bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatitis B virus infection is associated with deletion of chromosome 8p in multiple myeloma
Authors: Becker Nikolaus , Byl Anne , Friedrich Susanne , Jauch Anna , Schnitzler Paul , Egerer Gerlinde , Ho Anthony D , Goldschmidt Hartmut , Neben Kai 
Published: October 2012

AbstractSerological analyses within epidemiological cohort and case‐control studies indicate to an association between HBV infection and risk of multiple myeloma (MM). To verify the relationship with an independent approach, we investigated the correlation between HBV positivity and chromosomal aberrations within 680 patients of the National Center for Tumor Diseases Heidelberg for which the serological HBV status (HBsAg and anti‐HBc) and FISH data for five gains (1q21, 9q34, 11q23, 15q22, 19q13), five losses (6q21, 8p21, 13q14, 17p13, 22q11), and three IgH translocations [t(4,14), t(11,14), t(14,16)] were available. Deletion of 8p21 and 13q14 were shown associated with HBV positivity within hepatocellular carcinoma in other investigations. In the present evaluation, the odds ratio for loss of 8p21 was significantly elevated (OR = 2.74, 95% CL = 1.36–5.50, P = 0.0048) and for loss of 13q14 non‐significantly increased (OR = 1.40, 95% CL = 0.74–2.65) in anti‐HBc positive patients. The results provide further support for a role of HBV infection in the pathogenesis of MM.
A novel TRB@/NOTCH1 fusion gene in T‐cell lymphoblastic lymphoma with t(7;9)(q34;q34)
Authors: Yamamoto Katsuya , Nakamachi Yuji , Yakushijin Kimikazu , Miyata Yoshiharu , Okamura Atsuo , Kawano Seiji , Matsuoka Hiroshi , Minami Hironobu 
Published: October 2012

AbstractBackground: In T‐cell acute lymphoblastic leukemia/lymphoma (T‐ALL/LBL), activating mutations of NOTCH1 are observed in more than 50% of cases, whereas the t(7;9)(q34;q34) involving NOTCH1 at 9q34 and TRB@ at 7q34 is an extremely rare but recurrent translocation. Patient: A 41‐year‐old male with a large mediastinal mass, pleural effusion, and lymphadenopathy was diagnosed as having T‐LBL. Lymphoma cells were positive for CD4, CD8, CD2, CD3, CD5, CD7, CD10, and TdT. Results: G‐banding and spectral karyotyping of pleural effusion cells showed 47,XY,dup(1)(q21q32),t(7;9)(q34;q34),+20. Genomic polymerase chain reaction (PCR) revealed that the 5′ end of TRB@ J1‐5 was connected with the middle of NOTCH1 exon 25 (434 bp downstream from its 5′ end) in a ‘head‐to‐head’ configuration on the der(9)t(7;9), although nine extra bases were inserted between the two genes. Reverse transcription‐PCR confirmed expression of the TRB@/NOTCH1 fusion transcripts. Similarly, the 5′ end of J1‐5 was fused to the shortened exon 25 with nine extra bases. The NOTCH1 breakpoint in exon 25 was very close to transcription start sites of deleted Notch1 in murine T‐ALL. Conclusions: The TRB@/NOTCH1 fusion gene with a NOTCH1 breakpoint in exon 25, which has not previously been detected in four other reported cases with t(7;9), could lead to aberrant expression of the truncated NOTCH1 by TRB@ enhancer elements. The resultant NOTCH1 receptor deleting most of the extracellular domain may be implicated in the pathogenesis of T‐LBL by ligand‐independent, constitutive activation of the NOTCH1 pathway, suggesting avenues for future therapy with γ‐secretase inhibitors.
A sprayable luminescent pH sensor and its use for wound imaging in vivo
Authors: Schreml Stephan , Meier Robert J. , Weiß Katharina T. , Cattani Julia , Flittner Dagmar , Gehmert Sebastian , Wolfbeis Otto S. , Landthaler Michael , Babilas Philipp 
Published: October 2012

AbstractNon‐invasive luminescence imaging is of great interest for studying biological parameters in wound healing, tumors and other biomedical fields. Recently, we developed the first method for 2D luminescence imaging of pH in vivo on humans, and a novel method for one‐stop‐shop visualization of oxygen and pH using the RGB read‐out of digital cameras. Both methods make use of semitransparent sensor foils. Here, we describe a sprayable ratiometric luminescent pH sensor, which combines properties of both these methods. Additionally, a major advantage is that the sensor spray is applicable to very uneven tissue surfaces due to its consistency. A digital RGB image of the spray on tissue is taken. The signal of the pH indicator (fluorescein isothiocyanate) is stored in the green channel (G), while that of the reference dye [ruthenium(II)‐tris‐(4,7‐diphenyl‐1,10‐phenanthroline)] is stored in the red channel (R). Images are processed by rationing luminescence intensities (G/R) to result in pseudocolor pH maps of tissues, e.g. wounds.
Net greenhouse gas balance in response to nitrogen enrichment: perspectives from a coupled biogeochemical model
Authors: Lu Chaoqun , Tian Hanqin 
Published: October 2012

AbstractIncreasing reactive nitrogen (N) input has been recognized as one of the important factors influencing climate system through affecting the uptake and emission of greenhouse gases (GHG). However, the magnitude and spatiotemporal variations of N‐induced GHG fluxes at regional and global scales remain far from certain. Here we selected China as an example, and used a coupled biogeochemical model in conjunction with spatially explicit data sets (including climate, atmospheric CO2, O3, N deposition, land use, and land cover changes, and N fertilizer application) to simulate the concurrent impacts of increasing atmospheric and fertilized N inputs on balance of three major GHGs (CO2, CH4, and N2O). Our simulations showed that these two N enrichment sources in China decreased global warming potential (GWP) through stimulating CO2 sink and suppressing CH4 emission. However, direct N2O emission was estimated to offset 39% of N‐induced carbon (C) benefit, with a net GWP of three GHGs averaging −376.3 ± 146.4 Tg CO2 eq yr−1 (the standard deviation is interannual variability of GWP) during 2000–2008. The chemical N fertilizer uses were estimated to increase GWP by 45.6 ± 34.3 Tg CO2 eq yr−1 in the same period, and C sink was offset by 136%. The largest C sink offset ratio due to increasing N input was found in Southeast and Central mainland of China, where rapid industrial development and intensively managed crop system are located. Although exposed to the rapidly increasing N deposition, most of the natural vegetation covers were still showing decreasing GWP. However, due to extensive overuse of N fertilizer, China's cropland was found to show the least negative GWP, or even positive GWP in recent decade. From both scientific and policy perspectives, it is essential to incorporate multiple GHGs into a coupled biogeochemical framework for fully assessing N impacts on climate changes.
The ALK translocation in advanced non‐small‐cell lung carcinomas: preapproval testing experience at a single cancer centre
Authors: Conde Esther , Angulo Bárbara , Izquierdo Elisa , Muñoz Luna , Suárez‐Gauthier Ana , Plaza Carlos , Dominguez Nuria , Torres Maribel , Madrigal Luis , Rubio‐Viqueira Belén , Belda‐Iniesta Cristobal , Hidalgo Manuel , López‐Ríos Fernando 
Published: October 2012

AimsTo study the ALK translocation in patients with advanced non‐small‐cell lung carcinomas (NSCLCs) seen at a European cancer centre, and its association with EGFR mutations, KRAS mutations and MET amplification.Methods and resultsThe study included samples from 86 patients diagnosed with advanced NSCLC. ALK fluorescence in‐situ hybridization (FISH) was performed using the ALK break‐apart probe set (Vysis). ALK FISH‐positive cases were defined as those with more than 15% break‐apart signals or isolated red signals in 50 cells. EGFR and KRAS mutations were determined by direct sequencing. All ALK‐positive cases were analysed retrospectively for MET amplification using a FISH assay, and for ALK mutations by sequencing. We found nine (10.5%) ALK‐positive cases, all in adenocarcinomas and the majority in female patients (88.9%). Signet ring cells were observed in four (44.4%) of the nine patients. None of the ALK translocated cases showed MET amplifications or EGFR, KRAS and ALK mutations.ConclusionsThe prevalence of ALK translocation in an unselected population of European patients with advanced NSCLCs was 10%. This alteration was mutually exclusive with EGFR and KRAS mutations, as well as with MET amplification. If multiplexing is considered at the preanalytical phase, lung biopsy specimens are sufficient for performing several predictive assays.
Hotspots of exotic free‐spawning sex: man‐made environment facilitates success of an invasive seastar
Authors: Ling Scott D. , Johnson Craig R. , Mundy Craig N. , Morris Alice , Ross D. Jeff 
Published: October 2012

Summary1. The introduction of exotic species to new areas poses a major threat to the environment. For those introduced species that establish and survive beyond the short term, the opportunities to manage the risk of continuing spread often rest with limiting reproductive output. The introduced northern Pacific seastar Asterias amurensis is an ecologically important pest that has established in the Derwent Estuary (Australia). Driven by oversupply of bivalve prey, it is persistent, abundant and fecund when associated with man‐made structures such as docks, marinas, jetties and piers, that is, ‘wharves’.2. As a free‐spawning invertebrate, fertilization by A. amurensis is a critical life‐history stage constrained by strong Allee effects. Eggs must be released in close proximity to sperm sources because the chances of achieving fertilization drastically reduce with increasing distances of spawner separation.3. Investigation of zygote production in the Derwent Estuary using a spatially explicit model of free‐spawning fertilization shows that A. amurensis at wharves, while representing <10% of the total population in the estuary and concentrated in <0·1% of the total area, may contribute >90% of total zygote production. Given the seastars’ long‐lived and highly dispersive larvae, we show that wharves not only represent important sites of invasion but also facilitate propagule pressure promoting secondary invasions.4. Synthesis and applications. In the absence of effective pest control solutions, focusing on reproductive hotspots has the potential to reduce further spread of established marine pests and to alleviate ongoing ecological impacts. In the case of the northern Pacific seastar, elimination of highly localized wharf populations annually prior to spawning can reduce overall zygote production by up to estimated ∼90%. The long‐term protection of key sources of larval production is a common goal for marine reserve design and fisheries management. However, the same concept but in reverse, whereby larval production is minimized at key sources, could be effective in the management of introduced pests in subtidal marine environments.
Multi‐level functional responses for wildlife conservation: the case of threatened caribou in managed boreal forests
Authors: Moreau Guillaume , Fortin Daniel , Couturier Serge , Duchesne Thierry 
Published: October 2012

Summary1. The selection for particular habitat patches can vary as a function of local and regional levels of anthropogenic disturbance. Although such functional responses can better reveal habitat loss for species of precarious status faced with dwindling resources, they remain rarely used in conservation planning. We show that functional responses can occur at multiple levels, even as nested hierarchies, and that they can explain the plasticity in habitat selection observed in threatened forest‐dwelling caribou Rangifer tarandus caribou, within and among home‐ranges.2. Twenty‐seven caribou were followed with global positioning system collars between 2005 and 2010. Generalized linear mixed models served as the basis from which we built multi‐level functional responses characterizing how caribou alter their selection for closed‐canopy conifer forests, depending upon the availability of these forests and the amount of cutovers and roads.3. Caribou increased their selection for closed‐canopy conifer forests in areas of their home‐range that were comprised of a high proportion of recent cutovers during calving and summer and of high closed‐canopy conifer forests during winter. Also, caribou that were established in highly disturbed areas displayed an overall stronger selection for conifer forests. These individuals further adjusted their selection for conifer forests in areas of their home‐ranges that were largely comprised of recent cutovers. This concurrent response to local and global anthropogenic disturbances provides evidence of nested‐hierarchical functional responses.4. Synthesis and applications. Reliable characterization of disturbance effects on animals is necessary for conservation planning. Multi‐level functional responses can accurately describe animal distribution, and we provided a framework for modelling these responses. Our multi‐level functional responses indicate that fixing habitat requirements based on patterns of habitat selection for the average amount of disturbance can be misleading because it overlooks plasticity in the response of animals to habitat heterogeneity. For example, selection of closed‐canopy conifer forests by caribou generally became stronger with increasing disturbance levels. Anthropogenic disturbance thus could not only lead to the functional loss of residual habitat, but it can also increase the ‘relative value’ of residual patches. Our study provides a tool for more thorough assessments of spatial variation in the attractiveness of resource patches and, presumably, in the fitness benefits.
Cost–benefit analysis of ecological networks assessed through spatial analysis of ecosystem services
Authors: Newton Adrian C. , Hodder Kathy , Cantarello Elena , Perrella Lorretta , Birch Jennifer C. , Robins James , Douglas Sarah , Moody Christopher , Cordingley Justine 
Published: October 2012

Summary1. The development of ecological networks could enhance the ability of species to disperse across fragmented landscapes and could mitigate against the negative impacts of climate change. The development of such networks will require widespread ecological restoration at the landscape scale, which is likely to be costly. However, little information is available regarding the cost‐effectiveness of restoration approaches.2. We address this knowledge gap by examining the potential impact of landscape‐scale habitat restoration on the value of multiple ecosystem services across the catchment of the River Frome in Dorset, England. This was achieved by mapping the market value of four ecosystem services (carbon storage, crops, livestock and timber) under three different restoration scenarios, estimating restoration costs, and calculating net benefits.3. The non‐market value of additional services (cultural, aesthetic and recreational value) was elicited from local stakeholders using an online survey tool. Flood risk was assessed using a scoring approach. Spatial Multi‐Criteria Analysis (MCA) was conducted, incorporating both market and non‐market values, to evaluate the relative benefits of restoration scenarios. These were compared with impacts of restoration on biodiversity value.4. Multi‐Criteria Analysis results consistently ranked restoration scenarios above a non‐restoration comparator, reflecting the increased provision of multiple ecosystem services. Restoration scenarios also provided benefits to biodiversity, in terms of increased species richness and habitat connectivity. However, restoration costs consistently exceeded the market value of ecosystem services.5. Synthesis and applications. Establishment of ecological networks through ecological restoration is unlikely to deliver net economic benefits in landscapes dominated by agricultural land use. This reflects the high costs of ecological restoration in such landscapes. The cost‐effectiveness of ecological networks will depend on how the benefits provided to people are valued, and on how the value of non‐market benefits are weighted against the costs of reduced agricultural and timber production. Future plans for ecological restoration should incorporate local stakeholder values, to ensure that benefits to people are maximised.
Climate change as a main driver of ecological research
Authors: Pettorelli Nathalie 
Published: October 2012

Summary1. Climate change is a major threat to biodiversity, ecosystem services, and human well‐being. Mitigating its effects on living organisms and societies will be at the heart of most environmental management strategies, which will need to be informed by integrative scientific approaches. This Issue’s Special Profile provides examples of such approaches.2. Responses of species to change in climatic conditions will range from thriving (i.e. species capable of living under the new set of conditions) to adapting (i.e. species capable of surviving a change in global conditions by changing their ecology and/or distribution) and going extinct. Yet there is a need to identify which species will fall into which categories, as well as a need to understand how to facilitate species’ ability to adapt to change.3. Landscape management will be key to ensuring that functional, resilient ecosystems are maintained. Preserving the complexity and function of ecosystems can help mitigate the impact of extreme climatic conditions on the delivery of vital services such as climate regulation, primary production and water retention.4. To mitigate further biodiversity loss, healthy habitats will also need to be better connected. In many situations, developing ecological networks will require costly habitat restoration at large spatial scales: to maximise opportunities for these networks to be created and be successful, landscape‐scale assessments of the provision and value of multiple ecosystem services under alternative management regimes will need to inform decisions as to where and how to implement their creation.5. Synthesis and applications. Climate change is only starting to shape the ecological research agenda, as the complexity of the impact of this phenomenon on biodiversity and ecosystem services slowly unveils. Because changes in climatic conditions are expected to hit everyone everywhere, effective solutions for climate change mitigation will require science to truly engage with society and support decision‐making processes at local, national and international scales.
Integrating climate change into calcareous grassland management
Authors: Maalouf Jean‐Paul , Le Bagousse‐Pinguet Yoann , Marchand Lilian , Bâchelier Emilie , Touzard Blaise , Michalet Richard 
Published: October 2012

Summary1. Climate change is rarely taken into consideration in conservation management strategies aimed at protecting biodiversity from other threats. We examined the implications of this perspective in European calcareous grasslands, which are among the richest herbaceous systems of the continent and are therefore of high nature conservation interest. These systems are currently undergoing species loss because of the abandonment of agro‐pastoral practices. Classic ecological theory assumes that conservation management activities (such as regular mowing) and drought events should increase diversity through decreased plant competition in abandoned mesic communities. In turn, this could reduce diversity in xeric communities although positive plant interactions (facilitation) might buffer these negative effects and maintain diversity.2. We studied the effects of regular mowing and experimentally induced drought on diversity and biotic interactions between two transplanted species in mesic and xeric calcareous grasslands. The study sites in south‐western France have not been subjected to any management for the last 30 years.3. Drought did not affect mesic systems although mowing increased plant diversity through decreased competition. By contrast, mowing had no significant effect in xeric systems although drought decreased diversity. Interestingly, transplants were subject to neither competition nor facilitation in the xeric systems.4.
Synthesis and applications. Regular mowing and drought events impact plant diversity of mesic and xeric calcareous grassland communities in different ways. We recommend regular mowing of mesic grasslands, even in the context of climate change. By contrast, we recommend less‐frequent mowing of xeric grasslands together with specific interventions such as assisted migration for species with poor drought tolerance. Similar studies in other ecosystems on larger spatial and temporal scales should examine the dual effects of management and climate change to identify appropriate management programmes.
Identifying unidirectional and dynamic habitat filters to faunal recolonisation in restored mine‐pits
Authors: Craig Michael D. , Hardy Giles E. St J. , Fontaine Joseph B. , Garkakalis Mark J. , Grigg Andrew H. , Grant Carl D. , Fleming Patricia A. , Hobbs Richard J. 
Published: October 2012

Summary1. There is increasing evidence that passive faunal recolonisation of restored areas can take decades or even centuries, reducing benefits to biodiversity from restoration. Thus, there is a need to develop restoration and management strategies that facilitate and accelerate faunal recolonisation. This requires identification of habitat features that act as filters to slow or prevent recolonisation and whether those filters are temporally unidirectional or dynamic.2. We investigated successional patterns of reptiles and mammals in restored mine‐pits in south‐western Australia to identify potential filters to faunal recolonisation. We sampled reptiles and small mammals using 30 trapping grids across each of four restoration ages (4, 8, 12 and 17‐years old) and unmined forest and assessed vegetation structure to identify animal–habitat relationships.3. Mammal communities in restored areas converged on unmined forest communities as restoration matured, and all species recolonised rapidly, indicating there were no filters to mammal recolonisation. In contrast, reptile communities did not converge in the same way, indicating there were filters that slowed or prevented reptile recolonisation. We identified three reptile species that were slow, or failed, to recolonise restored areas and a fourth species that rapidly recolonised but disappeared as restoration matured. We identified low coarse woody debris (CWD) volumes and high overstorey stem densities as likely filters; the former is a unidirectional filter that will decrease gradually over long time frames, possibly centuries, while the latter is a dynamic filter that fluctuates in its intensity over short time frames of years.4. Synthesis and applications. Our study adds to growing evidence that filters to faunal recolonisation may be widespread in restored areas, with important implications for restoration practices. Firstly, examining individual species may more effectively identify filters than examining community successional patterns. Secondly, filters can persist over long time frames, possibly centuries, so management, such as the provision and accelerated development of CWD, may need to occur over similar time frames. Lastly, filters can be dynamic and repeated management interventions, such as thinning, may be required to overcome these filters. The growing evidence for filters suggests that facilitating faunal recolonisation is more complex than simply returning vegetation to restoration sites.