bluuebunny/crossref_metadata_2025 huggingface dataset:
CD-HIT-OTU-MiSeq, an Improved Approach for Clustering and Analyzing Paired End MiSeq 16S rRNA Sequences
Authors: Li Weizhong , Chang Yuanyuan
Published: June 2017

In recent years, Illumina MiSeq sequencers replaced pyrosequencing platforms and became dominant in 16S rRNA sequencing. One unique feature of MiSeq technology, compared with Pyrosequencing, is the Paired End (PE) reads, with each read can be sequenced to 250-300 bases to cover multiple variable regions on the 16S rRNA gene. However, the PE reads need to be assembled into a single contig at the beginning of the analysis. Although there are many methods capable of assembling PE reads into contigs, a big portion of PE reads can not be accurately assembled because the poor quality at the 3’ ends of both PE reads in the overlapping region. This causes that many sequences are discarded in the analysis. In this study, we developed a novel approach for clustering and annotation MiSeq-based 16S sequence data, CD-HIT-OTU-MiSeq. This new approach has four distinct novel features. (1) The package can clustering PE reads without joining them into contigs. (2) Users can choose a high quality portion of the PE reads for analysis (e.g. first 200 / 150 bases from forward / reverse reads), according to base quality profile. (3) We implemented a tool that can splice out the target region (e.g. V3-V4) from a full-length 16S reference database into the PE sequences. CD-HIT-OTU-MiSeq can cluster the spliced PE reference database together with samples, so we can derive Operational Taxonomic Units (OTUs) and annotate these OTUs concurrently. (4) Chimeric sequences are effectively identified throughde novoapproach. The package offers high speed and high accuracy. The software package is freely available as open source package and is distributed along with CD-HIT fromhttp://cd-hit.org. Within the CD-HIT package, CD-HIT-OTU-MiSeq is within the usecase folder.
Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer
Authors: Purcell Rachel V , Visnovska Martina , Biggs Patrick J , Schmeier Sebastian , Frizelle Frank A
Published: June 2017

Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding. 16S rRNA analysis showed enrichment of Fusobacteria and Bacteroidetes, and decreased levels of Firmicutes and Proteobacteria in CMS1. A more detailed analysis of bacterial taxa using non-human RNA-sequencing reads uncovered distinct bacterial communities associated with each molecular subtype. The most highly enriched species associated with CMS1 includedFusobacterium hwasookiiandPorphyromonas gingivalis. CMS2 was enriched forSelenomasandPrevotellaspecies, while CMS3 had few significant associations. Targeted quantitative PCR validated these findings and also showed an enrichment ofFusobacterium nucleatum, Parvimonas micraandPeptostreptococcus stomatisin CMS1. In this study, we have successfully associated individual bacterial species to CRC subtypes for the first time.
Variants at the ADAMTS13, BGALT5, SSBP2 and TKT Loci are associated with Post-term birth
Authors: Schierding William , Antony Jisha , Karhunen Ville , Vääräsmäki Marja , Franks Steve , Elliott Paul , Kajantie Eero , Sebert Sylvain , Blakemore Alex , Horsfield Julia A. , Järvelin Marjo-Riitta , O’Sullivan Justin M. , Cutfield Wayne S.
Published: June 2017

Gestation is a crucial timepoint in human development. Deviation from a term gestational age correlates with both acute and long-term adverse health effects for the child. Both being born pre and post-term,i.e.having short and long gestational ages, are heritable and influenced by the pre- and perinatal environment. Despite the obvious heritable component, specific genetic influences underlying differences in gestational age are poorly understood. Here we identify one globally significant intronic genetic variant within theADAMTS13gene that is associated with prolonged gestation in 9,141 white European individuals from the 1966 and 1986 Northern Finland birth cohorts. Additional variants that reached suggestive levels of significance were identified within introns at theTKT,andARGHAP42genes, and in the upstream (5’) intergenic regions of theB3GALT5andSSBP2genes. The variants near theADAMTS13, B3GALT5, SSBP2andTKTloci are linked to alterations in gene expression levels (cis-eQTLs). Luciferase assays confirmed the allele specific enhancer activity for theBGALT5andTKTloci. Our findings provide the first evidence of a specific genetic influence associated with prolonged gestation.
zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs
Authors: Parekh Swati , Ziegenhain Christoph , Vieth Beate , Enard Wolfgang , Hellmann Ines
Published: June 2017

Single cell RNA-seq (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification of the cDNA. The high throughput is made possible by the early introduction of sample-specific barcodes (BCs) and the amplification bias is alleviated by unique molecular identifiers (UMIs). Thus the ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according to both BC and UMI.zUMIsis such a pipeline, it can handle both known and random BCs and also efficiently collapses UMIs, either just for Exon mapping reads or for both Exon and Intron mapping reads. Another unique feature ofzUMIsis the adaptive downsampling function, that facilitates dealing with hugely varying library sizes, but also allows to evaluate whether the library has been sequenced to saturation.zUMIsflexibility allows to accommodate data generated with any of the major scRNA-seq protocols that use BCs and UMIs. To illustrate the utility ofzUMIs, we analysed a single-nucleus RNA-seq dataset and show that more than 35% of all reads map to Introns. We furthermore show that these intronic reads are informative about expression levels, significantly increasing the number of detected genes and improving the cluster resolution.Availability:https://github.com/sdparekh/zUMIs
Drug treatment efficiency depends on the initial state of activation in nonlinear pathways
Authors: Doldán-Martelli Victoria , Míguez David G.
Published: June 2017

An accurate prediction of the outcome of a given drug treatment requires quantitative values for all parameters and concentrations involved as well as a detailed characterization of the network of interactions where the target molecule is embedded. Here, we present a high-throughputin silicoscreening of all potential networks of three interacting nodes to study the effect of the initial conditions of the network in the efficiency of drug inhibition. Our study shows that most network topologies can induce multiple dose-response curves, where the treatment has an enhanced, reduced or even no effect depending on the initial conditions. The type of dual response observed depends on how the potential bistable regimes interplay with the inhibition of one of the nodes inside a nonlinear pathway architecture. We propose that this dependence of the strength of the drug on the initial state of activation of the pathway may be affecting the outcome and the reproducibility of drug studies and clinical trials.
Ectopic activation of the Spindle Assembly Checkpoint reveals its biochemical design and physiological operation
Authors: Chen Chu , Whitney Ian P. , Banerjee Anand , Sekhri Palak , Kern David M. , Fontan Adrienne , Tyson John J. , Cheeseman Iain M. , Joglekar Ajit P.
Published: June 2017

Switch-like activation of the Spindle Assembly Checkpoint (SAC) is critical for accurate chromosome segregation during cell division. To determine the mechanisms that implement it, we engineered an ectopic, kinetochore-independent SAC activator, the “eSAC”. The eSAC stimulates the SAC signaling cascade by artificially dimerizing the Mps1 kinase domain and a cytosolic KNL1 phosphodomain, the signaling scaffold in the kinetochore. Quantitative analyses and mathematical modeling of the eSAC reveal that the recruitment of multiple SAC proteins by the KNL1 phosphodomain stimulates synergistic signaling, which enables a small number of KNL1 molecules produce a disproportionately strong anaphase-inhibitory signal. However, when multiple KNL1 molecules signal concurrently, they compete for a limited cellular pool of SAC proteins. This frustrates synergistic signaling and modulates signal output. Together, these mechanisms institute automatic gain control – inverse, non-linear scaling between the signal output per kinetochore and the unattached kinetochore number, and thus enact the SAC switch.
A cadmium(II) coordination polymer with both polyrotaxane and polycatenane features constructed by a V-shaped semi-rigid ligand: synthesis and fluorescence properties
Authors: Xie Hua , Fang Wang-Jian , Yao Xiao-Qiang
Published: June 2017

One of the most interesting phenomena in coordination polymers (CPs) is the co-existence of different interlaced motifs. However, CPs having two different interlaced motifs at the same time are still rare. Colourless block-shaped crystals of the two-dimensional polymer poly[[aqua(μ2-naphthalene-2,6-dicarboxylato){μ2-4,4′-[oxybis(4,1-phenylene)]dipyridine}cadmium(II)] monohydrate], {[Cd(C12H6O4)(C22H16N2O)(H2O)]·H2O}
n
, (I), was synthesized under hydrothermal conditions by the self-assembly of 4,4′-[oxybis(4,1-phenylene)]dipyridine (OPY) with CdII in the presence of naphthalene-2,6-dicarboxylic acid (H2ndc). Each CdII ion is six-coordinated by two N atoms from the pyridine rings of two OPY ligands and by four O atoms, three of which are from two ndc2− ligands and one of which is from a water molecule. In (I), every two identical two-dimensional (2D) 63 layers are interpenetrated in a parallel fashion, resulting in an interesting 2D→2D framework with both polyrotaxane and polycatenane characteristics. The extension of these sheets into a three-dimensional supramolecular net is via O—H...O hydrogen bonds. The solid-state photoluminescence properties of (I) are also discussed.
DNA conformational transitions inferred from re-evaluation ofm|Fo| −D|Fc| electron-density maps
Authors: Sunami Tomoko , Chatake Toshiyuki , Kono Hidetoshi
Published: June 2017

Conformational flexibility of DNA plays important roles in biological processes such as transcriptional regulation and DNA packagingetc. To understand the mechanisms of these processes, it is important to analyse when, where and how DNA shows conformational variations. Recent analyses have indicated that conventional refinement methods do not always provide accurate models of crystallographic heterogeneities and that some information on polymorphism has been overlooked in previous crystallographic studies. In the present study, them|Fo| −D|Fc| electron-density maps of double-helical DNA crystal structures were calculated at a resolution equal to or better than 1.5 Å and potential conformational transitions were found in 27% of DNA phosphates. Detailed analyses of them|Fo| −D|Fc| peaks indicated that some of these unassigned densities correspond to ZI ↔ ZII or A/B → BI conformational transitions. A relationship was also found between ZI/ZII transitions and metal coordination in Z-DNA from the detected peaks. The present study highlights that frequent transitions of phosphate backbones occur even in crystals and that some of these transitions are affected by the local molecular environment.
Decisional dilemma in maintaining industrial peace in PSU in India
Authors: Mishra Sumit , Kant Shashi , Sharma Vinay , Agrawal Rajat
Published: June 2017

Subject area

Industrial Relations and People Management.

Study level/applicability

Graduate or Postgraduate level, Executive working in manufacturing sector.

Case overview

This case highlights the industrial relation issues in a public sector undertaking, a government-owned company in India. The case depicted the issues taken place in the company in the year 2015-2016. The primary data were collected by a working professional, who dealt with and was involved in the scenarios discussed in the case. Other modes such as in-depth interviews were also taken as per requirements. This case also highlights the importance of roles of unions and association in these organizations. Factors which are important to maintain industrial harmony were analyzed and their perspective with respect to production loss were addressed.

Expected learning outcomes

Every employee must be dealt with in a dignified manner with rationale. Hierarchy is required to be in place but doesn’t need to be authoritative. Be communicative and transparent while taking action. There should be no compromise on indiscipline at workplace and decision to be taken accordingly. Manage conflict by involving all the concerned authorities from outset. The analysis of the case shows that if the rationale was followed while managing the people it will lead to industrial harmony. Role of trade unions and association will prove beneficial as they will become a part of creating a solution in the matter of discords, ensuring growth for the company and its employees. It is important to mention here that the case was developed on the basis of the first-hand experience of the author.

Supplementary materials

Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS 6: Human Resource Management.
Revisiting the trajectory of IT implementation in organisations: an IT culture perspective
Authors: Abubakre Mumin , Ravishankar M.N. , Coombs Crispin
Published: June 2017

Purpose

Organisational implementations of information technology (IT) normally fail due to cultural forces that inhibit the usage levels required to facilitate successful IT implementation. The purpose of this paper is to explore IT implementation from an IT culture perspective (Leidner and Kayworth, 2006). In particular, it identifies and follows the trajectory of IT culture archetypes that emerge during the implementation process and further investigates their role in facilitating successful IT implementations.

Design/methodology/approach

This research adopts the qualitative single case study approach and draws on the implementation of a management information system in a Nigerian global bank.

Findings

The findings illustrate three different IT culture archetypes and provide insights into their dynamic nature. The progressive weakening of two IT culture archetypes and the corresponding strengthening of the third archetype shows how initial vision conflicts can get transformed into vision agreements.

Originality/value

This paper extends the IT culture perspective by illustrating how a congruence relationship between IT cultures and IT artefacts can be fostered. The paper shows how diverse IT cultures can develop reasonably quickly in line with initial user experiences of a system. When IT cultures are aligned with the values embedded in IT, positive engagement and usage of the technology results strengthening the presence of embracing IT cultures.
The importance of enhancing, maintaining and saving face in smartphone repurchase intentions of Chinese early adopters
Authors: Filieri Raffaele , Chen Wenshin , Lal Dey Bidit
Published: June 2017

Purpose

China is the world’s largest consumer market for smartphones. Early adopters are highly influential in consumers’ decisions of new technologies. Therefore, understanding Chinese early adopters’ decision making in the smartphone market is of crucial importance to smartphone companies. There is a dearth of in-depth studies on the factors affecting consumers’ repurchase intention for smartphones. The purpose of this paper is to narrow this knowledge gap by developing a new conceptual framework explaining early adopters’ repurchase intention of smartphones.

Design/methodology/approach

Using 30 face-to-face interviews with Chinese early adopters of smartphones, the authors built a new theoretical framework to explain the factors that influence their repurchase intention.

Findings

Repurchase intention of smartphones is determined by aesthetic and utilitarian product-related factors (design appeal, perceived usefulness), socio-cultural factors (subjective norms, mianzi/face considerations), and brand-related factors (brand popularity, brand’s country of origin, perceived brand quality, and brand loyalty). The emerging framework also explores the factors affecting enhancing, maintaining, and saving mianzi/face.

Originality/value

In contrast to existing technology-driven models, the study’s emerging framework shows how aesthetic, socio-cultural, and brand-related factors can offer new insights in understanding repurchase intention in a rapidly developing market. As these factors are rarely examined in the information technology and/or marketing literatures, potential knowledge contribution can be highly expected.
Effect of Chinese foreign direct investment on economic growth in Africa
Authors: Doku Isaac , Akuma John , Owusu-Afriyie John
Published: June 2017

Purpose

This study aims to examine the quantitative effect and direction of Chinese Foreign Direct Investment (FDI) on economic growth in Africa using a sample of 20 African countries from 2003 to 2012 with data obtained from United Nations Conference on Trade and Development and the World Bank.

Design/methodology/approach

The study used panel least squares regression, specifically fixed effect model to examine the quantitative effect of Chinese FDI on economic growth in Africa. The study also used Granger causality test to examine whether a causal relationship exists between economic growth and China’s FDI in Africa.

Findings

The study finds that a 1 per cent increase in China’s FDI stock in Africa significantly increases Africa’s gross domestic product (GDP) growth by 0.607 per cent, all things being equal. Furthermore, the study finds that a causal link exists between GDP growth in Africa and China’s FDI and the nature of causality is unidirectional.

Practical implications

The study recommends that to stimulate Chinese FDI in Africa, free visas must be given to Chinese investors coming into the continent, low tariffs should be imposed on inputs and intermediate goods from China and grant of business operation permit to Chinese investors must be made less bureaucratic.

Originality/value

This research has not been presented to any journal for publication and is originally written by the authors.
The importance of trust for inter-organizational relationships
Authors: Rad Alexander
Published: June 2017

Purpose

This paper aims to examine interbank market practices in a crisis to understand the importance of trust in dealing with control problems and managing risk in inter-organizational relationships (IORs).

Design/methodology/approach

A qualitative field study was conducted to collect data from two case-study banks and two key banking industry institutions.

Findings

The findings illustrate the use of trust-based partner-selection criteria such as guaranteed banks (i.e., banks granted special status by key banking industry institutions) and “clan-related” banks. In addition, the findings present several trust-based performance-control processes regarding the selected counterparties, such as negative expectations, goodwill and information sharing.

Research limitations/implications

This paper highlights IORs and considers how associated control problems and risks are affected by trust in the context of a large-scale crisis.

Practical implications

The findings provide insights into interbank market practices during the global financial crisis with respect to partner selection and performance control.

Originality/value

The empirical case of the banking industry helps broaden our understanding of inter-IORs.
How management accountants exert influence on managers – a micro-level analysis of management accountants’ influence tactics in budgetary control meetings
Authors: Mack Simone , Goretzki Lukas
Published: June 2017

Purpose

This paper aims to examine how remote (i.e. global, regional or divisional) management accountants communicate in interpersonal contacts with operational managers when trying to exert influence on them.

Design/methodology/approach

An ethnographic field study focusing on budgetary control meetings between regional management accountants and operational managers is used as the basis for a micro-level analysis of situated face-to-face interactions and communicative influence tactics.

Findings

Remote management accountants mainly use soft rather than hard influence tactics. They, furthermore, employ what is referred to as “panoramic knowledge” gained explicitly from their structurally as well as physically removed “meta-positioning” to suggest certain measures to operational managers that have proved successful in other units and – by doing so – try to exert influence on these managers. Moreover, they use information that they gain in their position in between senior and operational managers by acting as “double agents” – that is, informing operational managers about senior managers’ focus as well as making transparent to operational managers that they will inform senior management about specific operational matters. By doing so, they try to prompt operational managers to address these issues. Additionally, strengthening their verbally articulated suggestions, as “minute takers” they are able to document their suggestions by moving from spoken to a more binding written text. Through these purposeful and rather unobtrusive tactics, remote management accountants try to take influence on operational managers without generating their resistance.

Originality/value

The paper shows how remote management accountants (as staff members) can skillfully turn their apparently powerless position within the organization into a source of strength to exert influence on operational managers.
Alliance formation in high‐conflict custody mediation: a serial case analysis
Authors: Kjøs Peder , Weie Oddli Hanne
Published: June 2017

Through an in‐depth qualitative analysis of five cases of mandatory high‐conflict custody mediation, we analysed interpersonal processes associated with the early formation of a working alliance in a three‐way interaction. The analysis showed that the mediator efficiently managed the focus of the conversation and validated the parents’ perspectives, but was reticent in addressing interactional issues. Our findings suggest that mediators in high‐conflict custody mediation cases can facilitate the formation of an alliance between the parents, as well as between the mediator and the parents, by taking into account three main aspects of the interaction: (1) the management of the focus of the conversation; (2) validation of the parties’ perspectives; and (3) adapting interventions and tasks to the cohesion of the parent dyad.

Practitioner points

Mediators support the formation of a collaborative alliance by managing the focus of the conversation and validating parties’ perspectives

Low parent dyad cohesion may bar cooperation on seemingly minor issues and a working alliance should be established early on

Ample spacing between mediation sessions allows parents time to try out and evaluate different practical arrangements

Working on concrete items of a parenting plan contributes to improving cooperation
On the advancement of therapeutic penality: therapeutic authority, personality science and the therapeutic community
Authors: McBride Ruari‐Santiago
Published: June 2017

In this article I examine the advancement of therapeutic penality in the UK, a penal philosophy that reimagines prison policy, practices and environments utilising psychological knowledge. Adopting a historical approach, I show how modern therapeutic penality is linked to the emergence of personality science in the nineteenth century and the development of the democratic therapeutic community (DTC) model in the twentieth century. I outline how at the turn of the twenty‐first century a catalytic event generated a moral panic that led the British government to mobilise psychological knowledge and technologies in an attempt to manage dangerous people with severe personality disorder. Tracing subsequent developments, I argue psychological ways of talking, thinking and acting have obtained unparalleled salience in domains of penality and, in turn, radically transformed the conditions of imprisonment.
A Simple and Effective Physical Characteristic Profiling Method for Methamphetamine Tablet Seized in China
Authors: Li Tao , Hua Zhendong , Meng Xin , Liu Cuimei
Published: June 2017

Methamphetamine (MA) tablet production confers chemical and physical properties. This study developed a simple and effective physical characteristic profiling method for MA tablets with capital letter “WY” logos, which realized the discrimination between linked and unlinked seizures. Seventeen signature distances extracted from the “WY” logo were explored as factors for multivariate analysis and demonstrated to be effective to represent the features of tablets in the drug intelligence perspective. Receiver operating characteristic (ROC) curve was used to evaluate efficiency of different pretreatments and distance/correlation metrics, while “Standardization + Euclidean” and “Logarithm + Euclidean” algorithms outperformed the rest. Finally, hierarchical cluster analysis (HCA) was applied to the data set of 200 MA tablet seizures randomly selected from cases all around China in 2015, and 76% of them were classified into a group named after “WY‐001.” Moreover, the “WY‐001” tablets occupied 51–80% tablet seizures from 2011 to 2015 in China, indicating the existence of a huge clandestine factory incessantly manufacturing MA tablets.
Characteristics of Integrons and Associated Gene Cassettes in Antibiotic‐Resistant Escherichia coli Isolated from Free‐Ranging Food Animals in China
Authors: Rehman Mujeeb Ur , Zhang Hui , Huang Shucheng , Iqbal Muhammad Kashif , Mehmood Khalid , Luo Houqiang , Li Jiakui
Published: June 2017

We investigated the occurrence of integrons in antibiotic‐resistant Escherichia coli strains isolated from free‐ranging food animals, including yaks, piglets, and chickens, in China, and characterized the gene cassettes harbored within the integrons. We examined 432 E. coli strains that exhibited resistance to at least one class of antibiotics. Integrase genes and associated gene cassettes were characterized by polymerase chain reaction (PCR) analysis, restriction fragment‐length polymorphism, DNA sequencing, conjugation experiments, and plasmid analysis. Twenty‐nine (6.7%) integrons were amplified from the 432 antimicrobial‐resistant (AMR) isolates evaluated. Specifically, class 1 and 2 integrons were detected in 26 (6%) and 3 (0.7%) strains, respectively. Meanwhile, 6 different gene cassettes, dfrA1, dfr12, aadA1, aadA2, sat1, and orfF, were detected within 6 variable regions (VRs), of which the dfrA1 + aadA1 array was the most common, identified in 12 of 26 class 1 integrons (46.1%). Meanwhile, only one class 2 integron contained a cassette, and the remaining two contained undetermined VRs. Finally, a conjugation assay confirmed the transfer of 4 different types of class 1 integrons into recipient strains, with plasmid sizes ranging from 20 to 30 kb. This is the first report examining the baseline AMR characteristics of E. coli within an extensive farming system of livestock animals in China. Given that integrons were detected in >6% of resistant E. coli strains, precautionary measures are required to prevent the spread of mobile genetic resistance determinants in food animals and monitor their emergence.
Impact on survival of warfarin in patients with pulmonary arterial hypertension receiving subcutaneous treprostinil
Authors: Ascha Mona , Zhou Xuan , Rao Youlan , Minai Omar A. , Tonelli Adriano R.
Published: June 2017

Introduction

Anticoagulation is a common treatment modality in patients with pulmonary arterial hypertension (PAH). Further studies are needed to appropriately assess the risk/benefit ratio of anticoagulation, particularly in PAH patients receiving PAH‐specific therapies.

Aims

We use observational long‐term data on PAH patients treated with subcutaneous (SQ) treprostinil from a large open‐label study. Patients were followed for up to 4 years. The use of warfarin and bleeding events were recorded.

Results

At total of 860 patients (age [mean±SD] 46±15 years, 76% female, 83% Caucasian, 49% idiopathic PAH, and 76% New York Heart Association [NYHA] functional class III) were included. All patients received SQ treprostinil (15% also other pulmonary hypertension [PH]‐therapies) and 590 (69%) received warfarin during the study. The proportions of women, African American, and idiopathic pulmonary hypertension (IPAH) patients were higher in the group receiving warfarin. A higher proportion of patients with congenital heart disease and portopulmonary hypertension did not receive warfarin. There were no differences in unadjusted long‐term survival between PAH patients receiving warfarin or not (log‐rank test, P value=.69), even when only considering idiopathic PAH (P=.32). In addition, no difference was found in adjusted long‐term survival both in PAH (P=.84) and idiopathic PAH patients (P=.44) based on the use of warfarin. Furthermore, no survival difference based on the use of warfarin were noted between propensity score‐matched PAH patients (P=.37).

Conclusions

Long‐term anticoagulation with warfarin was not associated with any significant effect on survival in PAH or idiopathic PAH patients treated with SQ treprostinil.
Influence of academic training in endodontics and implantology on decision‐making in undergraduate students
Authors: Pineda Kenneth , Bueno Rufino , Alvarado Carlos , Abella Francesc , Roig Miguel , Duran‐Sindreu Fernando
Published: June 2017

Purpose

To evaluate the effect of academic training on decision‐making in a group of undergraduates who have undergone training in endodontics and implantology.

Basic procedures

A single group of undergraduate dentistry students (n = 65) was given a survey consisting of 15 endodontic cases. Each case included periapical radiographs and clinical photographs. Students were asked to select one of the eight proposed treatments. In their 4th year, the students first responded to the survey after completing endodontics. One year later, after completing their studies in implantology, the same students completed the same survey again.

Main findings

Under the conditions of this study, differences in undergraduate training significantly affected treatment decisions.

Principal Conclusions

Undergraduate decision‐making was affected by academic training.
Coding in surgery: impact of a specialized coding proforma in hepato‐pancreato‐biliary surgery
Authors: Murphy Jennifer , May Charlotte , Di Carlo Sara , Beckingham Ian , Cameron Iain C. , Gomez Dhanny
Published: June 2017

Background

Coding inaccuracies in surgery misrepresent the productivity of hospitals and outcome data of surgeons. The aim of this study was to audit the extent of coding inaccuracies in hepato‐pancreato‐biliary (HPB) surgery and assess the financial impact of introducing a coding proforma.

Methods

Coding of patients who underwent elective HPB surgery over a 3‐month period was audited. Codes were based on International Classification of Diseases 10 and Office of Population and Census Surveys‐4 codes. A coding proforma was introduced and assessed. New human resource group codes were re‐assigned and new tariffs calculated. A cost analysis was also performed.

Results

Prior to the introduction of the coding proforma, 42.0% of patients had the incorrect diagnosis and 48.5% had missing co‐morbidities. In addition, 14.5% of primary procedures were incorrect and 37.6% had additional procedures that were not coded for at all. Following the introduction of the coding proforma, there was a 27.5% improvement in the accuracy of primary diagnosis (P < 0.001) and 21% improvement in co‐morbidities (P = 0.002). There was a 7.2% improvement in the accuracy of coding primary procedures (P = not significant) and a 21% improvement in the accuracy of coding of additional procedures (P < 0.001). Financial loss as a result of coding inaccuracy over our 3‐month study period was £56 073 with an estimated annual loss of £228 292.

Conclusion

Coding in HPB surgery is prone to coding inaccuracies due to the complex nature of HPB surgery and the patient case‐mix. A specialized coding proforma completed ‘in theatre’ significantly improves the accuracy of coding and prevents loss of income.
The Social and Economic Complexity of Ancient Jerusalem as Seen Through Choices in Lighting Oils
Authors: Namdar D. , Amrani A. , Ben‐Ami D. , Hagbi M. , Szanton N. , Tchekhanovets Y. , Uziel J. , Dag A. , Rosen B. , Gadot Y.
Published: June 2017

This paper presents and discusses the results of residue analysis conducted on 78 ceramic lamps found in archaeological excavations in ancient Jerusalem, in an attempt to identify the types of oils used and the reasons for their preferential choice. The oil lamps chosen for the study were taken from a variety of contexts, which represent the different periods during which Jerusalem was settled and the different sectors of the city. The results of the study show that even the most mundane activity of lighting using oil held within it social and economic choices, as mirrored in the different excavation areas.
Pathways governing development of stem cell‐derived pancreatic β cells: lessons from embryogenesis
Authors: Al‐Khawaga Sara , Memon Bushra , Butler Alexandra E. , Taheri Shahrad , Abou‐Samra Abdul B. , Abdelalim Essam M.
Published: June 2017

The loss of functional β cells leads to development of diabetes. Several studies have shown that β cells are specified through several stages of progenitors during pancreas development, each stage defined by the expression of specific transcription factors (TFs). Understanding signalling pathways that control the differentiation and specification processes during embryogenesis will facilitate efforts to obtain functional β cells in vitro. Our current knowledge of the mechanisms involved in pancreatic β cell development and survival under normal or diabetic conditions has come largely from animal studies. However, there are marked differences in islet structure and physiological properties between humans and animals, and not all phenotypes of human diabetes can be recapitulated in animal models. Therefore, human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and human induced PSCs (hiPSCs) offer a great opportunity for increasing our understanding of the pathways regulating human pancreatic β‐cell development and survival. Furthermore, hPSCs provide a renewable source of functional pancreatic β cells for cell replacement therapy as well as disease modelling. Herein, we discuss the signalling pathways involved in the development of pancreatic β cells during embryogenesis. Additionally, we describe how these pathways are manipulated in vitro to differentiate hPSCs into functional β cells. Finally, we highlight the progress that has been made for the applications of those cells in treating and modelling diabetes.
Combined molecular modelling and 3D‐QSAR study for understanding the inhibition of NQO1 by heterocyclic quinone derivatives
Authors: López‐Lira Claudia , Alzate‐Morales Jans H. , Paulino Margot , Mella‐Raipán Jaime , Salas Cristian O. , Tapia Ricardo A. , Soto‐Delgado Jorge
Published: June 2017

A combination of three‐dimensional quantitative structure–activity relationship (3D‐QSAR), and molecular modelling methods were used to understand the potent inhibitory NAD(P)H:quinone oxidoreductase 1 (NQO1) activity of a set of 52 heterocyclic quinones. Molecular docking results indicated that some favourable interactions of key amino acid residues at the binding site of NQO1 with these quinones would be responsible for an improvement of the NQO1 activity of these compounds. The main interactions involved are hydrogen bond of the amino group of residue Tyr128, π‐stacking interactions with Phe106 and Phe178, and electrostatic interactions with flavin adenine dinucleotide (FADH) cofactor. Three models were prepared by 3D‐QSAR analysis. The models derived from Model I and Model III, shown leave‐one‐out cross‐validation correlation coefficients (q2LOO) of .75 and .73 as well as conventional correlation coefficients (R2) of .93 and .95, respectively. In addition, the external predictive abilities of these models were evaluated using a test set, producing the predicted correlation coefficients (r2pred) of .76 and .74, respectively. The good concordance between the docking results and 3D‐QSAR contour maps provides helpful information about a rational modification of new molecules based in quinone scaffold, in order to design more potent NQO1 inhibitors, which would exhibit highly potent antitumor activity.
Longitudinal Relations Among Positivity, Perceived Positive School Climate, and Prosocial Behavior in Colombian Adolescents
Authors: Luengo Kanacri Bernadette P. , Eisenberg Nancy , Thartori Eriona , Pastorelli Concetta , Uribe Tirado Liliana M. , Gerbino Maria , Caprara Gian V.
Published: June 2017

Bidirectional relations among adolescents’ positivity, perceived positive school climate, and prosocial behavior were examined in Colombian youth. Also, the role of a positive school climate in mediating the relation of positivity to prosocial behaviors was tested. Adolescents (N = 151; Mage of child in Wave 1 = 12.68, SD = 1.06; 58.9% male) and their parents (N = 127) provided data in two waves (9 months apart). A model of bidirectional relations between positivity and perceived positive school climate emerged. In addition, adolescents with higher levels of perceived positive school climate at age 12 showed higher levels of prosocial behaviors in the following year. Positive school climate related positivity to adolescents’ prosocial behavior over time.
Urbanscapes of Disaster: The Sociopolitical and Spatial Processes Underpinning Vulnerability within a Slum in Mexico
Authors: Güiza Frida , Méndez–Lemus Yadira , McCall Michael K.
Published: June 2017

Urbanscapes of disaster are socially and environmentally constituted. Drawing upon the theoretical framework of social vulnerability to disasters, the concept of urbanscape is enriched and empirically verified. This paper highlights how urban social hazards are more relevant for vulnerable people than the risk of experiencing the negative effects of extreme natural events. The analysis of floods in a slum located in a Mexican city reveals intricate socioenvironmental conditions underpinning a disaster process. Findings reveal that social, political, and economic hazards (including criminal hazards), imposed by the urban model on its inhabitants, are the most difficult to cope with and adapt to. This paper contributes to the wider literature on disasters, presenting an in–depth qualitative analysis of the factors propelling urban dwellers to endure in a vulnerable urbanscape, regardless of the physical and environmental conditions at the site.
Robotic vs laparoscopic rectal surgery in high‐risk patients
Authors: Ahmed J. , Cao H. , Panteleimonitis S. , Khan J. , Parvaiz A.
Published: June 2017

Aim

Laparoscopic rectal surgery is associated with a steep learning curve and high conversion rate despite progress in equipment design and consistent practice. The robotic system has shown an advantage over the laparoscopic approach due to stable three‐dimensional views, improved dexterity and better ergonomics. These factors make the robotic approach more favourable for rectal surgery. The aim of this study was to compare the perioperative outcomes of laparoscopic and robotic rectal cancer surgery in high‐risk patients.

Method

A prospectively collected dataset for high‐risk patients who underwent rectal cancer surgery between May 2013 and November 2015 was analysed. Patients with any of the following characteristics were defined as high risk: a body mass index ≥30, male gender, preoperative chemoradiotherapy, tumour <8 cm from the anal verge and previous abdominal surgery.

Results

In total, 184 high‐risk patients were identified: 99 in the robotic group and 85 in the laparoscopic group. Robotic surgery was associated with a significantly higher sphincter preservation rate (86% vs 74%, P = 0.045), shorter operative time (240 vs 270 min, P = 0.013) and hospital stay (7 vs 9 days, P = 0.001), less blood loss (10 vs 100 ml, P < 0.001) and a smaller conversion rate to open surgery (0% vs 5%, P = 0.043) compared with the laparoscopic technique. Reoperation, anastomotic leak rate, 30‐day mortality and oncological outcomes were comparable between the two techniques.

Conclusion

Robotic surgery in high‐risk patients is associated with higher sphincter preservation, reduced blood loss, smaller conversion rates, and shorter operating time and hospital stay. However, further studies are required to evaluate this notion.
Erythema multiforme‐like lesions in primary cutaneous aggressive cytotoxic epidermotropic CD8+ T‐cell lymphoma: A diagnostic and therapeutic challenge
Authors: Tomasini Carlo , Novelli Mauro , Fanoni Daniele , Berti Emilio F.
Published: June 2017

Primary cutaneous aggressive cytotoxic epidermotropic CD8+ T‐cell lymphoma is an extremely rare, rapidly progressing, cutaneous lymphoma, with frequent systemic involvement and poor prognosis, that still represents a diagnostic and therapeutic challenge, especially in the early stage. Herein, we report a case of an elderly woman with a fulminant course, who at onset presented with clinical and pathological features mimicking erythema multiforme (EM) and treated with cyclosporine that led to rapid deterioration with fatal outcome 6 months after disease onset. Histopathology showed a lichenoid, epidermotropic and nodular, angiocentric, dermal and subcutaneous infiltrate of sF1, CD8+, CD45RA+ small to medium‐sized atypical lymphoid cells, which strongly expressed cytotoxic markers. Monoclonal T‐cell‐γ receptor was clonally rearranged and array‐CGH showed numerous chromosomal imbalances. This case evidences the clinical, pathological and therapeutic challenges involved in this tumor. The first biopsy showed an interface dermatitis‐like pattern, revealing the deceptive features that early cutaneous infiltrates of this aggressive lymphoma may have. A high suspicion for aggressive CTCL and a low threshold for repeat biopsies should be maintained when faced with rapidly progressing and/or ulcerative EM‐like lesions, especially if immunomodulatory therapy is being considered.
Interictal oscillations and focal epileptic disorders
Authors: Lévesque Maxime , Salami Pariya , Shiri Zahra , Avoli Massimo
Published: June 2017

Neuronal network oscillations represent a main feature of the brain activity recorded in the EEG under normal and pathological conditions such as epilepsy. Specific oscillations occur between seizures in patients and in animal models of focal epilepsy, and thus, they are termed interictal. According to their shape and intrinsic signal frequency, interictal oscillations are classified as spikes and high‐frequency oscillations (HFOs). Interictal spikes are recorded in the ‘wideband’ EEG signal and consist of large‐amplitude events that usually last less than 1 s; HFOs, in contrast, are extracted by amplifying the appropriately filtered EEG signal and are usually categorized as ripples (80–200 Hz) and fast ripples (250–500 Hz). Interictal spikes and HFOs are used in clinical practice to localize the seizure onset zone in focal epileptic disorders, which is fundamental for performing successful surgical interventions in epileptic patients not responding to anti‐epileptic drug therapy. Both types of interictal oscillations have been widely studied in animal models of focal epilepsy to identify the mechanisms underlying their generation as well as to establish their role in ictogenesis and epileptogenesis. In this review, we will address the cellular mechanisms underlying the generation of interictal spikes and HFOs in animal models of epileptiform synchronization and of focal epilepsy. Moreover, we will highlight in vitro and in vivo evidence indicating that these interictal oscillations mirror specific, dynamic changes in neuronal network excitability causing seizure generation (i.e. ictogenesis) and leading to a chronic epileptic condition (i.e. epileptogenesis).
Incorporating evolutionary insights to improve ecotoxicology for freshwater species
Authors: Brady Steven P. , Richardson Jonathan L. , Kunz Bethany K.
Published: June 2017

Ecotoxicological studies have provided extensive insights into the lethal and sublethal effects of environmental contaminants. These insights are critical for environmental regulatory frameworks, which rely on knowledge of toxicity for developing policies to manage contaminants. While varied approaches have been applied to ecotoxicological questions, perspectives related to the evolutionary history of focal species or populations have received little consideration. Here, we evaluate chloride toxicity from the perspectives of both macroevolution and contemporary evolution. First, by mapping chloride toxicity values derived from the literature onto a phylogeny of macroinvertebrates, fish, and amphibians, we tested whether macroevolutionary relationships across species and taxa are predictive of chloride tolerance. Next, we conducted chloride exposure tests for two amphibian species to assess whether potential contemporary evolutionary change associated with environmental chloride contamination influences chloride tolerance across local populations. We show that explicitly evaluating both macroevolution and contemporary evolution can provide important and even qualitatively different insights from those obtained via traditional ecotoxicological studies. While macroevolutionary perspectives can help forecast toxicological end points for species with untested sensitivities, contemporary evolutionary perspectives demonstrate the need to consider the environmental context of exposed populations when measuring toxicity. Accounting for divergence among populations of interest can provide more accurate and relevant information related to the sensitivity of populations that may be evolving in response to selection from contaminant exposure. Our data show that approaches accounting for and specifically examining variation among natural populations should become standard practice in ecotoxicology.
A POEM, A DANCER, AND A PAINTING: RAINER MARIA RILKE'S ‘SPANISCHE TÄNZERIN’
Authors: Vilain Robert
Published: June 2017

Abstracts

After a reading of Rilke's ‘Spanische Tänzerin’ that unpicks the three main layers of imagery and explores how they interact, this article investigates Rilke's relationship with the Spanish painter Ignacio Zuloaga in order to dispel confusions about an event and a painting that are often felt to have inspired the poem. A fourth, poetological interpretative layer is exposed, and via the trope of the poet‐as‐magus, echoes (perhaps conscious) of the 1906 text in poems from the 1920s, and links with Die Aufzeichnungen des Malte Laurids Brigge are suggested.

Nach einer Deutung von Rilkes Gedicht ‘Spanische Tänzerin’, welche das Zusammenwirken der drei Hauptschichten der Bildsprache interpretiert, untersucht dieser Aufsatz Rilkes Verhältnis zum spanischen Maler Ignacio Zuloaga, um Fehlinterpretationen der Bedeutung einer Veranstaltung und eines Gemäldes zu beseitigen, die das Gedicht vermeintlich inspirierten. Eine vierte, poetologische Interpretationsschicht wird zutage gebracht, und schließlich wird durch den Tropus des Dichters‐als‐Magus auf (möglicherweise absichtliche) Anklänge an das 1906 entstandene Gedicht in Texten der 1920er Jahre und auf Beziehungen zu den Aufzeichnungen des Malte Laurids Brigge hingedeutet.