bluuebunny/crossref_metadata_2025 huggingface dataset:
Broadband enhancement of local density of states using silicon-compatible hyperbolic metamaterials
Authors: Wang Yu , Sugimoto Hiroshi , Inampudi Sandeep , Capretti Antonio , Fujii Minoru , Dal Negro Luca
Published: June 2015

Light emitting silicon quantum dots by colloidal synthesis were uniformly spin-coated into a 20 nm-thick film and deposited atop a hyperbolic metamaterial of alternating TiN and SiO2 sub-wavelength layers. Using steady-state and time-resolved photoluminescence spectroscopy as a function of the emission wavelength in partnership with rigorous electromagnetic modeling of dipolar emission, we demonstrate enhanced Local Density of States and coupling to high-k modes in a broad spectral range. These findings provide an alternative approach for the engineering of novel Si-compatible broadband sources that leverage the control of radiative transitions in hyperbolic metamaterials and the flexibility of the widespread Si platform.
Iterative experiment design guides the characterization of a light-inducible gene expression circuit
Authors: Ruess Jakob , Parise Francesca , Milias-Argeitis Andreas , Khammash Mustafa , Lygeros John
Published: June 2015

Significance

System identification addresses the problem of identifying unknown model parameters from measured data of a real system. In the case of biochemical reaction networks, the available measurements are typically sparse because of technical and/or economic reasons. Therefore, it is of paramount importance to maximize the information that can be gained by each experiment. Here, we apply a systematic design scheme for single-cell experiments based on information theoretic criteria. For the considered light-inducible gene expression circuit, we show that this scheme allows one to precisely identify model parameters that were practically unidentifiable from data measured in random experiments. This result provides evidence that optimal experiment design is a key requirement for the successful identification of biochemical reaction networks.
Retrieval of bindings between task-irrelevant stimuli and responses can facilitate behaviour under conditions of high response certainty
Authors: Horner Aidan J.
Published: June 2015

Repetition priming can be driven by the encoding and retrieval of stimulus–response (S–R) bindings. When a previously encoded S–R binding is retrieved, and is congruent with the response currently required, it can bias response-selection processes towards selecting the retrieved response, resulting in facilitation. Previous studies have used classification tasks at retrieval. Here, two (or more) response options are competing, and it is likely that any evidence (e.g., an S–R binding) in favour of one option will be utilized to effect a decision. Thus, S–R effects are likely to be seen when using such a task. It is unclear whether such effects can be seen under conditions of higher response certainty, when participants are explicitly cued to make a response. Across two experiments, evidence for a modulating influence of S–R bindings is seen despite using a response cueing method at retrieval to minimize response uncertainty and despite stimuli being task irrelevant. Finally, the results suggest that responses within these S–R bindings are coded at the level of left versus right hand, and not a more fine-grained within-hand thumb versus index finger. The results underline the resilience of S–R effects, suggesting that they are present even under conditions where no explicit object-oriented decision is required.
Whither development studies? Reflections on its relationship with social policy
Authors: Copestake James
Published: June 2015

This paper contributes to an ongoing conversation between development studies (DS) and social policy (SP) as academic fields, particularly in the UK. Using Andrew Abbott's analysis of the social sciences as an evolving system of knowledge lineages (KLs), it reflects on the status of DS and its relationship with SP. Defining DS as a distinctive KL centred on critical analysis of ideas and projects for advancing human well-being, I suggest that it has lost coherence even as research into international development thrives. Indeed it is easy to envisage its gradual assimilation into other KLs, including SP. The two increasingly overlap in their analysis of the causes of relative poverty and injustice, and what can be done to address them, within countries and globally. Strengthening links between the two fields can be justified as a political project, even at the risk of some loss of plurality and plenitude across the social sciences.
The Smith normal form of a matrix associated with Young’s lattice
Authors: Cai Tommy , Stanley Richard
Published: June 2015

We prove a conjecture of Miller and Reiner on the Smith normal form of the operator

D
U

DU

associated with a differential poset for the special case of Young’s lattice. Equivalently, this operator can be described as

∂

∂

p
1

p
1

\frac {\partial }{\partial p_1}p_1

acting on homogeneous symmetric functions of degree

n
n

.
Weak form of equidistribution theorem for harmonic measures of foliations by hyperbolic surfaces
Authors: Matsumoto Shigenori
Published: June 2015

We show that the equidistribution theorem of C. Bonatti and X. Gómez-Mont for a special kind of foliations by hyperbolic surfaces does not hold in general, and we seek a weaker form valid for general foliations by hyperbolic surfaces.
Introduction
Authors: Adams-Prassl Jeremias
Published: June 2015

This chapter charts the problems resulting from employment law’s near-exclusive focus on the classification of employees as party to a bilateral contract of employment, and suggests that the enquiry should be widened to encompass the concept of the employer. Subsequent sections then set out an overview of the central argument and overall structure of the work, and outline its scope and methodological approach. A final section sketches the broader implications of a reconceptualized definition of the employer for the personal scope of employment protective norms in English law: it is only by adopting a functional concept of the employer that coherent coverage can be restored, irrespective of the factual complexity of the underlying work arrangement.
Complex Employment Structures in Germany
Authors: Adams-Prassl Jeremias
Published: June 2015

This chapter presents a comparative exploration of the scope of employment regulation in multilateral structures under German law, particularly as regards the situation in corporate groups (the Konzern). It traces the evolution of a body of law at the intersection of company law and employment law, aimed at ensuring worker involvement throughout the enterprise as well as at the group level (codetermination, or Mitbestimmung), and explains the detailed operation of their different legal mechanisms. The comparative excursus concludes that any successful reconceptualization does not necessarily need to identify identical employers in different domains of labour law; that the unitary concept is particularly problematic insofar as it leads to rigidly formalistic outcomes; and that a reconceptualization needs to strive for a careful balance between overall coherence and flexibility, avoiding a radical departure from existing frameworks whilst at the same time remaining adaptable to future doctrinal development.
A Single Concept in Different Contexts
Authors: Adams-Prassl Jeremias
Published: June 2015

This chapter addresses the unitary strand to show that while some clear breaks have to be made from the existing setup, a unifying overarching concept of the employer can be maintained. Its opening sections return to the three main factors identified as driving the unitary strand in Chapter 1 (in particular privity of contract and separate legal personality), re-examining each one to demonstrate a growing incongruence between developments in the relevant areas and labour law’s rigid bilateral contractual analysis. The chapter then explores the need for an overarching concept of the employer to fulfil its key public-regulatory function of facilitating the risk/control trade-off at the heart of modern labour markets. Analysed thus, the received concept fails to achieve its basic tasks in nearly all situations beyond a unitary paradigm, whereas the reconceptualized strand ensures that the concept of the employer can grapple with complex multilateral manifestations of shared employer functions.
Gersonides
Authors: Glasner Ruth
Published: June 2015

Gersonides (Levi ben Gershom) was a highly original Jewish philosopher, scientist, and biblical exegete, active in Provence in the first half of the fourteenth century. The book focuses on his work as a scientist, arguing that the key to understanding his originality and his impressive achievements was his perspective of an applied mathematical scientist. It was this perspective that led him to examine Aristotelianism from points of view different from those usually adopted by contemporary scholastics. He started his way, as he himself states, as someone who is at once ‘mathematician, natural scientist and philosopher’, believing that it was in his power to solve the main problems of medieval science. He ended up concentrating on his work as a mathematical astronomer, developing techniques of observation and computation, and somewhat less optimistic about the prospect of scientific knowledge.
Does Healthy Food Access Matter in a French Urban Setting?
Authors: Caillavet France , Kyureghian Gayaneh , Nayga Rodolfo M. , Ferrant Coline , Chauvin Pierre
Published: June 2015

Limited access to healthy food is commonly regarded as a contributing factor to poor dietary choices. The objective of this article is to test this hypothesis in a French context given France's increasing obesity rates and incidence of poor dietary habits. We use data on fruit and vegetable consumption frequency and different food retail availability measures, for example the number of food stores, food surface area, and a dispersion measure based on store numbers, store types, and food area surface, from several data sources in France. We also employ different types of geographic units when measuring the food retail environment and instrumental variable model specifications to test the robustness of our results, which indicate that fewer but larger retail outlets increase the odds of consuming the recommended level of fruit and vegetables. We also find that an increase in food supply dispersion will improve fruit and vegetable consumption in Paris, but not in its suburbs.
Reconstructing 16S rRNA genes in metagenomic data
Authors: Yuan Cheng , Lei Jikai , Cole James , Sun Yanni
Published: June 2015

Metagenomic data, which contains sequenced DNA reads of uncultured microbial species from environmental samples, provide a unique opportunity to thoroughly analyze microbial species that have never been identified before. Reconstructing 16S ribosomal RNA, a phylogenetic marker gene, is usually required to analyze the composition of the metagenomic data. However, massive volume of dataset, high sequence similarity between related species, skewed microbial abundance and lack of reference genes make 16S rRNA reconstruction difficult. Generic de novo assembly tools are not optimized for assembling 16S rRNA genes. In this work, we introduce a targeted rRNA assembly tool, REAGO (REconstruct 16S ribosomal RNA Genes from metagenOmic data). It addresses the above challenges by combining secondary structure-aware homology search, zproperties of rRNA genes and de novo assembly. Our experimental results show that our tool can correctly recover more rRNA genes than several popular generic metagenomic assembly tools and specially designed rRNA construction tools.

Availability and implementation: The source code of REAGO is freely available at https://github.com/chengyuan/reago.

Contact:  yannisun@msu.edu
Identification of causal genes for complex traits
Authors: Hormozdiari Farhad , Kichaev Gleb , Yang Wen-Yun , Pasaniuc Bogdan , Eskin Eleazar
Published: June 2015

Motivation: Although genome-wide association studies (GWAS) have identified thousands of variants associated with common diseases and complex traits, only a handful of these variants are validated to be causal. We consider ‘causal variants’ as variants which are responsible for the association signal at a locus. As opposed to association studies that benefit from linkage disequilibrium (LD), the main challenge in identifying causal variants at associated loci lies in distinguishing among the many closely correlated variants due to LD. This is particularly important for model organisms such as inbred mice, where LD extends much further than in human populations, resulting in large stretches of the genome with significantly associated variants. Furthermore, these model organisms are highly structured and require correction for population structure to remove potential spurious associations.

Results: In this work, we propose CAVIAR-Gene (CAusal Variants Identification in Associated Regions), a novel method that is able to operate across large LD regions of the genome while also correcting for population structure. A key feature of our approach is that it provides as output a minimally sized set of genes that captures the genes which harbor causal variants with probability ρ. Through extensive simulations, we demonstrate that our method not only speeds up computation, but also have an average of 10% higher recall rate compared with the existing approaches. We validate our method using a real mouse high-density lipoprotein data (HDL) and show that CAVIAR-Gene is able to identify Apoa2 (a gene known to harbor causal variants for HDL), while reducing the number of genes that need to be tested for functionality by a factor of 2.

Availability and implementation: Software is freely available for download at genetics.cs.ucla.edu/caviar.

Contact: eeskin@cs.ucla.edu
Refined elasticity sampling for Monte Carlo-based identification of stabilizing network patterns
Authors: Childs Dorothee , Grimbs Sergio , Selbig Joachim
Published: June 2015

Motivation: Structural kinetic modelling (SKM) is a framework to analyse whether a metabolic steady state remains stable under perturbation, without requiring detailed knowledge about individual rate equations. It provides a representation of the system’s Jacobian matrix that depends solely on the network structure, steady state measurements, and the elasticities at the steady state. For a measured steady state, stability criteria can be derived by generating a large number of SKMs with randomly sampled elasticities and evaluating the resulting Jacobian matrices. The elasticity space can be analysed statistically in order to detect network positions that contribute significantly to the perturbation response. Here, we extend this approach by examining the kinetic feasibility of the elasticity combinations created during Monte Carlo sampling.

Results: Using a set of small example systems, we show that the majority of sampled SKMs would yield negative kinetic parameters if they were translated back into kinetic models. To overcome this problem, a simple criterion is formulated that mitigates such infeasible models. After evaluating the small example pathways, the methodology was used to study two steady states of the neuronal TCA cycle and the intrinsic mechanisms responsible for their stability or instability. The findings of the statistical elasticity analysis confirm that several elasticities are jointly coordinated to control stability and that the main source for potential instabilities are mutations in the enzyme alpha-ketoglutarate dehydrogenase.

Contact:  dorothee.childs@embl.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Robust reconstruction of gene expression profiles from reporter gene data using linear inversion
Authors: Zulkower Valentin , Page Michel , Ropers Delphine , Geiselmann Johannes , de Jong Hidde
Published: June 2015

Motivation: Time-series observations from reporter gene experiments are commonly used for inferring and analyzing dynamical models of regulatory networks. The robust estimation of promoter activities and protein concentrations from primary data is a difficult problem due to measurement noise and the indirect relation between the measurements and quantities of biological interest.

Results: We propose a general approach based on regularized linear inversion to solve a range of estimation problems in the analysis of reporter gene data, notably the inference of growth rate, promoter activity, and protein concentration profiles. We evaluate the validity of the approach using in silico simulation studies, and observe that the methods are more robust and less biased than indirect approaches usually encountered in the experimental literature based on smoothing and subsequent processing of the primary data. We apply the methods to the analysis of fluorescent reporter gene data acquired in kinetic experiments with Escherichia coli. The methods are capable of reliably reconstructing time-course profiles of growth rate, promoter activity and protein concentration from weak and noisy signals at low population volumes. Moreover, they capture critical features of those profiles, notably rapid changes in gene expression during growth transitions.

Availability and implementation: The methods described in this article are made available as a Python package (LGPL license) and also accessible through a web interface. For more information, see https://team.inria.fr/ibis/wellinverter.

Contact:  Hidde.de-Jong@inria.fr

Supplementary information: Supplementary data are available at Bioinformatics online.
cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions
Authors: Oliwa Tomasz , Shen Yang
Published: June 2015

Motivation: It remains both a fundamental and practical challenge to understand and anticipate motions and conformational changes of proteins during their associations. Conventional normal mode analysis (NMA) based on anisotropic network model (ANM) addresses the challenge by generating normal modes reflecting intrinsic flexibility of proteins, which follows a conformational selection model for protein–protein interactions. But earlier studies have also found cases where conformational selection alone could not adequately explain conformational changes and other models have been proposed. Moreover, there is a pressing demand of constructing a much reduced but still relevant subset of protein conformational space to improve computational efficiency and accuracy in protein docking, especially for the difficult cases with significant conformational changes.

Method and results: With both conformational selection and induced fit models considered, we extend ANM to include concurrent but differentiated intra- and inter-molecular interactions and develop an encounter complex-based NMA (cNMA) framework. Theoretical analysis and empirical results over a large data set of significant conformational changes indicate that cNMA is capable of generating conformational vectors considerably better at approximating conformational changes with contributions from both intrinsic flexibility and inter-molecular interactions than conventional NMA only considering intrinsic flexibility does. The empirical results also indicate that a straightforward application of conventional NMA to an encounter complex often does not improve upon NMA for an individual protein under study and intra- and inter-molecular interactions need to be differentiated properly. Moreover, in addition to induced motions of a protein under study, the induced motions of its binding partner and the coupling between the two sets of protein motions present in a near-native encounter complex lead to the improved performance. A study to isolate and assess the sole contribution of intermolecular interactions toward improvements against conventional NMA further validates the additional benefit from induced-fit effects. Taken together, these results provide new insights into molecular mechanisms underlying protein interactions and new tools for dimensionality reduction for flexible protein docking.

Availability and implementation: Source codes are available upon request.

Contact:  yshen@tamu.edu
In silicophenotyping via co-training for improved phenotype prediction from genotype
Authors: Roqueiro Damian , Witteveen Menno J. , Anttila Verneri , Terwindt Gisela M. , van den Maagdenberg Arn M.J.M. , Borgwardt Karsten
Published: June 2015

Motivation: Predicting disease phenotypes from genotypes is a key challenge in medical applications in the postgenomic era. Large training datasets of patients that have been both genotyped and phenotyped are the key requisite when aiming for high prediction accuracy. With current genotyping projects producing genetic data for hundreds of thousands of patients, large-scale phenotyping has become the bottleneck in disease phenotype prediction.

Results: Here we present an approach for imputing missing disease phenotypes given the genotype of a patient. Our approach is based on co-training, which predicts the phenotype of unlabeled patients based on a second class of information, e.g. clinical health record information. Augmenting training datasets by this type of in silico phenotyping can lead to significant improvements in prediction accuracy. We demonstrate this on a dataset of patients with two diagnostic types of migraine, termed migraine with aura and migraine without aura, from the International Headache Genetics Consortium.

Conclusions: Imputing missing disease phenotypes for patients via co-training leads to larger training datasets and improved prediction accuracy in phenotype prediction.

Availability and implementation: The code can be obtained at: http://www.bsse.ethz.ch/mlcb/research/bioinformatics-and-computational-biology/co-training.html

Contact:  karsten.borgwardt@bsse.ethz.ch or menno.witteveen@bsse.ethz.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Exploiting ontology graph for predicting sparsely annotated gene function
Authors: Wang Sheng , Cho Hyunghoon , Zhai ChengXiang , Berger Bonnie , Peng Jian
Published: June 2015

Motivation: Systematically predicting gene (or protein) function based on molecular interaction networks has become an important tool in refining and enhancing the existing annotation catalogs, such as the Gene Ontology (GO) database. However, functional labels with only a few (<10) annotated genes, which constitute about half of the GO terms in yeast, mouse and human, pose a unique challenge in that any prediction algorithm that independently considers each label faces a paucity of information and thus is prone to capture non-generalizable patterns in the data, resulting in poor predictive performance. There exist a variety of algorithms for function prediction, but none properly address this ‘overfitting’ issue of sparsely annotated functions, or do so in a manner scalable to tens of thousands of functions in the human catalog.

Results: We propose a novel function prediction algorithm, clusDCA, which transfers information between similar functional labels to alleviate the overfitting problem for sparsely annotated functions. Our method is scalable to datasets with a large number of annotations. In a cross-validation experiment in yeast, mouse and human, our method greatly outperformed previous state-of-the-art function prediction algorithms in predicting sparsely annotated functions, without sacrificing the performance on labels with sufficient information. Furthermore, we show that our method can accurately predict genes that will be assigned a functional label that has no known annotations, based only on the ontology graph structure and genes associated with other labels, which further suggests that our method effectively utilizes the similarity between gene functions.

Availability and implementation:  https://github.com/wangshenguiuc/clusDCA.

Contact:  jianpeng@illinois.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Inferring orthologous gene regulatory networks using interspecies data fusion
Authors: Penfold Christopher A. , Millar Jonathan B. A. , Wild David L.
Published: June 2015

Motivation: The ability to jointly learn gene regulatory networks (GRNs) in, or leverage GRNs between related species would allow the vast amount of legacy data obtained in model organisms to inform the GRNs of more complex, or economically or medically relevant counterparts. Examples include transferring information from Arabidopsis thaliana into related crop species for food security purposes, or from mice into humans for medical applications. Here we develop two related Bayesian approaches to network inference that allow GRNs to be jointly inferred in, or leveraged between, several related species: in one framework, network information is directly propagated between species; in the second hierarchical approach, network information is propagated via an unobserved ‘hypernetwork’. In both frameworks, information about network similarity is captured via graph kernels, with the networks additionally informed by species-specific time series gene expression data, when available, using Gaussian processes to model the dynamics of gene expression.

Results: Results on in silico benchmarks demonstrate that joint inference, and leveraging of known networks between species, offers better accuracy than standalone inference. The direct propagation of network information via the non-hierarchical framework is more appropriate when there are relatively few species, while the hierarchical approach is better suited when there are many species. Both methods are robust to small amounts of mislabelling of orthologues. Finally, the use of Saccharomyces cerevisiae data and networks to inform inference of networks in the budding yeast Schizosaccharomyces pombe predicts a novel role in cell cycle regulation for Gas1 (SPAC19B12.02c), a 1,3-beta-glucanosyltransferase.

Availability and implementation: MATLAB code is available from http://go.warwick.ac.uk/systemsbiology/software/.

Contact:  d.l.wild@warwick.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Integrative random forest for gene regulatory network inference
Authors: Petralia Francesca , Wang Pei , Yang Jialiang , Tu Zhidong
Published: June 2015

Motivation: Gene regulatory network (GRN) inference based on genomic data is one of the most actively pursued computational biological problems. Because different types of biological data usually provide complementary information regarding the underlying GRN, a model that integrates big data of diverse types is expected to increase both the power and accuracy of GRN inference. Towards this goal, we propose a novel algorithm named iRafNet: integrative random forest for gene regulatory network inference.

Results: iRafNet is a flexible, unified integrative framework that allows information from heterogeneous data, such as protein–protein interactions, transcription factor (TF)-DNA-binding, gene knock-down, to be jointly considered for GRN inference. Using test data from the DREAM4 and DREAM5 challenges, we demonstrate that iRafNet outperforms the original random forest based network inference algorithm (GENIE3), and is highly comparable to the community learning approach. We apply iRafNet to construct GRN in Saccharomyces cerevisiae and demonstrate that it improves the performance in predicting TF-target gene regulations and provides additional functional insights to the predicted gene regulations.

Availability and implementation: The R code of iRafNet implementation and a tutorial are available at: http://research.mssm.edu/tulab/software/irafnet.html

Contact:  zhidong.tu@mssm.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Predictors of 2010–2011 Michigan Medicaid Beneficiary Adverse E-Code Health Care Encounters
Authors: Corser William D. , Huebner Marianne , Zhu Qi
Published: June 2015

To inform Medicaid medication management and public health policymaking, the authors analyzed the major predictive factors influencing program-approved therapeutic use or poisoning E-coded encounters leading to emergency department visits and hospital admission for the totality of Michigan Medicaid beneficiaries during a 12-month 2010–2011 period. The analytic cohort was composed of 26,134 approved E-code encounters submitted for 19,865 discrete Michigan Medicaid beneficiaries.

More than 1% of all beneficiaries experienced at least one adverse medication/agent-related E-code encounter during the period. More such encounters and costlier approved encounters were recorded female subjects, African Americans, dually eligible adults, urban elderly, those with fee-for-service Medicaid coverage, and those residing in urban-density counties.

Especially notably for patient safety policymakers, more than 9% of total E-coded encounters for children and adults were primarily attributed by providers to likely preventable poisoning causes such as exposure to household cleaning agents/gases, cosmetic products, illicit drug/alcohol, or secondary tobacco smoke. Encounter costs for the total sample totaled $37 million but ranged considerably up to more than a quarter million dollars.

In view of the future expanding Medicaid-covered beneficiary cohorts, the authors propose several key patient safety/public health policy implications for researchers and policymakers striving to serve lower-income health care consumer groups.
Exploring Health Care Professionals' Perceptions of Incidents and Incident Reporting in Rehabilitation Settings
Authors: Espin Sherry , Carter Celina , Janes Nadine , McAllister Mary
Published: June 2015

Objectives

Research exploring patient safety in rehabilitation settings is limited. This study's aim was to describe team members' perceptions of incidents and incident reporting in rehabilitation settings.

Methods

Semistructured interviews were conducted with 18 health care professionals from multiple rehabilitation units (medical, neurological, and orthopedic) at 2 inner-city rehabilitation centers. Five hypothetical scenarios were presented to participants during the interviews. Participants were asked to classify the scenarios and whether they would report any identified incidents. Data were analyzed using a descriptive thematic approach.

Results

Participants classified events based on 2 parameters: the nature of the outcome and deviation from professional practice. Factors influencing participants' decisions to file incident reports included their classification of the events in the scenarios (i.e., events classified as critical incidents were more often reported than those classified as incident or near miss); the severity of the impact on the client; and their profession's perceived role in reporting specific incidents. When participants said they would report incidents, all agreed that they would report only objective facts.

Conclusions

The study findings demonstrate gaps between incident-reporting policy and practice, and opportunities to address these gaps. Organizational leaders can work with all health care professions to support their roles in reporting. Interprofessional team building, focused on valuing all team members, may improve interprofessional communication and reporting. Setting standards for classifying events could increase consistency in reporting. Ultimately, encouraging reporting of near misses and incidents can create a culture of learning focused on problem solving and improved patient safety.
Research Priorities in the Field of Patient Safety in Iran: Results of a Delphi Study
Authors: Ravaghi Hamid , Sajadi Haniye Sadat
Published: June 2015

There is inadequate evidence to direct and support patient safety practice. Therefore, identifying research priorities in this field is relevant for many stakeholders. This study, which was built on the World Health Organization work, aimed to identify and prioritize research topics for patient safety in Iran. A 3-round Modified Delphi process was used. We purposefully recruited a panel of 45 policy makers, planners, health care managers and staff, and academic members with experience or expertise in patient safety research. A review of the literature was used to develop the first questionnaire, including 24 research topics. Respondents were asked to rate their agreement with each research topic and propose new topics. Based on the results of round 1, the second questionnaire was developed and the respondents were requested to rate 45 research topics and also put similar research topics in the same groups. Given the responses of round 2, the third questionnaire including a list of 45 research priorities categorized in 4 groups was developed. Respondents were asked to reflect their opinions. Content analysis was used to analyze round 1 data and descriptive statistics for round 2 and round 3 data. Forty-five identified research topics in round 1 prioritized and grouped in subsequent rounds. Among 4 research groups, the extent and epidemiology threatening patient safety group received the highest priority; and among research topics, adverse drug events and its epidemiology were the top-ranked research priorities. In addition to the priorities identified in previous work, more research priorities that reflect important and needed issue related to patient safety, especially in Iran, were recognized. This priority research list, which most stakeholders agree with it, can serve as a blueprint for patient safety research.
Prauserella soli sp. nov., isolated from crude oil-contaminated soil
Authors: Almutairi Awatef
Published: June 2015

A novel actinomycete strain, designated 12-833T, was isolated from a crude oil-contaminated site north of Kuwait. The isolated strain showed the ability to degrade crude oil and various hydrocarbons. 16S rRNA gene sequence analysis showed that strain 12-833T belonged to the genus Prauserella and was closely related to Prauserella muralis 05-Be-005T (98.3 % 16S rRNA gene sequence similarity), Prauserella marina MS498T (96.9 %) and Prauserella rugosa DSM 43194T (96.7 %). The DNA G+C content of strain 12-833T was 71.1 mol%. Phenotypic, physiological, biochemical and chemotaxonomic characteristics and phylogenetic analysis indicated that strain 12-833T represents a novel species of the genus Prauserella, for which the name Prauserella soli sp. nov. is proposed. The type strain is 12-833T ( = DSM 45819T = LMG 28346T).
Probing the fabric of the rare biosphere
Authors: Crespo Bibiana G. , Wallhead Philip J. , Logares Ramiro , Pedrós-Alió Carlos
Published: June 2015

The relatively recent development of high-throughput sequencing (HTS) techniques has revealed a wealth of novel sequences found in very low abundance: the rare biosphere. Today, most studies of diversity of microorganisms are carried out almost exclusively with HTS techniques. However, culturing seems indispensable for diversity studies especially if the aim is exploring the rare biosphere. We have carried out a deep (1 million sequences per sample) pyrosequencing analysis of two marine bacterial samples and isolated a culture collection from one of them. We have shown that the collectors curves of the pyrosequencing data were close to reaching an asymptote. We have estimated the total richness of the samples and the sequencing effort necessary to obtain the total estimated richness experimentally. Comparing the pyrosequencing data and the isolates sequences we have found that isolation retrieves some of the rarest taxa and that the composition of rare taxa follows an annual succession. We have shown that increasing the number of tags sequenced would slowly uncover the isolated bacteria. However, even if the whole bacterial diversity was found by increasing the sampling depth, culturing would still be essential for the study of marine bacterial communities, especially if the target is the rare biosphere.
The Nature, Extent, and Consequences of Genetic Variation in theopaRepeats ofNotchinDrosophila
Authors: Rice Clinton , Beekman Danielle , Liu Liping , Erives Albert
Published: June 2015

ABTRACT

Polyglutamine (pQ) tracts are abundant in many proteins co-interacting on DNA. The lengths of these pQ tracts can modulate their interaction strengths. However, pQ tracts > 40 residues are pathologically prone to amyloidogenic self-assembly. Here, we assess the extent and consequences of variation in the pQ-encodingoparepeats ofNotch(N) inDrosophila melanogaster. We use Sanger sequencing to genotypeopasequences (5’-CAX repeats), which have resisted assembly using short sequence reads. While the majority ofNsequences pertain to referenceopa31(Q13HQ17) andopa32(Q13HQ18) allelic classes, several rare alleles encode tracts > 32 residues:opa33a(Q14HQ18),opa33b(Q15HQ17),opa34(Q16HQ17),opa35a1/opa35a2(Q13HQ21),opa36(Q13HQ22), andopa37(Q13HQ23). Only one rare allele encodes a tract < 31 residues:opa23(Q13–Q10). Thisopa23allele shortens the pQ tract while simultaneously eliminating the interrupting histidine. Homozygotes for the short and longopaalleles have defects in sensory bristle organ specification, abdominal patterning, and embryonic survival. Inbred stocks with wild-typeopa31alleles become more viable when outbred, while an inbred stock with the longeropa35becomes less viable after outcrossing to different backgrounds. In contrast, an inbred stock with the shortopa23allele is semi-viable in both inbred and outbred genetic backgrounds. Thisopa23 Notchallele also produces notched wings when recombined out of the X chromosome. Importantly,wa-linked X balancers carry theNalleleopa33band suppressAS-Cinsufficiency caused by thesc8inversion. Our results demonstrate potent pQ variation and epistatic sensitivity for theNlocus, and the need for long read genotyping of key repeat variables underlying gene regulatory networks.
Sentinel lymph node biopsy for 102 patients with primary cutaneous melanoma at a single Japanese institute
Authors: Otsuka Masaki , Yamasaki Osamu , Kaji Tatsuya , Iwatsuki Keiji , Asagoe Kenji
Published: June 2015

Sentinel lymph node biopsy (SLNB) is a widely accepted standard procedure for patients with clinically localized melanoma. Melanoma prevalence and Clark's subtype differ between Asians and Caucasians. Here, we evaluated our experience on SLNB for cutaneous melanoma in a Japanese population. SLNB was performed for patients with melanoma between July 2000 and June 2014. We retrospectively analyzed 102 patients regarding association of clinicopathological features with sentinel lymph node (SLN) status, melanoma‐specific survival (MSS) and disease‐free survival (DFS). A positive SLN was significantly associated with primary Breslow thickness. Compared with 43 patients with negative SLN, 59 patients with positive SLN had significantly shorter MSS (5‐year survival rate, 94.3% vs 63.2%; P = 0.0002) and DFS (5‐year survival rate, 92.7% vs 63.4%; P = 0.0004). According to our subgroup analyses, nine patients with positive non‐SLN had significantly shorter MSS compared with 32 patients with negative non‐SLN (5‐year survival rate, 32.4% vs 68.5%; P = 0.0273). The survival of 51 Japanese patients with acral lentiginous melanoma (ALM) was not inferior to the survival of patients with other Clark's subtype. Breslow thickness is an important factor for both MSS and DFS, and the status of SLN is the most predictive prognostic factor in Japanese patients with clinically localized melanomas, as in case of Caucasians. Features of ALM may be different between Asians and Caucasians.
Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity
Authors: Cheng Tao , Xu Chao , Lei Li , Li Changhao , Zhang Yu , Zhou Shiliang
Published: June 2015

The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant‐specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant‐specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common‐used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant‐specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.
Compensation in the Post‐FIN 48 Period: The Case of Contracting on Tax Performance and Uncertainty
Authors: Brown Jennifer L. , Drake Katharine D. , Martin Melissa A.
Published: June 2015

Academic and anecdotal evidence indicates that incentive systems often provide short‐term payouts without regard for long‐term consequences. New detailed disclosures mandated by FIN No. 48, Accounting for Uncertainty in Income Taxes, enable us to use a tax setting to investigate whether boards adjust performance‐based pay for uncertainty. We find managers’ bonus payouts are positively associated with tax performance; however, bonus payouts are lower when measures of ex ante tax uncertainty are higher. Our results are robust to tests of alternative explanations including financial reporting aggressiveness, overall firm risk, and other forms of compensation. Further, we document that the relation between bonus compensation and tax performance has changed in the post‐FIN No. 48 period. Specifically, we identify a significant association between bonus payout and GAAP ETR only in the pre‐FIN No. 48 period and a significant association between bonus payout and cash ETR only in the post‐FIN No. 48 period, suggesting that the relation between compensation and tax avoidance should be examined carefully with particular attention to the post‐FIN No. 48 period.
Weight loss and low age are associated with intensity of rooting behaviours in newborn infants
Authors: Takahashi Yuki , Jonas Wibke , Ransjö‐Arvidson Anna‐Berit , Lidfors Lena , Uvnäs Moberg Kerstin , Nissen Eva
Published: June 2015

Aim

Little is known about the developing breastfeeding behaviour of newborn infants. This study describes infants' prebreastfeeding behaviour during the second day of life and explores possible associations with infant characteristics.

Methods

We studied 13 mothers and healthy full‐term infants after normal births. At 24–48 hours of life, the newborns were placed in skin‐to‐skin contact with their mothers for breastfeeding and were video‐filmed. The order, frequency and duration of predefined infant prefeeding behaviours and suckling were coded and analysed using computer‐based video software.

Results

Prefeeding behaviours occurred in the following order: rooting, hand to mouth movements, licking of the nipple and hand to breast to mouth movements. The infants started to suckle at a median of one to two minutes. Rooting was the most common behaviour, observed in 12 infants. The duration of rooting movements during the last minute before breastfeeding was inversely related to neonatal age (p ≤ 0.001) and positively related to neonatal weight loss (p = 0.02) after birth.

Conclusion

Infants exhibited a distinct sequence of prefeeding behaviours during the second day of life, and our findings suggest that rooting movements were governed by mechanisms involved in the regulation of food intake and weight gain.
IPSAS or IFRS as the Framework for Public Sector Financial Reporting? New Zealand Preparers’ Perspectives
Authors: Laswad Fawzi , Redmayne Nives Botica
Published: June 2015

The last 30 years have seen public sector accounting in many countries undergo considerable change. More recently, some governments adopted accrual accounting and International Public Sector Accounting Standards (IPSAS), some adopted modified International Financial Reporting Standards (IFRS) while others continued with cash‐based accounting. New Zealand (NZ) has, for more than two decades, followed a sector neutral approach to financial reporting and standard setting where the same accounting standards were applied to all entities in all sectors: for‐profit, not‐for‐profit and the public sector. This period included the adoption of IFRS by for‐profit entities with minor modifications for the public sector. The suitability of IFRS for the public sector has been questioned and, recently, standard setters in NZ decided to adopt a sector‐specific standard‐setting approach with multiple tiers for each sector. The for‐profit sector will continue to follow IFRS but reporting standards for the public sector will be based on IPSAS. In this period of change we sought the views of preparers of public sector financial reports regarding the users of such reports and their preferences for the public sector reporting framework. We also sought the views of the preparers regarding the usefulness of each financial statement for users, and whether the benefits of reporting by their organisations exceeds the costs. The findings indicate support for maintaining IFRS as a basis for reporting in the NZ public sector. However, IPSAS modified to NZ conditions is also perceived as an acceptable option by respondents in this study. The income statement is, in the opinion of the respondents in this study, the most useful statement while cash flows appear to hold little value. A high proportion of respondents believe that the benefits of reporting exceed the costs, which contradicts the view that such reports are mainly compliance documents that provide little value. This finding contributes to the continuing debate on costs versus benefits on the recent introduction of IPSAS as the reporting framework for the public sector and the perceived appropriateness of IPSAS in public sector reporting.
Adopting International Financial Reporting Standards for Small and Medium‐sized Enterprises
Authors: Chand Parmod , Patel Arvind , White Michael
Published: June 2015

Diverse complications and controversial issues in the adoption of International Financial Reporting Standards (IFRS) for Small and Medium‐sized Enterprises (SMEs) have been reported by many jurisdictions, prompting them not to adopt this set of standards. Conversely many jurisdictions have adopted or are in the process of adopting IFRS for SMEs. This study considers the impetus for successfully achieving accounting convergence with IFRS for SMEs in those jurisdictions. The possible transition issues that may arise when countries adopt IFRS for SMEs are also highlighted. Furthermore, to provide pioneering evidence on the problems accountants encounter when applying IFRS for SMEs, we conduct a survey on accounting practitioners in Fiji – an early adopter of this set of standards. Both the insights provided on the process of embracing IFRS for SMEs in Fiji and the opinions elicited from accountants highlight new dimensions to the inherent problems in IFRS for SMEs. Scant attention has been given to this issue so far; hence the empirical evidence provided by our study informs not only the global convergence of SME accounting but also the quality of the current suite of IFRS for SMEs.