bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of carbon-to-sulfur (C/S) ratio and nitrate (N) dosage on Denitrifying Sulfur cycle-associated Enhanced Biological Phosphorus Removal (DS-EBPR)
Authors: Yu Mei , Lu Hui , Wu Di , Zhao Qing , Meng Fangang , Wang Yudan , Hao Xiaodi , Chen Guang-Hao 
Published: March 2016

AbstractIn this study, the Denitrifying Sulfur cycle-associated Enhanced Biological Phosphorous Removal (DS-EBPR) with 20 mg P/L/d of the volumetric P removal rate was successfully achieved in a Sequencing Batch Reactor (SBR). The effects of carbon-to-sulfur (C/S) mass ratio and nitrate (N) dosage were investigated through two batch tests to reveal the role of wastewater compositions in DS-EBPR performance. The optimal specific P release and uptake rates (0.4 and 2.4 mg P/g VSS/h, respectively) were achieved at C/S/P/N mass ratio of 150/200/20/20, and poly-S is supplied as a potential electron and energy storage. The nitrate dosage in a range of 10–50 mg N/L had no significant influence on P uptake rates (2.1 ~ 2.4 mg P/g VSS/h), but significantly affected the storage of inclusion poly-S, the poly-S oxidation rate was increased about 16% while dosing nitrate from 20 to 30 mg N/L. It implies that nitrate is denitrified in the P uptake phase, and excess nitrate is further consumed by poly-S. Moreover, the microbial analysis showed that the functional bacteria should mostly belong to denitrifying bacteria or Unclassified genera.
Hypoxia-induced sensitisation of TRPA1 in painful dysesthesia evoked by transient hindlimb ischemia/reperfusion in mice
Authors: So Kanako , Tei Yuna , Zhao Meng , Miyake Takahito , Hiyama Haruka , Shirakawa Hisashi , Imai Satoshi , Mori Yasuo , Nakagawa Takayuki , Matsubara Kazuo , Kaneko Shuji 
Published: March 2016

AbstractDysesthesia is an unpleasant abnormal sensation, which is often accompanied by peripheral neuropathy or vascular impairment. Here, we examined the roles of transient receptor potential ankyrin 1 (TRPA1) in dysesthesia-like behaviours elicited by transient hindlimb ischemia (15–60 min) by tightly compressing the hindlimb and reperfusion by releasing the ligature. The paw-withdrawal responses to tactile stimulation were reduced during ischemia and lasted for a while after reperfusion. Hindlimb ischemia/reperfusion elicited spontaneous licking of the ischemic hindpaw that peaked within 10 min. The licking was inhibited by reactive oxygen species (ROS) scavengers, a TRPA1 antagonist, or TRPA1 deficiency, but not by TRPV1 deficiency. In human TRPA1-expressing cells as well as cultured mouse dorsal root ganglion neurons, the H2O2-evoked TRPA1 response was significantly increased by pretreatment with hypoxia (80 mmHg) for 30 min. This hypoxia-induced TRPA1 sensitisation to H2O2 was inhibited by overexpressing a catalytically-inactive mutant of prolyl hydroxylase (PHD) 2 or in a TRPA1 proline mutant resistant to PHDs. Consistent with these results, a PHD inhibitor increased H2O2-evoked nocifensive behaviours through TRPA1 activation. Our results suggest that transient hindlimb ischemia/reperfusion-evoked spontaneous licking, i.e. painful dysesthesia, is caused by ROS-evoked activation of TRPA1 sensitised by hypoxia through inhibiting PHD-mediated hydroxylation of a proline residue in TRPA1.
Novel roles for class II Phosphoinositide 3-Kinase C2β in signalling pathways involved in prostate cancer cell invasion
Authors: Mavrommati Ioanna , Cisse Ouma , Falasca Marco , Maffucci Tania 
Published: March 2016

AbstractPhosphoinositide 3-kinases (PI3Ks) regulate several cellular functions such as proliferation, growth, survival and migration. The eight PI3K isoforms are grouped into three classes and the three enzymes belonging to the class II subfamily (PI3K-C2α, β and γ) are the least investigated amongst all PI3Ks. Interest on these isoforms has been recently fuelled by the identification of specific physiological roles for class II PI3Ks and by accumulating evidence indicating their involvement in human diseases. While it is now established that these isoforms can regulate distinct cellular functions compared to other PI3Ks, there is still a limited understanding of the signalling pathways that can be specifically regulated by class II PI3Ks. Here we show that PI3K-C2β regulates mitogen-activated protein kinase kinase (MEK1/2) and extracellular signal-regulated kinase (ERK1/2) activation in prostate cancer (PCa) cells. We further demonstrate that MEK/ERK and PI3K-C2β are required for PCa cell invasion but not proliferation. In addition we show that PI3K-C2β but not MEK/ERK regulates PCa cell migration as well as expression of the transcription factor Slug. These data identify novel signalling pathways specifically regulated by PI3K-C2β and they further identify this enzyme as a key regulator of PCa cell migration and invasion.
Cytokinin production by Pseudomonas fluorescens G20-18 determines biocontrol activity against Pseudomonas syringae in Arabidopsis
Authors: Großkinsky Dominik K. , Tafner Richard , Moreno María V. , Stenglein Sebastian A. , García de Salamone Inés E. , Nelson Louise M. , Novák Ondřej , Strnad Miroslav , van der Graaff Eric , Roitsch Thomas 
Published: March 2016

AbstractPlant beneficial microbes mediate biocontrol of diseases by interfering with pathogens or via strengthening the host. Although phytohormones, including cytokinins, are known to regulate plant development and physiology as well as plant immunity, their production by microorganisms has not been considered as a biocontrol mechanism. Here we identify the ability of Pseudomonas fluorescens G20-18 to efficiently control P. syringae infection in Arabidopsis, allowing maintenance of tissue integrity and ultimately biomass yield. Microbial cytokinin production was identified as a key determinant for this biocontrol effect on the hemibiotrophic bacterial pathogen. While cytokinin-deficient loss-of-function mutants of G20-18 exhibit impaired biocontrol, functional complementation with cytokinin biosynthetic genes restores cytokinin-mediated biocontrol, which is correlated with differential cytokinin levels in planta. Arabidopsis mutant analyses revealed the necessity of functional plant cytokinin perception and salicylic acid-dependent defence signalling for this biocontrol mechanism. These results demonstrate microbial cytokinin production as a novel microbe-based, hormone-mediated concept of biocontrol. This mechanism provides a basis to potentially develop novel, integrated plant protection strategies combining promotion of growth, a favourable physiological status and activation of fine-tuned direct defence and abiotic stress resilience.
Breaking the diffraction limit of light-sheet fluorescence microscopy by RESOLFT
Authors: Hoyer Patrick , de Medeiros Gustavo , Balázs Bálint , Norlin Nils , Besir Christina , Hanne Janina , Kräusslich Hans-Georg , Engelhardt Johann , Sahl Steffen J. , Hell Stefan W. , Hufnagel Lars 
Published: March 2016

Significance
Light-sheet fluorescence microscopy (LSFM) is an imaging modality in which a sample is illuminated from the side by a beam engineered into a wide and relatively thin “sheet.” This allows highly parallelized planewise scanning of volumes with inherent optical sectioning, offering a good balance between spatial and temporal resolution with reduced photostress. Unfortunately, the axial extent of the illuminated section is ultimately limited by diffraction. Here, we show that a RESOLFT [reversible saturable/switchable optical (fluorescence) transitions] strategy neutralizes the resolution-limiting role of diffraction in LSFM. While other LS strategies exist, which run into new hard axial limits of resolution, LS-RESOLFT is conceptually diffraction-unlimited and can be developed toward molecular-scale resolution.
Viral serine palmitoyltransferase induces metabolic switch in sphingolipid biosynthesis and is required for infection of a marine alga
Authors: Ziv Carmit , Malitsky Sergey , Othman Alaa , Ben-Dor Shifra , Wei Yu , Zheng Shuning , Aharoni Asaph , Hornemann Thorsten , Vardi Assaf 
Published: March 2016

SignificanceThis work investigates the metabolic basis of the interactions between the cosmopolitan bloom-forming algaEmiliania huxleyiand its specific large DNA virus. We demonstrate some of the basic metabolic principles used by the EhV virus to “engineer” its host sphingolipid metabolism, to produce a unique suite of virus-specific lipids. These sphingolipids were essential for the virus assembly and infectivity. These results present novel insight into the chemical “arm race” at sea that coevolved around a unique metabolic pathway. Furthermore, it may provide important evolutionary and biochemical insights into sphingolipid biosynthesis and its functional role in other host–pathogen interactions (e.g. HIV, hepatitis C virus, dengue virus).
Variation in the Effective Range of a Stereo-Video Lander in Relation to Near-Seafloor Water Clarity, Ambient Light and Fish Length
Authors: Hannah Robert W. , Blume Matthew T. O. 
Published: March 2016

Abstract
We studied how variation in seafloor water clarity, ambient light, and fish fork length influenced the maximum detection range of fish with a stereo-video lander on three temperate reefs of different depths (12–40, 44–91, and 144–149 m). Although the results are somewhat approximate and specific to the camera system, the methods we used can be applied to any stereo remote underwater visual survey system. In the 52 total lander deployments distributed between nearshore, mid-shelf and deep-shelf reefs in Oregon waters, seafloor light levels varied over 4 orders of magnitude, primarily as a function of depth. The seafloor scattering index was higher (low water clarity) and highly variable at the nearshore reef and lower (high water clarity) and less variable at the deeper reefs. In the 15 deployments with sufficient numbers of fish for detection range analysis, the mean maximum range of detection across species varied from 3.89 to 4.23 m at the deep-shelf reef, 3.32–5.55 m at the mid-shelf reef, and 1.57–3.42 m at the nearshore reef. Multiple regression analysis of the analyzed deployments showed a strong negative relationship between mean maximum detection range and the scattering index but no relationship with loge of seafloor ambient light. The lack of a light effect showed that the artificial lights were adequately illuminating the field of view in which fish were identifiable, potentially an important system test for sampling across a range of seafloor light levels. Analysis of detection range versus fish fork length for Blue Rockfish Sebastes mystinus and Deacon Rockfish S. diaconus from a single deployment showed a reduction in detection range for 10–20-cm fish of about 1.15 m relative to the detection range of 25–45-cm fish, or about 41%.
Received September 29, 2015; accepted December 14, 2015
EBglmnet: a comprehensive R package for sparse generalized linear regression models
Authors: Huang Anhui , Liu Dianting 
Published: March 2016

AbstractSummaryEBglmnet is an R package implementing empirical Bayesian method with both lasso (EBlasso) and elastic net (EBEN) priors for generalized linear models. In our previous studies, both EBlasso and EBEN outperformed other state-of-the-art methods such as lasso and elastic net in inferring sparse genotype and phenotype associations, in which the number of covariates is typically much larger than the sample size. While high density genetic markers can be easily obtained nowadays in genetics and population analysis thanks to the advancements in molecular high throughput technologies, EBglmnet will be a very useful tool for statistical modeling in this area.Availability and implementationEBglmnet package is freely available from the R archive CRAN (http://cran.r-project.org/).
Distribution of megafaunal species in the Southwestern Atlantic: key ecological areas and opportunities for marine conservation
Authors: González Carman V. , Mandiola A. , Alemany D. , Dassis M. , Seco Pon J. P. , Prosdocimi L. , Ponce de León A. , Mianzan H. , Acha E. M. , Rodríguez D. , Favero M. , Copello S. 
Published: March 2016

AbstractDuring the last centuries, populations of marine megafauna—such as seabirds, turtles, and mammals—were intensively exploited. At present, other threats such as bycatch and pollution affect these species, which play key ecological roles in marine ecosystems as apex consumers and/or nutrient transporters. This study analyses the distribution of six megafaunal species (Chelonia mydas, Caretta caretta, Dermochelys coriacea, Thalassarche melanophris, Otaria flavescens, and Arctocephalus australis) coexisting in the Southwestern Atlantic to discuss their protection in terms of current management strategies in the region. Through the prediction of the species potential distributions and their relation to bathymetry, sea temperature and oceanographic fronts, key ecological areas are defined from a multi-taxa perspective. Information on the distribution of 70 individuals (18 sea turtles, 19 albatrosses, and 33 otariids) was obtained through satellite tracking conducted during 2007–2013 and analysed using a Geographic Information System and maximum entropy models. During the autumn–winter period, megafaunal species were distributed over the continental shelves of Argentina, Uruguay, and Brazil, mainly over the Argentine Exclusive Economic Zone and the Argentina-Uruguay Common Fishing Zone. Despite some differences, all megafaunal species seems to have similar environmental requirements during the autumn–winter period. Mostly waters shallower than 50 m were identified as key ecological areas, with the Río de la Plata as the habitat with the highest suitability for all the species. This area is highly productive and sustains the main coastal fisheries of Uruguay and Argentina, yet its role as a key ecological area for megafaunal species has been underestimated until now. This approach provides a basis to analyse the effect of anthropic activities on megafaunal species through risk maps and, ultimately, to generate knowledge to improve national and bi-national management plans between Argentina and Uruguay.
Remote sensing of habitat characteristics using echo metrics and image-based seabed classes
Authors: Cutter George R. , Stierhoff Kevin L. , Demer David A. 
Published: March 2016

Abstract
The seabed can be classified using data from vertical, split-beam echosounders. This was demonstrated recently using a model parameterized with acoustic estimates of slope, roughness, normal-incidence backscattering strength, and variation of backscattering strength by frequency and incidence angle. These seabed classifications were interpreted and validated using published surficial geology maps, but the acoustic data indicated greater spatial variability. Here, classifications of sediment grain or feature size are ascribed to areas ∼10 m2. First, images of the seabed in the study area are ascribed, based on per cent coverage, to seven primary classes ranging from mud through high-relief rock, and 25 primary–secondary classes. Then, a refined seabed classifier, based on the acoustic model parameters is trained, using a nearest-neighbours algorithm, on a subset of the class data. The classifier accurately predicts 96% of the primary classes, and 93% of the primary–secondary classes from an independent data subset. These methods should be useful for characterizing, mapping, and quantifying potential seabed habitat domains of demersal fish and benthic invertebrates.
The role of climate and fisheries on the temporal changes in the Bothnian Bay foodweb
Authors: Pekcan-Hekim Zeynep , Gårdmark Anna , Karlson Agnes M. L. , Kauppila Pirkko , Bergenius Mikaela , Bergström Lena 
Published: March 2016

Abstract
Climate change, eutrophication, and fishing are main pressures associated with changes in the abiotic and biotic environment in several sub-basins of the Baltic Sea. Identifying the nature of such changes is of relative importance for fisheries and environmental management. The Bothnian Bay is the northernmost sub-basin in the Baltic Sea and the responses of the foodweb to long-term changes in combined pressures have not been investigated. In this study, we explore long-term changes in the Bothnian Bay foodweb, represented by key species across all trophic levels over the past 34 years, and identify potential environmental and anthropogenic drivers. The results indicate that salinity is the most important driver to explain changes in the composition of the offshore biota in the Bothnian Bay. These changes are probably driven by indirect effects of salinity rather than bottom-up effects. A decline in the herring spawning-stock biomass was most plausibly attributed to an increased competition for food due to a parallel increase in vendace, which uses the same food resources (zooplankton and zoobenthos) and may benefit from declining salinity due to its limnic origin. A strong increase in the abundance of grey seal and ringed seal populations was seen in the late 2000s but was not related to any of the pressure variables analysed. Temperature and nutrients were not identified as important drivers of changes in the overall biota. Our study explores correlative relationships between variables and identifies potential interactions in the foodweb to generate hypotheses for further studies.
Preliminary analysis of the sequential simultaneous integrated boost technique for intensity-modulated radiotherapy for head and neck cancers
Authors: Miyazaki Masayoshi , Nishiyama Kinji , Ueda Yoshihiro , Ohira Shingo , Tsujii Katsutomo , Isono Masaru , Masaoka Akira , Teshima Teruki 
Published: March 2016

Abstract
The aim of this study was to compare three strategies for intensity-modulated radiotherapy (IMRT) for 20 head-and-neck cancer patients. For simultaneous integrated boost (SIB), doses were 66 and 54 Gy in 30 fractions for PTVboost and PTVelective, respectively. Two-phase IMRT delivered 50 Gy in 25 fractions to PTVelective in the First Plan, and 20 Gy in 10 fractions to PTVboost in the Second Plan. Sequential SIB (SEQ-SIB) delivered 55 Gy and 50 Gy in 25 fractions, respectively, to PTVboost and PTVelective using SIB in the First Plan and 11 Gy in 5 fractions to PTVboost in the Second Plan. Conformity indexes (CIs) (mean ± SD) for PTVboost and PTVelective were 1.09 ± 0.05 and 1.34 ± 0.12 for SIB, 1.39 ± 0.14 and 1.80 ± 0.28 for two-phase IMRT, and 1.14 ± 0.07 and 1.60 ± 0.18 for SEQ-SIB, respectively. CI was significantly highest for two-phase IMRT. Maximum doses (Dmax) to the spinal cord were 42.1 ± 1.5 Gy for SIB, 43.9 ± 1.0 Gy for two-phase IMRT and 40.3 ± 1.8 Gy for SEQ-SIB. Brainstem Dmax were 50.1 ± 2.2 Gy for SIB, 50.5 ± 4.6 Gy for two-phase IMRT and 47.4 ± 3.6 Gy for SEQ-SIB. Spinal cord Dmax for the three techniques was significantly different, and brainstem Dmax was significantly lower for SEQ-SIB. The compromised conformity of two-phase IMRT can result in higher doses to organs at risk (OARs). Lower OAR doses in SEQ-SIB made SEQ-SIB an alternative to SIB, which applies unconventional doses per fraction.
Nol12 is a multifunctional endonuclease at the nexus of RNA and DNA metabolism
Authors: Scott D. D. , Trahan C. , Zindy P.J. , Aguilar L.C. , Delubac M.Y. , Wei K. E. , Oeffinger M. 
Published: March 2016

ABSTRACTEndo‐ and exonucleases are major contributors to RNA metabolism through their diverse roles in maturation and turnover of different species of RNA as well as transcription. Recent data suggests RNA nucleases also affect genome stability programs and act along DNA repair pathways. Here, we describe Nol12 as a multifunctional RNA/DNA endonuclease found in different subcellular compartments - the nucleoplasm, where it co-localizes with the RNA/DNA helicase Dhx9 and paraspeckles, nucleoli as well as GW/P-bodies. We show that Nol12 is required for a key step in ribosomal RNA processing, separating large and small subunit precursors at site 2, rerouting ribosome biogenesis via an alternative pathway in its absence to ensure ribosome production. Furthermore, loss of Nol12 results in increased oxidized DNA levels followed by a rapid p53-independent ATR-Chk1-mediated apoptotic response, suggesting a role for Nol12 in the prevention or resolution of oxidative DNA damage. Identification of a complex Nol12 interactome, which includes NONO, Dhx9 and DNA-PK, further supports its diverse functions in RNA metabolism and DNA maintenance, establishing Nol12 as a multifunctional endonuclease.
Implementing rapid, robust, cost-effective, patient-centred, routine genetic testing in ovarian cancer patients
Authors: George Angela , Riddell Daniel , Seal Sheila , Talukdar Sabrina , Mahamdallie Shazia , Ruark Elise , Cloke Victoria , Slade Ingrid , Kemp Zoe , Gore Martin , Strydom Ann , Banerjee Susana , Hanson Helen , Rahman Nazneen ,   for the Mainstreaming Cancer Genetics (MCG) Programme
Published: March 2016

SUMMARYBackground:Advances in DNA sequencing have made gene testing fast and affordable, but adaptation of clinical services to capitalise on this for patient benefit has been slow. Ovarian cancer exemplifies limitations of current systems and potential benefits of increased gene testing. Approximately 15% of ovarian cancer patients have a germline mutation inBRCA1orBRCA2(collectively termed ‘BRCA’) and this has substantial implications for their personal management and that of their relatives. However, in most countries implementation of BRCA testing in ovarian cancer has been inconsistent and largely unsuccessful.Methods:We developed a mainstream pathway in which BRCA testing was undertaken by cancer team members after 30 minutes online training. Patients with a mutation were sent a genetic appointment with their results. Cascade testing to relatives was performed via standard clinical genetic procedures.Findings:207 women with ovarian cancer were offered gene testing through the mainstream pathway and all accepted. 33 (16%) had a BRCA mutation. The result informed management of 79% (121/154) women with active disease including 97% (32/33) women with a mutation. All mutation-positive women and ~3.5 relatives per family have been seen in genetics. Patient and clinician feedback was very positive. >95% found the pathway to be simple and effective. The pathway offers considerable reduction in time (~5-fold) and resource requirements (~13-fold) compared to the traditional genetic pathway. We estimate it would deliver £2.6M NHS cost savings per year, and would allow implementation of national testing recommendations with existing infrastructure.Interpretation:Mainstream genetic testing is effective, efficient and patient-centred and offers a mechanism for large-scale implementation of BRCA gene testing in cancer patients. The principles could be applied in many other countries and to many other areas of genomic medicine.