bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growing evidence for facultative biotrophy in saprotrophic fungi: data from microcosm tests with 201 species of wood‐decay basidiomycetes
Authors: Smith Gabriel R. , Finlay Roger D. , Stenlid Jan , Vasaitis Rimvydas , Menkis Audrius 
Published: April 2017

Summary

Ectomycorrhizal (ECM) symbioses have evolved a minimum of 78 times independently from saprotrophic lineages, indicating the potential for functional overlap between ECM and saprotrophic fungi. ECM fungi have the capacity to decompose organic matter, and although there is increasing evidence that some saprotrophic fungi exhibit the capacity to enter into facultative biotrophic relationships with plant roots without causing disease symptoms, this subject is still not well studied.

In order to determine the extent of biotrophic capacity in saprotrophic wood‐decay fungi and which systems may be useful models, we investigated the colonization of conifer seedling roots in vitro using an array of 201 basidiomycete wood‐decay fungi. Microtome sectioning, differential staining and fluorescence microscopy were used to visualize patterns of root colonization in microcosm systems containing Picea abies or Pinus sylvestris seedlings and each saprotrophic fungus.

Thirty‐four (16.9%) of the tested fungal species colonized the roots of at least one tree species. Two fungal species showed formation of a mantle and one showed Hartig net‐like structures. These features suggest the possibility of an active functional symbiosis between fungus and plant.

The data indicate that the capacity for facultative biotrophic relationships in free‐living saprotrophic basidiomycetes may be greater than previously supposed.
Salivary microbiome of an urban Indian cohort and patterns linked to subclinical inflammation
Authors: Acharya A , Chan Y , Kheur S , Kheur M , Gopalakrishnan D , Watt RM , Mattheos N 
Published: April 2017

ObjectiveTo profile salivary microbiomes of an urban‐living, healthy Indian cohort and explore associations with proinflammatory status.MethodsFifty‐one clinically healthy Indian subjects’ salivary microbiomes were analyzed using 16S rRNA Illumina MiSeq sequencing. Community distribution was compared with salivary data from the Human Microbiome Project (HMP). Indian subjects were clustered using microbiome‐based “partitioning along medoids” (PAM), and relationships of interleukin‐1 beta levels with community composition were analyzed.ResultsIndian subjects presented higher phylogenetic diversity than HMP. Several taxa associated with traditional societies gut microbiomes (Bacteroidales, Paraprevotellaceae, and Spirochaetaceae) were raised. Bifidobacteriaceae and Lactobacillaceae were approximately fourfold greater. A PAM cluster enriched in several Proteobacteria, Actinobacteria, and Bacilli taxa and having almost twofold higher Prevotella to Bacteroides ratio showed significant overrepresentation of subjects within the highest quartile of salivary interleukin‐1 beta levels. Abiotrophia, Anaerobacillus, Micrococcus, Aggregatibacter, Halomonas, Propionivivrio, Paracoccus, Mannhemia, unclassified Bradyrhizobiaceae, and Caulobacteraceae were each significant indicators of presence in the highest interleukin‐1 beta quartile. 2 OTUs representing Lactobacillus fermentum and Cardiobacterium hominis significantly correlated with interleukin‐1 beta levels.ConclusionThe salivary microbiome of this urban‐dwelling Indian cohort differed significantly from that of a well‐studied Western cohort. Specific community patterns were putatively associated with subclinical inflammation levels.
Increased light‐use efficiency sustains net primary productivity of shaded coffee plants in agroforestry system
Authors: Charbonnier Fabien , Roupsard Olivier , le Maire Guerric , Guillemot Joannès , Casanoves Fernando , Lacointe André , Vaast Philippe , Allinne Clémentine , Audebert Louise , Cambou Aurélie , Clément‐Vidal Anne , Defrenet Elsa , Duursma Remko A. , Jarri Laura , Jourdan Christophe , Khac Emmanuelle , Leandro Patricia , Medlyn Belinda E. , Saint‐André Laurent , Thaler Philippe , Van Den Meersche Karel , Barquero Aguilar Alejandra , Lehner Peter , Dreyer Erwin 
Published: April 2017

AbstractIn agroforestry systems, shade trees strongly affect the physiology of the undergrown crop. However, a major paradigm is that the reduction in absorbed photosynthetically active radiation is, to a certain extent, compensated by an increase in light‐use efficiency, thereby reducing the difference in net primary productivity between shaded and non‐shaded plants. Due to the large spatial heterogeneity in agroforestry systems and the lack of appropriate tools, the combined effects of such variables have seldom been analysed, even though they may help understand physiological processes underlying yield dynamics.In this study, we monitored net primary productivity, during two years, on scales ranging from individual coffee plants to the entire plot. Absorbed radiation was mapped with a 3D model (MAESPA). Light‐use efficiency and net assimilation rate were derived for each coffee plant individually.We found that although irradiance was reduced by 60% below crowns of shade trees, coffee light‐use efficiency increased by 50%, leaving net primary productivity fairly stable across all shade levels.Variability of aboveground net primary productivity of coffee plants was caused primarily by the age of the plants and by intraspecific competition among them (drivers usually overlooked in the agroforestry literature) rather than by the presence of shade trees.
Identical Presentation of Scapular Osteolysis in Two Patients with Thoracic Kaposiform Hemangioendothelioma
Authors: Alonso Arroyo Verónica , Lopez‐Gutierrez Juan Carlos , Martinez Rox , Fernandez‐Pineda Israel 
Published: April 2017

AbstractKaposiform hemangioendothelioma (KHE) is a rare, locally aggressive vascular tumor that does not metastasize. We report two unique cases of KHE involving the right hemithorax and the upper ipsilateral extremity. Kasabach–Merrit phenomenon and osteolytic lesions in the scapula were observed in both cases.
Low‐Dose Cyclosporine A in the Treatment of Severe Atopic Dermatitis Complicated by Chronic Hepatitis C Virus Infection
Authors: Gnarra Maria , De Simone Clara , Garcovich Matteo , Garcovich Simone 
Published: April 2017

AbstractAtopic dermatitis (AD) is the most frequent chronic inflammatory skin disorder in children and is usually accompanied by genetic and environmental factors. Effective management and treatment of AD is challenging and often requires systemic immunosuppressive therapy when refractory to topical treatments. We report a rare association between chronic hepatitis C virus (HCV) and severe AD, management of which required systemic cyclosporine because of its favorable effects on inflammatory and viral‐related clinical outcomes.
Iatrogenic Calcinosis Cutis Successfully Treated with Topical Sodium Thiosulfate
Authors: García‐García Emilio , López‐López Rocío , Álvarez‐del‐Vayo Concepción , Bernabeu‐Wittel José 
Published: April 2017

AbstractCalcinosis cutis is a term used to describe a group of disorders in which calcium salt deposits form in the skin and subcutaneous tissue. We report a 6‐year‐old boy with hypoparathyroidism after thyroidectomy who was admitted to the hospital for severe hypocalcemia being treated with calcium gluconate intravenous infusion through peripheral veins. Within a few days we made a diagnosis of iatrogenic calcinosis cutis and treatment with 10% topical sodium thiosulfate was prescribed; complete resolution of lesions was achieved after 6 months, with no local or systemic adverse effects. Because of the lack of noninvasive alternatives and the good tolerance of the treatment, especially in childhood, we suggest the topical use of this drug as an option for this condition.
Changes in the stimulus‐preceding negativity and lateralized readiness potential during reinforcement learning
Authors: Ren Xi , Valle‐Inclán Fernando , Tukaiev Sergii , Hackley Steven A. 
Published: April 2017

AbstractAccording to reinforcement learning theory, dopamine‐dependent anticipatory processes play a critical role in learning from action outcomes such as feedback or reward. To better understand outcome anticipation, we examined variation in slow cortical potentials and assessed their changes over the course of motor‐skill acquisition. Healthy young adults learned a series of precisely timed, key press sequences. Feedback was delivered at a delay of either 2.5 or 8 s, to encourage use of either the striatally mediated, habit learning system or the hippocampus‐dependent, episodic memory system, respectively. During the 2.5‐s delay, the stimulus‐preceding negativity (SPN) was shown to decline in amplitude across trials, confirming previous results from a perceptual categorization task (Morís, Luque, & Rodríguez‐Fornells, 2013). This falsifies the hypothesis that SPN reflects specific outcome predictions, on the assumption that the ability to make such predictions should improve as a task is mastered. An SPN was also evident during the 8‐s delay, but it increased in amplitude across trials. At the conclusion of the 8‐s but not the 2.5‐s prefeedback interval, a reversed‐polarity lateralized readiness potential (LRP) was noted. It was suggested that this might indicate maintenance of an action representation for comparison with the feedback display. If so, this would constitute the first direct psychophysiological evidence for a popular hypothetical construct in quantitative models of reinforcement learning, the so‐called eligibility trace.
Nasopharyngeal viral PCR in immunosuppressed patients and its association with virus detection in bronchoalveolar lavage by PCR
Authors: Lachant Daniel J. , Croft Daniel P. , McGrane Minton Heather , Prasad Paritosh , Kottmann Robert M. 
Published: April 2017

ABSTRACTBackground and objectivePulmonary infiltrates are common in immunosuppressed patients. Bronchoscopy with bronchoalveolar lavage (BAL) is often used to evaluate their aetiology. However, it may not always be easily performed. Thus, alternative diagnostic strategies may be needed. There is limited data on the correlation of nasopharyngeal (NP) respiratory viral panel (RVP)‐PCR testing compared with BAL. We aimed to identify the predictive value of NP RVP‐PCR samples compared with samples obtained from BAL in immunosuppressed patients with pulmonary infiltrates.MethodsWe conducted an observational retrospective study of immunosuppressed adults who underwent bronchoscopy in the Pulmonary Department at the University of Rochester Medical Center between January 2011 and June 2016. We compared the positive and negative predictive values, sensitivity, specificity and false negative rate of NP RVP‐PCR and BAL RVP‐PCR, as well as identified clinical predictors of positive viral BAL RVP‐PCR.ResultsEighty‐nine immunosuppressed patients had both NP and bronchoalveolar RVP‐PCR testing. Twenty‐one patients had NP(+)BAL(+) RVP‐PCR testing. Seven patients had false negative (NP(−)BAL(+)) RVP‐PCR testing. Three patients had NP(+)BAL(−) RVP‐PCR testing. The positive and negative predictive values of NP RVP‐PCR testing were 88% and 89%, respectively. Allogeneic bone marrow transplantation and testing performed in the winter and spring months were significantly associated with positive BAL RVP‐PCR (OR = 3.3 (1.19–9.12); OR = 4.62 (1.64–12.99), respectively).Conclusion
NP RVP‐PCR testing has high concordance with testing performed on BAL samples. Repeat testing through BAL is beneficial when there is high concern for viral infection after initial NP RVP‐PCR testing is negative.
Dynamics of SIS Epidemic Model with Varying Total Population and Multivaccination Control Strategies
Authors: Zhang F. W. , Nie L. F. 
Published: April 2017

AbstractIn this paper, two susceptible‐infected‐susceptible epidemic models with varying total population size, continuous vaccination, and state‐dependent pulse vaccination are formulated to describe the transmission of infectious diseases, such as diphtheria, measles, rubella, pertussis, and so on. The first model incorporates the proportion of infected individuals in population as monitoring threshold value; we analytically show the existence and orbital asymptotical stability of positive order‐1 periodic solution for this control model. The other model determines control strategy by monitoring the proportion of susceptible individuals in population; we also investigate the existence and global orbital asymptotical stability of the disease‐free periodic solution. Theoretical results imply that the disease dies out in the second case. Finally, using realistic parameter values, we carry out some numerical simulations to illustrate the main theoretical results and the feasibility of state‐dependent pulse control strategy.
A Mathematical Model for the Propagation of an Animal Species on a Plain
Authors: Ndam Joel Nimyel , Dung Stephen 
Published: April 2017

A mathematical model for the dynamics of an animal species propagating on a plain is constructed. Travelling wave solutions are then sought for two cases, the case with constant diffusion coefficient and that with density-dependent diffusion coefficient. The results show the existence of travelling wave solutions in both cases. The existence of travelling wave solutions for the two-dimensional model is important as it captures more realistically the physical interactions of species in a habitat. The minimum wave speeds as well as the basins of attraction were determined. The results also indicate the occurrence of a saddle-node bifurcation in the case with density-dependent diffusion coefficient. The basins of attraction in both cases are functions of the wave speedВ and is still a subject for further investigation.
Identification of Virulent Capnocytophaga canimorsus Isolates by Capsular Typing
Authors: Hess Estelle , Renzi Francesco , Koudad Dunia , Dol Mélanie , Cornelis Guy R. 
Published: April 2017

ABSTRACT

Capnocytophaga canimorsus
is a dog oral commensal that causes rare but severe infections in humans.
C. canimorsus
was recently shown to be endowed with a capsular polysaccharide implicated in resistance to the innate immune system of the host. Here, we developed the first
C. canimorsus
capsular serotyping scheme. We describe nine different serovars (A to I), and this serotyping scheme allowed typing of 25/25 isolates from human infections but only 18/52 isolates from dog mouths, indicating that the repertoire of capsules in the species is vast. However, while only three serovars (A, B, and C) covered 88% of the human isolates tested (22/25), they covered only 7.7% of the dog isolates (4/52). Serovars A, B, and C were found 22.9-, 14.6-, and 4.2-fold more often, respectively, among human isolates than among dog isolates, with no geographical bias, implying that isolates endowed with these three capsular types are more virulent for humans than other isolates. Capsular serotyping would thus allow identification of virulent isolates in dogs, which could contribute to the prevention of these infections. To this end, we developed a PCR typing method based on the amplification of specific capsular genes.
Cbl E3 Ligase Mediates the Removal of Nectin-1 from the Surface of Herpes Simplex Virus 1-Infected Cells
Authors: Deschamps Thibaut , Dogrammatzis Christos , Mullick Ranajoy , Kalamvoki Maria 
Published: April 2017

ABSTRACT
The Cbl E3 ligase has been linked to the down-modulation of surface signaling responses by inducing internalization of surface receptors. The adaptor protein CIN85 is a partner of Cbl that augments many of these interactions. Previously, an interaction was demonstrated between ICP0 and CIN85, which results in the removal of epidermal growth factor receptor (EGFR) from the surface of the infected cells with a concomitant attenuation of EGFR signaling. Here, we examined whether Cbl mediates the removal of the herpes simplex virus 1 (HSV-1) entry receptor Nectin-1 from the surface of infected cells. We found the following: (i) that Cbl, Nectin-1, and the viral glycoprotein D (gD) form a complex in infected cells; (ii) that during infection Nectin-1 is removed from the surface of the infected cells but is retained on the surface of cells that have been depleted of Cbl; and (iii) that in cells infected with a ΔICP0 mutant virus, Nectin-1 remained on the cell surface. Thus, Cbl is necessary but not sufficient for the removal of Nectin-1 from the cell surface. In addition, we observed that in Cbl-depleted cells there was enhanced entry after infection. These cells were susceptible to secondary infections by HSV-1. Viral entry in CIN85-depleted cells was only moderately enhanced compared to that in the Cbl-depleted cells, suggesting that the Cbl–Nectin-1 interaction is likely the key to the downregulation of surface Nectin-1. The removal of the HSV-1 entry receptor Nectin-1 from the surface of the infected cells may be part of the strategy of the virus to efficiently spread to uninfected cells.

IMPORTANCE
The Cbl E3 ligase suppresses surface signaling responses by inducing internalization of surface components. The targets of Cbl include such components as immune system receptors, growth factor receptors, adhesion, and cell-to-cell contact molecules. The immediate early protein ICP0 of herpes simplex virus 1 (HSV-1) interacts with CIN85, an adaptor protein that augments Cbl functions. The consequence of this interaction is the removal of the epidermal growth factor receptor (EGFR) from the surface of the infected cells with concomitant suppression of the EGF ligand signaling. The viral entry receptor Nectin-1 is also internalized during HSV-1 infection in a Cbl-dependent mechanism, and that increases the opportunity of the virus to spread to uninfected cells. The diversion of the Cbl/CIN85 endocytic machinery may be a strategy utilized by the virus to alter the cell surface pattern to prevent detrimental host responses.
Environmental and nutrition impact of achieving new School Food Plan recommendations in the primary school meals sector in England
Authors: Wickramasinghe Kremlin , Rayner Mike , Goldacre Michael , Townsend Nick , Scarborough Peter 
Published: April 2017

ObjectivesThe aim of this modelling study was to estimate the expected changes in the nutritional quality and greenhouse gas emissions (GHGEs) of primary school meals due to the adoption of new mandatory food-based standards for school meals.SettingNationally representative random sample of 136 primary schools in England was selected for the Primary School Food Survey (PSFS) with 50% response rate.ParticipantsA sample of 6690 primary students from PSFS who consumed school meals.Outcome measuresPrimary School Food Plan (SFP) nutritional impact was assessed using both macronutrient and micronutrient quality. The environmental impact was measured by GHGEs.MethodsThe scenario tested was one in which every meal served in schools met more than half of the food-based standards mentioned in the SFP (SFP scenario). We used findings from a systematic review to assign GHGE values for each food item in the data set. The GHGE value and nutritional quality of SFP scenario meals was compared with the average primary school meal in the total PSFS data set (pre-SFP scenario). Prior to introduction of the SFP (pre-SFP scenario), the primary school meals had mandatory nutrient-based guidelines.ResultsThe percentage of meals that met the protein standard increased in the SFP scenario and the proportion of meals that met the standards for important micronutrients (eg, iron, calcium, vitamin A and C) also increased. However, the SFP scenario did not improve the salt, saturated fat and free sugar levels. The mean GHGE value of meals which met the SFP standards was 0.79 (95% CI 0.77 to 0.81) kgCO2e compared with a mean value of 0.72 (0.71 to 0.74) kgCO2e for all meals. Adopting the SFP would increase the total emissions associated with primary school meals by 22 000 000 kgCO2e per year.ConclusionsThe universal adoption of the new food-based standards, without reformulation would result in an increase in the GHGEs of school meals and improve some aspects of the nutritional quality, but it would not improve the average salt, sugar and saturated fat content levels.
Effects of injectable progestogen contraception versus the copper intrauterine device on HIV acquisition: sub-study of a pragmatic randomised controlled trial
Authors: Hofmeyr G Justus , Singata-Madliki Mandisa , Lawrie Theresa A , Bergel Eduardo , Temmerman Marleen 
Published: April 2017

BackgroundEvidence from observational studies suggests an increased risk of HIV acquisition among women using depot medroxyprogesterone acetate (DMPA) contraception.MethodsWithin the context of a South African programme to increase women's access to the intrauterine contraceptive device (IUD), we conducted a pragmatic, open-label, parallel-arm, randomised controlled trial (RCT) of the IUD versus injectable progestogen contraception (IPC) at two South African hospitals. The primary outcome was pregnancy; secondary outcomes included HIV acquisition. Consenting women attending termination of pregnancy services were randomised after pregnancy termination between July 2009 and November 2012. Condoms were promoted for the prevention of sexually transmitted infections. Voluntary HIV testing was offered at baseline and at 12 or more months later. Findings on HIV acquisition are reported in this article.ResultsHIV acquisition data were available for 1290 initially HIV-negative women who underwent a final study interview at a median of 20 months after randomisation to IPC or an IUD. Baseline group characteristics were comparable. In the IPC group, 545/656 (83%) of participants received DMPA, 96 (15%) received injectable norethisterone enanthate, 14 (2%) received the IUD and one received oral contraception. In the IUD group 609 (96%) received the IUD, 20 (3%) received IPC and 5 (1%) had missing data. According to intention-to-treat analysis, HIV acquisition occurred in 20/656 (3.0%) women in the IPC arm and 22/634 (3.5%) women in the IUD arm (IPC vs IUD, risk ratio 0.88; 95% confidence interval 0.48–1.59;p=0.7).ConclusionsThis sub-study was underpowered to rule out moderate differences in HIV risk, but confirms the feasibility of randomised trial methodology to address this question. Larger RCTs are needed to determine the relative risks of various contraceptive methods on HIV acquisition with greater precision.Trial registration numberPan African Clinical Trials Registry number PACTR201409000880157 (04-09-2014).
Formulae for low-energy secondary electron yield from different kinds of emitters as a function of measurable variables
Authors: Xie Ai-Gen , Zhon Kun , Zhao De-Lin , Xia Yu-Qing 
Published: April 2017

Based on the characteristics of secondary electron emission and the relationships among parameters of secondary electron yield [Formula: see text] in the low-energy range of [Formula: see text] eV (low-energy [Formula: see text]), the universal formula for low-energy [Formula: see text] as a function of [Formula: see text], [Formula: see text] and maximum [Formula: see text] was deduced, where [Formula: see text] and [Formula: see text] are the incident energies of primary electron and of [Formula: see text], respectively. From the deduced universal formula and experimental low-energy [Formula: see text] from metals, semiconductors and insulators, special formula for low-energy [Formula: see text] from metals as a function of [Formula: see text], [Formula: see text] and [Formula: see text] and that for low-energy [Formula: see text] from semiconductors and insulators as a function of [Formula: see text], [Formula: see text] and [Formula: see text] were deduced, respectively. The results were analyzed, it can be concluded that the two deduced special formulae can be used to calculate low-energy [Formula: see text] from metals, semiconductors and insulators, respectively.