bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethiopian agriculture has greater potential for carbon sequestration than previously estimated
Authors: Rimhanen Karoliina , Ketoja Elise , Yli‐Halla Markku , Kahiluoto Helena 
Published: March 2016

AbstractMore than half of the cultivation‐induced carbon loss from agricultural soils could be restored through improved management. To incentivise carbon sequestration, the potential of improved practices needs to be verified. To date, there is sparse empirical evidence of carbon sequestration through improved practices in East‐Africa. Here, we show that agroforestry and restrained grazing had a greater stock of soil carbon than their bordering pair‐matched controls, but the difference was less obvious with terracing. The controls were treeless cultivated fields for agroforestry, on slopes not terraced for terracing, and permanent pasture for restrained grazing, representing traditionally managed agricultural practices dominant in the case regions. The gain by the improved management depended on the carbon stocks in the control plots. Agroforestry for 6–20 years led to 11.4 Mg ha−1 and restrained grazing for 6–17 years to 9.6 Mg ha−1 greater median soil carbon stock compared with the traditional management. The empirical estimates are higher than previous process‐model‐based estimates and indicate that Ethiopian agriculture has greater potential to sequester carbon in soil than previously estimated.
Deep ploughing increases agricultural soil organic matter stocks
Authors: Alcántara Viridiana , Don Axel , Well Reinhard , Nieder Rolf 
Published: March 2016

AbstractSubsoils play an important role within the global C cycle, since they have high soil organic carbon (SOC) storage capacity due to generally low SOC concentrations. However, measures for enhancing SOC storage commonly focus on topsoils. This study assessed the long‐term storage and stability of SOC in topsoils buried in arable subsoils by deep ploughing, a globally applied method for breaking up hard pans and improving soil structure to optimize crop growing conditions. One effect of deep ploughing is translocation of SOC formed near the surface into the subsoil, with concomitant mixing of SOC‐poor subsoil material into the ‘new’ topsoil. Deep‐ploughed croplands represent unique long‐term in situ incubations of SOC‐rich material in subsoils. In this study, we sampled five loamy and five sandy soils that were ploughed to 55–90 cm depth 35–50 years ago. Adjacent, similarly managed but conventionally ploughed subplots were sampled as reference. The deep‐ploughed soils contained on average 42 ± 13% more SOC than the reference subplots. On average, 45 years after deep ploughing, the ‘new’ topsoil still contained 15% less SOC than the reference topsoil, indicating long‐term SOC accumulation potential in the topsoil. In vitro incubation experiments on the buried sandy soils revealed 63 ± 6% lower potential SOC mineralisation rates and also 67 ± 2% lower SOC mineralisation per unit SOC in the buried topsoils than in the reference topsoils. Wider C/N ratio in the buried sandy topsoils than in the reference topsoils indicates that deep ploughing preserved SOC. The SOC mineralisation per unit SOC in the buried loamy topsoils was not significantly different from that in the reference topsoils. However, 56 ± 4% of the initial SOC was preserved in the buried topsoils. It can be concluded that deep ploughing contributes to SOC sequestration by enlarging the storage space for SOC‐rich material.
A new global burned area product for climate assessment of fire impacts
Authors: Chuvieco Emilio , Yue Chao , Heil Angelika , Mouillot Florent , Alonso‐Canas Itziar , Padilla Marc , Pereira Jose Miguel , Oom Duarte , Tansey Kevin 
Published: March 2016

AbstractAim This paper presents a new global burned area (BA) product developed within the framework of the European Space Agency's Climate Change Initiative (CCI) programme, along with a first assessment of its potentials for atmospheric and carbon cycle modelling.Innovation Methods are presented for generating a new global BA product, along with a comparison with existing BA products, in terms of BA extension, fire size and shapes and emissions derived from biomass burnings.Main conclusions Three years of the global BA product were produced, accounting for a total BA of between 360 and 380 Mha year−1. General omission and commission errors for BA were 0.76 and 0.64, but they decreased to 0.51 and 0.52, respectively, for sites with more than 10% BA. Intercomparison with other existing BA datasets found similar spatial and temporal trends, mainly with the BA included in the Global Fire Emissions Database (GFED4), although regional differences were found (particularly in the 2006 fires of eastern Europe). The simulated carbon emissions from biomass burning averaged 2.1 Pg C year−1.
Spring growth stage detection in Italian ryegrass field using a ground‐based camera system
Authors: Fan Xinyan , Kawamura Kensuke , Lim Jihyun , Yoshitoshi Rena , Yuba Norio , Lee Hyo‐Jin , Kurokawa Yuzo , Tsumiyama Yoshimasa 
Published: March 2016

AbstractInformation on the spring growth status of winter forage crops is crucial for evaluating productivity and nutrient management. This study aimed to determine the spring quick growth stage (QGS) of Italian ryegrass using a ground‐based camera system. The camera system, installed in two Italian ryegrass fields at the farm of Hiroshima University, captured images automatically three times per day in red, green and blue channels over the growing season in 2012–13. Four presumed color intensities/indices were fitted using a logistic model to construct smoothed time‐series data. Among the color intensities/indices, excess green was suggested to be the best parameter for monitoring seasonal changes. The root mean squared error of the estimated phenology dates against plant height was 7.7 days for the start‐QGS and 2.8 days for the end‐QGS. These results from a single year should be broadened to examine other methodologies for image processing and extended to multi‐year data.
Usefulness of Housekeeping Genes for the Diagnosis of Helicobacter pylori Infection, Strain Discrimination and Detection of Multiple Infection
Authors: Palau Montserrat , Kulmann Marcos , Ramírez‐Lázaro María José , Lario Sergio , Quilez María Elisa , Campo Rafael , Piqué Núria , Calvet Xavier , Miñana‐Galbis David 
Published: March 2016

AbstractBackgroundHelicobacter pylori infects human stomachs of over half the world's population, evades the immune response and establishes a chronic infection. Although most people remains asymptomatic, duodenal and gastric ulcers, MALT lymphoma and progression to gastric cancer could be developed. Several virulence factors such as flagella, lipopolysaccharide, adhesins and especially the vacuolating cytotoxin VacA and the oncoprotein CagA have been described for H. pylori. Despite the extensive published data on H. pylori, more research is needed to determine new virulence markers, the exact mode of transmission or the role of multiple infection.Materials and MethodsAmplification and sequencing of six housekeeping genes (amiA, cgt, cpn60, cpn70, dnaJ, and luxS) related to H. pylori pathogenesis have been performed in order to evaluate their usefulness for the specific detection of H. pylori, the genetic discrimination at strain level and the detection of multiple infection. A total of 52 H. pylori clones, isolated from 14 gastric biopsies from 11 patients, were analyzed for this purpose.ResultsAll genes were specifically amplified for H. pylori and all clones isolated from different patients were discriminated, with gene distances ranged from 0.9 to 7.8%. Although most clones isolated from the same patient showed identical gene sequences, an event of multiple infection was detected in all the genes and microevolution events were showed for amiA and cpn60 genes.ConclusionsThese results suggested that housekeeping genes could be useful for H. pylori detection and to elucidate the mode of transmission and the relevance of the multiple infection.
Changes in the Functional Potential of the Gut Microbiome Following Probiotic Supplementation duringHelicobacter PyloriTreatment
Authors: Oh Bumjo , Kim Ji Won , Kim Bong‐Soo 
Published: March 2016

AbstractBackgroundProbiotic supplementation is utilized to alleviate the side effects associated with antibiotic therapy forHelicobacter pyloriinfection. Several studies have described the effects of administration of probiotics on the gut microbiota during antibiotic therapy. However, most of these studies have focused on specific bacteria, thereby providing limited information on the functional roles of the altered microbiota. Therefore, we examined the impact of probiotic supplementation on the structure and functional dynamics of the gut microbiota duringH. pylorieradication, using whole‐metagenomic sequence analysis.MethodsSubjects were divided into two groups: the antibiotics group, which received only antibiotics, and the probiotics group, which received antibiotics with probiotic supplementation. The structural and functional profiles of gut microbiota was analyzed using metagenomicDNAextracted from the feces during treatment by Illumina MiSeq system.ResultsThe overall alterations in microbiota, as revealed by whole metagenome sequencing, were similar with results from our previous 16SrRNAgene‐based analysis. The proportional shift in functional gene families was greater in the antibiotics group than in the probiotics group. In particular, the proportion of genes related to selenocompound metabolism was reduced in the probiotics group, whereas genes associated with the metabolism of nucleotide sugars were increased.ConclusionThe functional alterations of gut microbiota may link to the reduction in intestinal irritation and maintenance of bacterial diversity observed following probiotic supplementation with antibiotic therapy. The potential beneficial roles of altered gut microbiota following probiotic supplementation are expected a reduction in side effects such as intestinal irritation and antibiotics resistance.
Remote ischemic conditioning protects against acetaminophen‐induced acute liver injury in mice
Authors: Zheng Wei , Zhang Zhiyong , Liu Sushun , Bi Jianbin , Zhang Jingyao , Du Lixue , Ding Xiaoming , Liu Chang 
Published: March 2016

AimAcetaminophen (APAP) overdose is a major cause of drug‐induced acute liver failure. Studies have shown that remote ischemic pre‐ and post‐conditioning (R‐IPC and R‐IPOST) can protect the liver against ischemia–reperfusion (I/R) and lipopolysaccharide‐induced injuries. The aim of this study was to investigate the effect of R‐IPC and R‐IPOST on APAP‐induced hepatotoxicity in mice.MethodsMice were randomized (n = 6 per group) to seven major groups: (i) normal control; (ii) sham operated; (iii) APAP; (iv) R‐IPC + APAP; (v) R‐IPC + APAP + zinc protoporphyrin (ZnPP); (vi) R‐IPOST + APAP; and (vii) R‐IPOST + APAP + ZnPP. Sixteen hours after APAP treatment, mouse liver and serum were collected to determine the severity of liver injury.ResultsThe results showed that R‐IPC and R‐IPOST significantly decreased APAP‐induced serum levels of alanine aminotransferase, aspartate aminotransferase, tumor necrosis factor‐α, interleukin‐6, and hepatic malondialdehyde, as well as nitrotyrosine formation. Both R‐IPC and R‐IPOST could improve the hepatic superoxide dismutase, glutathione, and glutathione peroxidase activities and depress the expressions of pro‐inflammatory associated proteins, such as inducible nitric oxide synthetase and nuclear factor‐κB. They could also increase heme oxygenase‐1 expression; however, ZnPP could counteract this protective effect.ConclusionRemote ischemic conditioning has significant therapeutic potential in APAP‐induced hepatotoxicity by inhibiting oxidative stress and inflammation and promoting heme oxygenase‐1 expression.
Hypoxia‐inducible factor‐2α promotes hepatocyte apoptosis during cholestasis
Authors: Hua Xiangwei , Lu Tianfei , Zhang Jiang , Miao Qi , Bian Zhaolian , Zhang Haiyan , Huang Shanshan , Lin Weiwei , Xi Zhifeng , Zhang Ming , Chen Qimin , Ma Xiong , Zhang Jianjun , Xia Qiang 
Published: March 2016

AimHypoxia‐inducible factor‐2α (HIF‐2α) has been reported to play an important role in a host of pathophysiological processes, including cellular survival. This study explores the role of HIF‐2α in cholestasis‐mediated hepatocyte apoptosis.MethodsHypoxia‐inducible factor‐2α expression was measured by immunohistochemistry and confocal microscopy. Hepatic apoptosis was detected by terminal deoxynucleotidyl transferase‐mediated dUTP‐digoxigenin nick‐end labeling. The cholestatic mouse model was treated with bile duct ligation. The c‐myc, p53, and Bax protein levels were measured with Western blot analysis.ResultsIn pediatric and murine cholestatic liver tissues, HIF‐2α protein was widely expressed in the nucleus of parenchymal cells as well as in stromal cells. Hepatocyte HIF‐2α expression was significantly elevated at the early stage of pediatric cholestasis and decreased at the late stage. In both in vivo and in vitro murine studies, HIF‐2α deletion could alleviate cholestasis‐mediated hepatocyte apoptosis and regulate the expression of c‐myc, p53, and Bax proteins.ConclusionThese findings implied the contribution of HIF‐2α to cholestasis‐mediated hepatocyte apoptosis.
Fundic gland differentiation of oncocytic/pancreatobiliary subtypes of pancreatic intraductal papillary mucinous neoplasm
Authors: Mamat Osman , Fukumura Yuki , Saito Tsuyoshi , Takahashi Michiko , Mitomi Hiroyuki , Sai Jin Kan , Kawasaki Seiji , Yao Takashi 
Published: March 2016

AimsIntraductal papillary mucinous neoplasms (IPMNs) differentiate in several histological directions, which are related to their clinical behaviour. Differentiation of IPMNs to the gastric foveolar epithelium/pyloric gland (PG) is well known. However, no study has been conducted regarding fundic gland (FG) differentiation. The aim of this study was to determine the frequency of FG differentiation and its relationship with the clinicopathological features of IPMNs, by studying 48 surgically resected IPMN cases consisting of 17 gastric IPMNs, 15 intestinal IPMNs, 10 pancreatobiliary IPMNs, and six oncocytic IPMNs.Methods and resultsClinicopathological data, including histological tumour grade, immunohistochemical data for mucins (MUCs), pepsinogen I, pepsinogen II, and H,K‐ATPase, and GNAS/KRAS status, were analysed. Pepsinogen I and H,K‐ATPase were used to assess FG differentiation, and pepsinogen II and MUC6 were used to identify the equivalent cell type of the normal FG. Reverse transcription polymerase chain reaction (RT‐PCR) for PGA5/PGC (pepsinogen I and pepsinogen II mRNA, respectively) and quantitative real‐time RT‐PCR (qRT‐PCR) for PGA5 were performed to confirm the immunohistochemistry results. Pepsinogen I expression was detected in 12.5% (6/48) of total IPMNs, of which 66.7% (4/6) of oncocytic IPMNs and 20.0% (2/10) of pancreatobiliary IPMNs were pepsinogen I‐positive. No H,K‐ATPase‐positive cases were detected. Three oncocytic IPMNs with pepsinogen I expression showed similar histology to normal FG. RT‐PCR and qRT‐PCR confirmed the immunohistochemical results. All IPMNs with FG differentiation were of the oncocytic or pancreatobiliary subtype, were of histologically high grade, and were without GNAS mutation.ConclusionsThe differentiation of IPMNs to gastric FG is related to oncocytic and pancreatobiliary subtypes, and to high grade. This is the first report to describe differentiation of IPMNs to the FG, and to reveal its relationship with the clinicopathological features of IPMNs.
Correlating HIV tropism with immunological response under combination antiretroviral therapy
Authors: Bader J , Schöni‐Affolter F , Böni J , Gorgievski‐Hrisoho M , Martinetti G , Battegay M , Klimkait T ,   the Swiss HIV Cohort Study
Published: March 2016

ObjectivesA significant percentage of patients infected with HIV‐1 experience only suboptimal CD4 cell recovery while treated with combination therapy (cART). It is still unclear whether viral properties such as cell tropism play a major role in this incomplete immune response. This study therefore intended to follow the tropism evolution of the HIV‐1 envelope during periods of suppressive cART.MethodsViruses from two distinct patient groups, one with good and another one with poor CD4 recovery after 5 years of suppressive cART, were genotypically analysed for viral tropism at baseline and at the end of the study period.ResultsPatients with CCR5‐tropic CC‐motif chemokine receptor 5 viruses at baseline tended to maintain this tropism to the study end. Patients who had a CXCR4‐tropic CXC‐motif chemokine receptor 4 virus at baseline were overrepresented in the poor CD4 recovery group. Overall, however, the majority of patients presented with CCR5‐tropic viruses at follow‐up.ConclusionsOur data lend support to the hypothesis that tropism determination can be used as a parameter for disease progression even if analysed long before the establishment of a poorer immune response. Moreover, the lasting predominating CCR5‐tropism during periods of full viral control suggests the involvement of cellular mechanisms that preferentially reduce CXCR4‐tropic viruses during cART.
Chronic hepatitis B increases mortality and complexity among HIV‐coinfected patients in South Africa: a cohort study
Authors: Velen K , Charalambous S , Innes C , Churchyard GJ , Hoffmann CJ 
Published: March 2016

ObjectivesTo assess the effect of chronic hepatitis B on survival and clinical complexity among people living with HIV following antiretroviral therapy (ART) initiation.MethodsWe evaluated mortality and single‐drug substitutions up to 3 years from ART initiation (median follow‐up 2.75 years; interquartile range 2–3 years) among patients with and without chronic hepatitis B (CHB) enrolled in a workplace HIV care programme in South Africa.ResultsMortality was increased for CHB patients with hepatitis B virus (HBV) DNA levels > 10 000 copies/mL (adjusted hazard ratio 3.1; 95% confidence interval 1.2–8.0) compared with non‐CHB patients. We did not observe a similar difference between non‐CHB patients and those with CHB and HBV DNA < 10 000 copies/mL (adjusted hazard ratio 0.70; 95% confidence interval 0.2–2.3). Single‐drug substitutions occurred more frequently among coinfected patients regardless of HBV DNA level.ConclusionsOur findings suggest that CHB may increase mortality and complicate ART management.
Habitat complexity and the structure of vocalizations: a test of the acoustic adaptation hypothesis in three rail species (Rallidae)
Authors: Ręk Paweł , Kwiatkowska Katarzyna 
Published: March 2016

The acoustic adaptation hypothesis is based on the assumption that senders are directionally selected to maximize transmission and minimize degradation; however, the two aims are not necessarily convergent. In complex habitats, where more effects that might potentially cause attenuation and degradation co‐occur and longer transmission must incur a higher cost, signals should attenuate faster and have shorter transmission ranges. At the same time, such signals should be more resistant to degradation in order to preserve their communicatory function. Based on a sound transmission experiment, we tested the evidence for these predictions using territorial calls of three sympatric species of rails, inhabiting habitats with increasing complexity: Corncrake Crex crex, Spotted Crake Porzana porzana and Water Rail Rallus aquaticus. In the experiment, the calls were broadcasted with similar amplitudes through a heterogeneous habitat inhabited by all three species and rerecorded at different distances up to 320 m. Despite standardized amplitudes and habitats, calls of the species living in simpler habitats had longer transmission ranges but were more susceptible to degradation than calls of the species living in more complex habitats. Our results suggest that narrow frequency bandwidth is an adaptation of species inhabiting complex habitats that helps their calls to degrade less at the cost of stronger attenuation and shorter transmission range. By contrast, wide frequency bandwidth extends the range but increases degradation and thus it is used only by species inhabiting structurally simpler habitats. This study shows that, in more complex habitats, the clarity of the message is preserved at the cost of range.
Micro‐CT evaluation of several glide path techniques and ProTaper Next shaping outcomes in maxillary first molar curved canals
Authors: Alovisi M. , Cemenasco A. , Mancini L. , Paolino D. , Scotti N. , Bianchi C. C. , Pasqualini D. 
Published: March 2016

AbstractAimTo evaluate the ability of ProGlider instruments, PathFiles and K‐files to maintain canal anatomy during glide path preparation using X‐ray computed micro‐tomography (micro‐CT).MethodologyForty‐five extracted maxillary first permanent molars were selected. Mesio‐buccal canals were randomly assigned (n = 15) to manual K‐file, PathFile or ProGlider groups for glide path preparation. Irrigation was achieved with 5% NaOCl and 10% EDTA. After glide path preparation, each canal was shaped with ProTaper Next X1 and X2 to working length. Specimens were scanned (isotropic voxel size 9.1 μm) for matching volumes and surface areas and post‐treatment analyses. Canal volume, surface area, centroid shift, canal geometry variation through ratio of diameter ratios and ratio of cross‐sectional areas were assessed in the apical and coronal levels and at the point of maximum canal curvature. One‐way factorial anovas were used to evaluate the significance of instrument in the various canal regions.ResultsPost‐glide path analysis revealed that instrument factor was significant at the apical level for both the ratio of diameter ratios and the ratio of cross‐sectional areas (P < 0.001), with an improved maintenance of root canal geometry by ProGlider and PathFile. At the coronal level and point of maximum canal curvature, ProGlider demonstrated a tendency to pre‐flare the root canal compared with K‐file and PathFile. PathFile and ProGlider demonstrated a significantly lower centroid shift compared with K‐file at the apical level (P = 0.023). Post‐shaping analysis demonstrated a more centred preparation of ProGlider, compared with PathFile and K‐files, with no significant differences for other parameters.ConclusionsUse of ProGlider instruments led to less canal transportation than PathFiles and K‐files.
Effect of different freeze drying cycle in Semimembranous and Gluteus Medius bovine muscles: changes on microstructure, colour, texture and physicochemical parameters
Authors: Messina Valeria , Pieniazek Facundo , Sancho Ana 
Published: March 2016

SummaryThe aim of the present research was to evaluate effects of freeze drying cycle in Semimembranous and Gluteus Medius bovine muscles (sp: Aberdeen Angus) for instant meal. Samples were analysed by Scanning electron microscopy; texture and colour parameters were analysed by image analysis and physicochemical properties by instrumental assays. Micrographs revealed that a higher porous size structure and shrinkage of muscle fibre diameter were obtained at −40 °C. In Semimembranous and Gluteus Medius bovine muscles, significant difference (P < 0.0001) was obtained for texture, colour and physicochemical parameters. Results revealed that colour, texture and physicochemical parameters were less affected when freeze drying cycle was performed at −40 °C. Freeze drying cycle at −50 and −60 °C showed increases in lightness (L*) and yellowness (b*); decrease in redness (a*) and in water absorbing capability).