bluuebunny/crossref_metadata_2025_split huggingface dataset:
phenotools: An r package for visualizing and analysing phenomic datasets
Authors: Eliason Chad M. , Edwards Scott V. , Clarke Julia A. 
Published: May 2019

Abstract

Phenotypic data are crucial for understanding genotype–phenotype relationships, assessing the tree of life and revealing trends in trait diversity over time. Large‐scale description of whole organisms for quantitative analyses (phenomics) presents several challenges, and technological advances in the collection of genomic data outpace those for phenomic data. Reasons for this disparity include the time‐consuming and expensive nature of collecting discrete phenotypic data and mining previously published data on a given species (both often requiring anatomical expertise across taxa), and computational challenges involved with analysing high‐dimensional datasets.

One approach to building approximations of organismal phenomes is to combine published datasets of discrete characters assembled for phylogenetic analyses into a phenomic dataset. Despite a wealth of legacy datasets in the literature for many groups, relatively few methods exist for automating the assembly, analysis, and visualization of phenomic datasets in phylogenetic contexts. Here, we introduce a new r package phenotools for integrating (fusing original or legacy datasets), curating (finding and removing duplicates) and visualizing phenomic datasets.

We demonstrate the utility of the proposed toolkit with a morphological dataset for flightless birds and two morphological datasets for theropod dinosaurs and provide recommendations for character construction to maximize accessibility in future workflows. Visualization tools allow rapid identification of anatomical subregions with difficult or problematic histories of homology.

We anticipate these tools aiding automation of the assembly and visualization of phenomic datasets to inform evolutionary relationships and rates of phenotypic evolution.
Cannabis Use Disorder and Epilepsy: A Cross‐National Analysis of 657 072 Hospitalized Patients
Authors: Patel Rikinkumar S. , Mekala Hema M. , Tankersley William E. 
Published: May 2019

Background and ObjectivesRecent evidence has suggested that cannabis use precipitates cerebrovascular events. We investigated the relationship between cannabis use disorder (CUD) and hospitalization for epilepsy.MethodsNationwide inpatient sample (NIS) was analyzed from 2010 to 2014 for patients (age 15‐54) with a primary diagnosis of epilepsy (N = 657 072) and comparison was made between patients with ICD‐9 classification of CUD and without CUD. We utilized logistic regression to study the association (odds ratio [OR]) between CUD and epilepsy.ResultsThe incidence of CUD in epilepsy patients was 5.77%, and patients with CUD had a threefold higher likelihood of emergency admissions. Patients with CUD were younger (25‐34 years), male and African American. In regression analysis, adjusted for confounders, cannabis (OR, 1.56), tobacco (OR, 1.20), and alcohol (OR, 1.63) use disorders were found to be associated with higher odds of epilepsy hospitalization, but lower odds with cocaine (OR, 0.953), amphetamine (OR, 0.893), and opioid (OR, 0.828) use disorders.Conclusions and Scientific SignificanceWith the increasing prevalence of medical marijuana legalization, there is increased use of medicinal marijuana. Studies of cannabidiol and marijuana for epilepsy have been highly publicized, leading to its off‐label use for treatment. There is limited evidence to suggest that the cannabinoids may also induce a seizure. This study found that CUD is independently associated with a 56% increased likelihood of epilepsy hospitalization and this association persists even after adjusting for other substance use disorders and confounders. (Am J Addict 2019;28:353–360)
Determination of the minimally important difference in a nasal symptom score in house dust mite allergy
Authors: Devillier Philippe , Brüning Harald , Bergmann Karl‐Christian 
Published: May 2019

AbstractBackgroundHouse dust mite (HDM) allergens are responsible for the most prevalent persistent respiratory allergies. Clinical trials in this field often use a four‐component nasal symptom score (T4NSS) as a measure of efficacy.MethodsThe present observational, prospective, multinational, multicenter study determined the minimal important difference (MID) for a T4NSS in children, adolescents, and adults with physician‐diagnosed HDM‐induced allergic rhinoconjunctivitis (AR). Patients rated the T4NSS daily, a 15‐point global rating of change scale (GRCS) and the Rhinoconjunctivitis Quality of Life Questionnaire weekly. The MID was determined primarily by using a regression method with a GRCS threshold of 2.ResultsA total of 546 patients (210 adults, 133 adolescents, and 203 children) were included; 92.6% of the patients had moderate‐to‐severe AR, and 30.1% had concomitant mild asthma. During the first week, the mean ± standard deviation T4NSS was 5.68 ± 2.76 in adults, 5.34 ± 2.66 in adolescents, and 5.07 ± 2.48 in children. In a GRCS regression analysis, the MID [95% confidence interval] for the T4NSS was −0.90 [−1.06;‐0.75] overall (n = 509), −0.94 [−1.19;‐0.69] in children (n = 187), −0.74 [−1.07;‐0.41] in adolescents (n = 125), and −1.04 [−1.29;‐0.79] in adults (n = 197). The MID did not differ greatly from one disease severity tertile to another. Confirmatory distribution‐based analyses yielded overall MID values of −0.87 for the first week of the study and −0.93 for the week 2–week 1 difference.ConclusionThe MID for improvement in the T4NSS is at least −0.90 units in children, adolescents, and adults suffering from HDM‐induced AR This value could be rounded up to −1 unit for convenience.
The Life of Winds: Knowing the Namibian Weather from Someplace and from Noplace
Authors: Schnegg Michael 
Published: May 2019

ABSTRACTThis article brings the two questions, how and what we know, into a productive dialog to explain the difference between indigenous and scientific environmental knowledge. In the case I explore, scientists and Damara pastoralists (ǂnūkhoen) both relate the arrival of the rains in arid Namibia to the interplay between two winds. However, when it comes to explaining those observations, their accounts could hardly be more different. While Indigenous people understand the arrival of the rains as a play between loving and caring winds, scientists recognize them as a consequence of a shift of the Intertropical Convergence Zone. Building on Heidegger's phenomenology, I explore the relationship between the knower and the known. My main theoretical intervention is to show that Damara people and scientists have distinct ways of encountering the world: from someplace and from noplace. In those encounters, the weather is either enmeshed in forms of use in everyday skilled activity for rural pastoralists, or enframed by technology for scientists. By encountering the weather from someplace and from noplace, the world turns into a different place for each. The engagement with these weather worlds shows how ways of knowing the environment can be multiple, but they are not mutually exclusive. [Indigenous knowledge, weather, phenomenology, ontology, Heidegger]
Vitamin A levels are comparable between children with newly diagnosed coeliac disease and non‐coeliac controls
Authors: Weintraub Yael , Ben‐Tov Amir , Dotan Gad , Yerushalmy‐Feler Anat , Weiner Dror , Levy Dina , Lubetzky Ronit , Cohen Shlomi 
Published: May 2019

AbstractAimNutritional deficiencies associated with coeliac disease include iron, folic acid and fat‐soluble vitamins. This study compared the prevalence and degree of vitamin A deficiency among newly diagnosed coeliac disease patients to controls in a developed country.MethodsThis prospective cohort study included all children evaluated by gastroscopy at Dana‐Dwek Children's Hospital, Israel, between September 2014 and February 2017. Vitamin A, haemoglobin, C‐reactive protein (CRP), ferritin, tissue transglutaminase, immunoglobulin A and vitamin D levels were measured.ResultsOf the 113 children (69% females), 47 were diagnosed with coeliac disease whereas the others were the controls (mean age of 8.2 ± 3.8 years and 12.4 ± 3.5 years, respectively). There was no group difference in vitamin A, vitamin D or CRP levels. Among coeliac children, two had true vitamin A deficiency compared with three controls, while 18 coeliac children had subclinical vitamin A deficiency compared with 25 controls (p > 0.05).ConclusionPaediatric coeliac disease was not associated with increased prevalence of vitamin A deficiency. Children evaluated for gastrointestinal complaints in a developed country were found to have an unexpectedly high prevalence of subclinical vitamin A deficiency. Further prevalence and causality assessments of vitamin A deficiency in developed countries are needed.
Thalassaemia intermedia caused by coinheritance of a β‐thalassaemia mutation and a de novo duplication of α‐globin genes in the paternal allele
Authors: Pang Dejian , Shang Xuan , Cai Decheng , Zhu Fei , Cheng Yi , Zhong Jianmei , Yi Sheng , Zhang Qianqian , Xu Xiangmin 
Published: May 2019

SummaryNext generation sequencing identified a de novo, 204 kb, tandem duplication (αααα204) in the α‐globin gene cluster of a Chinese thalassaemia intermedia patient. Haplotype analysis showed that the duplicated chromosome was of paternal origin. Molecular analysis of genomic DNA from the patient's lymphocytes, hair follicles, buccal mucosa cells, his father's lymphocytes and sperm cells excluded the possibility of somatic or germinal mosaicism. The analysis also indicated that this duplication arose during spermatogenesis. The microhomology in the breakpoint was found and suggested that this duplication could be formed by a coupled homologous and non‐homologous recombination mechanism.
Longitudinal sequencing of RUNX1 familial platelet disorder: new insights into genetic mechanisms of transformation to myeloid malignancies
Authors: Duarte Bruno K. L. , Yamaguti‐Hayakawa Gabriela G. , Medina Samuel S. , Siqueira Lúcia H. , Snetsinger Brooke , Costa Fernando F. , Rauh Michael J. , Ozelo Margareth C. 
Published: May 2019

SummaryThe mechanisms by which patients with RUNX1 familial platelet disorder with propensity to myeloid malignancies (FPDMM) develop myeloid malignancies (MM) are not fully understood. We report the results of targeted next‐generation sequencing on three patients with RUNX1 FPDMM who developed acute myeloid leukaemia or myelodysplastic syndromes (AML/MDS). DNA samples were collected from bone marrow, peripheral blood and buccal swabs at different time points. One patient had clonal haematopoiesis, represented by an SRSF2 p.P95R variant, prior to his AML diagnosis, when he developed an additional NRAS p.G12D variant. His sister presented to us with MDS, with a TET2 p.S471fs and identical NRAS p.G12D variant. The third patient, from another family, had an additional RUNX1 p.R204X and an NFE2 p.Q139fs variant at AML diagnosis. This constitutes the first report of NFE2 variants in AML without extramedullary disease and NRAS variants in AML/MDS in the setting of FPDMM. A systematic review of the literature including our findings distinguishes two genetic landscapes at AML transformation from FPDMM characterized by either the presence or absence of somatic abnormalities in RUNX1 with or without variants in genes usually associated with MM. Whether clonal haematopoiesis precedes transformation only in patients without somatic abnormalities in RUNX1 needs further confirmation.
Trends in biodiversity and habitat quantification tools used for market‐based conservation in the United States
Authors: Chiavacci Scott J. , Pindilli Emily J. 
Published: May 2019

AbstractMarket‐based conservation mechanisms are designed to facilitate the mitigation of harm to and conservation of habitats and biodiversity. Their potential is partly hindered, however, by the quantification tools used to assess habitat quality and functionality. Of specific concern are the lack of transparency and standardization in tool development and gaps in tool availability. To address these issues, we collected information via internet and literature searchers and through conversations with tool developers and users on tools used in U.S. conservation mechanisms, such as payments for ecosystem services (PES) and ecolabel programs, conservation banking, and habitat exchanges. We summarized information about tools and explored trends among and within mechanisms based on criteria detailing geographic, ecological, and technical features of tools. We identified 69 tools that assessed at least 34 species and 39 habitat types. Where tools reported pricing, 98% were freely available. More tools were applied to states along the U.S. West Coast than elsewhere, and the level of tool transferability varied markedly among mechanisms. Tools most often incorporated conditions at numerous spatial scales, frequently addressed multiple risks to site viability, and required 1–83 data inputs. Most tools required a moderate or greater level of user skill. Average tool‐complexity estimates were similar among all mechanisms except PES programs. Our results illustrate the diversity among tools in their ecological features, data needs, and geographic application, supporting concerns about a lack of standardization. However, consistency among tools in user skill requirements, incorporation of multiple spatial scales, and complexity highlight important commonalities that could serve as a starting point for establishing more standardized tool development and feature‐incorporation processes. Greater standardization in tool design may expand market participation and facilitate a needed assessment of the effectiveness of market‐based conservation.
Acute and chronic pain in orofacial trauma patients
Authors: Khan Junad , Zusman Tal , Wang Qian , Eliav Eli 
Published: May 2019

AbstractTrauma or injury to the dentition and supporting tissues is associated with pain and discomfort, as expected, that may present immediately, shortly afterwards, or within a few days. Pain is an essential response to injury because it allows the organism to develop avoidance behavior to potential threats and helps the organism to avoid usage of the injured organ during the healing process. Not only does external trauma induce pain, but also essential invasive dental procedures such as extractions, dental implant insertions, root canal treatments, and oral surgeries are accompanied by similar post‐surgical (post‐traumatic) pain. The pain intensity after trauma varies and does not always correlate with the extent of injury. Trauma to the orofacial region or the teeth may also indirectly affect and induce pain in other orofacial structures such as the masticatory muscles, the temporomandibular joint, and even the cervical spine. In most cases, the pain will resolve as soon as healing of the affected tissue occurs or after dental and routine palliative treatment. In a limited number of cases, the pain persists beyond healing and evolves into a chronic pain state. Chronic pain in the orofacial region presents diagnostic and management challenges. Misdiagnosis or delayed diagnosis of the oral chronic pain condition may lead to unnecessary dental treatment. This article will discuss diagnosis and treatment for acute and chronic pain as well as potential mechanisms involved in the undesirable transition from acute to chronic pain.
Microbiological aspects of traumatic injuries
Authors: Fouad Ashraf F. 
Published: May 2019

AbstractAfter traumatic injuries to teeth, microorganisms may invade the compromised pulp tissue and initiate pulp infection and periapical inflammation. In addition to bone resorption that typically accompanies pulp necrosis, root resorption frequently occurs. Root resorption has several variants that may occur shortly after the trauma or at a later stage. The pathological changes seen after traumatic injuries to teeth are invariably linked to the presence of microbial irritants. The presence of bacterial biofilms in the dental pulp space can be treated with regenerative or therapeutic endodontic procedures. However, necrosis of periodontal ligament is usually terminal for the tooth involved. In this review, the sources of bacteria after traumatic injuries are discussed. The types and role of microorganisms involved in the pathogenesis of endodontic pathosis after traumatic injuries are presented, and contemporary approaches for the management of these conditions are reviewed. Contemporary antimicrobial strategies are discussed. The rationale for the use of systemic and topical antimicrobials is presented. Finally, novel approaches to the use of antimicrobial therapies, particularly in regenerative procedures, are reviewed.
Long‐acting antipsychotic medication as first‐line treatment of first‐episode psychosis with comorbid substance use disorder
Authors: Abdel‐Baki Amal , Thibault Dominic , Medrano Sofia , Stip Emmanuel , Ladouceur Martin , Tahir Ramzan , Potvin Stephane 
Published: May 2019

AbstractAimSubstance use disorder (SUD) is highly prevalent among patients with first‐episode psychosis (FEP) and associated with poor adherence and worst treatment outcomes. Although relapses are frequent in FEP, current literature on long‐acting injectable antipsychotics (LAI‐AP) use in FEP is scarce and studies often exclude patients with SUD.ObjectivesTo determine the impact of LAI‐AP as first‐line treatment on psychotic relapses or rehospitalizations in FEP patients with comorbid SUD (FEP‐SUD).MethodsThis is a naturalistic, longitudinal, 3‐year prospective and retrospective study on 237 FEP‐SUD admitted in two EIS in Montreal, between 2005 and 2012. The patients were divided on the basis of first‐line medication introduced, either oral antipsychotics (OAP, n = 206) or LAI‐AP (n = 31). Baseline characteristics were compared using χ² test and analysis of variance, and Kaplan‐Meier survival analysis was performed on relapse and rehospitalization.ResultsCompared to the OAP group, patients in the LAI‐AP group presented worse prognostic factors (eg, history of homelessness). Despite this, the LAI‐AP group presented a lower relapse rate (67.7% vs 76.7%), higher relapse‐free survival time (694 vs 447 days, P = 0.008 in Kaplan‐Meier analysis), and trends for reduced rehospitalization rates (48.4% vs 57.3%) and hospitalization‐free survival time (813 vs 619 days, P = 0.065 Kaplan‐Meier analysis). Of those receiving OAP as first‐line, 41.3% were eventually switched to LAI‐AP and displayed worst outcome in relapse and rehospitalization.ConclusionLAI‐AP should be strongly considered as first‐line treatment of FEP‐SUD patients since this pharmacological option reduces the risk of relapse and rehospitalization even in the individuals with poor prognostic factors.
Atraumatic vs conventional restorative treatment for root caries lesions in older patients: Meta‐ and trial sequential analysis
Authors: Göstemeyer Gerd , da Mata Cristiane , McKenna Gerald , Schwendicke Falk 
Published: May 2019

AbstractObjectivesWe aimed to appraise the comparative clinical efficacy of atraumatic restorative treatment (ART) versus conventional restorative treatment (CT) using a meta‐analysis, and assessed the robustness of evidence by trial sequential analysis (TSA).BackgroundDue to its simplified clinical approach, ART may be advantageous over CT for restoration of root caries lesions in institutionalised older patients.MethodsThree electronic databases (PubMed, Embase and Cochrane CENTRAL) were screened, and hand searches and cross‐referencing performed to identify randomised controlled trials reporting on survival of ART vs CT for restoration of root caries in older patients. Trial selection, data extraction and risk of bias assessment were performed by two independent reviewers. ART and CT were compared using fixed‐ or random‐effects pairwise meta‐analysis for per‐protocol (PP), intention‐to‐treat (ITT) and best‐case scenarios. TSA was used to control for risk of random errors.ResultsA total of 235 studies were identified, and three trials involving 130 patients (463 restorations) were included. Risk of bias was high or moderate in all but one trial. ART was associated with a significantly increased risk of failure (OR [95% CI] 2.06 [1.06/4.00]) in PP‐ but not in ITT analysis (1.36 [0.92/2.02]). Analyses for best‐case scenarios found great uncertainty introduced by attrition. No firm evidence was reached according to TSA.ConclusionsFor restoration of root caries, there is insufficient data to clearly rule out whether differences between ART and CT exist. Limited available data indicate there might be an increased risk of failure for ART.
Mirror meetings with frail older people and multidisciplinary primary care teams: Process and impact analysis
Authors: Grol Sietske , Molleman Gerard , Schers Henk 
Published: May 2019

AbstractObjectivesTo analyse the process and impact of confronting multidisciplinary teams (MTs) in primary care with the experiences of frail older patients through mirror meetings (MMs), with the aim of supporting teams to organize care in a more patient‐oriented way.MethodsProcess and impact analyses were performed using a mixed‐method approach. MMs were held with 14 frail older patients and four MTs comprising 23 health‐care professionals (HCPs) in primary care in the Netherlands.ResultsMirror meetings were feasible for frail older people living at home, although their recruitment was time‐consuming. Interaction between the patients was scarce, but they valued the opportunity to share their stories. HCPs preferred MMs overwritten reports about patient experiences. An impact analysis revealed four dominant professional areas for improvement: improve alignment with patient goals, improved communication with patients both orally and in writing, developing new pathways to connect with informal caregivers and an increased understanding that most HCPs are relative strangers to their patients.ConclusionsMirror meetings are a relatively simple and promising method for exploring the ways in which frail older patients experience care.Practice implicationsGiven the right conditions, MMs could result in valuable processes to enable MTs to improve their working methods.
Aleurone cells are the primary contributor to arabinoxylan oligosaccharide production from wheat bran after treatment with cell wall‐degrading enzymes
Authors: Vangsøe Cecilie Toft , Sørensen Jens Frisbæk , Bach Knudsen Knud Erik 
Published: May 2019

SummaryArabinoxylans and in particular arabinoxylan oligosaccharides (AXOS) from wheat are recognised for their prebiotic potential. A high‐yield, non‐chemical production of AXOS is therefore of interest when producing functional foods. This study investigated the enzymatic production of AXOS from wheat bran with the aim of establishing the main fraction contributing to production of AXOS. Fractions of wheat bran, outer pericarp and aleurone with two different purities were treated with the cell wall‐degrading enzymes: xylanase, cellulase and β‐glucanase. The yield of solubilised arabinoxylans upon treatment was greatest in the most pure aleurone fraction (164 g kg−1) and lowest in the outer pericarp fraction (15 g kg−1). The yield was mainly recovered as AXOS rather than soluble arabinoxylans and was negatively related to the arabinose/xylose ratio found in the raw material. In conclusion, wheat aleurone cell walls are the main contributor to the production of AXOS from wheat bran and this seems to depend on the A/X ratio of the raw material.