bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candida glabrata's recurrent infections: biofilm formation during Amphotericin B treatment
Authors: Rodrigues C.F. , Silva S. , Azeredo J. , Henriques M. 
Published: June 2016

Abstract
Candida species are responsible for recurrent human infections, mostly in immunocompromised patients, due to their high vulnerability. Candida glabrata has a major role in systemic candidiasis and Amphotericin B (AmB), a polyene only used in hospitals, is frequently used to treat this disease. Lately, however, clinical evidences of Candida recurrent infections during these treatments are being described, probably due to biofilm (re)formation during this therapy. Thus, this work aims at inferring if C. glabrata biofilms are still being formed during AmB treatment. For that, C. glabrata biofilms were formed in the presence of AmB and analysed by dry weight. Matrix composition was analysed quantifying carbohydrates and, specifically, β-1,3 glucans. Results demonstrated that, although in a lesser extent, C. glabrata is able to develop biofilms in the presence of AmB, with a thick extracellular matrix, with an increase on carbohydrates, especially β-1,3 glucans. Therefore, it is confirmed that complex biofilms of C. glabrata can be formed during an AmB treatment.

Significance and Impact of the Study
This study shows new insights regarding recurrent candidiasis. The authors demonstrated that Amphotericin B did not totally prevent the development of biofilms during Candida glabrata's infection treatment and that the change in the biofilm matrices may have a high responsibility for the fail in the treatment of systemic candidiasis.
Depth‐dependent plasticity in opsin gene expression varies between damselfish (Pomacentridae) species
Authors: Stieb Sara M. , Carleton Karen L. , Cortesi Fabio , Marshall N. Justin , Salzburger Walter 
Published: June 2016

AbstractPhenotypic plasticity plays an important role in adapting the visual capability of many animal species to changing sensory requirements. Such variability may be driven by developmental change or may result from environmental changes in light habitat, thereby improving performance in different photic environments. In this study, we examined inter‐ and intraspecific plasticity of visual sensitivities in seven damselfish species, part of the species‐rich and colourful fish fauna of the Great Barrier Reef in Australia. Our goal was to test whether the visual systems of damselfish were tuned to the prevailing light environment in different habitats and/or other aspects of their lifestyle. More specifically, we compared the opsin gene expression levels from individuals living in different photic habitats. We found that all species expressed rod opsin (RH1) used for dim‐light vision, and primarily three cone opsins (SWS1, RH2B and RH2A) used for colour vision. While RH1 levels changed exclusively following a diurnal cycle, cone opsin expression varied with depth in four of the seven species. Estimates of visual pigment performance imply that changes in opsin expression adjust visual sensitivities to the dominant photic regime. However, we also discovered that some species show a more stable opsin expression profile. Further, we found indication that seasonal changes, possibly linked to changes in the photic environment, might also trigger opsin expression. These findings suggest that plasticity in opsin gene expression of damselfish is highly species‐specific, possibly due to ecological differences in visual tasks or, alternatively, under phylogenetic constraints.
Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap
Authors: Gokul Jarishma K. , Hodson Andrew J. , Saetnan Eli R. , Irvine‐Fynn Tristram D. L. , Westall Philippa J. , Detheridge Andrew P. , Takeuchi Nozomu , Bussell Jennifer , Mur Luis A. J. , Edwards Arwyn 
Published: June 2016

AbstractMicrobial colonization of glacial ice surfaces incurs feedbacks which affect the melting rate of the ice surface. Ecosystems formed as microbe–mineral aggregates termed cryoconite locally reduce ice surface albedo and represent foci of biodiversity and biogeochemical cycling. Consequently, greater understanding the ecological processes in the formation of functional cryoconite ecosystems upon glacier surfaces is sought. Here, we present the first bacterial biogeography of an ice cap, evaluating the respective roles of dispersal, environmental and biotic filtration occurring at local scales in the assembly of cryoconite microbiota. 16S rRNA gene amplicon semiconductor sequencing of cryoconite colonizing a Svalbard ice cap coupled with digital elevation modelling of physical parameters reveals the bacterial community is dominated by a ubiquitous core of generalist taxa, with evidence for a moderate pairwise distance–decay relationship. While geographic position and melt season duration are prominent among environmental predictors of community structure, the core population of taxa appears highly influential in structuring the bacterial community. Taxon co‐occurrence network analysis reveals a highly modular community structured by positive interactions with bottleneck taxa, predominantly Actinobacteria affiliated to isolates from soil humus. In contrast, the filamentous cyanobacterial taxon (assigned to Leptolyngbya/Phormidesmis pristleyi) which dominates the community and binds together granular cryoconite are poorly connected to other taxa. While our study targeted one ice cap, the prominent role of generalist core taxa with close environmental relatives across the global cryosphere indicate discrete roles for cosmopolitan Actinobacteria and Cyanobacteria as respective keystone taxa and ecosystem engineers of cryoconite ecosystems colonizing ice caps.
The Causal Effects of Income Support and Housing Benefits on Mental Well‐Being: An Application of a Bayesian Network
Authors: Ozdamar Oznur , Giovanis Eleftherios 
Published: June 2016

AbstractThis study explores the causal effects of air pollution, income support, housing benefits and household income on the subjective mental well‐being in United Kingdom (UK). Additionally, the analysis considers the effects of air pollution and weather conditions. The estimates are based on data from the British Household Panel Survey. The results show that those who are unemployed or who have a low income and who claim the benefits report higher levels of mental well‐being than those who do not claim them. Moreover, the marginal willingness to pay (MWTP) for an improvement on air quality are lower in the case of the Bayesian Network.
ThrR, a DNA‐binding transcription factor involved in controlling threonine biosynthesis in Bacillus subtilis
Authors: Rosenberg Jonathan , Müller Peter , Lentes Sabine , Thiele Martin J. , Zeigler Daniel R. , Tödter Dominik , Paulus Henry , Brantl Sabine , Stülke Jörg , Commichau Fabian M. 
Published: June 2016

SummaryThe threonine dehydratase IlvA is part of the isoleucine biosynthesis pathway in the Gram‐positive model bacterium Bacillus subtilis. Consequently, deletion of ilvA causes isoleucine auxotrophy. It has been reported that ilvA pseudo‐revertants having a derepressed hom‐thrCB operon appear in the presence of threonine. Here we have characterized two classes of ilvA pseudo‐revertants. In the first class the hom‐thrCB operon was derepressed unmasking the threonine dehydratase activity of the threonine synthase ThrC. In the second class of mutants, threonine biosynthesis was more broadly affected. The first class of ilvA pseudo‐revertants had a mutation in the Phom promoter (P*hom), resulting in constitutive expression of the hom‐thrCB operon. In the second class of ilvA pseudo‐revertants, the thrR gene encoding a putative DNA‐binding protein was inactivated, also resulting in constitutive expression of the hom‐thrCB operon. Here we demonstrate that ThrR is indeed a DNA‐binding transcription factor that regulates the hom‐thrCB operon and the thrD aspartokinase gene. DNA binding assays uncovered the DNA‐binding site of ThrR and revealed that the repressor competes with the RNA polymerase for DNA binding. This study also revealed that ThrR orthologs are ubiquitous in genomes from the Gram‐positive phylum Firmicutes and in some Gram‐negative bacteria.
Pseudopilin residue E5 is essential for recruitment by the type 2 secretion system assembly platform
Authors: Nivaskumar Mangayarkarasi , Santos‐Moreno Javier , Malosse Christian , Nadeau Nathalie , Chamot‐Rooke Julia , Tran Van Nhieu Guy , Francetic Olivera 
Published: June 2016

SummaryType II secretion systems (T2SSs) promote secretion of folded proteins playing important roles in nutrient acquisition, adaptation and virulence of Gram‐negative bacteria. Protein secretion is associated with the assembly of type 4 pilus (T4P)‐like fibres called pseudopili. Initially membrane embedded, pseudopilin and T4 pilin subunits share conserved transmembrane segments containing an invariant Glu residue at the fifth position, E5. Mutations of E5 in major T4 pilins and in PulG, the major pseudopilin of the Klebsiella T2SS abolish fibre assembly and function. Among the four minor pseudopilins, only PulH required E5 for secretion of pullulanase, the substrate of the Pul T2SS. Mass‐spectrometry analysis of pili resulting from the co‐assembly of PulGE5A variant and PulGWT ruled out an E5 role in pilin processing and N‐methylation. A bacterial two‐hybrid analysis revealed interactions of the full‐length pseudopilins PulG and PulH with the PulJ‐PulI‐PulK priming complex and with the assembly factors PulM and PulF. Remarkably, PulGE5A and PulHE5A variants were defective in interaction with PulM but not with PulF, and co‐purification experiments confirmed the E5‐dependent interaction between native PulM and PulG. These results reveal the role of E5 in a recruitment step critical for assembly of the functional T2SS, likely relevant to T4P assembly systems.
Diversity of Phytophthora species in natural ecosystems of Taiwan and association with disease symptoms
Authors: Jung T. , Chang T. T. , Bakonyi J. , Seress D. , Pérez‐Sierra A. , Yang X. , Hong C. , Scanu B. , Fu C. H. , Hsueh K. L. , Maia C. , Abad‐Campos P. , Léon M. , Horta Jung M. 
Published: June 2016

In 2013 a survey of Phytophthora diversity was performed in 25 natural and seminatural forest stands and 25 rivers in temperate montane and subtropical lowland regions of Taiwan. Using baiting assays, 10 described species and 17 previously unknown taxa of Phytophthora were isolated from 71.5% of the 144 rhizosphere soil samples from 33 of 40 tree species sampled in 24 forest stands, and from 19 rivers: P. capensis, P. citrophthora, P. plurivora, P. tropicalis, P. citricola VII, P. sp. × botryosa‐like, P. sp. × meadii‐like and P. sp. occultans‐like from Clade 2; P. palmivora from Clade 4; P. castaneae and P. heveae from Clade 5; P. chlamydospora and P. sp. forestsoil‐like from Clade 6; P. cinnamomi (Pc), P. parvispora, P. attenuata nom. prov., P. flexuosa nom. prov., P. formosa nom. prov., P. intricata nom. prov., P. × incrassata nom. prov. and P. × heterohybrida nom. prov. from Clade 7; P. sp. palustris and five new hybrid species from Clade 9. The A1 mating type of Pc was widespread in both montane and lowland forests and rarely associated with disease, whereas the A2 mating type was limited to lowland forests and in some cases causing severe dieback. Most other Phytophthora species were not associated with obvious disease symptoms. It is concluded that (i) Taiwan is within the centre of origin of most Phytophthora taxa found, (ii) Pc A2 is an introduced invasive pathogen, and (iii) interspecific hybridizations play a major role in speciation and species radiations in diverse natural ecosystems.
Diversity of genusLasiodiplodiaassociated with perennial tropical fruit plants in northeastern Brazil
Authors: Coutinho I. B. L. , Freire F. C. O. , Lima C. S. , Lima J. S. , Gonçalves F. J. T. , Machado A. R. , Silva A. M. S. , Cardoso J. E. 
Published: June 2016

Until now, onlyLasiodiplodia theobromaehas been reported in association with gummosis and dieback of cashew plants and other tropical fruit plants in northeastern Brazil. This study aims to identify and characterize species ofLasiodiplodiaassociated with gummosis and dieback on tropical fruit plants grown in Ceará, Paraíba, Pernambuco, Piauí and Rio Grande do Norte States in northeastern Brazil with a description of two new species:Lasiodiplodia caatinguensissp. nov. andLasiodiplodia pontaesp. nov. Fungal identification was accomplished using a combination of morphophysiological and pathogenic characteristics, together with phylogenetic analyses based on partial translation elongation factor 1‐α sequence (TEF1‐α), internal transcribed spacer (ITS) and β‐tubulin (β‐tub). Six species ofLasiodiplodiawere identified as being associated with several tropical fruit species:Lasiodiplodia brasiliense(Manilkara zapota,Mangifera indicaandSpondias purpurea),L. caatinguensissp. nov. (Anacardium occidentale,Citrus sinensis,S. purpureaandS. lutea),L. euphorbicola(Annona muricataandCocos nucifera),L. pontaesp. nov. (A. occidentaleandS. purpurea),L. pseudotheobromae(A. occidentale,S. purpureaandTamarindus indica) andL. theobromae(A. occidentale,S. purpureaandTalisia esculenta).This is the first study to use molecular data ofLasiodiplodiataken from the stems and branches ofAnnonaspp.,A. occidentale,M. zapota,T. indica,T. esculentaandSpondiasspp. AfterL. caatinguensissp. nov., the speciesL. pseudotheobromaeandL. theobromaewere the second most frequent species. All identified species were able to cause necrotic lesions at different levels of severity when inoculated on mango fruits and young plants ofAnnonaspp., cashew andSpondiasspp.
Vesicles Cytoplasmic Injection: An Efficient Technique to Produce Porcine Transgene‐Expressing Embryos
Authors: Luchetti CG , Bevacqua RJ , Lorenzo MS , Tello MF , Willis M , Buemo CP , Lombardo DM , Salamone DF 
Published: June 2016

ContentsThe use of vesicles co‐incubated with plasmids showed to improve the efficiency of cytoplasmic injection of transgenes in cattle. Here, this technique was tested as a simplified alternative for transgenes delivery in porcine zygotes. To this aim, cytoplasmic injection of the plasmid alone was compared to the injection with plasmids co‐incubated with vesicles both in diploid parthenogenic and IVF zygotes. The plasmid pcx‐egfp was injected circular (CP) at 3, 30 and 300 ng/μl and linear (LP) at 30 ng/μl. The experimental groups using parthenogenetic zygotes were as follows: CP naked at 3 ng/μl (N = 105), 30 ng/μl (N = 95) and 300 ng/μl (N = 65); Sham (N = 105); control not injected (N = 223); LP naked at 30 ng/μl (N = 78); LP vesicles (N = 115) and Sham vesicles (N = 59). For IVF zygotes: LP naked (N = 44) LP vesicles (N = 94), Sham (N = 59) and control (N = 79). Cleavage, blastocyst and GFP+ rates were analysed by Fisher's test (p < 0.05). The parthenogenic CP naked group showed lower cleavage respect to control (p < 0.05). The highest concentration of plasmids to allow development to blastocyst stage was 30 ng/μl. There were no differences in DNA fragmentation between groups. The parthenogenic LP naked group resulted in high GFP rates (46%) and also allowed the production of GFP blastocysts (33%). The cytoplasmic injection with LP vesicles into parthenogenic zygotes allowed 100% GFP blastocysts. Injected IVF showed higher cleavage rates than control (p < 0.05). In IVF zygotes, only the use of vesicles produced GFP blastocysts. The use of vesicles co‐incubated with plasmids improves the transgene expression efficiency for cytoplasmic injection in porcine zygotes and constitutes a simple technique for easy delivery of plasmids.
Sperm Morphology Assessment in Captive Neotropical Primates
Authors: Swanson WF , Valle RR , Carvalho FM , Arakaki PR , Rodas‐Martínez AZ , Muniz JAPC , García‐Herreros M 
Published: June 2016

ContentsThe main objective of this study was to evaluate sperm morphology in four neotropical primate species to compare the sperm morphological traits and the sperm morphometric parameters as a basis for establishing normative sperm standards for each species. Data from 80 ejaculates collected from four primate species, Callithrix jacchus, Callimico goeldii, Alouatta caraya and Ateles geoffroyi, were analysed for detection of sperm morphological alterations using subjective World Health Organization (WHO‐2010) standards and Sperm Deformity Index (SDI) criteria, objective computer‐assisted sperm morphometry analysis (CASMA) and subpopulation sperm determination (SSD) methods. There were multiple differences (p < 0.01) observed among primate species in values obtained from WHO‐2010, SDI, CASMA and SSD sperm analysis methods. In addition, multiple significant positive and negative correlations were observed between the sperm morphological traits (SDI, Sperm Deformity Index Head Defects, Sperm Deformity Index Midpiece Defects, Sperm Deformity Index Tail Defects, Normal Sperm, Head Defects, Midpiece Defects and Tail Defects) and the sperm morphometric parameters (SSD, Area (A), Perimeter (P), Length (L), Width (W), Ellipticity, Elongation and Rugosity) (p ≤ 0.046). In conclusion, our findings using different evaluation methods indicate that pronounced sperm morphological variation exists among these four neotropical primate species. Because of the strong relationship observed among morphological and morphometric parameters, these results suggest that application of objective analysis methods could substantially improve the reliability of comparative studies and help to establish valid normative sperm values for neotropical primates.
Morphological expression of bedforms formed by supercritical sediment density flows on four fjord‐lake deltas of the south‐eastern Canadian Shield (Eastern Canada)
Authors: Normandeau Alexandre , Lajeunesse Patrick , Poiré Antoine G. , Francus Pierre 
Published: June 2016

AbstractHigh‐resolution swath bathymetry data collected in fjord‐lakes Pentecôte, Walker and Pasteur (eastern Québec, Canada) allowed imaging in great detail the deltas of four rivers in order to understand the factors controlling the formation and downslope evolution of bedforms present on their slopes. The morphometry and morphology of 199 bedforms reflect the behaviour of sediment density flows. The shape of the bedforms, mostly crescentic, and the relationships between their morphological properties indicate that they were formed by supercritical density flows and that they are cyclic steps. The crescentic shape suggests an upslope migration while the aspect ratios and increasing wavelengths with distance from the shore (and decreasing slopes) are compatible with a cyclic step origin. At the rollover point, the acceleration of the density flows on steep slopes produces tightly spaced hydraulic jumps and favours short wavelength and symmetrical bedforms. Further downslope, decreasing slopes and increasing specific discharge increase the wavelength and asymmetry of the bedforms. The wavelength and asymmetry are increased because density flows require longer distances to become supercritical again on lower slopes after each successive hydraulic jump. Bedform morphometry and morphology are used to reconstruct density flow behaviour downslope. Froude numbers are high near the rollover point and gradually decrease downslope as the slope becomes gentler. Conversely, the specific discharge and flow depth are low near the rollover point and gradually increase downslope as the flow either erodes sediments or becomes more dilute due to sediment deposition and water entrainment. The supercritical density flows are believed to be triggered mainly by hyperpycnal flows but some evidence of delta‐front slope failures is also observed. The differences in delta morphology and bedform development between the four deltas are linked to basin morphology and watershed hydrology, but also mainly to the fjord heritage of the lakes that allowed the focusing of sediment at the delta front.
Post‐transplant monitoring of NK cell counts as a simple approach to predict the occurrence of opportunistic infection in liver transplant recipients
Authors: Fernández‐Ruiz M. , Silva J.T. , López‐Medrano F. , Allende L.M. , San Juan R. , Cambra F. , Justo I. , Paz‐Artal E. , Jiménez C. , Aguado J.M. 
Published: June 2016

AbstractBackgroundMonitoring of peripheral blood lymphocyte subpopulation (PBLS) counts might be useful for estimating the risk of infection after liver transplantation (LT).MethodsWe prospectively measured total lymphocyte and PBLS counts at baseline and post‐transplant months 1 and 6 in 92 LT recipients. PBLS were enumerated by single‐platform 6‐color flow cytometry technology. Areas under receiver operating characteristic (ROC) curves were used to evaluate the accuracy of different PBLS for predicting cytomegalovirus (CMV) disease and overall opportunistic infection (OI). Adjusted hazard ratios (aHRs) for both outcomes were estimated by Cox regression.ResultsAfter a median follow‐up of 730.0 days, 29 patients (31.5%) developed 38 episodes of OI (including 22 episodes of CMV disease). The counts of CD3+, CD4+, and CD8+ T cells, and CD56+ CD16+ natural killer (NK) cells at month 1 were significantly lower in patients subsequently developing OI. The NK cell count was the best predictive parameter (area under ROC curve for predicting CMV disease: 0.78; P‐value = 0.001). Patients with an NK cell count <0.050 × 103 cells/μL had higher cumulative incidences of CMV disease (P‐value = 0.001) and overall OI (P‐value <0.001). In the multivariate models, an NK cell count <0.050 × 103 cells/μL at month 1 post transplantation remained as an independent risk factor for CMV disease (aHR: 5.54; P‐value = 0.003) and overall OI (aHR: 7.56; P‐value <0.001).ConclusionPost‐transplant kinetics of NK cell counts may be used as a simple and affordable proxy to the cell‐mediated immunity status in LT recipients and to their associated risk of OI.
Outcomes of spontaneous bacterial peritonitis in liver transplant recipients with allograft failure
Authors: Leong J. , Huprikar S. , Schiano T. 
Published: June 2016

AbstractBackgroundSpontaneous bacterial peritonitis (SBP) carries appreciable morbidity and mortality in the pre‐liver transplant (LT) setting. However, the occurrence of SBP and its consequences in the post‐LT setting have not been well characterized.MethodsThis is a retrospective study of SBP occurring in post‐LT patients between January 2007 and December 2012. Outcomes were compared to a cohort of post‐LT patients with allograft failure and ascites without SBP.ResultsThe most common indication for liver transplantation in this cohort was hepatitis C. A total of 29 episodes of SBP in 21 patients were identified. Escherichia coli (19%) and Klebsiella pneumoniae (10%) were the most frequent pathogens identified. Six patients died during their first episode of SBP. Ten patients were eventually listed for liver re‐transplantation (re‐LT) after their first episode of SBP; 5 of these patients were transplanted and the other 5 died. Of the 5 who were transplanted, 2 died shortly after re‐transplant, and 3 are still alive. The cause of death in the majority of patients was infection (83.3%). The median time from onset of ascites to death was 214 days (range: 10–1085 days) and from the first episode of SBP to death was 50.5 days (range: 4–549 days). In contrast, the median time from onset of ascites to death in patients with allograft failure and ascites without SBP was 331.5 days (45–2400 days).ConclusionsAllograft failure with ascites is a poor prognostic factor and these patients should be considered high risk for re‐LT. SBP may accelerate the time to mortality.