bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increasing picocyanobacteria success in shelf waters contributes to long‐term food web degradation
Authors: Schmidt Katrin , Birchill Antony J. , Atkinson Angus , Brewin Robert J. W. , Clark James R. , Hickman Anna E. , Johns David G. , Lohan Maeve C. , Milne Angela , Pardo Silvia , Polimene Luca , Smyth Tim J. , Tarran Glen A. , Widdicombe Claire E. , Woodward E. Malcolm S. , Ussher Simon J. 
Published: June 2020

AbstractContinental margins are disproportionally important for global primary production, fisheries and CO2 uptake. However, across the Northeast Atlantic shelves, there has been an ongoing summertime decline of key biota—large diatoms, dinoflagellates and copepods—that traditionally fuel higher tropic levels such as fish, sea birds and marine mammals. Here, we combine multiple time series with in situ process studies to link these declines to summer nutrient stress and increasing proportions of picophytoplankton that can comprise up to 90% of the combined pico‐ and nanophytoplankton biomass in coastal areas. Among the pico‐fraction, it is the cyanobacterium Synechococcus that flourishes when iron and nitrogen resupply to surface waters are diminished. Our field data show how traits beyond small size give Synechococcus a competitive edge over pico‐ and nanoeukaryotes. Key is their ability to grow at low irradiances near the nutricline, which is aided by their superior light‐harvesting system and high affinity to iron. However, minute size and lack of essential biomolecules (e.g. omega‐3 polyunsaturated fatty acids and sterols) render Synechococcus poor primary producers to sustain shelf sea food webs efficiently. The combination of earlier spring blooms and lower summer food quantity and quality creates an increasing period of suboptimal feeding conditions for zooplankton at a time of year when their metabolic demand is highest. We suggest that this nutrition‐related mismatch has contributed to the widespread, ~50% decline in summer copepod abundance we observe over the last 60 years. With Synechococcus clades being prominent from the tropics to the Arctic and their abundances increasing worldwide, our study informs projections of future food web dynamics in coastal and shelf areas where droughts and stratification lead to increasing nutrient starvation of surface waters.
Permafrost nitrogen status and its determinants on the Tibetan Plateau
Authors: Mao Chao , Kou Dan , Chen Leiyi , Qin Shuqi , Zhang Dianye , Peng Yunfeng , Yang Yuanhe 
Published: June 2020

AbstractIt had been suggested that permafrost thaw could promote frozen nitrogen (N) release and modify microbial N transformation rates, which might alter soil N availability and then regulate ecosystem functions. However, the current understanding of this issue is confined to limited observations in the Arctic permafrost region, without any systematic measurements in other permafrost regions. Based on a large‐scale field investigation along a 1,000 km transect and a laboratory incubation experiment with a 15N pool dilution approach, this study provides the comprehensive evaluation of the permafrost N status, including the available N content and related N transformation rates, across the Tibetan alpine permafrost region. In contrast to the prevailing view, our results showed that the Tibetan alpine permafrost had lower available N content and net N mineralization rate than the active layer. Moreover, the permafrost had lower gross rates of N mineralization, microbial immobilization and nitrification than the active layer. Our results also revealed that the dominant drivers of the gross N mineralization and microbial immobilization rates differed between the permafrost and the active layer, with these rates being determined by microbial properties in the permafrost while regulated by soil moisture in the active layer. In contrast, soil gross nitrification rate was consistently modulated by the soil

content in both the permafrost and the active layer. Overall, patterns and drivers of permafrost N pools and transformation rates observed in this study offer new insights into the potential N release upon permafrost thaw and provide important clues for Earth system models to better predict permafrost biogeochemical cycles under a warming climate.
Elevated temperature increases the accumulation of microbial necromass nitrogen in soil via increasing microbial turnover
Authors: Wang Xu , Wang Chao , Cotrufo M. Francesca , Sun Lifei , Jiang Ping , Liu Ziping , Bai Edith 
Published: June 2020

AbstractMicrobial‐derived nitrogen (N) is now recognized as an important source of soil organic N. However, the mechanisms that govern the production of microbial necromass N, its turnover, and stabilization in soil remain poorly understood. To assess the effects of elevated temperature on bacterial and fungal necromass N production, turnover, and stabilization, we incubated 15N‐labeled bacterial and fungal necromass under optimum moisture conditions at 10°C, 15°C, and 25°C. We developed a new 15N tracing model to calculate the production and mineralization rates of necromass N. Our results showed that bacterial and fungal necromass N had similar mineralization rates, despite their contrasting chemistry. Most bacterial and fungal necromass 15N was recovered in the mineral‐associated organic matter fraction through microbial anabolism, suggesting that mineral association plays an important role in stabilizing necromass N in soil, independently of necromass chemistry. Elevated temperature significantly increased the accumulation of necromass N in soil, due to the relatively higher microbial turnover and production of necromass N with increasing temperature than the increases in microbial necromass N mineralization. In conclusion, we found elevated temperature may increase the contribution of microbial necromass N to mineral‐stabilized soil organic N.
Application of Four Measurement Techniques to Understand Natural Source Zone Depletion Processes at an LNAPL Site
Authors: Kulkarni Poonam R. , Newell Charles J. , King David C. , Molofsky Lisa J. , Garg Sanjay 
Published: June 2020

AbstractThere are several key data gaps in our understanding of Natural Source Zone Depletion (NSZD) processes at sites impacted by light nonaqueous phase liquid (LNAPL), and quantifying NSZD rates can be challenging due to the inherent differences in measurement methods. In this study, four different NSZD measurement methods (oxygen influx measured by the Gradient Method, long‐term carbon dioxide efflux measured with Carbon Traps, instantaneous carbon dioxide efflux measured with Dynamic Closed Chambers (DCC LI‐COR), and the long‐term heat flux from biodegradation measured by Thermal NSZD monitoring), as well as LNAPL composition and dissolved gas sampling, were applied at a site in Southern California. These techniques were used to evaluate key questions such as: (1) how do different NSZD rate measurement methods compare, and what causes variability in NSZD results?; (2) to what extent NSZD processes are occurring in LNAPL within the saturated zone?; and (3) how is NSZD related to LNAPL composition change over time? Carbon Traps and Thermal NSZD monitoring measurement methods provided the most consistent NSZD data at this geologically heterogeneous site, with two location average NSZD rates of 540 and 480 gal/acre/year, respectively. Overall, comparisons of NSZD rates between methods were challenging due to different measurement timeframes, significant temporal and spatial heterogeneity, and operational challenges with two of the NSZD methods. Finally, samples of subsurface LNAPL were collected for analysis in 2007 and 2016; results indicated that diesel‐range constituents were already very degraded and anaerobic degradation of gasoline‐range constituents was ongoing. A LNAPL depletion model (Douglas et al. 1996) applied to the measured LNAPL composition change appeared to greatly overestimate the amount of LNAPL depletion compared to the measured NSZD rate, but did provide an independent semiqualitative line of evidence that LNAPL was being depleted by active NSZD processes at the site.
Epstein–Barr virus‐positive inflammatory follicular dendritic cell sarcoma presenting as a solitary colonic mass: two rare cases and a literature review
Authors: Ke Xiaokang , He Huihua , Zhang Qingping , Yuan Jingping , Ao Qilin 
Published: June 2020

AimsFollicular dendritic cell (FDC) sarcoma is a rare neoplasm originating from follicular dendritic cells in germinal centres. It is classified as conventional and Epstein–Barr virus (EBV)‐positive inflammatory FDC sarcoma according to the 2019 World Health Organization classification of digestive system tumours; the latter is rarer. So in view of the rarity and difficulty in diagnosis, the aim of the manuscript is to share our experience of diagnosing EBV‐positive inflammatory FDC sarcoma.Methods and resultsHere, we describe the clinicopathological features, gross description, histomorphology, immunophenotype, EBV‐encoded mRNA (EBER) in‐situ hybridisation, gene rearrangement and clinical follow‐up of two patients with EBV‐positive inflammatory FDC sarcoma in the colon, and review the relevant literature. The tumours were found in two males, aged 53 and 48 years, respectively, with a tumour diameter between 10 and 45 mm. Both cases occurred in the colon and presented as pedunculated colonic masses. Microscopically, scanty atypical ovoid to spindle neoplastic cells were mixed in a background of florid lymphoplasmacytic infiltration. The nuclei of these atypical cells showed vesicular chromatin and small, distinct nucleoli. Immunohistochemistry demonstrated that the atypical stromal cells were positive for CD21, CD23, CD35, and D2‐40. EBER in‐situ hybridisation also gave positive results in two cases. There was a mean follow‐up of 9 months (range, 7–11 months).ConclusionEBV‐positive inflammatory FDC sarcoma is an extremely rare tumour with a distinct morphology and phenotype. Therefore, it is very important to recognise it particularly for correct diagnosis and prevention of misdiagnosis and mistreatment.
Synovial chondrosarcoma: a single‐institution experience with molecular investigations and review of the literature
Authors: Gambarotti Marco , Pacheco Marina , Ruengwanichayakun Poosit , Silvino Vega Jiménez Brayan , Benini Stefania , Bianchi Giuseppe , Sbaraglia Marta , Vanel Daniel , Carretta Elisa , Bertoni Franco , Franchi Alessandro , Dei Tos Angelo P , Righi Alberto 
Published: June 2020

AimsTo evaluate the available diagnostic histological criteria for synovial chondrosarcoma and to screen for the presence of IDH1/IDH2 mutations in a series of cases of this malignant cartilaginous neoplasm.Methods and resultsTen cases of synovial chondrosarcoma diagnosed at our institute were reviewed. At presentation, all tumours occurred in adults (median age, 62 years). The most common location was the knee joint (five cases), and the size at diagnosis ranged from 30 mm to 170 mm. Eight patients had secondary synovial chondrosarcomas associated with pre‐existing/recurrent or concomitant synovial chondromatosis. Five patients had local recurrences and three had lung metastases. All patients with intralesional excisions developed local recurrences, whereas those who underwent wide resections did not. At last follow‐up (mean, 91 months), available for nine patients, seven patients were alive and disease‐free, one patient had died of disease, and one was alive with paravertebral metastases. Frequent histological features observed included loss of clustering of chondrocytes (nine cases), the presence of variable amounts of myxoid matrix (eight cases), peripheral hypercellularity (eight cases), tumour necrosis (six cases), and spindling of chondrocytes (four cases). Of the seven cases for which it was possible to evaluate bone permeation, six showed infiltration of bone marrow. All seven cases screened for mutations of exon 4 of IDH1 and IDH2 were found to be wild‐type.ConclusionsHistological criteria in correlation with clinical and radiological features allow the recognition of synovial chondrosarcoma. IDH1/IDH2 mutations were not present in synovial chondrosarcoma. Adequate surgical margins are important for disease control.
Promising effect of intravenous immunoglobulin therapy for epidermolysis bullosa pruriginosa
Authors: Ertop Pelin , Vural Secil , Gökpınar Ili Ezgi , Durmaz Ceren D. , Heper Aylin O. , McGrath John A. , Ilgın Ruhi H. , Boyvat Ayse 
Published: June 2020

AbstractBackgroundEpidermolysis bullosa pruriginosa (EBP) is rare a clinical variant of dystrophic epidermolysis bullosa characterized by trauma‐induced bullae formation, milia and nail dystrophy accompanied by severe pruritus. Treatment pruritus of EBP focuses on immunosuppressive treatment with limited efficacy. Treatment strategies are not well‐established.AimTo provide the genetic characterization of a multi‐generational EBP family and discuss the efficacy of intravenous immunoglobulin treatment in EBP.Materials & methodsThe clinical characteristics of patients diagnosed with EBP in three consecutive generations were determined. The mutation is analyzed in the index patient's genomic DNA by Sanger sequencing, and this mutation was confirmed in other affected members of the family. Index case with severe phenotype was treated with intravenous immunoglobulin (IVIG).ResultsA heterozygous single nucleotide transition, c.6127G>A, in exon 73 of COL7A1 was identified in all affected members. Physical examination of patients revealed lichenoid papules on extensor surfaces of extremities, excoriations, milia formation and nail dystrophy. Majority of patients had elevated serum IgE levels (%86 (6/7)) without a medical history for atopy. Female patients had generalized involvement and severe phenotype. The skin lesions of the index case were refractory to high dose systemic steroids and cyclosporine treatment. Lesions improved significantly with intravenous immunoglobulin therapy.ConclusionIn severe cases, unresponsive to other therapies, IVIG may be a preferable therapeutic approach to modulate the inflammatory response in patients with EBP.
Clinical and histological characteristics, and management of melanoma in French Guiana, 2007–2018
Authors: Broly Marine , Drak Alsibai Kinan , Cenciu Beatrice , Guevara Hemerson , Fayette Jerome , Neidhardt Eve‐Marie , Demar Magalie , Couppie Pierre , Blaizot Romain 
Published: June 2020

AbstractThere are few studies available on melanoma in Afro‐Caribbean and Amerindian populations of South America. French Guiana deserves a study due to its specific health system and diversity of phototypes. The objectives of this study were to evaluate the incidence, histological and clinical characteristics of melanoma in French Guiana. A retrospective study was conducted from October 2007 to January 2018 on all primary melanomas observed at the Cayenne Hospital Centre. Thirty‐nine patients were included. The incidence rate (1.61/106 inhabitants/year) was low compared with mainland France. Median age was 58, and gender ratio 1 : 16. Clear phototype (I/II) patients were the most frequent (38.5%), but a significant amount of melanoma also occurred in darker skin. Median Breslow was higher in dark phototypes than in fair‐skinned patients. Superficial spreading melanoma (SSM) was the most common histological type (33.3%), particularly in patients with clear phototype (61.5%). Acral lentiginous melanoma was found only in darker‐skinned patients (29.1%). The trunk was involved in 66.6% in the clearest group whereas foot was the most common location in the darkest group (60% in V/VI phototypes). Surgery was the most frequently used treatment (79.5%). At the end of the study period, 53.8% had been lost to follow‐up. In conclusion, the incidence of melanoma in French Guiana is lower than in mainland France but remains a public health concern, as dark‐skinned populations often present with advanced diseases. Awareness and prevention in these communities must be improved.
Landscape of variable domain of heavy‐chain‐only antibody repertoire from alpaca
Authors: Tu Zhui , Huang Xiaoqiang , Fu Jinheng , Hu Na , Zheng Wei , Li Yanping , Zhang Yang 
Published: June 2020

SummaryHeavy‐chain‐only antibodies (HCAbs), which are devoid of light chains, have been found naturally occurring in various species including camelids and cartilaginous fish. Because of their high thermostability, refoldability and capacity for cell permeation, the variable regions of the heavy chain of HCAbs (VHHs) have been widely used in diagnosis, bio‐imaging, food safety and therapeutics. Most immunogenetic and functional studies of HCAbs are based on case studies or a limited number of low‐throughput sequencing data. A complete picture derived from more abundant high‐throughput sequencing (HTS) data can help us gain deeper insights. We cloned and sequenced the full‐length coding region of VHHs in Alpaca (Vicugna pacos) via HTS in this study. A new pipeline was developed to conduct an in‐depth analysis of the HCAb repertoires. Various critical features, including the length distribution of complementarity‐determining region 3 (CDR3), V(D)J usage, VJ pairing, germline‐specific mutation rate and germline‐specific scoring profiles (GSSPs), were systematically characterized. The quantitative data show that V(D)J usage and VHH recombination are highly biased. Interestingly, we found that the average CDR3 length of classical VHHs is longer than that of non‐classical ones, whereas the mutation rates are similar in both kinds of VHHs. Finally, GSSPs were built to quantitatively describe and compare sequences that originate from each VJ pair. Overall, this study presents a comprehensive landscape of the HCAb repertoire, which can provide useful guidance for the modeling of somatic hypermutation and the design of novel functional VHHs or VHH repertoires via evolutionary profiles.
Crack initiation, propagation, and arrest in sintering powder aggregates
Authors: Carazzone Joseph R. , Martin Christophe L. , Cordero Zachary C. 
Published: June 2020

AbstractCracking during sintering is a common problem in powder processing and is usually caused by constraint that prevents the sintering material from shrinking in one or more directions. Different factors influence sintering‐induced cracking, including temperature schedule, packing density, and specimen geometry. Here we use the discrete element method to directly observe the stress distribution and sinter‐cracking behavior in edge notched panels sintered under a uniaxial restraint. This geometry allows an easy comparison with traditional fracture mechanics parameters, facilitating analysis of sinter‐cracking behavior. We find that cracking caused by self‐stress during sintering resembles the growth of creep cracks in fully dense materials. By deriving the constrained densification rate from the appropriate constitutive equations, we discover that linear shrinkage transverse to the loading axis is accelerated by a contribution from the effective Poisson's ratio of a sintering solid. Simulation of different notch geometries and initial relative densities reveals conditions that favor densification and minimize crack growth, alluding to design methods for avoiding cracking in actual sintering processes. We combine the far‐field stress and crack length to compute the net section stress, finding that it characterizes the stress profile between the notches and correlates with the sinter‐crack growth rate, demonstrating its potential to quantitatively describe sinter‐cracking.
Optical properties of Er3+ and Yb3+/Er3+‐doped NaF‐Na2SO4‐Al(PO3)3 fluoro‐sulfo‐phosphate glasses
Authors: Ji Yao , Xiao Yongbao , Huang Shujing , Wang Weichao 
Published: June 2020

AbstractFluoro‐sulfo‐phosphate (FPS) glass is of current interest as potential material for laser application due to its good glass‐forming ability, thermal, and chemical stability as well as the complicated local environment for incorporated species. Herein, the physical and luminescent properties of Er3+ and Yb3+/Er3+‐doped FPS glasses vs S/F ratio are investigated comprehensively. The low melting temperature (750°C) leads to fewer ingredients evaporation and easier operation. The sulfate addition depolymerizes the structure of FPS glasses, leading to either monotonic or nonmonotonic variations of physical properties, while no deterioration in thermal and limited one in chemical stability is caused. The addition of sulfate also modifies the local structure around optical active species and thus, leading to higher emission cross section (1.52 × 10−20 cm2), effective linewidth (68.4 nm), figure of merit (5.61 × 10−23 s cm2), gain bandwidth (102.44 × 10−27 cm3), and energy‐transfer microparameters (51.87 × 10−39 cm6/s), implying high possibility to serve as 1.5 μm laser application.
Thermally grown oxide in water vapor on coated and uncoated SiC
Authors: Kowalski Benjamin , Harder Bryan 
Published: June 2020

AbstractCoupons of Hexoloy®, CVD SiC, and SiO2 were thermally cycled in a flowing steam atmosphere of 90%/10% H2O/O2 at 1426°C in order to simulate the water vapor partial pressure of a turbine environment. The paralinear model for oxidation and volatilization is examined and a condensed version is provided that allows for extraction of the oxidation (kp) and volatilization (kl) rates from only a few measured data points across a small time window. Due to high Si(OH)4 (g) volatility rates, SiO2 scale thickness approached nearly invariant paralinear limiting values (~3‐6 μm) for all conditions, including cycle frequency or material. However, a disparity still exists between weight changes measured and the thickness of the resulting oxide as well as the contribution from the material properties to the oxidation and volatilization rates. Comparisons are made for the oxidation and volatilization rates, specific weight changes, and oxide thicknesses for a number of cycle times for both uncoated and environmental barrier coated SiC.
Ca2+/Sr2+/Ba2+ dependent phase separation, nanocrystallization and photoluminescence in fluoroaluminosilicate glass
Authors: Xu Xiuxia , Zhao Junjie , Chen Xiaotong , Xu Qian , Wang Ting , Yu Siu Fung , Xu Xuhui , Qiao Xvsheng , Du Jincheng , Fan Xianping , Qiu Jianbei , Qian Guodong 
Published: June 2020

AbstractFluoride phase separation is the initial stage of nanocrystallization in oxyfluoride glasses, and it is a key step in achieving transparent glass‐ceramics with good luminescence. In this work, we combine molecular dynamics (MD) simulations and experimental studies to investigate the phase separation, nanocrystallization and photoluminescence in fluoroaluminosilicate glass and glass‐ceramics containing alkali earth fluoride (MF2). The results reveal different phase separation behaviors due to the field strength difference of M2+. The composition and size similarity between the fluoride‐rich regions in the MD simulated glass and the fluoride nanocrystals in the experimental prepared glass‐ceramics are observed, suggesting that the separated fluoride phase is the structural origin of the observed MF2 nanocrystals. Besides, in order to understand the M2+ dependent glass structural features, the crystallization temperatures, the luminescent properties of Eu3+ and Eu2+ doped glass‐ceramics, and the lasing performance of Er3+ doped glass‐ceramics are discussed. Based on these comprehensions, some strategies are proposed to help to efficiently design oxyfluoride glass with desired luminescence performance.