bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protective effects of the egg stalk ofParatrioza sinica(Hemiptera: Psyllidae) at various angles and spacings against three predaceous coccinellids,Harmonia axyridis,Coccinella septempunctataandHippodamia variegata(Coleoptera: Coccinellidae)
Authors: Wu Pengxiang , Ma Baoxu , Yan Shuo , Xu Jing , He Jia , Zhang Rong , Zhang Runzhi 
Published: August 2017

AbstractBACKGROUNDParatrioza sinicais a major pest of wolfberry (Lycium barbarum). Coccinellids can effectively control various developmental stages ofP. sinicabut not the stalked egg. To investigate the protective role of egg stalks against the predaceous coccinellidsHarmonia axyridis,Coccinella septempunctataandHippodamia variegata, we studied the functional responses to, and effects of, two factors: the angle between the egg stalk and the leaf plane, and the spacing between egg stalks.RESULTSThe searching rate, handling time and theoretical maximum egg consumption ofH. variegatawere optimal among the three ladybug species. Egg consumption by coccinellids was maximum and minimum at stalk angles of 0° and 90°, respectively. The average reduction in the rate of egg consumption when the stalk angle was 90° relative to 0° was significantly smaller for larvae of coccinellids compared with adults, and forH. variegatacompared with the other two species. Optimal spacing of eggs for consumption by predators varied with the predator species and their developmental stage, and was close to the body length of the predators.CONCLUSIONThe egg stalk serves as a physical protection against predators. The evolutionary selective advantage of the egg stalk in providing protection against predators requires more attention. Appropriate selection of predators and irrigation strategies may improve control ofP. sinica. © 2017 Society of Chemical Industry
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

AbstractBACKGROUNDUse 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.RESULTSAnalysis 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.CONCLUSIONMn 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

AbstractThis 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.
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

Abstract

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

AbstractToday 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.
A review of methods and databases for metagenomic classification and assembly
Authors: Breitwieser Florian P , Lu Jennifer , Salzberg Steven L 
Published: August 2017

AbstractMicrobiome 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

AbstractThe 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

Abstract
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

Abstract
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

AbstractThe 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

ABSTRACTPeripheral 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

AbstractThe 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

AbstractFoliar 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.