bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and Pathogenicity of Fungal Species Associated with Canker Diseases of Pistachio in California
Authors: Nouri Mohamed T. , Lawrence Daniel P. , Holland Leslie A. , Doll David A. , Kallsen Craig E. , Culumber Catherine M. , Trouillas Florent P.
Published: April 2019

A survey was conducted during 2015 and 2016 in pistachio orchards throughout the San Joaquin Valley of California to investigate the occurrence of canker diseases and identify the pathogens involved. Cankers and dieback symptoms were observed mainly in orchards aged >15 years. Symptoms of canker diseases included brown to dark brown discoloration of vascular tissues, wood necrosis, and branch dieback. In total, 58 fungal isolates were obtained from cankers and identified based on multilocus phylogenetic analyses (internal transcribed spacer, glyceraldehyde 3-phosphate dehydrogenase, β-tubulin, calmodulin, actin 1, and translation elongation factor 1α) representing 11 fungal species: Colletotrichum karstii, Cytospora californica, Cytospora joaquinensis, Cytospora parapistaciae, Cytospora pistaciae, Diaporthe ambigua, Didymella glomerata, Diplodia mutila, Neofusicoccum mediterraneum, Phaeoacremonium canadense, and Schizophyllum commune. Pathogenicity tests conducted in the main pistachio cultivars Kerman, Golden Hills, and Lost Hills using the mycelium-plug method indicated that all fungal species were pathogenic to Pistacia vera. All species tested caused cankers in pistachio branches, although virulence among species varied from high to moderate. Overall, N. mediterraneum and Cytospora spp. were the most widespread and virulent species associated with canker diseases of pistachio in California.
Uncommon Histopathological Variants of Malignant Melanoma. Part 2
Authors: Saggini Andrea , Cota Carlo , Lora Viviana , Kutzner Heinz , Rütten Arno , Sangüeza Omar , Requena Luis , Cerroni Lorenzo
Published: April 2019

Despite new horizons opened by recent advances in molecular pathology, histological evaluation still remains the diagnostic gold standard regarding cutaneous melanocytic neoplasms. Several histological variants of melanoma have been described, and their knowledge is crucial for accurate diagnosis and classification of cases with unusual clinico-pathological features. Uncommon histological variants of melanoma have been described based on a broad constellation of features, including architectural pattern, stromal alterations, cytological attributes, and other morphological properties. This review is aimed at providing an extensive discussion of unusual but distinctive histopathological variants of melanoma.
Clinical and Demographic Trends in Cardiac Rehabilitation: 1996-2015
Authors: Gaalema Diann E. , Savage Patrick D. , Leadholm Kevin , Rengo Jason , Naud Shelly , Priest Jeffrey S. , Ades Philip A.
Published: April 2019

Purpose:

Clinical interventions in programs such as cardiac rehabilitation (CR) are guided by clinical characteristics of participating patients. This study describes changes in CR participant characteristics over 20 yr.

Methods:

To examine changes in patient characteristics over time, we analyzed data from 1996 to 2015 (n = 5396) garnered from a systematically and prospectively gathered database. Linear, logistic, multinomial logistic or negative binomial regression was used, as appropriate. Effects of sex and index diagnosis were considered both as interactions and as additive effects.

Results:

Analyses revealed that mean age increased (from 60.7 to 64.2 yr), enrollment of women increased (from 26.8% to 29.6%), and index diagnosis has shifted; coronary artery bypass surgery decreased (from 37.2% to 21.6%), whereas heart valve repair/replacement increased (from 0% to 10.6%). Risk factors also shifted with increases in body mass index (28.7 vs 29.6 kg/m2), obesity (from 33.2% to 39.6%), hypertension (from 51% to 62.5%), type 2 diabetes mellitus (from 17.3% to 21.7%), and those reporting current smoking (from 6.6% to 8.4%). Directly measured peak aerobic capacity remained relatively stable throughout. The proportion of patients on statin therapy increased from 63.6% to 98.9%, coinciding with significant improvements in lipid levels.

Conclusions:

Compared with 1996, participants entering CR in 2015 were older, more overweight, and had a higher prevalence of coronary risk factors. Lipid values improved substantially concurrent with increased statin use. While the percentage of female participants increased, they continue to be underrepresented. Patients with heart valve repair/replacement now constitute 10.6% of the patients enrolled. Clinical programs need to recognize changing characteristics of attendees to best tailor interventions.
Effects of Soft Toric, Rigid Gas-Permeable, and Mini-Scleral Lenses on Corneal Microstructure Using Confocal Microscopy
Authors: Alipour Fateme , Soleimanzade Mahya , Latifi Golshan , Aghaie Sepideh Haji , Kasiri Maryam , Dehghani Shima
Published: April 2019

Objective:

To determine effects of wearing soft toric silicone hydrogel, rigid gas-permeable (RGP), and mini-scleral lenses on corneal microstructure using confocal microscopy.

Method:

A prospective cohort study was conducted on 33 neophyte patients fitted with contact lenses (avg. age: 26±7 years) in the tertiary eye center. Patients were instructed to wear soft toric silicone hydrogel, RGP, or mini-scleral lenses based on clinical diagnoses. Inclusion criteria were age greater than 18 years and best-corrected visual acuity ≥3/10. Patients with a history of eye-involving systemic diseases were excluded. Baseline examinations included log of minimal angle of resolution visual acuity (Early Treatment Diabetic Retinopathy Study chart), refraction, slit-lamp, and fundoscopy. Confocal microscopy was used to measure subbasal nerve (SBN) density (mm/mm2), keratocyte cell density (cells/mm2), basal epithelial cell density (cells/mm2), and endothelial cell density (cells/mm2). Data were gathered on the first and follow-up visits. The follow-up visit happened after 6 months when the subjects had stopped wearing contact lenses for 12 hr. Comparative analysis was conducted within each group using the paired t test.

Results:

The changes in visual acuity, SBN, and keratocyte cell density were insignificant after 6 months of wearing lenses in all three groups. The basal epithelial cell density significantly decreased (P<0.05) in RGP and mini-scleral groups. In addition, the endothelial cell density decreased significantly (P<0.05) in the RGP group. No significant changes were detected in soft toric silicone hydrogel lens wearers.

Conclusions:

Soft toric silicone hydrogel lenses seemed to have the least impact on the corneal cellular microstructure for a wear period of 6 months, controlling confounding factors of prior cross-sectional investigations. The coarse (three layers) versus fine (five layers) division of stroma, the repeatability and reproducibility of stromal layers' demarcation, and the cohort size and its diversity in terms of initial corneal diagnoses (particularly in the mini-scleral wearing group) can potentially influence the outcomes, and their impact remains to be further investigated.
Improving Pharmacology Standardized Test and Final Examination Scores Through Team-Based Learning
Authors: El-Banna Majeda M. , Whitlow Malinda , McNelis Angela M.
Published: April 2019

Background

Team-based learning (TBL) is a collaborative teaching and learning strategy emphasizing student engagement and application of knowledge.

Purpose

The purpose of the study was to compare the differences in scores on pharmacology course final and standardized criterion-referenced examinations between students taught in a traditional lecture-based approach and those taught under the TBL approach.

Methods

Using a before-and-after design, 338 prelicensure students were taught pharmacology using either a traditional lecture-based approach or a TBL approach.

Results

Significant differences on course final and standardized examination scores were found between the groups, with students taught using TBL scoring higher than students in the traditional lecture-based group.

Conclusions

Team-based learning had a positive impact on learning outcomes. Moreover, TBL may be a more efficient approach to teaching, as students in the TBL group had only 3 credit hours of content versus students in the traditional lecture-based group, who had 4 credit hours.
PD-L1 Expression and Tumor-infiltrating Lymphocytes in Uterine Smooth Muscle Tumors
Authors: Shanes Elisheva D. , Friedman Lisa A. , Mills Anne M.
Published: April 2019

Immunotherapies targeting the PD-1/PD-L1 checkpoint axis are of growing interest for the treatment of mesenchymal neoplasms. However, PD-L1 expression and tumor-associated lymphocytes have not been well-investigated in uterine smooth muscle tumors. Forty-nine uterine smooth muscle tumors (23 leiomyosarcomas, 8 smooth muscle tumors of uncertain malignant potential [STUMP], 7 atypical leiomyomas, and 11 benign leiomyomas) were evaluated for tumoral and tumor-associated immune PD-L1 expression and tumor-associated T-cell infiltration. ALK immunohistochemistry was performed to exclude inflammatory myofibroblastic tumors. Tumor PD-L1 expression was seen in 70% of leiomyosarcomas and 14% of atypical leiomyomas; no cases of STUMP or benign leiomyoma demonstrated tumoral PD-L1. PD-L1 positivity was seen in tumor-associated immune cells in 78% of leiomyosarcomas, 25% of STUMP, no cases of atypical leiomyomas, and 9% of benign leiomyomas. Of the 23 leiomyosarcomas, 15 (65%) had a combined positive score ≥1, while of the 26 other uterine smooth muscle tumors, only 2 (8%) had a combined positive score ≥1. Tumor-associated CD8+ cells were highest among leiomyosarcomas (mean: 87/high-power fields vs. 17/high-power fields for nonleiomyosarcomas), and were significantly associated with PD-L1 expression. One PD-L1+, CD8-enriched leiomyosarcoma showed an ALK overexpression suggesting possible classification as inflammatory myofibroblastic tumor, but otherwise lacked morphologic features of this entity. Leiomyosarcomas demonstrate significantly higher PD-L1 expression and cytotoxic T-cell infiltration when compared with other uterine smooth muscle tumors. These data suggest the possibility that treatment with targeted immunotherapy may be appropriate in a selected population of patients with leiomyosarcoma and, potentially, in related tumors bearing ALK rearrangements.
Memory inception and preservation in slime moulds: the quest for a common mechanism
Authors: Boussard A. , Delescluse J. , Pérez-Escudero A. , Dussutour A.
Published: April 2019

Learning and memory are indisputably key features of animal success. Using information about past experiences is critical for optimal decision-making in a fluctuating environment. Those abilities are usually believed to be limited to organisms with a nervous system, precluding their existence in non-neural organisms. However, recent studies showed that the slime mouldPhysarum polycephalum, despite being unicellular, displays habituation, a simple form of learning. In this paper, we studied the possible substrate of both short- and long-term habituation in slime moulds. We habituated slime moulds to sodium, a known repellent, using a 6 day training and turned them into a dormant state named sclerotia. Those slime moulds were then revived and tested for habituation. We showed that information acquired during the training was preserved through the dormant stage as slime moulds still showed habituation after a one-month dormancy period. Chemical analyses indicated a continuous uptake of sodium during the process of habituation and showed that sodium was retained throughout the dormant stage. Lastly, we showed that memory inception via constrained absorption of sodium for 2 h elicited habituation. Our results suggest that slime moulds absorbed the repellent and used it as a ‘circulating memory’.

This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
The plant body as a network of semi-autonomous agents: a review
Authors: Oborny Beata
Published: April 2019

Plants can solve amazingly difficult tasks while adjusting their growth and development to the environment. They can explore and exploit several resources simultaneously, even when the distributions of these vary in space and time. The systematic study of plant behaviour goes back to Darwin's book
The power of movement in plants
. Current research has highlighted that modularity is a key to understanding plant behaviour, as the production, functional specialization and death of modules enable the plant to adjust its movement to the environment. The adjustment is assisted by a flow of information and resources among the modules. Experiments have yielded many results about these processes in various plant species. Theoretical research, however, has lagged behind the empirical studies, possibly owing to the lack of a proper modelling framework that could encompass the high number of components and interactions. In this paper, I propose such a framework on the basis of network theory, viewing the plant as a group of connected, semi-autonomous agents. I review some characteristic plant responses to the environment through changing the states of agents and/or links. I also point out some unexplored areas, in which a dialogue between plant science and network theory could be mutually inspiring.

This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
Phigaro: high throughput prophage sequence annotation
Authors: Starikova Elizaveta V. , Tikhonova Polina O. , Prianichnikov Nikita A. , Rands Chris M. , Zdobnov Evgeny M. , Govorun Vadim M.
Published: April 2019

Phigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated “prophage genome maps” and marks possible transposon insertion spots inside prophages. It provides putative taxonomic annotations that can distinguish tailed from non-tailed phages. It is applicable for mining prophage regions from large metagenomic datasets.

Availability

Source code for Phigaro is freely available for download at https://github.com/bobeobibo/phigaro along with test data. The code is written in Python.
No evidence for disruption of global patterns of nest predation in shorebirds
Authors: Bulla Martin , Reneerkens Jeroen , Weiser Emily L. , Sokolov Aleksandr , Taylor Audrey R. , Sittler Benoît , McCaffery Brian J. , Ruthrauff Dan R. , Catlin Daniel H. , Payer David C. , Ward David H. , Solovyeva Diana V. , Santos Eduardo S.A. , Rakhimberdiev Eldar , Nol Erica , Kwon Eunbi , Brown Glen S. , Hevia Glenda D. , Gates H. River , Johnson James A. , van Gils Jan A. , Hansen Jannik , Lamarre Jean-François , Rausch Jennie , Conklin Jesse R. , Liebezeit Joe , Bêty Joёl , Lang Johannes , Alves José A. , Fernández-Elipe Juan , Michael-Exo Klaus , Bollache Loïc , Bertellotti Marcelo , Giroux Marie-Andrée , van de Pol Martijn , Johnson Matthew , Boldenow Megan L. , Valcu Mihai , Soloviev Mikhail , Sokolova Natalya , Senner Nathan R. , Lecomte Nicolas , Meyer Nicolas , Schmidt Niels Martin , Gilg Olivier , Smith Paul A. , Machín Paula , McGuire Rebecca L. , Cerboncini Ricardo A.S. , Ottvall Richard , van Bemmelen Rob S.A. , Swift Rose J. , Saalfeld Sarah T. , Jamieson Sarah E. , Brown Stephen , Piersma Theunis , Albrecht Tomas , D’Amico Verónica , Lanctot Richard B. , Kempenaers Bart
Published: April 2019

Kubelka et al. (Science, 9 November 2018, p. 680-683) claim that climate change has disrupted patterns of nest predation in shorebirds. They report that predation rates have increased since the 1950s, especially in the Arctic. We describe methodological problems with their analyses and argue that there is no solid statistical support for their claims.
Excess significance bias in repetitive transcranial magnetic stimulation literature for neuropsychiatric disorders
Authors: Amad Ali , Jardri Renaud , Rousseau Chloé , Larochelle Yann , Ioannidis John P.A. , Naudet Florian
Published: April 2019

Introduction

Repetitive transcranial magnetic stimulation (rTMS) has been widely tested and promoted for use in multiple neuropsychiatric conditions, but as for many other medical devices, some gaps may exist in the literature and the evidence base for rTMS clinical efficacy remains under debate. We aimed to empirically test for an excess number of statistically significant results in the literature on rTMS therapeutic efficacy across a wide range of meta-analyses and to characterize the power of studies included in these meta-analyses.

Methods

Based on power calculations, we computed the expected number of “positive” datasets for a medium effect-size (standardized mean difference, SMD=0.30) and compared it with the number of observed “positive” datasets. Sensitivity analyses considered small (SMD=0.20), modest (SMD=0.50), and large (SMD=0.80) effect sizes.

Results

14 meta-analyses with 228 datasets (110 for neurological disorders and 118 for psychiatric disorders) were assessed. For SMD=0.3, the number of observed “positive” studies (n=94) was larger than expected (n=35). We found evidence for an excess of significant findings overall (p<0.0001) and in 8/14 meta-analyses. Evidence for an excess of significant findings was also observed for SMD=0.5 for neurological disorders. 0 (0 %), 0 (0 %), 3 (1 %), and 53 (23 %) of the 228 datasets had power >0.80, respectively for SMDs of 0.30, 0.20, 0.50, and 0.80.

Conclusion

Most studies in the rTMS literature are underpowered. This results in fragmentation and waste of research efforts. The somewhat high frequency of “positive” results seems spurious and may reflect bias.

Trial Registration: PROSPERO 2017 CRD42017056694
A Genetically Encoded Fluorescent Sensor Enables Real-time Detection of the Intracellular GTP:GDP Ratio
Authors: Zhang Jiayuan , Song Yuxin , Liu Shuzhang , Wang Weibo , Zhang Meiqi , Yang Guangfu , Zou Peng , Wang Jing
Published: April 2019

The interconversion of guanosine triphosphate (GTP) and guanosine diphosphate (GDP) is integral to a wide variety of biological cellular activities. However, analytical methods which directly detect the ratio of intracellular GTP and GDP concentrations have not been available. Herein, we report GNEPS, a genetically encoded fluorescent sensor that enables real-time monitoring of the GTP:GDP ratio, which is a fusion protein comprising a eukaryotic G-protein and a circularly permuted yellow fluorescent protein. GNEPS has distinct fluorescence spectra between its GTP-bound and GDP-bound states. Its apparent fluorescence signal therefore depends upon the competitive binding of GTP and GDP. Live cell imaging experiments demonstrated that GNEPS can be used to monitor spatiotemporal changes in the intracellular GTP:GDP ratio in various cell types and organelles in response to metabolic perturbations. We anticipate that GNEPS will become a valuable tool for understanding the metabolic and regulatory contributions of guanosine nucleotides.
State-dependent differences in the frequency of TMS-evoked potentials between resting and active states
Authors: Stanfield Candice T. , Wiener Martin
Published: April 2019

Previous evidence suggests different cortical areas naturally oscillate at distinct frequencies, reflecting tuning properties of each region. The concurrent use of transcranial magnetic stimulation (TMS) and electroencephalography (EEG) has been used to perturb cortical regions, resulting in an observed post-stimulation response that is maximal at the natural frequency of that region. However, little is known about the spatial extent of TMS-induced activation differences in cortical regions when comparing resting state (passive) versus active task performance. Here, we employed TMS-EEG to directly perturb three cortical areas in the right hemisphere while measuring the resultant changes in maximal evoked frequency in healthy human subjects during a resting state (N=12) and during an active sensorimotor task (N=12). Our results revealed that the brain engages a higher dominant frequency mode when actively engaged in a task, such that the frequency evoked during a task is consistently higher across cortical regions, regardless of the region stimulated. These findings suggest that a distinct characteristic of active performance versus resting state is a higher state of natural cortical frequencies.
Direct Comparative Analysis of 10X Genomics Chromium and Smart-seq2
Authors: Wang Xiliang , He Yao , Zhang Qiming , Ren Xianwen , Zhang Zemin
Published: April 2019

Single cell RNA sequencing (scRNA-seq) is widely used for profiling transcriptomes of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently-used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Here, by directly comparing the scRNA-seq data by the two platforms from the same samples of CD45-cells, we systematically evaluated their features using a wide spectrum of analysis. Smart-seq2 detected more genes in a cell, especially low abundance transcripts as well as alternatively spliced transcripts, but captured higher proportion of mitochondrial genes. The composite of Smart-seq2 data also resembled bulk RNA-seq data better. For 10X-based data, we observed higher noise for mRNA in the low expression level. Despite the poly(A) enrichment, approximately 10-30% of all detected transcripts by both platforms were from non-coding genes, with lncRNA accounting for a higher proportion in 10X. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. However, 10X-data can better detect rare cell types given its ability to cover a large number of cells. In addition, each platform detected different sets of differentially expressed genes between cell clusters, indicating the complementary nature of these technologies. Our comprehensive benchmark analysis offers the basis for selecting the optimal scRNA-seq strategy based on the objectives of each study.
A weighted sequence alignment strategy for gene structure annotation lift over from reference genome to a newly sequenced individual
Authors: Song Baoxing , Sang Qing , Wang Hai , Pei Huimin , Wang Fen , Gan XiangChao
Published: April 2019

Genome sequences and gene structure annotation are very important for genomic analysis, while only the reference gene structure annotation is widely used for a wide range of investigations of different natural variation individuals. Herein, we are reporting the software GEAN which could lift over the reference gene structure annotation to other individuals belonging to the same or closely related species whose genome sequence was determined by whole-genome resequencing or de novo assembly. We found that inconsistent sequence alignment makes the coordinate lift over between different individual genomes unreliable, thus obscuring the lift over of gene structure annotations and genomic variants functional prediction. We designed a zebraic dynamic programming (ZDP) algorithm by providing different weights to different genetic features to refine the gene structure lift over. Using the lift over gene structure annotation as anchors, a base-pair resolution whole-genome-wide sequence alignment and variant calling pipeline for de novo assembly have been implemented. Taking Arabidopsis thaliana as example, we show that the natural variation alleles expression level of apoptosis death and defence response related genes might could be better quantified using GEAN. And GEAN could be used to refine the functional annotation of genetic variants, annotate de novo assembly genome sequence, detect syntenic blocks, improve the quantification of gene expression levels using RNA-seq data and genomic variants encoding for population genetic analysis. We expect that GEAN will be a standard gene structure annotation lift over and genome sequence alignment tool for the coming age of de novo assembly population genetics analysis.
Brown Adipose Tissue Remodeling Precedes Cardiometabolic Abnormalities Independent of Overweight in Fructose-Feed Mice
Authors: Machado Thaissa Queiroz , Pereira-Silva Debora Cristina , Gonçalves Leidyanne Ferreira , Fernandes-Santos Caroline
Published: April 2019

Objectives

To investigate the early cardiometabolic abnormalities along with WAT and BAT remodeling in short-term fructose feeding mice model.

Methods

Mice (n=10-11/group) were fed for four weeks with control diet (AIN93-M) or experimental diets rich in glucose or fructose. We investigated body weight, body adiposity, blood glucose, lipid and hepatic parameters, and white (WAT) and brown adipose tissue (BAT) histopathology.

Results

Fructose feeding promoted neither weight gain nor hypertrophy of visceral and subcutaneous WAT depots, but the fat was redistributed toward visceral depots. Glucose, lipid and hepatic metabolic dysfunction were not yet noticed in fructose-fed mice, with the exception for an elevation in total cholesterol and hepatic weight without steatosis. BAT mass did not increase, and it was proportionally reduced compared with visceral WAT in fructose feed mice. BAT suffered premature adverse morphological remodeling, characterized by increased lipid deposition per tissue area in enlarged intracellular lipid droplets.

Conclusion

Short-term fructose feeding redistributes body fat, changes the proportion of BAT to visceral fat, and promotes BAT adverse remodeling, characterized by enlarged intracellular lipid droplets.
Structures of a highly variable cell‐wall anchored protein‐encoding the spj gene from ST8/SCCmecIVl community‐associated methicillin‐resistant Staphylococcus aureus (CA‐MRSA/J) isolated from 2003 onwards: An indicator of a strongly invasive pathotype
Authors: Wan Tsai‐Wen , Teng Lee‐Jene , Yamamoto Tatsuo
Published: April 2019

The cell wall‐anchored protein‐encoding spj gene on staphylococcal cassette chromosome mec IVl (SCCmecIVl) was found to vary in size because of its 22‐ and 86‐aa repeat domains. The 22‐aa repeats are the more flexible of the two repeats, comprising three 11‐aa units, and were classified into three groups with eleven types. The 11/22‐aa repeats are longer in individuals with bullous impetigo, shorter in those with invasive disease and were absent in a fatal case, this last one having been rapidly diagnosed by PCR. IS431‐flanking pUB110 (bleO, aadD) is present on SCCmecIVl at 90%. The bacterial surface has the spj product and a unique surface layer.
A fast and robust two‐point ray tracing method in layered media with constant or linearly varying layer velocity
Authors: Fang Xinding , Chen Xiaofei
Published: April 2019

A fast and robust method for two‐point ray tracing in one‐dimensional layered media is presented. This method is applicable to layered models with constant or linearly varying isotropic layer velocity. For given model properties and source and receiver positions, a ray path can be uniquely determined once its ray parameter (i.e. horizontal slowness) is known. The ray parameter can be obtained by numerically solving the nonlinear offset (i.e. source–receiver horizontal distance) equation using Newton's method, which generally works well at near and mid offsets. However, Newton's method becomes hard to converge at large offsets due to the oversensitivity of offset to ray parameter. Based on the analysis of the characteristic of the offset equation, a modified ray parameter is proposed and used to replace the generic ray parameter in numerical calculation. Numerical experiments show that the iteration process becomes stable and converges rapidly with the modified ray parameter. Moreover, a rational function that asymptotically approximates the shape of the offset equation is introduced for obtaining good initial estimates of the modified ray parameter. Numerical tests show that this method is robust in any situation, and an accurate ray parameter can be obtained within two or three iterations for a wide range of model velocity structure and source–receiver distance. Furthermore, the proposed two‐point ray tracing method is easy to implement.
Real‐time compensation of magnetic data acquired by a single‐rotor unmanned aircraft system
Authors: Tuck L. , Samson C. , Polowick C. , Laliberté J.
Published: April 2019

Two methods for low‐altitude calibration of a single‐rotor unmanned aircraft system using a real‐time compensator are tested: (1) a stationary calibration where the unmanned aircraft system executes manoeuvres while hovering in order to minimize ambient field changes due to the local geology; and (2) an adapted box calibration flown in four orthogonal directions. Both methods use two compensator‐specific limits derived from established methods for manned airborne calibration: the lowest frequency used by the compensator for the calibration algorithm and the maximum variation of the ambient magnetic intensity experienced by the unmanned aircraft system during calibration. Prior to flying, the unmanned aircraft system was magnetically characterized using the heading error and fourth difference. Magnetic interference was mitigated by extending the magnetometer‐unmanned aircraft system separation distance to 1.7 m, shielding, and demagnetization. The stationary calibration yielded an improvement ratio of 8.595 and a standard deviation of the compensated total magnetic intensity of 0.075 nT (estimated Figure‐of‐Merit of 3.8 nT). The box calibration also yielded an improvement ratio of 3.989 and a standard deviation of the compensated total magnetic intensity of 0.083 nT (estimated Figure‐of‐Merit of 4.2 nT). The stationary and box calibration solutions were robust with low cross‐correlation indexes (1.090 and 1.048, respectively) when applied to a non‐native data set.
Root‐feeding larvae increase their performance by inducing leaf volatiles that attract above‐ground conspecific adults
Authors: Sun Xiao , Siemann Evan , Liu Zhen , Wang Qiyun , Wang Dingli , Huang Wei , Zhang Chujun , Ding Jianqing
Published: April 2019

Herbivore‐induced changes in plant volatile emissions mediate above–below‐ground interactions by determining host plant colonization of different herbivores. By changing shoot‐emitted volatiles, below‐ground herbivores may use the plant to extend their capacity to interact with above‐ground con‐ and heterospecifics.

We investigated the attractiveness of Triadica sebifera plants infested by larvae of a specialist beetle or root‐knot nematodes to above‐ground herbivores. We then determined the contribution of leaf volatiles to the observed recruitment patterns using olfactometer experiments. We also identified volatiles through gas chromatography–mass spectrometry (GC–MS) and electroantennography, and conducted field experiments to confirm their effects.

Leaf volatiles induced by the root‐feeding larvae attracted above‐ground conspecific adults in laboratory and field experiments, but repelled a heterospecific specialist weevil, whereas induction by root‐knot nematodes had no effects on either. Greater leaf consumption by conspecific adults increased root nutrients, decreased root defences and facilitated root feeding larval performance. Thus, larvae and adults appear to manipulate their host plant, which increases aggregation above‐ground and feeding below‐ground.

Synthesis. The resulting colonization dynamics may shape the composition of plant rhizosphere and phyllosphere herbivore communities by enhancing conspecific establishment and reducing colonization by other herbivores. By modifying above‐ground volatiles and above‐ground herbivore behaviour, root feeders could mediate plant and leaf herbivore interactions and benefit via plant responses to above‐ground feeding.
Optimal Monetary Policy in China with Money as Not Redundant
Authors: Zhang Guoxiong
Published: April 2019

This article provides three pieces of evidence to show that money is not redundant in China: aggregate real money balance can affect aggregate demand even when its effect through short‐term interest rates is controlled. I estimate a DSGE model using Chinese data. With the estimated model, I find that monetary policy that controls the money supply (the quantity rule) is better than the one that controls the short‐term interest rate (the price rule) in terms of minimising welfare loss. I then discuss the optimal monetary policy that combines both the price rule and the quantity rule.
Organisational culture and enterprise risk management: The Australian not‐for‐profit context
Authors: Chen Jinhua , Jiao Lu , Harrison Graeme
Published: April 2019

With the increasing emphasis on risk management in not‐for‐profit organisations, this study is timely in its examination of risk management practices in the Australian not‐for‐profit sector. Specifically, the study investigates the relation between not‐for‐profits’ organisational culture and the maturity of enterprise risk management (ERM) practices. The results show that the organisational culture factors of Outcome Orientation (valuing achievements and results) and Innovation (valuing receptivity and adaptability to change) are associated with the maturity of not‐for‐profits’ ERM. This finding demonstrates the important role that organisational culture plays in shaping ERM practices in not‐for‐profit organisations and the crucial role that leaders play in creating and nurturing such a culture within their organisations. The results also have implications for regulatory policy‐making in, and for, the not‐for‐profit sector.
Survey mode effects and insurance coverage estimates in the redesigned Gallup well‐being index
Authors: Sommers Benjamin D. , Goldman Anna L. , Lee Dennis , Epstein Arnold M.
Published: April 2019

Objective

To test whether a change from a telephone to mail and Internet survey in January 2018 affected the sample composition and uninsured estimates in the Gallup‐Sharecare Well‐Being Index.

Data Sources

Gallup‐Sharecare Well‐Being Index (2013‐2018).

Study Design

Regression discontinuity analysis identified changes after the survey redesign in the estimated U.S. uninsured rate (adults 18‐64) and in the sample's demographic composition.

Principal Findings

After the survey redesign, the estimated uninsured rate fell 5.3 percentage points (P < 0.001), respondents were older and disproportionately white, more likely to have a college degree, and had higher average incomes. These changes were modestly reduced by survey weights.

Conclusions

The shift to a mail survey (with a web option) led to an older, more educated sample with fewer minorities, and a significant break in trend in the estimated uninsured rate.
Conservation and the Environment in US Farm Legislation
Authors: Lichtenberg Erik
Published: April 2019

Conservation programmes have been a feature of US agricultural policy since the 1930s. Farmers are paid to take farmland out of production and to install or maintain farming practices to reduce erosion and runoff or to protect wildlife habitat. Budgets for these programmes have grown substantially over the past two decades and they have become major vehicles for making payments to farmers. The goals are to promote agricultural sustainability and to enhance environmental quality. Providing income support to farmers is an explicit goal of some of the programmes and an implicit function of others. They operate by paying farmers to convert environmentally sensitive land to more sustainable uses; to adopt or maintain runoff‐ and erosion‐reducing practices on working farmland; or to preserve land of environmental or cultural importance in its current condition. The benefits of conserving agriculture's natural resource base are largely private while the benefits of environmental quality improvements are largely public. Income support (and thus political) considerations have dominated the geographic distribution of spending, to the detriment of potential achievements in environmental quality improvement. These programmes remain important as virtually the only means by which non‐point source pollution from agriculture is addressed in the United States.
EU and US Agricultural Policies: Commonalities and Contrasts
Authors: Blandford David , Matthews Alan
Published: April 2019

The fact that the EU and the United States are revising their farm legislation at the same time provides a good opportunity to compare the direction of farm policy in the two jurisdictions. In both cases policy developments are required to satisfy budgetary constraints, which on this occasion appear to be more stringent for the EU. Farm‐oriented spending in both regions continues to be largely directed to farm income support – the farm safety net in the US and direct payments in the EU. Policy changes in the US have aimed to increase the likelihood that financial support will be provided to farmers. The EU, at least in the rhetorical justification for its legal proposal, gives greater priority to incentivising farmers to adopt practices friendlier to the environment and is more focused on climate mitigation and adaptation. However, the key innovation in the EU proposal revolves around the management of the policy, with the aim of steering the decisions of Member States through a results‐based rather than compliance‐based approach. This introduction highlights some background and context for the articles to follow that explore these themes in greater depth.
Environment and Climate in the Common Agricultural Policy
Authors: Dupraz Pierre , Guyomard Hervé
Published: April 2019

In the 2014–20 CAP, environment is targeted through a combination of measures in both Pillar 1, through cross‐compliance and green payments, and Pillar 2, mainly through voluntary measures with compensation for cost incurred and income forgone. The European Commission's legislative proposals for the CAP after 2020 would suppress green payments but their objectives would be retained as part of new conditionality requirements. A new environmental instrument would be introduced in Pillar 1, the ‘eco‐scheme’, and the CAP would be implemented through national strategic plans offering Member States large room for manoeuvre in application of the principle of subsidiarity. This article explains the weak environmental effectiveness of the CAP until now. It then analyses the extent to which the European Commission's proposals could improve the regulation of the environment and climate impacts of European agriculture. Pillar 2 measures are largely unchanged with their strengths and weaknesses. There is a risk that short‐run political pressures will lead numerous countries to opt for limited ambition in their eco‐schemes. However, there is an urgent need to tackle climate and biodiversity issues seriously. This could be done following the principles of public economics and environmental federalism. In that perspective, defining simple and robust agri‐environmental indicators is crucial.
New evolving strategies revealed by transcriptomic analysis of a fur− mutant of the cyanotrophic bacterium Pseudomonas pseudoalcaligenes CECT 5344
Authors: Becerra Gracia , Igeño María Isabel , Merchán Faustino , Sánchez‐Clemente Rubén , Blasco Rafael
Published: April 2019

The transcriptomic analysis (RNA‐seq) of a fur mutant of P. pseudoalcaligenes CECT 5344 has revealed that Fur regulates the expression of more than 100 genes in this bacterial strain, most of them negatively. The highest upregulated genes in response to fur deletion, with respect to the wild type, both cultivated in LB medium, corresponded to genes implicated in iron uptake. They include both TonB‐dependent siderophore transporters for the active transport across the outer membrane, and ABC‐type and MSF‐type transporters for the active transport across the cytoplasmic membrane. Therefore, the main response of this bacterium to iron limitation is expressing genes necessary for metabolism of Fe siderophores produced by other microorganisms (xenosiderophores). The number of genes whose expression decreased in the fur− mutant, as well as its normalized expression (fold change), was lower. Among them, it is remarkable the presence of one of the two cas operons of the two CRISP/Cas clusters was detected in the genome of this bacterium. The transcriptome was validated by qPCR, including the decrease in the expression of cas genes (cse1). The expression of cse1 was also decreased by limiting the amount of iron, carbon or nitrogen in the medium, or by adding menadione, a compound that causes oxidative stress. The higher decrease in cse1 expression was triggered by the addition of cyanide in minimal medium. These results suggest that this bacterium responds to stress conditions, and especially to cyanide, taking a reasonable risk with respect to both the uptake of (TonB‐dependent receptors gates) and the tolerance to (reduced immunity) foreign nucleic acids. In conjunction, this can be considered a yet unknown molecular mechanism forcing bacterial evolution.
A Rapid Response Survey to Characterize the Impacts of the 2017 High Water Event on Lake Ontario
Authors: Steinschneider Scott , Styler Alex , Stedman Richard , Austerman Mary
Published: April 2019

In the spring and summer of 2017, communities along the Lake Ontario shoreline suffered from the worst flood event on record. In late May, daily water levels reached their highest point in over 100 years, and flooding continued throughout much of the summer as lake levels slowly declined, with inundation and erosion significantly impacting shoreline homes and businesses. In this work, we present results from a rapid response online survey of property owners along the New York Lake Ontario shoreline to quantify the perceived flood impacts of the 2017 extended high water event. The survey focused on the degree and spatial distribution of inundation and erosion; the duration and drivers of inundation; the associated damages to different property features, with an emphasis on shoreline protection; and the degree of disruption to business and other activities and services. Photographic documentation of inundation extent and property damage also was provided by survey respondents. We demonstrate the potential utility of this dataset by characterizing key features of inundation and erosion impacts across the shoreline, and by using classification and regression trees to explore the predictability of inundation and erosion based on property characteristics. This work is part of a larger effort to develop models of inundation and erosion that can support flood impact assessments across the shoreline and help communities better prepare for future extended high water events.
Multivariate Analyses Reveal Biological Components Related to Neuronal Signaling and Immunity Mediating Electroencephalograms Abnormalities in Alcohol‐Dependent Individuals from the Collaborative Study on the Genetics of Alcoholism Cohort
Authors: Meda Shashwath A. , Narayanan Balaji , Chorlian David , Meyers Jacquelyn L. , Gelernter Joel , Hesselbrock Victor , Bauer Lance , Calhoun Vince D. , Porjesz Bernice , Pearlson Godfrey D.
Published: April 2019

Background

The underlying molecular mechanisms associated with alcohol use disorder (AUD) risk have only been partially revealed using traditional approaches such as univariate genomewide association and linkage‐based analyses. We therefore aimed to identify gene clusters related to Electroencephalograms (EEG) neurobiological phenotypes distinctive to individuals withAUDusing a multivariate approach.

Methods

The current project adopted a bimultivariate data‐driven approach, parallel independent component analysis (para‐ICA), to derive and explore significant genotype–phenotype associations in a case–control subset of the Collaborative Study on the Genetics of Alcoholism (COGA) dataset. Para‐ICAsubjects comprisedN = 799 self‐reported European Americans (367 controls and 432AUDcases), recruited fromCOGA, who had undergone restingEEGand genotyping. BothEEGand genomewide single nucleotide polymorphism (SNP) data were preprocessed prior to being subjected to para‐ICA in order to derive genotype–phenotype relationships.

Results

From the data, 4EEGfrequency and 4SNPcomponents were estimated, with 2 significantly correlatedEEG–genetic relationship pairs. The first such pair primarily represented theta activity, negatively correlated with a genetic cluster enriched for (but not limited to) ontologies/disease processes representing cell signaling, neurogenesis, transmembrane drug transportation, alcoholism, and lipid/cholesterol metabolism. The second component pair represented mainly alpha activity, positively correlated with a genetic cluster with ontologies similarly enriched as the first component. Disease‐related enrichments for this component revealed heart and autoimmune disorders as top hits. Loading coefficients for both the alpha and theta components were significantly reduced in cases compared to controls.

Conclusions

Our data suggest plausible multifactorial genetic components, primarily enriched for neuronal/synaptic signaling/transmission, immunity, and neurogenesis, mediating low‐frequency alpha and theta abnormalities in alcohol addiction.
Novel Role of Macrophage Migration Inhibitory Factor in Upstream Control of the Unfolded Protein Response After Ethanol Feeding in Mice
Authors: Poulsen Kyle Lauren , McMullen Megan R. , Huang Emily , Kibler Christopher D. , Sheehan Megan M. , Leng Lin , Bucala Richard , Nagy Laura E.
Published: April 2019

Background

Macrophage migration inhibitory factor (MIF), a pluripotent immune regulator, is an emerging mediator in alcohol‐related liver disease (ALD).MIFis associated withALDprogression through its chemokine‐ and cytokine‐like activities.

Methods

Mechanistic studies into the role ofMIFin ethanol (EtOH)‐induced liver injury were performed inMif−/−mice and in C57BL/6J mice treated with a small‐moleculeMIFantagonist,MIF098, after Gao‐Binge (acute‐on‐chronic) EtOH feeding, an EtOH feeding protocol associated with hepatic neutrophilia and induction of the unfolded protein response (UPR).

Results

TheMIFaxis, for example,MIFandMIFreceptors invariant polypeptide of major histocompatibility complex, class II antigen‐associated (CD74),CXCR2,CXCR4, andCXCR7, was enhanced in the livers of alcoholic hepatitis (AH) patients as compared to healthy controls.Mif−/−mice were protected from hepatocellular injury after Gao‐Binge feeding, independent of neutrophilia and inflammation, but were associated with theUPR. Interestingly, theUPRsignature inAHpatients and in mice following Gao‐Binge feeding was biased toward cell death with increased expression of pro‐cell death CCAAT–enhancer‐binding protein homologous protein (CHOP) and decreased prosurvivalGRP78. TheUPRand liver injury 6 hours after binge were prevented both inMif−/−mice and inMIF098‐treated mice. However, bothMIFinterventions led to increased liver injury and exacerbated the hepaticUPR9 hours after binge. Induction of upstreamUPRsignaling and expression ofCHOPprotein by thapsigargin in alpha mouse liver 12 hepatocytes were blunted by coexposure toMIF098, directly connectingMIFtoUPRin hepatocytes.

Conclusions

The current study revealed that, in addition to its cytokine/chemokine functions,MIFis an upstream regulator ofUPRin response to EtOH feeding in mice. Importantly, bothMIFandUPRcan either protect or contribute to liver injury, dependent upon the stage or severity of EtOH‐induced liver injury.