bluuebunny/crossref_metadata_2025_split huggingface dataset:
The nitrification inhibitor dicyandiamide increases mineralization–immobilization turnover in slurry-amended grassland soil
Authors: ERNFORS M. , BRENNAN F. P. , RICHARDS K. G. , MCGEOUGH K. L. , GRIFFITHS B. S. , LAUGHLIN R. J. , WATSON C. J. , PHILIPPOT L. , GRANT J. , MINET E. P. , MOYNIHAN E. , MÜLLER C. 
Published: January 2014

SUMMARYNitrification inhibitors are used in agriculture for the purpose of decreasing nitrogen (N) losses, by limiting the microbially mediated oxidation of ammonium (NH4+) to nitrate (NO3−). Successful inhibition of nitrification has been shown in numerous studies, but the extent to which inhibitors affect other N transformations in soil is largely unknown. In the present study, cattle slurry was applied to microcosms of three different grassland soils, with or without the nitrification inhibitor dicyandiamide (DCD). A solution containing NH4+and NO3−, labelled with15N either on the NH4+or the NO3−part, was mixed with the slurry before application. Gross N transformation rates were estimated using a15N tracing model. In all three soils, DCD significantly inhibited gross autotrophic nitrification, by 79–90%. Gross mineralization of recalcitrant organic N increased significantly with DCD addition in two soils, whereas gross heterotrophic nitrification from the same pool decreased with DCD addition in two soils. Fungal to bacterial ratios were not significantly affected by DCD addition. Total gross mineralization and immobilization increased significantly across the three soils when DCD was used, which suggests that DCD can cause non-target effects on soil N mineralization–immobilization turnover.
Early effects of slash-and-burn cultivation on soil physicochemical properties of small-scale farms in the Tapajós region, Brazilian Amazon
Authors: BÉLIVEAU A. , DAVIDSON R. , LUCOTTE M. , DO CANTO LOPES L. OTÁVIO , PAQUET S. , VASSEUR C. 
Published: January 2014

SUMMARYIncreasing human occupation of the Brazilian Amazon has led to the intensification of deforestation over the last 50 years. The present study is aimed at analysing the impacts of the first year of slash-and-burn cultivation on soil physicochemical properties. Sampling was done in 26 small-scale farms of the Tapajós River basin. In August 2004, soil samples were collected from primary forest plots planned for slash-and-burn cultivation. In September 2005, 1 year after the initial burning and the beginning of cultivation, the same sites were re-sampled. The results indicated that soil fertility after burning was relatively moderate, as the increase of base cations was not particularly marked. Moreover, although an increase of some nutrients (such as exchangeable phosphorus) was observed at soil surface, total carbon and nitrogen (N) pools did not change significantly. Nutrient leaching was also detected through the accumulation of both forms of available nitrogen (NO3 and NH4) as well as potassium in subsoil horizons. In addition, signs of erosion were seen, as a significant increase surface density occurred, coupled with up to 25% fine particle loss at the surface. The present study draws attention to the early impacts of slash-and-burn agriculture on soil properties within a year of cultivation. Furthermore, its regional dimension highlights undisturbed soils natural variability as well as differentiated responses to deforestation according to soil texture.
Ulceration of the nasal dorsum: a rare cause?
Authors: Salim F , Joshi A , Hopkins C 
Published: January 2014

AbstractIntroduction:Non-healing ulcers can be caused by a number of conditions, including vascular disease, diabetes, malignancy and some infections. Drug-related ulcers are rare, and a high index of clinical suspicion is required for diagnosis, in parallel with exclusion of more sinister underlying causes.Case report:We present a patient with a complex medical background, who had a 10-week history of a non-healing ulcer on his nasal bridge. Inflammatory, autoimmune and malignant causes for the ulcer were excluded by histopathology.Conclusion:Nicorandil was deemed to be the most likely cause for the patient's ulcer. Nicorandil is an anti-anginal medication known to cause oral ulceration and skin lesions in the perianal and peristomal regions and around surgical wounds. However, there are no previously reported cases of facial ulcers. The ulcer required surgical debridement and healed completely within six months, following discontinuation of nicorandil. This case highlights the importance of having a high index of clinical suspicion regarding non-healing ulcers, and of considering drugs as an aetiological factor, especially in patients with a complex medical background who are taking numerous medications.
Molecular characterization of an endo-type chitosanase from the fish pathogenRenibacteriumsp. QD1
Authors: Xing Peichuan , Liu Dan , Yu Wen-Gong , Lu Xinzhi 
Published: January 2014

Renibacteriumsp. QD1, a bacteria strain capable of hydrolysing chitosan, was isolated from the homogenate of small crabs. An extracellular chitosanase, Csn-A, was purified from the QD1 fermentation broth. The enzyme was purified to homogeneity, with a yield of eight-fold, 67% recovery and a specific activity of 1575 U/mg proteins. The molecular weight of Csn-A was estimated to be 26.1 kDa by SDS-PAGE. Unlike other chitosanases, the purified Csn-A displayed maximal activity at a pH range of 5.3–6.5, and it was stable in a broad pH range of 5.0–10.0. The optimum temperature for chitosanlytic activity was 55°C. The enzyme activity was strongly stimulated by Mn2+but inhibited by Fe3+, Cu2+, Al3+, Zn2+and SDS. TLC analysis demonstrated that Csn-A hydrolysed N-deacetylated polymeric glucosamines into chito-biose and -triose in an endo-type manner. The amino acid seuquence of Csn-A showed close identity with an uncharacterized chitosanase of strain ATCC33209.
Trophic structure of the bathyal benthos at an area with evidence of methane seep activity off southern Chile (~45°S)
Authors: Zapata-Hernández Germán , Sellanes Javier , Thurber Andrew R. , Levin Lisa A. 
Published: January 2014

Through application of carbon (C) and nitrogen (N) stable isotope analyses, we investigated the benthic trophic structure of the upper-slope off southern Chile (~45°S) including a recent methane seep area discovered as part of this study. The observed fauna comprised 53 invertebrates and seven fish taxa, including remains of chemosymbiotic fauna (e.g.chemosymbiotic bivalves and siboglinid polychaetes), which are typical of methane seep environments. While in close-proximity to a seep, the heterotrophic fauna had a nutrition derived predominantly from photosynthetic sources (δ13C > –21‰). The absence of chemosynthesis-based nutrition in the consumers was likely a result of using an Agassiz trawl to sample the benthos, a method that is likely to collect a mix of fauna including individuals from adjacent non-seep bathyal environments. While four trophic levels were estimated for invertebrates, the fish assemblage was positioned within the third trophic level of the food web. Differences in corrected standard ellipse area (SEAC), which is a proxy of the isotopic niche width, yielded differences for the demersal fishNotophycis marginata(SEAC = 5.1‰) andCoelorinchus fasciatus(SEAC = 1.1‰), suggesting distinct trophic behaviours. No ontogenic changes were detected inC. fasciatusregarding food sources and trophic position. The present study contributes the first basic trophic data for the bathyal area off southern Chile, including the identification of a new methane seep area, among the furthest south ever discovered. Such information provides the basis for the proper sustainable management of the benthic environments present along the vast Chilean continental margin.
Fires and Recoveries Witnessed by the Dutch in Edo and Nagasaki: The Great Fire of Meireki in 1657 and the Great Fire of Kanbun in 1663
Authors: Fuyuko Matsukata 
Published: January 2014

Kaji to kenka ha Edo no hana (Fires and fights are the highlights of Edo) is a famous phrase to illustrate that fires plagued the city of Edo (now known as Tokyo) during the Tokugawa period (1603–1868). Fires seem to have been considered not only terrible disasters, but also a symbol of a busy, active metropolis. The same is true in other early-modern Japanese cities, particularly those facing the Pacific Ocean or the East China Sea, such as Nagasaki.The geographical setting of these two cities, among others, is one of four factors that contributed to many of the fires in Japan. The winter monsoon from the north or northwest caused by the Siberia anticyclone is steady and powerful from December to February, and the first summer monsoon from the south, called haru ichiban (the first wind of spring) in March or April is also quite strong. During these months, the combination of dry air, strong winds, and individual fires set to keep homes warm create fire hazard conditions. Even today, the season when most fires occur is winter.As Edo lies in the center of the Kanto plain, there is nothing to prevent strong winds. Between 1601 and 1867, there were 1,798 fires in Edo, including 49 large fires, whereas Osaka experienced only six large fires and Kyoto nine. Although it is open to the sea on the south-west, Nagasaki is surrounded by mountains, so the winds blow from the north-east to the south-west. There were smaller fires in Nagasaki, which is a smaller city than Edo, but the number of incidents was still high. Nagasaki suffered from 232 fires during the period 1633–1868, including those that occurred in suburban areas.
Spectroscopic characterization of laser-ablated manganese sulfate plasma
Authors: Salik M. , Hanif M. , Wang J. , Zhang X. Q. 
Published: January 2014

AbstractIn this work, we present the spectroscopic studies of the plasma generated at the surface of manganese sulfate by the fundamental (1064 nm) and second harmonic (532 nm) of a Q-switched Nd:YAG laser. The 4s4p 4F7/2→ 4s 2H9/2 at 438.80 nm, 4p 2I11/2 → 4s22I11/2 at 440.80 nm, 4p 4G11/2 → 4s 2H9/2 at 464.27 nm, 4p 4F5/2→ 4s 4D7/2 at 467.16, 4p 4F5/2 → 4s24G 7/2 at 515.08 nm, and 4p 4F7/2 → 4s2 4G 9/2 at 519.65 nm transitions have been used to estimate the electron temperature through the Boltzmann plot method. The number density has been estimated from the Stark broadened profiles of the spectral line 348.30 nm. The spatial behavior of the electron temperature and number density has been examined at different ambient air pressures and with laser irradiance. The temperature and number density are found to be in the range from 9842 K to 9371 K and 1.58 × 1017 to 3.26 × 1016 cm−3 for the 1064 nm laser, from 9668 to 9297 K and 2.27 × 1017 to 5.79 × 1016 cm−3 for the 532 nm laser.
Command-based voice teleoperation of a mobile robot via a human-robot interface
Authors: Poncela Alberto , Gallardo-Estrella Leticia 
Published: January 2014

SUMMARYVerbal communication is the most natural way of human–robot interaction. Such an interaction is usually achieved by means of a human-robot interface (HRI). In this paper, a HRI is presented to teleoperate a robotic platform via the user's voice. Hence, a speech recognition system is necessary. In this work, a user-dependent acoustic model for Spanish speakers has been developed to teleoperate a robot with a set of commands. Experimental results have been successful, both in terms of a high recognition rate and the navigation of the robot under the control of the user's voice.
Bridging climate science to adaptation action in data sparse Tanzania
Authors: GIRVETZ EVAN H. , GRAY ELIZABETH , TEAR TIMOTHY H. , BROWN MATTHEW A. 
Published: January 2014

SUMMARYIn the face of an already changing climate, conservation practitioners and local communities face the major challenge of how to plan for a future climate. In data-sparse areas of the world, where action is often most needed, the daunting scope of the problem can lead to inaction. This paper shows that climate adaptation planning can be accomplished successfully with publicly and globally available data by linking science and stakeholders through a facilitated process. Working with local stakeholders in the western Tanzanian Greater Mahale and Greater Gombe Ecosystems, future climate projections produced using Climate Wizard and analyses of literature provided an understanding of the climate vulnerabilities of local ecosystems and human livelihoods. Facilitated workshops enabled local stakeholders to use this information to develop conceptual models and hypotheses of change for these systems, and to identify possible modifications to conservation plans. Here, climate change planning required the modification of most current conservation strategies, developing some new strategies and abandoning others. The paper indicates that climate adaptation planning is achievable even in data-sparse rural and developing areas, but requires appropriate scientific analyses, engaged stakeholders and a facilitated process.
Dehydration and crystallization of amorphous calcium carbonate in solution and in air
Authors: Ihli Johannes , Wong Wai Ching , Noel Elizabeth H. , Kim Yi-Yeoun , Kulak Alexander N. , Christenson Hugo K. , Duer Melinda J. , Meldrum Fiona C. 
Published: January 2014

AbstractThe mechanisms by which amorphous intermediates transform into crystalline materials are poorly understood. Currently, attracting enormous interest is the crystallization of amorphous calcium carbonate, a key intermediary in synthetic, biological and environmental systems. Here we attempt to unify many contrasting and apparently contradictory studies by investigating this process in detail. We show that amorphous calcium carbonate can dehydrate before crystallizing, both in solution and in air, while thermal analyses and solid-state nuclear magnetic resonance measurements reveal that its water is present in distinct environments. Loss of the final water fraction—comprising less than 15% of the total—then triggers crystallization. The high activation energy of this step suggests that it occurs by partial dissolution/recrystallization, mediated by surface water, and the majority of the particle then crystallizes by a solid-state transformation. Such mechanisms are likely to be widespread in solid-state reactions and their characterization will facilitate greater control over these processes.
A novel computational biostatistics approach implies impaired dephosphorylation of growth factor receptors as associated with severity of autism
Authors: Wittkowski K M , Sonakya V , Bigio B , Tonn M K , Shic F , Ascano M , Nasca C , Gold-Von Simson G 
Published: January 2014

AbstractThe prevalence of autism spectrum disorders (ASDs) has increased 20-fold over the past 50 years to >1% of US children. Although twin studies attest to a high degree of heritability, the genetic risk factors are still poorly understood. We analyzed data from two independent populations usingu-statistics for genetically structured wide-locus data and added data from unrelated controls to explore epistasis. To account for systematic, but disease-unrelated differences in (non-randomized) genome-wide association studies (GWAS), a correlation between P-values and minor allele frequency with low granularity data and for conducting multiple tests in overlapping genetic regions, we present a novel study-specific criterion for ‘genome-wide significance’. From recent results in a comorbid disease, childhood absence epilepsy, we had hypothesized that axonal guidance and calcium signaling are involved in autism as well. Enrichment of the results in both studies with related genes confirms this hypothesis. Additional ASD-specific variations identified in this study suggest protracted growth factor signaling as causing more severe forms of ASD. Another cluster of related genes suggests chloride and potassium ion channels as additional ASD-specific drug targets. The involvement of growth factors suggests the time of accelerated neuronal growth and pruning at 9–24 months of age as the period during which treatment with ion channel modulators would be most effective in preventing progression to more severe forms of autism. By extension, the same computational biostatistics approach could yield profound insights into the etiology of many common diseases from the genetic data collected over the last decade.
Phosphatidylserine and FVa regulate FXa structure
Authors: Srivasatava Kinshuk Raj , Majumder Rinku , Kane William H. , Quinn-Allen Mary Ann , Lentz Barry R. 
Published: January 2014

Human coagulation FXa (Factor Xa) plays a key role in blood coagulation by activating prothrombin to thrombin on ‘stimulated’ platelet membranes in the presence of its cofactor FVa (Factor Va). PS (phosphatidylserine) exposure on activated platelet membranes promotes prothrombin activation by FXa by allosterically regulating FXa. To identify the structural basis of this allosteric regulation, we used FRET to monitor changes in FXa length in response to (i) soluble short-chain PS [C6PS (dicaproylphosphatidylserine)], (ii) PS membranes, and (iii) FVa in the presence of C6PS and membranes. We incorporated a FRET pair with donor (fluorescein) at the active site and acceptor (Alexa Fluor® 555) at the FXa N-terminus near the membrane. The results demonstrated that FXa structure changes upon binding of C6PS to two sites: a regulatory site at the N-terminus [identified previously as involving the Gla (γ-carboxyglutamic acid) and EGFN (N-terminus of epidermal growth factor) domains] and a presumptive protein-recognition site in the catalytic domain. Binding of C6PS to the regulatory site increased the interprobe distance by ~3 Å (1 Å=0.1 nm), whereas saturation of both sites increased the distance by a further ~6.4 Å. FXa binding to a membrane produced a smaller increase in length (~1.4 Å), indicating that FXa has a somewhat different structure on a membrane from when bound to C6PS in solution. However, when both FVa2 (a FVa glycoform) and either C6PS- or PS-containing membranes were bound to FXa, the overall change in length was comparable (~5.6–5.8 Å), indicating that C6PS- and PS-containing membranes in conjunction with FVa2 have comparable regulatory effects on FXa. We conclude that the similar functional regulation of FXa by C6PS or membranes in conjunction with FVa2 correlates with similar structural regulation. The results demonstrate the usefulness of FRET in analysing structure–function relationships in FXa and in the FXa·FVa2 complex.
Phosphorylation by Akt within the ST loop of AMPK-α1 down-regulates its activation in tumour cells
Authors: Hawley Simon A. , Ross Fiona A. , Gowans Graeme J. , Tibarewal Priyanka , Leslie Nicholas R. , Hardie D. Grahame 
Published: January 2014

The insulin/IGF-1 (insulin-like growth factor 1)-activated protein kinase Akt (also known as protein kinase B) phosphorylates Ser487 in the ‘ST loop’ (serine/threonine-rich loop) within the C-terminal domain of AMPK-α1 (AMP-activated protein kinase-α1), leading to inhibition of phosphorylation by upstream kinases at the activating site, Thr172. Surprisingly, the equivalent site on AMPK-α2, Ser491, is not an Akt target and is modified instead by autophosphorylation. Stimulation of HEK (human embryonic kidney)-293 cells with IGF-1 caused reduced subsequent Thr172 phosphorylation and activation of AMPK-α1 in response to the activator A769662 and the Ca2+ ionophore A23187, effects we show to be dependent on Akt activation and Ser487 phosphorylation. Consistent with this, in three PTEN (phosphatase and tensin homologue deleted on chromosome 10)-null tumour cell lines (in which the lipid phosphatase PTEN that normally restrains the Akt pathway is absent and Akt is thus hyperactivated), AMPK was resistant to activation by A769662. However, full AMPK activation could be restored by pharmacological inhibition of Akt, or by re-expression of active PTEN. We also show that inhibition of Thr172 phosphorylation is due to interaction of the phosphorylated ST loop with basic side chains within the αC-helix of the kinase domain. Our findings reveal that a previously unrecognized effect of hyperactivation of Akt in tumour cells is to restrain activation of the LKB1 (liver kinase B1)–AMPK pathway, which would otherwise inhibit cell growth and proliferation.
A neuromorphic network for generic multivariate data classification
Authors: Schmuker Michael , Pfeil Thomas , Nawrot Martin Paul 
Published: January 2014

Significance
One primary goal of computational neuroscience is to uncover fundamental principles of computations that are performed by the brain. In our work, we took direct inspiration from biology for a technical application of brain-like processing. We make use of neuromorphic hardware—electronic versions of neurons and synapses on a microchip—to implement a neural network inspired by the sensory processing architecture of the nervous system of insects. We demonstrate that this neuromorphic network achieves classification of generic multidimensional data—a widespread problem with many technical applications. Our work provides a proof of concept for using analog electronic microcircuits mimicking neurons to perform real-world computing tasks, and it describes the benefits and challenges of the neuromorphic approach.
JAK2V
617
F-positive endothelial cells contribute to clotting abnormalities in myeloproliferative neoplasms
Authors: Etheridge S. Leah , Roh Michelle E. , Cosgrove Megan E. , Sangkhae Veena , Fox Norma E. , Chen Junmei , López José A. , Kaushansky Kenneth , Hitchcock Ian S. 
Published: January 2014

Significance
The myeloproliferative neoplasms (MPNs) are a group of hematological malignancies characterized by increased numbers of myeloid blood cells, such as platelets, erythrocytes, and neutrophils. The main causes of illness and death in patients with MPNs are arterial and venous clotting and also, conversely, bleeding complications. However, the causes of these conditions are poorly understood. In this paper, we use a mouse model of MPNs to determine the cell types responsible for abnormal clotting in MPNs. We demonstrate that endothelial cells, the cell type that lines all blood vessels, have a significant role to play in MPN bleeding complications, potentially identifying a new cellular target for MPN therapies.
Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy
Authors: Cerase Andrea , Smeets Daniel , Tang Y. Amy , Gdula Michal , Kraus Felix , Spivakov Mikhail , Moindrot Benoit , Leleu Marion , Tattermusch Anna , Demmerle Justin , Nesterova Tatyana B. , Green Catherine , Otte Arie P. , Schermelleh Lothar , Brockdorff Neil 
Published: January 2014

Significance
Polycomb repressor proteins are recruited to the inactive X chromosome in mammals, and this has been attributed to a biochemical interaction between the non–protein-coding RNA X-inactive specific transcript (Xist), which initiates the X inactivation process, and core polycomb subunits. We have studied this using a combination of genome mapping analysis and 3D structured illumination microscopy (3D-SIM) that allows 3D imaging with eightfold volumetric resolution improvement compared with previous state-of-the-art confocal microscopy. Our findings reveal that Xist-mediated recruitment of polycomb repressors does not correlate well with gene silencing and, moreover, that using 3D-SIM, polycomb proteins and Xist RNA show significant spatial separation. These observations challenge prevailing models and prompt a reappraisal of the role of Xist RNA in polycomb recruitment.