bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of potassium and manganese phosphites in the control of Pythium damping‐off in soybean: a feasible alternative to fungicide seed treatments
Authors: Carmona Marcelo A , Sautua Francisco J , Grijalba Pablo E , Cassina Mariano , Pérez‐Hernández Oscar
Published: August 2017

BACKGROUND

Use of fungicide seed treatments for control of soybean soilborne diseases such as Pythium damping‐off has increased worldwide. However, emergence of Pythium strains resistant to metalaxyl‐M has prompted the need for alternative technologies to fungicides for damping‐off control. The use of phosphites (Phis) has been proposed as a method to control oomycetes, but their use as seed treatments in soybean is limited by the lack of information on their efficacy. The effect of potassium (K) and manganese (Mn) Phis (as seed treatments) in the control of Pythium damping‐off in soybean was evaluated in vitro and in vivo. In vitro, treated seeds and a control were placed on potato dextrose agar and the damping‐off severity caused by Pythium aphanidermatum (Edson) Fitzpatrick, Pythium irregulare Buisman, and Pythium ultimum Trow was assessed 5 days after incubation using an ordinal scale. In vivo, treated seeds and a control were planted in polystyrene pots and emergence was evaluated 21 days after planting.

RESULTS

Analysis of the in vitro data using a multinomial generalized linear model showed that the probabilities of non‐germinated, dead seeds ranged from 0.64 to 1.00 in the control and from 0 to 0.13 in the Phi treatments in each of the Pythium species. Probabilities of seed germination without or with damping‐off symptoms were significantly higher for seeds treated with the Phi products than for the control. In the in vivo experiment, the Phi‐based products increased seedling emergence by up to 29% on average compared with the untreated control.

CONCLUSION

Mn and K Phis are feasible alternatives as seed treatments to control Pythium damping‐off in soybean. This study is the first, worldwide, to document the efficacy of K and Mn Phis in the control of soybean Pythium damping‐off. © 2017 Society of Chemical Industry
Dietary behaviour changes to improve nutritional quality and health outcomes☆
Authors: Tapsell Linda C.
Published: August 2017

This narrative review examines the changes required in dietary behaviours to address the current global burden of disease resulting from diet‐associated cardiometabolic dysfunction. Beginning with known relationships between nutritional factors and health outcomes, the review identifies a number of problems with current dietary behaviours, using examples from the Australian context. Implications for practice are then discussed drawing on insights from research in dietary trials. From a concerted research effort across the globe, the effects of foods, food components and dietary patterns on cardiometabolic parameters have been reasonably well exposed. The evidence base for these effects underpins dietary guidelines, which aim to meet nutritional requirements and protect against cardiometabolic disease. Thus foods recommended in dietary guidelines tend to be consistent with research that identifies foods that appear protective and those that appear detrimental to health. The need for dietary behaviour change is apparent through analyses that have exposed increasing consumption of detrimental foods, despite the availability of healthy foods. However, behaviour change is a complex area, and where weight loss is also required, there is high level evidence that interdisciplinary efforts combining diet, physical activity and psychological support are warranted. Insights from dietary trials and research indicate that focussing on foods and dietary patterns is integral to the specific dietary change required for health outcomes, but social and behavioural factors will influence the achievement of these changes.
Patriarcado, violencia, injusticia: sobre las (im)posibilidades de la democracia
Authors: Rios Alves Nunes da Costa Marta
Published: August 2017

Qual a relação entre patriarcado, capitalismo, violência e (in)justiça? De que forma a violência contra a mulher se traduz numa violência contra a própria política e condena o sucesso de um projeto democrático? Este artigo visa responder a estas questões, desdobrando-se em duas tarefas distintas: por um lado, a tarefa descritiva do que é, nomeadamente, a representação da sociedade brasileira marcada por uma lógica de violência contra a mulher que assenta num modelo patriarcal; por outro lado, a tarefa prescritiva de comopode ser, mostrando que um real compromisso com a democracia passa necessariamente pela superação de todas as lógicas de dominação e opressão, o que significa que a questão de gênero assume papel central na busca de emancipação humana.
Análisis envolvente de datos. Un caso de estudio para una universidad argentina
Authors: Villarreal Fernanda , Tohmé Fernando
Published: August 2017

Este artículo presenta un caso de estudio en el que se analiza la eficiencia relativa del plan de estudios de un programa universitario. Esta cuestión es muy relevante, ya que los cursos del plan están financiados con fondos públicos y por lo tanto afectan la eficiencia del gasto público global. El método aplicado es el análisis envolvente de datos (DEA, por sus iniciales en inglés). Los resultados permiten identificar los cursos optativos ineficientes que deberían aumentar el número de estudiantes y reducir al mismo tiempo el número de miembros del cuerpo docente asignados a ellos para mejorar su eficiencia. En el caso de cursos obligatorios, la mejora también requiere reducir el número de docentes auxiliares.
Longitudinal Patterns of Occurrence and Remission of Erectile Dysfunction in Men with Type 1 Diabetes
Authors: Palmer Melody R. , Holt Sarah K. , Sarma Aruna V. , Dunn Rodney L. , Hotaling James M. , Cleary Patricia A. , Braffett Barbara H. , Martin Catherine , Herman William H. , Jacobson Alan M. , Wessells Hunter ,   Diabetes Control and Complications Trial and Epidemiology of Diabetes Interventions and Complications Research Group
Published: August 2017

Background

Men with diabetes are at greater risk of erectile dysfunction (ED).

Aim

To describe the natural history of ED in men with type 1 diabetes.

Methods

We examined up to 30 years of prospectively collected annual ED status and demographic and clinical variables from 600 male participants in the Diabetes Control and Complications Trial (DCCT; 1983–1993) and its follow-up study, the Epidemiology of Diabetes Interventions and Complications (1994–present; data in this study are through 2012).

Outcomes

Yes vs no response to whether the participant had experienced impotence in the past year and whether he had used ED medication.

Results

Sixty-one percent of men reported ED at least once during the study. For some men, the initial report of ED was permanent. For others, potency returned and was lost multiple times. Visual display of the data showed four longitudinal ED phenotypes: never (38.7%), isolated (6.7%), intermittent (41.8%), and persistent (12.8%). Men who never reported ED or in only 1 isolated year were younger, had lower body mass index, and better glycemic control than men in the intermittent and persistent groups at DCCT baseline. In a multivariable logistic model comparing men at their first year reporting ED, men who were older had lower odds of remission and men who were in the conventional DCCT treatment group had higher odds of remission.

Clinical Translation

If validated in other cohorts, such findings could be used to guide individualized interventions for patients with ED.

Strengths and Limitations

This is the first examination of ED with repeated measures at an annual resolution, with up to 30 years of responses for each participant. However, the yes vs no response is a limitation because the real phenotype is not binary and the question can be interpreted differently depending on the participant.

Conclusions

Age, glycemic control, and BMI were important longitudinal predictors of ED. We have described a more complex ED phenotype, with variation in remission patterns, which could offer insight into different mechanisms or opportunities for intervention. If validated in other cohorts, such findings could be used to establish more accurate prognostication of outcomes for patients with ED to guide individualized interventions.
Distribution of genes encoding resistance to aminoglycoside modifying enzymes in methicillin‐resistant Staphylococcus aureus (MRSA) strains
Authors: Khosravi Azar Dokht , Jenabi Atefeh , Montazeri Effat Abbasi
Published: August 2017

Today Methicillin‐Resistant Staphylococcus aureus (MRSA) have acquired multiple resistance to a wide range of antibiotics including aminoglycosides. So, this study was aimed to investigate the rate of aminoglycoside resistance and the frequency of aminoglycoside resistance mediated genes of aac(Ia)‐2, aph(3)‐IIIa and ant(4′)‐Ia among MRSA strains. A total of 467 staphylococci isolates were collected from various clinical samples. S. aureus strains were identified by standard culture and identification criteria and investigating of presence of 16S rRNA and nuc genes. Cefoxitin disk diffusion, and oxacillin‐salt agar screening methods were used to detect the MRSA strains with subsequent molecular identification for the presence of mecA gene. Antibiotic susceptibility of MRSA strains against aminoglycoside antibiotics was evaluated by using agar disk diffusion method. Multiplex PCR for the presence of aac(Ia)‐2, aph(3)‐IIIa and ant(4′)‐Ia encoding genes for aminoglycosides were performed for MRSA strains. From total staphylococci tested isolates, 262 (56.1%) were identified as S. aureus, of which 161 (61.45%) were detected as MRSA and all comprised mecA gene. The resistance pattern of MRSA strains to aminoglycoside antibiotics were: gentamicin 136 (84.5%); amikacin 125 (77.6%); kanamycin 139 (86.3%); tobramycin 132 (82%); and neomycin 155 (96.3%). The frequency of aac(Ia)‐2, aph(3)‐IIIa, and ant(4′)‐Ia genes among MRSA strains, were 64%, 42% and 11.8% respectively. In conclusion, as MRSA strains are of great concern in human infections, the results of present study could provide a useful resource for health sectors for choosing appropriate antibiotics for the effective treatment of infections due to MRSA strains.
Transcription and translation of APOL1 variants
Authors: Ejaz Samina
Published: August 2017

It is highly important to document the molecular alterations existing in normal cells prior to the onset of any disease. Knowledge of genetic mutations and associated molecular mechanisms will be helpful for better diagnosis and management of disease. The major focus of this commentary on providing understanding about the apolipoprotein 1 (APOL1) gene, the protein encoded by this gene (apoL1) and the mechanistic details regarding the role of apoL1 in the lysis of Trypanosoma brucei. Information about APOL1 genetic variants, APOL1G1 and APOL1G2, is provided along with the association of these variants with hypertension-attributed end-stage renal disease (ESRD) and focal segmental glomerulosclerosis (FSGS). Moreover, this commentary presents a brief overview of how the authors of a recent Bioscience Reports article [Haque et al (2017) 37, BSR20160531, doi: 10.1042/BSR20160531] have evaluated the functional impact of G1 and G2 alleles on the transcription and translation of APOL1 mRNA.
Impaired innate immune gene profiling in airway smooth muscle cells from chronic cough patients
Authors: Rossios Christos , Pavlidis Stelios , Gibeon David , Mumby Sharon , Durham Andrew , Ojo Oluwaseun , Horowitz Daniel , Loza Matt , Baribaud Fred , Rao Navin , Chung Kian Fan , Adcock Ian M.
Published: August 2017

Chronic cough is associated with airway inflammation and remodelling. Abnormal airway smooth muscle cell (ASMC) function may underlie mechanisms of chronic cough. Our objective was to examine the transcriptome and focused secretome of ASMCs from chronic cough patients and healthy non-cough volunteers. ASMC gene expression profiling was performed at baseline and/or after stimulation with polyinosinic:polycytidylic acid (poly(I:C)) to mimic viral infection. Supernatants were collected for multiplex analysis. Our results showed no significant differentially expressed genes (DEGs, false discovery rate (FDR) <0.05) between chronic cough and healthy non-cough ASMCs at baseline. Poly(I:C) stimulation resulted in 212 DEGs (>1.5 fold-change, FDR <0.05) in ASMCs from chronic cough patients compared with 1674 DEGs in healthy non-cough volunteers. The top up-regulated genes included chemokine (C–X–C motif) ligand (CXCL) 11 (CXCL11), CXCL10, chemokine (C–C motif) ligand (CCL) 5 (CCL5) and interferon-induced protein 44 like (IFI44L) corresponding with inflammation and innate immune response pathways. ASMCs from cough subjects had enhanced activation of viral response pathways in response to poly(I:C) compared with healthy non-cough subjects, reduced activation of pathways involved in chronic inflammation and equivalent activation of neuroregulatory genes. The poly(I:C)-induced release of inflammatory mediators, including CXCL8, interleukin (IL)-6 and CXCL1, from ASMCs from cough patients was significantly impaired compared with healthy non-cough subjects. Addition of fluticasone propionate (FP) to poly(I:C)-treated ASMCs resulted in greater gene expression changes in healthy non-cough ASMCs. FP had a differential effect on poly(I:C)-induced mediator release between chronic cough and healthy non-cough volunteers. In conclusion, altered innate immune and inflammatory gene profiles within ASMCs, rather than infiltrating cells or nerves, may drive the cough response following respiratory viral infection.
Role of conformational change and K-path ligands in controlling cytochrome c oxidase activity
Authors: Liu Jian , Hiser Carrie , Ferguson-Miller Shelagh
Published: August 2017

Given the central role of cytochrome c oxidase (CcO) in health and disease, it is an increasingly important question as to how the activity and efficiency of this key enzyme are regulated to respond to a variety of metabolic states. The present paper summarizes evidence for two modes of regulation of activity: first, by redox-induced conformational changes involving the K-proton uptake path; and secondly, by ligand binding to a conserved site immediately adjacent to the entrance of the K-path that leads to the active site. Both these phenomena highlight the importance of the K-path in control of CcO. The redox-induced structural changes are seen in both the two-subunit and a new four-subunit crystal structure of bacterial CcO and suggest a gating mechanism to control access of protons to the active site. A conserved ligand-binding site, first discovered as a bile salt/steroid site in bacterial and mammalian oxidases, is observed to bind an array of ligands, including nucleotides, detergents, and other amphipathic molecules. Highly variable effects on activity, seen for these ligands and mutations at the K-path entrance, can be explained by differing abilities to inhibit or stimulate K-path proton uptake by preventing or allowing water organization. A new mutant form in which the K-path is blocked by substituting the conserved carboxyl with a tryptophan clarifies the singularity of the K-path entrance site. Further study in eukaryotic systems will determine the physiological significance and pharmacological potential of ligand binding and conformational change in CcO.
Visualising pattern recognition receptor signalling
Authors: Macleod Charlotte , Bryant Clare E.
Published: August 2017

Signalling by pattern recognition receptors (PRRs) is critical for protecting the host against pathogens. Disruption of these signalling pathways has been implicated in many diseases ranging from infection susceptibility to cancer and autoimmune disease. Understanding how PRRs signal is of critical importance due to their potential as therapeutic targets to ameliorate symptoms of inflammatory diseases. The recent advances in microscopy, such as the discovery of fluorescent proteins and the breaking of the diffraction limit of light, offer a unique opportunity to visualise receptor signalling at a single protein level within living cells. Many different microscopy techniques have been developed and used for dissecting different aspects of PRR signalling pathways. This review will provide an overview of the main microscopy techniques used for dissecting these pathways with a focus on Toll-like receptor and NOD-like receptor signalling.
Structure of the Holliday junction: applications beyond recombination
Authors: Ho P. Shing
Published: August 2017

The Holliday junction (HJ) is an essential element in recombination and related mechanisms. The structure of this four-stranded DNA assembly, which is now well-defined alone and in complex with proteins, has led to its applications in areas well outside of molecular recombination, including nanotechnology and biophysics. This minireview explores some interesting recent research on the HJ, as it has been adapted to design regular two- or three-dimensional lattices for crystal engineering, and more complex systems through DNA origami. In addition, the sequence dependence of the structure is discussed in terms how it can be applied to characterize the geometries and energies of various noncovalent interactions, including halogen bonds in oxidatively damaged (halogenated) bases and hydrogen bonds associated with the epigenetic 5-hydroxylmethylcytosine base.
Short‐term ice accretion forecasting model for transmission lines with modified time‐series analysis by fireworks algorithm
Authors: Huang Xin‐Bo , Li Hong‐Bo , Zhu Yong‐Can
Published: August 2017

In order to reduce the damages of transmission line icing, an effective ice accretion forecasting can be used to guide the de‐icing work. The ice accretion on transmission lines varies slowly over time, and the icing data series is characteristic of timing sequence and autocorrelation. Time‐series analysis is suitable for analysing the similar data series, and fireworks algorithm (FA) is used to determine the autoregressive order and the moving average order of time‐series analysis. Then a short‐term ice accretion forecasting for transmission lines with modified time‐series analysis by FA is built. The ice accretion experiments were done in artificial icing laboratory. The results show that the modified time‐series analysis model by the FA has higher accuracy than another five models, whose relative errors are <1.3% and closer to the experimental data. Field applications also show that the modified time‐series analysis model has higher accuracy than the traditional one for the short‐term ice accretion forecasting, whose average error rates are separately 2.6723 and 5.2654%.
Contrast‐aware power control method for mobile active‐matrix organic light‐emitting diode display
Authors: Shin Jeyong , Park Rae‐Hong
Published: August 2017

Mobile display technology has been developed fast and low‐power design for the display is more important than ever. Hardware techniques for low‐power design are not flexible and the existing software techniques are not considering the characteristics of the display panels. In this study, a histogram‐based contrast‐aware power control method for active‐matrix organic light‐emitting diode display is proposed. The proposed power control method solves an optimisation problem to achieve power control with maximum contrast available. A new histogram representation is also proposed to calculate the power consumption of an image efficiently in the optimisation process. Simulation results and hardware experiment results show that the proposed method provides both precise power control and better contrast of the output image.
Improved chamfer matching method for surface mount component positioning
Authors: Bai Lifei , Yang Xianqiang , Gao Huijun
Published: August 2017

This study is concerned with the surface mount component positioning problem and an improved chamfer matching method based on iterative position and rotation angle estimation approach is proposed. Instead of performing matching of the image with different pre‐specified angle templates pixel by pixel, as does in traditional chamfer matching methods, the gradient information of the distance transform image is incorporated into the chamfer matching method and reduced computational cost of the method is achieved. The iterative formulas to update the translation and rotation angle are derived by reference to the characteristic of rigid body motion. The criterions of search region establishment, seed point selection and terminal conditions are given. The effectiveness of the proposed method is verified by applying the method to component positioning with actual captured images.
Super‐resolution reconstruction: using non‐local structure similarity and edge sharpness dictionary
Authors: Zhao Jianwei , Hu Heping , Zhou Zhenghua , Cao Feilong
Published: August 2017

Image super‐resolution (SR) reconstruction, which gains high‐pixel and multi‐detail image from single or several low‐pixel images, has attracted increasing interest in recent years. This study proposes a new SR method based on sparse representation, which made good use of the non‐local (NL) structure similarity and edge sharpness dictionary. Firstly, all the training patches are classified into different clusters according to diverse edge sharpness of patches. Secondly, different dictionaries are trained for different training patches in each cluster. Thirdly, the NL structure similarity is added into the constraint of NL structure similarity model, and the suitable dictionary is selected for current patch to achieve the coefficients according to the value of edge sharpness of patch. Finally, the high‐resolution (HR) image is obtained by integrating HR patches obtained by the product of HR dictionaries and coefficients. Moreover, by calculating edge sharpness, the different dictionaries which adapt to patches with different structure are obtained, and the NL similarity is well utilised and more details are added to HR patch. Compared to some classical and common methods, the proposed method possesses better reconstruction effects in numerical and visual aspects.
Reconstruction of three‐dimensional linear structures in the breast from craniocaudal and mediolateral oblique mammographic views
Authors: Akhtar Yusuf , Mukherjee Dipti Prasad
Published: August 2017

A three‐dimensional (3D) representation of the linear structures in a breast has been constructed by utilising information of the ridges in the craniocaudal (CC) and the mediolateral oblique (MLO) mammographic views of the breast. Blood vessels and ducts appear as ridges in the mammogram. The position and shape of the ridges in the breast are an indicator of malignancy. In the first stage of the proposed 3D reconstruction problem, an algorithm has been developed to find out which linear structure in the CC view and a linear structure in the MLO view correspond to the same 3D structure in the breast. The 3D view of the linear structures is constructed from the abovementioned correspondences. The positional error (per unit length of the reconstructed linear structure) between the manual reconstruction and the algorithmic reconstruction of a linear structure turns out to be better by 20% than a competing approach.
AC coefficient and K‐means cuckoo optimisation algorithm‐based segmentation and compression of compound images
Authors: Manju Vethamuthu Nesamony , Lenin Fred Alfred
Published: August 2017

Compound images are containing palletise regions including text or graphics and continuous tone images. The compression of compound images is a challenging function and which is complicated to achieve it without degrading the quality of the images. This document is mainly used to improve the compression ratio and an efficient segmentation method is created to separate the background image, text and graphics from the compound images for to make the compression independently. The segmentation is performed through AC coefficient‐based segmentation method resulting in smooth and non‐smooth regions. The non‐smooth region is again segmented by means of K‐means cuckoo optimisation algorithm. In the second phase, the segmented background image, text and graphics were compressed by means of arithmetic coder, Huffman coder and JPEG coder, respectively. This proposed technique is implemented in the working platform of MATLAB and the results were analysed.
X‐band antenna array for low‐cost beam scanning
Authors: Yashchyshyn Yevhen , Godziszewski Konrad , Bogdan Grzegorz , Piasecki Przemysław
Published: August 2017

A concept of a low‐cost beamforming system is investigated by developing an inexpensive microstrip antenna array and proposing an appropriate approach for a beamforming. The antenna structure is composed of individually fabricated linear sub‐arrays suspended over the ground plane. The design is scalable, because an antenna array with required radiation pattern can be designed by using adequate number of linear sub‐arrays. A novel cone‐shaped transition surrounding the probe feed has been applied to decrease an inductive reactance of the input impedance. The antenna array composed of four linear sub‐arrays has been designed, fabricated and measured to validate performance of the proposed low‐cost design. The measured gain of a fabricated antenna is >26 dBi and the reflection coefficient is better than −10 dB. Each sub‐array has a separate coaxial connector, therefore beam scanning can be achieved by controlling radio frequency signals in each sub‐array. Two methods of beam scanning, a phased array approach and a time modulation approach, have been proposed and compared in terms of efficiency, cost and functionality.
Study on the phase factor of phase retrieval algorithm for surface diagnosis of large reflector antennas
Authors: Liu Kangkang , Ye Qian , Meng Guoxiang
Published: August 2017

Surface diagnosis methods based on phase retrieval algorithm have been successfully applied to many large reflector antennas. In the phase retrieval algorithm, surface distortion is retrieved by multiple far field patterns. The different far field patterns are connected to each other by an important element called ‘phase factor’. This study investigates the effect of the phase factor on the phase retrieval algorithm. Generally, the phase factor is simple for the phase retrieval algorithm. In this study, a new method based on the active surface system is proposed to produce more flexible and diverse phase factors. Through digital simulations, the effect of different kinds of phase factors on the phase retrieval algorithm is discussed. In addition, the inaccuracy of the phase factor caused by the mechanism error is considered.
A review of methods and databases for metagenomic classification and assembly
Authors: Breitwieser Florian P , Lu Jennifer , Salzberg Steven L
Published: August 2017

Microbiome research has grown rapidly over the past decade, with a proliferation of new methods that seek to make sense of large, complex data sets. Here, we survey two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly, and we review some of the challenges facing these methods. All of the methods rely on public genome databases, and we also discuss the content of these databases and how their quality has a direct impact on our ability to interpret a microbiome sample.
Neurological manifestations related to Crohn’s disease: a boon for the workforce
Authors: Nemati Reza , Mehdizadeh Somayeh , Salimipour Hooman , Yaghoubi Ehsan , Alipour Zeinab , Tabib Seyed Masoud , Assadi Majid
Published: August 2017

The neurological manifestations of Crohn’s disease and its prevalence are not well known. Here, we report five patients of confirmed Crohn’s disease with different neurological presentations. The neurological presentations include anterior ischemic optic neuropathy, myelopathy, posterior reversible encephalopathy syndrome, chronic inflammatory demyelinating polyneuropathy, and chronic axonal sensory and motor polyneuropathy. These manifestations should be kept in mind in the assessment of Crohn’s disease.
The draft genome assembly of Rhododendron delavayi Franch. var. delavayi
Authors: Zhang Lu , Xu Pengwei , Cai Yanfei , Ma Lulin , Li Shifeng , Li Shufa , Xie Weijia , Song Jie , Peng Lvchun , Yan Huijun , Zou Ling , Ma Yongpeng , Zhang Chengjun , Gao Qiang , Wang Jihua
Published: August 2017

Rhododendron delavayi Franch. is globally famous as an ornamental plant. Its distribution in southwest China covers several different habitats and environments. However, not much research had been conducted on Rhododendron spp. at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to different environments. Here, we report the genome assembly and gene annotation of R. delavayi var. delavayi (the second genome sequenced in the Ericaceae), which will facilitate the study of the family. The genome assembly will have further applications in genome-assisted cultivar breeding. The final size of the assembled R. delavayi var. delavayi genome (695.09 Mb) was close to the 697.94 Mb, estimated by k-mer analysis. A total of 336.83 gigabases (Gb) of raw Illumina HiSeq 2000 reads were generated from 9 libraries (with insert sizes ranging from 170 bp to 40 kb), achieving a raw sequencing depth of ×482.6. After quality filtering, 246.06 Gb of clean reads were obtained, giving ×352.55 coverage depth. Assembly using Platanus gave a total scaffold length of 695.09 Mb, with a contig N50 of 61.8 kb and a scaffold N50 of 637.83 kb. Gene prediction resulted in the annotation of 32 938 protein-coding genes. The genome completeness was evaluated by CEGMA and BUSCO and reached 95.97% and 92.8%, respectively. The gene annotation completeness was also evaluated by CEGMA and BUSCO and reached 97.01% and 87.4%, respectively. Genome annotation revealed that 51.77% of the R. delavayi genome is composed of transposable elements, and 37.48% of long terminal repeat elements (LTRs). The de novo assembled genome of R. delavayi var. delavayi (hereinafter referred to as R. delavayi) is the second genomic resource of the family Ericaceae and will provide a valuable resource for research on future comparative genomic studies in Rhododendron species. The availability of the R. delavayi genome sequence will hopefully provide a tool for scientists to tackle open questions regarding molecular mechanisms underlying environmental interactions in the genus Rhododendron, more accurately understand the evolutionary processes and systematics of the genus, facilitate the identification of genes encoding pharmaceutically important compounds, and accelerate molecular breeding to release elite varieties.
The human NAIP-NLRC4-inflammasome senses the Pseudomonas aeruginosa T3SS inner-rod protein
Authors: Grandjean Teddy , Boucher Anne , Thepaut Marion , Monlezun Laura , Guery Benoit , Faudry Eric , Kipnis Eric , Dessein Rodrigue
Published: August 2017

While NLRC4-dependent sensing of intracellular Gram-negative pathogens such as Salmonella enterica serovar typhimurium is a beneficial host response, NLRC4-dependent sensing of the Pseudomonas aeruginosa type 3 secretion system (T3SS) has been shown to be involved in pathogenicity. In mice, different pathogen-associated microbial patterns are sensed by the combination of the NLRC4-inflammasome with different neuronal apoptosis inhibitory proteins (NAIPs). NAIP2 is involved in sensing PscI, an inner-rod protein of the P. aeruginosa T3SS. Surprisingly, only a single human NAIP (hNAIP) has been found. Moreover, there is no description of hNAIP-NLRC4 inflammasome recognition of T3SS inner-rod proteins in humans. Here, we show that the P. aeruginosa T3SS inner-rod protein PscI and needle protein PscF are both sensed by the hNAIP-NLRC4 inflammasome in human macrophages and PBMCs from healthy donors, allowing caspase-1 and IL-1β maturation and resulting in a robust inflammatory response. TLR4 and TLR2 are involved in redundantly sensing these two T3SS components.
A practical solution for preserving single cells for RNA sequencing
Authors: Attar Moustafa , Sharma Eshita , Li Shuqiang , Bryer Claire , Cubitt Laura , Broxholme John , Lockstone Helen , Kinchen James , Simmons Alison , Piazza Paolo , Buck David , Livak Kenneth J. , Bowden Rory
Published: August 2017

The design and implementation of single-cell experiments is often limited by their requirement for fresh starting material. We have adapted a method for histological tissue fixation using dithio-bis(succinimidyl propionate) (DSP), or Lomant’s Reagent, to stabilise cell samples for single-cell transcriptomic applications. DSP is a reversible cross-linker of free amine groups that has previously been shown to preserve tissue integrity for histology while maintaining RNA integrity and yield in bulk RNA extractions. Although RNA-seq data from DSP-fixed single cells appears to be prone to characteristic artefacts, such as slightly reduced yield of cDNA and a detectable 3’ bias in comparison with fresh cells, cell preservation using DSP does not appear to substantially reduce RNA complexity at the gene level. In addition, there is evidence that instantaneous fixation of cells can reduce inter-cell technical variability. The ability of DSP-fixed cells to retain commonly used dyes, such as propidium iodide, enables the tracking of experimental sub-populations and the recording of cell viability at the point of fixation. Preserving cells using DSP will remove several barriers in the staging of single-cell experiments, including the transport of samples and the scheduling of shared equipment for downstream single-cell isolation and processing.
Macrophage-to-sensory neuron crosstalk mediated by Angiotensin II type-2 receptor elicits neuropathic pain
Authors: Shepherd Andrew J. , Mickle Aaron D. , Copits Bryan A. , Karlsson Páll , Kadunganattil Suraj , Golden Judith P. , Tadinada Satya M. , Mack Madison R. , Haroutounian Simon , de Kloet Annette D. , Samineni Vijay K. , Valtcheva Manouela V. , McIlvried Lisa A. , Sheahan Tayler D. , Jain Sanjay , Ray Pradipta R. , Usachev Yuriy M. , Dussor Gregory , Kim Brian S. , Krause Eric G. , Price Theodore J. , Gereau Robert W. , Mohapatra Durga P.
Published: August 2017

Peripheral nerve damage initiates a complex series of cellular and structural processes that culminate in chronic neuropathic pain. Our study defines local angiotensin signaling via activation of the Angiotensin II (Ang II) type-2 receptor (AT2R) on macrophages as the critical trigger of neuropathic pain. An AT2R-selective antagonist attenuates neuropathic, but not inflammatory pain hypersensitivity in mice, and requires the cell damage-sensing ion channel transient receptor potential family-A member-1 (TRPA1). Mechanical and cold pain hypersensitivity that are characteristic of neuropathic conditions can be attenuated by chemogenetic depletion of peripheral macrophages and AT2R-null hematopoietic cell transplantation. Our findings show no AT2R expression in mouse or human sensory neurons, rather AT2R expression and activation in macrophages triggers production of reactive oxygen/nitrogen species, which trans-activate TRPA1 on sensory neurons. Our study defines the precise neuro-immune crosstalk underlying nociceptor sensitization at the site of nerve injury. This form of cell-to-cell signaling represents a critical peripheral mechanism for chronic neuropathic pain, and therefore identifies multiple analgesic targets.
GPU-accelerated alignment of bisulfite-treated short-read sequences
Authors: Wilton Richard , Li Xin , Feinberg Andrew P. , Szalay Alexander S.
Published: August 2017

The alignment of bisulfite-treated DNA sequences (BS-seq reads) to a large genome involves a significant computational burden beyond that required to align non-bisulfite-treated reads. In the analysis of BS-seq data, this can present an important performance bottleneck that can potentially be addressed by appropriate software-engineering and algorithmic improvements. One strategy is to integrate this additional programming logic into the read-alignment implementation in a way that the software becomes amenable to optimizations that lead to both higher speed and greater sensitivity than can be achieved without this integration.

We have evaluated this approach using Arioc, a short-read aligner that uses GPU (general-purpose graphics processing unit) hardware to accelerate computationally-expensive programming logic. We integrated the BS-seq computational logic into both GPU and CPU code throughout the Arioc implementation. We then carried out a read-by-read comparison of Arioc's reported alignments with the alignments reported by the most widely used BS-seq read aligners. With simulated reads, Arioc's accuracy is equal to or better than the other read aligners we evaluated. With human sequencing reads, Arioc's throughput is at least 10 times faster than existing BS-seq aligners across a wide range of sensitivity settings.

The Arioc software is available athttps://github.com/RWilton/Arioc. It is released under a BSD open-source license.
Dew-induced transpiration suppression impacts the water and isotope balances ofColocasialeaves
Authors: Gerlein-Safdi Cynthia , Gauthier Paul P.G. , Caylor Kelly K.
Published: August 2017

Foliar uptake of water from the surface of leaves is common when rainfall is scarce and non-meteoric water such as dew or fog is more abundant. However, many species in more mesic environments have hydrophobic leaves that do not allow the plant to uptake water. Unlike foliar uptake, all species can benefit from dew- or fog-induced transpiration suppression, but despite its ubiquity, transpiration suppression has so far never been quantified. Here, we investigate the effect of dew-induced transpiration suppression on the water balance and the isotope composition of leaves via a series of experiments. Characteristically hydrophobic leaves of a tropical plant,Colocasia esculenta, are misted with isotopically enriched water to reproduce dew deposition. This species does not uptake water from the surface of its leaves. We measure leaf water isotopes and water potential and find that misted leaves exhibit a higher water potential (p< 0.05) and a more depleted water isotope composition than dry leaves (p< 0.001), suggesting a ~30% decrease in transpiration rate (p< 0.001) compared to control leaves. We propose three possible mechanisms governing the interaction of water droplets with leaf energy balance: increase in albedo from the presence of dew droplets, decrease in leaf temperature from the evaporation of dew, and local decrease in vapor pressure deficit. Comparing previous studies on foliar uptake to our results, we conclude that transpiration suppression has an effect of similar amplitude, yet opposite sign to foliar uptake on leaf water isotopes.
De novoassembly and phasing of dikaryotic genomes from two isolates ofPuccinia coronataf. sp.avenae, the causal agent of oat crown rust
Authors: Miller Marisa E. , Zhang Ying , Omidvar Vahid , Sperschneider Jana , Schwessinger Benjamin , Raley Castle , Palmer Jonathan M. , Garnica Diana , Upadhyaya Narayana , Rathjen John , Taylor Jennifer M. , Park Robert F. , Dodds Peter N. , Hirsch Cory D. , Kianian Shahryar F. , Figueroa Melania
Published: August 2017

Oat crown rust, caused by the fungusPuccinia coronataf. sp.avenae(Pca), is a devastating disease that impacts worldwide oat production. For much of its life cycle,Pcais dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguousde novogenome assemblies of twoPcaisolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for a total assembly length of 99.16 Mbp for 12SD80 and 777 primary contigs with a total length of 105.25 Mbp for 12NC29, and approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of co-expressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms inPca.

Importance

Disease management strategies for oat crown rust are challenged by the rapid evolution ofPuccinia coronataf. sp.avenae(Pca), which renders resistance genes in oat varieties ineffective. Despite the economic importance of understandingPca, resources to study the molecular mechanisms underpinning pathogenicity and emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle ofPcaas well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations ofPca.
Primary cilia mediate diverse kinase inhibitor resistance mechanisms in cancer
Authors: Jenks Andrew D. , Vyse Simon , Wong Jocelyn P. , Keller Deborah , Burgoyne Tom , Shoemark Amelia , de la Roche Maike , Tsalikis Athanasios , Michaelis Martin , Cinatl Jindrich , Huang Paul H. , Tanos Barbara E.
Published: August 2017

Primary cilia are microtubule-based organelles that detect mechanical and chemical stimuli. Although cilia house a number of oncogenic molecules (including Smoothened, KRAS, EGFR, and PDGFR), their precise role in cancer remains unclear. We have interrogated the role of cilia in acquired andde novoresistance to a variety of kinase inhibitors, and found that in several examples, resistant cells are distinctly characterized by an increase in the number and/or length of cilia with altered structural features. Changes in cilia length seem to be linked to the lack of recruitment of Kif7 and IFT81 to cilia tips, and result in enhanced hedgehog pathway activation. Notably, Kif7 knockdown is sufficient to confer drug resistance in drug sensitive cells. Conversely, targeting of cilia length or integrity through genetic and pharmacological approaches overcomes kinase inhibitor resistance. The identification of a broad mechanism of pathway-unbiased drug resistance, represents a major advancement in oncology, and helps define a specific and important role for cilia in human cancer.
Prevalence ofMycoplasma genitaliumin different population groups: systematic review and meta-analysis
Authors: Baumann Lukas , Cina Manuel , Egli-Gany Dianne , Goutaki Myrofora , Halbeisen Florian , Lohrer Gian-Reto , Ali Hammad , Scott Pippa , Low Nicola
Published: August 2017

Background

Mycoplasma genitaliumis a common cause of non-gonococcal non-chlamydial urethritis and cervicitis. Testing of asymptomatic populations has been proposed, but prevalence rates in asymptomatic populations are not well established. We aimed to estimate the prevalence ofM. genitaliumin adults in the general population, in clinic-based samples, pregnant women, men who have sex with men (MSM) and female sex workers (FSW).

Methods

We searched Embase, Medline, IndMED, AIM and LILACS from 1 January 1991 to 12 July 2016 without language restrictions. We included studies with 500 participants or more. We screened and selected studies and extracted data in duplicate. We examined eligible studies in forest plots and conducted random effects meta-analysis to estimate prevalence, if appropriate. Between study heterogeneity was examined using the I2statistic and meta-regression.

Results

Of 3,316 screened records, 63 were included. In randomly selected samples from the general population, the summary prevalence estimate was 1.3% (95% confidence intervals, CI 1.0 to 1.8%, I241.5%, 3 studies) in countries with higher levels of development and 3.9% (95% CI 2.2 to 6.7, I289.2%, 3 studies) in countries with lower levels. Prevalence estimates were similar in women and men (p=0.47). In clinic-based samples prevalence estimates were higher, except in asymptomatic patients (0.8%, 95% CI 0.4 to 1.4, I20.0%, 3 studies). Summary prevalence estimates were: pregnant women 0.9% (95% CI 0.6 to 1.4%, I20%, 4 studies); MSM in the community 3.2% (95% CI 2.1 to 5.1, I278.3%, 5 studies); FSW in the community 15.9% (95% CI 13.5 to 18.9, I2=79.9%, 4 studies).

Discussion

This systematic review can inform testing guidelines forM. genitaliuminfection. The low estimated prevalence ofM. genitaliumin the general population, pregnant women and asymptomatic attenders at clinics does not support expansion of testing to asymptomatic people in these groups.

Registration Numbers

PROSPERO: CRD42015020420
Notos - a Galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types
Authors: Bulla Ingo , Aliaga Benoît , Lacal Virginia , Bulla Jan , Grunau Christoph , Chaparro Cristian
Published: August 2017

Background

DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it remains challenging to infer kingdom-wide general rules about the functions and evolutionary conservation of DNA methylation. Methylated cytosine is often found in specific CpN dinucleotides, and the frequency distributions of, for instance, CpG observed/expected (CpG o/e) ratios have been used to infer DNA methylation types based on higher mutability of methylated CpG.

Results

Predominantly model-based approaches essentially founded on mixtures of Gaussian distributions are currently used to investigate questions related to the number and position of modes of CpG o/e ratios. These approaches require the selection of an appropriate criterion for determining the best model and will fail if empirical distributions are complex or even merely moderately skewed. We use a kernel density estimation (KDE) based technique for robust and precise characterization of complex CpN o/e distributions withouta prioriassumptions about the underlying distributions.

Conclusions

We show that KDE delivers robust descriptions of CpN o/e distributions. For straightforward processing, we have developed a Galaxy tool, called Notos and available at the ToolShed, that calculates these ratios of input FASTA files and fits a density to their empirical distribution. Based on the estimated density the number and shape of modes of the distribution is determined, providing a rational for the prediction of the number and the types of different methylation classes. Notos is written in R and Perl.