bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of differentially expressed genes in the oviduct of two rabbit lines divergently selected for uterine capacity using suppression subtractive hybridization
Authors: Ballester M. , Castelló A. , Peiró R. , Argente M. J. , Santacreu M. A. , Folch J. M. 
Published: November 2012

SummarySuppressive subtractive hybridization libraries from oviduct at 62 h post‐mating of two lines of rabbits divergently selected for uterine capacity were generated to identify differentially expressed genes. A total of 438 singletons and 126 contigs were obtained by cluster assembly and sequence alignment of 704 expressed sequence tags (ESTs), of which 54% showed homology to known proteins of the non‐redundant NCBI databases. Differential screening by dot blot validated 71 ESTs, of which 47 showed similarity to known genes. Transcripts of genes were functionally annotated in the molecular function and the biological process gene ontology categories using the blast2go software and were assigned to reproductive developmental process, immune response, amino acid metabolism and degradation, response to stress and apoptosis terms. Finally, three interesting genes, PGR, HSD17B4 and ERO1L, were identified as overexpressed in the low line using RT‐qPCR. Our study provides a list of candidate genes that can be useful to understanding the molecular mechanisms underlying the phenotypic differences observed in early embryo survival and development traits.
Lipids are required for the development of Brazil nut allergy: the role of mouse and human iNKT cells
Authors: Mirotti L. , Florsheim E. , Rundqvist L. , Larsson G. , Spinozzi F. , Leite‐de‐Moraes M. , Russo M. , Alcocer M. 
Published: November 2012

AbstractBackgroundLipids are required for mice sensitization to Ber e 1, Brazil nut major allergen. Here, we characterized different lipid fractions extracted from Brazil nuts and the lipid‐binding ability of Ber e 1. Further, we determined their in vivo ability to induce Ber‐specific anaphylactic antibodies and the role of invariant natural killer T (iNKT) cells in this process.MethodsWild‐type (WT) and iNKT cell‐deficient mice were sensitized with Ber e 1 and specific lipid fractions, and anaphylactic antibodies were measured by enzyme‐linked immunosorbent assay (ELISA) and passive cutaneous anaphylaxis (PCA). The lipid‐binding characteristic of Ber e 1 (Ber) was established by using fluorescent probes and 15N‐labeled NMR. In vitro production of IL‐4 was determined in Ber/lipid C‐stimulated mouse iNKT cells and human T‐cell lines containing NKTs primed with CD1d+C1R transfectants by flow cytometry and ELISA, respectively.ResultsOnly one specific lipid fraction (lipid C), containing neutral and common phospholipids, induced Ber anaphylactic antibodies in mice. Ber e 1 has a lipid‐binding site, and our results indicated an interaction between Ber e 1 and lipid C. iNKT‐deficient mice produced lower levels of anaphylactic antibodies than WT mice. In vitro, Ber/lipid C‐stimulated murine iNKT cells produced IL‐4 but not IFN‐gamma. Human T‐cell lines derived from nut‐allergic patients produced IL‐4 to Ber/lipid C in a CD1d− and dose‐dependent manner.ConclusionLipid fraction C from Brazil nut presents an essential adjuvant activity to Ber e 1 sensitization, and iNKT cells play a critical role in the development of Brazil nut‐allergic response.
Functional variants in the thromboxane A2 receptor gene are associated with lung function in childhood‐onset asthma
Authors: Takeuchi K. , Mashimo Y. , Shimojo N. , Arima T. , Inoue Y. , Morita Y. , Sato K. , Suzuki S. , Nishimuta T. , Watanabe H. , Hoshioka A. , Tomiita M. , Yamaide A. , Watanabe M. , Okamoto Y. , Kohno Y. , Hata A. , Suzuki Y. 
Published: November 2012

SummaryBackgroundThe thromboxane A2 receptor (TBXA2R) gene is associated with asthma, but no functional genetic variations are known to associate with the disease or its related phenotypes.ObjectiveTo investigate the association of TBXA2R polymorphisms with asthma susceptibility and related phenotypes and to identify functionally relevant polymorphisms.MethodsWe performed comprehensive sequencing of the TBXA2R gene in 48 Japanese control subjects and found a set of variants (SNP1 G>T rs2238634, SNP2 T>G rs2238633, SNP3 C>T rs2238632 and SNP4 G>A rs2238631) in intron 1 in linkage disequilibrium with c.795 T>C rs1131882, which was previously reported to be associated with asthma and related phenotypes. To investigate the effect of four common haplotypes (H1, H2, H3 and H4) on transcriptional activity, we performed a luciferase assay in primary bronchial smooth muscle cells (BSMCs) and human airway epithelial cells (BEAS‐2B). We also studied the haplotype association with lung function, TBXA2R mRNA levels, and eosinophil fraction/count in peripheral blood in childhood‐onset asthma patients and/or controls.ResultsH2 and H4, containing minor alleles of SNP2 and SNP3, had significantly higher transcriptional activities than H1 consisting of major alleles (P < 0.001 in BSMCs and BEAS‐2B). Homozygotes for redefined haplotype h2 corresponding to minor alleles of SNP2 and SNP3 were associated with lower lung function in childhood‐onset asthma patients compared to other zygotes (baseline Forced expiratory volume in one second (FEV1)/ Forced vital capacity (FVC) and Forced expiratory flow between 25% and 75% of the FVC (%FEF25–75%): P = 0.00201 and 0.0128, respectively, and post‐bronchodilator FEV1/FVC and %FEF25–75%: P = 0.00224 and 0.0393 respectively). Haplotype h2 was also associated with higher mRNA levels in control peripheral blood cells and higher blood eosinophil fractions and counts in female controls.Conclusions and Clinical RelevanceGenetic variants were identified in the TBXA2R gene that influenced transcriptional activity and were associated with asthma‐related phenotypes. Thromboxane pathways may therefore play important roles in airway inflammation and remodelling in asthma patients.
Plasma oxidative stress is induced by single‐sprint anaerobic exercise in young cigarette smokers
Authors: Taito Shunsuke , Sekikawa Kiyokazu , Oura Keisuke , Kamikawa Norimichi , Matsuki Ryosuke , Kimura Tatsushi , Takahashi Makoto , Inamizu Tsutomu , Hamada Hironobu 
Published: November 2012

SummaryCigarette smoking increases oxidative stress, which is a risk factor for several diseases. Smoking has also been reported to enhance plasma oxidative stress during strenuous exercise. However, no prior study has examined the changes in plasma oxidative stress after single‐sprint anaerobic exercise in cigarette smokers. The purpose of this study was to investigate these changes in young cigarette smokers by measuring reactive oxygen species generation and total antioxidant content. Participants were 15 male smokers (mean age: 25·9 ± 2·9 years) and 18 male non‐smokers (mean age: 24·2 ± 4·3 years). Hydroperoxide concentration and biological antioxidant potential (BAP) in plasma were measured at baseline and after the Wingate anaerobic test. A significant interaction between group and time was observed for plasma hydroperoxide concentration (P = 0·037). Plasma hydroperoxide concentration was significantly increased after exercise in both smokers and non‐smokers (P = 0·001 and <0·001, respectively). However, no significant interaction was observed between groups by time on plasma BAP (P = 0·574), and a main effect of time was observed (P<0·001). Plasma BAP was significantly increased after exercise in both groups (both, P<0·001). These findings indicate that plasma oxidative stress is higher in cigarette smokers than in non‐smokers after single‐sprint anaerobic exercise, which may increase the risk of oxidative damage.
Wildcat occurrence in Scotland: food really matters
Authors: Silva André P. , Kilshaw Kerry , Johnson Paul J. , Macdonald David W. , Rosalino Luís M. 
Published: November 2012

AbstractAimEuropean wildcat Felis silvestris silvestris (Schreber, 1775) populations are suffering considerable threats, making conservation action a priority. In Scotland, the establishment of Special Areas of Wildcat Conservation (SAWC) have been recommended; however, few studies have addressed wildcat ecological requirements in this region. Our goal was to identify the environmental determinants limiting wildcat occurrence at a broad scale in Scotland.LocationScotland, Europe.MethodsWe examined data from the recent Scottish wildcat survey (2006–2008) and the National Biodiversity Network (NBN) Gateway. Presence and pseudo‐absence data from 71 sampling units (10 km × 10 km) were used to generate models explaining probable wildcat occurrence. Models were built based on three pre‐established hypotheses using generalized linear models (GLM‐Logit).ResultsEuropean rabbit presence, high rodent diversity and the prevalence of large grassland areas were positively associated with probable wildcat occurrence. Heather moorland, sampling units with few grassland patches or secondary watercourses and higher elevation ranges were associated with probable wildcat absence. We found no evidence that forested areas or human disturbance were influential.Main conclusionsOur results suggest that wildcats may benefit from heterogeneity within the landscape matrix, reinforcing the idea that the wildcat is not primarily a forest species (as has traditionally been inferred from studies of the species elsewhere). We conclude that less mountainous areas, with a diverse landscape including woodland and grassland supporting rabbits and a diversity of small rodents are a priority for wildcat conservation efforts.
Does local habitat fragmentation affect large‐scale distributions? The case of a specialist grassland bird
Authors: Reino Luís , Beja Pedro , Araújo Miguel B. , Dray Stéphane , Segurado Pedro 
Published: November 2012

AbstractAimAlthough the negative effects of habitat fragmentation have been widely documented at the landscape scale, much less is known about its impacts on species distributions at the biogeographical scale. We hypothesize that fragmentation influences the large‐scale distribution of area‐ and edge‐sensitive species by limiting their occurrence in regions with fragmented habitats, despite otherwise favourable environmental conditions. We test this hypothesis by assessing the interplay of climate and landscape factors influencing the distribution of the calandra lark, a grassland specialist that is highly sensitive to habitat fragmentation.LocationIberia Peninsula, Europe.MethodsEcological niche modelling was used to investigate the relative influence of climate/topography, landscape fragmentation and spatial structure on calandra lark distribution. Modelling assumed explicitly a hierarchically structured effect among explanatory variables, with climate/topography operating at broader spatial scales than landscape variables. An eigenvector‐based spatial filtering approach was used to cancel bias introduced by spatial autocorrelation. The information theoretic approach was used in model selection, and variation partitioning was used to isolate the unique and shared effects of sets of explanatory variables.ResultsClimate and topography were the most influential variables shaping the distribution of calandra lark, but incorporating landscape metrics contributed significantly to model improvement. The probability of calandra lark occurrence increased with total habitat area and declined with the number of patches and edge density. Variation partitioning showed a strong overlap between variation explained by climate/topography and landscape variables. After accounting for spatial structure in species distribution, the explanatory power of environmental variables remained largely unchanged.Main conclusionsWe have shown here that landscape fragmentation can influence species distributions at the biogeographical scale. Incorporating fragmentation metrics into large‐scale ecological niche models may contribute for a better understanding of mechanism driving species distributions and for improving predictive modelling of range shifts associated with land use and climate changes.
Managing sun bears in a changing tropical landscape
Authors: Wong Wai‐Ming , Linkie Matthew 
Published: November 2012

AbstractAimAcross the tropics, large‐bodied mammal species are threatened by rapid and widespread forest habitat conversion by either commercial logging or agricultural expansion. How such species use these habitats is an important area of research for guiding their future management. The tropical forest‐dwelling sun bear, Helarctos malayanus, is the least known of the eight bear species. Consequently, the IUCN/SSC Bear Specialist Group ranks research on this species as a top priority. This study aims to investigate landscape variables that influence sun bear habitat use in forests under varying levels of degradation and protection.LocationA 20,998 km2 Sumatra forest landscape covering Kerinci Seblat National Park (KSNP), Batang Hari Protection Forest (BHPF) and neighbouring logging and agricultural concessions.MethodsAn occupancy‐based sampling technique using detection/non‐detection data with 10 landscape covariates was applied in six study areas that operated a total of 125 camera traps. The potential differences between habitat use (ψ) of sun bears were first modelled with broad‐scale covariates of study area, land‐use types and forest type. Sun bear habitat use was then investigated with the finer‐scale landscape features associated within these areas.ResultsFrom 10,935 trap nights, sun bears were recorded at altitudes ranging from 365 to 1791 m. At a broad‐scale, habitat use increased with protection status, being highest in KSNP (0.688 ± 0.092, ± SE) and BHPF (0.621 ± 0.110) compared to production (0.418 ± 0.121) and convertible (0.286 ± 0.122) forests. Within these areas, sun bears showed a preference for forest that was further from public roads and villages and at a lower elevation.Main conclusionsThe habitat suitability model identified several high‐quality habitat patches outside of the priority conservation areas for immediate protection. Consequently, conservation management strategies should emphasize the importance of high conservation value forests and prohibit further conversion of threatened lowland forests.
A blinded study of bone marrow examinations in patients with primary immune thrombocytopenia
Authors: Mahabir Vishwanath K. , Ross Catherine , Popovic Snezana , Sur Mona Lisa , Bourgeois Jacqueline , Lim Wendy , George James N. , Wang Grace , Cook Richard J. , Toltl Lisa J. , Nazi Ishac , Kelton John G. , Arnold Donald M. 
Published: November 2012

AbstractObjectiveThe role of bone marrow examinations in patients with primary immune thrombocytopenia (ITP) is uncertain. The objectives of this study were to determine the inter‐rater reliability of bone marrow examinations and to identify distinguishing morphological features of ITP bone marrows under controlled conditions.MethodsHistological slides of bone marrow biopsy specimens and aspirates from 32 adult patients with severe primary ITP who had failed a median of two treatments, and 51 non‐thrombocytopenic controls were retrieved from hospital archives. Slides were arranged in random order in a slide box and coded. Blinded to the diagnosis and platelet counts, three independent hematopathologists were asked to identify the ITP bone marrows and to evaluate megakaryocyte number, morphology, and distribution.ResultsOverall chance‐corrected agreement on ITP classification among the three raters was poor [kappa (κ) = 0.30; 95% confidence interval 0.22–0.38]. Raters were generally unable to correctly identify the ITP bone marrows from controls. Increased number of megakaryocytes, while an uncommon finding, was more frequent among ITP patients compared with controls (6/32, 18.8%; vs. 2/51, 3.9%; P = 0.05), and abnormal megakaryocyte morphology often led individual raters to reach a diagnosis of ITP. Overall sensitivity and specificity of bone marrow examinations were 24% and 90%, respectively.ConclusionsThis study confirms methodologically that bone marrow examinations are unreliable and frequently non‐diagnostic in ITP. Thus, they are not useful for patients with typical disease. Rare subsets of patients with severe ITP demonstrated unique features such as increased number of megakaryocytes.
Rational design, synthesis, evaluation and enzyme–substrate structures of improved fluorogenic substrates for family 6 glycoside hydrolases
Authors: Wu Miao , Nerinckx Wim , Piens Kathleen , Ishida Takuya , Hansson Henrik , Sandgren Mats , Ståhlberg Jerry 
Published: November 2012

Methylumbelliferyl‐β–cellobioside (MUF–G2) is a convenient fluorogenic substrate for certain β–glycoside hydrolases (GH). However, hydrolysis of the aglycone is poor with GH family 6 enzymes (GH6), despite strong binding. Prediction of the orientation of the aglycone of MUF–G2 in the +1 subsite of Hypocrea jecorina Cel6A by automated docking suggested umbelliferyl modifications at C4 and C6 for improved recognition. Four modified umbelliferyl‐β–cellobiosides [6–chloro‐4–methyl‐ (ClMUF); 6–chloro‐4‐trifluoromethyl‐ (ClF3MUF); 4–phenyl‐ (PhUF); 6–chloro‐4–phenyl‐ (ClPhUF)] were synthesized and tested with GH6, GH7, GH9, GH5 and GH45 cellulases. Indeed the rate of aglycone release by H. jecorina Cel6A was 10–150 times higher than with MUF–G2, although it was still three orders of magnitude lower than with H. jecorina Cel7B. The 4–phenyl substitution drastically reduced the fluorescence intensity of the free aglycone, while ClMUF–G2 could be used for determination of kcat and KM for H. jecorina Cel6A and Thermobifida fusca Cel6A. Crystal structures of H. jecorina Cel6A D221A mutant soaked with the MUF‐, ClMUF‐ and ClPhUF‐β–cellobioside substrates show that the modifications turned the umbelliferyl group ‘upside down’, with the glycosidic bond better positioned for protonation than with MUF–G2.DatabaseStructural data have been submitted to the Protein Data Bank under accession numbers pdb 4AU0, 4AX7, 4AX6Structured digital abstract• http://mint.bio.uniroma2.it/mint/search/interaction.do?interactionAc=MINT-7260296• Cel6A and Cel6A bind by x-ray crystallography (View Interaction: 1, 2)
Overload effect on the fatigue crack propagation in large‐scale tubular joints
Authors: QIAN X. , SWADDIWUDHIPONG S. , NGUYEN C. T. , PETCHDEMANEENGAM Y. , MARSHALL P. , OU Z. 
Published: November 2012

ABSTRACTThis paper examines the overloading effect on the fatigue crack propagations monitored in a large‐scale tubular X‐joint specimen under two separate cyclic tests. The first cyclic test applies a constant‐amplitude brace in‐plane bending to the joint, with a single cycle of 150% overload before the crack depth reaches the mid‐thickness of the chord. The second fatigue test applies two batches of cyclic loads, with the amplitude of the second batch at 66% of the former. The X‐joint specimen experiences a 150% overload cycle during the first batch of loading, followed by the second batch after it has recovered from the overload effect. The experimental results reveal that deep surface cracks experience more significant overload retardation than does a shallow fatigue crack. The Paris law estimation indicates that the single overload cycle applied in the first specimen leads to a 7% increase in the fatigue life of the X‐joint.
Niche segregation of coexisting Arctic charr (Salvelinus alpinus) and brown trout (Salmo trutta) constrains food web coupling in subarctic lakes
Authors: ELORANTA ANTTI P. , KNUDSEN RUNE , AMUNDSEN PER‐ARNE 
Published: November 2012

Summary1. Generalist fish species are recognised as important couplers of benthic and pelagic food‐web compartments in lakes. However, interspecific niche segregation and individual specialisation may limit the potential for generalistic feeding behaviour.2. We studied summer habitat use, stomach contents and stable isotopic compositions of the generalist feeder Arctic charr coexisting with its common resource competitor brown trout in five subarctic lakes in northern Norway to reveal population‐level and individual‐level niche plasticity.3. Charr and trout showed partial niche segregation in all five lakes. Charr used all habitat types and a wide variety of invertebrate prey including zooplankton, whereas trout fed mainly on insects in the littoral zone. Hence, charr showed a higher potential to promote habitat and food‐web coupling compared to littoral‐dwelling trout.4.  The level of niche segregation between charr and trout and between pelagic‐caught and littoral‐caught charr depended on the prevailing patterns of interspecific and intraspecific resource competition. The two fish species had partially overlapping trophic niches in one lake where charr numerically dominated the fish community, whereas the most segregated niches occurred in lakes where trout were more abundant.5. In general, pelagic‐caught charr had substantially narrower dietary and isotopic niches and relied less on littoral carbon sources compared to littoral‐caught conspecifics that included generalist as well as specialised benthivorous and planktivorous individuals. Despite the partially specialised planktivorous niche and thus reduced potential of pelagic‐dwelling charr to promote benthic–pelagic coupling, the isotopic compositions of both charr subpopulations suggested a significant reliance on both littoral and pelagic carbon sources in all five study lakes.6. Our study demonstrates that both interspecific niche segregation between and individual trophic specialisation within generalist fish species can constrain food‐web coupling and alter energy mobilisation to top consumers in subarctic lakes. Nevertheless, pelagic and littoral habitats and food‐web compartments may still be highly integrated due to the potentially plastic foraging behaviour of top consumers.
Spatial patterns and climate drivers of carbon fluxes in terrestrial ecosystems of China
Authors: Yu Gui‐Rui , Zhu Xian‐Jin , Fu Yu‐Ling , He Hong‐Lin , Wang Qiu‐Feng , Wen Xue‐Fa , Li Xuan‐Ran , Zhang Lei‐Ming , Zhang Li , Su Wen , Li Sheng‐Gong , Sun Xiao‐Min , Zhang Yi‐Ping , Zhang Jun‐Hui , Yan Jun‐Hua , Wang Hui‐Min , Zhou Guang‐Sheng , Jia Bing‐Rui , Xiang Wen‐Hua , Li Ying‐Nian , Zhao Liang , Wang Yan‐Fen , Shi Pei‐Li , Chen Shi‐Ping , Xin Xiao‐Ping , Zhao Feng‐Hua , Wang Yu‐Ying , Tong Cheng‐Li 
Published: November 2012

AbstractUnderstanding the dynamics and underlying mechanism of carbon exchange between terrestrial ecosystems and the atmosphere is one of the key issues in global change research. In this study, we quantified the carbon fluxes in different terrestrial ecosystems in China, and analyzed their spatial variation and environmental drivers based on the long‐term observation data of ChinaFLUX sites and the published data from other flux sites in China. The results indicate that gross ecosystem productivity (GEP), ecosystem respiration (ER), and net ecosystem productivity (NEP) of terrestrial ecosystems in China showed a significantly latitudinal pattern, declining linearly with the increase of latitude. However, GEP, ER, and NEP did not present a clear longitudinal pattern. The carbon sink functional areas of terrestrial ecosystems in China were mainly located in the subtropical and temperate forests, coastal wetlands in eastern China, the temperate meadow steppe in the northeast China, and the alpine meadow in eastern edge of Qinghai‐Tibetan Plateau. The forest ecosystems had stronger carbon sink than grassland ecosystems. The spatial patterns of GEP and ER in China were mainly determined by mean annual precipitation (MAP) and mean annual temperature (MAT), whereas the spatial variation in NEP was largely explained by MAT. The combined effects of MAT and MAP explained 79%, 62%, and 66% of the spatial variations in GEP, ER, and NEP, respectively. The GEP, ER, and NEP in different ecosystems in China exhibited ‘positive coupling correlation’ in their spatial patterns. Both ER and NEP were significantly correlated with GEP, with 68% of the per‐unit GEP contributed to ER and 29% to NEP. MAT and MAP affected the spatial patterns of ER and NEP mainly by their direct effects on the spatial pattern of GEP.