bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy of image analysis tools for functional root traits: A comment on Delory et al. (2017)
Authors: Rose Laura , Lobet Guillaume 
Published: January 2019

Abstract

Root traits get increasing attention as functional equivalents of above‐ground traits. Image analysis software such as WinRhizo™ and IJ_Rhizo facilitate root trait analyses. Delory et al. () presented a comparison between the accuracy of WinRhizo™ and IJ_Rhizo for measuring root length. We complement their analyses with a comparison of diameter and volume estimates and a comparison of different image resolutions with manual and automatic threshold.

We analysed 100 images of fibrous and taproot systems, which were obtained using the root model ArchiSimple. As a result, for each image, diameter, length and volume were known. The images were analysed with WinRhizo™ and IJ_Rhizo and we compared the estimates of diameter, length and volume to ground‐truth values. We further computed relative errors and their magnitude and analysed their dependency on image characteristics and root system properties.

At 1,200 and 800 dpi, diameter and length estimates provided by WinRhizo™ and IJ_Rhizo were of comparable accuracy. Diameter errors were balanced. Volume estimates were subjected to a systematic error caused by the assumption of constant diameter. WinRhizo™, however, provides the opportunity to calculate correctly computed volumes from diameter classes. At 1,200 dpi, IJ_Rhizo failed to automatically find an appropriate threshold for pixel classification, which fundamentally decreased accuracy.

The magnitude of diameter errors increased with root overlap for IJ_Rhizo. The length errors increased with increasing root length, overlap and root length density for WinRhizo™. The magnitude of underestimation of the volume (WinRhizo™) decreased with volume. It was higher for taproot than for fibrous root systems. All errors increased with lower resolution.

Our results confirm the results of Delory et al. () regarding the accuracy for length. They further confirm that estimates derived from different software packages or at different resolution should not be compared directly. The characteristics of root systems should be standardized for image analysis. The dependency of errors on the response variable of interest can influence the effect size and increase the probability of errors. Validation of methods should be conducted for each analysed dataset. New image analysis tools should be validated against a real ground‐truth.
Clinical implications of the association between fluoroquinolones and tendon rupture: The magnitude of the effect with and without corticosteroids
Authors: Persson Rebecca , Jick Susan 
Published: January 2019

AimsTo estimate the relative, absolute and attributable risk of non‐traumatic tendon rupture, at various sites, associated with use of fluoroquinolones, with and without concomitant corticosteroids.MethodsWe conducted cohort and nested case–control studies among fluoroquinolone users in the United Kingdom Clinical Practice Research Datalink Gold. We estimated the excess risk (cohort analysis) and odds ratios (ORs) (case control) of tendon rupture by fluoroquinolone (current, recent and past use versus unexposed) and corticosteroid (current versus unexposed) use.ResultsAmong 740 926 patients with a fluoroquinolone prescription, 3957 cases of tendon rupture were identified. The excess risk due to current fluoroquinolone use was low: any tendon rupture 3.73 (95% confidence interval, CI, 2.08–5.39) per 10 000 person‐years (PY) and Achilles tendon rupture 2.91 (1.71–4.11) per 10 000 PY. The excess risk of any tendon rupture was much higher for current concomitant fluoroquinolone and corticosteroid use versus corticosteroids alone: 21.2 (11.3–31.2) per 10 000 PY. In the case–control, OR (95% CI) among current fluoroquinolone users versus unexposed patients was elevated: any tendon rupture 1.60 (1.22–2.09), Achilles tendon 2.71 (1.76–4.17) and bicep tendon 1.53 (0.85–2.73). The risk of any tendon rupture was higher among women (OR 2.27 [1.54–3.34]), patients aged 60+ (OR 2.42 [1.74–3.37]), and concomitant corticosteroid use (OR 6.64 [3.99–11.1]).ConclusionsFluoroquinolones increase the risk of Achilles tendon rupture and, to a lesser extent, bicep tendon rupture, but the attributable risk is low. The risk is materially increased with concomitant use of corticosteroids.
Respect for autonomy in systems of postmortem organ procurement: A comment
Authors: den Hartogh Govert 
Published: January 2019

AbstractIn 2015 Robert Veatch published the second edition of his Transplantation ethics, this time together with Lainie Ross. The chapters on postmortem organ procurement distinguish between ‘giving’ and ‘taking’ systems, and argue that ‘taking’ systems may promise a greater yield of organs for transplantation, but inevitably violate a requirement of respect for the deceased's autonomy. That argument has been very influential, and is also representative of a way of thinking that is widespread in the literature and in public debate. In this paper I contend that it is conceptually flawed in a number of important respects. These concern the understanding of both the concept of ‘consent’ and the requirement of respect for autonomy, the role of the relatives in any procurement system, and the factors that actually determine the extent to which a system respects autonomy, under any interpretation of that requirement.
Can an integrated obstetric emergency simulation training improve respectful maternity care? Results from a pilot study in Ghana
Authors: Afulani Patience A. , Aborigo Raymond A. , Walker Dilys , Moyer Cheryl A. , Cohen Susanna , Williams John 
Published: January 2019

AbstractBackgroundFew evidence‐based interventions exist on how to improve respectful maternity care (RMC) in low‐resource settings. We sought to evaluate the effect of an integrated simulation‐based training on provision of RMC.MethodsThe pilot project was in East Mamprusi District in northern Ghana. We integrated specific components of RMC, emphasizing dignity and respect, communication and autonomy, and supportive care, into a simulation training to improve identification and management of obstetric and neonatal emergencies. Forty‐three providers were trained. For evaluation, we conducted surveys at baseline (N = 215) and endline (N = 318) 6 months later, with recently delivered women to assess their experiences of care using the person‐centered maternity care scale. Higher scores on the scale represent more respectful care.ResultsCompared to the baseline, women in the endline reported more respectful care. The average person‐centered maternity care score increased from 50 at baseline to 72 at endline, a relative increase of 43%. Scores on the subscales also increased between baseline and endline: 15% increase for dignity and respect, 87% increase for communication and autonomy, and 55% increase for supportive care. These differences remained significant in multivariate analysis controlling for several potential confounders.ConclusionsThe findings suggest that integrated provider trainings that give providers the opportunity to learn, practice, and reflect on their provision of RMC in the context of stressful emergency obstetric simulations have the potential to improve women's childbirth experiences in low‐resource settings. Incorporating such trainings into preservice and in‐service training of providers will help advance global efforts to promote RMC.
Expression of ELF1, a lymphoid ETS domain‐containing transcription factor, is recurrently lost in classical Hodgkin lymphoma
Authors: Paczkowska Julia , Soloch Natalia , Bodnar Magdalena , Kiwerska Katarzyna , Janiszewska Joanna , Vogt Julia , Domanowska Ewa , Martin‐Subero José I. , Ammerpohl Ole , Klapper Wolfram , Marszalek Andrzej , Siebert Reiner , Giefing Maciej 
Published: January 2019

SummaryLoss of B cell‐specific transcription factors (TFs) and the resulting loss of B‐cell phenotype of Hodgkin and Reed‐Sternberg (HRS) cells is a hallmark of classical Hodgkin lymphoma (cHL). Here we have analysed two members of ETS domain containing TFs, ELF1 and ELF2, regarding (epi)genomic changes as well as gene and protein expression. We observed absence or lower levels of ELF1 protein in HRS cells of 31/35 (89%) cases compared to the bystander cells and significant (P < 0·01) downregulation of the gene on mRNA as well as protein level in cHL compared to non‐cHL cell lines. However, no recurrent loss of ELF2 protein was observed. Moreover, ELF1 was targeted by heterozygous deletions combined with hypermethylation of the remaining allele(s) in 4/7 (57%) cell lines. Indeed, DNA hypermethylation (range 95–99%, mean 98%) detected in the vicinity of the ELF1 transcription start site was found in all 7/7 (100%) cHL cell lines. Similarly, 5/18 (28%) analysed primary biopsies carried heterozygous deletions of the gene. We demonstrate that expression of ELF1 is impaired in cHL through genetic and epigenetic alterations, and thus, it may represent an additional member of a TF network whose downregulation contributes to the loss of B‐cell phenotype of HRS cells.
Contribution of immunoglobulin lambda light chain gene rearrangement analysis in the diagnosis of B‐cell neoplasms
Authors: Paterson Anna L. , El‐Daly Hesham , Raso‐Barnett Livia , Du Ming‐Qing , Giger Olivier , Soilleux Elizabeth , Roberts Thomas , Huang Yuanxue , Bibawi Hani , Matharu Baljinder , Bench Anthony , Scott Mike A. , Liu Hongxiang 
Published: January 2019

SummaryIdentification of clonal IGH, IGK and IGL gene rearrangements offers diagnostic adjunct in suspected B‐cell neoplasms. However, many centres omit IGL analysis as its value is uncertain. A review of 567 cases with IGH, IGK and IGL rearrangement assessed using BIOMED‐2 assays showed clonal immunoglobulin gene rearrangement in 54% of cases, of which 24% had a clonal IGL rearrangement. In two cases, the clonal rearrangement was detected exclusively by IGL analysis. This finding demonstrates the added value of IGL analysis for clonality assessment, especially in suspected B‐cell neoplasms in which a clonal IGH and/or IGK rearrangement is not detected or is equivocal.
Cell type‐specific structural plasticity of the ciliary transition zone in C. elegans
Authors: Akella Jyothi S. , Silva Malan , Morsci Natalia S. , Nguyen Ken C. , Rice William J. , Hall David H. , Barr Maureen M. 
Published: January 2019

Background informationThe current consensus on cilia development posits that the ciliary transition zone (TZ) is formed via extension of nine centrosomal microtubules. In this model, TZ structure remains unchanged in microtubule number throughout the cilium life cycle. This model does not however explain structural variations of TZ structure seen in nature and could also lend itself to the misinterpretation that deviations from nine‐doublet microtubule ultrastructure represent an abnormal phenotype. Thus, a better understanding of events that occur at the TZ in vivo during metazoan development is required.ResultsTo address this issue, we characterized ultrastructure of two types of sensory cilia in developing Caenorhabditis elegans. We discovered that, in cephalic male (CEM) and inner labial quadrant (IL2Q) sensory neurons, ciliary TZs are structurally plastic and remodel from one structure to another during animal development. The number of microtubule doublets forming the TZ can be increased or decreased over time, depending on cilia type. Both cases result in structural TZ intermediates different from TZ in cilia of adult animals. In CEM cilia, axonemal extension and maturation occurs concurrently with TZ structural maturation.Conclusions and SignificanceOur work extends the current model to include the structural plasticity of metazoan transition zone, which can be structurally delayed, maintained or remodelled in cell type‐specific manner.
Pharmacological impact of antiretroviral therapy on platelet function to investigate human immunodeficiency virus‐associated cardiovascular risk
Authors: Taylor Kirk A. , Smyth Erica , Rauzi Francesca , Cerrone Maddalena , Khawaja Akif A. , Gazzard Brian , Nelson Mark , Boffito Marta , Emerson Michael 
Published: January 2019

Background and purposeSome clinical studies have reported increased myocardial infarction in people living with human immunodeficiency virus (HIV) taking the antiretroviral abacavir sulphate (ABC). Given that clinical studies contain confounding variables (e.g., HIV‐associated factors), we investigated the pharmacological effects of antiretrovirals on platelet function in HIV‐negative volunteers in order to identify mechanisms of increased cardiovascular risk.Experimental approachPlatelets were isolated from healthy volunteers and HIV‐negative subjects enrolled on a Phase I clinical trial and platelet function evaluated using aggregometry and flow cytometry. In vivo platelet thromboembolism was monitored in anaesthetized mice.Key resultsHuman platelet aggregation was unaffected by all antiretrovirals tested, but ABC treatment led uniquely to increased platelet granule release. ABC also interrupted NO‐mediated inhibition of platelet aggregation and increased in vivo aggregation in mice. Another antiretroviral, tenofovir, did not affect platelet function. Furthermore, aggregation and activation of platelets isolated from 20 subjects taking clinically relevant doses of tenofovir were comparable to baseline samples.Conclusions and implicationsABC can enhance platelet activation, independently of variables that confound clinical studies, suggesting a potential pharmacological effect that is absent with tenofovir. Mechanistically, we propose that ABC enhances platelet degranulation and interrupts NO‐mediated platelet inhibition. The interaction of ABC with NO signalling is demonstrated by ABC‐mediated enhancement of aggregation in vivo and in vitro that persisted in the presence of NO. Although an association between ABC and platelet activation has not been confirmed in patients, these findings provide evidence of a mechanistic link between platelet activation and antiretroviral therapy.
The growth ring concept: seeking a broader and unambiguous approach covering tropical species
Authors: Silva Marcelo dos S. , Funch Ligia S. , da Silva Lazaro B. 
Published: January 2019

ABSTRACTThe concept of growth rings is little discussed in the literature and their treatment remains somewhat confusing in terms of the diversity of structures described. This situation has a major impact on the study of growth rings in tropical species, in which variations and complexity are greater and accuracy of identification less good. The rigid conceptual delimitations used by dendrochronologists and wood anatomists of temperate regions cannot be applied to the study of growth rings in most tropical species, which has led to neglect of this subject. With the objective of discussing the concept of growth rings, the present study consists of a survey of anatomical, periodicity, causal and evolutionary aspects of the treatment of these structures as evidenced in previous studies, and the evaluation of their application and limitations to the development of this concept. Anatomical aspects arise through radial integrity, or the presence of early and late wood; the degree of distinction of the rings, which may vary from well to poorly defined; and tangential continuity, meaning that rings may form a complete circle in the transverse section of the trunk, or instead be tangentially discontinuous, lens‐shaped or in wedges. In addition there are a diversity of anatomical markers which enable us to recognize growth rings. Regarding periodicity, the rings may be annual, infra‐annual or supra‐annual. Causal aspects include genetic, endogenous and environmental components. Evolutionary aspects continue to be insufficiently investigated, and although most comparative studies treat growth rings recognized by different markers as though they were a single character, it remains questionable whether they can be regarded as homologous or the result of homoplasy. We conclude that the elaboration of a robust but broad definition which can include all the variation observed in growth rings of tropical species is a complex task, which is only possible by overcoming the restrictions adopted by dendrochronologists and wood anatomists of temperate regions for whom growth rings are essentially annual, strongly demarcated, tangentially continuous and restricted to the most pronounced markers.
Screening for hand dermatitis in healthcare workers: Comparing workplace screening with dermatologist photo screening
Authors: Nichol Kathryn , Copes Ray , Kersey Karon , Eriksson Jonas , Holness Dorothy L. 
Published: January 2019

BackgroundHealthcare workers are at increased risk for occupational contact dermatitis, owing to wet work exposure. Early detection and management improves outcomes. Although several diagnostic tools are available, none is appropriate for rapid screening.ObjectivesTo assess the validity and feasibility of the Hand Dermatitis Screening Tool in the acute healthcare sector.MethodsScreening of 508 employees at three hospitals in Ontario, Canada was performed with the Hand Dermatitis Screening Tool either by an occupational health nurse (N = 225) or by self‐administration (N = 283). Two occupational dermatologists rated photographs of participants’ hands.ResultsOf the participants, 30.5% screened positive for hand dermatitis. A positive screen was associated with wet work, history of eczema, dermatitis, or other rash, and currently having a rash. Ninety‐four per cent of participants reported that using the tool took <2 minutes, 99% indicated that the tool was easy to use, and 86% stated that workplace screening was very important. Workplace and dermatologist photo screening showed fair agreement.ConclusionsThe prevalence of hand dermatitis and identified risk factors were consistent with the literature. These findings, along with positive feasibility results, support further testing of the tool despite only fair agreement between workplace and dermatologist screening.
Alcohol consumption and suicide risk in medical internship: A Peruvian multicentric study
Authors: Carrasco‐Farfan Carlos A. , Alvarez‐Cutipa Daniela , Vilchez‐Cornejo Jennifer , Lizana‐Medrano Magaly , Durand‐Anahua Paula A. , Rengifo‐Sanchez Jorge A. , Rebatta‐Acuña Alexis , Cubas Wildor S. , Arroyo‐Hernandez Hugo , Toro‐Huamanchumo Carlos J. 
Published: January 2019

AbstractIntroduction and AimSuicide and harmful alcohol consumption are major health problems, especially in medical students. This study aimed to evaluate the association between risk for alcohol abuse and suicide risk in medical interns of Peruvian hospitals.Design and MethodsWe conducted a multicentre cross‐sectional study in medical interns from 18 Peruvian hospitals. We measured suicide risk, risk for alcohol abuse, depression and self‐esteem using the Plutchik Suicide Risk Scale, CAGE, Zung Self‐Rating Depression Scale and Rosenberg Self‐Esteem Scale, respectively. We used χ2 and Student t‐tests for descriptive analysis. To evaluate the association between risk for alcohol abuse and suicide risk we generated crude and adjusted Poisson regression models with robust variance and estimated prevalence ratios with 95% confidence intervals.ResultsWe surveyed 433 medical interns. The prevalence of suicide risk and risk for alcohol abuse was 19.6% and 27.5%, respectively. We found significant differences in suicide risk according to age (P < 0.001), region of origin (P = 0.002), with whom the participant lived (P < 0.001), university of origin (P = 0.040), type of hospital (P = 0.042), family history of attempted suicide (P = 0.043), self‐esteem level (P < 0.001) and alcohol consumption (P < 0.001). In the adjusted model, age (PRa: 1.11, 95% confidence interval 1.05–1.17) and risk for alcohol abuse (PRa: 7.60, 95% confidence interval 4.46–12, 96) were associated with suicide risk.Discussion and ConclusionsTwo out of 10 medical interns had a positive screening for suicide risk. Age and especially risk for alcohol abuse were the associated variables.
Gene mutations in paediatric epilepsies cause NMDA‐pathy, and phasic and tonic GABA‐pathy
Authors: Gataullina Svetlana , Bienvenu Thierry , Nabbout Rima , Huberfeld Gilles , Dulac Olivier 
Published: January 2019

The aim of this study was to disentangle mechanisms of epileptogenesis in monogenic epilepsies in children. We reviewed paediatric monogenic epilepsies excluding brain malformation or an inborn error of metabolism, but including the gene function whether there is loss‐of‐function or gain‐of‐function, age at gene expression when available, and associated epilepsy syndrome. Genes for which at least five patients with similar epilepsy phenotype had been reported were selected. Three mechanisms are shared by most monogenic epilepsies: (1) excess of N‐methyl‐d‐aspartate (NMDA) transmission activation (NMDA‐pathies); (2) abnormal gamma‐aminobutyric acid (GABA) transmission with reduced inhibition (phasic GABA‐pathies); and (3) tonic activation of extrasynaptic GABAA receptors by extracellular GABA (tonic GABA‐pathies). NMDA‐pathies comprise early epileptic encephalopathy with suppression‐burst, neonatal/infantile benign seizures, West and Lennox–Gastaut syndromes, and encephalopathy with continuous spike waves in slow sleep, thus brief seizures with major interictal spiking. Phasic GABA‐pathies comprise mostly generalized epilepsy with febrile seizures plus and Dravet syndrome, thus long‐lasting seizures with mild interictal spiking. Tonic GABA‐pathies cause epilepsy with myoclonic–atonic seizures and Angelman syndrome, thus major high‐amplitude slow‐wave activity. This pathophysiological approach to monogenic epilepsies provides diagnostic clues and helps to guide treatment strategy.What this paper adds

In paediatric monogenic epilepsies, electroclinical patterns point to three main mechanisms: NMDA‐pathies, and phasic and tonic GABA‐pathies.

Antiepileptic treatment choice could be guided by each of these mechanisms.
Speech and language in bilateral perisylvian polymicrogyria: a systematic review
Authors: Braden Ruth O , Leventer Richard J , Jansen Anna , Scheffer Ingrid E , Morgan Angela T 
Published: January 2019

AimWe aimed to systematically review the speech production, language, and oral function phenotype of bilateral perisylvian polymicrogyria (BPP), and examine the correlation between the topography of polymicrogyria and the severity of speech, language, and oral functional impairment.MethodA systematic search of MEDLINE, Embase, and PubMed databases was completed on 26th October 2017 using Medical Subject Heading terms synonymous with BPP and speech, language, or oral motor impairment. In total, 2411 papers were identified and 48 met inclusion criteria.ResultsExpressive and receptive language impairment and oral structural and functional deficits are frequent in BPP. Expressive deficits are frequently more severe than receptive. Only one study used formal assessments to demonstrate the presence of speech disorder, namely dysarthria. Seven studies reported an association between diffuse BPP and more severe language impairment.InterpretationFindings confirmed that language deficits are common in BPP, though assessment of the specific speech phenotype is limited. The paucity of high quality studies detailing the specific communication phenotype of BPP highlights the need for further investigation. Improving understanding of this phenotype will inform the development of targeted therapies and lead to better long‐term outcomes.What this paper adds

Speech, language, and oral functional impairments are common in individuals with bilateral perisylvian polymicrogyria.

Posterior polymicrogyria is associated with a less severe language impairment than anterior polymicrogyria.

Deeper investigation of speech is needed to understand implicated networks in this malformation.