bluuebunny/crossref_metadata_2025 huggingface dataset:
Stress and strain analysis of Si-based III – V template fabricated by ion-slicing*
Authors: Zhao Shuyan , Song Yuxin , Liang Hao , Jin Tingting , Lin Jiajie , Yue Li , You Tiangui , Wang Chang , Ou Xin , Wang Shumin
Published: April 2020

Strain and stress were simulated using finite element method (FEM) for three III–V-on-Insulator (III–VOI) structures, i.e., InP/SiO2/Si, InP/Al2O3/SiO2/Si, and GaAs/Al2O3/SiO2/Si, fabricated by ion-slicing as the substrates for optoelectronic devices on Si. The thermal strain/stress imposes no risk for optoelectronic structures grown on InPOI at a normal growth temperature using molecular beam epitaxy. Structures grown on GaAsOI are more dangerous than those on InPOI due to a limited critical thickness. The intermedia Al2O3 layer was intended to increase the adherence while it brings in the largest risk. The simulated results reveal thermal stress on Al2O3 over 1 GPa, which is much higher than its critical stress for interfacial fracture. InPOI without an Al2O3 layer is more suitable as the substrate for optoelectronic integration on Si.
Negative thermal expansion of Ca2RuO4 with oxygen vacancies*
Authors: Xu Sen , Hu Yangming , Liang Yuan , Shi Chenfei , Su Yuling , Guo Juan , Gao Qilong , Chao Mingju , Liang Erjun
Published: April 2020

Oxygen vacancies have a profound effect on the magnetic, electronic, and transport properties of transition metal oxides but little is known about their effect on thermal expansion. Herein we report the effect of oxygen defects on the structure formation and thermal expansion properties of the layered perovskite Ca2RuO4 (CRO). It is shown that the CRO containing excess oxygen crystallizes in a metallic L-CRO phase without structure transition from 100 K to 500 K and displays a normal thermal expansion behavior, whereas those with oxygen vacancies adopt at room temperature an insulating S-CRO phase and exhibit an enormous negative thermal expansion (NTE) from 100 K to about 360 K, from where they undergo a structure transition to a high temperature metallic L-CRO phase. Compared to the L-CRO containing excess oxygen, the S-CRO structure has increasingly large orthorhombic strain and distinctive in-plane distortion upon cooling. The in-plane distortion of the RuO6 octahedra reaches a maximum across 260 K and then relaxes monotonically, providing a structure evidence for the appearance of an antiferromagnetic orbital ordering in the paramagnetic phase and the Ag
phonon mode suppression and phase flip across the same temperature found recently. Both the L- and S-CRO display an antiferromagnetic ordering at about 150–110 K, with ferromagnetic ordering components at lower temperature. The NTE in S-CRO is a result of a complex interplay among the spin, orbital, and lattice.
Past long-term summer warming over western Europe in new generation climate models: role of large-scale atmospheric circulation
Authors: Boé Julien , Terray Laurent , Moine Marie-Pierre , Valcke Sophie , Bellucci Alessio , Drijfhout Sybren , Haarsma Rein , Lohmann Katja , Putrasahan Dian A. , Roberts Chris , Roberts Malcom , Scoccimarro Enrico , Seddon Jon , Senan Retish , Wyser Klaus
Published: April 2020

Past studies have concluded that climate models of previous generations tended to underestimate the large warming trend that has been observed in summer over western Europe in the last few decades. The causes of this systematic error are still not clear. Here, we investigate this issue with a new generation of climate models and systematically explore the role of large-scale circulation in that context.

As an ensemble, climate models in this study warm less over western Europe and warm more over eastern Europe than observed on the 1951–2014 period, but it is difficult to conclude this is directly due to systematic errors given the large potential impact of internal variability. These differences in temperature trends are explained to an important extent by an anti-correlation of sea level pressure trends over the North Atlantic / Europe domain between models and observations. The observed trend tends to warm (cool) western (eastern) Europe but the simulated trends generally have the opposite effect, both in new generation and past generation climate models. The differences between observed and simulated sea level pressure trends are likely the result of systematic model errors, which might also impact future climate projections. Neither a higher resolution nor the realistic representation of the evolution of sea surface temperature and sea ice leads to a better simulation of sea level pressure trends.
Antibacterial and anticancer activity of hydrothermally-synthesized zinc oxide nanomaterials using natural extracts of neem, pepper and turmeric as solvent media
Authors: Abinaya C , Manjula Devi R , Suresh P , Balasubramanian N , Muthaiya N , Kannan N D , Annaraj J , Shanmugaiah V , Pearce J M , Shanmugapriya P , Mayandi J
Published: April 2020

A novel and simple wet chemical hydrothermal synthesis method was employed in the preparation of zinc oxide (ZnO) nanoparticles using neem (N), pepper (P) and turmeric (T) extracts as solvent media. The structural and optical properties as well as the antibacterial and anticancer properties of all the samples (ZnO, N/ZnO, P/ZnO, T/ZnO and NPT/ZnO) were characterized and analyzed. Solvent media was found to have an effect on both the size and the morphology of the nanoparticles, which in turn effected their optical and cytotoxic properties. The colony forming unit (CFU) assays were done for E. coli, S. aureus and S. typhi in which T/ZnO (∼2) and P/ZnO (∼3) showed a remarkable effect on S. aureus for 100 μg ml−1 and nearly zero for 150 μg/ml. The zone of inhibition (ZoI) was measured for S. agalactiae, S. dysgalactiae and S. pyogenes.The results showed that S. dysgalactiae is more sensitive to N/ZnO.Finally, the anticancer properties of these compounds towardsprostate cancer cells was investigated. Among the active compounds T ZnO showed the highest activity with low IC50 value (37.751 μg/ml) followed by P ZnO (45.68 μg ml−1).
Relativism and the Metaphysics of Value: A Comment on Daan Evers
Authors: Wright Crispin
Published: April 2020

Daan Evers argues that relativists about aesthetic and other types of evaluative language face some distinctive and largely overlooked metaphysical difficulties concerning the nature of the states of affairs that such statements are intended to be about. These difficulties, as Evers notes, all rest on the assumption that evaluative language is representational. Evers takes it that it is only on this assumption that evaluative relativism is distinguished from expressivism. I argue that this is incorrect and that, without falling into some form of expressivism, relativists can and must drop the representational assumption, but that the resulting position is one in which relativism no longer offers any distinctive dialectical or theoretical advantage.
GlyGen data model and processing workflow
Authors: Kahsay Robel , Vora Jeet , Navelkar Rahi , Mousavi Reza , Fochtman Brian C , Holmes Xavier , Pattabiraman Nagarajan , Ranzinger Rene , Mahadik Rupali , Williamson Tatiana , Kulkarni Sujeet , Agarwal Gaurav , Martin Maria , Vasudev Preethi , Garcia Leyla , Edwards Nathan , Zhang Wenjin , Natale Darren A , Ross Karen , Aoki-Kinoshita Kiyoko F , Campbell Matthew P , York William S , Mazumder Raja
Published: April 2020

Glycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is critical. This application note describes the GlyGen data model, processing workflow and the data access interfaces featuring programmatic use case example queries based on specific biological questions. The GlyGen project is a data integration, harmonization and dissemination project for carbohydrate and glycoconjugate-related data retrieved from multiple international data sources including UniProtKB, GlyTouCan, UniCarbKB and other key resources.

Availability and implementation

GlyGen web portal is freely available to access at https://glygen.org. The data portal, web services, SPARQL endpoint and GitHub repository are also freely available at https://data.glygen.org, https://api.glygen.org, https://sparql.glygen.org and https://github.com/glygener, respectively. All code is released under license GNU General Public License version 3 (GNU GPLv3) and is available on GitHub https://github.com/glygener. The datasets are made available under Creative Commons Attribution 4.0 International (CC BY 4.0) license.

Supplementary information

Supplementary data are available at Bioinformatics online.
SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants
Authors: Kuksa Pavel P , Lee Chien-Yueh , Amlie-Wolf Alexandre , Gangadharan Prabhakaran , Mlynarski Elizabeth E , Chou Yi-Fan , Lin Han-Jen , Issen Heather , Greenfest-Allen Emily , Valladares Otto , Leung Yuk Yee , Wang Li-San
Published: April 2020

We report Spark-based INFERence of the molecular mechanisms of NOn-coding genetic variants (SparkINFERNO), a scalable bioinformatics pipeline characterizing non-coding genome-wide association study (GWAS) association findings. SparkINFERNO prioritizes causal variants underlying GWAS association signals and reports relevant regulatory elements, tissue contexts and plausible target genes they affect. To achieve this, the SparkINFERNO algorithm integrates GWAS summary statistics with large-scale collection of functional genomics datasets spanning enhancer activity, transcription factor binding, expression quantitative trait loci and other functional datasets across more than 400 tissues and cell types. Scalability is achieved by an underlying API implemented using Apache Spark and Giggle-based genomic indexing. We evaluated SparkINFERNO on large GWASs and show that SparkINFERNO is more than 60 times efficient and scales with data size and amount of computational resources.

Availability and implementation

SparkINFERNO runs on clusters or a single server with Apache Spark environment, and is available at https://bitbucket.org/wanglab-upenn/SparkINFERNO or https://hub.docker.com/r/wanglab/spark-inferno.

Contact

lswang@pennmedicine.upenn.edu

Supplementary information

Supplementary data are available at Bioinformatics online
Efficient posterior sampling for high-dimensional imbalanced logistic regression
Authors: Sen Deborshee , Sachs Matthias , Lu Jianfeng , Dunson David B
Published: April 2020

Classification with high-dimensional data is of widespread interest and often involves dealing with imbalanced data. Bayesian classification approaches are hampered by the fact that current Markov chain Monte Carlo algorithms for posterior computation become inefficient as the number $p$ of predictors or the number $n$ of subjects to classify gets large, because of the increasing computational time per step and worsening mixing rates. One strategy is to employ a gradient-based sampler to improve mixing while using data subsamples to reduce the per-step computational complexity. However, the usual subsampling breaks down when applied to imbalanced data. Instead, we generalize piecewise-deterministic Markov chain Monte Carlo algorithms to include importance-weighted and mini-batch subsampling. These maintain the correct stationary distribution with arbitrarily small subsamples and substantially outperform current competitors. We provide theoretical support for the proposed approach and demonstrate its performance gains in simulated data examples and an application to cancer data.
Successful Community Resettlement of Men with Learning Disabilities Who Have Completed a Hospital-Based Treatment for Sexual Offending
Authors: Hollomotz Andrea
Published: April 2020

Treatment for sexual offending equips men with learning disabilities with tools required for pro-social community living. In the past, risk aversiveness prevented discharges from hospital, but fieldwork took place at the time of the Transforming Care Agenda, which sought to enable more people to return to their communities. This offered the opportunity to gain unique insights into community resettlement planning in cases that require ongoing risk management. Eleven case studies were examined through qualitative interviews with the men and professionals. A realist evaluation methodology was applied to examine how treatment outcomes manifested longer term. It was evidenced that treatment had equipped men with risk management tools, as well as encouraged them to develop realistic visions for their pro-social futures and that both outcomes come to fruition under conditions that allow positive risk taking. The welfareist and user-led nature of working towards pro-social community living makes this a useful toolkit for social work, whilst input from forensic health services was valued for skilling up the social care workforce. However, discharge practices continued to be influenced by contextual factors, including local availability of resources and personal attributes, such as men’s sexual preferences and levels of compliance and some men remained in hospital.
Sensitivity and Specificity of Treponemal-specific Tests for the Diagnosis of Syphilis
Authors: Park Ina U , Tran Anthony , Pereira Lara , Fakile Yetunde
Published: April 2020

We conducted a systematic review of relevant syphilis diagnostic literature to address the question, “What is the sensitivity and specificity of the treponemal tests currently approved by the Food and Drug Administration (FDA) for the diagnosis of syphilis (by stage)?” There were 16 treponemal assays evaluated: 13 immunoassays and 3 manual assays (fluorescent treponemal antibody absorbed test [FTA-ABS], microhemagglutination assay for Treponema pallidum antibodies [MHA-TP], Treponema pallidum particle agglutination assay [TP-PA]). MHA-TP and FTA-ABS were less sensitive in primary and secondary syphilis than TP-PA; TP-PA is the most specific manual treponemal assay. There is insufficient evidence to recommend one particular treponemal immunoassay (eg, enzyme immunoassays, chemiluminescence immunoassays, microbead immunoassays) over another based on published performance data. For diagnosis of neurosyphilis, cerebrospinal fluid (CSF) TP-PA has similar performance to CSF FTA-ABS in studies with patients with definitive or presumptive neurosyphilis. However, CSF treponemal testing has limitations in its sensitivity and specificity and should be interpreted within the context of the clinical scenario, additional CSF test results and syphilis prevalence.
Testing for SARS-CoV-2: Can We Stop at 2?
Authors: Lee Tau Hong , Junhao Lin Ray , Lin Raymond T P , Barkham Timothy , Rao Pooja , Leo Yee-Sin , Chien Lye David , Young Barnaby ,   for the National Centre for Infectious Diseases COVID-19 Outbreak Research Team
Published: April 2020

The COVID-19 epidemic requires accurate identification and isolation of confirmed cases for effective control. This report describes the effectiveness of our testing strategy and highlights the importance of repeat testing in suspected cases in our cohort.
Intra-Tile Parallelization for Two-Level Perfectly Nested Loops With Non-Uniform Dependences
Authors: Abdi Reyhan Zahra , Lotfi Shahriar , Isazadeh Ayaz , Karimpour Jaber
Published: April 2020

Most important scientific and engineering applications have complex computations or large data. In all these applications, a huge amount of time is consumed by nested loops. Therefore, loops are the main source of the parallelization of scientific and engineering programs. Many parallelizing compilers focus on parallelization of nested loops with uniform dependences, and parallelization of nested loops with non-uniform dependences has not been extensively investigated. This paper addresses the problem of parallelizing two-level nested loops with non-uniform dependences. The aim is to minimize the execution time by improving the load balancing and minimizing the inter-processor communication. We propose a new tiling algorithm, k-StepIntraTiling, using bin packing problem to minimize the execution time. We demonstrate the effectiveness of the proposed method in several experiments. Simulation and experimental results show that the algorithm effectively reduces the total execution time of several benchmarks compared to the other tiling methods.
The harm of delayed diagnosis of arrhythmogenic cardiac sarcoidosis: a case series
Authors: Hoogendoorn Jarieke C , Ninaber Maarten K , Piers Sebastiaan R D , de Riva Marta , Grauss Robert W , Bogun Frank M , Zeppenfeld Katja
Published: April 2020

Aims

Cardiac sarcoidosis (CS) is a known cause of ventricular tachycardia (VT). However, an arrhythmogenic presentation may not prompt immediate comprehensive evaluation. We aimed to assess the diagnostic and disease course of patients with arrhythmogenic cardiac sarcoidosis (ACS).

Methods and results

From the Leiden VT-ablation-registry, consecutive patients with CS as underlying aetiology were retrospectively included. Data on clinical presentation, time-to-diagnosis, cardiac function, and clinical outcomes were collected. Patients were divided in early (<6 months from first cardiac presentation) and late diagnosis. After exclusion of patients with known causes of non-ischaemic cardiomyopathy (NICM), 15 (12%) out of 129 patients with idiopathic NICM were ultimately diagnosed with CS and included. Five patients were diagnosed early; all had early presentation with VTs. Ten patients had a late diagnosis with a median delay of 24 (IQR 15–44) months, despite presentation with VT (n = 5) and atrioventricular block (n = 4). In 6 of 10 patients, reason for suspicion of ACS was the electroanatomical scar pattern. In patients with early diagnosis, immunosuppressive therapy was immediately initiated with stable cardiac function during follow-up. Adversely, in 7 of 10 patients with late diagnosis, cardiac function deteriorated before diagnosis, and in only one cardiac function recovered with immunosuppressive therapy. Six (40%) patients died (five of six with late diagnosis).

Conclusion

Arrhythmogenic cardiac sarcoidosis is an important differential diagnosis in NICM patients referred for VT ablation. Importantly, the diagnosis is frequently delayed, which leads to a severe disease course, including irreversible cardiac dysfunction and death. Early recognition, which can be facilitated by electroanatomical mapping, is crucial.
The Foreclosure Crisis, Community Change, and the Cognitive Health of Older Adults
Authors: Friedman Esther M , Houle Jason N , Cagney Kathleen A , Slaughter Mary E , Shih Regina A
Published: April 2020

Objectives

While home foreclosures are often thought of as a household-level event, the consequences may be far-reaching, and spill over to the broader community. Older adults, in particular, could be affected by the spiral of community changes that result from foreclosures, but we know very little about how the foreclosure crisis is related to older adult health, in particular cognition.

Method

This article uses growth curve models and data from the Health and Retirement Study matched to Census and county-level foreclosure data to examine whether community foreclosures are related to older adults’ cognitive health and the mechanisms responsible.

Results

We find that higher rates of county-level foreclosures are associated with a faster decline in individual cognition at older ages. Although we examined an extensive number of individual and community mechanisms, including individual housing wealth and depressive symptoms, community structural factors, social factors, and perceptions of physical disorder and cohesion, none of the mechanisms examined here explained this relationship.

Discussion

This study shows that the adverse consequences of home foreclosures spill over to the local community, with implications for the cognitive health of older adults.
Natural, Everyday Language Use Provides a Window Into the Integrity of Older Adults’ Executive Functioning
Authors: Polsinelli Angelina J , Moseley Suzanne A , Grilli Matthew D , Glisky Elizabeth L , Mehl Matthias R
Published: April 2020

Objectives

Language markers derived from structured clinical interviews and assessments have been found to predict age-related normal and pathological cognitive functioning. An important question, then, is the degree to which the language that people use in their natural daily interactions, rather than their language elicited within and specifically for clinical assessment, carries information about key cognitive functions associated with age-related decline. In an observational study, we investigated how variability in executive functioning (EF) manifests in patterns of daily word use.

Method

Cognitively normal older adults (n = 102; mean age 76 years) wore the electronically activated recorder, an ambulatory monitoring device that intermittently recorded short snippets of ambient sounds, for 4 days, yielding an acoustic log of their daily conversations as they naturally unfolded. Verbatim transcripts of their captured utterances were text-analyzed using linguistic inquiring and word count. EF was assessed with a validated test battery measuring WM, shifting, and inhibitory control.

Results

Controlling for age, education, and gender, higher overall EF, and particularly working memory, was associated with analytic (e.g., more articles and prepositions), complex (e.g., more longer words), and specific (e.g., more numbers) language in addition to other language markers (e.g., a relatively less positive emotional tone, more sexual and swear words).

Discussion

This study provides first evidence that the words older adults use in daily life provide a window into their EF.
Low-frequency noise attenuation in seismic and microseismic data using mathematical morphological filtering
Authors: Huang Weilin , Wang Runqiu , Zu Shaohuan , Chen Yangkang
Published: April 2020

Low-frequency noise is one of the most common types of noise in seismic and microseismic data. Conventional approaches, such as the high-pass filtering method, utilize the low-frequency nature and distinguish between signal and noise based on their different frequency contents. However, conventional approaches are limited or even invalid when the signal and noise shares the same frequency band. Moreover, high-pass filtering method will suppress not only low-frequency noise but also low-frequency signal when they overlap in a same frequency band, which is extremely important in the inversion process for building the subsurface velocity model. To overcome the drawbacks of conventional high-pass filtering approach, we developed a novel method based on the mathematical morphology theorem to separate signal and noise using their differences in morphological scale. We extracted empirical relation between morphological scale and frequency band so that the mathematical morphology based approach can be conveniently used in low-frequency noise attenuation. The proposed method is termed as the mathematical morphological filtering (MMF) method. We compare the MMF approach with high-pass filtering and empirical mode decomposition (EMD) approaches using synthetic, reflection seismic and microseismic examples. The various examples demonstrate that the proposed MMF method can preserve more low-frequency signal than the high-pass filtering approach, and is more efficient and causes fewer artefacts than the EMD approach.
Plane-wave orthogonal polynomial transform for amplitude-preserving noise attenuation
Authors: Chen Yangkang , Huang Weilin , Zhou Yatong , Liu Wei , Zhang Dong
Published: April 2020

Amplitude-preserving data processing is an important and challenging topic in many scientific fields. The amplitude-variation details in seismic data are especially important because the amplitude variation is directly related with the subsurface wave impedance and fluid characteristics. We propose a novel seismic noise attenuation approach that is based on local plane-wave assumption of seismic events and the amplitude preserving capability of the orthogonal polynomial transform (OPT). The OPT is a way for representing spatially correlative seismic data as a superposition of polynomial basis functions, by which the random noise is distinguished from the useful energy by the high orthogonal polynomial coefficients. The seismic energy is the most correlative along the structural direction and thus the OPT is optimally performed in a flattened gather. We introduce in detail the flattening operator for creating the flattened dimension, where the OPT can be applied subsequently. The flattening operator is created by deriving a plane-wave trace continuation relation following the plane-wave equation. We demonstrate that both plane-wave trace continuation and OPT can well preserve the strong amplitude variation existing in seismic data. In order to obtain a robust slope estimation performance in the presence of noise, a robust slope estimation approach is introduced to substitute the traditional method. A group of synthetic, pre-stack and post-stack field seismic data are used to demonstrate the potential of the proposed framework in realistic applications.
Hydrodynamic Simulations of the Performance Landscape for Suction-Feeding Fishes Reveal Multiple Peaks for Different Prey Types
Authors: Olsson Karin H , Martin Christopher H , Holzman Roi
Published: April 2020

The complex interplay between form and function forms the basis for generating and maintaining organismal diversity. Fishes that rely on suction-feeding for prey capture exhibit remarkable phenotypic and trophic diversity. Yet the relationships between fish phenotypes and feeding performance on different prey types are unclear, partly because the morphological, biomechanical, and hydrodynamic mechanisms that underlie suction-feeding are complex. Here we demonstrate a general framework to investigate the mapping of multiple phenotypic traits to performance by mapping kinematic variables to suction-feeding capacity. Using a mechanistic model of suction-feeding that is based on core physical principles, we predict prey capture performance across a broad range of phenotypic trait values, for three general prey types: mollusk-like prey, copepod-like prey, and fish-like prey. Mollusk-like prey attach to surfaces, copepod-like prey attempt to escape upon detecting the hydrodynamic disturbance produced by the predator, and fish-like prey attempt to escape when the predator comes within a threshold distance. This approach allowed us to evaluate suction-feeding performance for any combination of six key kinematic traits, irrespective of whether these trait combinations were observed in an extant species, and to generate a multivariate mapping of phenotype to performance. We used gradient ascent methods to explore the complex topography of the performance landscape for each prey type, and found evidence for multiple peaks. Characterization of phenotypes associated with performance peaks indicates that the optimal kinematic parameter range for suction-feeding on different prey types are narrow and distinct from each other, suggesting different functional constraints for the three prey types. These performance landscapes can be used to generate hypotheses regarding the distribution of extant species in trait space and their evolutionary trajectories toward adaptive peaks on macroevolutionary fitness landscapes.
Optimal-order error estimates of finite element approximations to variable-order time-fractional diffusion equations without regularity assumptions of the true solutions
Authors: Zheng Xiangcheng , Wang Hong
Published: April 2020

We study a fully discretized finite element approximation to variable-order Caputo and Riemann–Liouville time-fractional diffusion equations (tFDEs) in multiple space dimensions, which model solute transport in heterogeneous porous media and related applications. We prove error estimates for the proposed methods, which are discretized on an equidistant or graded temporal partition predetermined by the behavior of the variable order at the initial time, only under the regularity assumptions of the variable order, coefficients and the source term but without any regularity assumption of the true solutions. Roughly, we prove that the finite element approximations to variable-order Caputo tFDEs have optimal-order convergence rates on a uniform temporal partition. In contrast the finite element approximations to variable-order Riemann–Liouville tFDEs discretized on a uniform temporal partition achieve an optimal-order convergence rate if $\alpha (0)=\alpha ^{\prime}(0) = 0$ but a suboptimal-order convergence rate if $\alpha (0)>0$. In the latter case, optimal-order convergence rate can be proved by employing the graded temporal partition. We conduct numerical experiments to investigate the performance of the numerical methods and to verify the mathematical analysis.
Artificial intelligence: opportunities and implications for the health workforce
Authors: Hazarika Indrajit
Published: April 2020

Healthcare involves cyclic data processing to derive meaningful, actionable decisions. Rapid increases in clinical data have added to the occupational stress of healthcare workers, affecting their ability to provide quality and effective services. Health systems have to radically rethink strategies to ensure that staff are satisfied and actively supported in their jobs. Artificial intelligence (AI) has the potential to augment provider performance. This article reviews the available literature to identify AI opportunities that can potentially transform the role of healthcare providers. To leverage AI’s full potential, policymakers, industry, healthcare providers and patients have to address a new set of challenges. Optimizing the benefits of AI will require a balanced approach that enhances accountability and transparency while facilitating innovation.
Brown bear den characteristics and selection in eastern Transylvania, Romania
Authors: Faure Ulysse , Domokos Csaba , Leriche Agathe , Cristescu Bogdan
Published: April 2020

Dens are important for species that need to survive and reproduce during harsh winters. Brown bears (Ursus arctos) in Romania, listed by the European Union as a population of concern, use dens for several months each year. To date, few quantitative assessments of denning habitat have been carried out for this population or others in Europe. In 2008–2013 and 2015–2017, we used local knowledge and telemetry data from brown bears fitted with GPS collars to identify 115 winter dens and eight open ground nests used by bears in eastern Transylvania, Romania. We located most dens in mountainous areas (64%) and fewer in foothills (36%). Den entrances in mountainous areas were significantly narrower than entrances in foothills, likely due to the need for reduced thermal loss during more severe winters at higher elevations. We selected seven habitat characteristics (abiotic and biotic) and human-related covariates associated with known locations of dens and open nests to identify potential brown bear denning habitat using maximum entropy modeling. We found that terrain ruggedness was the single most important factor when predicting bear denning habitat. The habitat map derived from this study can be used in the future to safeguard bear denning areas from potential human disturbances.
A comparison of density estimation methods in plateau pika populations in an alpine meadow ecosystem
Authors: Wei Wanrong , He Jundong , Zheng Qiaoyan , He Yuli , Oosthuizen Maria K
Published: April 2020

Plateau pikas are a keystone species and ecosystem engineers in alpine meadow ecosystems. A number of surveying methods have been used to estimate pika density, but the reliability of these methods is not known. In addition, better population density methodologies allow for more reliable density estimates. We therefore compared the relationship among several commonly used methods of estimating pika relative density and the absolute density (AD) of pika populations. This relationship was investigated in summer and winter pastures to determine whether distribution pattern of the pikas (patchy or uniform) would influence this relationship. During August of 2015 and August of 2016, we measured the relative and absolute population density of pikas in an alpine meadow in the County, Gansu province, northwestern China. Relative density was measured with three indirect and direct methods: the total burrow density (TBD), the active burrow density (ABD), and the direct counting density (DCD) at the peak of pika activity. AD was assessed by removal sampling. Our results showed that the relative population density with all three survey methods was significantly related to the absolute population density. In particular, DCD at the peak of the pika activity showed the best correlation with AD. A simple linear model showed the effect of grazing time by livestock had a significant effect on TBD and ABD. These results imply that using DCD as a method to survey at the peak of the pika activity is more reliable than other methods.
Sustained Reductions in Children's Risk Taking from Peer-Communicated Behavioral Safety Norms
Authors: Morrongiello Barbara A , Weinberger Emily , Seasons Mackenzie
Published: April 2020

Objective

This research examined whether the positive effects of a peer-communicated social norm that reduces risk-taking behaviors persist over time and if a reminder of this peer-communicated safety message has any impact on this outcome.

Methods

Positive mood in 7- to 9-year olds was induced experimentally and risk taking intentions and behaviors were measured when the child was in a positive and neutral mood state and after they had been exposed to either a safety or neutral peer-communicated social norm message. A few weeks later, half of the participants who experienced the safety social norm message were exposed to a reminder of this message via a slogan and risk-taking measures were taken again when in a heightened positive mood state.

Results

Exposure to a safety norm successfully counteracted the increase in risk taking associated with a positive mood state. These effects persisted for several weeks regardless of whether the children were exposed to a reminder.

Conclusion

Manipulating peer social norms holds promise as an approach to produce reductions in children’s risk taking and these effects persist at least over several weeks.
A glutathione-dependent control of the indole butyric acid pathway supports Arabidopsis root system adaptation to phosphate deprivation
Authors: Trujillo-Hernandez José A , Bariat Laetitia , Enders Tara A , Strader Lucia C , Reichheld Jean-Philippe , Belin Christophe
Published: April 2020

Root system architecture results from a highly plastic developmental process to adapt to environmental conditions. In particular, the development of lateral roots and root hair growth are constantly optimized to the rhizosphere properties, including biotic and abiotic constraints. The development of the root system is tightly controlled by auxin, the driving morphogenic hormone in plants. Glutathione, a major thiol redox regulator, is also critical for root development but its interplay with auxin is scarcely understood. Previous work showed that glutathione deficiency does not alter root responses to indole acetic acid (IAA), the main active auxin in plants. Because indole butyric acid (IBA), another endogenous auxinic compound, is an important source of IAA for the control of root development, we investigated the crosstalk between glutathione and IBA during root development. We show that glutathione deficiency alters lateral roots and root hair responses to exogenous IBA but not IAA. Detailed genetic analyses suggest that glutathione regulates IBA homeostasis or conversion to IAA in the root cap. Finally, we show that both glutathione and IBA are required to trigger the root hair response to phosphate deprivation, suggesting an important role for this glutathione-dependent regulation of the auxin pathway in plant developmental adaptation to its environment.
Modified initial power spectrum and too big to fail problem
Authors: Kameli Hamed , Baghram Shant
Published: April 2020

The galactic scale challenges of dark matter such as ‘missing satellite’ problem and ‘too big to fail’ problem are the main caveats of standard model of cosmology. These challenges could be solved either by implementing the complicated baryonic physics or it could be considered as an indication to a new physics beyond the standard model of cosmology. The modification of collisionless dark matter models or the standard initial conditions are two promising venues for study. In this work, we investigate the effects of the deviations from scale invariant initial curvature power spectrum on number density of dark matter haloes. We develop the non-Markov extension of the excursion set theory to calculate the number density of dark matter substructures and dark matter halo progenitor mass distribution. We show that the plausible solution to ‘too big to fail’ problem could be obtained by a Gaussian excess in initial power in the scales of k* ∼ 3 h Mpc−1 that is related to the mass scale of M* ∼ 1011 M⊙. We show that this deviation leads to the decrement of dark matter subhaloes in galactic scale, which is consistent with the current status of the non-linear power spectrum. Our proposal also has a prediction that the number density of Milky Way-type galaxies must be higher than the standard case.
Kidney disease pathways, options and decisions: an environmental scan of international patient decision aids
Authors: Winterbottom Anna E , Mooney Andrew , Russon Lynne , Hipkiss Vicki , Ziegler Lucy , Williams Richard , Finderup Jeanette , Bekker Hilary L
Published: April 2020

Background

Conservative management is recognized as an acceptable treatment for people with worsening chronic kidney disease; however, patients consistently report they lack understanding about their changing disease state and feel unsupported in making shared decisions about future treatment. The purpose of this review was to critically evaluate patient decision aids (PtDAs) developed to support patient–professional shared decision-making between dialysis and conservative management treatment pathways.

Methods

We performed a systematic review of resources accessible in English using environmental scan methods. Data sources included online databases of research publications, repositories for clinical guidelines, research projects and PtDAs, international PtDA expert lists and reference lists from relevant publications. The resource selection was from 56 screened records; 17 PtDAs were included. A data extraction sheet was applied to all eligible resources, eliciting resource characteristics, decision architecture to boost/bias thinking, indicators of quality such as International Standards for Patient Decision Aids Standards checklist and engagement with health services.

Results

PtDAs were developed in five countries; eleven were publically available via the Internet. Treatment options described were dialysis (n = 17), conservative management (n = 9) and transplant (n = 5). Eight resources signposted conservative management as an option rather than an active choice. Ten different labels across 14 resources were used to name ‘conservative management’. The readability of the resources was good. Six publications detail decision aid development and/or evaluation research. Using PtDAs improved treatment decision-making by patients. Only resources identified as PtDAs and available in English were included.

Conclusions

PtDAs are used by some services to support patients choosing between dialysis options or end-of-life options. PtDAs developed to proactively support people making informed decisions between conservative management and dialysis treatments are likely to enable services to meet current best practice.
Return to work interventions for chronic pain: a systematic review
Authors: Wegrzynek P A , Wainwright E , Ravalier J
Published: April 2020

Background

Chronic pain (CP) remains the second commonest reason for being off work. Tertiary return to work (RTW) interventions aim to improve psychological and physical capacity amongst workers already off sick. Their effectiveness for workers with CP is unclear.

Aims

To explore which tertiary interventions effectively promote RTW for CP sufferers.

Methods

We searched eight databases for randomized controlled trials evaluating the effectiveness of tertiary RTW interventions for CP sufferers. We employed the Cochrane Risk of Bias (ROB) and methodological quality assessment tools for all included papers. We synthesized findings narratively. Meta-analysis was not possible due to heterogeneity of study characteristics.

Results

We included 16 papers pertaining to 13 trials. The types, delivery format and follow-up schedules of RTW interventions varied greatly. Most treatments were multidisciplinary, comprising psychological, physical and workplace elements. Five trials reported that tertiary interventions with multidisciplinary elements promoted RTW for workers with CP compared to controls. We gave a high ROB rating for one or more assessment criteria to three out of the five successful intervention trials. Two had medium- and low-risk elements across all categories. One compared different intensity multidisciplinary treatment and one comprised work-hardening with a job coach. Seven trials found treatment effects for secondary outcomes but no RTW improvement.

Conclusions

There is no conclusive evidence to support any specific tertiary RTW intervention for workers with CP, but multidisciplinary efforts should be considered. Workers’ compensation is an important area for RTW policymakers to consider.
The Proline-Rich Family Protein EXTENSIN33 Is Required for Etiolated Arabidopsis thaliana Hypocotyl Growth
Authors: Zdanio Malgorzata , Boron Agnieszka Karolina , Balcerowicz Daria , Schoenaers Sébastjen , Markakis Marios Nektarios , Mouille Grégory , Pintelon Isabel , Suslov Dmitry , Gonneau Martine , Höfte Herman , Vissenberg Kris
Published: April 2020

Growth of etiolated Arabidopsis hypocotyls is biphasic. During the first phase, cells elongate slowly and synchronously. At 48 h after imbibition, cells at the hypocotyl base accelerate their growth. Subsequently, this rapid elongation propagates through the hypocotyl from base to top. It is largely unclear what regulates the switch from slow to fast elongation. Reverse genetics-based screening for hypocotyl phenotypes identified three independent mutant lines of At1g70990, a short extensin (EXT) family protein that we named EXT33, with shorter etiolated hypocotyls during the slow elongation phase. However, at 72 h after imbibition, these dark-grown mutant hypocotyls start to elongate faster than the wild type (WT). As a result, fully mature 8-day-old dark-grown hypocotyls were significantly longer than WTs. Mutant roots showed no growth phenotype. In line with these results, analysis of native promoter-driven transcriptional fusion lines revealed that, in dark-grown hypocotyls, expression occurred in the epidermis and cortex and that it was strongest in the growing part. Confocal and spinning disk microscopy on C-terminal protein-GFP fusion lines localized the EXT33-protein to the ER and cell wall. Fourier-transform infrared microspectroscopy identified subtle changes in cell wall composition between WT and the mutant, reflecting altered cell wall biomechanics measured by constant load extensometry. Our results indicate that the EXT33 short EXT family protein is required during the first phase of dark-grown hypocotyl elongation and that it regulates the moment and extent of the growth acceleration by modulating cell wall extensibility.
Performance of the 2019 ACR/EULAR classification criteria for IgG4-related disease and clinical phenotypes in a Spanish multicentre registry (REERIGG4)
Authors: Fernández-Codina Andreu , Pinilla Blanca , Pinal-Fernández Iago , Carballo Iago , Feijoo-Massó Carlos , Toledano-Macías María , de Miguel-Campo Borja , Fonseca-Aizpuru Eva , Sáez-Comet Luis , López-Dupla Miguel , Hernández-Rodríguez José , Martínez-Valle Fernando
Published: April 2020

Objectives

Several IgG4-related disease (IgG4-RD) phenotypes have been proposed and the first set of classification criteria have been recently created. Our objectives were to assess the phenotype distribution and the performance of the classification criteria in Spanish patients as genetic and geographical differences may exist.

Methods

We performed a cross-sectional multicentre study (Registro Español de Enfermedad Relacionada con la IgG4, REERIGG4) with nine participating centres from Spain. Patients were recruited from November 2013 to December 2018. The 2019 American College of Rheumatology/European League Against Rheumatism classification criteria (AECC) were used.

Results

We included 105 patients; 88% had Caucasian ethnicity. On diagnosis, 86% met the international pathology consensus while 92% met the Japanese comprehensive criteria. The phenotype distribution was head and neck 25%, Mikulicz and systemic (MS) 20%, pancreato-hepato-biliary (PHB) 13%, retroperitoneal and aorta (RA) 26%. Sixteen per cent had an undefined phenotype. Seventy-seven per cent of the cases met the AECC. From the 24 patients not meeting the AECC, 33% met exclusion criteria, and 67% did not get a score ≥20 points. Incomplete pathology reports were associated to failure to meet the AECC.

Conclusions

The PHB phenotype was rare among Spanish IgG4-RD patients. The MS phenotype was less frequent and the RA phenotype was more prevalent than in other, Asian patient series. An undefined phenotype should be considered as some patients do not fall into any of the categories. Three quarters of the cases met the 2019 AECC. Incomplete pathology reports were the leading causes of failure to meet the criteria.
Association Between Childhood Green Space, Genetic Liability, and the Incidence of Schizophrenia
Authors: Engemann Kristine , Pedersen Carsten Bøcker , Agerbo Esben , Arge Lars , Børglum Anders Dupont , Erikstrup Christian , Hertel Ole , Hougaard David Michael , McGrath John J , Mors Ole , Mortensen Preben Bo , Nordentoft Merete , Sabel Clive Eric , Sigsgaard Torben , Tsirogiannis Constantinos , Vilhjálmsson Bjarni Jóhann , Werge Thomas , Svenning Jens-Christian , Horsdal Henriette Thisted
Published: April 2020

Childhood exposure to green space has previously been associated with lower risk of developing schizophrenia later in life. It is unclear whether this association is mediated by genetic liability or whether the 2 risk factors work additively. Here, we investigate possible gene–environment associations with the hazard ratio (HR) of schizophrenia by combining (1) an estimate of childhood exposure to residential-level green space based on the normalized difference vegetation index (NDVI) from Landsat satellite images, with (2) genetic liability estimates based on polygenic risk scores for 19 746 genotyped individuals from the Danish iPSYCH sample. We used information from the Danish registers of health, residential address, and socioeconomic status to adjust HR estimates for established confounders, ie, parents’ socioeconomic status, and family history of mental illness. The adjusted HRs show that growing up surrounded by the highest compared to the lowest decile of NDVI was associated with a 0.52-fold (95% confidence interval [CI]: 0.40 to 0.66) lower schizophrenia risk, and children with the highest polygenic risk score had a 1.24-fold (95% CI: 1.18 to 1.30) higher schizophrenia risk. We found that NDVI explained 1.45% (95% CI: 1.07 to 1.90) of the variance on the liability scale, while polygenic risk score for schizophrenia explained 1.01% (95% CI: 0.77 to 1.46). Together they explained 2.40% (95% CI: 1.99 to 3.07) with no indication of a gene–environment interaction (P = .29). Our results suggest that risk of schizophrenia is associated additively with green space exposure and genetic liability, and provide no support for an environment-gene interaction between NDVI and schizophrenia.