bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal perturbations of gravitationally unstable, transient boundary layers in porous media
Authors: Daniel Don , Tilton Nils , Riaz Amir 
Published: July 2013

AbstractWe study the linear stability of gravitationally unstable, transient, diffusive boundary layers in porous media using non-modal stability theory. We first perform a classical optimization procedure, using an adjoint-based method, to obtain the perturbations at the initial time $t= {t}_{p} $ that have a maximum amplification at a final time $t= {t}_{f} $. We then investigate the sensitivity of the optimal perturbations to the initial time, ${t}_{p} $, and the final time, ${t}_{f} $, as well as different measures of perturbation amplification. Due to the transient nature of the base state, we demonstrate that there is an optimal initial perturbation time, ${ t}_{p}^{o} $. By rescaling the problem, we develop analytical relationships for the optimal initial time and wavenumber in terms of aquifer properties. We also demonstrate that the classical optimization procedure essentially recovers the dominant perturbation structures predicted by a quasi-steady modal analysis. Although the classical optimal perturbations are mathematically valid, we observe that due to physical constraints, they are unlikely to reflect analogous laboratory experiments. Therefore, we propose a modified optimization procedure (MOP) that constrains the optimization to physically admissible initial perturbation fields. We compare the results of the classical and modified optimization procedures with quasi-steady modal analyses and initial value problems commonly used in the literature. Finally, we validate the predictions of the modified optimization scheme by performing direct numerical simulations (DNS) that emulate the onset of convection in physical systems.
Recovery: an international perspective
Authors: Slade Mike , Amering Michaela , Oades Lindsay 
Published: July 2013

SummaryAims– To review developments in recovery-focussed mental health services internationally.Methods– Two forms of ‘recovery’ which have been used in the literature are considered, and international examples of recovery-focussed initiatives reviews. A ‘litmus test’ for a recovery-focussed service is proposed.Results– ‘Clinical recovery’ has emerged from professional literature, focuses on sustained remission and restoration of functioning, is invariant across individuals, and has been used to establish rates of recovery. ‘Personal recovery’ has emerged from consumer narratives, focuses on living a satisfying, hopeful and contributing life even with limitations caused by the illness, varies across individuals, and the empirical evidence base relates to stages of change more than overall prevalence rates. Clinical and personal recovery are different. Two innovative, generalisable and empirically investigated examples are given of implementing a focus on personal recovery: the Collaborative Recovery Model in Australia, and Trialogues in German-speaking Europe. The role of medication is an indicator: services in which all service users are prescribed medication, in which the term ‘compliance’ is used, in which the reasoning bias is present of attributing improvement to medication and deterioration to the person, and in which contact with and discussion about the service user revolves around medication issues, are not personal recovery-focussed services.Conclusions– The term ‘Recovery’ has been used in different ways, so conceptual clarity is important. Developing a focus on personal recovery is more than a cosmetic change – it will entail fundamental shifts in the values of mental health services.Declaration of Interest: None.
Spt6 prevents transcription-coupled loss of posttranslationally modified histone H3
Authors: Kato Hiroaki , Okazaki Kosuke , Iida Tetsushi , Nakayama Jun-ichi , Murakami Yota , Urano Takeshi 
Published: July 2013

AbstractThe tail of histone H3 is an ideal medium for storing epigenetic information because displacement of histone H3 is heavily restricted during transcription. To maintain the locus-specific modifications of histone H3, histone molecules should be retained locally at the original position through multiple rounds of transcription. Here, we found that fission yeast Spt6, a highly conserved RNA polymerase II-interacting histone H3–H4 chaperone, is essential for the maintenance of Lys-4 and Lys-9 methylation of histone H3 in euchromatin and heterochromatin, respectively. In euchromatin, loss of Lys-4 methylated histone H3 and deposition of newly synthesized Lys-56 acetylated histone H3 induced by Spt6 inactivation were coupled with transcription. While in heterochromatin, Spt6 prevents histone turnover and cryptic transcription in parallel with Clr3 histone deacetylase. We propose that Spt6 retains posttranslationally modified histone H3 during transcription to maintain epigenome integrity.
Modeling combined coherent and incoherent scattering structures for light trapping in solar cells
Authors: Abass Aimi , Trompoukis Christos , Leyre Sven , Burgelman Marc , Maes Bjorn 
Published: July 2013

Current structures for solar cells or LEDs often incorporate layers of various optical regimes, with a mixture of coherent, partially coherent or incoherent behavior. We developed a simple and efficient calculation method to study such combined solar cell structures with both wave and ray optics sections. These One-Pass Coherent calculations take wave effects into account where they matter the most, while avoiding a large computational domain to model rough structures. The method simulates a general diffuser by working directly with the reflected wavefronts, instead of using its geometry. We utilize this method to study thin film silicon solar cell structures with a grating on the front and a diffuser at the back. More absorption is obtained with the combined light trapping scheme of appropriate characteristics, compared with grating-only or diffuser-only counterparts. Finally, we report a significant effect of incoherence on the absorption of fairly thin (∼10 μm) cells. We demonstrate that partially incoherent light can be more efficiently absorbed than fully coherent light on average over a broad wavelength range. It turns out that the scarcity of guided modes for fully coherent light can hinder the grating enhancement, leading to a consistently better performance when light coherence is limited or lost.
A scenario for impacts of water availability loss due to climate change on riverine fish extinction rates
Authors: Tedesco Pablo A. , Oberdorff Thierry , Cornu Jean‐François , Beauchard Olivier , Brosse Sébastien , Dürr Hans H. , Grenouillet Gaël , Leprieur Fabien , Tisseuil Clément , Zaiss Rainer , Hugueny Bernard 
Published: July 2013

Summary

Current models estimating impact of habitat loss on biodiversity in the face of global climate change usually project only percentages of species ‘committed to extinction’ on an uncertain time‐scale. Here, we show that this limitation can be overcome using an empirically derived ‘background extinction rate–area’ curve to estimate natural rates and project future rates of freshwater fish extinction following variations in river drainage area resulting from global climate change.

Based on future climatic projections, we quantify future active drainage basin area losses and combine them with the extinction rate–area curve to estimate the future change in extinction rate for each river basin. We then project the number of extinct species in each river basin using a global data base of freshwater fish species richness.

The median projected extinction rate owing to climate change conditions is c. 7% higher than the median background extinction rate. A closer look at the pattern reveals great geographical variations highlighting an amplification of aridity by 2090 and subsequent increase in extinction rates in presently semi‐arid and Mediterranean regions. Among the 10% most‐impacted drainage basins, water availability loss will increase background extinction rates by 18·2 times (median value).

Projected numbers of extinct species by 2090 show that only 20 river basins among the 1010 analysed would experience fish species extinctions attributable to water availability loss from climate change. Predicted numbers of extinct species for these rivers range from 1 to 5.

Synthesis and applications. Our results strongly contrast with previous alarming predictions of huge surface‐dependent climate change–driven extinctions for riverine fishes and other taxonomic groups. Furthermore, based on well‐documented fish extinctions from Central and North American drainages over the last century, we also show that recent extinction rates are, on average, 130 times greater than our projected extinction rates from climate change. This last result implies that current anthropogenic threats generate extinction rates in rivers far greater than the ones expected from future water availability loss. We thus argue that conservation actions should be preferentially focused on reducing the impacts of present‐day anthropogenic drivers of riverine fish extinctions.
EDITORIAL: Ecological science for ecosystem services and the stewardship of Natural Capital
Authors: Hails Rosemary S. , Ormerod Steve J. 
Published: July 2013

Summary

National and international assessments are increasingly highlighting the unsustainable use of earth's natural resources in the face of population increase, growing material affluence and global change. In all likelihood, the use and degradation of natural resources will continue.

In contrast to resource depletion, the concept of natural capital emphasises how the environment is an asset to be managed, to ensure that the benefits which flow from it are sustained for future generations. These benefits are the ecosystem goods and services upon which all people rely for their continued survival and well‐being both now and, ideally, in perpetuity.

Despite their importance, the evidence‐base and quantitative understanding of links between biodiversity, ecosystem function and ecosystem services are insufficient to allow informed use and management. Moreover, the concepts of natural capital and ecosystem services are insufficiently mainstream to influence decisions that currently favour the production of food and fibre rather than less tangible services such as climate regulation, air and water purification, pollination or the contributions of environment to health.

There are specific challenges to ecological science in this interdisciplinary endeavour: specifically, to develop frameworks for identifying and monitoring natural capital; to parameterise factors affecting ecosystem services and their resilience to change; to integrate the complexity of ecological systems into ecosystem service valuation; and to characterise the synergies and trade‐offs between ecosystem services in different management and policy scenarios.

Synthesis and applications. The five papers in this Special Profile exemplify just some of the leading work through which ecologists in the UK are contributing nationally and internationally to these needs, stemming from the UK National Ecosystem Assessment ‐ the first national scale exercise of its type in the world. We expect a major, worldwide increase in work on ecosystem services and natural capital in future as decisions on ecosystem use of management are squeezed increasingly between the needs of exploitation and protection.
Greening of arid Australia: New insights from extreme years
Authors: Wardle Glenda M. , Pavey Chris R. , Dickman Chris R. 
Published: July 2013

AbstractIn comparison with drylands elsewhere, the unpredictability of rainfall in central Australia is globally distinctive. The transformative rhythms of arid Australia reflect extremes of climatic conditions rather than seasons, and are characterized by irregular pulses of productivity that punctuate long periods of drought. These decadal‐scale dynamics are only now beginning to be understood. Further complications in predicting and managing the biological processes within these landscapes arise from the vast spatial extent of arid and semi‐arid communities, and increasing recognition of the heterogeneities that drive the formation of patterns across multiple scales. In 2010 and 2011 flooding rains broke long‐standing rainfall records and triggered an anticipated greening of the typically dry red landscapes of central Australia. These unusual climatic events provided an unparalleled opportunity to test ideas about productivity and function, bottom‐up versus top‐down effects, and differential responses of biota that reflect landscape connections and heterogeneity. Migrations of species outside their known ranges, irruptions of rodents and redistribution of resources are just a few of the novel observations that were reported. The transformation of the landscape also presented land managers with challenges stemming from the influx of invasive species that trigger novel ecological interactions and processes. The papers presented in this special issue describe how ecologists and managers responded to the unprecedented rainfall events, key lessons that we have learnt, and practical recommendations on how to improve conservation outcomes for the fragile inland environment into the future.
Three‐Dimensional Architecture of the Ovine Oviductal Mucosa
Authors: Yániz J. L. , Carretero T. , Recreo P. , Arceiz E. , Santolaria P. 
Published: July 2013

SummaryThe objective of this work was to establish for the first time a complete three‐dimensional model of the ovine oviductal mucosa. The oviducts of 15 cyclic ewes were examined combining the direct examination of the mucosa, by scanning electron microscopy (SEM) and histology, with the SEM observation of resin moulds of the oviductal lumen. Around the ostium abdominale, all longitudinal primary folds and wide secondary are seen to form cul‐de‐sacs, with their opening pointing in the ovarian direction were observed. At the connection of the ampulla to the isthmus, there is a sharp change in the morphology, from a high folded structure to a smoother one. In the utero‐tubal junction, the primary folds broaden and become more voluminous, the lumen has a slit‐like appearance, and secondary folds form cul‐de‐sacs with their opening oriented towards the uterus. The areas between the folds throughout the lumen of the oviduct show a high degree of complexity. The presence of crypts was observed in all the regions studied, branched in the ampulla and spiniform in the isthmus. Marked variations were observed in the oviductal epithelium depending on the oviductal segment and the basal or apical areas of the folds. The variations found regarding the phase of the oestrous cycle were similar to those described in studies of other species. The anatomy of the oviductal mucosa provides a complex system that seems to be designed to regulate the movement of fluids and the passage of cells within the oviductal canal.
Causal Responsibility and Counterfactuals
Authors: Lagnado David A. , Gerstenberg Tobias , Zultan Ro'i 
Published: July 2013

AbstractHow do people attribute responsibility in situations where the contributions of multiple agents combine to produce a joint outcome? The prevalence of over‐determination in such cases makes this a difficult problem for counterfactual theories of causal responsibility. In this article, we explore a general framework for assigning responsibility in multiple agent contexts. We draw on the structural model account of actual causation (e.g., Halpern & Pearl, 2005) and its extension to responsibility judgments (Chockler & Halpern, 2004). We review the main theoretical and empirical issues that arise from this literature and propose a novel model of intuitive judgments of responsibility. This model is a function of both pivotality (whether an agent made a difference to the outcome) and criticality (how important the agent is perceived to be for the outcome, before any actions are taken). The model explains empirical results from previous studies and is supported by a new experiment that manipulates both pivotality and criticality. We also discuss possible extensions of this model to deal with a broader range of causal situations. Overall, our approach emphasizes the close interrelations between causality, counterfactuals, and responsibility attributions.
Immune responses to an upper body tri‐set resistance training session
Authors: Brunelli Diego T. , Caram Kaue , Nogueira Felipe R. D. , Libardi Cleiton A. , Prestes Jonato , Cavaglieri Cláudia R. 
Published: July 2013

SummaryThe purpose of this study was to evaluate the acute immune responses to an upper body tri‐set resistance training (RT) session in RT trained individuals. Eighteen young trained men (22·0 ± 1·8 years) were randomly assigned to an exercise group (EG; n = 9) or control group (CG; n = 9). The EG completed an acute tri‐set RT protocol using two combinations of three exercises for the same muscle group with six to eight repetitions at 75% of one repetition maximum (1RM) for each exercise. Blood samples were collected before (Pre), and 15 min (Post) and 24 h (P24h) after the acute RT protocol to determine basal and acute total leucocytes and leucocyte subsets counting, interleukin‐6 (IL‐6), tumour necrosis factor‐α (TNF‐α) and cortisol. There were significant increases in total leucocytes, monocytes and neutrophils at Post as compared with Pre (P<0·05). Additionally, total leucocytes and monocytes were reduced even at P24h when compared to Pre (P<0·05). There were no significant changes in plasma concentrations of TNF‐α, IL‐6 and cortisol throughout the measured moments. As compared to CG, EG demonstrated very large effect sizes for total leucocytes, neutrophils and monocytes 15 min postprotocol and a reduction (trivial and small effect sizes) P24h. These results suggest that the tri‐set RT session did not exacerbate the acute inflammatory response and might be a good option for variations in RT methods for trained individuals.
Learning curve of conventional transbronchial needle aspiration
Authors: Tutar Nuri , Büyükoğlan Hakan , Yılmaz İnsu , Kanbay Asiye , Önal Ömer , Bilgin Mehmet , Canöz Özlem , Demir Ramazan , Oyak Fatma Sema , Gülmez İnci , Çetinkaya Erdoğan 
Published: July 2013

AbstractBackground and AimsIntrathoracic lymphadenopathy usually occurs as a result of neoplasm, granulomatous diseases, infections or reactive hyperplasia. Conventional transbronchial needle aspiration (C‐TBNA) is a cheap and safe procedure for diagnosing intrathoracic lymphadenopathy. The aim of this study was to assess the learning curve and diagnostic accuracy of C‐TBNA after an observational education programme.MethodsIn the present study, we retrospectively evaluated our first 62 C‐TBNA procedures at Erciyes University between May 2012 and December 2012 after an observational education programme. The first 31 patients were defined as group A, and the second 31 patients as group B.ResultsOne hundred and seven lymph nodes were sampled in 62 patients by C‐TBNA. Adequate lymph node samples were obtained in 52 of the 62 patients (83.8%). In these 52 patients, two patients had a diagnosis of ‘suspicious of malignancy’ by C‐TBNA, and these patients were excluded from the analysis. In the remaining 50 cases who had adequate results, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and diagnostic accuracy per patient were 80.6%, 92.9%, 96.7%, 65.0% and 84.0%, respectively. The diagnostic accuracy rates of C‐TBNA for Group A and B were 72.0% (18/25) and 96.0% (24/25), and the difference was statistically significant (P < 0.05).ConclusionC‐TBNA is a useful diagnostic procedure for sampling intrathoracic lymphadenopathies and masses that are adjacent to the bronchial system. An observational education programme is helpful for learning C‐TBNA. The diagnostic yield improves in time, and approximately 30 procedures may be sufficient to achieve successful results.
Maspin expression in the invasive margin of primary melanomas may reflect an aggressive tumor phenotype
Authors: Pföhler Claudia , Knöpflen Tobias , Körner Rebecca , Vogt Thomas , Rösch Alexander , Müller Cornelia S.L. 
Published: July 2013

SummaryBackgroundThe role of maspin has been discussed controversially in different tumors. In the majority of malignant tumors, maspin seems to act as a tumor suppressor. However, data about maspin expression as well as its function in melanoma are very inconsistent.ObjectiveTo investigate the expression of maspin in melanomas and to correlate the intensity of maspin staining with prognostic parameters of the tumor and with progression‐free and overall survival.Patients and MethodsPrimary melanomas from 47 patients were investigated for maspin expression using immunohistochemistry.ResultsMaspin was heterogeneously expressed predominantly in the cytoplasm of melanoma cells. Maspin staining intensity in the invasive part of the tumor correlated with parameters of prognosis such as Clark level (p = 0.05), tumor thickness (p = 0.002) and stage of disease (p = 0.023). Maspin staining intensity in the invasive front of the tumor significantly correlated with death from disease (p = 0.007) and shortened overall survival (p = 0.007).ConclusionsIn accordance with data concerning maspin expression in colorectal cancers, the expression of this protein in the invasive front of primary melanomas seems to correlate with local infiltration and tumor aggressiveness. Strong maspin expression in the invasive margin of primary melanomas therefore might reflect an aggressive tumor phenotype.
Species‐based risk assessments for biological invasions: advances and challenges
Authors: Kumschick Sabrina , Richardson David M. 
Published: July 2013

AbstractAimAn increasingly important component of invasive species management involves the formal assessment of risks associated with particular species becoming invasive and causing impact. We evaluated recent developments in risk assessment (RA) for alien species, with special emphasis on species‐based pre‐border assessments for intentional introductions. Our aim was to identify important advances and key challenges.LocationGlobal.MethodsA literature review was done to determine which approaches have been developed and fine‐tuned over the last two decades, which of these have worked best and which are most widely used. We identified priorities for improving our ability to assess risks.ResultsThe review is divided into sections on various types and foci of RAs: invasion stage, taxon, ecosystem, assessment method and impact type. RAs for plants are the most advanced, with the Australian Weed Risk Assessment (A‐WRA) being the most widely applied and tested protocol. Based on the history of the A‐WRA, we highlight advances that have been made in assessing risk of alien species for pre‐border control and identify remaining challenges.Main conclusionsCurrently available RAs have proven to be cost‐effective, but there is room for substantial improvement. Further work is needed to separate likelihood and consequence more explicitly, and provide better and more objective means for assessing risks of impact. Types and levels of uncertainty need to be more effectively incorporated. Advanced RA protocols are needed for taxa other than plants and vertebrates. The latest insights from research in invasion ecology need to be incorporated, and advances in other fields must also be taken into account.