bluuebunny/crossref_metadata_2025 huggingface dataset:
Cosmological N-body simulations including radiation perturbations
Authors: Brandbyge Jacob , Rampf Cornelius , Tram Thomas , Leclercq Florent , Fidler Christian , Hannestad Steen
Published: November 2016

Cosmological N-body simulations are the standard tools to study the emergence of the observed large-scale structure of the Universe. Such simulations usually solve for the gravitational dynamics of matter within the Newtonian approximation, thus discarding general relativistic effects such as the coupling between matter and radiation (≡ photons and neutrinos). In this Letter, we investigate novel hybrid simulations that incorporate interactions between radiation and matter to the leading order in General Relativity, whilst evolving the matter dynamics in full non-linearity according to Newtonian theory. Our hybrid simulations come with a relativistic space–time and make it possible to investigate structure formation in a unified framework. In this work, we focus on simulations initialized at z = 99 and show that the extracted matter power spectrum receives up to 3 per cent corrections on very large scales through radiation. Our numerical findings compare favourably with linear analytical results from Fidler et al., from which we deduce that there cannot be any significant non-linear mode-coupling induced through linear radiation corrections.
Feasibility of Implementing a Hospital-Based “Opt-Out” Tobacco-Cessation Service
Authors: Nahhas Georges J , Wilson Dianne , Talbot Vince , Cartmell Kathleen B , Warren Graham W , Toll Benjamin A , Carpenter Matthew J , Cummings K Michael
Published: November 2016

Objective

To assess the feasibility and outcomes of implementing a hospital-based “opt-out” tobacco-cessation service.

Methods

In 2014, the Medical University of South Carolina adopted a policy that all hospitalized patients who self-report using tobacco be referred to tobacco-cessation service. This is a descriptive study of a real-world effort to implement guidelines for a hospital-based cessation service consistent with Joint Commission’s standards. Between February 2014 and May 2015, 42 061 adults were admitted to the Medical University of South Carolina Hospital. Eligible current cigarette smokers were referred to the tobacco-cessation service, which consisted of a bedside consult and phone follow-up 3, 14, and 30 days after hospital discharge using interactive-voice-response. The primary study outcomes evaluated the proportions of smokers reached by the bedside counselor and/or phone follow-up, smokers who opted out, and smokers who self-reported not smoking when last contacted by phone.

Results

Records identified 8423 smokers, of whom 69.4% (n = 5843) were referred into the service. One full-time bedside counselor was able to speak with 1918 (32.8%) patients, of whom 96 (5%) denied currently smoking and 287 (14.9%) refused counselling. Reach at follow-up was achieved for 703 (55%) smokers who received bedside counselling and 1613 (49%) who did not, yielding an overall follow-up reach rate of 60%. Of those reached by phone, 36.4% reported not smoking (51% vs. 27% for those who did and did not receive bedside counselling, respectively). Intent-to-treat abstinence rate was 13.5% according to the last known smoking status.

Conclusions

Findings from this study suggest that an inpatient smoking-cessation service with an “opt-out” approach can positively impact short-term cessation outcomes.

Implications

(1)The findings demonstrate the feasibility of implementing an automated large-scale opt-out tobacco-cessation service for hospitalized patients that is consistent with the Joint Commission recommended standards for treating tobacco dependence. (2) Receiving a bedside tobacco-cessation consult while hospitalized increased the use of stop smoking medications and abstinence from smoking after discharge from the hospital. (3) Even in those patients who did not receive a bedside consult, 5% accepted a referral to the South Carolina Tobacco Quitline to get help to stop smoking.
Laccase Gene Sh-lac Is Involved in the Growth and Melanin Biosynthesis of Scleromitrula shiraiana
Authors: Lǚ Zhiyuan , Kang Xin , Xiang Zhonghuai , He Ningjia
Published: November 2016

Scleromitrula shiraiana causes the popcorn disease in mulberry trees resulting in severe economic losses. Previous studies have shown that melanin may play a vital role in establishing the pathogenicity of fungi. In the present study, we identified the melanin produced in S. shiraiana belongs to DHN melanin by gas chromatography-mass spectrometry, and cloned the laccase Sh-lac, a potential DHN melanin biosynthesis gene from S. shiraiana. We obtained two stable Sh-lac silenced transformants using RNAi, ilac-4 and 8 to elucidate the DHN melanin biosynthetic pathway in S. shiraiana. The melanin production of ilac-4 and ilac-8 was significantly reduced, and their vegetative growth was also suppressed. Results such as these led to a proposal that Sh-lac played a key role in DHN melanin formation in S. shiraiana and may function differentially with other melanin biosynthetic genes. The inhibition of melanin was accompanied by the decrease of oxalic acid and the adhesion of hyphae was impaired. Our results indicated that laccase was an important enzyme in the synthesis of melanin and might play a critical role in the pathogenicity of S. shiraiana.
Immunological Patterns from Four Melioidosis Cases: Constant and Variable Protein Antigens
Authors: Yi Jinhee , Herring Kelsey , Sanchez Timothy C. , Iyer Srinivas , Stone Joshua K. , Lee Judy , Mayo Mark , Currie Bart J. , Tuanyok Apichai , Keim Paul
Published: November 2016

Burkholderia pseudomallei is the causative agent of the melioidosis and is endemic to Southeast Asia and northern Australia. There is no available vaccine and accurate diagnosis is difficult, time-consuming and labor intensive. Early diagnosis is an important part of successful treatment and current serological tests are inadequate and based upon multiple antigens. Identifying specific immunogenic proteins which are highly seroreactive may yield potential diagnostic targets for detecting antibodies and antigens specific to melioidosis. We have used 2D gel electrophoresis and Western blotting analysis to analyze protein antigenicity of whole cell lysates extracted from four B. pseudomallei strains and the sera from the specific infected humans. We found a total of 135 immunogenic proteins, 62 of which we were able to identify to a specific gene by mass-spectrometry. Results from the Western blotting of each strain’s proteins and the corresponding patient serum reveal between 30 – 40% serum x strain specific immunogenic proteins. In most cases, these differences exist despite the fact that the genes encoding these proteins were present among all four B. pseudomallei strains. Eight particular proteins were immunogenic in all four strain x serum combinations and could represent novel diagnostic and vaccine subunit targets.
Simulations ofCYP51AfromAspergillus fumigatusin a model bilayer provide insights into triazole drug resistance
Authors: Nash Anthony , Rhodes Johanna
Published: November 2016

1

Azole antifungal drugs targetCYP51AinAspergillus fumigatusby binding with the active site of the protein, blocking ergosterol biosynthesis. Resistance to azole anti-fungal drugs is now common, with a leucine to histidine amino acid substitution at position 98 the most frequent, conferring resistance to itraconazole. In this study, we create a homology model ofCYP51Ausing a recently published crystal structure of the paralog proteinCYP51B. The derived structures, wild-type and L98H mutant, are positioned within a lipid membrane bilayer and subjected to molecular dynamics simulations in order improve the accuracy of both models. The structural analysis from our simulations suggests a decrease in active site surface from the formation of hydrogen bonds between the histidine substitution and neighbouring polar side chains, potentially preventing the binding of azole drugs. This study yields a biologically relevant structure and set dynamics of theA. fumigatusLanosterol 14 alpha-demethylase enzyme and provides further insight into azole antifungal drug resistance.
Floral Radiometry: A Biophysical Basis to Characterize Landscapes
Authors: Jaishanker R. , Sooraj N.P. , Somasekheran Pillai M. , Athira K. , Joseph Ammini , Krishna Aswathy , Indu I , SarojKumar V
Published: November 2016

This paper presents early results on studies of floral spectral reflectance of angiosperms and introduces floral radiometry as an emergent dimension of ecological research in India. Floral spectral reflectance of 121 angiosperm species was measured using hand-held spectroradiometer. The authors describe spectral reflectance of seven representative species within 350-800 nanometer region of the electromagnetic spectrum. Characteristic absorption and reflection of flowers, in ultraviolet and visible regions of the spectrum is reported. Near infrared reflectance was consistently high for all species studied. Flower color is unique to a species and importance of understanding flower color from pollinator’s perspective is highlighted.
Engineered tRNA suppression of a CFTR nonsense mutation
Authors: Lueck John D. , Infield Daniel T. , Mackey Adam L. , Pope R. Marshall , McCray Paul B. , Ahern Christopher A.
Published: November 2016

Ten percent of human diseases are caused by ‘nonsense’ mutations that lead to premature truncation of the protein reading frame. Small molecules that promote read-through of such PTC have significant clinical promise but current iterations suffer from lowin vivoefficacy and the nonselective amino acid incorporation. Alternatively, while gene-modifying approaches, such as CRISPR/Cas9, represent a long-term solution, such treatments may be far from reaching the clinical setting. Building on previous work by our group and others, we describe a tRNA engineering approach that enables the conversion of an in frame nonsense stop mutation to the naturally occurring amino acid, thus rescuing the full-length wild type protein. Data is presented demonstrating the functionality of the approach with the rescue of CFTR W1282X, a human mutation that causes cystic fibrosis (CF). The stringency of the approach is confirmed by mass spectrometry in a model protein indicating the encoding of only tryptophan at the TGA suppression site. The data describe the first use of an edited tRNA to repair a CF causative mutation and serve a proof of principle for the eventual use of codon-edited tRNA for the therapeutic rescue of PTC disease codons.
Identification of clinically predictive metagenes that encode components of a network coupling cell shape to transcription by image-omics
Authors: Sailem Heba Z. , Bakal Chris
Published: November 2016

The associations between clinical phenotypes (tumor grade, survival) and cell phenotypes, such as shape, signaling activity, and gene expression, are the basis for cancer pathology, but the mechanisms explaining these relationships are not always clear. The generation of large data sets containing information regarding cell phenotypes and clinical data provides an opportunity to describe these mechanisms. Here, we develop an image-omics approach to integrate quantitative cell imaging data, gene expression, and protein–protein interaction data to systematically describe a “shape-gene network” that couples specific aspects of breast cancer cell shape to signaling and transcriptional events. The actions of this network converge on NF-κB, and support the idea that NF-κB is responsive to mechanical stimuli. By integrating RNAi screening data, we identify components of the shape-gene network that regulate NF-κB in response to cell shape changes. This network was also used to generate metagene models that predict NF-κB activity and aspects of morphology such as cell area, elongation, and protrusiveness. Critically, these metagenes also have predictive value regarding tumor grade and patient outcomes. Taken together, these data strongly suggest that changes in cell shape, driven by gene expression and/or mechanical forces, can promote breast cancer progression by modulating NF-κB activation. Our findings highlight the importance of integrating phenotypic data at the molecular level (signaling and gene expression) with those at the cellular and tissue levels to better understand breast cancer oncogenesis.
Life-cycle information management using open-standard BIM
Authors: Hoeber Hans , Alsem Daan
Published: November 2016

Purpose

The purpose of this paper is to present a way of working with open-standard building information modeling (BIM), object type libraries, systems engineering and an Information Delivery Manual for the management of information over the life-cycle of infrastructure assets. The concept is presented as a source of inspiration, proof of concept and to underpin the value of different parts of the concept leading to an integrated approach to life-cycle information management.

Design/methodology/approach

The paper presents a concept for a way of working. A proof of concept is provided in the form of a case study in which this concept is operational. It shows that this way of working using open-standard BIM can be applied to manage information in the life-cycle. It does not provide, nor suggest to provide, empirical evidence for specific benefits in terms of efficiency.

Findings

The paper shows that open-standard BIM can be applied for information management in the life-cycle of (construction) assets. The specific approach that is applied in practice in a Dutch Infrastructure Project is explained including a case project.

Research limitations/implications

The example of Traverse Dieren attests to a implementation of the approach in practice. From this case it can be concluded that the suggested approach is feasible in the initiation and design phase and applicable during realization. Based on the example as described in this paper it cannot be concluded to what extent the known information management problems in the life-cycle are solved. Therefore a detailed evaluation on the information exchange would be required which is beyond the scope of this paper.

Practical implications

This paper shows how different (theoretical) concepts are successfully combined and implemented in practice to attain the defined BIM goals.

Originality/value

This paper shows a practical case implementation of open-standard BIM (using COINS). It provides a way of working that combines BIM, systems engineering, libraries and contractual arrangements for the management of information over the life-cycle of infrastructure assets.
Fog computing architectures for healthcare
Authors: Prieto González Lisardo , Jaedicke Corvin , Schubert Johannes , Stantchev Vladimir
Published: November 2016

Purpose

The purpose of this study is to analyze how embedding of self-powered wireless sensors into cloud computing further enables such a system to become a sustainable part of work environment.

Design/methodology/approach

This is exemplified by an application scenario in healthcare that was developed in the context of the OpSIT project in Germany. A clearly outlined three-layer architecture, in the sense of Internet of Things, is presented. It provides the basis for integrating a broad range of sensors into smart healthcare infrastructure. More specifically, by making use of short-range communication sensors (sensing layer), gateways which implement data transmission and low-level computation (fog layer) and cloud computing for processing the data (application layer).

Findings

A technical in-depth analysis of the first two layers of the infrastructure is given to prove reliability and to determine the communication quality and availability in real-world scenarios. Furthermore, two example use-cases that directly apply to a healthcare environment are examined, concluding with the feasibility of the presented approach.

Practical implications

Finally, the next research steps, oriented towards the semantic tagging and classification of data received from sensors, and the usage of advanced artificial intelligence-based algorithms on this information to produce useful knowledge, are described together with the derived social benefits.

Originality/value

The work presents an innovative, extensible and scalable system, proven to be useful in healthcare environments.
Clinical factors predicting the therapeutic response to ustekinumab in patients with moderate to severe chronic plaque psoriasis
Authors: Hwang Young Ji , Youn Sang Woong , Kim Bo Ri , Yu Dae Young , Kim Youngdoe , Pires Antonio , Cho Soyun , Seo Seong Jun , Lee Eun So , Roh Joo Young , Choi Gwang Seong , Lee Min Geol ,   the MARCOPOLO investigators
Published: November 2016

While ustekinumab has been widely used as an effective biologic for the treatment of chronic plaque psoriasis, no prospective studies have specifically investigated the clinical factors that may influence treatment outcomes with ustekinumab. This post‐hoc analysis aimed to identify specific clinical factors that may influence treatment outcomes with ustekinumab in psoriasis patients. In the MARCOPOLO study, 102 Korean patients with moderate to severe psoriasis were analyzed to assess the influence of baseline characteristics as clinical factors on clinical response (improvement in Psoriasis Area and Severity Index by ≥75%/90% [PASI75/PASI90]) to ustekinumab. In addition, differences in PASI75 and PASI90 responses between the responder group and non‐responders were evaluated at weeks 28 and 52. Multiple logistic regression analysis was used to determine adjusted clinical factors predicting treatment outcomes among patient characteristics. At week 28, there was a significant difference in PASI75/PASI90 response based on prior biologic experience, although the difference did not persist at week 52. In addition, after adjusting for the effects of relevant clinical factors, biologic experience was significantly associated with less PASI75 (odds ratio [OR] = 0.14, P = 0.001) and PASI90 (OR = 0.22, P = 0.036) responses at week 28. The presence of comorbidities was higher among non‐responders than among PASI75/PASI90 responders at both weeks 28 and 52, but was not statistically significant. Previous biologic use was the only clinical factor predicting less response at week 28, although it did not influence the clinical response after week 52. Further studies are warranted to investigate the association between presence of comorbidities and clinical response.
First‐arrival traveltime tomography with modified total‐variation regularization
Authors: Jiang Wenbin , Zhang Jie
Published: November 2016

First‐arrival traveltime tomography is a robust tool for near‐surface velocity estimation. A common approach to stabilizing the ill‐posed inverse problem is to apply Tikhonov regularization to the inversion. However, the Tikhonov regularization method recovers smooth local structures while blurring the sharp features in the model solution. We present a first‐arrival traveltime tomography method with modified total‐variation regularization to preserve sharp velocity contrasts and improve the accuracy of velocity inversion. To solve the minimization problem of the new traveltime tomography method, we decouple the original optimization problem into the two following subproblems: a standard traveltime tomography problem with the traditional Tikhonov regularization and a L2 total‐variation problem. We apply the conjugate gradient method and split‐Bregman iterative method to solve these two subproblems, respectively. Our synthetic examples show that the new method produces higher resolution models than the conventional traveltime tomography with Tikhonov regularization, and creates less artefacts than the total variation regularization method for the models with sharp interfaces. For the field data, pre‐stack time migration sections show that the modified total‐variation traveltime tomography produces a near‐surface velocity model, which makes statics corrections more accurate.
Abundant and rare picoeukaryotic sub‐communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean
Authors: Wu Wenxue , Logares Ramiro , Huang Bangqin , Hsieh Chih‐hao
Published: November 2016

In this work, they compared patterns of abundant and rare picoeukaryotic sub‐communities in the epipelagic waters (surface and 40–75 m depth subsurface layers) of the East and South China Seas across seasons via 454 pyrosequencing of the V4 region of 18S rDNA. They also examined the relative effects of environmental filtering, dispersal limitations and seasonality on community assembly. Their results indicated that (i) in the surface layer, abundant taxa are primarily influenced by dispersal limitations and rare taxa are primarily influenced by environmental filtering, whereas (ii) in the subsurface layer, both abundant and rare sub‐communities are only weakly influenced by environmental filtering but are strongly influenced by dispersal limitations. Moreover, (iii) abundant taxa exhibit stronger temporal variability than rare taxa. They also found that abundant and rare sub‐communities display similar spatial richness patterns that are negatively correlated with latitude and chlorophyll a and positively correlated with temperature. In summary, environmental filtering and dispersal limitations have different effects on abundant and rare picoeukaryotic sub‐communities in different layers. Thus, depth appears as an essential variable that governs the structuring patterns of picoeukaryotic communities in the oceans and should be thoroughly considered to develop a more comprehensive understanding of oceanic microbial assemblages.
PAAR‐Rhs proteins harbor various C‐terminal toxins to diversify the antibacterial pathways of type VI secretion systems
Authors: Ma Jiale , Sun Min , Dong Wenyang , Pan Zihao , Lu Chengping , Yao Huochun
Published: November 2016

The type VI secretion system (T6SS) of bacteria plays a key role in competing for specific niches by the contact‐dependent killing of competitors. Recently, Rhs proteins with polymorphic C‐terminal toxin‐domains that inhibit or kill neighboring cells were identified. In this report, we identified a novel Rhs with an MPTase4 (Metallopeptidase‐4) domain (designated as Rhs‐CT1) that showed an antibacterial effect via T6SS in Escherichia coli. We managed to develop a specific strategy by matching the diagnostic domain‐architecture of Rhs‐CT1 (Rhs with an N‐terminal PAAR‐motif and a C‐terminal toxin domain) for effector retrieval and discovered a series of Rhs‐CTs in E. coli. Indeed, the screened Rhs‐CT3 with a REase‐3 (Restriction endonuclease‐3) domain also mediated interbacterial antagonism. Further analysis revealed that vgrGO1 and eagR/DUF1795 (upstream of rhs‐ct) were required for the delivery of Rhs‐CTs, suggesting eagR as a potential T6SS chaperone. In addition to chaperoned Rhs‐CTs, neighborless Rhs‐CTs could be classified into a distinct family (Rhs‐Nb) sharing close evolutionary relationship with T6SS2‐Rhs (encoded in the T6SS2 cluster of E. coli). Notably, the Rhs‐Nb‐CT5 was confirmed bioinformatically and experimentally to mediate interbacterial antagonism via Hcp2B‐VgrG2 module. In a further retrieval analysis, we discovered various toxin/immunity pairs in extensive bacterial species that could be systematically classified into eight referential clans, suggesting that Rhs‐CTs greatly diversify the antibacterial pathways of T6SS.
Eye of the Finch: characterization of the ocular microbiome of house finches in relation to mycoplasmal conjunctivitis
Authors: Thomason Courtney A. , Leon Ariel , Kirkpatrick Laila T. , Belden Lisa K. , Hawley Dana M.
Published: November 2016

Vertebrate ocular microbiomes are poorly characterized and virtually unexplored in wildlife species. Pathogen defense is considered a key function of microbiomes, but determining microbiome stability during disease is critical for understanding the role of resident microbial communities in infectious disease dynamics. Here, we characterize the ocular bacterial microbiome of house finches (Haemorhous mexicanus), prior to and during experimental infection with an inflammatory ocular disease, Mycoplasmal conjunctivitis, caused by Mycoplasma gallisepticum. In ocular tissues of healthy house finches, we identified 526 total bacterial operational taxonomic units (OTUs, 97% similarity), primarily from Firmicutes (92.6%) and Proteobacteria (6.9%), via 16S rRNA gene amplicon sequencing. Resident ocular communities of healthy female finches were characterized by greater evenness and phylogenetic diversity compared to healthy male finches. Regardless of sex, ocular microbiome community structure significantly shifted 11 days after experimental inoculation with M. gallisepticum. A suite of OTUs, including taxa from the genera Methylobacterium, Acinetobacter and Mycoplasma, appear to drive these changes, indicating that the whole finch ocular microbiome responds to infection. Further study is needed to quantify changes in absolute abundance of resident taxa and to elucidate potential functional roles of the resident ocular microbiome in mediating individual responses to this common songbird bacterial pathogen.
Sex, Statistics, Peacekeepers and Power: UN Data on Sexual Exploitation and Abuse and the Quest for Legal Reform
Authors: Grady Kate
Published: November 2016

The UN Secretariat provides annual statistics on allegations of sexual exploitation and abuse made against peacekeeping personnel, with reduced numbers of allegations leading to claims of success for the UN's ‘zero tolerance’ policy. This article explores the use of data as ‘technologies’ of global governance, to examine the function that these annual statistics serve for the UN and the impact that they have on calls for legal reform. Thus far, the statistics have attracted little academic appraisal. Yet, they have been used to establish the UN's authority to resolve the ‘problem’ of sexual exploitation and abuse, diminishing the space for critique of UN policy and undermining the quest for improved legal arrangements.
Responses to Salduz: Procedural Tradition, Change and the Need for Effective Defence
Authors: Jackson John D.
Published: November 2016

This article examines the responses of national courts to the ECtHR's decision in Salduz v Turkey that suspects be provided with access to a lawyer before they are first interrogated by the police. It argues that harmonious application of human rights standards in criminal proceedings should build upon common values underpinning the procedural traditions of member states. ECtHR success in gaining acceptance for the principle of access to a lawyer during police interrogation, anchoring it in the privilege against incrimination, is contrasted with resistance towards giving the defence any active role during criminal investigations. It is argued that this resistance can be overcome by an appeal to safeguards that have long dominated the trial process. As the investigation phase increasingly determines the outcome of criminal proceedings, standards of fairness traditionally reserved for the trial process should be applied also to this phase in order to provide suspects with an effective defence.
Education in a mobile modernity
Authors: Forsey Martin
Published: November 2016

The main contention of this paper is that education helps frame a modernity in which individual progress and achievement are increasingly linked to the sheer physical act of movement. Thinking of modernisation as a trajectory of progress and development symbolised by industrialisation and a reordering of ‘traditional societies’ through rational forms of governance, we can begin to recognise the importance of the disembedding of people and communities from local institutions and relations that these modernising processes continue to require. Individual education stories are filled with movement that often reflect a commitment to the mobility imperatives of modernity. Reflecting the different scales of practice evident in this mobile modernity, the empirical focus ranges from rural settings to urban mobilities and then out to transnational mobilities and the educational choices exercised by the global middle classes. The paper explores the profound and the mundane ways in which educational structures affect family and individual mobilities.
phylodyn: an R package for phylodynamic simulation and inference
Authors: Karcher Michael D. , Palacios Julia A. , Lan Shiwei , Minin Vladimir N.
Published: November 2016

We introduce phylodyn, an r package for phylodynamic analysis based on gene genealogies. The package's main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes several Markov chain Monte Carlo‐based methods and an integrated nested Laplace approximation‐based approach for phylodynamic inference that have been developed in recent years. Genealogical data describe the timed ancestral relationships of individuals sampled from a population of interest. Here, individuals are assumed to be sampled at the same point in time (isochronous sampling) or at different points in time (heterochronous sampling); in addition, sampling events can be modelled with preferential sampling, which means that the intensity of sampling events is allowed to depend on the effective population size trajectory. We assume the coalescent and the sequentially Markov coalescent processes as generative models of genealogies. We include several coalescent simulation functions that are useful for testing our phylodynamics methods via simulation studies. We compare the performance and outputs of various methods implemented in phylodyn and outline their strengths and weaknesses. r package phylodyn is available at https://github.com/mdkarcher/phylodyn.
Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables
Authors: Clark Lindsay V. , Schreier Andrea Drauch
Published: November 2016

A major limitation in the analysis of genetic marker data from polyploid organisms is non‐Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here, we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci. We present an algorithm to take advantage of this mathematical property, sorting alleles into isoloci based on correlations, then refining the allele assignments after checking for consistency with individual genotypes. We demonstrate the utility of our method on simulated data, as well as a real microsatellite data set from a natural population of octoploid white sturgeon (Acipenser transmontanus). Our methodology is implemented in the R package polysat version 1.6.
Policy Diffusion: A Regime‐sensitive Conceptual Framework
Authors: Tosun Jale , Croissant Aurel
Published: November 2016

The analysis of diffusion processes is an expanding field of research in the social and economic sciences. However, prolific scholarship has highlighted the transnational diffusion of policy innovations, but the insights provided – at least for policies – are limited by a ‘democracy bias’, that is, the focus of most studies is on democracies. This limitation concerns both the empirical scope of most diffusion studies and their theoretical underpinning. Furthermore, the emphasis placed on the diffusion mechanisms has hindered the development of conceptual frameworks that systematically account for political regime characteristics and their role for policy diffusion. To take a first step towards reducing this gap, we propose an alternative conceptual framework. It builds on the existing literature on policy diffusion, but shifts the perspective from the international to the national context. In the subsequent discussion we put forward a theoretical framework that explicitly accounts for the role of political regime types in policy diffusion and shifts the analytical focus from mechanisms to ‘routes’ of diffusion.
Patterns of Diffusion: Comparing Democratic and Autocratic Waves
Authors: Weyland Kurt
Published: November 2016

This essay examines why the diffusion of autocratic rule tends to unfold more slowly, yet with greater effectiveness (‘success’) than pro‐democratic waves often do. A precedent of progressive regime change often inspires fairly unorganized crowds in many other countries to initiative spontaneous emulation efforts, as it happened in the revolutions of 1848 and the Arab Spring of 2011. Yet this lack of organization creates a high risk of failure. By contrast, the overthrow of democracy, which can also stimulate imitation attempts, is usually spearheaded by well‐established organizations, such as the military, which jump on the bandwagon less rashly, but pursue their goals more effectively. Therefore, autocratic waves advance with lower speed, yet greater ‘success’ than pro‐democratic riptides often do, as was evident in the diffusion of authoritarianism and fascism during the interwar years and the spread of military dictatorships in Latin America during the 1960s and 1970s.
Inferring diet from dental morphology in terrestrial mammals
Authors: Pineda‐Munoz Silvia , Lazagabaster Ignacio A. , Alroy John , Evans Alistair R.
Published: November 2016

Dietary inferences are a key foundation for paleoecological, ecomorphological and macroevolutionary studies because they inform us about the direct relationships between the components of an ecosystem. However, we need to consider the range of dietary variation we want to investigate and characterize before choosing a proxy. The goal of the present work is to evaluate the differences in dietary discrimination power between our new method, the multidimensional multi‐proxy dental morphology analysis (MPDMA) and unidimensional dental morphology proxies such as orientation patch count (OPCR), relief index (RI) or slope.

In order to do that, we three‐dimensionally scanned the dentitions of 134 extant mammals including 28 marsupials (order Diprotodontia) and 106 placentals (orders Carnivora, Primates and Rodentia) and classified their diets using a new classification scheme that emphasizes the primary resource in a given diet. Diet categories included herbivory, carnivory, frugivory, granivory, insectivory, fungivory, gumivory and generalist.

Unidimensional proxies significantly discriminate (P < 0·05) between one or two diet categories on the one hand and the rest on the other. For example, OPCR discriminates well between carnivorous and non‐carnivorous species. However, none of the individual proxies discriminate all eight dietary categories. Multi‐proxy dental morphology analysis demonstrates significant morphological differences across diets (MANOVA, d.f. = 7; F = 7·56; P < 0·05) and correctly discriminates diet for 67–82% of the specimens in the data set including and excluding rodents respectively.

Combining different morphological variables makes it possible to draw better dietary inferences and fully represent the multidimensional nature of dental morphology and dietary specializations. Our results have important applications in ecological, paleoecological and evolutionary research.
Infections and exposure to anti‐infective agents and the risk of severe mental disorders: a nationwide study
Authors: Köhler O. , Petersen L. , Mors O. , Mortensen P. B. , Yolken R. H. , Gasse C. , Benros M. E.
Published: November 2016

Objective

Severe infections are associated with increased risks of mental disorders; however, this is the first large‐scale study investigating whether infections treated with anti‐infective agents in the primary care setting increase the risks of schizophrenia and affective disorders.

Method

We identified all individuals born in Denmark 1985–2002 (N = 1 015 447) and studied the association between infections treated with anti‐infective agents and the subsequent risk of schizophrenia and affective disorders during 1995–2013. Cox regression analyses were adjusted for important confounders.

Results

Infections treated with anti‐infective agents were associated with increased risks of schizophrenia by a hazard rate ratio (HRR) of 1.37 (95%‐CI = 1.20–1.57) and affective disorders by a HRR of 1.64 (95%‐CI = 1.48–1.82), fitting a dose–response and temporal relationship (P < 0.001). The excess risk was primarily driven by infections treated with antibiotics, whereas infections treated with antivirals, antimycotics, and antiparasitic agents were not significant after mutual adjustment. Individuals with infections requiring hospitalization had the highest risks for schizophrenia (HRR = 2.05; 95%‐CI = 1.77–2.38) and affective disorders (HRR = 2.59; 95%‐CI = 2.31–2.89).

Conclusion

Infections treated with anti‐infective agents and particularly infections requiring hospitalizations were associated with increased risks of schizophrenia and affective disorders, which may be mediated by effects of infections/inflammation on the brain, alterations of the microbiome, genetics, or other environmental factors.
When the neighbourhood goes bad: can endangered black robins adjust nest‐site selection in response to the risk of an invasive predator?
Authors: Lawrence C. , Paris D. , Briskie J. V. , Massaro M.
Published: November 2016

The introduction of exotic predators into new areas has had significant impacts on naïve prey species, which initially lack behavioural mechanisms to avoid predation. Understanding a species’ ability to respond appropriately to novel threats may inform in situ management options for threatened island populations. In the presence of nest predators, physical characteristics of the nest site can influence the likelihood that eggs or chicks are lost to predation. Some birds that evolved under high nest predation pressure show predictable changes in nest‐site selection following nest predation, but the ability of naïve island birds to alter nest‐site decisions based on experience with novel nest predators has not been well studied. We examined nest‐site choices of re‐nesting Chatham Island black robins Petroica traversi following nest predation by invasive European starlings Sturnus vulgaris. Robins whose first nests were depredated re‐nested in a new location that was significantly lower to the ground than pairs whose first nests were lost through other causes. As predation risk increases with nest height, the lower placement of re‐nests is consistent with a movement towards safer nest sites. The cause of nest failure did not influence the choice of substrate for a replacement nest, nor did individual pairs re‐nest further away from depredated nests. Changes in nest‐site selection did not carry over into subsequent nesting seasons. Our results suggest that some evolutionarily naïve species may be capable of assessing immediate risk through individual experience with novel predators, and modifying their nest‐site decisions accordingly.
Potential risks of orthodontic therapy: a critical review and conceptual framework
Authors: Wishney M
Published: November 2016

This review examines some of the potential risks of orthodontic therapy along with their evidence base. The risks of orthodontic treatment include periodontal damage, pain, root resorption, tooth devitalization, temporomandibular disorder, caries, speech problems and enamel damage. These risks can be understood to arise from a synergy between treatment and patient factors. In general terms, treatment factors that can influence risk include appliance type, force vectors and duration of treatment whilst relevant patient factors are both biological and behavioural. Hence, the natural variation between orthodontic treatment plans and patients gives rise to variations in risk. A good understanding of these risks is required for clinicians to obtain informed consent before starting treatment as well as to reduce the potential for harm during treatment. After considering each of these risks, a conceptual framework is presented to help clinicians better understand how orthodontic risks arise and may therefore be mitigated.
Is the Memorial Sloan Kettering Cancer Centre (MSKCC) sarcoma nomogram useful in an Asian population?
Authors: Ng Deanna Wan Jie , Tan Grace Hwei Ching , Chia Claramae Shulyn , Lim Cindy Xindi , Chee Soo Khee , Quek Richard Hong Hui , Farid Mohamad , Teo Melissa Ching Ching
Published: November 2016

Aim

A nomogram for prediction of 12‐year sarcoma‐specific survival has been developed based on patients with soft tissue sarcomas treated in Memorial Sloan Kettering Cancer Centre (MSKCC). We aim to evaluate the predictive accuracy of the MSKCC sarcoma nomogram in a cohort of patients treated at an Asian institution. This has not been validated in an Asian population and thus its universal applicability remains unproven.

Materials and methods

Between 1990 and 2013, 840 adult patients underwent treatment for primary soft tissue sarcoma (STS) at the National Cancer Centre Singapore. Patients who presented with locally recurrent or metastatic disease were excluded from the analysis. The variables included in the MSKCC nomogram included age at diagnosis, tumor size, histologic grade, histologic subtype, depth and site. A total of 399 patients were left for analysis. The nomogram was validated by assessing its extent of discrimination and level of calibration.

Results

All patients had deep tumors. Disease occurred most commonly in the lower extremity (n = 149 [37.3%]), the most common histologic subtype was “Others” (angiosarcoma, ewing's sarcoma, endometrial stromal sarcoma, sarcoma NOS [not otherwise specified] and rhabdomyosarcoma). Sixty‐four percent of all patients had high‐grade tumors while 36% had low‐grade tumors. The median patient age at diagnosis was 54 years (range: 17–88 years). The median follow up time for all patients and surviving patients were 29 (range: 1–174) and 33 (range: 1–157) months, respectively. The observed 5‐ and 10‐year sarcoma‐specific survival were 55% and 33%, respectively. The concordance index was 0.71. For level of calibration, the observed correspondence between predicted and actual outcomes suggest that the MSKCC nomogram generally predicts well for patients with higher survival probability, but consistently overpredicts survival for the other groups, in our cohort of patients.

Conclusion

The MSKCC sarcoma nomogram was found to be accurate in terms of extent of discrimination. In terms of level of calibration, it generally predicts well for patients with higher survival probability, but consistently overpredicts survival for the other groups in our population.
Attitudes of local people towards the mountain nyala (Tragelaphus buxtoni) in Munessa, Ethiopia
Authors: Tadesse Solomon A. , Kotler Burt P.
Published: November 2016

Due to their direct dependence on wildlife products for subsistent use, people living in poverty are often viewed as being in conflict with wildlife conservation. We studied the attitudes of local people towards mountain nyala (Tragelaphus buxtoni) in Munessa, Ethiopia. A household survey (n = 214) was used to examine the socio‐economic characteristics and beliefs of local people from three peasant associations and one village. Generally, the study revealed that local people had positive attitudes towards mountain nyala, its conservation and population increase, which is consistent with our predictions. For example, a greater percentage of the respondents had positive (62.5%) rather than negative (37.5%) attitudes towards mountain nyala and its conservation. Moreover, the larger proportion of the respondents had positive (66.67%) rather than negative (33.3%) attitudes towards an increase in mountain nyala population. However, compared to socio‐economic characteristics, beliefs towards mountain nyala were more powerful and consistent predictor of attitudes and explained much of the variances of the two groups of the dependent variables. Thus, informing local communities about the value of mountain nyala (e.g. recreational and economic) through conservation education, advocating the need for sustainable utilization and introducing an economic benefit sharing may improve positive attitude and increase participation of local people in conservation and management of the mountain nyala population in Munessa.
Agreement and accuracy using the FIGO, ACOG and NICE cardiotocography interpretation guidelines
Authors: Santo Susana , Ayres‐de‐Campos Diogo , Costa‐Santos Cristina , Schnettler William , Ugwumadu Austin , Da Graça Luís M. ,   the FM‐Compare Collaboration
Published: November 2016

Introduction

One of the limitations reported with cardiotocography is the modest interobserver agreement observed in tracing interpretation. This study compared agreement, reliability and accuracy of cardiotocography interpretation using the International Federation of Gynecology and Obstetrics, American College of Obstetrics and Gynecology and National Institute for Health and Care Excellence guidelines.

Material and methods

A total of 151 tracings were evaluated by 27 clinicians from three centers where International Federation of Gynecology and Obstetrics, American College of Obstetrics and Gynecology and National Institute for Health and Care Excellence guidelines were routinely used. Interobserver agreement was evaluated using the proportions of agreement and reliability with the κ statistic. The accuracy of tracings classified as “pathological/category III” was assessed for prediction of newborn acidemia. For all measures, 95% confidence interval were calculated.

Results

Cardiotocography classifications were more distributed with International Federation of Gynecology and Obstetrics (9, 52, 39%) and National Institute for Health and Care Excellence (30, 33, 37%) than with American College of Obstetrics and Gynecology (13, 81, 6%). The category with the highest agreement was American College of Obstetrics and Gynecology category II (proportions of agreement = 0.73, 95% confidence interval 0.70–76), and the ones with the lowest agreement were American College of Obstetrics and Gynecology categories I and III. Reliability was significantly higher with International Federation of Gynecology and Obstetrics (κ = 0.37, 95% confidence interval 0.31–0.43), and National Institute for Health and Care Excellence (κ = 0.33, 95% confidence interval 0.28–0.39) than with American College of Obstetrics and Gynecology (κ = 0.15, 95% confidence interval 0.10–0.21); however, all represent only slight/fair reliability. International Federation of Gynecology and Obstetrics and National Institute for Health and Care Excellence showed a trend towards higher sensitivities in prediction of newborn acidemia (89 and 97%, respectively) than American College of Obstetrics and Gynecology (32%), but the latter achieved a significantly higher specificity (95%).

Conclusions

With American College of Obstetrics and Gynecology guidelines there is high agreement in category II, low reliability, low sensitivity and high specificity in prediction of acidemia. With International Federation of Gynecology and Obstetrics and National Institute for Health and Care Excellence guidelines there is higher reliability, a trend towards higher sensitivity, and lower specificity in prediction of acidemia.