bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small wetlands are critical for safeguarding rare and threatened plant species
Authors: Richardson Sarah J. , Clayton Richard , Rance Brian D. , Broadbent Hazel , McGlone Matt S. , Wilmshurst Janet M. 
Published: October 2014

AbstractQuestionRare and threatened species are a common focus of natural area protection, but selecting sites to protect them must be balanced against other conservation objectives. Using a series of wetlands as a case study, we ask: (i) will protecting sites based on species rarity capture all critical community types; (ii) do rare plant species occur in rare environments; and (iii) will safeguarding large wetlands protect taxonomic and functional richness of rare and threatened species?LocationSouthern New Zealand.MethodsWe used lists of vascular plant species from 118 wetlands (66 fens, 35 bogs and 17 marshes). The resulting species lists included 29 rare and threatened species. Nine functional attributes of the rare and threatened species were compiled. Species assemblages were ordinated using non‐metric multidimensional scaling. Permutational multivariate ANOVA tested for a difference in assemblages between wetlands with or without rare and threatened species. Wetlands were classified according to a rare environment scheme. SLOSS (single‐large‐or‐several‐small) accumulation curves determined whether species and functional richness of rare and threatened species were best captured by groups of small or large wetlands.ResultsWetlands with rare and threatened species supported species assemblages, which were different from those without rare or threatened plant species. Rare and threatened species were not associated with rare environments. The presence or richness of rare and threatened species was not associated with wetland size. SLOSS analyses revealed that small wetlands were critical for capturing rare and threatened species and their functional richness.ConclusionsPrioritizing wetlands with rare and threatened plant species will not meet other conservation objectives, such as the preservation of all critical community types, rare environments or large wetlands. Networks of small wetlands will be necessary to safeguard rare and threatened plant species. Complementary objectives targeted at wetlands of varying size will be necessary to protect the full range of biodiversity and ecosystem services that wetlands offer.
Areas of China predicted to have a suitable climate for Anoplophora chinensis under a climate‐warming scenario
Authors: Ge Xuezhen , Zong Shixiang , He Shanyong , Liu Yiting , Kong Xiangqi 
Published: October 2014

AbstractAnoplophora chinensis (Forster) (Coleoptera: Cerambycidae) is an A1 class quarantine pest, native to China, Japan, and North Korea. The A. chinensis outbreak in China has severely affected the local environment and economic development. This study investigates potential areas in China with suitable climate for A. chinensis using historical climate data (1971–2000) and future climate‐warming estimates generated by CLIMEX1.1. These future estimates are based on simulated climate data (2010–2039) provided by the Tyndall Centre for Climate Change Research (TYN SC 2.0). The results suggest that a wide area of China will have a climate suitable for A. chinensis, and every province may contain some suitable areas for this pest. The predicted areas are distributed primarily in central and southern China, with an estimated distribution range of 18.2–49.5°N and 81.3–135.0°E. Using a global‐warming scenario and predictions based on historical climate data, the areas in China with a climate generally suitable for A. chinensis are predicted to decline, whereas the areas that are highly suitable for A. chinensis are predicted to expand particularly to the northeast and northwest. The estimated distribution range covered 18.2–49.1°N and 73.6–135.0°E. Anoplophora chinensis hosts grow in much of China; therefore, the pest could possibly establish this entire predicted area. These results support enhanced quarantine and control measures combined with stronger monitoring systems to prevent the spread and export of A. chinensis.
Ectomycorrhizal impacts on plant nitrogen nutrition: emerging isotopic patterns, latitudinal variation and hidden mechanisms
Authors: Mayor Jordan , Bahram Mohammad , Henkel Terry , Buegger Franz , Pritsch Karin , Tedersoo Leho 
Published: October 2014

AbstractEctomycorrhizal (EcM)‐mediated nitrogen (N) acquisition is one main strategy used by terrestrial plants to facilitate growth. Measurements of natural abundance nitrogen isotope ratios (denoted as δ15N relative to a standard) increasingly serve as integrative proxies for mycorrhiza‐mediated N acquisition due to biological fractionation processes that alter 15N:14N ratios. Current understanding of these processes is based on studies from high‐latitude ecosystems where plant productivity is largely limited by N availability. Much less is known about the cause and utility of ecosystem δ15N patterns in the tropics. Using structural equation models, model selection and isotope mass balance we assessed relationships among co‐occurring soil, mycorrhizal plants and fungal N pools measured from 40 high‐ and 9 low‐latitude ecosystems. At low latitudes 15N‐enrichment caused ecosystem components to significantly deviate from those in higher latitudes. Collectively, δ15N patterns suggested reduced N‐dependency and unique sources of EcM 15N‐enrichment under conditions of high N availability typical of the tropics. Understanding the role of mycorrhizae in global N cycles will require reevaluation of high‐latitude perspectives on fractionation sources that structure ecosystem δ15N patterns, as well as better integration of EcM function with biogeochemical theories pertaining to climate‐nutrient cycling relationships.
Balance of Treg versus T‐effector cells during systemic treatment with adalimumab and topical treatment with calcipotriol–betamethasone dipropionate ointment
Authors: Keijsers Romy R. M. C. , Joosten Irma , Hendriks Anke G. M. , Koenen Hans J. P. M , van Erp Piet E. J , van de Kerkhof Peter C. M. 
Published: October 2014

AbstractDiminished suppressive capacity of regulatory T cells (Treg) has been demonstrated in blood and in lesional skin of psoriatic patients. Treatment with anti‐TNFα restored the number and function of circulating Treg in psoriasis. We aimed to study Treg in the skin of psoriatic patients undergoing topical treatment with calcipotriol–betamethasone dipropionate (CBD) ointment (n = 12) or systemic treatment with anti‐TNFα agent adalimumab (n = 10). Skin biopsies were collected from patients with chronic plaque psoriasis who responded to the above‐mentioned treatments with a SUM‐score improvement of at least 50% (at the end of treatment). Biopsies were processed for immunohistochemistry. As Treg function is associated with a numerical balance between Treg and effector T cells, Foxp3/CD4 ratios were calculated. It appeared that both treatments cause a significant decrease in the presence of Foxp3+ cells. However, in patients that were treated with CBD ointment, we observed lower Foxp3/CD4 ratios after 8 weeks of treatment compared to baseline (t = 0: 0.41 ± 0.08; t = 8: 0.22 ± 0.04, P = 0.033), whereas in patients who were treated with adalimumab we observed an increase of the Foxp3/CD4 ratios after 1.5 and 16 weeks of treatment compared to baseline (t = 0: 0.25 ± 0.04; t = 1.5: 0.32 ± 0.06; t = 16: 0.49 ± 0.10, P = 0.15). Based on Foxp3/CD4 ratios, we can conclude that adalimumab treated skin differs from CBD treated skin with regard to the anti‐inflammatory/inflammatory balance. We suggest that, in contrast to CBD ointment, adalimumab favours local Treg function in the skin.
Reflectance confocal microscopy: non‐invasive distinction between actinic keratosis and squamous cell carcinoma
Authors: Peppelman M. , Nguyen K.P. , Hoogedoorn L. , van Erp P.E.J. , Gerritsen M.‐J.P. 
Published: October 2014

AbstractBackgroundEarly recognition of squamous cell carcinoma (SCC) is difficult. Non‐invasive reflectance confocal microscopic (RCM) imaging of the skin is a promising diagnostic technique. Although several RCM features for SCC and AK have been described, it is not determined whether RCM has the ability to distinguish between SCC and actinic keratosis (AK).ObjectiveTo determine in vivo reflectance confocal microscopic features that are specific for making a distinction between AK and SCC.MethodsIn 24 patients, 30 lesions clinically suspicious for AK or SCC were selected for RCM imaging. Following the imaging procedure, a 3 mm skin biopsy was obtained for confirmation of the histopathological diagnosis. Two observers evaluated the RCM images according to a literature based list of RCM features. The obtained data were evaluated by an univariate and forward multivariate logistic regression analysis, kappa analysis and independent T‐test.ResultsThe univariate logistic regression showed statistically significant odds ratios for several RCM features, including architectural disarray in the stratum granulosum, architectural disarray in the spinous layer and nest‐like structures in the dermis. The forward multivariate logistic regression analysis showed that the combination of these features increased the ability to make the correct diagnosis AK and SCC non‐invasively. The interobserver agreement between a starting and an experienced RCM observer ranged from poor to no agreement.ConclusionThis study revealed specific RCM features that can distinguish between AK and SCC, stimulating further prospective, large cohort research in this field. This will result in correct, efficient and adequate diagnosis and treatment of clinically difficult to distinguish AK and SCC lesions.
Effects of tree architecture on pollen dispersal and mating patterns inAbies pinsapoBoiss. (Pinaceae)
Authors: Sánchez‐Robles Jose M. , García‐Castaño Juan L. , Balao Francisco , Terrab Anass , Navarro‐Sampedro Laura , Tremetsberger Karin , Talavera Salvador 
Published: October 2014

AbstractPlant architecture is crucial to pollination and mating in wind‐pollinated species. We investigated the effect of crown architecture on pollen dispersal, mating system and offspring quality, combining phenotypic and genotypic analyses in a low‐density population of the endangered speciesAbies pinsapo. A total of 598 embryos from three relative crown height levels (bottom, middle and top) in five mother plants were genotyped using eleven nuclear microsatellite markers (nSSRs). Paternity analysis and mating system models were used to infer mating and pollen dispersal parameters. In addition, seeds were weighed (N = 16 110) and germinated (N = 736), and seedling vigour was measured to assess inbreeding depression. Overall,A. pinsaposhows a fat‐tailed dispersal kernel, with an average pollen dispersal distance of 113–227 m, an immigration rate of 0.84–26.92%, and a number of effective pollen donors (Nep) ranging between 3.5 and 11.9. We found an effect of tree height and relative crown height levels on mating parameters. A higher proportion of seeds with embryo (about 50%) and a higher rate of self‐fertilization (about 60%) were found at the bottom level in comparison with the top level. Seed weight and seedling vigour are positively related. Nevertheless, no differences were found in seed weight or in seedling‐related variables such as weight and length of aerial and subterranean parts among the different relative crown height levels, suggesting that seeds from the more strongly inbred bottom level are not affected by inbreeding depression. Our results point to vertical isotropy for outcross‐pollen and they suggest that self‐pollen may ensure fertilization when outcross‐pollen is not available in low‐density population.
Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing
Authors: Ghai Rohit , Mizuno Carolina Megumi , Picazo Antonio , Camacho Antonio , Rodriguez‐Valera Francisco 
Published: October 2014

AbstractFreshwater ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even the most abundant components, freshwater Actinobacteria, remain largely unknown. Here, applying deep metagenomic sequencing to the microbial community of a freshwater reservoir, we were able to circumvent this traditional bottleneck and reconstruct de novo seven distinct streamlined actinobacterial genomes. These genomes represent three new groups of photoheterotrophic, planktonic Actinobacteria. We describe for the first time genomes of two novel clades, acMicro (Micrococcineae, related to Luna2,) and acAMD (Actinomycetales, related to acTH1). Besides, an aggregate of contigs belonged to a new branch of the Acidimicrobiales. All are estimated to have small genomes (approximately 1.2 Mb), and their GC content varied from 40 to 61%. One of the Micrococcineae genomes encodes a proteorhodopsin, a rhodopsin type reported for the first time in Actinobacteria. The remarkable potential capacity of some of these genomes to transform recalcitrant plant detrital material, particularly lignin‐derived compounds, suggests close linkages between the terrestrial and aquatic realms. Moreover, abundances of Actinobacteria correlate inversely to those of Cyanobacteria that are responsible for prolonged and frequently irretrievable damage to freshwater ecosystems. This suggests that they might serve as sentinels of impending ecological catastrophes.
PstS‐1, the 38‐kDaMycobacterium tuberculosisGlycoprotein, is an Adhesin, Which Binds the Macrophage Mannose Receptor and Promotes Phagocytosis
Authors: Esparza M. , Palomares B. , García T. , Espinosa P. , Zenteno E. , Mancilla R. 
Published: October 2014

AbstractMycobacterium tuberculosis, the primary causative agent of tuberculosis, infects macrophages and transforms the hostile intracellular environment into a permissive niche.M. tuberculosisinfects macrophages using a variety of microbial ligand/cell receptor systems. In this study, binding assays with biotin‐labelled mycobacterial cell wall proteins revealed five Concanavalin A‐reactive proteins that bind macrophages. Among these proteins, we identified PstS‐1, a 38‐kDaM. tuberculosismannosylated glycolipoprotein, and characterized it as an adhesin. Inhibition assays with mannan and immunoprecipitation demonstrated that PstS‐1 binds the mannose receptor. We purified PstS‐1 to 95.9% purity using ion exchange chromatography. The presence of mannose in purified PstS‐1 was demonstrated by Concanavalin A interaction, which was abolished in the presence of sodiumm‐periodate and α‐D‐mannosidase. Gas chromatography revealed that purified PstS‐1 contained 1% of carbohydrates by weight, which was mainly mannose. Finally, we used fluorescent microbeads coated with purified PstS‐1 in phagocytosis assays and discovered that microbead uptake was inhibited by the pre‐incubation of cells with GlcNAc, mannan and α‐methyl mannoside. The interaction of PstS‐1 coated beads with the mannose receptor was confirmed by confocal colocalization studies that showed high Pearson and Manders's colocalization coefficients. Our findings contribute to a better understanding of the strategiesM. tuberculosisuses to infect host cells, the critical first step in the pathogenesis of tuberculosis.
Whole blood treated with riboflavin and ultraviolet light: quality assessment of all blood components produced by the buffy coat method
Authors: Schubert Peter , Culibrk Brankica , Karwal Simrath , Serrano Katherine , Levin Elena , Bu Daniel , Bhakta Varsha , Sheffield William P. , Goodrich Raymond P. , Devine Dana V. 
Published: October 2014

BackgroundPathogen inactivation (PI) technologies are currently licensed for use with platelet (PLT) and plasma components. Treatment of whole blood (WB) would be of benefit to the blood banking community by saving time and costs compared to individual component treatment. However, no paired, pool‐and‐split study directly assessing the impact ofWB PIon the subsequently produced components has yet been reported.Study Design and MethodsIn a “pool‐and‐split” study,WBeither was treated with riboflavin and ultraviolet (UV) light or was kept untreated as control. The buffy coat (BC) method produced plasma,PLT, and red blood cell (RBC) components.PLTunits arising from the untreatedWBstudy arm were treated with riboflavin andUVlight on day of production and compared toPLTconcentrates (PCs) produced from the treatedWBunits. A panel of common in vitro variables for the three types of components was used to monitor quality throughout their respective storage periods.ResultsPCsderived from theWB PItreatment were of significantly better quality than treatedPLTcomponents for most variables.RBCsproduced from theWBtreatment deteriorated earlier during storage than untreated units. Plasma components showed a 3% to 44% loss in activity for several clotting factors.ConclusionTreatment ofWBwith riboflavin andUVbefore production of components by theBCmethod shows a negative impact on all three blood components.PLTunits produced fromPI‐treatedWBexhibited less damage compared toPLTcomponent treatment.
Prostate CT segmentation method based on nonrigid registration in ultrasound‐guided CT‐based HDR prostate brachytherapy
Authors: Yang Xiaofeng , Rossi Peter , Ogunleye Tomi , Marcus David M. , Jani Ashesh B. , Mao Hui , Curran Walter J. , Liu Tian 
Published: October 2014

Purpose:The technological advances in real‐time ultrasound image guidance for high‐dose‐rate (HDR) prostate brachytherapy have placed this treatment modality at the forefront of innovation in cancer radiotherapy. Prostate HDR treatment often involves placing the HDR catheters (needles) into the prostate gland under the transrectal ultrasound (TRUS) guidance, then generating a radiation treatment plan based on CT prostate images, and subsequently delivering high dose of radiation through these catheters. The main challenge for this HDR procedure is to accurately segment the prostate volume in the CT images for the radiation treatment planning. In this study, the authors propose a novel approach that integrates the prostate volume from 3D TRUS images into the treatment planning CT images to provide an accurate prostate delineation for prostate HDR treatment.Methods:The authors’ approach requires acquisition of 3D TRUS prostate images in the operating room right after the HDR catheters are inserted, which takes 1–3 min. These TRUS images are used to create prostate contours. The HDR catheters are reconstructed from the intraoperative TRUS and postoperative CT images, and subsequently used as landmarks for the TRUS–CT image fusion. After TRUS–CT fusion, the TRUS‐based prostate volume is deformed to the CT images for treatment planning. This method was first validated with a prostate‐phantom study. In addition, a pilot study of ten patients undergoing HDR prostate brachytherapy was conducted to test its clinical feasibility. The accuracy of their approach was assessed through the locations of three implanted fiducial (gold) markers, as well as T2‐weighted MR prostate images of patients.Results:For the phantom study, the target registration error (TRE) of gold‐markers was 0.41 ± 0.11 mm. For the ten patients, the TRE of gold markers was 1.18 ± 0.26 mm; the prostate volume difference between the authors’ approach and the MRI‐based volume was 7.28% ± 0.86%, and the prostate volume Dice overlap coefficient was 91.89% ± 1.19%.Conclusions:The authors have developed a novel approach to improve prostate contour utilizing intraoperative TRUS‐based prostate volume in the CT‐based prostate HDR treatment planning, demonstrated its clinical feasibility, and validated its accuracy with MRIs. The proposed segmentation method would improve prostate delineations, enable accurate dose planning and treatment delivery, and potentially enhance the treatment outcome of prostate HDR brachytherapy.
Super‐resolution reconstruction for 4D computed tomography of the lung via the projections onto convex sets approach
Authors: Zhang Yu , Wu Xiuxiu , Yang Wei , Feng Qianjin , Chen Wufan 
Published: October 2014

Purpose:The use of 4D computed tomography (4D‐CT) of the lung is important in lung cancer radiotherapy for tumor localization and treatment planning. Sometimes, dense sampling is not acquired along the superior–inferior direction. This disadvantage results in an interslice thickness that is much greater than in‐plane voxel resolutions. Isotropic resolution is necessary for multiplanar display, but the commonly used interpolation operation blurs images. This paper presents a super‐resolution (SR) reconstruction method to enhance 4D‐CT resolution.Methods:The authors assume that the low‐resolution images of different phases at the same position can be regarded as input “frames” to reconstruct high‐resolution images. The SR technique is used to recover high‐resolution images. Specifically, the Demons deformable registration algorithm is used to estimate the motion field between different “frames.” Then, the projection onto convex sets approach is implemented to reconstruct high‐resolution lung images.Results:The performance of the SR algorithm is evaluated using both simulated and real datasets. Their method can generate clearer lung images and enhance image structure compared with cubic spline interpolation and back projection (BP) method. Quantitative analysis shows that the proposed algorithm decreases the root mean square error by 40.8% relative to cubic spline interpolation and 10.2% versus BP.Conclusions:A new algorithm has been developed to improve the resolution of 4D‐CT. The algorithm outperforms the cubic spline interpolation and BP approaches by producing images with markedly improved structural clarity and greatly reduced artifacts.