bluuebunny/crossref_metadata_2025 huggingface dataset:
Poincaré-Birkhoff Theorems in random dynamics
Authors: Pelayo Álvaro , Rezakhanlou Fraydoun
Published: May 2016

We propose a generalization of the Poincaré-Birkhoff Theorem on area-preserving twist maps to area-preserving twist maps

F
F

that are random with respect to an ergodic probability measure. In this direction, we will prove several theorems concerning existence, density, and type of the fixed points. To this end first we introduce a randomized version of generalized generating functions, and verify the correspondence between its critical points and the fixed points of

F
F

, a fact which we successively exploit in order to prove the theorems. The study we carry out needs to combine probabilistic techniques with methods from nonlinear PDE, and from differential geometry, notably Moser’s method and Conley-Zehnder theory. Our stochastic model in the periodic case coincides with the classical setting of the Poincaré-Birkhoff Theorem.
Dual function of cTAGE5 in collagen export from the endoplasmic reticulum
Authors: Tanabe Tomoya , Maeda Miharu , Saito Kota , Katada Toshiaki
Published: May 2016

Two independent functions of cTAGE5 have been reported in collagen VII export from the endoplasmic reticulum (ER). cTAGE5 not only forms a cargo receptor complex with TANGO1, but it also acts as a scaffold to recruit Sec12, a guanine-nucleotide exchange factor for Sar1 GTPase, to ER exit sites. However, the relationship between the two functions remains unclear. Here we isolated point mutants of cTAGE5 that lost Sec12-binding ability but retained binding to TANGO1. Although expression of the mutant alone could not rescue the defects in collagen VII secretion mediated by cTAGE5 knockdown, coexpression with Sar1, but not with the GTPase-deficient mutant, recovered secretion. The expression of Sar1 alone failed to rescue collagen secretion in cTAGE5-depleted cells. Taken together, these results suggest that two functionally irreplaceable and molecularly separable modules in cTAGE5 are both required for collagen VII export from the ER. The recruitment of Sec12 by cTAGE5 contributes to efficient activation of Sar1 in the vicinity of ER exit sites. In addition, the GTPase cycle of Sar1 appears to be responsible for collagen VII exit from the ER.
SimLoRD: Simulation of Long Read Data
Authors: Stöcker Bianca K. , Köster Johannes , Rahmann Sven
Published: May 2016

Motivation: Third generation sequencing methods provide longer reads than second generation methods and have distinct error characteristics. While there exist many read simulators for second generation data, there is a very limited choice for third generation data.

Results: We analyzed public data from Pacific Biosciences (PacBio) SMRT sequencing, developed an error model and implemented it in a new read simulator called SimLoRD. It offers options to choose the read length distribution and to model error probabilities depending on the number of passes through the sequencer. The new error model makes SimLoRD the most realistic SMRT read simulator available.

Availability and Implementation: SimLoRD is available open source at http://bitbucket.org/genomeinformatics/simlord/ and installable via Bioconda ( http://bioconda.github.io ).

Contact:  Bianca.Stoecker@uni-due.de or Sven.Rahmann@uni-due.de .

Supplementary information:  Supplementary data are available at Bioinformatics online.
Stirred but not shaken: population and recruitment genetics of the scallop (Pecten fumatus) in Bass Strait, Australia
Authors: Ovenden Jennifer R. , Tillett Bree J. , Macbeth Michael , Broderick Damien , Filardo Fiona , Street Raewyn , Tracey Sean R. , Semmens Jayson
Published: May 2016

We report population genetic structure and fine-scale recruitment processes for the scallop beds (Pecten fumatus) in Bass Strait and the eastern coastline of Tasmania in southern Australia. Conventional population pairwise FST analyses are compared with novel discriminant analysis of principal components (DAPC) to assess population genetic structure using allelic variation in 11 microsatellite loci. Fine-scale population connectivity was compared with oceanic features of the sampled area. Disjunct scallop beds were genetically distinct, but there was little population genetic structure between beds connected by tides and oceanic currents. To identify recruitment patterns among and within beds, pedigree analyses determined the distribution of parent–offspring and sibling relationships in the sampled populations. Beds in northeastern Bass Strait were genetically distinct to adjacent beds (FST 0.003–0.005) and may not contribute to wider recruitment based on biophysical models of larval movement. Unfortunately, pedigree analyses lacked power to further dissect fine-scale recruitment processes including self-recruitment. Our results support the management of disjunct populations as separate stocks and the protection of source populations among open water beds. The application of DAPC and parentage analyses in the current study provided valuable insight into their potential power to determine population connectivity in marine species with larval dispersal.
Roles of regulatory T cells in cancer immunity
Authors: Takeuchi Yoshiko , Nishikawa Hiroyoshi
Published: May 2016

CD4 + regulatory T cells (T regs ) expressing the transcription factor FoxP3 are highly immune suppressive and play central roles in the maintenance of self-tolerance and immune homeostasis, yet in malignant tumors they promote tumor progression by suppressing effective antitumor immunity. Indeed, higher infiltration by T regs is observed in tumor tissues, and their depletion augments antitumor immune responses in animal models. Additionally, increased numbers of T regs and, in particular, decreased ratios of CD8 + T cells to T regs among tumor-infiltrating lymphocytes are correlated with poor prognosis in various types of human cancers. The recent success of cancer immunotherapy represented by immune checkpoint blockade has provided a new insight in cancer treatment, yet more than half of the treated patients did not experience clinical benefits. Identifying biomarkers that predict clinical responses and developing novel immunotherapies are therefore urgently required. Cancer patients whose tumors contain a large number of neoantigens stemming from gene mutations, which have not been previously recognized by the immune system, provoke strong antitumor T-cell responses associated with clinical responses following immune checkpoint blockade, depending on the resistance to T reg -mediated suppression. Thus, integration of a strategy restricting T reg -mediated immune suppression may expand the therapeutic spectrum of cancer immunotherapy towards patients with a lower number of neoantigens. In this review, we address the current understanding of T reg -mediated immune suppressive mechanisms in cancer, the involvement of T regs in cancer immunotherapy, and strategies for effective and tolerable T reg -targeted therapy.
Excited-state hydroxyl maser catalogue from the methanol multibeam survey – I. Positions and variability
Authors: Avison A , Quinn L J , Fuller G A , Caswell J L , Green J A , Breen S L , Ellingsen S P , Gray M D , Pestalozzi M , Thompson M A , Voronkov M A
Published: May 2016

We present the results of the first complete unbaised survey of the Galactic plane for 6035-MHz excited-state hydroxyl (ex-OH) masers undertaken as part of the methanol multibeam (MMB) survey. These observations cover the Galactic longitude ranges 186° < l < 60° including the Galactic Centre. We report the detection of 127 ex-OH masers within the survey region, 47 being new sources. The positions of new detections were determined from interferometric observations with the Australia Telescope Compact Array. We discuss the association of 6035-MHz masers in our survey with the 6668-MHz masers from the MMB Survey, finding 37 likely CH3OH–ex-OH maser pairs with physical separations of ≤0.03 pc and 55 pairings separated by ≤0.1 pc. Using these we calculate for the first time an ex-OH maser lifetime of between 3.3 × 103 and 8.3 × 103 yr. We also discuss the variability of the 6035-MHz masers and detection rates of counterpart 6030-MHz ex-OH masers (28 per cent of our sample having detection at both frequencies).
The build-up of the red sequence in the Hercules cluster
Authors: Agulli I. , Aguerri J. A. L. , Dominguez Palmero L. , Diaferio A.
Published: May 2016

We present the study of the colour–magnitude diagram of the cluster Abell 2151 (A 2151), with a particular focus on the low-mass end. The deep spectroscopy with AF2/WYFFOS@WHT and the caustic method enable us to obtain 360 members within 1.3 R200 and absolute magnitude $M_r \lesssim M_r^{\ast }+6$. This nearby cluster shows a well defined red sequence up to Mr ∼ −18.5; at fainter magnitudes only 36 per cent of the galaxies lie on the extrapolation of the red sequence. We compare the red sequences of A 2151 and Abell 85, which is another nearby cluster with similar spectroscopic data, but with different mass and dynamical state. Both clusters show similar red sequences at the bright end (Mr ≤ −19.5), whereas large differences appear at the faint end. This result suggests that the reddening of bright galaxies is independent of environment, unlike the dwarf population (Mr ≥ −18.0).
Disseminated Talaromyces marneffei and Mycobacterium abscessus in a Patient With Anti-Interferon-γ Autoantibodies
Authors: Pruetpongpun Nattapol , Khawcharoenporn Thana , Damronglerd Pansachee , Suthiwartnarueput Worapop , Apisarnthanarak Anucha , Rujanavej Sasinuch , Suwantarat Nuntra
Published: May 2016

Anti-interferon (IFN)-γ autoantibodies are increasingly recognized as a cause of adult-onset immunodeficiency and increased risk for infections with intracellular pathogens. We report on disseminated Talaromyces (Penicillium) marneffei and Mycobacterium abscessus infection in a 72-year-old, human immunodeficiency virus noninfected, Thai man with anti-IFN-γ autoantibody. The patient was successfully treated with antimicrobial therapy and rituximab to control B cell-derived autoantibodies.
Dynamic modulation of visual and electrosensory gains for locomotor control
Authors: Sutton Erin E. , Demir Alican , Stamper Sarah A. , Fortune Eric S. , Cowan Noah J.
Published: May 2016

Animal nervous systems resolve sensory conflict for the control of movement. For example, the glass knifefish,Eigenmannia virescens, relies on visual and electrosensory feedback as it swims to maintain position within a moving refuge. To study how signals from these two parallel sensory streams are used in refuge tracking, we constructed a novel augmented reality apparatus that enables the independent manipulation of visual and electrosensory cues to freely swimming fish (n= 5). We evaluated the linearity of multisensory integration, the change to the relative perceptual weights given to vision and electrosense in relation to sensory salience, and the effect of the magnitude of sensory conflict on sensorimotor gain. First, we found that tracking behaviour obeys superposition of the sensory inputs, suggesting linear sensorimotor integration. In addition, fish rely more on vision when electrosensory salience is reduced, suggesting that fish dynamically alter sensorimotor gains in a manner consistent with Bayesian integration. However, the magnitude of sensory conflict did not significantly affect sensorimotor gain. These studies lay the theoretical and experimental groundwork for future work investigating multisensory control of locomotion.
Does moving up a food chain increase aggregation in parasites?
Authors: Lester R. J. G. , McVinish R.
Published: May 2016

General laws in ecological parasitology are scarce. Here, we evaluate data on numbers of fish parasites published by over 200 authors to determine whether acquiring parasites via prey is associated with an increase in parasite aggregation. Parasite species were grouped taxonomically to produce 20 or more data points per group as far as possible. Most parasites that remained at one trophic level were less aggregated than those that had passed up a food chain. We use a stochastic model to show that high parasite aggregation in predators can be solely the result of the accumulation of parasites in their prey. The model is further developed to show that a change in the predators feeding behaviour with age may further increase parasite aggregation.
Antimicrobial defence and persistent infection in insects revisited
Authors: Makarova Olga , Rodriguez-Rojas Alex , Eravci Murat , Weise Chris , Dobson Adam , Johnston Paul , Rolff Jens
Published: May 2016

Insects show long-lasting antimicrobial immune responses that follow the initial fast-acting cellular processes. These immune responses are discussed to provide a form of phrophylaxis and/or to serve as a safety measure against persisting infections. The duration and components of such long-lasting responses have rarely been studied in detail, a necessary prerequisite to understand their adaptive value. Here, we present a 21 day proteomic time course of the mealworm beetleTenebrio molitorimmune-challenged with heat-killedStaphylococcus aureus. The most upregulated peptides are antimicrobial peptides (AMPs), many of which are still highly abundant 21 days after infection. The identified AMPs included toll and imd-mediated AMPs, a significant number of which have no known function againstS. aureusor other Gram-positive bacteria. The proteome reflects the selective arena for bacterial infections. The results also corroborate the notion of synergistic interactionsin vivothat are difficult to modelin vitro.

This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.
Analytical considerations for comparative transcriptomics of wild organisms
Authors: Krabbenhoft Trevor J. , Turner Thomas F.
Published: May 2016

Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome-environment interactions. However, important data handling and quality control challenges remain, particularly when working with non-model species outside of a controlled laboratory environment. Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes). We present computational solutions for processing, annotating and summarizing comparative transcriptome data for assessing genome-environment interactions across species. The resulting bioinformatics pipeline addresses the following points: (1) the potential importance of “essential genes”, (2) the influence of microbiomes and other exogenous DNA, (3) potentially novel, species-specific genes, and (4) genomic rearrangements (e.g., whole genome duplication). Quantitative consideration of these points contributes to a firmer foundation for future comparative work across distantly related taxa for a variety of sub-disciplines, including stress and immune response, community ecology, ecotoxicology, and climate change.
HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads
Authors: Mangul Serghei , Yang Harry (Taegyun) , Hormozdiari Farhad , Tseng Elizabeth , Zelikovsky Alex , Eskin Eleazar
Published: May 2016

Sequencing of RNA provides the possibility to study an individual’s transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental haplotypes. While the read length of the single-molecule protocols is long, the relatively high error rate limits the ability to accurately detect the genetic variants and assemble them into the haplotype-specific isoforms. In this paper, we present HapIso (Haplotype-specific Isoform Reconstruction), a method able to tolerate the relatively high error-rate of the single-molecule platform and partition the isoform reads into the parental alleles. Phasing the reads according to the allele of origin allows our method to efficiently distinguish between the read errors and the true biological mutations. HapIso uses a k-means clustering algorithm aiming to group the reads into two meaningful clusters maximizing the similarity of the reads within cluster and minimizing the similarity of the reads from different clusters. Each cluster corresponds to a parental haplotype. We use family pedigree information to evaluate our approach. Experimental validation suggests that HapIso is able to tolerate the relatively high error-rate and accurately partition the reads into the parental alleles of the isoform transcripts. Furthermore, our method is the first method able to reconstruct the haplotype-specific isoforms from long single-molecule reads.

The open source Python implementation of HapIso is freely available for download at https://github.com/smangul1/HapIso/
From cytoskeletal dynamics to organ asymmetry: a non-linear, regulative pathway underlies left-right patterning
Authors: McDowell Gary S. , Rajadurai Suvithan , Levin Michael
Published: May 2016

Consistent left-right asymmetry is a fundamental aspect of the bodyplan across phyla, and errors of laterality form an important class of human birth defects. Its molecular underpinning was first discovered as a sequential pathway of left-and right-sided gene expression that controlled positioning of the heart and visceral organs. Recent data have revised this picture in two important ways. First, the physical origin of chirality has been identified; cytoskeletal dynamics underlie the asymmetry of single cell behavior and of patterning of the left-right axis. Second, the pathway is not linear: early disruptions that alter the normal sidedness of upstream asymmetric genes do not necessarily induce defects in the laterality of the downstream genes or in organsitus. Thus, the LR pathway is a unique example of two fascinating aspects of biology: the interplay of physics and genetics in establishing large-scale anatomy, and regulative (shape-homeostatic) pathways that correct errors of patterning over time. Here, we review aspects of asymmetry from its intracellular, cytoplasmic origins to the recently-uncovered ability of the LR control circuitry to achieve correct gene expression and morphology despite reversals of key “determinant” genes. We provide novel functional data, inXenopus laevis, on conserved elements of the cytoskeleton that drive asymmetry, and repair of downstream gene expression anomalies over developmental time. LR patterning can thus serve as a paradigm of how subcellular physics and gene expression cooperate to achieve developmental robustness of a body axis.
myCircos: Facilitating the Creation and Use of Circos Plots Online
Authors: Labelle Caroline , Boucher Geneviève , Lemieux Sébastien
Published: May 2016

Circos plots were designed to display large amounts of processed genomic information on a single graphical representation. The creation of such plots remains challenging for less technical users as the leading tool requires command-line proficiency. Here, we introduce myCircos, a web application that facilitates the generation of Circos plots by providing an intuitive user interface, adding interactive functionalities to the representation and providing persistence of previous requests. myCircos is available at:http://mycircos.iric.ca. Non registered users can explore the application through the Guest user. Source code (for local server installation) is available upon request.
Crystal structure of [tris(pyridin-2-ylmethyl)amine-κ4N]copper(II) bromide
Authors: Bridgman Emma C. , Doherty Megan M. , Ellis Kaleigh A. , Homer Elizabeth A. , Lashbrook Taylor N. , Mraz Margaret E. , Pernesky Gina C. , Vreeke Emma M. , Oshin Kayode D. , Oliver Allen G.
Published: May 2016

In the asymmetric unit of the title compound, [CuBr(C18H18N4)]Br, there are three crystallographically independent cations. One of the cations exhibits positional disorder of the pyridin-2-ylmethyl groups over two sets of sites with refined occupancies of 0.672 (8) and 0.328 (8). The outer-sphere bromine counter-ion is severely disordered over multiple sites. In each cation, the CuIIion is coordinated by the four N atoms of the tris(pyridin-2-ylmethyl)amine ligand and one bromine and adopts a slightly distorted trigonal–bipyramidal geometry.
2-Amino-6-methylpyridinium 2-hydroxybenzoate
Authors: Sivakumar P. , Sudhahar S. , Israel S. , Chakkaravarthi G.
Published: May 2016

In the title molecular salt, C6H9N2+·C7H5O3−, the cation is protonated at its pyridine N atom and and makes a dihedral angle of 16.26 (9)° with the plane of the six-membered ring of the anion. The six-membered ring makes a dihedral angle of 6.09 (3)° with the attached carboxylate group. In the anion, an intramolecular O—H...O hydrogen bond generates anS(6) ring motif and a pair of N—H...O hydrogen bonds generates anR22(8) ring motif. In the crystal, the anions and cations are linkedviaN—H...O hydrogen bonds to form a tetramer.
Should the international accounting standards board have responsibility for human rights?
Authors: McPhail Ken , Macdonald Kate , Ferguson John
Published: May 2016

Purpose

– The purpose of this paper is to explore the basis for, and ramifications of, applying relevant human rights norms – such as the United Nations Guiding Principles on Business and Human Rights – to the International Accounting Standards Board (IASB). In doing so, the paper seeks to contribute to scholarship on the political legitimisation of the IASB’s structure and activities under prevailing global governance conditions.

Design/methodology/approach

– The paper explores three distinct argumentative logics regarding responsibilities for justice and human rightsvis-à-visthe IASB. First, the authors explore the basis for applying human rights responsibilities to the IASB through reasoning based on the analysis of “public power” (Macdonald, 2008) and public authorisation. Second, the authors develop the reasoning with reference to recent attempts by legal scholars and practitioners to apply human rights obligations to other non-state and transnational institutions. Finally, the authors develop reasoning based on Thomas Pogge’s (1992b) ideas about institutional harms and corresponding responsibilities.

Findings

– The three distinct argumentative logic rest on differing assumptions – the goal is not to reconcile or synthesise these approaches, but to propose that these approaches offer alternative and in some ways complementary insights, each of which contributes to answering questions about how human rights obligations of the IASB should be defined, and how such a responsibility could be “actually proceduralised”.

Originality/value

– The analysis provides an important starting point for beginning to think about how responsibilities for human rights might be applied to the operation of the IASB.
Rana Plaza collapse aftermath: are CSR compliance and auditing pressures effective?
Authors: Sinkovics Noemi , Hoque Samia Ferdous , Sinkovics Rudolf R.
Published: May 2016

Purpose

– The purpose of this paper is to investigate the intended and unintended consequences of compliance and auditing pressures in the Bangladeshi garment industry. To explore this issue the authors draw on three medium-sized suppliers. The institutional changes that followed the Rana Plaza accident in April 2013 make Bangladesh in general and the garment industry in particular an interesting and suitable research setting for standards compliance.

Design/methodology/approach

– The study adopts a multiple case study approach. Face-to-face interviews have been conducted with the owners of three Bangladeshi garment manufacturing firms and several workers. Additionally, organisational documents and local newspaper articles had been collected wherever possible.

Findings

– The results indicate that the pressure for compliance has led the case companies to prioritise the implementation of measurable standards over the socially grounded needs and priorities of workers. As a consequence certain initiatives instead of adding new social value in fact destroyed previously existing social value. Furthermore, the pressure for compliance created the necessity to find ways to cover the sizable cost of compliance. This prompted firms to pursue process upgrading through technological advancements and increased work pressures on the labour force. These initiatives led to an increased power imbalance and the exclusion of unskilled workers from the job market.

Research limitations/implications

– The paper contributes to the understanding of the human rights implications of compliance and auditing pressures and initiatives. Furthermore, in order to further enrich existing knowledge in the critical accounting literature, the study draws on insights from the global value chains (GVC) and international business (IB) literatures.

Originality/value

– The paper contributes to the understanding of the human rights implications of compliance and auditing pressures and initiatives. Furthermore, in order to further enrich existing knowledge in the critical accounting literature, the study draws on insights from the GVC and IB literatures.
The use of imagery in the campaign speeches of Barack Hussein Obama and John McCain during the 2008 US Presidential Election
Authors: McGuire David , Garavan Thomas N. , Cunningham James , Duffy Greg
Published: May 2016

Purpose

– The use of imagery in leadership speeches is becoming increasingly important in shaping the beliefs and actions of followers. The purpose of this paper is to investigate the use of speech imagery and linguistic features employed during the 2008 US Presidential Election campaign.

Design/methodology/approach

– The authors analysed a total of 264 speeches (160 speeches from Obama and 104 speeches from McCain) delivered throughout the 2008 US Presidential Election and identified 15 speech images used by the two candidates. Both descriptive coding and axial coding approaches were applied to the data and speech images common to both candidates were further subjected to Pennebakeret al.(2003) linguistic inquiry methodology.

Findings

– The analysis revealed a number of important differences with Obama using inclusive language and nurturing communitarian values, whereas McCain focusing on personal actions and strict, conservative individualistic values. The use of more inclusive language by Obama was found to be significant in three of the five speech images common to both candidates.

Research limitations/implications

– The research acknowledges the difficulty of measuring the effectiveness of speech images without taking into account wider factors such as tone of voice, facial expression and level of conviction. It also recognises the heavy use of speechwriters by presidential candidates whilst on the campaign trail, but argues that candidates still exert a strong influence through instructions to speechwriters and that speeches should reflect the candidate’s values and beliefs.

Originality/value

– The research findings contribute to the emerging stream of leadership research that addresses language content issues surrounding and embedded in the leadership process. The research argues that leaders’ speeches provide a fertile ground for conducting research and for examining the evolving relationship between leaders and followers.
What helps successful community groups (involving peers support workers) to develop?
Authors: Deering Kris , Fieldhouse Jon , Parmenter Vanessa
Published: May 2016

Purpose

– The purpose of this paper is to explore features of successful peer supported community support groups hosted by St Mungo’s and partners.

Design/methodology/approach

– Literature review and theme construction.

Findings

– Overall the review confirmed existing findings that successful support groups foster mutually supportive, reciprocal relationships capable of inspiring hope among group members. This paper will concentrate on findings that co-production was indicative of successful groups in terms of shared aims, negotiated agendas, clear communication, and engagement with the wider community.

Research limitations/implications

– A group’s success was seen in terms of growth in members’ self-esteem, empowerment, and optimism, which this paper proposes could become part of a conceptual framework of a learning organisational culture.

Originality/value

– Developing understanding of a rapidly growing phenomenon in community-based mental health care and presenting this in terms of a particular organisational culture.
Repeated fires trap Amazonian blackwater floodplains in an open vegetation state
Authors: Flores Bernardo M. , Fagoaga Raquel , Nelson Bruce W. , Holmgren Milena
Published: May 2016

Climate change may increase the occurrence of droughts and fires in the Amazon. Most of our understanding on how fire affects tropical ecosystems is based on studies of non‐flooded forest–savanna ecotones. Nonetheless, tropical floodplain forests in the Amazon can burn severely during extreme droughts. The mechanisms slowing down forest regeneration in these ecosystems remain poorly understood and have never been assessed in the field.

We studied the recovery of Amazonian blackwater floodplain forests after one and two fire events. We used Landsat images to map fire history and conducted field surveys to measure forest structure, tree species richness, tree seed bank and post‐fire invasion of herbaceous plants.

Sites burnt once had on average 0% trees, 6% tree seed abundance, 23% tree seed species richness and 8% root mat thickness compared to unburnt forests. In contrast, herbaceous cover increased from 0 to 72%. Nonetheless, forest structure and diversity recovered slowly towards pre‐burn levels, except for tree seed banks that remained depleted even 15 years after fire.

Sites burnt twice had on average 0% trees, 1% tree seed abundance, 3% tree seed species richness and 1% root mat thickness compared to unburnt forests. Herbaceous cover increased to 100%. Mean recovery of tree basal area was 50% slower and of root mat thickness 93% slower compared to recovery in sites burnt once. Tree seed banks did not recover at all, and herbaceous cover persisted close to 100% for more than 20 years after the second fire.

Synthesis and applications. Our results indicate that after a second fire event, Amazonian blackwater floodplain forests lose their recovery capacity, and persist in a non‐forested state dominated by herbaceous vegetation. Such fragility implies that preventing human ignited fires during drought episodes is a particularly important conservation strategy for these ecosystems.
Status Incentives and Corporate Giving: Evidence From China's Political Reform On Private Enterprises
Authors: Chen Zhao , Zhang Jipeng
Published: May 2016

In this paper, we estimate the effect of status incentives on charitable giving by exploiting a natural experiment during China's political reform in 2002 that significantly improved the status of private entrepreneurs and their enterprises. We find that exogenous changes in social, political and economic status of private entrepreneurs led to a significant increase in the corporate giving of their privately owned firms. The findings are robust when we use different samples of the data and when we control for a large set of entrepreneurs and firm characteristics in the regression analysis.
Evaluation and establishment of a ward‐based geriatric liaison service for older urological surgical patients: Proactive care of Older People undergoing Surgery (POPS)‐Urology
Authors: Braude Philip , Goodman Anna , Elias Tania , Babic‐Illman Gordana , Challacombe Ben , Harari Danielle , Dhesi Jugdeep K.
Published: May 2016

Objective

To assess the impact of introducing and embedding a structured geriatric liaison service, Proactive care of Older People undergoing Surgery (POPS)‐Urology, using comprehensive geriatric assessment methodology, on an inpatient urology ward.

Patients and Methods

A phased quality improvement project was undertaken using stepwise interventions. Phase 1 was a before‐and‐after study with initiation of a daily board round, weekly multidisciplinary meeting, and targeted geriatrician‐led ward rounds for elective and emergency urology patients aged ≥65 years admitted over two 1‐month periods. Outcomes were recorded from medical records and discharge documentation, including length of inpatient stay, medical and surgical complications, and 30‐day readmission and mortality rates. Phase 2 was a quality improvement project involving Plan‐Do‐Study‐Act cycles and qualitative staff surveys in order to create a Geriatric Surgical Checklist (GSCL) to standardize the intervention in Phase 1, improve equity of care by extending it to all ages, improve team‐working and streamline handovers for multidisciplinary staff.

Results

Phase 1 included 112 patients in the control month and 130 in the intervention month. The length of inpatient stay was reduced by 19% (mean 4.9 vs 4.0 days; P = 0.01), total postoperative complications were lower (risk ratio 0.24 [95% confidence interval 0.10, 0.54]; P = 0.001). A non‐significant trend was seen towards fewer cancellations of surgery (10 vs 5%; P = 0.12) and 30‐day readmissions (8 vs 3%; P = 0.07). In Phase 2, the GSCL was created and incrementally improved. Questionnaires repeated at intervals showed that the GSCL helped staff to understand their role better in multidisciplinary meetings, improved their confidence to raise issues, reduced duplication of handovers and standardized identification of geriatric issues. Equity of care was improved by providing the intervention to patients of all ages, despite which the time taken for the daily board round did not lengthen.

Conclusion

This is the first known paper describing the benefits of daily proactive geriatric intervention in elective and emergency urological surgery. The results suggest that using a multidisciplinary team board round helps to facilitate collaborative working between surgical and geriatric medicine teams. The GSCL enables systematic identification of patients who require a focused comprehensive geriatric assessment. There is potential to transfer the GSCL package to other surgical specialties and hospitals to improve postoperative outcomes.
Combination of panobinostat with ponatinib synergistically overcomes imatinib‐resistant CML cells
Authors: Matsuda Yasufumi , Yamauchi Takahiro , Hosono Naoko , Uzui Kanako , Negoro Eiju , Morinaga Koji , Nishi Rie , Yoshida Akira , Kimura Shinya , Maekawa Taira , Ueda Takanori
Published: May 2016

The major mechanism of imatinib (IM) resistance of CML is the reactivation of ABL kinase either through BCR‐ABL gene amplification or mutation. We investigated the cytotoxicity of a pan‐ABL tyrosine kinase inhibitor, ponatinib, and a pan‐histone deacetylase inhibitor, panobinostat, against IM‐resistant CML cells in vitro. Two different IM‐resistant cell lines, K562/IM‐R1 and Ba/F3/T315I were evaluated in comparison with their respective, parental cell lines, K562 and Ba/F3. K562/IM‐R1 overexpressed BCR‐ABL due to gene amplification. Ba/F3/T315I was transfected with a BCR‐ABL gene encoding T315I‐mutated BCR‐ABL. Ponatinib inhibited the growth of both K562/IM‐R1 and Ba/F3/T315I as potently as it inhibited their parental cells with an IC50 of 2–30 nM. Panobinostat also similarly inhibited the growth of all of the cell lines with an IC50 of 40–51 nM. This was accompanied by reduced histone deacetylase activity, induced histone H3 acetylation, and an increased protein level of heat shock protein 70, which suggested disruption of heat shock protein 90 chaperone function for BCR‐ABL and its degradation. Importantly, the combination of ponatinib with panobinostat showed synergistic growth inhibition and induced a higher level of apoptosis than the sum of the apoptosis induced by each agent alone in all of the cell lines. Ponatinib inhibited phosphorylation not only of BCR‐ABL but also of downstream signal transducer and activator of transcription 5, protein kinase B, and ERK1/2 in both K562/IM‐R1 and Ba/F3/T315I, and the addition of panobinostat to ponatinib further inhibited these phosphorylations. In conclusion, panobinostat enhanced the cytotoxicity of ponatinib towards IM‐resistant CML cells including those with T315I‐mutated BCR‐ABL.
The amount of care delivered: challenges of indices in oral health studies
Authors: van Dommelen Paula , Schuller Annemarie A.
Published: May 2016

Objectives

Untreated dental caries is the most prevalent medical condition worldwide, with considerable variations in prevalence between regions and countries. The care index (CI) and the restorative index (RI) are generally used to make comparisons between and within countries of levels of care delivered. However, several methodological challenges can be identified that limit the interpretation and comparison of these indices. The objective of this manuscript was to evaluate these challenges and to provide solutions.

Methods

Five challenges were identified: (i) the comparability of CI and RI, (ii) the use of multiple definitions of CI and RI, (iii) CI and RI measured for surfaces or teeth, (iv) the skewness of F/D(M)F (restored teeth or surfaces as a fraction of the total number of decayed, (missing), and filled teeth or surfaces), and (v) the relationship between CI, RI and D(M)F. Time‐series data were obtained – for people aged 25–44 years with low socioeconomic status – from four cross‐sectional studies performed in 1995, 2002, 2007 and 2013 in the Netherlands, and those data were subjected to descriptive analyses.

Results

The analyses showed that the choice of index and definition had a major impact on the results, which varied in terms of absolute size and trends. Moreover, CI and RI are expressed as mean scores, but the distributions of F/DMF and F/DF were highly skewed. CI and RI may therefore mask groups of individuals who still need care. The proportion of individuals receiving most restorative care was much higher in the group with low levels of caries than in the groups with more caries. This implies that, when the need for care decreases over time, the restorative care indices can be expected to increase, even though there may be no improvement in the amount of care delivered.

Conclusions

We argue that epidemiological studies of oral health in the future should clarify the definitions used to describe the care delivered and investigate subgroups of F/DMF or F/DF in categories based on the extent of caries. These figures could be used to monitor changes in treatment provision and to highlight inequalities in the provision of care.
Early Recanalization Postintravenous Thrombolysis in Ischemic Stroke with Large Vessel Occlusion: A Digital Subtraction Angiography Study
Authors: Mao Yi‐Ting , Mitchell Peter , Churilov Leonid , Dowling Richard , Dong Qiang , Yan Bernard
Published: May 2016

Aims

We aimed to evaluate early recanalization postintravenous (i.v.) tissue plasminogen activator (t‐PA) by digital subtraction angiography (DSA) in acute ischemic stroke (AIS) with large vessel occlusion (LVO).

Methods

We performed baseline CT angiography to identify LVO in AIS. Recanalization pre‐ and post‐intra‐arterial therapy (IAT) was categorized to none, partial, and global recanalization (GR). Modified Rankin Scale score ≤2 at 3 months was considered a favorable outcome.

Results

Among 1610 patients with AIS, 286 received IV t‐PA. Of these, 55 patients with LVO were included. The median time from IV t‐PA to DSA was 120 min (interquartile range, 79–152). Recanalization post‐IV t‐PA was observed in seven patients (12.7%). By occlusion sites, the recanalization rates were as follows: extracranial internal carotid artery 2 of 14 (14.3%); intracranial internal carotid artery 3 of 24 (12.5%); M1 of middle cerebral artery 3 of 39 (7.7%); M2 of middle cerebral artery 1 of 40 (2.5%); vertebral artery 0 of 4; and basilar artery 0 of 7. GR post‐IAT was associated with favorable outcomes (odds ratio: 8.6; 95% confidence interval, 1.5–48.0; P = 0.014).

Conclusion

Early recanalization assessed by DSA post‐IV t‐PA is rarely observed in acute ischemic stroke patients with LVO.
Weigh Forward: a clinical audit of weight management in Australian general practice
Authors: Hemmes R. A. , Adam N. , Dixon J. B.
Published: May 2016

Weigh Forward was a prospective clinical audit, aimed to assess the use and efficacy of 12‐week weight management program in general practice. Twenty‐eight practitioners participated in the audit, with a total of 258 patients observed. Of these, 147 (57%) were retained to 24 weeks. Practices were asked to implement a structured 12‐week weight loss program, and encouraged to utilize relevant weight management guidelines as necessary. Patients were followed up regularly, and comprehensively assessed at baseline, 12 and 24 weeks. Evaluations were made of patient weight loss, practitioner willingness to utilize available weight loss interventions, practitioner set weight loss goals and the appropriateness of such goals. Overall, the 57% of completing patients lost an average of 6.1% ± 0.5% body weight, with 27.2% losing ≥10% body weight. Practitioners were hesitant to intensify treatment, and those with comorbidities were less likely (odds ratio 1.8; 95% CI 1.4–2.4) to receive intensified treatment than those without. Practitioners also tended to set high weight loss goals, with a mean goal of 17.3% body‐weight loss. The clinically significant mean weight loss demonstrates that practitioners are able to generate meaningful weight loss in primary care settings, however, could benefit from increased use of available interventions.
Lymph node size is not a reliable criterion for predicting nodal metastasis in rectal neuroendocrine tumours
Authors: Kim B. C. , Kim Y. E. , Chang H. J. , Lee S. H. , Youk E. G. , Lee D.‐S. , Lee J. B. , Lee E.‐J. , Kim M. J. , Sohn D. K. , Oh J. H.
Published: May 2016

Aim

The study was designed to assess the correlation between lymph node (LN) size and LN metastasis in patients with rectal neuroendocrine tumours (NETs).

Method

Forty patients who underwent curative resection with lymphadenectomy for a rectal NET between January 2007 and December 2012 were included. The short and long diameters of entire nodes were microscopically measured using a slide gauge.

Results

In all, 1052 LNs were collected from the 40 patients, with 49 (4.7%) showing evidence of metastasis. Metastasis‐positive LNs had significantly greater long and short diameters (P < 0.001) than metastasis‐negative LNs. Of the 49 metastatic LNs, 29 (59.2%) were ≤ 5 mm in largest diameter. In five patients, the largest metastatic LN was only 2–3 mm in diameter. In clinically node‐negative (cN0) patients, 18 (51.4%) patients had metastatic LNs (pN1).

Conclusion

The size of LNs containing metastasis varied widely, with some being very small. LN size alone is therefore not a sufficient predictor of tumour metastasis in rectal NETs. Radical surgery with lymphadenectomy should be considered for patients with rectal NETs with high risk factors for LN metastasis, even those without LN enlargement.
INEQUALITY: AN INTRODUCTION
Authors: Kumar Ravi
Published: May 2016

(JEL D3)
Drivers of Extinction Risk in Terrestrial Vertebrates
Authors: Ducatez Simon , Shine Richard
Published: May 2016

Rising rates of extinction create an urgent need to identify the mechanisms and drivers of endangerment. One critical question is whether major phylogenetic lineages are equally at risk to the same threats. We used the IUCN Red List classification to explore the effect of four major threatening processes (habitat alteration, invasive species, climate change and overexploitation) on 7,441 species in four terrestrial vertebrate classes. As expected, species rated as vulnerable to a higher number of threats were also at greater risk of extinction. However, this pattern differed strongly among classes. Notably, invasive species and climate change were strongly associated with increased risk of extinction in birds but not mammals. These large‐scale differences might be artifacts of differing methodologies used by class specialists to classify species vulnerability; or might reflect biological differences. That ambiguity needs to be resolved, because it has strong implications for the assessment and amelioration of threatening processes.
Nicotinamide Phosphoribosyltransferase Attenuates Methotrexate Response in Juvenile Idiopathic Arthritis and In Vitro
Authors: Funk RS , Singh R , Pramann L , Gigliotti N , Islam S , Heruth DP , Ye SQ , Chan MA , Leeder JS , Becker ML
Published: May 2016

Variability in response to methotrexate (MTX) in the treatment of juvenile idiopathic arthritis (JIA) remains unpredictable and poorly understood. Based on previous studies implicating an interaction between nicotinamide phosphoribosyltransferase (NAMPT) expression and MTX therapy in inflammatory arthritis, we hypothesized that increased NAMPT expression would be associated with reduced therapeutic response to MTX in patients with JIA. A significant association was found between increased plasma concentrations of NAMPT and reduced therapeutic response in patients with JIA treated with MTX. Inhibition of NAMPT in cell culture by either siRNA‐based gene silencing or pharmacological inhibition with FK‐866 was found to result in a fourfold increase in the pharmacological activity of MTX. Collectively, these findings provide evidence that NAMPT inhibits the pharmacological activity of MTX and may represent a predictive biomarker of response, as well as a therapeutic target, in the treatment of JIA with MTX.
Characterizing social–ecological units to inform biodiversity conservation in cultural landscapes
Authors: Hanspach Jan , Loos Jacqueline , Dorresteijn Ine , Abson David J. , Fischer Joern
Published: May 2016

Aim

Cultural landscapes and their biodiversity are threatened by land use changes and the abandonment of traditional farming techniques. Conceptualizing cultural landscapes as social–ecological systems can be useful to develop strategies for biodiversity conservation. First, this study aimed to develop a typology of social–ecological units based on land use patterns. Second, we sought to relate this typology to biophysical and socio‐demographic drivers as well as to biodiversity outcomes.

Location

Southern Transylvania (Romania).

Methods

We developed a typology of villages in Southern Transylvania based on land use data. We collected species richness data for plants, butterflies and birds, modelled local richness data for each village and related these values to the village typology. Also, we related village typology to biophysical and socio‐demographic variables.

Results

We identified four types of villages that showed distinct species richness patterns. Bird richness was highest in forest‐dominated and mixed‐land use villages; plant richness was highest in pasture‐dominated villages; and butterfly richness was high in arable‐dominated, mixed‐land use and pasture‐dominated villages. The four types of villages had distinct topographic characteristics and also differed in terms of ethnic composition, migration patterns and geographic location. Drawing on a combined understanding of social–ecological variables, different conservation actions could be prioritized for each of the four village types.

Main conclusions

Applying social–ecological approaches has the potential to inform biodiversity conservation in cultural landscapes. Social–ecological typologies can improve our understanding of complex systems and provide useful input for the development of effective strategies for biodiversity conservation.
The Importance of Product Reformulation Versus Consumer Choice in Improving Diet Quality
Authors: Griffith Rachel , O'Connell Martin , Smith Kate
Published: May 2016

Improving diet quality has been a target of public health policy. Governments have encouraged consumers to make healthier food choices and firms to reformulate food products. Evaluation of such policies has focused on the impact on consumer behaviour; firm behaviour has been less well studied. We show that the recent decline in dietary salt intake in the UK was entirely attributable to product reformulation; consumer switching between products worked in the opposite direction and led to a slight increase in grocery salt intensity. These findings point to the important role that firms can play in achieving public policy goals.