bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of soil organic carbon in arable soil in Belgium and Luxembourg with the LUCAS topsoil database
Authors: Castaldi F. , Chabrillat S. , Chartin C. , Genot V. , Jones A. R. , van Wesemael B. 
Published: April 2018

SummaryQuantification of the soil organic carbon (SOC) content over large areas is mandatory to obtain accurate soil characterization and classification, which can improve site‐specific management at local or regional scales. In this context, soil spectroscopy is a well‐consolidated and widespread method to estimate soil variables, and in particular SOC content, at a low cost for routine analysis. The increasing number of large soil spectral libraries collected worldwide reflects the importance of spectroscopy in soil science. These large libraries contain soil samples derived from a large number of pedological regions and thus from different parent materials and soil types. In the light of the huge variation in the spectral responses to SOC content and composition, a rigorous process is necessary to subdivide large spectral libraries to avoid calibration with global models that fail to predict local variation in SOC content. Here, we propose to classify the European LUCAS topsoil database with a cluster analysis based on a large number of soil properties. The soil samples collected from arable land in the LUCAS database were chosen to apply a standardized multivariate calibration approach, valid for large areas, to calibrate local models without the need for further field and laboratory work. Cluster analysis detected seven soil classes and the samples belonging to each class were used to calibrate specific partial least squares regression (PLSR) models to estimate SOC content in three spectral libraries collected in Belgium and Luxembourg. Soil organic carbon was predicted with good accuracy, both within each library (root mean square error (RMSE), 1.2–5.1 g kg−1; ratio of performance to prediction (RPD), 1.41–2.24) and for the samples of the three libraries together (RMSE, 3.7 g kg−1; RPD, 2.54). The proposed approach could enable SOC to be estimated for arable soils in Europe with only the spectra of soil samples and without the need for laboratory analyses.HighlightsWe investigated the potential of the LUCAS database to estimate SOC in spectral libraries.
We proposed a routine approach to estimate SOC with less laboratory work.
The classification of the LUCAS topsoil dataset improved estimation accuracy of SOC
SOC content can be predicted from soil spectra with models calibrated on the LUCAS database.
Biochemical and biomechanical characterisation of equine cervical facet joint cartilage
Authors: O'Leary S. A. , White J. L. , Hu J. C. , Athanasiou K. A. 
Published: April 2018

SummaryBackgroundThe equine cervical facet joint is a site of significant pathology. Located bilaterally on the dorsal spine, these diarthrodial joints work in conjunction with the intervertebral disc to facilitate appropriate spinal motion. Despite the high prevalence of pathology in this joint, the facet joint is understudied and thus lacking in viable treatment options.ObjectiveThe goal of this study was to characterise equine facet joint cartilage and provide a comprehensive database describing the morphological, histological, biochemical and biomechanical properties of this tissue.Study designDescriptive cadaver studies.MethodsA total of 132 facet joint surfaces were harvested from the cervical spines of six skeletally mature horses (11 surfaces per animal) for compiling biomechanical and biochemical properties of hyaline cartilage of the equine cervical facet joints. Gross morphometric measurements and histological staining were performed on facet joint cartilage. Creep indentation and uniaxial strain‐to‐failure testing were used to determine the biomechanical compressive and tensile properties. Biochemical assays included quantification of total collagen, sulfated glycosaminoglycan andDNAcontent.ResultsThe facet joint surfaces were ovoid in shape with a flat articular surface. Histological analyses highlighted structures akin to articular cartilage of other synovial joints. In general, biomechanical and biochemical properties did not differ significantly between the inferior and superior joint surfaces as well as among spinal levels. Interestingly, compressive and tensile properties of cervical facet articular cartilage were lower than those of articular cartilage from other previously characterised equine joints. Removal of the superficial zone reduced the tissue's tensile strength, suggesting that this zone is important for the tensile integrity of the tissue.Main limitationsFacet surfaces were sampled at a single, central location and do not capture the potential topographic variation in cartilage properties.ConclusionsThis is the first study to report the properties of equine cervical facet joint cartilage and may serve as the foundation for the development of future tissue‐engineered replacements as well as other treatment strategies.
The FGF‐23/klotho axis and its relationship with phosphorus, calcium, vitamin D, PTH, aldosterone, severity of disease, and outcome in hospitalised foals
Authors: Kamr A. M. , Dembek K. A. , Hildreth B. E. , Morresey P. R. , Rathgeber R. A. , Burns T. A. , Zaghawa A. A. , Toribio R. E. 
Published: April 2018

SummaryBackgroundFibroblast growth factor‐23 (FGF‐23) and klotho are key regulators of vitamin D and parathyroid hormone (PTH) synthesis as well as phosphorus and calcium homeostasis; however, information on the FGF‐23/klotho axis in healthy and hospitalised foals is lacking.ObjectivesThe aims of this study were to measure serum FGF‐23 and klotho concentrations and determine their association with serum phosphorus, total calcium (TCa), vitamin D metabolite [25(OH)D, 1,25(OH)2D], PTH, and aldosterone concentrations, disease severity, and mortality in hospitalised foals.Study designProspective, multicentre, cross‐sectional study.MethodsA total of 91 foals ≤72 h old were classified as hospitalised (n = 81; 58 septic; 23 sick non‐septic [SNS]) and healthy (n = 10). Blood samples were collected on admission. Hormone concentrations were determined by immunoassays.ResultsSerum FGF‐23, PTH, phosphorus, and aldosterone concentrations were higher while klotho, 25(OH)D, 1,25(OH)2D, and TCa concentrations were lower in septic and SNS compared to healthy foals (P<0.05). In hospitalised and septic foals, increased FGF‐23 and aldosterone concentrations were associated with high phosphorus and PTH but not with TCa and vitamin D metabolite concentrations. Hospitalised foals with the highest FGF‐23 and lowest klotho concentrations were more likely to die (odds ratio (OR): 3.3; 95% confidence interval (CI): 1.1–10.3 and OR: 3.1; CI: 1.1–8.0, respectively).Main limitationsBlood gas, ionised calcium, blood culture information not being available for many foals, and use of the sepsis score to classify hospitalised foals.ConclusionsImbalances in the FGF‐23/klotho axis may contribute to mineral dyshomeostasis and disease progression in critically ill foals. Elevated FGF‐23 and reduced klotho, together with high phosphorus and PTH concentrations suggests FGF‐23 resistance. FGF‐23 and klotho are good markers of disease severity and likelihood of mortality in hospitalised foals. Aldosterone may influence phosphorus and PTH dynamics in hospitalised foals. Routine measurement of phosphorus concentrations in sick foals is recommended.
Descriptive vs mechanistic scientific approach to study wound healing and its inhibition: Is there a value of translational research involving human subjects?
Authors: Pastar Irena , Wong Lulu L. , Egger Andjela N. , Tomic‐Canic Marjana 
Published: April 2018

AbstractThe clinical field of wound healing is challenged by numerous hurdles. Not only are wound‐healing disorders complex and multifactorial, but the corresponding patient population is diverse, often elderly and burdened by multiple comorbidities such as diabetes and cardiovascular disease. The care of such patients requires a dedicated, multidisciplinary team of physicians, surgeons, nurses and scientists. In spite of the critical clinical need, it has been over 15 years since a treatment received approval for efficacy by the FDA in the United States. Among the reasons contributing to this lack of effective new treatment modalities is poor understanding of mechanisms that inhibit healing in patients. Additionally, preclinical models do not fully reflect the disease complexity of the human condition, which brings us to a paradox: if we are to use a “mechanistic” approach that favours animal models, we can dissect specific mechanisms using advanced genetic, molecular and cellular technologies, with the caveat that it may not be directly applicable to patients. Traditionally, scientific review panels, for either grant funding or manuscript publication purposes, favour such “mechanistic” approaches whereby human tissue analyses, deemed “descriptive” science, are characterized as a “fishing expedition” and are considered “fatally flawed.” However, more emerging evidence supports the notion that the use of human samples provides significant new knowledge regarding the molecular and cellular mechanisms that control wound healing and contribute to inhibition of the process in patients. Here, we discuss the advances, benefits and challenges of translational research in wound healing focusing on human subject research.
Structural and molecular dynamics studies of a C1‐oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition
Authors: Liu Bing , Kognole Abhishek A. , Wu Miao , Westereng Bjørge , Crowley Michael F. , Kim Seonah , Dimarogona Maria , Payne Christina M. , Sandgren Mats 
Published: April 2018

Lytic polysaccharide monooxygenases (LPMOs) are a group of recently discovered enzymes that play important roles in the decomposition of recalcitrant polysaccharides. Here, we report the biochemical, structural, and computational characterization of an LPMO from the white‐rot fungus Heterobasidion irregulare (HiLPMO9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of HiLPMO9B was determined at 2.1 Å resolution using X‐ray crystallography. Unlike the majority of the currently available C1‐specific LPMO structures, the HiLPMO9B structure contains an extended L2 loop, connecting β‐strands β2 and β3 of the β‐sandwich structure. Molecular dynamics (MD) simulations suggest roles for both aromatic and acidic residues in the substrate binding of HiLPMO9B, with the main contribution from the residues located on the extended region of the L2 loop (Tyr20) and the LC loop (Asp205, Tyr207, and Glu210). Asp205 and Glu210 were found to be involved in the hydrogen bonding with the hydroxyl group of the C6 carbon of glucose moieties directly or via a water molecule. Two different binding orientations were observed over the course of the MD simulations. In each orientation, the active‐site copper of this LPMO preferentially skewed toward the pyranose C1 of the glycosidic linkage over the targeted glycosidic bond. This study provides additional insight into cellulose binding by C1‐specific LPMOs, giving a molecular‐level picture of active site substrate interactions.DatabaseThe atomic coordinates and structure factors for HiLPMO9B have been deposited in the Protein Data Bank with accession code 5NNS.
Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)
Authors: Argentina Jane E. , Angermeier Paul L. , Hallerman Eric M. , Welsh Stuart A. 
Published: April 2018

Abstract

Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.

As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.

Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or loss of genetic diversity, they reduce population connectivity and may impact long‐term population persistence.

The broad spatial scale of this study demonstrated the large spatial extent of some variegate darter populations and indicated that dispersal is more extensive than expected given the movement patterns typically observed for small‐bodied, benthic fish. Dam impacts depended on underlying population size and stability, with larger populations more resilient to genetic drift and allelic richness loss than smaller populations.

Other darters that inhabit large river habitats may show similar patterns in landscape‐scale studies, and large river barriers may impact populations of small‐bodied fish more than previously expected. Estimation of dispersal rates and behaviours is critical to conservation of imperilled riverine species such as darters.
A global climate niche for giant trees
Authors: Scheffer Marten , Xu Chi , Hantson Stijn , Holmgren Milena , Los Sietse O. , van Nes Egbert H. 
Published: April 2018

AbstractRainforests are among the most charismatic as well as the most endangered ecosystems of the world. However, although the effects of climate change on tropical forests resilience is a focus of intense research, the conditions for their equally impressive temperate counterparts remain poorly understood, and it remains unclear whether tropical and temperate rainforests have fundamental similarities or not. Here we use new global data from high precision laser altimetry equipment on satellites to reveal for the first time that across climate zones ‘giant forests’ are a distinct and universal phenomenon, reflected in a separate mode of canopy height (~40 m) worldwide. Occurrence of these giant forests (cutoff height > 25 m) is negatively correlated with variability in rainfall and temperature. We also demonstrate that their distribution is sharply limited to situations with a mean annual precipitation above a threshold of 1,500 mm that is surprisingly universal across tropical and temperate climates. The total area with such precipitation levels is projected to increase by ~4 million km2 globally. Our results thus imply that strategic management could in principle facilitate the expansion of giant forests, securing critically endangered biodiversity as well as carbon storage in selected regions.
High‐grade PanIN presenting with localised stricture of the main pancreatic duct: A clinicopathological and molecular study of 10 cases suggests a clue for the early detection of pancreatic cancer
Authors: Yokode Masataka , Akita Masayuki , Fujikura Kohei , Kim Mi‐Ju , Morinaga Yukiko , Yoshikawa Seiichi , Terada Takuro , Matsukiyo Hiroshi , Tajiri Takuma , Abe‐Suzuki Shiho , Itoh Tomoo , Hong Seung‐Mo , Zen Yoh 
Published: April 2018

AimsThis study aimed to identify the pathological features of high‐grade PanIN that presents with imaging‐detectable abnormalities.Methods and resultsTen cases of isolated, main‐duct, high‐grade PanIN as the primary clinical presentation were identified. All patients presented with stenosis of the main pancreatic duct, with two being associated with extensive upstream duct dilatation (>5 mm in diameter). Pancreatic juice cytology suggested adenocarcinoma in all seven cases examined. In resected specimens, high‐grade PanIN was present chiefly in the main pancreatic duct, with longitudinal extension ranging between 3 and 40 mm in length (median = 18 mm). In four cases, in which hypoechoic or hypovascular masses were observed on imaging, radiopathology correlations suggested that they represented parenchymal atrophy and subsequent fibrosis around affected ducts, but not invasive malignancy. On immunohistochemistry, the loss of p16 expression was found in five (50%), p53 overexpression in two (20%) and loss of SMAD4 expression in none (0%). KRAS mutations were detected in nine cases, with two dominant clones being found in three by ultrasensitive droplet digital polymerase chain reaction, suggesting the genetic heterogeneity of dysplastic cells composing individual lesions. Mutant GNAS was also observed in one case.ConclusionsIsolated high‐grade PanIN may present with pancreatic duct stenosis. Therefore, intensive investigations including pancreatic juice cytology will be required for patients with unexplained pancreatic duct stenosis. The abnormal expression of p53 and SMAD4 is infrequent, while GNAS may be mutated in premalignant lesions mainly affecting the main pancreatic duct, similar to KRAS.
DICER1 hot‐spot mutations in ovarian gynandroblastoma
Authors: Wang Yemin , Karnezis Anthony N , Magrill Jamie , Tessier‐Cloutier Basile , Lum Amy , Senz Janine , Gilks C Blake , McCluggage W Glenn , Huntsman David G , Kommoss Friedrich 
Published: April 2018

AimsGynandroblastoma is a rare ovarian sex cord‐stromal tumour characterised by the presence of both male (Sertoli and/or Leydig cells) and female (granulosa cells) components. We investigated the mutational status of DICER1, FOXL2 and AKT1 genes at hot‐spot regions that are known to be the key driving events in the development of Sertoli–Leydig cell tumour (SLCT), adult granulosa cell tumour (aGCT) and juvenile granulosa cell tumour (jGCT), respectively, to gain insights into the molecular pathogenesis of gynandroblastoma.Methods and resultsSixteen cases of gynandroblastoma were studied. All contained SLCT or Sertoli cell tumour components. aGCT and jGCT components were identified in seven and 10 cases, respectively, with one presenting both components. Heterozygous hot‐spot mutations in the RNase IIIb domain of DICER1 were discovered in three cases, including one case with heterologous mucinous elements, all of which were composed of moderately or poorly differentiated SLCT and jGCT components, and harboured the mutations in both histological components. None of the 16 cases displayed mutations at the p.C134W (c.402C→G) of FOXL2 or within the pleckstrin‐homology domain of AKT1. All cases showed FOXL2 immunostaining in both male and female components.ConclusionDICER1 hot‐spot mutation is the key‐driving event in a subset of gynandroblastomas containing components of SLCT and jGCT. Gynandroblastomas composed of SLCT and jGCT may represent morphological variants of SLCT. The molecular basis of gynandroblastoma containing a component of aGCT is different from pure aGCT.
Geochemical and geochronological studies of the Muong Hum alkaline granitic pluton from the Phan Si Pan Zone, northwest Vietnam: Implications for petrogenesis and tectonic setting
Authors: Minh Pham , Hieu Pham T. , Hoang Nguyen K. 
Published: April 2018

AbstractThe Phan Si Pan zone in northwest Vietnam is an important tectonic unit for understanding the geological evolution of the southeast Asian Block. Numerous late Permian A‐type granites outcrop in this zone. In this study, new geochemical and geochronological data derived from the Muong Hum alkaline granitic pluton in the Phan Si Pan zone were investigated for its petrogenesis and tectonic setting. Zircon U–Pb analyses of three samples yielded 206Pb/238U ages of (251.1 ±3.5) Ma, (251.2 ±3.8) Ma, and (253.9 ±1.5) Ma, respectively, coinciding with the ages of the acid member of magma from Emeishan large igneous province, southwest China. The Muong Hum granite has 10 000 × Ga/Al and A/CNK values of 4.70–4.93 and 0.87–0.90, respectively, as well as negative Eu anomalies. It shows significant depletion of Ba, Sr, Ti, and P, similar to features of A‐type granite. Zircons have positive εHf(t) values (+1.9 to +8.6) and Hf model ages (TDM1) of 595–846 Ma, originating a mantle source. Compared with the Panzhihua A‐type granite of the southwest China domain and other A‐type plutons of the Phan Si Pan zone, including Ye Yen Sun, Phu Sa Phin, Nam Xe, Tam Duong Phan Si Pan, and Taihe, the geochemical characteristics and zircon Hf isotopic compositions of the Muong Hum granite demonstrate an affinity of mantle magma. It is believed that the Phan Si Pan zone is an important part of Emeishan large igneous province. It was reworked by the Cenozoic Aillaoshan‐Red River shear fault to its present location.
Late Cretaceous uplift history of the Cretaceous volcanic arc in Southwest Japan: Provenance analysis of the Yuasa–Aridagawa basin based on U–Pb zircon ages
Authors: Shunori Ryosuke , Takeuchi Makoto , Yamamoto Koshi 
Published: April 2018

AbstractThe Ryoke Metamorphic complex has undergone low‐P/T metamorphism and was intruded by granitic magmas around 100 Ma. Subsequently, the belt was uplifted and exposed by the time deposition of the Izumi Group began. The tectonic history of uplift, such as the timing and processes, are poorly known despite being important for understanding the spatiotemporal evolution of the Ryoke Metamorphic Belt. U–Pb zircon ages from sedimentary rocks in the forearc and backarc basins are useful for constraining uplift and magmatism in the provenance. U–Pb dating of detrital zircons from 12 samples (four sandstones and eight granitic clasts) in the Yuasa–Aridagawa basin, a Cretaceous forearc basin in the Chichibu Belt of Southwest Japan, gave mostly ages of 60–110 Ma. Granitic clasts contained in conglomerate suggest that granitic intrusions predate the formation of Coniacian and Maastrichtian conglomerate. Emplacement ages of granitic bodies originated from granitic clasts in Coniacian conglomerate are (110.2 ±1.3) Ma, (106.1 ±1.8) Ma, (101.8+5.8–3.8) Ma, and (95.3 ±1.4) Ma; for granitic clasts in Maastrichtian conglomerate, (89.6 ±1.8) Ma, (87.3+2.4–1.8) Ma, (85.7 ±1.2) Ma, and (82.7 ±1.2) Ma. The results suggest that detrital zircons in the sandstones were mainly derived from volcanic eruptions contemporaneous with depositional age, and plutonic rocks of the Ryoke Metamorphic Belt. Zircon ages of the granitic clast samples also indicate that uplift in the provenance began after Albian and occurred at least during the Coniacian to Maastrichtian. Our results, together with the difference of provenance between backarc and forearc basins suggest that the southern marginal zone of the Ryoke Metamorphic Belt was uplifted and supplied a large amount of clastic materials to the forearc basins during the Late Cretaceous.