bluuebunny/crossref_metadata_2025 huggingface dataset:
Bighead is a Wnt antagonist secreted by the
Xenopus
Spemann organizer that promotes Lrp6 endocytosis
Authors: Ding Yi , Colozza Gabriele , Sosa Eric A. , Moriyama Yuki , Rundle Samantha , Salwinski Lukasz , De Robertis Edward M.
Published: September 2018

The
Xenopus laevis
embryo has been subjected to almost saturating screens for molecules specifically expressed in dorsal Spemann organizer tissue. In this study, we performed high-throughput RNA sequencing of ectodermal explants, called animal caps, which normally give rise to epidermis. We analyzed dissociated animal cap cells that, through sustained activation of MAPK, differentiate into neural tissue. We also microinjected mRNAs for Cerberus, Chordin, FGF8, BMP4, Wnt8, and Xnr2, which induce neural or other germ layer differentiations. The searchable database provided here represents a valuable resource for the early vertebrate cell differentiation. These analyses resulted in the identification of a gene present in frog and fish, which we call Bighead. Surprisingly, at gastrula, it was expressed in the Spemann organizer and endoderm, rather than in ectoderm as we expected. Despite the plethora of genes already mined from Spemann organizer tissue, Bighead encodes a secreted protein that proved to be a potent inhibitor of Wnt signaling in a number of embryological and cultured cell signaling assays. Overexpression of Bighead resulted in large head structures very similar to those of the well-known Wnt antagonists Dkk1 and Frzb-1. Knockdown of Bighead with specific antisense morpholinos resulted in embryos with reduced head structures, due to increased Wnt signaling. Bighead protein bound specifically to the Wnt coreceptor lipoprotein receptor-related protein 6 (Lrp6), leading to its removal from the cell surface. Bighead joins two other Wnt antagonists, Dkk1 and Angptl4, which function as Lrp6 endocytosis regulators. These results suggest that endocytosis plays a crucial role in Wnt signaling.
AP2 transcription factor CBX1 with a specific function in symbiotic exchange of nutrients in mycorrhizal
Lotus japonicus
Authors: Xue Li , Klinnawee Lompong , Zhou Yue , Saridis Georgios , Vijayakumar Vinod , Brands Mathias , Dörmann Peter , Gigolashvili Tamara , Turck Franziska , Bucher Marcel
Published: September 2018

Significance

Arbuscular mycorrhizal (AM) fungi promote phosphorus uptake into host plants in exchange for organic carbon. Physiological tracer experiments showed that up to 100% of acquired phosphate can be delivered to plants via the mycorrhizal phosphate uptake pathway (MPU). Previous studies revealed that the CTTC
cis
-regulatory element (CRE) is required for promoter activation of mycorrhiza-specific phosphate transporter and H
+
-ATPase genes. However, the precise transcriptional mechanism directly controlling MPU is unknown. Here, we show that CBX1 binds CTTC and AW-box CREs and coregulates mycorrhizal phosphate transporter and H
+
-ATPase genes. Interestingly, genes involved in lipid biosynthesis are also regulated by CBX1 through binding to AW box, including
RAM2
. Our work suggests a common regulatory mechanism underlying complex trait control of symbiotic exchange of nutrients.
Spatiotemporal Patterns and Diffusion of the 1918 Influenza Pandemic in British India
Authors: Reyes Olivia , Lee Elizabeth C , Sah Pratha , Viboud Cécile , Chandra Siddharth , Bansal Shweta
Published: September 2018

The factors that drive spatial heterogeneity and diffusion of pandemic influenza remain debated. We characterized the spatiotemporal mortality patterns of the 1918 influenza pandemic in British India and studied the role of demographic factors, environmental variables, and mobility processes on the observed patterns of spread. Fever-related and all-cause excess mortality data across 206 districts in India from January 1916 to December 1920 were analyzed while controlling for variation in seasonality particular to India. Aspects of the 1918 autumn wave in India matched signature features of influenza pandemics, with high disease burden among young adults, (moderate) spatial heterogeneity in burden, and highly synchronized outbreaks across the country deviating from annual seasonality. Importantly, we found population density and rainfall explained the spatial variation in excess mortality, and long-distance travel via railroad was predictive of the observed spatial diffusion of disease. A spatiotemporal analysis of mortality patterns during the 1918 influenza pandemic in India was integrated in this study with data on underlying factors and processes to reveal transmission mechanisms in a large, intensely connected setting with significant climatic variability. The characterization of such heterogeneity during historical pandemics is crucial to prepare for future pandemics.
BhGLM: Bayesian hierarchical GLMs and survival models, with applications to genomics and epidemiology
Authors: Yi Nengjun , Tang Zaixiang , Zhang Xinyan , Guo Boyi
Published: September 2018

BhGLM is a freely available R package that implements Bayesian hierarchical modeling for high-dimensional clinical and genomic data. It consists of functions for setting up various Bayesian hierarchical models, including generalized linear models (GLMs) and Cox survival models, with four types of prior distributions for coefficients, i.e. double-exponential, Student-t, mixture double-exponential and mixture Student-t. These functions adapt fast and stable algorithms to estimate parameters. BhGLM also provides functions for summarizing results numerically and graphically and for evaluating predictive values. The package is particularly useful for analyzing large-scale molecular data, i.e. detecting disease-associated variables and predicting disease outcomes. We here describe the models, algorithms and associated features implemented in BhGLM.

Availability and implementation

The package is freely available from the public GitHub repository, https://github.com/nyiuab/BhGLM.
Human Immunodeficiency Virus-associated Neurocognitive Impairment in Diverse Resource-limited Settings
Authors: Robertson Kevin R , Jiang Hongyu , Kumwenda Johnstone , Supparatpinyo Khuanchai , Marra Christina M , Berzins Baiba , Hakim James , Sacktor Ned , Campbell Thomas B , Schouten Jeffrey , Mollan Katie , Tripathy Srikanth , Kumarasamy Nagalingeswaran , La Rosa Alberto , Santos Breno , Silva Marcus T , Kanyama Cecilia , Firhnhaber Cindy , Murphy Robert , Hall Colin , Marcus Cheryl , Naini Linda , Masih Reena , Hosseinipour Mina C , Mngqibisa Rosie , Badal-Faesen Sharlaa , Yosief Sarah , Vecchio Alyssa , Nair Apsara ,   AIDS Clinical Trials Group
Published: September 2018

Background

Neurocognitive impairment remains a common complication of human immunodeficiency virus (HIV) despite effective antiretroviral therapy (ART). We previously reported improved neurocognitive functioning with ART initiation in 7 resource-limited countries for HIV+ participants from the AIDS Clinical Trials Group (ACTG) 5199 International Neurological Study (INS). Here, we apply normative data from the International Neurocognitive Normative Study (INNS) to INS to provide previously unknown rates of neurocognitive impairment.

Methods

The A5199 INS assessed neurocognitive and neurological performance within a randomized clinical trial with 3 arms containing World Health Organization first-line recommended ART regimens (ACTG 5175; PEARLS). The ACTG 5271 INNS collected normative comparison data on 2400 high-risk HIV-negative participants from 10 voluntary counseling and testing sites aligned with INS. Normative comparison data were used to create impairment ratings for HIV+ participants in INS; associations were estimated using generalized estimating equations.

Results

Among 860 HIV+ adults enrolled in ACTG 5199, 55% had no neurocognitive impairment at baseline. Mild neurocognitive impairment was found in 25%, moderate in 17%, and severe in 3% of participants. With the initiation of ART, the estimated odds of impairment were reduced 12% (95% confidence interval, 9%, 14%) for every 24 weeks (P < .0001) on ART. Mild impairment dropped slightly and then remained at about 18% out to week 168.

Conclusions

Almost half of HIV+ participants had neurocognitive impairment at baseline before ART, based on local norms. With ART initiation, there were significant overall reductions in neurocognitive impairment over time, especially in those with moderate and severe impairments.

Clinical Trials Registration

NCT00096824.
Pattern of antibiotic prescriptions for outpatients with acute respiratory tract infections in Japan, 2013–15: a retrospective observational study
Authors: Teratani Yusuke , Hagiya Hideharu , Koyama Toshihiro , Adachi Mayu , Ohshima Ayako , Zamami Yoshito , Tanaka Hiroyoshi Y , Tatebe Yasuhisa , Tasaka Ken , Mikami Naoko , Shinomiya Kazuaki , Kitamura Yoshihisa , Kano Mitsunobu R , Hinotsu Shiro , Sendo Toshiaki
Published: September 2018

Background

In this age of antimicrobial resistance, unnecessary use of antibiotics to treat non-bacterial acute respiratory tract infections (ARTIs) and inappropriate use of antibiotics in treating bacterial ARTIs are public health concerns.

Purpose

Our aim is to identify the pattern of oral antibiotic prescriptions for outpatients with ARTIs in Japan.

Methods

We analysed health insurance claims data of patients (aged ≤74 years) from 2013 to 2015, to determine the pattern of antibiotic prescriptions for outpatient ARTIs and calculated the proportion of each antibiotic.

Results

Data on 4.6 million antibiotic prescriptions among 1559394 outpatients with ARTIs were analysed. The most commonly prescribed classes of antibiotics included cephalosporins (41.9%), macrolides (32.8%) and fluoroquinolones (14.7%). The proportion of first-, second- and third-generation cephalosporins was 1.0%, 1.7% and 97.3%, respectively. Fluoroquinolones accounted for a quarter of the prescriptions for ARTIs in patients aged >20 years. In contrast, penicillins accounted for just 8.0% of the total number of antibiotic prescriptions for ARTIs.

Conclusions

According to clinical guidelines, penicillins are first-line antibiotics against ARTIs. However, third-generation cephalosporins, macrolides and fluoroquinolones are more frequently prescribed in Japan. Although we could not assess the extent to which appropriate antibiotics are selected, our results support the necessity of improving antibiotic choices in the treatment of ARTIs.
Cordycepin activates autophagy through AMPK phosphorylation to reduce abnormalities in Machado–Joseph disease models
Authors: Marcelo Adriana , Brito Filipa , Carmo-Silva Sara , Matos Carlos A , Alves-Cruzeiro João , Vasconcelos-Ferreira Ana , Koppenol Rebekah , Mendonça Liliana , de Almeida Luís Pereira , Nóbrega Clévio
Published: September 2018

Machado–Joseph disease (MJD) is a neurodegenerative disorder caused by an abnormal expansion of citosine-adenine-guanine trinucleotide repeats in the disease-causing gene. This mutation leads to an abnormal polyglutamine tract in the protein ataxin-3 (Atx3), resulting in formation of mutant Atx3 aggregates. Despite several attempts to develop a therapeutic option for MJD, currently there are no available therapies capable of delaying or stopping disease progression. Recently, our group reported that reducing the expression levels of mutant Atx3 lead to a mitigation of several MJD-related behavior and neuropathological abnormalities. Aiming a more rapid translation to the human clinics, in this study we investigate a pharmacological inhibitor of translation—cordycepin—in several preclinical models. We found that cordycepin treatment significantly reduced (i) the levels of mutant Atx3, (ii) the neuropathological abnormalities in a lentiviral mouse model, (iii) the motor and neuropathological deficits in a transgenic mouse model and (iv) the number of ubiquitin aggregates in a human neural model. We hypothesize that the effect of cordycepin is mediated by the increase of phosphorylated adenosine monophosphate-activated protein kinase (AMPK) levels, which is accompanied by a reduction in the global translation levels and by a significant activation of the autophagy pathway. Overall, this study suggests that cordycepin might constitute an effective and safe therapeutic approach for MJD, and probably for the other polyglutamine diseases.
A century of change in North Sea plankton communities explored through integrating historical datasets
Authors: Bedford Jacob , Johns David , McQuatters-Gollop Abigail
Published: September 2018

Plankton communities make useful ecosystem indicators, and taking a historical perspective on plankton community composition provides insights into large-scale environmental change. Much of our understanding of long temporal-scale change in plankton communities in the North Sea has been provided by the Continuous Plankton Recorder (CPR) survey, operating since 1931, with consistent time-series data available since 1958. This article further increases the temporal scale of our understanding of community change in the North Sea by combining the CPR dataset with a digitized collection of plankton surveys undertaken by ICES from 1902 to 1912. After steps taken to integrate the two disparate datasets, differences in overall community composition between time periods suggest that the multidecadal changes observed through the CPR survey time period may have occurred from a non-stable baseline that was already on a trajectory of change. Therefore, a stable historical time period in which plankton communities are assessed against for any impact of human pressures may be hard to define for the North Sea and instead underlying variation needs to be encompassed within any baseline chosen. Further evidence for the influence of large-scale changes in sea surface temperature driving change in plankton community composition was found using the extended dataset.
Using voice to create inpatient progress notes: effects on note timeliness, quality, and physician satisfaction
Authors: Payne Thomas H , Alonso W David , Markiel J Andrew , Lybarger Kevin , Lordon Ross , Yetisgen Meliha , Zech Jennifer M , White Andrew A
Published: September 2018

Objectives

We describe the evaluation of a system to create hospital progress notes using voice and electronic health record integration to determine if note timeliness, quality, and physician satisfaction are improved.

Materials and methods

We conducted a randomized controlled trial to measure effects of this new method of writing inpatient progress notes, which evolved over time, on important outcomes.

Results

Intervention subjects created 709 notes and control subjects created 1143 notes. When adjusting for clustering by provider and secular trends, there was no significant difference between the intervention and control groups in the time between when patients were seen on rounds and when progress notes were viewable by others (95% confidence interval −106.9 to 12.2 min). There were no significant differences in physician satisfaction or note quality between intervention and control.

Discussion

Though we did not find support for the superiority of this system (Voice-Generated Enhanced Electronic Note System [VGEENS]) for our 3 primary outcomes, if notes are created using voice during or soon after rounds they are available within 10 min. Shortcomings that likely influenced subject satisfaction include the early state of our VGEENS and the short interval for system development before the randomized trial began.

Conclusion

VGEENS permits voice dictation on rounds to create progress notes and can reduce delay in note availability and may reduce dependence on copy/paste within notes. Timing of dictation determines when notes are available. Capturing notes in near-real-time has potential to apply NLP and decision support sooner than when notes are typed later in the day, and to improve note accuracy.
Diet Macronutrient Composition, Physical Activity, and Body Composition in Soldiers During 6 Months Deployment
Authors: Nykänen Tarja , Pihlainen Kai , Santtila Matti , Vasankari Tommi , Fogelholm Mikael , Kyröläinen Heikki
Published: September 2018

Introduction

Optimal diet together with good physical fitness maintains readiness and military performance during longer deployments. The purpose of this study was to describe changes in dietary macronutrient and energy intake, total physical activity and body composition during a 6-month deployment in South Lebanon. Furthermore, associations of diet macronutrient intake and physical activity on body composition were also studied.

Materials and Methods

Forty male soldiers kept a 3-day food diary and their body composition was measured via bioimpedance and ultrasonography. Total physical activity was evaluated by accelerometers in a subgroup of participants. Measurements were conducted in the PRE-, MID-, and POST-deployment.

Results

Mean carbohydrate intakes were 39.5–42.6 E%, protein intakes 18.7–22.3 E%, and fat intakes 34.9–35.7 E%. Daily energy intake remained stable (10.1–10.3 MJ/D). Total physical activity was decreased during deployment (e.g., step count from 9,835 ± 2,743 to 8,388 ± 2,875 steps/day, p = 0.007). Skeletal muscle mass and subcutaneous fat increased by 1.3% (p = 0.019) and 1.9% (p = 0.006), respectively. Energy and fat intake associated positively with body mass and skeletal muscle mass (r = 0.31–0.48, p < 0.05–0.001).

Conclusions

Carbohydrate intakes and physical activity were low, compared with the general recommendations. Protein intakes were relatively high. Skeletal muscle mass and subcutaneous fat increased. Suboptimal diet together with low level of physical activity may have a negative impact on body composition, physical performance, and cardiometabolic health. Consequently, soldiers should be encouraged to consume more fiber-rich carbohydrates and less saturated fatty acids as well as maintain a high level of physical fitness to sustain military readiness during long-term deployments.
Epidemiological survey of onychomycosis pathogens in Japan by real-time PCR
Authors: Shimoyama Harunari , Satoh Kazuo , Makimura Koichi , Sei Yoshihiro
Published: September 2018

In Japan, an epidemiological survey of onychomycosis pathogens was performed using culture methods; however, the positive culture rate was 40% or less. As part of an epidemiological survey of dermatomycoses in Japan, we overcame this low positive rate by employing a real-time polymerase chain reaction (PCR) assay that allowed rapid and accurate detection and identification. In 2011, nail specimens were collected from patients at nine institutes in various prefectures in Japan and diagnosed as onychomycosis. For the detection and identification of the main pathogens causing onychomycosis, we performed real-time PCR using specific TaqMan® MGB probes and primer sets. Of the 496 onychomycosis samples, real-time PCR detected 382 cases (77.0%) caused by Trichophyton rubrum; 74 cases (15.0%) caused by Trichophyton interdigitale; and eight cases (1.6%) caused by Candida albicans. The real-time PCR positive rate was 96.2%. The most frequent pathogen was T. rubrum throughout life, with the number of patients affected peaking in the range of 60 to 69 years of age and no significant differences in the composition of causative pathogens by sex. We were able to detect and identify pathogens from almost all specimens and succeeded in analyzing the pathogens involved in onychomycosis cases in Japan. These data confirmed that our real-time PCR method was effective for detecting and identifying the main fungal pathogens from onychomycosis specimens.
Effect of ferric citrate on serum phosphate and fibroblast growth factor 23 among patients with nondialysis-dependent chronic kidney disease: path analyses
Authors: Block Geoffrey A , Pergola Pablo E , Fishbane Steven , Martins Julian G , LeWinter Robin D , Uhlig Katrin , Neylan John F , Chertow Glenn M
Published: September 2018

Background

Among patients with nondialysis-dependent chronic kidney disease (NDD-CKD) and iron-deficiency anemia (IDA), ferric citrate increases hemoglobin and iron parameters and reduces serum phosphate and fibroblast growth factor 23 (FGF23), a key phosphate-regulating hormone. We conducted post hoc analyses of a phase 3 trial to explore associations between iron replacement, serum phosphate changes and FGF23 regulation.

Methods

We employed multivariable regression and longitudinal mixed-effects models to identify and confirm, respectively, whether baseline demographic and laboratory variables were associated with ferric citrate-induced changes in serum phosphate or FGF23 concentrations. We employed path analyses to determine whether changes in FGF23 concentrations were mediated via changes in serum phosphate and/or transferrin saturation (TSAT).

Results

We analyzed a total of 117 and 115 ferric citrate-treated and placebo-treated patients, respectively. At 16 weeks, ferric citrate significantly reduced serum phosphate versus placebo (P = 0.006) only among patients with elevated baseline serum phosphate (≥4.5 mg/dL) and did not reduce serum phosphate among patients with baseline serum phosphate within the population reference range. Ferric citrate reduced intact FGF23 and C-terminal FGF23 partially via changes in TSAT (for C-terminal FGF23) and serum phosphate (for intact FGF23) and partially via unknown/unmeasured mechanisms.

Conclusions

Ferric citrate reduced serum FGF23 concentrations (partially via effects on serum phosphate and iron balance) and did not reduce serum phosphate among patients with baseline serum phosphate concentrations within the population reference range.
Accelerating Soybean Breeding in a CO2-Supplemented Growth Chamber
Authors: Nagatoshi Yukari , Fujita Yasunari
Published: September 2018

Soybean (Glycine max) is the most important dicot crop worldwide, and is increasingly used as a model legume due to the wide availability of genomic soybean resources; however, the slow generation times of soybean plants are currently a major hindrance to research. Here, we demonstrate a method for accelerating soybean breeding in compact growth chambers, which greatly shortens the generation time of the plants and accelerates breeding and research projects. Our breeding method utilizes commonly used fluorescent lamps (220 ï¿½mol m–2 s–1 at the canopy level), a 14 h light (30ï¿½C)/10 h dark (25ï¿½C) cycle and carbon dioxide (CO2) supplementation at >400 p.p.m. Using this approach, the generation time of the best-characterized elite Japanese soybean cultivar, Enrei, was shortened from 102–132 d reported in the field to just 70 d, thereby allowing up to 5 generations per year instead of the 1–2 generations currently possible in the field and/or greenhouse. The method also facilitates the highly efficient and controlled crossing of soybean plants. Our method uses CO2 supplementation to promote the growth and yield of plants, appropriate light and temperature conditions to reduce the days to flowering, and the reaping and sowing of immature seeds to shorten the reproductive period greatly. Thus, the appropriate parameters enable acceleration of soybean breeding in the compact growth chambers commonly used for laboratory research. The parameters used in our method could therefore be optimized for other species, cultivars, accessions and experimental designs to facilitate rapid breeding in a wide range of crops.
Randomised study demonstrates sustained benefits of a pre-school intervention designed to improve nutrition and physical activity practices
Authors: de Zwarte Diewerke , Kearney John , Corish Clare A , Glennon Corina , Maher Lorraine , Johnston Molloy Charlotte
Published: September 2018

Background

Health-promoting programmes must demonstrate sustained efficacy in order to make a true impact on public health. This study aimed to determine the effect of the Healthy Incentive for Pre-schools project on health-promoting practices in full-day-care pre-schools 18 months after a training intervention.

Methods

Thirty-seven pre-schools completed the initial study and were included in this follow-up study. The intervention consisted of one training session with either the pre-school ‘manager-only’ or ‘manager and staff’ using a specifically developed needs-based training resource pack comprised of written educational material and a validated health-promoting practice evaluation tool. Direct observation data of health-promoting practices were collected and allocated a score using the evaluation tool by a research dietitian at three time points; pre-intervention, between 6 and 9 months post-intervention and at 18-month follow-up. An award system was used to incentivise pre-schools to improve their scores.

Results

Health-promoting practice scores improved significantly (P < 0.001) from the 6–9 month post-intervention to the 18-month follow-up evaluation. No significant differences were observed between ‘manager-only’ and ‘manager and staff’ trained pre-schools.

Conclusions

The introduction of a pre-school evaluation tool supported by a training resource was successfully used to incentivise pre-schools to sustain and improve health-promoting practices 18 months after intervention training.
A SCREENING SURVEY EXERCISE FOR THYROID INTERNAL EXPOSURE FROM RADIOIODINE AFTER A NUCLEAR ACCIDENT
Authors: Yajima Kazuaki , Kim Eunjoo , Tani Kotaro , Tatsuzaki Hideo , Li Chunsheng , Kurihara Osamu
Published: September 2018

In the aftermath of the 2011 Fukushima nuclear disaster, a screening survey for thyroid internal exposure from intake of radioiodine was performed on 1080 children using handheld NaI(Tl) survey meters. This article presents the design and results of a practical exercise conducted to develop the skills of personnel who would be potentially engaged in such a survey. Participants of this exercise were asked to measure manikin heads in which point sources were installed under normal (~0.05 μSv h−1) and elevated (~0.5 μSv h−1) background conditions. The results demonstrated that the measurements were less dependent on the background radiation level, and the deviation of net signals obtained by the participants were within 10–20% for dose rates above 0.2 μSv h−1. This result suggests that dose rates can be reliably obtained above a provisional operational intervention level for the device, 0.5 μSv h−1 under a real nuclear accident situation.
Development and Evaluation of a Triplex TaqMan Assay and Next-Generation Sequence Analysis for Improved Detection of Xylella in Plant Material
Authors: Bonants Peter , Griekspoor Yvonne , Houwers Ilse , Krijger Marjon , van der Zouwen Patricia , van der Lee Theo A. J. , van der Wolf Jan
Published: September 2018

Xylella fastidiosa is a heterogenous gram-negative bacterial plant pathogen with a wide host range covering over 300 plant species. Since 2013, in Europe, the presence of the pathogen is increasing in a part of the Mediterranean area, but it causes in particular severe disease problems in olive orchards in the Southern part of Italy. Various subspecies of the pathogen were also diagnosed in natural outbreaks and intercepted ornamental plants in Europe, among them Olea europaea, Coffea arabica, and Nerium oleander. The host range of the pathogen can vary, depending on the subspecies and even the strain. The availability of fast and reliable diagnostic tools is indispensable in management strategies to control diseases caused by X. fastidiosa. To improve the reliability of the TaqMan assay, currently widely used in surveys, a triplex TaqMan assay was developed in which two specific and sensitive TaqMan assays, previously designed for X. fastidiosa, were combined with an internal control. The triplex assay exhibited the same diagnostic sensitivity as the simplex assays. In addition, the usefulness of a metagenomic approach using next-generation sequencing (NGS) was demonstrated, in which total DNA extracted from plant material was sequenced. DNA extracts from plant material free of X. fastidiosa, from artificially inoculated hosts plants or from naturally infected plants sampled in France, Spain, and Italy, or intercepted in Austria and the Netherlands, were analyzed for the presence of X. fastidiosa using the metagenomic approach. In all samples, even in samples with a low infection level, but not in the pathogen-free samples, DNA reads were detected specific for X. fastidiosa. In most cases, the pathogen could be identified to the subspecies level, and for one sample even the whole genome could be assembled and the sequence type could be determined. All results of NGS-analyzed samples were confirmed with the triplex TaqMan polymerase chain reaction and loop-mediated isothermal amplification.
Efficacy of In-Furrow Fungicides for Management of Field Pea Root Rot Caused by Fusarium avenaceum and F. solani Under Greenhouse and Field Conditions
Authors: Modderman Chryseis T. , Markell Samuel , Wunsch Michael , Pasche Julie S.
Published: September 2018

Field pea (Pisum sativum L.) root rot has resulted in substantial yield losses in North Dakota, with symptoms ranging from small lesions to complete root destruction. Traditional management practices such as seed treatment fungicides and crop rotation have proven insufficient under high disease pressure. The objective of this research was to determine the efficacy of in-furrow fungicide applications for management of field pea root rot under greenhouse and field conditions. In-furrow fungicides generally reduced root rot severity, sometimes significantly over the seed treatment in the field; however, the level of control varied across hosts and pathogens in both greenhouse and field trials. Prothioconazole, fluopyram, and penthiopyrad provided the most consistent results across trials. The results of these studies indicate that the use of in-furrow fungicides provides growers with another tool for managing Fusarium root rot.
Measuring accessibility using gravity and radiation models
Authors: Piovani Duccio , Arcaute Elsa , Uchoa Gabriela , Wilson Alan , Batty Michael
Published: September 2018

Since the presentation of the radiation model, much work has been done to compare its findings with those obtained from gravitational models. These comparisons always aim at measuring the accuracy with which the models reproduce the mobility described by origin–destination matrices. This has been done at different spatial scales using different datasets, and several versions of the models have been proposed to adjust to various spatial systems. However, the models, to our knowledge, have never been compared with respect to policy testing scenarios. For this reason, here we use the models to analyse the impact of the introduction of a new transportation network, a bus rapid transport system, in the city of Teresina in Brazil. We do this by measuring the estimated variation in the trip distribution, and formulate an accessibility to employment indicator for the different zones of the city. By comparing the results obtained with the two approaches, we are able to not only better assess the goodness of fit and the impact of this intervention, but also understand reasons for the systematic similarities and differences in their predictions.
Effect of carboxylic group on the compatibility with retarder and the retarding side effect of the fluid loss control additive used in oil well cement
Authors: Guo Shenglai , Lu Yao , Bu Yuhuan , Li Benlin
Published: September 2018

The retarding side effect and the compatibility with other additives are the main problems that limit the field application of the synthesized fluid loss control additive (FLCA). The effect of the type and content of carboxylic acid groups on the retarding side effect of FLCA and the compatibility between FLCA and the retarder AMPS-IA synthesized using 2-acrylamido-2-methyl propane sulfonic acid (AMPS) and itaconic acid (IA) was studied in this paper. The type and content of carboxylic acid group have a great influence on the fluid loss control ability, the compatibility with retarder and the retarding side effect of FLCA. FLCA containing IA or maleic acid (MA) shows better compatibility with retarder than FLCA containing acrylic acid, but the retarding side effect of FLCA containing MA is weaker than that of FLCA containing IA. Thus, MA is the most suitable monomer for synthesizing FLCA having good compatibility with retarder AMPS-IA.
A microfluidic chip-based co-culture of fibroblast-like synoviocytes with osteoblasts and osteoclasts to test bone erosion and drug evaluation
Authors: Ma Hui-Peng , Deng Xue , Chen Deng-Yi , Zhu Di , Tong Jin-Ling , Zhao Ting , Ma Jin-Hui , Liu Yan-Qiu
Published: September 2018

Targeting fibroblast-like synoviocyte (FLS) migration and invasion-mediated bone erosion is a promising clinical strategy for the treatment of rheumatoid arthritis (RA). Drug sensitivity testing is fundamental to this scheme. We designed a microfluidic chip-based, cell co-cultured platform to mimic RA FLS-mediated bone erosion and perform drug-sensitive assay. Human synovium SW982 cells were cultured in the central channel and migrated to flow through matrigel-coated side channels towards cell culture chamber where RANKL-stimulated osteoclastic RAW264.7 and osteogenic medium (OS)-stimulated bone marrow mesenchymal stem cells (BMSC) were cultured in the microfluidic chip device, mimicking FLS migration and invasion-mediated bone erosion in RA. These SW982 cells showed different migration potentials to osteoclasts and BMSC. The migration of SW982 cells with high expression of cadherin-11 was more potent when SW982 cells were connected with the co-culture of RAW264.7 and BMSC. Simultaneously, in the co-cultured chamber, tartrate-resistant acid phosphatase (TRAP) activity of RANKL-stimulated RAW264.7 cells was enhanced, but alkaline phosphatase (ALP) activity was decreased in comparison with mono-cultured chamber. Furthermore, it was confirmed that celastrol, a positive drug for the treatment of RA, inhibited SW982 cell migration as well as TRAP activity in the cell-cultured microfluidic chips. Thus, the migration and invasion to bone-related cells was reconstituted on the microfluidic model. It may provide an effective anti-RA drug screen model for targeting FLS migration-mediated bone erosion.
Facile synthesis of palladium nanoparticles on hierarchical hollow silica spheres and its catalytic properties in Suzuki-reaction
Authors: Liu Mao , Wu Liuli , Han Jianjie , Xu Xiuhong , He Chengyuan , Wang Peng , Wei Qian , Yang Wanliang
Published: September 2018

A novel well-dispersed Pd@HHSS catalyst was synthesized by reduction of Pd(OAc)
2
immobilized on HHSS we reported. When the ratios of Pd/SiO
2
were 5 : 100 and 10 : 100, the Pd nanoparticles size was about 5–10 nm. The Pd@HHSS catalyst (Pd/SiO
2
= 10 : 100) showed high catalytic activity in Suzuki-reaction with yields of 91–99% and the catalyst is reusable after four successive cycles without obvious loss of catalytic activity.
Network resilience of mutualistic ecosystems and environmental changes: an empirical study
Authors: Nagaishi Ellie , Takemoto Kazuhiro
Published: September 2018

It is theorized that a mutualistic ecosystem's resilience against perturbations (e.g. species extinction) is determined by a single macroscopic parameter (network resilience), calculable from the network. Given that such perturbations occur owing to environmental changes (e.g. climate change and human impact), it has been predicted that mutualistic ecosystems that exist despite extensive environmental changes exhibit higher network resilience; however, such a prediction has not been confirmed using real-world data. Thus, in this study, the effects of climate change velocity and human activities on mutualistic network resilience were investigated. A global dataset of plant–animal mutualistic networks was used, and spatial analysis was performed to examine the effects. Moreover, the potential confounding effects of network size, current climate and altitude were statistically controlled. It was demonstrated that mutualistic network resilience was globally influenced by warming velocity and human impact, in addition to current climate. Specifically, pollination network resilience increased in response to human impact, and seed-dispersal network resilience increased with warming velocity. The effect of environmental changes on network resilience for plants was remarkable. The results confirmed the prediction obtained based on the theory and imply that real-world mutualistic networks have a structure that increases ecosystem resilience against environmental changes. These findings will enhance the understanding of ecosystem resilience.
Tailoring morphology of cobalt–nickel layered double hydroxide via different surfactants for high-performance supercapacitor
Authors: Xiao Bangqing , Zhu Wenliang , Li Zhong , Zhu Jiliang , Zhu Xiaohong , Pezzotti Giuseppe
Published: September 2018

Tailoring the morphology of cobalt–nickel layered double hydroxide (LDH) electrode material was successfully achieved via the process of cathodic electrodeposition by adding different surfactants (hexamethylenetetramine, dodecyltrimethylammonium bromide (DTAB) or cetyltrimethylammonium bromide). The as-prepared Co
0.75
Ni
0.25
(OH)
2
samples with surfactants exhibited wrinkle-like, cauliflower-like or net-like structures that corresponded to better electrochemical performances than the untreated one. In particular, a specific capacitance of 1209.1 F g
−1
was found for the cauliflower-like Co
0.75
Ni
0.25
(OH)
2
electrode material using DTAB as the surfactant at a current density of 1 A g
−1
, whose structure boosted ion diffusion to present a good rate ability of 64% with a 50-fold increase in current density from 1 A g
−1
to 50 A g
−1
. Accordingly, the asymmetric supercapacitor assembled by current LDH electrode and activated carbon electrode showed an energy density as high as 21.3 Wh kg
−1
at a power density of 3625 W kg
−1
. The relationship between surfactant and electrochemical performance of the LDH electrode materials has been discussed.
Facile synthesis of NiCo
2
S
4
/CNTs nanocomposites for high-performance supercapacitors
Authors: Huang Yunxia , Cheng Ming , Xiang Zhongcheng , cui Yimin
Published: September 2018

Herein, porous NiCo
2
S
4
/CNTs nanocomposites were synthesized via a simple hydrothermal method followed by the sulphurization process using different sulfide sources. By comparing two different sulfur sources, the samples using thioacetamide as sulfide source delivered more remarkable electrochemical performance with a high specific capacitance of 1765 F g
−1
at 1 A g
−1
and an admirable cycling stability with capacitance retention of 71.7% at a high current density of 10 A g
−1
after 5000 cycles in 2 M KOH aqueous electrolyte. Furthermore, an asymmetric supercapacitor (ASC) device was successfully fabricated with the NiCo
2
S
4
/CNTs electrode as the positive electrode and graphene as the negative electrode. The device provided a maximum energy density of 29.44 W h kg
−1
at a power density of 812 W kg
−1
. Even at a high power density of 8006 W kg
−1
, the energy density still reaches 16.68 W h kg
−1
. Moreover, the ASC presents 89.8% specific capacitance retention after 5000 cycles at 5 A g
−1
. These results reveal its great potential for supercapacitors in electrochemical energy storage field.
Bayesian adaptation of chaos representations using variational inference and sampling on geodesics
Authors: Tsilifis P. , Ghanem R. G.
Published: September 2018

A novel approach is presented for constructing polynomial chaos representations of scalar quantities of interest (QoI) that extends previously developed methods for adaptation in Homogeneous Chaos spaces. In this work, we develop a Bayesian formulation of the problem that characterizes the posterior distributions of the series coefficients and the adaptation rotation matrix acting on the Gaussian input variables. The adaptation matrix is thus construed as a new parameter of the map from input to QoI, estimated through Bayesian inference. For the computation of the coefficients' posterior distribution, we use a variational inference approach that approximates the posterior with a member of the same exponential family as the prior, such that it minimizes a Kullback–Leibler criterion. On the other hand, the posterior distribution of the rotation matrix is explored by employing a Geodesic Monte Carlo sampling approach, consisting of a variation of the Hamiltonian Monte Carlo algorithm for embedded manifolds, in our case, the Stiefel manifold of orthonormal matrices. The performance of our method is demonstrated through a series of numerical examples, including the problem of multiphase flow in heterogeneous porous media.
Local root growth and death are mediated by contrasts in nutrient availability and root quantity between soil patches
Authors: Wang Peng , Yang Yan , Mou Pu , Zhao Qingzhou , Li Yunbin
Published: September 2018

Plants are thought to be able to regulate local root growth according to its overall nutrient status as well as nutrient contents in a local substrate patch. Therefore, root plastic responses to environmental changes are probably co-determined by local responses of root modules and systematic control of the whole plant. Recent studies showed that the contrast in nutrient availability between different patches could significantly influence the growth and death of local roots. In this study, we further explored, beside nutrient contrast, whether root growth and death in a local patch are also affected by relative root quantity in the patch. We conducted a split-root experiment with different splitting ratios of roots of Canada goldenrod (Solidago canadensis) individuals, as well as high- (5× Hoagland solution versus water) or low- (1× Hoagland solution versus water) contrast nutrient conditions for the split roots. The results showed that root growth decreased in nutrient-rich patches but increased in nutrient-poor patches when more roots co-occurred in the same patches, irrespective of nutrient contrast condition. Root mortality depended on contrasts in both root quantity and nutrients: in the high-nutrient-contrast condition, it increased in nutrient-rich patches but decreased in nutrient-poor patches with increasing root proportion; while in the low-nutrient-contrast condition, it showed the opposite trend. These results demonstrated that root growth and death dynamics were affected by the contrast in both nutrient availability and root quantity between patches. Our study provided ecological evidence that local root growth and death are mediated by both the responses of root modules to a nutrient patch and the whole-plant nutrient status, suggesting that future work investigating root production and turnover should take into account the degree of heterogeneity in nutrient and root distribution.
Stratigraphic signatures of mass extinctions: ecological and sedimentary determinants
Authors: Nawrot Rafał , Scarponi Daniele , Azzarone Michele , Dexter Troy A. , Kusnerik Kristopher M. , Wittmer Jacalyn M. , Amorosi Alessandro , Kowalewski Michał
Published: September 2018

Stratigraphic patterns of last occurrences (LOs) of fossil taxa potentially fingerprint mass extinctions and delineate rates and geometries of those events. Although empirical studies of mass extinctions recognize that random sampling causes LOs to occur earlier than the time of extinction (Signor–Lipps effect), sequence stratigraphic controls on the position of LOs are rarely considered. By tracing stratigraphic ranges of extant mollusc species preserved in the Holocene succession of the Po coastal plain (Italy), we demonstrated that, if mass extinction took place today, complex but entirely false extinction patterns would be recorded regionally due to shifts in local community composition and non-random variation in the abundance of skeletal remains, both controlled by relative sea-level changes. Consequently, rather than following an apparent gradual pattern expected from the Signor–Lipps effect, LOs concentrated within intervals of stratigraphic condensation and strong facies shifts mimicking sudden extinction pulses. Methods assuming uniform recovery potential of fossils falsely supported stepwise extinction patterns among studied species and systematically underestimated their stratigraphic ranges. Such effects of stratigraphic architecture, co-produced by ecological, sedimentary and taphonomic processes, can easily confound interpretations of the timing, duration and selectivity of mass extinction events. Our results highlight the necessity of accounting for palaeoenvironmental and sequence stratigraphic context when inferring extinction dynamics from the fossil record.
Parent–offspring facial resemblance increases with age in rhesus macaques
Authors: Kazem Anahita J. N. , Barth Yvonne , Pfefferle Dana , Kulik Lars , Widdig Anja
Published: September 2018

Kin recognition is a key ability which facilitates the acquisition of inclusive fitness benefits and enables optimal outbreeding. In primates, phenotype matching is considered particularly important for the recognition of patrilineal relatives, as information on paternity is unlikely to be available via social familiarity. Phenotypic cues to both paternal and maternal relatedness exist in the facial features of humans and other primates. However, theoretical models suggest that in systems with uncertainty parentage it may be adaptive for offspring to conceal such cues when young, in order to avoid potential costs of being discriminated against by unrelated adults. Using experienced human raters, we demonstrate in a computer-based task that detection of parent–offspring resemblances in the faces of rhesus macaques (
Macaca mulatta
) increases significantly with offspring age. Moreover, this effect is specific to information about kinship, as raters were extremely successful at discriminating individuals even among the youngest animals. To our knowledge, this is the first evidence in non-humans for the age-dependent expression of visual cues used in kin recognition.
How does parental environment influence the potential for adaptation to global change?
Authors: Chirgwin Evatt , Marshall Dustin J. , Sgrò Carla M. , Monro Keyne
Published: September 2018

Parental environments are regularly shown to alter the mean fitness of offspring, but their impacts on the genetic variation for fitness, which predicts adaptive capacity and is also measured on offspring, are unclear. Consequently, how parental environments mediate adaptation to environmental stressors, like those accompanying global change, is largely unknown. Here, using an ecologically important marine tubeworm in a quantitative-genetic breeding design, we tested how parental exposure to projected ocean warming alters the mean survival, and genetic variation for survival, of offspring during their most vulnerable life stage under current and projected temperatures. Offspring survival was higher when parent and offspring temperatures matched. Across offspring temperatures, parental exposure to warming altered the distribution of additive genetic variance for survival, making it covary across current and projected temperatures in a way that may aid adaptation to future warming. Parental exposure to warming also amplified nonadditive genetic variance for survival, suggesting that compatibilities between parental genomes may grow increasingly important under future warming. Our study shows that parental environments potentially have broader-ranging effects on adaptive capacity than currently appreciated, not only mitigating the negative impacts of global change but also reshaping the raw fuel for evolutionary responses to it.