bluuebunny/crossref_metadata_2025_split huggingface dataset:
A first step towards best practice recommendations for the design and statistical analyses of pragmatic clinical trials: A modified Delphi approach
Authors: Palin Victoria , Van Staa Tjeerd P. , Steels Stephanie , Troxel Andrea B. , Groenwold Rolf H. H. , MacDonald Tom M. , Torgerson David , Faries Douglas , Mancini Pierre , Ouwens Mario , Frith Lucy J. , Tsirtsonis Kate , MacLennan Graham , Nordon Clementine ,   GetReal Initiative
Published: June 2022

AimPragmatic clinical trials (PCTs) are randomized trials implemented through routine clinical practice, where design parameters of traditional randomized controlled trials are modified to increase generalizability. However, this may introduce statistical challenges. We aimed to identify these challenges and discuss possible solutions leading to best practice recommendations for the design and analysis of PCTs.MethodsA modified Delphi method was used to reach consensus among a panel of 11 experts in clinical trials and statistics. Statistical issues were identified in a focused literature review and aggregated with insights and possible solutions from experts collected through a series of survey iterations. Issues were ranked according to their importance.ResultsTwenty‐seven articles were included and combined with experts' insight to generate a list of issues categorized into participants, recruiting sites, randomization, blinding and intervention, outcome (selection and measurement) and data analysis. Consensus was reached about the most important issues: risk of participants' attrition, heterogeneity of “usual care” across sites, absence of blinding, use of a subjective endpoint and data analysis aligned with the trial estimand. Potential issues should be anticipated and preferably be addressed in the trial protocol. The experts provided solutions regarding data collection and data analysis, which were considered of equal importance.DiscussionA set of important statistical issues in PCTs was identified and approaches were suggested to anticipate and/or minimize these through data analysis. Any impact of choosing a pragmatic design feature should be gauged in the light of the trial estimand.
Elastic Analysis of Irregularly or Sparsely Sampled Curves
Authors: Steyer Lisa , Stöcker Almond , Greven Sonja 
Published: June 2022

Abstract
We provide statistical analysis methods for samples of curves in two or more dimensions, where the image, but not the parameterization of the curves, is of interest and suitable alignment/registration is thus necessary. Examples are handwritten letters, movement paths, or object outlines. We focus in particular on the computation of (smooth) means and distances, allowing, for example, classification or clustering. Existing parameterization invariant analysis methods based on the elastic distance of the curves modulo parameterization, using the square-root-velocity framework, have limitations in common realistic settings where curves are irregularly and potentially sparsely observed. We propose using spline curves to model smooth or polygonal (Fréchet) means of open or closed curves with respect to the elastic distance and show identifiability of the spline model modulo parameterization. We further provide methods and algorithms to approximate the elastic distance for irregularly or sparsely observed curves, via interpreting them as polygons. We illustrate the usefulness of our methods on two datasets. The first application classifies irregularly sampled spirals drawn by Parkinson's patients and healthy controls, based on the elastic distance to a mean spiral curve computed using our approach. The second application clusters sparsely sampled GPS tracks based on the elastic distance and computes smooth cluster means to find new paths on the Tempelhof field in Berlin. All methods are implemented in the R-package “elasdics” and evaluated in simulations.
The Keloid Area and Severity Index (KASI): an objective tool for the evaluation of keloids
Authors: Limmer Emily E. , Kerby Eva , Lies Shelby , Limmer Byron , Limmer Rachel , Teske Noelle , Savory Stephanie , Reisch Joan S. , Glass Donald A. 
Published: June 2022

Abstract
To aid in the standardization of evaluating patients with multiple keloids, a Keloid Area and Severity Index (KASI) was developed using patient feedback, previous literature, and clinical expertise. The system was validated using intrarater and interrater reliability assessments. Here, we present a verified, reliable method of assessing keloid area and severity in clinical and research settings.
Emotional quality of early education programs improves language learning: A within‐child across context design
Authors: Rankin Peter Sheldon , Staton Sally , Potia Azhar Hussain , Houen Sandy , Thorpe Karen 
Published: June 2022

AbstractObservational studies comparing child outcomes in early care and education classrooms of differing quality are often confounded by between‐child differences. A within‐child design, tracking children across contexts, can identify the effects of quality with less confounding. An analysis of Australian children (N = 1128, mean age 5 years, 48% female, 2.9% Indigenous, ethnicity data unavailable) tracked across pre‐K, K, and year 1 (2010–2012) was conducted to assess how changes in observed quality (Classroom Assessment Scoring System) were associated with changes in cognitive development (Woodcock–Johnson III). Thresholds of quality were also investigated. Increases in Emotional Support were associated with improved language development (β = 0.54, 95% CI [0.1–0.99], approximating 2.6 weeks development). Results highlight that emotional quality is an integral and potent component of early learning.
A qualitative assessment of patient satisfaction with remote dermatology consultations utilized during the UK's first wave of the COVID-19 pandemic in a single secondary care dermatology department
Authors: Livesey Amy , Plant Alice , Simmonds Roshni , Mitchell Charles 
Published: June 2022

Abstract
During the first wave of the SARS-CoV-2 coronavirus (COVID-19) pandemic, many dermatology departments in the UK delivered remote consultations in order to minimize viral transmission. To assess patient perception of remote consultations delivered in a single dermatology department during this time, we retrospectively contacted patients via an electronic questionnaire and the responses are summarized. We anticipate that increased use of remote consultations will be a legacy of the pandemic, although healthcare professionals will have a responsibility for ensuring appropriate patient suitability.
Where are we with developing diagnostic criteria for skin diseases? Mapping the evidence in 2021
Authors: Luke Jessie , Burden-Teh Esther 
Published: June 2022

Abstract
The breadth and scope of dermatological diagnostic criteria is currently unknown. We created a map of diagnostic criteria to provide a panoramic view of past and ongoing research to develop dermatological diagnostic criteria. We analysed studies for which the primary research aim was to develop, validate or critically appraise diagnostic criteria for dermatological conditions identified with a PubMed search conducted in July 2021. The researched skin diseases were grouped based on similarities in pathogenesis. In total, 166 studies covering 104 skin diseases were included in the data extraction. The two largest disease categories were autoimmune diseases (17%) and rare disorders and genetic syndromes (17%). Of the total studies analysed, 28% included a type of validation and 64% provided diagnostic accuracy data. This map of diagnostic criteria covers a vast range of dermatological conditions, but many common skin diseases were under-represented. We plan to update the map and make it available for all health professionals and researchers.
Outcome of implants placed to retain craniofacial prostheses – A retrospective cohort study with a follow‐up of up to 30 years
Authors: Alberga Jamie , Eggels Iris , Visser Anita , van Minnen Baucke , Korfage Anke , Vissink Arjan , Raghoebar Gerry 
Published: June 2022

AbstractObjectivesTo retrospectively assess the treatment outcomes of endosseous implants placed to retain craniofacial prostheses.Material and MethodsPatients with craniofacial defects resulting from congenital disease, trauma, or oncologic treatment had implant retained prostheses placed in the mastoid, orbital, or nasal region and then assessed over a period of up to 30 years. Implant survival rates were calculated with the Kaplan–Meier method. Clinical assessments consisted of scoring skin reactions under the prosthesis and the peri‐implant skin reactions. Possible risk factors for implant loss were identified. Patient satisfaction was evaluated using a 10‐point VAS‐scale.ResultsA total of 525 implants placed in 201 patients were included. The median follow up was 71 months (IQR 28–174 months). Implants placed in the mastoid and nasal region showed the highest overall implant survival rates (10‐year implant survival rates of 93.7% and 92.5%, respectively), while the orbital implants had the lowest overall survival rate (84.2%). Radiotherapy was a significant risk factor for implant loss (HR 3.14, p < 0.001). No differences in implant loss were found between pre‐ and post‐operative radiotherapy (p = 0.89). Soft tissue problems were not frequently encountered, and the patients were highly satisfied with their implant‐retained prosthesis.ConclusionImplants used to retain craniofacial prostheses have high survival and patient satisfaction rates and can thus be considered as a predictable treatment option. Radiation is the most important risk factor for implant loss.
Illicit drug use and male barroom aggression among members of the Australian construction industry: Associations with personality and masculinity factors
Authors: Litherland Steven , Miller Peter G. , Hyder Shannon 
Published: June 2022

AbstractIntroductionIllicit drug use has been found to increase the risks of male barroom aggression (MBA). Personality traits such as dispositional aggressiveness have been associated with illicit substance use and aggressive behaviour, along with social normative masculinity factors. The present study assessed the relationships between illicit drug use, key personality (trait aggression, impulsivity, narcissism) and masculinity (conformity to masculine norms, male honour) variables with physical MBA perpetration and victimisation among male Australian construction workers.MethodsA purposive, high‐risk sample of male construction workers aged 18–69 years (n = 476, Mage = 25.90 years, SDage = 9.44) completed interviews at their place of work or training.ResultsParticipants reported high rates of both physical MBA perpetration (21%; n = 100) and victimisation (31.1%; n = 148) as well as any illicit drug use (33.61%; n = 160). Logistic regressions revealed the use of amphetamine‐type stimulants (methamphetamine, ecstasy) was associated with violence perpetration, even after accounting for high‐intensity drinking (HID) which was the strongest predictor of MBA involvement. Trait variables (Trait Physical aggressiveness, narcissism) and the masculine norm CMNI Violence were also risk factors for MBA perpetration while CMNI Playboy was protective against MBA.Discussion and ConclusionsThe use of amphetamine‐type stimulants is a risk‐factor for MBA perpetration, as are key personality traits such as aggressiveness and narcissism. Most aspects of masculinity, including male honour, were either unrelated to or protective against involvement in physical violence in bars, clubs or pubs.
Predicting potential distributions of large carnivores in Kenya: An occupancy study to guide conservation
Authors: Broekhuis Femke , Ngene Shadrack , Gopalaswamy Arjun M. , Mwaura Anastacia , Dloniak Stephanie M. , Ngatia Dedan K. , Tyrrell Peter D. , Yamane Yumi , Elliot Nicholas B. 
Published: June 2022

AbstractAimSpecies‐specific conservation strategies are frequently formulated based on species distribution maps, which are challenging to produce, especially at large spatial scales. Our aim was to use a novel empirical approach to predict the national distribution for all six large carnivore species found in Kenya to guide conservation and management decisions by identifying knowledge and conservation gaps.LocationKenya.MethodsWe collected data on carnivore presence and absence through questionnaire and sightings‐based surveys and analysed the combined data set using single‐season false‐positive occupancy models, which account for imperfect detections and false positives. To predict potential distributions and inform conservation strategies, we used the occupancy outputs to make predictions for unsampled areas and create occupancy‐based distribution maps where ψ > 0.50, to (1) quantify differences with IUCN Red List range maps, (2) quantify overlap with wildlife areas and (3) identify areas of high carnivore richness.ResultsLarge carnivore occupancy was associated with land conversion, habitat and prey availability. Our results suggest that all six species are widely distributed across Kenya and reveal substantial differences to distribution maps compiled by the IUCN Red List. More specifically, our occupancy‐based distribution maps predict much larger distribution for African wild dog (5.09X), lion (4.77X) and leopard (1.46X), similar distribution for cheetah, and smaller distribution for spotted hyaena (0.84X) and striped hyaena (0.65X). For all large carnivores, the vast majority (~80%) of their predicted distribution falls outside wildlife areas and northern Kenya is predicted to have the highest large carnivore richness.Main conclusionsOur results are encouraging as large carnivores may be widely distributed across Kenya, in some cases potentially more so than previously acknowledged. However, much of this range lies outside wildlife areas and represent areas of concern both for conservation and human livelihoods illustrating the challenges of conserving large carnivores across their range.
The global exposure of species ranges and protected areas to forest management
Authors: Jung Martin , Lewis Matthew , Lesiv Myroslava , Arnell Andy , Fritz Steffen , Visconti Piero 
Published: June 2022

AbstractAimMany vertebrate species globally are dependent on forests, most of which require active protection to safeguard global biodiversity. Forests, however, are increasingly either being disturbed, planted or managed in the form of timber or food plantations. Because of a lack of spatial data, forest management has commonly been ignored in previous conservation assessments.LocationGlobal.MethodsWe combine a new global map of forest management types created solely from remote sensing imagery with spatially explicit information on the distribution of forest‐associated vertebrate species and protected areas globally. Using Bayesian logistic regressions, we explore whether the amount of forested habitat available to a species as well as information on species‐specific threats can explain differences in IUCN extinction risk categories.ResultsWe show that disturbed and human‐managed forests dominate the distributional ranges of most forest‐associated species. Species considered as non‐threatened had on average larger amounts of non‐managed forests within their range. A greater amount of planted forests did not decrease the probability of species being threatened by extinction. Even more worrying, protected areas are increasingly being established in areas dominated by disturbed forests.ConclusionOur results imply that species extinction risk and habitat assessments might have been overly optimistic with forest management practices being largely ignored so far. With forest restoration being at the centre of climate and conservation policies in this decade, we caution that policy makers should explicitly consider forest management in global and regional assessments.
Cross‐scale drivers of woody plant species commonness and rarity in the Brazilian drylands
Authors: Pinho Bruno X. , Trindade Diego P. F. , Peres Carlos A. , Jamelli Davi , de Lima Renato A. F. , Ribeiro Elâine M. S. , Melo Felipe P. L. , Leal Inara R. , Tabarelli Marcelo 
Published: June 2022

AbstractAimLocally abundant species are typically widespread, while locally scarce species are geographically restricted—the so‐called abundance‐occupancy relationships (AORs). AORs help explain the drivers of species rarity and community assembly, but little is known about how variation around such relationship is driven by species traits and niche‐based processes, particularly in tropical woody plants. We tested the hypothesis that AORs in tropical dryland woody plants are positive and mediated by niche and functional traits along environmental gradients.LocationThe Caatinga dry forest and Cerrado savannah, Brazil.MethodsWe aggregated abundance and occurrence data into grid‐cells representing local (10‐km) to landscape scales (50‐km). We calculated species mean relative abundance at occupied grid‐cells (local abundance) and the proportion of grid‐cells occupied (occupancy), and estimated their niche breadth and marginality along multivariate environmental gradients.ResultsAORs were positive but weak at different scales in both regions due to some locally abundant but geographically restricted species, with most species being both locally and geographically rare. Cross‐species variation in local abundance was largely unpredictable, but occupancy was strongly driven by niche and functional traits, with a prominent negative effect of niche marginality. Geographically restricted species were associated with rare habitats, such as wetter and less intensively used habitats. Large seeds and abiotic dispersal favoured occupancy in Caatinga at small and large spatial scales, respectively, whereas species with conservative leaves were more widespread across scales in Cerrado.Main conclusionsWoody plants in dry tropical biotas exhibit weak AORs, a pattern likely related to low habitat availability and dispersal limitation. Caatinga and Cerrado biotas emerge as environmentally structured at multiple spatial scales, with several habitat‐specialist rare species bearing specific regenerative and resource‐use traits and relying on conditions threatened by climate change and land‐use intensification. Examining AORs through the lens of niche, functional traits and spatial scales enables mapping patterns and drivers of species commonness and rarity, enhancing understanding of species assembly and providing tools for biodiversity conservation.
The Rx transcription factor is required for determination of the retinal lineage and regulates the timing of neuronal differentiation
Authors: Yamamoto Maho , Ong Agnes Lee Chen , Shinozuka Takuma , Sasai Noriaki 
Published: June 2022

AbstractUnderstanding the molecular mechanisms leading to retinal development is of great interest for both basic scientific and clinical applications. Several signaling molecules and transcription factors involved in retinal development have been isolated and analyzed; however, determining the direct impact of the loss of a specific molecule is problematic, due to difficulties in identifying the corresponding cellular lineages in different individuals. Here, we conducted genome‐wide expression analysis with embryonic stem (ES) cells devoid of theRxgene, which encodes one of several homeobox transcription factors essential for retinal development. We performed three‐dimensional differentiation of wild‐type and mutant cells and compared their gene‐expression profiles. The mutant tissue failed to differentiate into the retinal lineage and exhibited precocious expression of genes characteristic of neuronal cells. Together, these results suggest that Rx expression is an important biomarker of the retinal lineage and that it helps regulates appropriate differentiation stages.
Olfactory outcomes in Zika virus‐associated Guillain–Barré syndrome
Authors: Lazarini Françoise , Lannuzel Annie , Cabié André , Michel Vincent , Madec Yoann , Chaumont Hugo , Calmont Isabelle , Favrat Mathilde , Montagutelli Xavier , Roze Emmanuel , Lledo Pierre‐Marie ,   for the ZikaSmell Working Group
Published: June 2022

AbstractBackground and purposeZika virus (ZIKV) infection has been associated with Guillain–Barré syndrome (GBS). However, little is known about the consequence of ZIKV infection on olfaction in humans.MethodsImmediately before the COVID‐19 outbreak, we prospectively investigated the olfactory capacities of 19 patients with ZIKV‐associated GBS from the French West Indies and compared them to nine controls from the same population, with GBS of similar severity but independent of ZIKV infection. To provide further evidence that ZIKV infection induces smell alteration, we investigated the consequences of ZIKV infection on olfactory abilities using a mouse model.ResultsPatients with GBS‐ZIKA+ had poorer olfactory function than GBS‐non‐ZIKA, even 1–2 years after the acute phase. The proportion of patients with hyposmia was significantly higher in the GBS‐ZIKA+ than in the GBS‐non‐ZIKA group (68.4% vs. 22.2%, p = 0.042). These deficits were characterized by lower threshold and identification scores and were independent from GBS severity. Additionally, ZIKV infection was found to impair olfaction in immunodeficient mice infected with ZIKV. High viral load was observed in their olfactory system and downstream brain structures. ZIKV promoted both cellular damage in the olfactory neuroepithelium and protracted inflammation of the olfactory bulb, likely accounting for smell alteration.ConclusionsPatients with ZIKV‐related GBS had poorer long‐term olfactory function than patients with GBS‐non‐ZIKA, and ZIKV‐infected mice are hyposmic. These observations suggest that ZIKV belongs on the list of viruses affecting the olfactory system. Clinical evaluation of the olfactory system should be considered for ZIKV‐infected patients.
Neural distinctiveness of fatigue and low sleep quality in multiple sclerosis
Authors: Ruiz‐Rizzo Adriana L. , Bublak Peter , Kluckow Steffen , Finke Kathrin , Gaser Christian , Schwab Matthias , Güllmar Daniel , Müller Hermann J. , Witte Otto W. , Rupprecht Sven 
Published: June 2022

AbstractBackground and purposeFatigue and low sleep quality in multiple sclerosis (MS) are closely related symptoms. Here, the associations between the brain's functional connectivity (FC) and fatigue and low sleep quality were investigated to determine the degree of neural distinctiveness of these symptoms.MethodA hundred and four patients with relapsing–remitting MS (age 38.9 ± 10.2 years, 66 females) completed the Modified Fatigue Impact Scale and the Pittsburgh Sleep Quality Index and underwent resting‐state functional magnetic resonance imaging. FC was analyzed using independent‐component analysis in sensorimotor, default‐mode, fronto‐parietal and basal‐ganglia networks. Multiple linear regression models allowed us to test the association between FC and fatigue and sleep quality whilst controlling for one another as well as for demographic, disease‐related and imaging variables.ResultsHigher fatigue correlated with lower sleep quality (r = 0.54, p < 0.0001). Higher fatigue was associated with lower FC of the precentral gyrus in the sensorimotor network, the precuneus in the posterior default‐mode network and the superior frontal gyrus in the left fronto‐parietal network, independently of sleep quality. Lower sleep quality was associated with lower FC of the left intraparietal sulcus in the left fronto‐parietal network, independently of fatigue. Specific associations were found between fatigue and the sensorimotor network's global FC and between low sleep quality and the left fronto‐parietal network's global FC.ConclusionDespite the high correlation between fatigue and low sleep quality in the clinical picture, our findings clearly indicate that, on the neural level, fatigue and low sleep quality in MS are associated with decreased FC in distinct functional brain networks.