bluuebunny/crossref_metadata_2025 huggingface dataset:
The transcription factors Slug (SNAI2) and Snail (SNAI1) regulate phospholipase D (PLD) promoter in opposite ways towards cancer cell invasion
Authors: Ganesan Ramya , Mallets Elizabeth , Gomez-Cambronero Julian
Published: December 2015

Slug (SNAI2) and Snail (SNAI1) are master regulatory transcription factors for organogenesis and wound healing, and they are involved in the epithelial to mesenchymal transition (EMT) of cancer cells. We found that the activity of phospholipase D isoform 2 (PLD2) is highly increased in cancers with larger size and poor prognosis (MDA‐MB‐231 versus MCF‐7 cells), so we determined if Snail or Slug were responsible for PLD2 gene transcription regulation. Unexpectedly, we found that PLD2 expression was positively regulated by Slug but negatively regulated by Snail. The differential effects are amplified in breast cancer cells over normal cells and with MDA‐MB‐231 more robustly than MCF‐7. Slug putatively binds to the PLD2 promoter and transactivates it, which is negated when Slug and Snail compete with each other. Meanwhile, PLD2 has a negative effect on Snail expression and a positive effect on Slug, thus closing a feedback loop between the lipase and the transcription factors. Further, PA, the product of PLD2 enzymatic reaction, has profound effects on its own and it further regulates the transcription factors. Thus, we show for the first time that the overexpressed PLD2 in human breast tumors is regulated by Slug and Snail transcription factors. The newly uncovered feedback loops in highly invasive cancer cells have important implications in the process of EMT.
Liquid biopsy utility for the surveillance of cutaneous malignant melanoma patients
Authors: Huang Sharon K. , Hoon Dave S.B.
Published: December 2015

Cutaneous melanoma is one of the highest incident‐rate cancers with increasing prevalence in Western societies. Despite the advent of new approved therapeutics, the 5‐year overall survival rate of stage IV melanoma patients remains below 15%. Current treatments for late stage disease have shown higher efficacy when treated at a lower disease burden. Thus, blood‐based biomarkers capable of detecting melanoma prior to clinically evident distant metastasis, will improve the treatment and outcomes for melanoma patients. To that end, effective treatment of melanoma necessitates identification of patients at risk for developing distant metastases. Furthermore, employing blood biomarkers that monitor cancer progression over the course of treatment is a promising solution to post‐treatment drug resistance often developed in melanoma patients. Non‐invasive blood biomarker assays allow for regular dynamic monitoring of disease. “Liquid Biopsy” of blood, which exploits circulating tumor cells (CTCs), cell‐free circulating tumor DNA (ctDNA) and cell‐free circulating microRNA (cmiRNA), has been shown to detect prognostic factors for relapse in AJCC stage III and stage IV melanoma patients. Moreover, molecular characterization of CTC and analysis of various forms of ctDNA present promising potential in development of individualized therapy for melanoma patients. New approaches such as massive parallel sequencing (MPS) provide a comprehensive view of the disease progression, allowing for the selection of therapeutic options for individual patients. With advancements of improving molecular assays, liquid biopsy analysis as a powerful, routine clinical assay for melanoma patients, is highly promising prospective.
miRNA 206 and miRNA 574-5p are highly expression in coronary artery disease
Authors: Zhou Jianqing , Shao Guofeng , Chen Xiaoliang , Yang Xi , Huang Xiaoyan , Peng Ping , Ba Yanna , Zhang Lin , Jehangir Tashina , Bu Shizhong , Liu Ningsheng , Lian Jiangfang
Published: December 2015

Coronary artery disease (CAD) is the leading cause of human morbidity and mortality worldwide. Innovative diagnostic biomarkers are a pressing need for this disease. miRNAs profiling is an innovative method of identifying biomarkers for many diseases and could be proven as a powerful tool in the diagnosis and treatment of CAD. We performed miRNA microarray analysis from the plasma of three CAD patients and three healthy controls. Subsequently, we performed quantitative real-time PCR (qRT-PCR) analysis of miRNA expression in plasma of another 67 CAD patients and 67 healthy controls. We identified two miRNAs (miR-206 and miR-574-5p) that were significantly up-regulated in CAD patients as compared with healthy controls (P<0.05). The receiver operating characteristic (ROC) curves indicated these two miRNAs had great potential to provide sensitive and specific diagnostic value for CAD.
Management of Giant Calcified Thoracic Disks and Description of the Trench Vertebrectomy Technique
Authors: Al-Mahfoudh Rafid , Mitchell Paul S. , Wilby Martin , Crooks Daniel , Barrett Chris , Pillay Robin , Pigott Tim
Published: December 2015

Study Design

Case series and review of the literature.

Objective

To review the management of giant calcified disks in our large cohort and compare with the existing literature. We discuss our surgical technique.

Methods

Twenty-nine cases of herniated thoracic disk between 2000 and 2013 were reviewed. Eighteen patients were identified as having giant calcified thoracic disks, defined as diffusely calcified disks occupying at least 40% of the spinal canal. Demographic data was collected in addition to presentation, imaging findings, operative details, and outcomes using the modified Japanese Orthopaedic Association (mJOA) scale.

Results

Giant calcified thoracic disks (GCTDs) are unique clinical entities that require special neurosurgical consideration owing to significant (≥40%) involvement of the spinal canal and compression of the spinal cord, often leading to myelopathy. The median age at diagnosis was 51.2 years (range 37 to 70) with the mean duration of presenting symptoms being 9.9 months (range 2 weeks to 3 years). Seventeen (94.4%) patients presented with at least one sign of myelopathy (hyperreflexia, hypertonia, bladder or bowel dysfunction) with the remaining 1 (5.6%) patient presenting with symptoms in keeping with radiculopathy. Thoracotomy was performed on 17 (94.4%) patients, and 1 (5.6%) patient had a costotransverse approach. Mean follow-up was 19.8 months (range 7 months to 2 years). mJOA score improved in 15 (83.3%) patients. mJOA scores in the other patients remained stable.

Conclusions

GCTDs are difficult neurosurgical challenges owing to their size, degree of spinal cord compression, and consistency. We recommend a trench vertebrectomy via a thoracotomy in their surgical management. This procedure safely allows the identification of normal dura on either side of the compressed segment prior to performing a diskectomy. Excellent fusion rates were achieved with insertion of rib head autograft in the trench.
Turning statistical physics models into materials design engines
Authors: Miskin Marc Z. , Khaira Gurdaman , de Pablo Juan J. , Jaeger Heinrich M.
Published: December 2015

Significance

A fundamental tenet of science is that the properties of a material are intimately linked to the nature of the constituent components. Although there are powerful methods to predict such properties for given components, a key challenge for materials design is the inverse process: identifying the required components and their structural configuration for given target properties. This paper presents a new approach to this challenge. A formalism is introduced that generates algorithms for materials design both under equilibrium and under nonequilibrium conditions and operates without the need for user input beyond a design goal. This formalism is broadly applicable, fast, and robust, and it provides a powerful tool for materials optimization as well as discovery.
Ethnic Minorities and the Politics of Identity in Iran
Authors: Elling Rasmus Christian , Saleh Alam
Published: December 2015

The present review essay is of a novel format: two authors working in the same field introduce each other's works, and then pose a number of questions to each other. The aim is to facilitate dialogue between scholars occupied with similar issues, theories, methods or problems, and to share their discussions with others. Here, Alam Saleh, Lecturer in Middle Eastern Politics, University of Exeter, and Rasmus Christian Elling, Assistant Professor of Iranian Studies, University of Copenhagen, introduce each other's recent books on ethnic minorities, identity and nationalism in post-revolution Iran. These introductions are then followed by questions and answers in relation to the topics covered by the books.
Pulse DC electrodeposition of Zn–Ni–Co coatings
Authors: Choudhary R. K. , Mishra P. , Kain V.
Published: December 2015

Anomalous co-deposition of Zn–Ni–Co ternary alloy on carbon steel and copper substrates was attempted using pulse direct current electrodeposition technique. The obtained coatings were characterised for their crystal structure, chemical composition and surface morphology by X-ray diffractometry, energy dispersive X-ray spectroscopy and scanning electron microscopy, respectively. X-ray diffraction measurement showed peaks for Zn, Ni and Co. The concentration of Ni and Co in the ternary alloy increased with decrease in pulse frequency as confirmed by energy dispersive X-ray measurement. Scanning electron microscopy revealed uniform morphology of the coating surface with an average grain size of 1 µm. Potentiodynamic polarisation and electrochemical impedance spectroscopy tests conducted in 3% NaCl solution confirmed improved corrosion behaviour of the coatings deposited at lower current pulse frequencies.
Plasma nitriding of AISI 2205 steel: effects of surface mechanical attrition treatment and chemical etching
Authors: Gatey Atul M. , Hosmani Santosh S. , Arya Shashi B. , Figueroa Carlos A. , Singh Rajkumar P.
Published: December 2015

In the present study, surface mechanical attrition treatment (SMAT) and plasma nitriding were conducted on AISI 2205 steel. SMAT was effective in enhancing the surface hardness of the steel by about 80%. The influence of SMAT on the corrosion behaviour of the steel was studied in a 3.5 wt-% NaCl solution. Due to the stable and thicker passive layer, improved corrosion resistance was observed for the SMATed steel. However, nitrogen diffusion during plasma nitriding was impeded by the improved passivation, especially for the lower duration (30 min) of chemical etching/cleaning (i.e. sputter cleaning in hydrogen plasma) of the specimen's surface. Furthermore, high chemical etching duration (120 min) resulted in improved surface hardness and nitriding kinetics.
Training Opioid Addiction Treatment Providers to Adopt Contingency Management: A Prospective Pilot Trial of a Comprehensive Implementation Science Approach
Authors: Becker Sara J. , Squires Daniel D. , Strong David R. , Barnett Nancy P. , Monti Peter M. , Petry Nancy M.
Published: December 2015

Background

Few prospective studies have evaluated theory-driven approaches to the implementation of evidence-based opioid treatment. This study compared the effectiveness of an implementation model (Science to Service Laboratory; SSL) to training as usual (TAU) in promoting the adoption of contingency management across a multisite opioid addiction treatment program. We also examined whether the SSL affected putative mediators of contingency management adoption (perceived innovation characteristics and organizational readiness to change).

Methods

Sixty treatment providers (39 SSL, 21 TAU) from 15 geographically diverse satellite clinics (7 SSL, 8 TAU) participated in the 12-month study. Both conditions received didactic contingency management training and those in the predetermined experimental region received 9 months of SSL-enhanced training. Contingency management adoption was monitored biweekly, whereas putative mediators were measured at baseline, 3 months, and 12 months.

Results

Relative to providers in the TAU region, treatment providers in the SSL region had comparable likelihood of contingency management adoption in the first 20 weeks of the study, and then significantly higher likelihood of adoption (odds ratios = 2.4–13.5) for the remainder of the study. SSL providers also reported higher levels of one perceived innovation characteristic (Observability) and one aspect of organizational readiness to change (Adequacy of Training Resources), although there was no evidence that the SSL affected these putative mediators over time.

Conclusions

Results of this study indicate that a fully powered randomized trial of the SSL is warranted. Considerations for a future evaluation are discussed.
Clinician Recommendation of 12-Step Meeting Attendance and Discussion regarding Disclosure of Buprenorphine use among Patients in Office-Based Opioid Treatment
Authors: Suzuki Joji , Dodds Tyler
Published: December 2015

Background

Clinicians are encouraged to include 12-step meetings, such as Alcoholics or Narcotics Anonymous (AA/NA), as ancillary services for the treatment for opioid use disorders (OUDs), even though some of these groups may not fully accept individuals receiving buprenorphine. Little is known about whether clinicians actually discuss with patients the issue of disclosure of buprenorphine use at 12-step meetings.

Methods

An anonymous survey was offered to patients enrolled in office-based opioid treatment with buprenorphine to assess whether their clinicians recommended attendance at 12-step meetings and discussed the issue of disclosing their use of buprenorphine to other members. The patients’ attendance at 12-step meetings was also assessed, as well as beliefs and prior experiences related to disclosure of buprenorphine use at 12-step meetings.

Results

Thirty patients completed the survey. Twenty-one respondents (75.0%) indicated that they were encouraged to attend meetings, but only 9 (33.3%) reported having any discussion with their clinicians about the issue of disclosing their use of buprenorphine at meetings. The majority (76.7%) reported attending 12-step meetings at least occasionally, and 70% reported finding the meetings helpful. Nearly one third (30%) expressed concerns that other 12-step members would not accept them if their buprenorphine status were known, and a similar proportion (37%) frequently avoided disclosing their use of buprenorphine.

Conclusions

Clinicians recommended 12-step meetings to most patients but did not routinely discuss issues of disclosure. Despite utilizing 12-step meetings and reporting them to be helpful, many avoided disclosing their use of buprenorphine to others. More research is needed to better understand how clinicians may assist patients to best utilize 12-step meetings.
Primary Care Providers’ Experiences with Urine Toxicology Tests to Manage Prescription Opioid Misuse and Substance use among Chronic Noncancer Pain Patients in Safety Net Health Care Settings
Authors: Ceasar Rachel , Chang Jamie , Zamora Kara , Hurstak Emily , Kushel Margot , Miaskowski Christine , Knight Kelly
Published: December 2015

Background

Guideline recommendations to reduce prescription opioid misuse among patients with chronic noncancer pain include the routine use of urine toxicology tests for high-risk patients. Yet little is known about how the implementation of urine toxicology tests among patients with co-occurring chronic noncancer pain and substance use impacts primary care providers’ management of misuse. Clinicians’ perspectives on the benefits and challenges of implementing urine toxicology tests in the monitoring of opioid misuse and substance use in safety net health care settings are presented in this paper.

Methods

Twenty-three primary care providers from 6 safety net health care settings whose patients had a diagnosis of co-occurring chronic noncancer pain and substance use were interviewed. Interviews were transcribed, coded, and analyzed using grounded theory methodology.

Results

The benefits of implementing urine toxicology tests for primary care providers included less reliance on intuition to assess for misuse and the ability to identify unknown opioid misuse and/or substance use. The challenges of implementing urine toxicology tests included insufficient education and training about how to interpret and implement tests, and a lack of clarity on how and when to act on tests that indicated misuse and/or substance use.

Conclusions

These data suggest that primary care clinicians’ lack of education and training to interpret and implement urine toxicology tests may impact their management of patient opioid misuse and/or substance use. Clinicians may benefit from additional education and training about the clinical implementation and use of urine toxicology tests. Additional research is needed on how primary care providers implementation and use of urine toxicology tests impacts chronic noncancer pain management in primary care and safety net health care settings among patients with co-occurring chronic non cancer pain and substance use.
Barriers to Implementation of Opioid Overdose Prevention Programs in Ohio
Authors: Winstanley Erin L. , Clark Angela , Feinberg Judith , Wilder Christine M.
Published: December 2015

Background

Nationally, overdose fatalities have reached epidemic proportions. Ohio has one of the highest overdose death rates in the country, as well as high rates of prescription opioid trafficking.

Methods

A cross-sectional self-report survey of opioid overdose prevention programs (OOPPs) in Ohio was conducted between August and October 2014 to characterize programs and ascertain barriers to successful implementation. A 91% response rate was achieved with 18 programs participating in the study.

Results

The first Ohio OOPP opened in August 2012, a second program opened in 2013, and the remaining programs began in 2014. All of the programs distribute nasal naloxone and provide overdose prevention education, and 89% ( n = 16) provide overdose kits for free. Six OOPPs are funded by the Ohio Department of Health, 3 programs are funded by a local health foundation, and several other public and private funding sources were reported. The OOPPs have funding to distribute a combined total of 8,670 overdose kits and had distributed 1998 kits by October 2014. The OOPPs reported 149 overdose reversals. Fifteen programs (83%) reported implementation barriers that were categorized as stigma-, cost-, staffing-, legal, regulatory, and client-related problems. Legislative changes aimed at removing some of the obstacles to distribution and lay administration of naloxone have recently been enacted in Ohio.

Conclusions

OOPPs have rapidly expanded in Ohio during the past 3 years. Although recent legislative changes have addressed some of the reported implementation barriers, stigma and the cost of naloxone remain significant problems.
Bayesian Estimation of Possibly Similar Yield Densities: Implications for Rating Crop Insurance Contracts
Authors: Ker Alan P. , Tolhurst Tor N. , Liu Yong
Published: December 2015

The Agricultural Act of 2014 solidified insurance as the cornerstone of U.S. agricultural policy. The Congressional Budget Office (2014) estimates that this act will increase spending on agricultural insurance programs by $5.7 billion to a total of $89.8 billion over the next decade. In light of the sizable resources directed toward these programs, accurate rating of insurance contracts is of the utmost importance to producers, private insurance companies, and the federal government. Unlike most forms of insurance, agricultural insurance is plagued by a paucity of spatially correlated data. A novel interpretation of Bayesian Model Averaging is used to estimate a set of possibly similar densities that offers greater efficiency if the set of densities are similar while seemingly not losing any if the set of densities are dissimilar. Simulations indicate that finite sample performance—in particular small sample performance—is quite promising. The proposed approach does not require knowledge of the form or extent of any possible similarities, is relatively easy to implement, admits correlated data, and can be used with either parametric or nonparametric estimators. We use the proposed approach to estimate U.S. crop insurance premium rates for area‐type programs and develop a test to evaluate its efficacy. An out‐of‐sample game between private insurance companies and the federal government highlights the policy implications for a variety of crop‐state combinations. Consistent with the simulation results, the performance of the proposed approach with respect to rating area‐type insurance—in particular small sample performance—remains quite promising.
Challenges of Conducting Contingent Valuation Studies in Developing Countries
Authors: Durand-Morat Alvaro , Wailes Eric J. , Nayga Rodolfo M.
Published: December 2015

We review the experiences and challenges that researchers can face when conducting contingent valuation studies in developing countries. We discuss these challenges based on our own experiences of conducting field‐contingent valuation studies about genetically modified rice in five developing countries that represent different regions of the world and diverse cultures; we also base our discussion on results from a survey we conducted of agricultural and applied economists regarding their own experiences. The issues covered include the selection and training of local personnel, the recruitment of participants, sampling challenges, participants' compensation, survey methods and implementation, elicitation methods, the literacy rate of the population, and security/safety issues in developing countries. We also discuss the implications of our findings to other well‐established stated‐preference methods such as choice experiments.
PaxtoolsR: pathway analysis in R using Pathway Commons
Authors: Luna Augustin , Babur Özgün , Aksoy Bülent Arman , Demir Emek , Sander Chris
Published: December 2015

Purpose: PaxtoolsR package enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons webservice for users of the R language to aid in advanced pathway analyses. Features include the extraction, merging and validation of pathway data represented in the BioPAX format. This package also provides novel pathway datasets and advanced querying features for R users through the Pathway Commons webservice allowing users to query, extract and retrieve data and integrate these data with local BioPAX datasets.

Availability and implementation: The PaxtoolsR package is compatible with versions of R 3.1.1 (and higher) on Windows, Mac OS X and Linux using Bioconductor 3.0 and is available through the Bioconductor R package repository along with source code and a tutorial vignette describing common tasks, such as data visualization and gene set enrichment analysis. Source code and documentation are at http://www.bioconductor.org/packages/paxtoolsr. This plugin is free, open-source and licensed under the LGPL-3.

Contact:  paxtools@cbio.mskcc.org or lunaa@cbio.mskcc.org
Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration
Authors: Shavit Yoli , Walker Barnabas James , Lio’ Pietro
Published: December 2015

Motivation: Recent advancements in molecular methods have made it possible to capture physical contacts between multiple chromatin fragments. The resulting association matrices provide a noisy estimate for average spatial proximity that can be used to gain insights into the genome organization inside the nucleus. However, extracting topological information from these data is challenging and their integration across resolutions is still poorly addressed. Recent findings suggest that a hierarchical approach could be advantageous for addressing these challenges.

Results: We present an algorithmic framework, which is based on hierarchical block matrices (HBMs), for topological analysis and integration of chromosome conformation capture (3C) data. We first describe chromoHBM, an algorithm that compresses high-throughput 3C (HiT-3C) data into topological features that are efficiently summarized with an HBM representation. We suggest that instead of directly combining HiT-3C datasets across resolutions, which is a difficult task, we can integrate their HBM representations, and describe chromoHBM-3C, an algorithm which merges HBMs. Since three-dimensional (3D) reconstruction can also benefit from topological information, we further present chromoHBM-3D, an algorithm which exploits the HBM representation in order to gradually introduce topological constraints to the reconstruction process. We evaluate our approach in light of previous image microscopy findings and epigenetic data, and show that it can relate multiple spatial scales and provide a more complete view of the 3D genome architecture.

Availability and implementation: The presented algorithms are available from: https://github.com/yolish/hbm.

Contact:  ys388@cam.ac.uk or pl219@cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
FluxModeCalculator: an efficient tool for large-scale flux mode computation
Authors: van Klinken Jan Bert , Willems van Dijk Ko
Published: December 2015

Summary: Elementary flux mode (EFM) analysis is a powerful technique for determining the metabolic capacities and robustness of stoichiometric networks. Recently, several improvements have been made to the algorithm for enumerating the EFMs, making the study of large models possible. However, currently these tools require high performance workstations to perform large-scale EFM computations, thus limiting their applicability. We developed a more time and memory efficient implementation of the algorithm for EFM enumeration in MATLAB, called FluxModeCalculator, which enables large-scale EFM computation on ordinary desktop computers.

Availability and implementation: FluxModeCalculator is open source and freely available under the terms of the GNU General Public License v3.0 at http://www.lumc.nl/jan-bert-van-klinken

Contact:  j.b.van_klinken@lumc.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fast integration-based prediction bands for ordinary differential equation models
Authors: Hass Helge , Kreutz Clemens , Timmer Jens , Kaschek Daniel
Published: December 2015

Motivation: To gain a deeper understanding of biological processes and their relevance in disease, mathematical models are built upon experimental data. Uncertainty in the data leads to uncertainties of the model’s parameters and in turn to uncertainties of predictions. Mechanistic dynamic models of biochemical networks are frequently based on nonlinear differential equation systems and feature a large number of parameters, sparse observations of the model components and lack of information in the available data. Due to the curse of dimensionality, classical and sampling approaches propagating parameter uncertainties to predictions are hardly feasible and insufficient. However, for experimental design and to discriminate between competing models, prediction and confidence bands are essential. To circumvent the hurdles of the former methods, an approach to calculate a profile likelihood on arbitrary observations for a specific time point has been introduced, which provides accurate confidence and prediction intervals for nonlinear models and is computationally feasible for high-dimensional models.

Results: In this article, reliable and smooth point-wise prediction and confidence bands to assess the model’s uncertainty on the whole time-course are achieved via explicit integration with elaborate correction mechanisms. The corresponding system of ordinary differential equations is derived and tested on three established models for cellular signalling. An efficiency analysis is performed to illustrate the computational benefit compared with repeated profile likelihood calculations at multiple time points.

Availability and implementation: The integration framework and the examples used in this article are provided with the software package Data2Dynamics, which is based on MATLAB and freely available at http://www.data2dynamics.org.

Contact:  helge.hass@fdm.uni-freiburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics
Authors: Goldfarb Dennis , Wang Wei , Major Michael B.
Published: December 2015

Summary: Data-dependent acquisition (DDA) is the most common method used to control the acquisition process of shotgun proteomics experiments. While novel DDA approaches have been proposed, their evaluation is made difficult by the need of programmatic control of a mass spectrometer. An alternative is in silico analysis, for which suitable software has been unavailable. To meet this need, we have developed MSAcquisitionSimulator—a collection of C ++ programs for simulating ground truth LC-MS data and the subsequent application of custom DDA algorithms. It provides an opportunity for researchers to test, refine and evaluate novel DDA algorithms prior to implementation on a mass spectrometer.

Availability and implementation: The software is freely available from its Github repository http://www.github.com/DennisGoldfarb/MSAcquisitionSimulator/ which contains further documentation and usage instructions.

Contact:  weiwang@cs.ucla.edu or ben_major@med.unc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Impact of high pCO2 and warmer temperatures on the process of silica biomineralization in the sponge Mycale grandis
Authors: Vicente Jan , Silbiger Nyssa J. , Beckley Billie A. , Raczkowski Charles W. , Hill Russell T.
Published: December 2015

Siliceous sponges have survived pre-historical mass extinction events caused by ocean acidification and recent studies suggest that siliceous sponges will continue to resist predicted increases in ocean acidity. In this study, we monitored silica biomineralization in the Hawaiian sponge Mycale grandis under predicted pCO2 and sea surface temperature scenarios for 2100. Our goal was to determine if spicule biomineralization was enhanced or repressed by ocean acidification and thermal stress by monitoring silica uptake rates during short-term (48 h) experiments and comparing biomineralized tissue ratios before and after a long-term (26 d) experiment. In the short-term experiment, we found that silica uptake rates were not impacted by high pCO2 (1050 µatm), warmer temperatures (27°C), or combined high pCO2 with warmer temperature (1119 µatm; 27°C) treatments. The long-term exposure experiments revealed no effect on survival or growth rates of M. grandis to high pCO2 (1198 µatm), warmer temperatures (25.6°C), or combined high pCO2 with warmer temperature (1225 µatm, 25.7°C) treatments, indicating that M. grandis will continue to prosper under predicted increases in pCO2 and sea surface temperature. However, ash-free dry weight to dry weight ratios, subtylostyle lengths, and silicified weight to dry weight ratios decreased under conditions of high pCO2 and combined pCO2 warmer temperature treatments. Our results show that rising ocean acidity and temperature have marginal negative effects on spicule biomineralization and will not affect sponge survival rates of M. grandis.
Effects of spatial heterogeneity in growth and fishing effort on yield-per-recruit models: an application to the US Atlantic sea scallop fishery
Authors: Truesdell Samuel B. , Hart Deborah R. , Chen Yong
Published: December 2015

Conventional yield-per-recruit (Y/R) and spawning-stock biomass-per-recruit (SSB/R) models make no allowance for spatial heterogeneity in fishing mortality, natural mortality, or growth across the stock area, although variability in these processes can affect model results. For example, areas with higher growth and/or lower natural mortality rates should be fished at a lower rate to maximize Y/R; however, these areas may be especially attractive to fishers and are often fished harder. Here, Y/R and SSB/R models are developed that simultaneously account for spatial heterogeneity in growth and fishing effort. These models are applied to the US Atlantic sea scallop (Placopecten magellanicus) fishery. The spatial variability in growth uses depth-integrated models from the literature and variability in effort is based on, alternatively, uniform, observed, and relative-optimal spatial harvesting distributions. The observed effort patterns are derived from vessel monitoring system positions, and illustrate one application for these widely collected but underutilized spatial data. In this example, the distribution of observed fishing effort reduces Y/R compared with the relative-optimal, or the uniform effort distribution implicitly assumed by conventional Y/R analysis. SSB/R was in some cases considerably higher under the relative-optimal distribution of effort than when calculated using observed or uniform effort patterns. Such more realistic spatially integrated Y/R and SSB/R models can help to evaluate the impact of effort patterns on fishery yield and stock egg production. These models demonstrate that the spatial distribution of effort can be as important as the overall average fishing mortality when managing fisheries to optimize Y/R, SSB/R, and yield.
Dynamics of European eel landings and stocks in the coastal waters of Estonia
Authors: Bernotas P. , Vetemaa M. , Saks L. , Eschbaum R. , Verliin A. , Järvalt A.
Published: December 2015

European eel stocks are in a decline all over Europe. In Estonia, we analysed three different dataseries (commercial landings 1969–2014, scientific eel monitoring 1998–2014, and recreational catches 2005–2012). In the commercial fishery, the biggest drop in landings occurred in the 1980s, with a small recovery in the end of the 1990s. We also interviewed fishers to evaluate the quality of the official catch figures. In the monitoring dataseries, gathered by the use of special eel fykenets, the steepest cpue decline occurred in the last 5 years. Finally, recreational eel fishery has almost stopped: in 2012, catches were only 3% of that in 2005. In conclusion, both professional and recreational eel catches have declined in all the coastal areas of Estonia. The number of professional and recreational fishers specialized to eel fishing has decreased and the number of licences for eel-specific fishing gear has been reduced.
“Whatever it takes”: An Empirical Assessment of the Value of Policy Actions in Banking
Authors: Fiordelisi Franco , Ricci Ornella
Published: December 2015

What types of policy intervention had a greater impact during the financial crisis? By using a detailed dataset of worldwide policy, we answer this question focusing on Global Systemically Important banks (G-SIBs), looking both to stock returns and Credit Default Swap (CDS) spreads reactions. As robustness checks, we also analyze a control sample of 31 large Non-Financial Companies (NFCs). Overall, we show that different policy interventions from governments and central banks have produced diverse market reactions: investors generally appreciate monetary policy interventions for G-SIBs (but not for NFCs) and do not welcome bank failures and bailouts (for both G-SIBs and NCFs).
A Meta-Analysis Examining Differences in Short-Term Outcomes between Sutureless and Conventional Aortic Valve Prostheses
Authors: Hurley Eoghan T. , O'Sullivan Katie E. , Segurado Ricardo , Hurley John P.
Published: December 2015

Objective

Sutureless aortic valve prostheses are anchored by radial force in a mechanism similar to that of transcatheter aortic valve implantation. Transcatheter aortic valve implantation is associated with an increased permanent pacemaker (PPM) requirement in a significant proportion of patients. We undertook a meta-analysis to examine the incidence of PPM insertion associated with sutureless compared with conventional surgical aortic valve replacement.

Methods

A systematic review was conducted in accordance with the Prisma guidelines.1 All searches were performed on August 10, 2014. Studies between 2007 and 2014 were included in the search.

Results

A total of 832 patients were included in the sutureless group and 3,740 in the conventional group. Aortic cross-clamp (39.8 vs 62.4 minutes; P < 0.001) and cardiopulmonary bypass (64.9 vs 86.7 minutes; P = 0.002) times were shorter in the sutureless group. Permanent pacemaker implantation rate was higher in the sutureless cohort (9.1% vs 2.4%; P = 0.025).

Conclusions

Sutureless aortic valve prostheses are associated with significantly shorter cardiopulmonary bypass and aortic cross-clamp times and a higher incidence of PPM insertion than conventional. Further investigation of the prognostic significance is required.
The proteome of the infectious bronchitis virus Beau-R virion
Authors: Dent Stuart D. , Xia Dong , Wastling Jonathan M. , Neuman Benjamin W. , Britton Paul , Maier Helena J.
Published: December 2015

Infectious bronchitis is a highly contagious respiratory disease of poultry caused by the coronavirus infectious bronchitis virus (IBV). It was thought that coronavirus virions were composed of three major viral structural proteins until investigations of other coronaviruses showed that the virions also include viral non-structural and genus-specific accessory proteins as well as host-cell proteins. To study the proteome of IBV virions, virus was grown in embryonated chicken eggs, purified by sucrose-gradient ultracentrifugation and analysed by mass spectrometry. Analysis of three preparations of purified IBV yielded the three expected structural proteins plus 35 additional virion-associated host proteins. The virion-associated host proteins had a diverse range of functional attributions, being involved in cytoskeleton formation, RNA binding and protein folding pathways. Some of these proteins were unique to this study, while others were found to be orthologous to proteins identified in severe acute respiratory syndrome coronavirus virions and also virions from a number of other RNA and DNA viruses.
Insect Wing Classification of Mosquitoes and Bees Using CO1 Image Recognition
Authors: Vyas-Patel Nayna , Ravela Sai , Mafra-Neto Agenor , Mumford John D
Published: December 2015

The certainty that a species is accurately identified is the cornerstone of appearance based classification; however the methods used in classical taxonomy have yet to fully catch up with the digital age. Recognising this, the CO1 algorithm presented on the StripeSpotter platform was used to identify different species and sexes of mosquito wings (Diptera: Culicidae) and honey bee and bumblebee wings (Hymenoptera: Apidae). Images of different species of mosquito and bee wings were uploaded onto the CO1 database and test wing images were analysed to determine if this resulted in the correct species being identified. Out of a database containing 925 mosquito and bee wing images, the CO1 algorithm correctly identified species and sexes of test wing image presented, with a high degree of accuracy (80% to 100% depending on the species and database used, excluding sibling species) highlighting the usefulness of CO1 in identifying medically important as well as beneficial insect species. Using a larger database of wing images resulted in significantly higher numbers of test images being correctly identified than using a smaller database. The hind wings of Hymenoptera provided higher levels of correctly identified results than using the fore wings. The software should be used in conjunction with other identifying criteria (salient morphological features) in addition to the wings. CO1 is a powerful algorithm to use in identifying insect wings in its current form and has great potential if it is adapted and tailored for insect species identification. It is suggested that a primary aim in the digital age should be the production of a ‘World Wide Database’ of insect images, where all known insect images can be made available to everyone, with image recognition and species knowledge at its core.
Octopamine release impairs courtship conditioning in Drosophila melanogaster
Authors: Chartove Julia , Zhang Mengxi Cici , Zhang Edward
Published: December 2015

Octopamine is known to have an appetitive role in odor conditioning paradigms in Drosophila melanogaster. We sought to test whether octopamine could also act as an appetitive stimulus in courtship conditioning, a paradigm in which training with an unreceptive female (such as a decapitated virgin) causes a subsequent decrease in courtship behavior in male Drosophila. To control octopamine release, we used the Tdc2-Gal4 and UAS-dTRPa1 genes in conjunction to depolarize octopaminergic neurons at 27 C in experimental flies. We hypothesized that inducing octopamine release during courtship training would decrease the aversive impact of training and cause less subsequent suppression of courtship behavior. Our findings confirmed this hypothesis: Tdc2-Gal4/UAS-dTRPa1 flies trained at 27 degrees showed significantly more courtship behavior than controls during testing, and in fact showed no significant effect of courtship training. This confirms that octopamine release counteracts the aversive stimulus of failure to copulate, indicating that octopamine may have an appetitive role in courtship.
Hippocampal circuit abnormalities in MeCP2+/- mouse model of Rett syndrome
Authors: Chartove Julia , Liao Wenlin , Hassan Aniqa , McMullen Mary , White Rachel , Kim Sangwon , Carlson Gregory
Published: December 2015

Rett syndrome (RTT) has a complex developmental course over childhood and adolescence. Patients with RTT often have a pre-symptomatic period with no or little outward signs of the disorder, followed by developmental arrest and regression. Following regression, the individual's condition is not static, as they often progress into defined stages with unique neurological symptoms. Similarly, the progression of RTT-like symptoms in female mice heterozygous for a null-mutation has a prodromal and symptomatic period. Change in functional local circuit connectivity was studied using hippocampal slices, assaying Schaffer evoked activity in area CA1 using fast voltage sensitive dye imaging. With this technique the local functional interactions between the excitatory and inhibitory components of the circuit can be characterized. The prodromal period was associated with a shift in extent of excitation into the stratum oriens of the hippocampus and reduced sensitivity to changes in divalent cation concentration. These data suggest that hyperexcitability of the hippocampus at the circuit level may contribute to the prodromal reduction in cognitive performance and the onset of developmental regression.
Who's Afraid of Postcolonial Theory?
Authors: Roy Ananya
Published: December 2015

Recent assertions of urban theory have dismissed the value of postcolonial critique in urban studies. This essay draws on postcolonial theory to demonstrate key flaws in such theoretical formulations. In doing so, it returns to the puzzle of how and why studying urbanism in the global South might matter for the reconceptualization of critical urban theory. Instead of a universal grammar of cityness, modified by (exotic) empirical variation, the essay foregrounds forms of theorization that are attentive to historical difference as a fundamental constituent of global urbanization. What is at stake, the essay concludes, is a culture of theory, one that in its Eurocentrism tends to foreclose multiple concepts of the urban and alternative understandings of political economy. A concern with the relationship between place, knowledge and power—a key insight of postcolonial critique—might make possible new practices of theory in urban studies.
It's Just the City after All!
Authors: Simone Abdoumaliq
Published: December 2015

Long a site for incessant worry, revision or redemption, it is unclear what the ‘city' is today. Yet, in face of the near‐apocalyptic readjustments potentiated by human‐engineered global warming, there is an exigency about getting cities to function right. It is no wonder, then, that contemporary theories of cities and urbanization attempt to restore some common sense, to get to the heart of critical matters in a world where urbanization disrupts once‐normative assumptions about the nature of territory, scale and politics. But what is the nature of that ‘common sense'? How does one engage the very concrete efforts that constructed the city, with all the layers of physical and cultural memory that new regimes usually attempt to cover up, and all that the city does not show, either because its inhabitants are prohibited from paying attention or because whatever is considered normative or spectacular in city life has to get rid of the messy labor and politics that brought it about? Invoking blackness as an analytical method, these questions are addressed through thinking about how long histories of urban practices deployed by black residents of cities across the world might challenge and reinvent the sense of an urban commons.

‘Living just enough, just enough for the city…'

Stevie Wonder (1973)
LAST CHANCE SALOON
Authors: Johnston Anna
Published: December 2015

While Daniel Effron's research might not see the end of cheating, it does uncover a new concept: the cheat‐at‐the‐end effect
MAXIMISING CARE
Authors: Crainer Stuart
Published: December 2015

Find out how students from London Business School worked with the NHS to improve maternity services and delivery of cancer treatment
WHY SHOULD ANYONE WORK HERE?
Authors: Goffee Rob , Jones Gareth
Published: December 2015

Rob Goffee and Gareth Jones argue that ‘authentic’ organisations help employees to thrive
NETWORKING YOUR WAY TO INNOVATION
Authors: Perle Judith
Published: December 2015

Networks are vital to innovation. Judith Perle demonstrates how and why
BLAZING A TRAIL
Authors: Caulkin Simon , Birkinshaw Julian
Published: December 2015

Simon Caulkin and Julian Birkinshaw report on the reinvention of an iconic public service, and the lessons business can learn from this amazing transformation
SELLING INVESTORS SHORT?
Authors: Crainer Stuart
Published: December 2015

New research by Francesca Cornelli and Bilge Yamaz sheds new light on the mysteries of shorting
CHARM SCHOOL
Authors: Marsh Hannah
Published: December 2015

Your reputation as a charismatic leader could be profoundly affected by the informal advice ties in your team
EUROZONE IN PERIL
Authors: Portes Richard , Reichlin Lucrezia
Published: December 2015

The biggest threat to the EU is contractionary fiscal policy, claim Richard Portes and Lucrezia Reichlin
DANGER IN THE SHADOWS?
Authors: Connon Heather
Published: December 2015

New research by Ralph Koijen of London Business School identifies shadow insurance as a key area of risk
SIR ALEX FERGUSON'S WINNING WAY
Authors: Hytner Richard
Published: December 2015

Consistent adherence to beliefs is the key to the former Manchester United manager's unparalleled leadership, says Richard Hytner
RECOMMENDED READING
Authors: Peterson Randall S
Published: December 2015

Randall S Peterson, Professor of Organisational Behaviour; Academic Director of the Leadership Institute at London Business School, selects eight inspiring reads on leadership by some of history's most famous (and infamous) figureheads
MY DAY
Authors: Johnston Anna
Published: December 2015

A day in the life of Dr Jamie Wilson, founder and CEO of London‐based HomeTouch