bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genome/transcriptome analysis probes Boraginales' phylogenetic position, WGDs in Boraginales, and key enzyme genes in the alkannin/shikonin core pathway
Authors: Tang Cheng‐Yi , Li Song , Wang Yun‐Tong , Wang Xi 
Published: October 2019

AbstractBoraginales (the forget‐me‐not order) is a core group within the lamiids clade. However, until now, no genome from Boraginales has been reported, and published transcriptomes are also rare. Here, we report the first Boraginales species de novo genome (i.e. Echium plantagineum genome) and seven other Boraginales species transcriptomes to probe three issues: (i) Boraginales' phylogenetic position within the lamiids clade; (ii) potential whole genome duplications (WGDs) in Boraginales; and (iii) candidate key enzyme genes in the alkannin/shikonin core pathway. The results showed that: (i) Boraginales was most probably closer to the Solanales/Gentianales clade than the Lamiales clade, at least based on the single‐copy orthologous genes from genome/transcriptome data; (ii) after the gamma (γ) event, Boraginaceae (classified into the Boraginales I clade) probably underwent at least two rounds of WGD, whereas Heliotropiaceae and Ehretiaceae (classified into the Boraginales II clade) probably underwent only one round of WGD; and (iii) several candidate key enzyme genes in the alkannin/shikonin core pathway were inferred, e.g. genes corresponding to geranyl cyclase, naphthol hydroxylase and O‐acyl transferase.
The Machado–Joseph disease deubiquitylase ataxin‐3 interacts with LC3C/GABARAP and promotes autophagy
Authors: Herzog Laura K. , Kevei Éva , Marchante Ricardo , Böttcher Claudia , Bindesbøll Christian , Lystad Alf Håkon , Pfeiffer Annika , Gierisch Maria E. , Salomons Florian A. , Simonsen Anne , Hoppe Thorsten , Dantuma Nico P. 
Published: October 2019

AbstractThe pathology of spinocerebellar ataxia type 3, also known as Machado‐Joseph disease, is triggered by aggregation of toxic ataxin‐3 (ATXN3) variants containing expanded polyglutamine repeats. The physiological role of this deubiquitylase, however, remains largely unclear. Our recent work showed that ATX‐3, the nematode orthologue of ATXN3, together with the ubiquitin‐directed segregase CDC‐48, regulates longevity in Caenorhabditis elegans. Here, we demonstrate that the long‐lived cdc‐48.1; atx‐3 double mutant displays reduced viability under prolonged starvation conditions that can be attributed to the loss of catalytically active ATX‐3. Reducing the levels of the autophagy protein BEC‐1 sensitized worms to the effect of ATX‐3 deficiency, suggesting a role of ATX‐3 in autophagy. In support of this conclusion, the depletion of ATXN3 in human cells caused a reduction in autophagosomal degradation of proteins. Surprisingly, reduced degradation in ATXN3‐depleted cells coincided with an increase in the number of autophagosomes while levels of lipidated LC3 remained unaffected. We identified two conserved LIR domains in the catalytic Josephin domain of ATXN3 that directly interacted with the autophagy adaptors LC3C and GABARAP in vitro. While ATXN3 localized to early autophagosomes, it was not subject to lysosomal degradation, suggesting a transient regulatory interaction early in the autophagic pathway. We propose that the deubiquitylase ATX‐3/ATXN3 stimulates autophagic degradation by preventing superfluous initiation of autophagosomes, thereby promoting an efficient autophagic flux important to survive starvation.
Hot Off the Press: Chemical Versus Electrical Cardioversion for Atrial Fibrillation
Authors: Bond Christopher , Morgenstern Justin , Heitz Corey , Milne William K. 
Published: October 2019

AbstractAtrial fibrillation (AF) is a significant dysrhythmia that often requires treatment in the emergency department (ED). This can be performed with rhythm control using electrical or chemical cardioversion or with rate control. There is widespread variation in management of AF within Canada and worldwide. This study focuses on rhythm control techniques, comparing ED length of stay when using an electrical‐first strategy versus a chemical‐first strategy of cardioversion.
Power calculation for cross‐sectional stepped wedge cluster randomized trials with variable cluster sizes
Authors: Harrison Linda J , Chen Tom , Wang Rui 
Published: October 2019

AbstractStandard sample size calculation formulas for stepped wedge cluster randomized trials (SW‐CRTs) assume that cluster sizes are equal. When cluster sizes vary substantially, ignoring this variation may lead to an under‐powered study. We investigate the relative efficiency of a SW‐CRT with varying cluster sizes to equal cluster sizes, and derive variance estimators for the intervention effect that account for this variation under a mixed effects model—a commonly used approach for analyzing data from cluster randomized trials. When cluster sizes vary, the power of a SW‐CRT depends on the order in which clusters receive the intervention, which is determined through randomization. We first derive a variance formula that corresponds to any particular realization of the randomized sequence and propose efficient algorithms to identify upper and lower bounds of the power. We then obtain an “expected” power based on a first‐order approximation to the variance formula, where the expectation is taken with respect to all possible randomization sequences. Finally, we provide a variance formula for more general settings where only the cluster size arithmetic mean and coefficient of variation, instead of exact cluster sizes, are known in the design stage. We evaluate our methods through simulations and illustrate that the average power of a SW‐CRT decreases as the variation in cluster sizes increases, and the impact is largest when the number of clusters is small.
On Mendelian randomization analysis of case‐control study
Authors: Zhang Han , Qin Jing , Berndt Sonja I. , Albanes Demetrius , Deng Lu , Gail Mitchell H. , Yu Kai 
Published: October 2019

AbstractMendelian randomization (MR) analysis uses genotypes as instruments to estimate the causal effect of an exposure in the presence of unobserved confounders. The existing MR methods focus on the data generated from prospective cohort studies. We develop a procedure for studying binary outcomes under a case‐control design. The proposed procedure is built upon two working models commonly used for MR analyses and adopts a quasi‐empirical likelihood framework to address the ascertainment bias from case‐control sampling. We derive various approaches for estimating the causal effect and hypothesis testing under the empirical likelihood framework. We conduct extensive simulation studies to evaluate the proposed methods. We find that the proposed empirical likelihood estimate is less biased than the existing estimates. Among all the approaches considered, the Lagrange multiplier (LM) test has the highest power, and the confidence intervals derived from the LM test have the most accurate coverage. We illustrate the use of our method in MR analysis of prostate cancer case‐control data with vitamin D level as exposure and three single nucleotide polymorphisms as instruments.
Effects of plant diversity on soil carbon in diverse ecosystems: a global meta‐analysis
Authors: Chen Xinli , Chen Han Y. H. , Chen Chen , Ma Zilong , Searle Eric B. , Yu Zaipeng , Huang Zhiqun 
Published: October 2019

ABSTRACTSoil organic carbon (SOC) is a valuable resource for mediating global climate change and securing food production. Despite an alarming rate of global plant diversity loss, uncertainties concerning the effects of plant diversity on SOC remain, because plant diversity not only stimulates litter inputsviaincreased productivity, thus enhancing SOC, but also stimulates microbial respiration, thus reducing SOC. By analysing 1001 paired observations of plant mixtures and corresponding monocultures from 121 publications, we show that both SOC content and stock are on average 5 and 8% higher in species mixtures than in monocultures. These positive mixture effects increase over time and are more pronounced in deeper soils. Microbial biomass carbon, an indicator of SOC release and formation, also increases, but the proportion of microbial biomass carbon in SOC is lower in mixtures. Moreover, these species‐mixture effects are consistent across forest, grassland, and cropland systems and are independent of background climates. Our results indicate that converting 50% of global forests from mixtures to monocultures would release an average of 2.70 Pg C from soil annually over a period of 20 years: about 30% of global annual fossil‐fuel emissions. Our study highlights the importance of plant diversity preservation for the maintenance of soil carbon sequestration in discussions of global climate change policy.
The effect of conspecific density, herbivory, and bamboo on seedling dynamics of a dominant oak in a Neotropical highland forest
Authors: Calderón‐Sanou Irene , Ríos Luis Diego , Cascante‐Marín Alfredo , Barrantes Gilbert , Fuchs Eric J. 
Published: October 2019

AbstractConspecific negative density dependence (CNDD) is one of the main mechanisms influencing diversity maintenance in tropical forests. Tropical highland forests, in contrast to most lowland forests, are commonly dominated by a few tree species, and testing the importance of density dependence effects on seedling establishment of dominant trees may provide insights on the mechanisms regulating population dynamics and forest composition of tropical highlands. We tested the effect of CNDD regulation on seedling survival and recruitment of Quercus costaricensis, a monodominant oak in the Talamanca highland forests of Costa Rica. We used Ripley's K and generalized linear mixed models to test the effects of conspecific density, distance to the nearest adult, density of Chusquea bamboo shoots, and herbivory on the annual survival probability of 3579 seedlings between 2014 and 2017. We did not find a significant effect of CNDD on seedling survival. However, bamboo density and herbivory both significantly decreased oak seedling survival. All seedlings had signs of herbivory and predator satiation may explain the lack of density dependent regulation in seedlings of this species. We argue that the lack of intraspecific density regulation at the seedling stage may contribute to explain the dominance of Q. costaricensis in the highland forests of Costa Rica. Local seedling dynamics of this endemic oak are instead regulated by herbivory and the density of Chusquea.Abstract in Spanish is available with online material.
Retrospective evaluation of marginal bone loss around implants in a mandibular locator‐retained denture using panoramic radiographic images and finite element analysis: A pilot study
Authors: Tercanli Alkis Humeyra , Turker Nurullah 
Published: October 2019

AbstractBackgroundThe follow‐up of the peri‐implant marginal bone loss is the most important criterion for the determination of implant success.PurposeThe purpose of this study is to measure marginal bone loss using panoramic radiographic images (PRI) of patients treated using a mandibular, two implant–supported, locator‐retained denture and to evaluate the compatibility of these findings with those of the finite element analysis (FEA).Materials and MethodsThe PRI of patients who had a mandibular, two implant–supported, locator‐retained denture were assessed, and the mesial and distal marginal bone loss of both right‐ and left‐sided implants was measured. Mandibular and maxillary models, which have the features of bilateral balanced occlusion, were created. The surfaces of the generated models were converted in a computer‐aided design model that could be transferred to the FEA software, and the forces were defined on contacts formed in maximum intercuspation, lateral, and protrusive movement position for bilateral balanced occlusion.ResultsThe bone loss in the mesial and distal regions at the right‐ and left‐sided implants was not statistically significant. Higher stresses were formed on the vestibular side under protrusive movement, on the lingual side under maximum intercuspation, on the distolingual side under left unilateral biting, and on the mesiolingual side under right unilateral biting in the FEA.ConclusionAccording to FEA, peri‐implant bone resorption may be higher in the buccal and palatal regions, implying that panoramic radiographs can be misleading in understanding the amount of peri‐implant bone resorption.
Prevalence of contact allergy to metals: nickel, palladium, and cobalt in Southern Sweden from 1995–2016
Authors: Rosholm Comstedt Lisbeth , Dahlin Jakob , Bruze Magnus , Åkesson Anna , Hindsén Monica , Pontén Ann , Isaksson Marléne , Svedman Cecilia 
Published: October 2019

AbstractBackgroundIn 2001, the EU nickel directive was introduced to prevent contact allergy to nickel. Contact allergy to palladium and/or cobalt is often seen together with contact allergy to nickel.ObjectivesTo compare the contact allergy prevalence of nickel, palladium, and cobalt allergy before and after the introduction of the EU nickel directive in consecutive patients with dermatitis.MethodsA retrospective analysis of patch test results from 1995–2016 was performed (n = 18 264). Chi‐square tests were used to examine trends for nickel, palladium, and cobalt across test years. Logistic regression was used for associations.ResultsThe prevalence of nickel allergy decreased significantly in the youngest age group (6–30 years) for both female and male patients from 1995–1999 to 2012–2016: females: 33.4% to 19.1% (P< .001); males: 5.9% to 2.1% (P< .05). The concomitant reactions between nickel and palladium and nickel and cobalt among young females, respectively, also decreased significantly. Isolated palladium and cobalt allergy remained stable (1.4% and 2.3%, respectively) during the same time period for both men and women.ConclusionsThe prevalence of nickel has decreased among young females and males suspected of contact allergy in Southern Sweden after the introduction of the EU nickel directive. There has been no change in isolated palladium or cobalt allergy.
Pancreas transplantation following total pancreatectomy for chronic pancreatitis
Authors: Cerise Adam , Nagaraju Santosh , Powelson John A. , Lutz Andrew , Fridell Jonathan A. 
Published: October 2019

AbstractBackgroundTotal pancreatectomy for chronic pancreatitis leads to brittle diabetes and challenging glycemic control with half of all patients experiencing severe hypoglycemia, many requiring medical intervention or hospitalization. Pancreas transplantation has the potential to manage both the endocrine and the exocrine insufficiency in this patient population.MethodsBetween June 1, 2005, and July 1, 2016, 8 patients with brittle diabetes following total pancreatectomy underwent pancreas transplantation. All grafts had systemic venous and enteric exocrine drainage. Data included demographics, graft and patient survival, pre‐ and post‐transplant supplementation with pancreatic enzymes, and narcotic usage.ResultsPatient survival rate at 1 and 3 years was 88%. Pancreas graft survival rate of those alive at 1 year was 100% and 86%, respectively. About 75% of these patients remained insulin‐free until their time of death, loss of follow‐up, or present day. Of the patients with maintained graft function at 3 years, none required further hospitalization for glycemic control. About 75% of these patients have also maintained exocrine function without pancreatic enzyme supplementation.ConclusionsPancreas transplant can treat both exocrine and endocrine insufficiency and give long‐term insulin‐free survival and should be considered as a viable treatment option for patients who have undergone total pancreatectomy for chronic pancreatitis.
Stress coping strategies and their clinical correlates in patients with psychosis at various stages of illness: A case‐control study
Authors: Piotrowski Patryk , Rymaszewska Joanna , Stańczykiewicz Bartłomiej , Małecka Monika , Kotowicz Kamila , Samochowiec Jerzy , Samochowiec Agnieszka , Plichta Piotr , Kalinowska Sylwia , Misiak Błażej 
Published: October 2019

AbstractAimsThere is evidence that individuals with psychosis adopt inefficient coping styles. Moreover, it has been hypothesized that inefficient coping styles might serve as trait‐dependent characteristics of psychosis. Therefore, we aimed to explore coping styles and their clinical correlates at various stages of psychosis.MethodsWe recruited 37 individuals at familial high risk of psychosis (FHR‐P), 42 individuals with first‐episode psychosis (FEP), 28 acutely relapsed schizophrenia (SCZ‐AR) subjects and 40 healthy controls. Coping strategies were assessed using the Coping Inventory for Stressful Situations.ResultsIndividuals with FEP were less likely to use task‐focused coping, while SCZ‐AR subjects preferred using distraction when compared to controls. Both groups of participants did not differ significantly in terms of using specific coping styles. No significant differences in the use of various coping strategies between FHR‐P individuals and controls were found. Higher odds of using emotion‐focused coping and distraction were associated with more severe depressive symptoms in individuals with psychosis. Moreover, higher frequency of using distraction was associated with worse functioning in individuals with psychosis. However, this association appeared to be insignificant after adjustment for multiple testing.ConclusionsCoping styles are similar in FEP and SCZ‐AR subjects. However, decreased use of task‐focused coping is more specific for FEP individuals while a preference of distraction might be more typical for SCZ‐AR individuals. The use of various coping styles is similar in FHR‐P individuals and controls. Preference of distraction and emotion‐focused coping might be related to more severe depressive symptoms and poor functioning in individuals with psychosis.
Extensive mismatches between species distributions and performance and their relationship to functional traits
Authors: Bohner Teresa , Diez Jeffrey 
Published: October 2019

AbstractMismatches between species distributions and their optimal habitat are predicted by ecological theory and will affect species responses to changing climate. However, empirical tests lack consensus on the prevalence of such mismatches and their underlying mechanisms. Here we present a conceptual framework to quantify the mismatch between optimal conditions for species occurrence and multiple measures of population and individual performance (density, adult growth and survival, and recruitment) and the associated performance reduction, or cost. We quantified these mismatches for 59 tree species in the western US along a soil water balance gradient and found high variability in mismatches among species and among performance measures, often resulting in high costs. We used functional traits to explore how dispersal limitation, migration lags, and competitive exclusion may cause mismatches. Overall, the large variability in mismatches, their costs and the relationship with functional traits highlight the nuanced relationships between species’ performance and their distributions.
Using the Joint Standards to Design Postsecondary Assessments With Evidence of Validity and Reliability: An Approach to CAEP Accreditation
Authors: Wilkerson Judy R. 
Published: October 2019

AbstractValidity and reliability are a major focus in teacher education accreditation by the Council for Accreditation of Educator Preparation (CAEP). CAEP requires the use of “accepted research standards,” but many faculty and administrators are unsure how to meet this requirement. The Standards of Educational and Psychological Testing abbreviated Joint Standards, are the implied accepted research standards. The purpose of this study was to test empirically the extent to which the Joint Standards could serve this purpose. The primary outcome of this study is a pragmatic set of implementation strategies organized into assessment specifications connecting CAEP requirements to the Joint Standards. An example set of assessment specifications is provided. Use of this process can improve assessments in any academic discipline for any accreditation agency, become a faculty professional development tool, raise assessment literacy, and potentially impact instruction of future educators.
Quantitative analysis of phenotypic elements augments traditional electroclinical classification of common familial epilepsies
Authors:   Epi4K Consortium
Published: October 2019

AbstractObjectiveClassification of epilepsy into types and subtypes is important for both clinical care and research into underlying disease mechanisms. A quantitative, data‐driven approach may augment traditional electroclinical classification and shed new light on existing classification frameworks.MethodsWe used latent class analysis, a statistical method that assigns subjects into groups called latent classes based on phenotypic elements, to classify individuals with common familial epilepsies from the Epi4K Multiplex Families study. Phenotypic elements included seizure types, seizure symptoms, and other elements of the medical history. We compared class assignments to traditional electroclinical classifications and assessed familial aggregation of latent classes.ResultsA total of 1120 subjects with epilepsy were assigned to five latent classes. Classes 1 and 2 contained subjects with generalized epilepsy, largely reflecting the distinction between absence epilepsies and younger onset (class 1) versus myoclonic epilepsies and older onset (class 2). Classes 3 and 4 contained subjects with focal epilepsies, and in contrast to classes 1 and 2, these did not adhere as closely to clinically defined focal epilepsy subtypes. Class 5 contained nearly all subjects with febrile seizures plus or unknown epilepsy type, as well as a few subjects with generalized epilepsy and a few with focal epilepsy. Family concordance of latent classes was similar to or greater than concordance of clinically defined epilepsy types.SignificanceQuantitative classification of epilepsy has the potential to augment traditional electroclinical classification by (1) combining some syndromes into a single class, (2) splitting some syndromes into different classes, (3) helping to classify subjects who could not be classified clinically, and (4) defining the boundaries of clinically defined classifications. This approach can guide future research, including molecular genetic studies, by identifying homogeneous sets of individuals that may share underlying disease mechanisms.