authors: Janik Vincent M. , Knörnschild Mirjam 
Published: September 2021

Vocal production learning, the ability to modify the structure of vocalizations as a result of hearing those of others, has been studied extensively in birds but less attention has been given to its occurrence in mammals. We summarize the available evidence for vocal learning in mammals from the last 25 years, updating earlier reviews on the subject. The clearest evidence comes from cetaceans, pinnipeds, elephants and bats where species have been found to copy artificial or human language sounds, or match acoustic models of different sound types. Vocal convergence, in which parameter adjustments within one sound type result in similarities between individuals, occurs in a wider range of mammalian orders with additional evidence from primates, mole-rats, goats and mice. Currently, the underlying mechanisms for convergence are unclear with vocal production learning but also usage learning or matching physiological states being possible explanations. For experimental studies, we highlight the importance of quantitative comparisons of seemingly learned sounds with vocal repertoires before learning started or with species repertoires to confirm novelty. Further studies on the mammalian orders presented here as well as others are needed to explore learning skills and limitations in greater detail.This article is part of the theme issue ‘Vocal learning in animals and humans’.
Re-evaluating vocal production learning in non-oscine birds
Authors: ten Cate Carel 
Published: September 2021

The study of vocal production learning in birds is heavily biased towards oscine songbirds, making the songbird model the reference for comparative studies. However, as vocal learning was probably ancestral in songbirds, interspecific variations might all be variations on a single theme and need not be representative of the nature and characteristics of vocal learning in other bird groups. To assess the possible mechanisms of vocal learning and its evolution therefore requires knowledge about independently evolved incidences of vocal learning. This review examines the presence and nature of vocal production learning in non-songbirds. Using a broad definition of vocal learning and a comparative phylogenetic framework, I evaluate the evidence for vocal learning and its characteristics in non-oscine birds, including well-known vocal learners such as parrots and hummingbirds but also (putative) cases from other taxa. Despite the sometimes limited evidence, it is clear that vocal learning occurs in a range of different, non-related, taxa and can be caused by a variety of mechanisms. It is more widespread than often realized, calling for more systematic studies. Examining this variation may provide a window onto the evolution of vocal learning and increase the value of comparative research for understanding vocal learning in humans.
This article is part of the theme issue ‘Vocal learning in animals and humans’.
Species information in whistle frequency modulation patterns of common dolphins
Authors: Oswald Julie N. , Walmsley Sam F. , Casey Caroline , Fregosi Selene , Southall Brandon , Janik Vincent M. 
Published: September 2021

The most flexible communication systems are those of open-ended vocal learners that can acquire new signals throughout their lifetimes. While acoustic signals carry information in general voice features that affect all of an individual's vocalizations, vocal learners can also introduce novel call types to their repertoires. Delphinids are known for using such learned call types in individual recognition, but their role in other contexts is less clear. We investigated the whistles of two closely related, sympatric common dolphin species,Delphinus delphisandDelphinus bairdii, to evaluate species differences in whistle contours. Acoustic recordings of single-species groups were obtained from the Southern California Bight. We used an unsupervised neural network to categorize whistles and compared the resulting whistle types between species. Of the whistle types recorded in more than one encounter, 169 were shared between species and 60 were species-specific (32D. delphistypes, 28D. bairdiitypes).Delphinus delphisused 15 whistle types with an oscillatory frequency contour while only one such type was found inD. bairdii. Given the role of vocal learning in delphinid vocalizations, we argue that these differences in whistle production are probably culturally driven and could help facilitate species recognition betweenDelphinusspecies.This article is part of the theme issue ‘Vocal learning in animals and humans’.
Development of a multimodal machine-learning fusion model to non-invasively assess ileal Crohn’s disease endoscopic activity
Authors: Guez Itai , Focht Gili , C.Greer Mary-Louise , Cytter-Kuint Ruth , Pratt Li-Tal , Castro Denise A. , Turner Dan , Griffiths Anne M. , Freiman Moti 
Published: September 2021

AbstractBackground and ObjectiveRecurrent attentive non-invasive observation of intestinal inflammation is essential for the proper management of Crohn’s disease (CD). The goal of this study was to develop and evaluate a multimodal machine-learning (ML) model to assess ileal CD endoscopic activity by integrating information from Magnetic Resonance Enterography (MRE) and biochemical biomarkers.MethodsWe obtained MRE, biochemical and ileocolonoscopy data from the multi-center ImageKids study database. We developed an optimized multimodal fusion ML model to non-invasively assess terminal ileum (TI) endoscopic disease activity in CD from MRE data. We determined the most informative features for model development using a permutation feature importance technique. We assessed model performance in comparison to the clinically recommended linear-regression MRE model in an experimental setup that consisted of stratified 2-fold validation, repeated 50 times, with the ileocolonoscopy-based Simple Endoscopic Score for CD at the TI (TI SES-CD) as a reference. We used the predictions’ mean-squared-error (MSE) and the receiver operation characteristics (ROC) area under curve (AUC) for active disease classification (TI SEC-CD≥3) as performance metrics.Results121 subjects out of the 240 subjects in the ImageKids study cohort had all required information (Non-active CD: 62 [51%], active CD: 59 [49%]). Length of disease segment and normalized biochemical biomarkers were the most informative features. The optimized fusion model performed better than the clinically recommended model determined by both a better median test MSE distribution (7.73 vs. 8.8, Wilcoxon test, p<1e-5) and a better aggregated AUC over the folds (0.84 vs. 0.8, DeLong’s test, p<1e-9).ConclusionsOptimized ML models for ileal CD endoscopic activity assessment have the potential to enable accurate and non-invasive attentive observation of intestinal inflammation in CD patients. The presented model will be made available to the community through a dedicated website upon acceptance.
Elevation of Neurodegenerative Serum Biomarkers among Hospitalized COVID-19 Patients
Authors: Frontera Jennifer A. , Boutajangout Allal , Masurkar Arjun V. , Betensky Rebecca A. , Ge Yulin , Vedvyas Alok , Debure Ludovic , Moreira Andre , Lewis Ariane , Huang Joshua , Thawani Sujata , Balcer Laura , Galetta Steven , Wisniewski Thomas 
Published: September 2021

ABSTRACTINTRODUCTIONOlder adults hospitalized with COVID-19 are susceptible to neurological complications, particularly encephalopathy, which may reflect age-related neurodegenerative processes.METHODSSerum total tau, ptau-181, GFAP, NFL, UCHL1, and amyloid-beta(Aβ-40,42) were measured in hospitalized COVID-19 patients without a history of dementia, and compared among patients with or without encephalopathy, in-hospital death versus survival, and discharge home versus other dispositions using multivariable Cox proportional hazards regression analyses.RESULTSAmong 251 patients, admission serum ptau-181 and UCHL1 were significantly elevated in patients with encephalopathy (both P<0.05) and total tau, GFAP, and NFL were significantly lower in those discharged home(all P<0.05). These markers correlated significantly with severity of COVID illness. NFL, GFAP and UCH-L1 were significantly higher in hospitalized COVID patients than in non-COVID controls with mild cognitive impairment or Alzheimer’s disease(AD).DISCUSSIONAge-related neurodegenerative biomarkers were elevated to levels observed in AD and associated with encephalopathy and worse outcomes among hospitalized COVID-19 patients.
Efficacy versus abundancy: which vaccination schemes can better prohibit deaths and active infections?
Authors: Deeb Omar El , Jalloul Maya 
Published: September 2021

AbstractIn this paper, we introduce a general novel compartmental model accounting for the effects of vaccine efficacy, deployment rates and timing of initiation of deployment. It consists of compartments corresponding to susceptible, vaccinated susceptible, infectious, vaccinated infectious, active, and dead populations with various vaccine efficacies and vaccination deployment rates.We simulate different scenarios and initial conditions, and we find that the abundance and higher rate of deployment of low efficacy vaccines would lower the cumulative number of deaths in comparison to slower deployment of high efficacy vaccines. However, the latter can lower the number of active cases and achieve faster and higher herd immunity. We also forecast that, at the same daily deployment rate, the earlier introduction of vaccination schemes with lower efficacy would also lower the number of deaths with respect to a delayed introduction of high efficacy vaccines, which can however, still achieve lower numbers of infections and better herd immunity.