bluuebunny/crossref_metadata_2025_split huggingface dataset:
Divergent drivers of leaf trait variation within species, among species, and among functional groups
Authors: Osnas Jeanne L. D. , Katabuchi Masatoshi , Kitajima Kaoru , Wright S. Joseph , Reich Peter B. , Van Bael Sunshine A. , Kraft Nathan J. B. , Samaniego Mirna J. , Pacala Stephen W. , Lichstein Jeremy W. 
Published: May 2018

Significance
Leaf traits, such as photosynthetic capacity, nitrogen concentration, and leaf mass per area, strongly affect plant growth and nutrient cycles. Understanding relationships among leaf traits is, therefore, a fundamental challenge in plant biology, crop science, and ecology. Different groups of leaves exhibit distinct relationships among pairs of traits. For example, photosynthetic capacity per unit leaf area increases strongly with leaf mass per area from sun to shade within species, but these same traits are only weakly related across global species. Our analysis suggests that divergent trait relationships can be understood by partitioning leaf mass into photosynthetic and structural support components. Our paper clarifies the causes of relationships among traits and why those relationships differ among different groups of plants.
Evolution of increased competitive ability and shifting defence hypotheses.
Authors: Müller C. 
Published: May 2018

Abstract

This chapter focuses on two of the various hypotheses that take into account the role of biotic interactions in invasion biology, namely the evolution of increased competitive ability (EICA) hypothesis and the shifting defence hypothesis (SDH). Both hypotheses mainly consider changes in concentrations of chemical defences in plant individuals from native vs exotic populations and are studied independently of the novelty of the chemical metabolite in the invasive range. The EICA hypothesis predicts that chemical defences should be lower in plants of invasive populations because enemy pressure is reduced in the exotic range. The SDH predicts a shift in chemical defences by discriminating between qualitative and quantitative defences. Qualitative defences (toxins) are cheaper to produce and expected to increase in invasive populations because they are needed as defence against generalists, whereas expensive quantitative defences (digestibility reducers) may be reduced in plants of the invasive range owing to the overall lower enemy pressure. Methodological issues are pointed out that should be considered when testing the differences in plant traits between native and invasive populations. A literature review on qualitative and quantitative defence traits, which were compared between plants of native and invasive origin grown under standardized common-garden conditions, revealed 37 studies, comprising 22 plant species. The results of the review infrequently support predictions for defence distributions of the EICA hypothesis, whereas predictions of the SDH are supported by somewhat more traits. The definition of qualitative vs quantitative defences has shortcomings, however. In particular, actual costs of these defences are difficult to estimate but should be investigated in future studies. Furthermore, instead of focusing on individual defences, multiple defences should be considered in plant species that are invasive to gain a more complete understanding of resource-allocation patterns.
Analytic treatment of the thermoelectric properties for two coupled
quantum dots threaded by magnetic fields
Authors: Menichetti G , Grosso G , Parravicini G Pastori 
Published: May 2018

Abstract
Coupled double quantum dots (c-2QD) connected to leads have been widely adopted
as prototype model systems to verify interference effects on quantum transport
at the nanoscale. We provide here an analytic study of the thermoelectric
properties of c-2QD systems pierced by a uniform magnetic field. Fully analytic
and easy-to-use expressions are derived for all the kinetic functionals of
interest. Within the Green’s function formalism, our
results allow a simple inexpensive procedure for the theoretical description of
the thermoelectric phenomena for different chemical potentials and temperatures
of the reservoirs, different threading magnetic fluxes, dot energies and
interdot interactions; moreover they provide an intuitive guide to parametrize
the system Hamiltonian for the design of best performing realistic devices. We
have found that the thermopower S can be enhanced by more than
ten times and the figure of merit ZT by more than hundred times
by the presence of a threading magnetic field. Most important, we show that the
magnetic flux increases also the performance of the device under maximum power
output conditions.
The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease
Authors: Cremers Amelieke J H , Mobegi Fredrick M , van der Gaast–de Jongh Christa , van Weert Michelle , van Opzeeland Fred J , Vehkala Minna , Knol Mirjam J , Bootsma Hester J , Välimäki Niko , Croucher Nicholas J , Meis Jacques F , Bentley Stephen , van Hijum Sacha A F T , Corander Jukka , Zomer Aldert L , Ferwerda Gerben , de Jonge Marien I 
Published: May 2018

Abstract

Background
Different clinical manifestations of invasive pneumococcal disease (IPD) have thus far mainly been explained by patient characteristics. Here we studied the contribution of pneumococcal genetic variation to IPD phenotype.

Methods
The index cohort consisted of 349 patients admitted to 2 Dutch hospitals between 2000–2011 with pneumococcal bacteremia. We performed genome-wide association studies to identify pneumococcal lineages, genes, and allelic variants associated with 23 clinical IPD phenotypes. The identified associations were validated in a nationwide (n = 482) and a post–pneumococcal vaccination cohort (n = 121). The contribution of confirmed pneumococcal genotypes to the clinical IPD phenotype, relative to known clinical predictors, was tested by regression analysis.

Results
Among IPD patients, the presence of pneumococcal gene slaA was a nationwide confirmed independent predictor of meningitis (odds ratio [OR], 10.5; P = .001), as was sequence cluster 9 (serotype 7F: OR, 3.68; P = .057). A set of 4 pneumococcal genes co-located on a prophage was a confirmed independent predictor of 30-day mortality (OR, 3.4; P = .003). We could detect the pneumococcal variants of concern in these patients’ blood samples.

Conclusions
In this study, knowledge of pneumococcal genotypic variants improved the clinical risk assessment for detrimental manifestations of IPD. This provides us with novel opportunities to target, anticipate, or avert the pathogenic effects related to particular pneumococcal variants, and indicates that information on pneumococcal genotype is important for the diagnostic and treatment strategy in IPD. Ongoing surveillance is warranted to monitor the clinical value of information on pneumococcal variants in dynamic microbial and susceptible host populations.
Assessing Dependency in a Multiethnic Community Cohort of Individuals With Alzheimer’s Disease
Authors: Meinerding Maria , DeFeis Brittany , Sunderaraman Preeti , Azar Martina , Lawless Siobhan , Perez-Vivaldo Carlos , Gu Yian , Stern Yaakov , Cosentino Stephanie 
Published: May 2018

Abstract

Background and Objectives
Clinic-based studies of patients with Alzheimer’s disease (AD) have demonstrated the value of assessing dependence when characterizing patients’ functional status. The Dependence Scale, a validated tool to assess level of caregiving needs, is associated with markers of disease severity, cost, and progression, while offering independent functional information about patients. This study examines whether such associations between the Dependence Scale and markers of disease severity demonstrated in clinical cohorts are similarly exhibited in a multiethnic community population of individuals with AD.

Research Design and Methods
One hundred fifty four elders with AD enrolled in the Predictors 3 cohort were assessed with the Dependence Scale, modified Mini-Mental State Examination (mMMS), instrumental (IADL) and basic (BADL) activities of daily living, and Clinical Dementia Rating (CDR) Scale, and were assigned an Equivalent Institutional Care (EIC) rating. Cross-sectional associations were examined using bivariate correlations and one-way analysis of variance analyses. Fisher-z tests examined differences in strengths of associations across previous clinic and current community cohorts.

Results
Dependence Scale scores were associated with CDR (r = .20, p = .013), mMMS (r = −.23, p = .005), IADL (r = .39, p &lt; .001), BADL (r = .65, p &lt; .001), and EIC (r = .51, p &lt; .001). Dependence was unassociated with ethnicity (F[3,144] = 1.027, p = .3822), age (r = .120, p = .145), and education (r = −.053, p = .519). The strength of the correlations was comparable across cohorts except that BADLs were more strongly associated with dependence (z = −4.60, p &lt; .001) in the community cohort, and living arrangement was not associated with dependence (r = .13, p = .130).

Discussion and Implications
Associations between the Dependence Scale and markers of disease severity in a clinic-based cohort of AD patients are similar to associations in a multiethnic community cohort of individuals diagnosed with AD. The Dependence Scale relates to markers of disease severity rather than demographic factors, and may offer an unbiased assessment of care required in multiethnic and community populations.
Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files
Authors: Sun Xiaobo , Gao Jingjing , Jin Peng , Eng Celeste , Burchard Esteban G , Beaty Terri H , Ruczinski Ingo , Mathias Rasika A , Barnes Kathleen , Wang Fusheng , Qin Zhaohui S ,   CAAPA consortium
Published: May 2018

Abstract

Background
Sorted merging of genomic data is a common data operation necessary in many sequencing-based studies. It involves sorting and merging genomic data from different subjects by their genomic locations. In particular, merging a large number of variant call format (VCF) files is frequently required in large-scale whole-genome sequencing or whole-exome sequencing projects. Traditional single-machine based methods become increasingly inefficient when processing large numbers of files due to the excessive computation time and Input/Output bottleneck. Distributed systems and more recent cloud-based systems offer an attractive solution. However, carefully designed and optimized workflow patterns and execution plans (schemas) are required to take full advantage of the increased computing power while overcoming bottlenecks to achieve high performance.

Findings
In this study, we custom-design optimized schemas for three Apache big data platforms, Hadoop (MapReduce), HBase, and Spark, to perform sorted merging of a large number of VCF files. These schemas all adopt the divide-and-conquer strategy to split the merging job into sequential phases/stages consisting of subtasks that are conquered in an ordered, parallel, and bottleneck-free way. In two illustrating examples, we test the performance of our schemas on merging multiple VCF files into either a single TPED or a single VCF file, which are benchmarked with the traditional single/parallel multiway-merge methods, message passing interface (MPI)–based high-performance computing (HPC) implementation, and the popular VCFTools.

Conclusions
Our experiments suggest all three schemas either deliver a significant improvement in efficiency or render much better strong and weak scalabilities over traditional methods. Our findings provide generalized scalable schemas for performing sorted merging on genetics and genomics data using these Apache distributed systems.
Assessment of rosacea symptom severity by genome-wide association study and expression analysis highlights immuno-inflammatory and skin pigmentation genes
Authors: Aponte Jennifer L , Chiano Mathias N , Yerges-Armstrong Laura M , Hinds David A , Tian Chao , Gupta Akanksha , Guo Cong , Fraser Dana J , Freudenberg Johannes M , Rajpal Deepak K , Ehm Margaret G , Waterworth Dawn M 
Published: May 2018

AbstractRosacea is a common, chronic skin disease of variable severity with limited treatment options. The cause of rosacea is unknown, but it is believed to be due to a combination of hereditary and environmental factors. Little is known about the genetics of the disease. We performed a genome-wide association study (GWAS) of rosacea symptom severity with data from 73 265 research participants of European ancestry from the 23andMe customer base. Seven loci had variants associated with rosacea at the genome-wide significance level (P < 5 × 10−8). Further analyses highlighted likely gene regions or effector genes including IRF4 (P = 1.5 × 10−17), a human leukocyte antigen (HLA) region flanked by PSMB9 and HLA-DMB (P = 2.2 × 10−15), HERC2-OCA2 (P = 4.2 × 10−12), SLC45A2 (P = 1.7 × 10−10), IL13 (P = 2.8 × 10−9), a region flanked by NRXN3 and DIO2 (P = 4.1 × 10−9), and a region flanked by OVOL1and SNX32 (P = 1.2 × 10−8). All associations with rosacea were novel except for the HLA locus. Two of these loci (HERC-OCA2 and SLC45A2) and another precedented variant (rs1805007 in melanocortin 1 receptor) with an association P value just below the significance threshold (P = 1.3 × 10−7) have been previously associated with skin phenotypes and pigmentation, two of these loci are linked to immuno-inflammation phenotypes (IL13 and PSMB9-HLA-DMA) and one has been associated with both categories (IRF4). Genes within three loci (PSMB9-HLA-DMA, HERC-OCA2 and NRX3-DIO2) were differentially expressed in a previously published clinical rosacea transcriptomics study that compared lesional to non-lesional samples. The identified loci provide specificity of inflammatory mechanisms in rosacea, and identify potential pathways for therapeutic intervention.
Comparing Negative Attitudes Toward the Unemployed Across European Countries in 2008 and 2016: The Role of the Unemployment Rate and Job Insecurity
Authors: Buffel Veerle , Van de Velde Sarah 
Published: May 2018

AbstractWe explore how negative attitudes toward the unemployed are related to countries’ overall and long-term (LT) unemployment rate. Insights from the risk attribution and position theory are combined with the in-group–out-group conflict model, derived from migration literature. Multilevel analyses are performed on two waves (2008 and 2016) of the European Social Survey. Negative attitudes toward the unemployed are measured via the item “most unemployed people do not really try to find a job.” Results show that in countries with a high LT unemployment rate and/or an increase in this rate, people are more likely to hold negative attitudes toward the unemployed. Moreover, this is more pronounced among people in secure job conditions (those with a permanent contract and/or perceiving job security).
Accuracy of the medication list in the electronic health record—implications for care, research, and improvement
Authors: Walsh Kathleen E , Marsolo Keith A , Davis Cori , Todd Theresa , Martineau Bernadette , Arbaugh Carlie , Verly Frederique , Samson Charles , Margolis Peter 
Published: May 2018

AbstractObjectiveElectronic medication lists may be useful in clinical decision support and research, but their accuracy is not well described. Our aim was to assess the completeness of the medication list compared to the clinical narrative in the electronic health record.MethodsWe reviewed charts of 30 patients with inflammatory bowel disease (IBD) from each of 6 gastroenterology centers. Centers compared IBD medications from the medication list to the clinical narrative.ResultsWe reviewed 379 IBD medications among 180 patients. There was variation by center, from 90% patients with complete agreement between the medication list and clinical narrative to 50% agreement.ConclusionsThere was a range in the accuracy of the medication list compared to the clinical narrative. This information may be helpful for sites seeking to improve data quality and those seeking to use medication list data for research or clinical decision support.
Ultrasound-guided Pulsed Radiofrequency in the Management of Thoracic Postherpetic Neuralgia
Authors: Makharita Mohamed Y. , El Bendary Hanaa M. , Sonbul Zainab M. , Ahmed Salma E.S. , Latif Mahmoud A. 
Published: May 2018

Objectives:
This study was designed to evaluate the efficacy and safety of ultrasound-guided pulsed radiofrequency (PRF) for the intercostal nerves (ICNs) in the management of thoracic postherpetic neuralgia.

Methods:
After 2 weeks of treatment by pregabalin 150 mg/12 hours, patients were randomly allocated into 2 groups. The PRF group, after ultrasound-guided localization of the ICN of the affected thoracic dermatome, sensory stimulation of the ICN was tested. Thereafter, the patient received 2 cycles PRF at 42°C temperature, for 120 seconds. The sham group, after stimulation, the same time was spent to mimic PRF. The same procedures were repeated to the upper and lower adjacent ICNs. Pain intensity using Visual Analogue Scale (VAS), and total analgesics consumption were assessed at the baseline, every 2 weeks for 6 months then after 9 and 12 months. The duration of effective pain relief was recorded. Quality of life was evaluated using self-evaluation questionnaires (SF-36) at baseline then after 1, 3, 6, and 12 months.

Results:
PRF group expressed a significant decrease on the VAS throughout the study period. VAS<30 was reported in the PRF group until the 22nd week. Pregabalin and acetaminophen consumption was significantly lower in the PRF group. The 8 domains of the SF-36 revealed a significant improvement in the PRF group when compared with the sham group throughout the study period except for the physical role which displayed nonsignificant improvement.

Conclusions:
Ultrasound-guided PRF for ICNs in combination with pharmacotherapy seems to be a safe and effective treatment modality for postherpetic neuralgia.
Classification of Foreign Body Reactions due to Industrial Silicone Injection
Authors: Harlim Ago , Kanoko Mpu , Aisah Siti 
Published: May 2018

BACKGROUND
A foreign body reaction (FBR) is a typical tissue response to a biomaterial that has been injected or implanted in human body tissue. There has been a lack of data on the classification of foreign body reaction to silicone injection, which can describe the pattern of body tissue responses to silicone.

OBJECTIVE
Determine the foreign body reaction to silicone injection.

METHOD
We modified the classification proposed by Duranti and colleagues, which has categorized a FBR to hyaluronic acid injection into a new classification of an FBR to silicone injection. A cohort study of 31 women suffering from silicone-induced granulomas on their chin was conducted. Granulomatous tissue and submental skin were stained with hematoxylin–eosin and evaluated.

RESULTS
Our data revealed that there were at least 7 categories of FBRs to silicone injection that could be developed. Categories 1 to 4 showed inflammatory activity, and categories 5 to 8 showed tissue repair by fibrosis.

CONCLUSION
Using histopathological staining, we are able to sequence the steps of body reactions to silicone injection. Initial inflammatory reaction is then replaced by fibrosis process repairing the damaged tissues. The process depends on the host immune tolerance.
Comparison of Corneal Collagen Cross-Linking Protocols Measured With Scheimpflug Tomography
Authors: Shajari Mehdi , Sowwa Gabriela , Steinwender Gernot , Hofmann Christian , Pahlitzsch Marie-Luise , Petermann Kerstin , Kohnen Thomas 
Published: May 2018

Purpose:
To evaluate the effectiveness of corneal collagen cross-linking with Dresden and accelerated protocols to treat keratoconus by Scheimpflug tomography.

Methods:
Fifty-eight eyes with manifest keratoconus were measured preoperatively at least twice with the Pentacam. The difference of relevant variables for keratoconus progression (eg, D value, thinnest pachymetry, Kmax) was established. After evident progression, patients underwent corneal cross-linking (29 eyes with the Dresden protocol and 29 eyes with the accelerated protocol). Postoperatively, variables used for defining manifest progression were compared again by measuring the difference between 2 measurements.

Results:
Preoperatively, the mean D value was 9.6 ± 4.8 for the Dresden cohort and 8.3 ± 5.1 for the accelerated cohort. There was no significant difference between both cohorts in terms of the mean preoperative difference in the D value (0.59 ± 1.7 for the Dresden cohort vs. 0.4 ± 1.49, P = 1). Postoperatively, however, a significant difference (P < 0.01 for the accelerated corhort) was found (Dresden: −0.47 ± 0.88 vs. accelerated: 0.04 ± 0.67). Regression analysis showed that keratoconus progression was significant in both study groups preoperatively (with a significant reduction of corneal thickness and increase in the D value). Postoperative data show an improvement in all observed keratoconus indices in both study groups and stagnation in progression for the accelerated cohort, P = 0.774, for the D value and a regression in manifestation for the Dresden cohort (decrease in the D value, P < 0.01).

Conclusions:
Before operative intervention, Scheimpflug imaging showed signs of a progressive disease in all eyes. Both conventional Dresden protocol and accelerated pulsed corneal collagen cross-linking techniques effectively stopped this progression.
Effect of Posterior Corneal Vesicles on Corneal Endothelial Cell Density and Anisometropic Amblyopia
Authors: Noguchi Atsushi , Okumura Naoki , Sotozono Chie , Kinoshita Shigeru 
Published: May 2018

Purpose:
To evaluate the effect of corneal vesicles in patients with posterior corneal vesicles (PCV) on corneal endothelial cell (CEC) density and the acquisition of amblyopia.

Methods:
In this retrospective study of patients with PCV (18 eyes of 14 patients), CEC density was examined by noncontact specular microscopy during each follow-up examination. Best-corrected visual acuity and the objective refractive error were also examined.

Results:
Of the 14 total patients, 10 were diagnosed with PCV and 4 were diagnosed with bilateral suspected PCV or posterior polymorphous corneal dystrophy (PPCD), and in all patients, no ocular abnormality other than corneal vesicles was observed. In patients with PCV and patients with bilateral suspected PCV or PPCD, mean CEC density was 1131 ± 338 and 1095 ± 492 cells/mm2, respectively. In both PCV group and the bilateral suspected PCV or PPCD-group patients who were followed for 164.2 ± 25.4 months (range: 123–186 months), CEC density tended not to decrease. In patients with PCV, the mean best-corrected visual acuity of the unaffected eyes was significantly higher than that of the affected eyes with corneal vesicles (−0.10 ± 0.06 and 0.05 ± 0.13, respectively, P = 0.012). Four of 9 affected eyes (1 eye was excluded because of retinal atrophy) exhibited amblyopia, and all 4 eyes had astigmatism higher than 2 diopters.

Conclusions:
Although CEC density of patients with PCV in this study was found to be stable over a long-term follow-up period, strict attention should be given to the possibility of amblyopia in eyes with PCV.