bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic regulation of transcriptional variation in naturalArabidopsis thalianaaccessions
Authors: Zan Yanjun , Shen Xia , Forsberg Simon K. G. , Carlborg Örjan
Published: January 2016

An increased knowledge of the genetic regulation of expression inArabidopsis thalianais likely to provide important insights about the basis of the plant’s extensive phenotypic variation. Here, we reanalysed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of naturalA. thalianaaccessions. Transcripts from more than half of all genes were detected in the leaf of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions but no transcripts at all in others and this pattern was correlated with the genome-wide genotype. In total, 2,669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. 646 cis-eQTLs regulated genes that lacked detectable transcripts in some accessions, and for 159 of these we identified one, or several, common structural variants in the populations that were shown to be likely contributors to the lack of detectable RNA-transcripts for these genes. This study thus provides new insights on the overall genetic regulation of global gene-expression diversity in the leaf of naturalA. thalianaaccessions. Further, it also shows that strong cis-acting polymorphisms, many of which are likely to be structural variations, make important contributions to the transcriptional variation in the worldwideA. thalianapopulation.
Fine-scale crossover rate variation on theC. elegansX chromosome
Authors: Bernstein Max R. , Rockman Matthew V.
Published: January 2016

Meiotic recombination creates genotypic diversity within species. Recombination rates vary substantially across taxa and the distribution of crossovers can differ significantly among populations and between sexes. Crossover locations within species have been found to vary by chromosome and by position within chromosomes, where most crossover events occur in small regions known as recombination hotspots. However, several species appear to lack hotspots despite significant crossover heterogeneity. The nematodeCaenorhabditis eleganswas previously found to have the least fine-scale variation in crossover distribution among organisms studied to date. It is unclear whether this pattern extends to the X chromosome given its unique compaction through the pachytene stage of meiotic prophase in hermaphrodites. We generated 798 recombinant nested near-isogenic lines (NILs) with crossovers in a 1.41 Mb region on the left arm of the X chromosome to determine if its recombination landscape is similar to that of the autosomes. We find that the fine-scale variation in crossover rate is lower than that of other model species and is inconsistent with hotspots. The relationship of genomic features to crossover rate is dependent on scale, with GC content, histone modifications, and nucleosome occupancy being negatively associated with crossovers. We also find that the abundances of 4-6 base pair DNA motifs significantly explain crossover density. These results are consistent with recombination occurring at unevenly distributed sites of open chromatin.
Reduction of lattice disorder in protein crystals by high-pressure cryocooling
Authors: Huang Qingqiu , Gruner Sol M. , Kim Chae Un , Mao Yuxin , Wu Xiaochun , Szebenyi Doletha M. E.
Published: January 2016

High-pressure cryocooling (HPC) has been developed as a technique for reducing the damage that frequently occurs when macromolecular crystals are cryocooled at ambient pressure. Crystals are typically pressurized at around 200 MPa and then cooled to liquid nitrogen temperature under pressure; this process reduces the need for penetrating cryoprotectants, as well as the damage due to cryocooling, but does not improve the diffraction quality of the as-grown crystals. Here it is reported that HPC using a pressure above 300 MPa can reduce lattice disorder, in the form of high mosaicity and/or nonmerohedral twinning, in crystals of three different proteins, namely human glutaminase C, the GTP pyrophosphokinase YjbM and the uncharacterized protein lpg1496. Pressure lower than 250 MPa does not induce this transformation, even with a prolonged pressurization time. These results indicate that HPC at elevated pressures can be a useful tool for improving crystal packing and hence the quality of the diffraction data collected from pressurized crystals.
Online data analysis at the ESRF bioSAXS beamline, BM29
Authors: Brennich Martha Elisabeth , Kieffer Jérôme , Bonamis Guillaume , De Maria Antolinos Alejandro , Hutin Stephanie , Pernot Petra , Round Adam
Published: January 2016

High-throughput small-angle X-ray scattering on proteins in solution (bioSAXS) at synchrotron sources is a commonly used technique in structural biology, which relies on highly automated data acquisition. Data reduction and primary analysis for bioSAXS experiments consist of a well defined series of individual tasks, the automation of which allows a first easy assessment of the quality of collected data and the adjustment of collection strategies if necessary. This article describes both the logic and the technical implementation of the automated processing pipeline for bioSAXS data at the ESRF BM29 beamline using theEDNAframework.
Salt forms of the pharmaceutical amide dihydrocarbamazepine
Authors: Buist Amanda R. , Kennedy Alan R.
Published: January 2016

Carbamazepine (CBZ) is well known as a model active pharmaceutical ingredient used in the study of polymorphism and the generation and comparison of cocrystal forms. The pharmaceutical amide dihydrocarbamazepine (DCBZ) is a less well known material and is largely of interest here as a structural congener of CBZ. Reaction of DCBZ with strong acids results in protonation of the amide functionality at the O atom and gives the salt forms dihydrocarbamazepine hydrochloride {systematic name: [(10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)(hydroxy)methylidene]azanium chloride, C15H15N2O+·Cl−}, dihydrocarbamazepine hydrochloride monohydrate {systematic name: [(10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)(hydroxy)methylidene]azanium chloride monohydrate, C15H15N2O+·Cl−·H2O} and dihydrocarbamazepine hydrobromide monohydrate {systematic name: [(10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)(hydroxy)methylidene]azanium bromide monohydrate, C15H15N2O+·Br−·H2O}. The anhydrous hydrochloride has a structure with two crystallographically independent ion pairs (Z′ = 2), wherein both cations adoptsynconformations, whilst the two hydrated species are mutually isostructural and have cations withanticonformations. Compared to neutral dihydrocarbamazepine structures, protonation of the amide group is shown to cause changes to both the molecular (C=O bond lengthening and C—N bond shortening) and the supramolecular structures. The amide-to-amide and dimeric hydrogen-bonding motifs seen for neutral polymorphs and cocrystalline species are replaced here by one-dimensional polymeric constructs with no direct amide-to-amide bonds. The structures are also compared with, and shown to be closely related to, those of the salt forms of the structurally similar pharmaceutical carbamazepine.
2-({[(Pyridin-1-ium-2-ylmethyl)carbamoyl]formamido}methyl)pyridin-1-ium bis(3,5-dicarboxybenzoate): crystal structure and Hirshfeld surface analysis
Authors: Jotani Mukesh M. , Syed Sabrina , Halim Siti Nadiah Abdul , Tiekink Edward R. T.
Published: January 2016

The asymmetric unit of the title salt, C14H16N4O22+·2C9H5O6−, comprises half a dication, being located about a centre of inversion, and one anion, in a general position. The central C4N2O2group of atoms in the dication are almost planar (r.m.s. deviation = 0.009 Å), and the carbonyl groups lie in anantidisposition to enable the formation of intramolecular amide-N—H...O(carbonyl) hydrogen bonds. To a first approximation, the pyridinium and amide N atoms lie to the same side of the molecule [Npy—C—C—Namidetorsion angle = 34.8 (2)°], and theantipyridinium rings are approximately perpendicular to the central part of the molecule [dihedral angle = 68.21 (8)°]. In the anion, one carboxylate group is almost coplanar with the ring to which it is connected [Cben—Cben—Cq—O torsion angle = 2.0 (3)°], whereas the other carboxylate and carboxylic acid groups are twisted out of the plane [torsion angles = 16.4 (3) and 15.3 (3)°, respectively]. In the crystal, anions assemble into layers parallel to (10-4)viahydroxy-O—H...O(carbonyl) and charge-assisted hydroxy-O—H...O(carboxylate) hydrogen bonds. The dications are linked into supramolecular tapes by amide-N—H...O(amide) hydrogen bonds, and thread through the voids in the anionic layers, being connected by charge-assisted pyridinium-N—O(carboxylate) hydrogen bonds, so that a three-dimensional architecture ensues. An analysis of the Hirshfeld surface points to the importance of O—H...O hydrogen bonding in the crystal structure.
Integrating ISSM into TAM to enhance digital library services
Authors: Chen Jung-Fang , Chang Jui-Fang , Kao Cheng-Wan , Huang Yueh-Min
Published: January 2016

Purpose

This study aims to propose a new model by incorporating information system success model (ISSM) into technology acceptance model (TAM) with an “attitude toward using” as the connection variable. The new model is then adopted to analyse and investigate empirical data and develop relevant factors, which affect the personal usage behaviour and net benefits for National Central Library in Taiwan to enhance digital library services. The research results can benefit future establishment and design of library information system or improvement of website service procedures.

Design/methodology/approach

This study selected National Central Library Taiwan Digital Meta-Library as the research theme, and used stratified convenience sampling to perform interviews in various colleges and universities in the southern Taiwan. A total of 264 valid questionnaires were returned, and this study used structural equation modelling (SEM) to perform analyses.

Findings

The results reveal that attitude toward using is significantly and positively affected by perceived usefulness, perceived ease of use and user satisfaction. However, service quality of information system and personal net benefits do not have a significant and positive effect on attitude toward using, while they have an indirect and significant effect on attitude toward using through user satisfaction. Based on the results above, “user satisfaction” is the critical factor affecting the attitude toward using. Therefore, to strengthen users’ positive attitude toward using, the factor of user satisfaction is a key for enhancing digital library service.

Originality/value

This study constructed the “New Technology Information Assessment Model” as the reference for improving practical assessment. Moreover, this study also proposed the suggestions concerning digital library information services.
Two complimentary duties under corporate social responsibility
Authors: Nwoke Uchechukwu
Published: January 2016

Purpose

– The purpose of this paper is to critically examine the concept of corporate social responsibility (CSR) in Nigeria’s Delta region and draw a distinction between philanthropic CSR (positive affirmative CSR) and the more demanding duty not to harm the ecosystem (negative injunction CSR). It suggests that for CSR to contribute to sustainable development, oil multinational corporations (MNCs) need to perform the more demanding duties and not only philanthropy.

Design/methodology/approach

– The method applied is a critical evaluation of the nature and categories of CSR. It thoroughly reviews existing literature on CSR and uses them to identify and separate for analytical purposes, the different obligations arising from the concept.

Findings

– The paper highlights the inability of oil MNCs in Nigeria to differentiate between philanthropic CSR and the more demanding duty to care for the host communities and their environment. It suggests that this failure, arguably attributable to the “shareholder value” model of corporate governance, appears to lie at the heart of the unrest in the region.

Practical

– By performing only the positive CSR duties, while neglecting the negative injunction obligations, oil MNCs continue to attract hostility from the host communities who feel that their survival is at stake.

Originality/value

– The paper extends the knowledge of the CSR practices of MNCs in Nigeria, by clearly delineating the two CSR duties and by linking the failure of MNCs to perform the negative injunctions to the shareholder value model of corporate governance.
Universal learning: findings from an analysis of serious case review executive summaries
Authors: Aylett Jay
Published: January 2016

Purpose

– The purpose of this paper is to report and discuss the findings of a thematic analysis from a survey of 114 serious case review (SCR) executive summaries in adult safeguarding. The Care Act 2014 (Section 44) makes the establishment of Safeguarding Adults Boards a statutory requirement. One of their responsibilities/functions is to undertake Safeguarding Adults Reviews (SAR-previously known as SCRs). They must also publish an annual report which includes the recommendations and actions from these SAR’s. This paper draws attention to the potential of SCR as national learning materials, and offers recommendations for strengthening the scope for interpretation in practice.

Design/methodology/approach

– This paper maps the findings and recommendations from 114 SCRs undertaken in England and Wales between 2000 and 2012. It then identifies the dominant themes and universal lessons to emerge, and makes suggestions for the improvement of learning.

Findings

– The demographic profile of SCRs bore some correlation to UK prevalence reports on perpetrator characteristics, but there was variance in relation to victim characteristics, where people with mental illness were the subject of SCRs with a level of frequency that does not mirror the prevalence of mental illness in reported abuse in the UK. The thematic analysis of conclusions and recommendations identified that these could be categorised as either idiosyncratic or bureaucratic.

Research limitations/implications

– The quality and quantity of information contained within the various SCR executive summary reports collated evidenced the lack of consistency/standardisation. Consequently, the analysis of demographic characteristics from these reports was compromised by incomplete data. In order to strengthen the scope of interpretation and understanding from future SARs to inform wider learning within the safeguarding community some national collation and standardisation is necessary.

Originality/value

– This paper offers an analysis of the demographic profile and common themes emerging from an examination of the largest survey of SCR executive summaries reported on in the UK so far.
Fundamental Islamic perspective of work ethics
Authors: Aldulaimi Saeed Hameed
Published: January 2016

Purpose

– This paper debates the Islamic perspective on the work ethics employed in an organization. It aims to discuss the issues of assumptions involving the Islamic Work Ethic (IWE). Therefore, this paper addresses the gap in the management literature and suggests a group of dimensions from fundamentals of Islam.

Design/methodology/approach

– The paper reviews the foundations of IWE and investigates various empirical studies conducted in several countries. Then, briefly presents a short historical and conceptual review of the work ethic construct, suggests a general conceptual definition of work ethic, and offers multidimensional model including a series of constructs which can enable researchers to evaluate and measure work ethic in Islamic societies.

Findings

– The study reveals that there is an evidence of ethics formulation depending on Islamic literature which constructs Islamic values for work. This paper proposes new perspective about the right ethics of work in Islam. Further, multidimensional model including 18 dimensions has been developed to evaluate work ethic in Islamic societies.

Research limitations/implications

– This field needs to reconsider the constructs of IWEs where it is far from reflecting Islamic theory. This paper presents new dimensions which can be utilized to enrich this area.

Originality/value

– This is one of the few attempts to suggest the appropriate constructs of IWE in the management literature. It provides 18 elements responsible and have the promise to strengthen individual transparency and morally which eventually enhance economic progress in Islamic world.
TOPSIS method for intuitionistic fuzzy multiple-criteria decision making and its application to investment selection
Authors: Zeng Shouzhen , Xiao Yao
Published: January 2016

Purpose

– The purpose of this paper is to present a hybrid intuitionistic fuzzy technique for order preference by similarity to ideal solution (TOPSIS) method, called intuitionistic fuzzy ordered weighted averaging weighted averaging (OWAWA) distance TOPSIS (IFOWAWAD-TOPSIS) method for intuitionistic fuzzy multiple-criteria decision making (MCDM) problems.

Design/methodology/approach

– Based on the OWAWA operator, the authors develop the intuitionistic fuzzy OWAWA distance measure, then the IFOWAWAD-TOPSIS method is obtained by using the IFOWAWAD and traditional TOPSIS.

Findings

– The developed IFOWAWAD-TOPSIS method can overcome the drawback of traditional TOPSIS method that cannot consider both the subjective information of attributes and the attitudinal character of decision maker.

Research limitations/implications

– Clearly, this paper is devoted to the OWA operator, MCDM and intuitionistic fuzzy theory.

Practical implications

– The developed method is applicable in a wide range of situations such as decision-making, statistics, engineering and economics. A numerical example concerning investment selection is given to illustrate the practicability and usefulness of the proposed approach.

Originality/value

– This paper fulfils an identified need to study how to make a decision considering both the subjective information of attribute and the attitudinal character of decision maker in intuitionistic fuzzy environment.
Interpreting and presenting marginalized voices through intersubjective accounts
Authors: Phillips David P
Published: January 2016

Purpose

– The purpose of this paper is to introduce a unique approach to accessing, interpreting, and presenting issues concerning the lives of social science research participants. It particularly focuses on accessing those considered to be economically, socially, or politically marginalized and where there is reliance upon intersubjective accounts in two languages.

Design/methodology/approach

– The conceptual and empirical material referred to in this paper is drawn from the author’s doctoral research of a Fair Trade case study in Malawi. The approach presented is influenced by concepts derived from postcolonial theory, grounded theory, and intersubjectivity.

Findings

– For the community empowerment research focus it was important to provide space to capture voices of all participants, accounting for the hierarchical socio-political context in which people were embedded. This required the use of interpreters, introducing challenges related to intersubjectivity such as recognizing and accounting for positionalities and impressions of multiple parties collaborating in the process of collecting and interpreting qualitative research material.

Practical implications

– Investing in trained and engaged interpreters, using pilot interviews, including participants’ data in the field research design process, and capturing marginalized voices helps a researcher to mitigate challenges related to bias and power relations.

Originality/value

– Recognizing inherent shortcomings related to interpreter-facilitated research and power relations, the framework presented provides a reflective and practical methodological approach for qualitative researchers.
Influence of mechanical exposures on electrical properties of thin and thick-film flexible resistors and conductors
Authors: Osypiuk Paweł , Dziedzic Andrzej , Stęplewski Wojciech
Published: January 2016

Purpose

– The purpose of this paper is to determine the influence of mechanical factors (such as longitudinal elongation or cyclic compressive and tensile stresses) on electrical properties of thin- or thick-film resistors or conductors.

Design/methodology/approach

– All test samples were made on Kapton foil. Copper foil or silver-based polymer thick-film conductive inks were used for fabrication of conductors. Resistive structures were made with the aid of two polymer thick-film resistive inks or OhmegaPly Ni-P resistive foil. Test structures differ not only in materials applied for resistors or conductors but also in geometrical shape of functional tracks (meanders consisted of many horse-shoes, semicircles, squares or triangles).

Findings

– Presented results showed significant role of material on range of reversible resistance changes. But shape of test samples also affects relation between relative resistance changes and relative elongation.

Originality/value

– In general, changes induced by cyclic compressive and stretching stresses were smaller than those caused by substrate elongation.
Prenatal parental depression and preterm birth: a national cohort study
Authors: Liu C , Cnattingius S , Bergström M , Östberg V , Hjern A
Published: January 2016

Objective

To investigate the effects of maternal and paternal depression on the risk for preterm birth.

Design

National cohort study.

Setting

Medical Birth Register of Sweden, 2007–2012.

Population

A total of 366 499 singleton births with linked information for parents’ filled drug prescriptions and hospital care.

Methods

Prenatal depression was defined as having filled a prescription for an antidepressant drug or having been in outpatient or inpatient hospital care with a diagnosis of depression from 12 months before conception until 24 weeks after conception. An indication of depression after 12 months with no depression was defined as ‘new depression’, whereas all other cases were defined as ‘recurrent depression’.

Main outcome measures

Odds ratios (ORs) for very preterm (22–31 weeks of gestation) and moderately preterm (32–36 weeks of gestation) births were estimated using multinomial logistic regression models.

Results

After adjustment for maternal depression and sociodemographic covariates, new paternal prenatal depression was associated with very preterm birth [adjusted OR (aOR) 1.38, 95% confidence interval (95% CI) 1.04–1.83], whereas recurrent paternal depression was not associated with an increased risk of preterm birth. Both new and recurrent maternal prenatal depression were associated with an increased risk of moderately preterm birth (aOR 1.34, 95% CI 1.22–1.46, and aOR 1.42, 95% CI 1.32–1.53, respectively).

Conclusions

New paternal and maternal prenatal depression are potential risk factors for preterm birth. Mental health problems in both parents should be addressed for the prevention of preterm birth.

Tweetable abstract

Depression in both mothers and fathers is associated with an increased risk of preterm birth.
Development of species‐specific primers for rapid diagnosis of Tetranychus urticae, T. kanzawai, T. phaselus and T. truncatus (Acari: Tetranychidae)
Authors: Shim Jae‐Kyoung , Khaing Tin Moe , Seo Han‐Eul , Ahn Jun‐Yung , Jung Duck‐Oung , Lee Jong‐Ho , Lee Kyeong‐Yeoll
Published: January 2016

Species diagnosis is of the utmost importance to both pest management and plant quarantine services. Because of difficulties in the morphological diagnosis of spider mites, molecular techniques are of great value to rapidly and accurately diagnose closely related species. We examined four species of genus Tetranychus (the green and red forms of T. urticae, and T. kanzawai, T. phaselus and T. truncatus), which are found in Korea and are of significance to plant quarantine services. DNA samples isolated from a single egg, larva or adult weighed 64–188 ng. We designed species‐specific primers by performing sequence alignment for 107 sequences of the ribosomal internal transcribed spacer 2 (ITS2) region, which we obtained from GenBank, and sequences generated in this study. Specific nucleotides of each species were selected for designing primers specific for each species. Each species‐specific primer pair, when used to perform PCR analyses, detected only the species from which it originated. However, a T. urticae‐specific primer pair did not discriminate between the green and red forms of this species. These species‐specific primers can be applied in practice for the rapid and accurate diagnosis of spider mite species in plant quarantine and in agricultural fields.
Quaternary vicariance of tiger beetle, Cicindela chinensis, in Ryukyu, Japan, Taiwan and Korea–China
Authors: Osozawa Soichi , Fukuda Haruo , Kwon Hyeok‐Yeong , Wakabayashi John
Published: January 2016

We show vicariance of Cicindela chinensis in Okinawa, Japan (differentiated within Japan) and Korea–China through construction of Bayesian inference trees by BEAST2. Calibration was done using an assumption of the MRCA expansion of C. chinensis at 1.55 Ma (=geologically obtained formative time of the Ryukyu islands) following the protocol of BEAUti. We derived substitution rates for mitochondrial COI (1.66%/m.y.) and nuclear 28SrRNA (0.109%/m.y.) of analyzed Cicindela. Cicindela ferriei is a sister of C. chinensis, and these two species differentiated from each other at ca. 3 Ma before the expansion of C. chinensis. However, they are not strongly differentiated between Amami‐Oshima and Tokuno‐shima, although they display different color. Vicariance at 1.55 Ma is also recognized between Cicindela batesi in Taiwan and Cicindela aurulenta and virgula in continental China. From the sequence data we obtained, it is also evident that C. c. okinawana recently colonized Ishigaki‐jima from Okinawa‐jima, as did C. batesi in Iriomote‐jima from Taiwan.
Cocaine addiction is associated with abnormal prefrontal function, increased striatal connectivity and sensitivity to monetary incentives, and decreased connectivity outside the human reward circuit
Authors: Vaquero Lucía , Cámara Estela , Sampedro Frederic , Pérez de los Cobos José , Batlle Francesca , Fabregas Josep Maria , Sales Joan Artur , Cervantes Mercè , Ferrer Xavier , Lazcano Gerardo , Rodríguez‐Fornells Antoni , Riba Jordi
Published: January 2016

Cocaine addiction has been associated with increased sensitivity of the human reward circuit to drug‐related stimuli. However, the capacity of non‐drug incentives to engage this network is poorly understood. Here, we characterized the functional sensitivity to monetary incentives and the structural integrity of the human reward circuit in abstinent cocaine‐dependent (CD) patients and their matched controls. We assessed the BOLD response to monetary gains and losses in 30 CD patients and 30 healthy controls performing a lottery task in a magnetic resonance imaging scanner. We measured brain gray matter volume (GMV) using voxel‐based morphometry and white matter microstructure using voxel‐based fractional anisotropy (FA). Functional data showed that, after monetary incentives, CD patients exhibited higher activation in the ventral striatum than controls. Furthermore, we observed an inverted BOLD response pattern in the prefrontal cortex, with activity being highest after unexpected high gains and lowest after losses. Patients showed increased GMV in the caudate and the orbitofrontal cortex, increased white matter FA in the orbito‐striatal pathway but decreased FA in antero‐posterior association bundles. Abnormal activation in the prefrontal cortex correlated with GMV and FA increases in the orbitofrontal cortex. While functional abnormalities in the ventral striatum were inversely correlated with abstinence duration, structural alterations were not. In conclusion, results suggest abnormal incentive processing in CD patients with high salience for rewards and punishments in subcortical structures but diminished prefrontal control after adverse outcomes. They further suggest that hypertrophy and hyper‐connectivity within the reward circuit, to the expense of connectivity outside this network, characterize cocaine addiction.
Cirrhosis is under‐recognised in patients subsequently diagnosed with hepatocellular cancer
Authors: Walker M. , El‐Serag H. B. , Sada Y. , Mittal S. , Ying J. , Duan Z. , Richardson P. , Davila J. A. , Kanwal F.
Published: January 2016

Background

Most clinical practice guidelines recommend screening for HCC in patients with cirrhosis. However, patients with compensated cirrhosis are often asymptomatic and may remain unrecognised for years.

Aims

To determine the extent to which cirrhosis is unrecognised in a US Veteran population with HCC, and to evaluate the association between lack of cirrhosis recognition and stage of HCC at diagnosis.

Methods

We reviewed the electronic medical records of a random sample of HCC cases diagnosed in the national Veterans Affairs system between 2005 and 2011. We conducted multivariable analyses adjusting for patients’ demographics, comorbidity, aetiology of underlying disease and healthcare utilisation including HCC surveillance.

Results

Of 1201 patients with HCC and cirrhosis, 24.6% had unrecognised cirrhosis prior to HCC diagnosis. Older patients [>65 years, odds ratio (OR) 2.32], African Americans (OR 1.93), patients with alcoholic or NAFLD liver disease (OR 1.69 and 4.77 respectively), HIV (OR 3.02), and fewer comorbidities (Deyo 0 vs. 3, OR 2.42) had significantly higher odds of having unrecognised cirrhosis than comparison groups. Furthermore, patients with unrecognised cirrhosis were 6.5 times more likely to have advanced stage HCC at diagnosis. The effect of cirrhosis recognition on HCC stage remained significant after adjusting for pre‐specified covariates (OR 3.37).

Conclusions

In one quarter of patients, cirrhosis was unrecognised prior to HCC diagnosis, and this group was significantly more likely to have advanced stage HCC. These findings emphasise the importance of timely evaluation for cirrhosis in at‐risk populations as a critical step to improving outcomes for patients with HCC.
Direct measurement of oscillatory RhoA activity in embryonic cortical neurons stimulated with the axon guidance cue netrin‐1 using fluorescence resonance energy transfer
Authors: Antoine‐Bertrand Judith , Fu Min , Lamarche‐Vane Nathalie
Published: January 2016

Background Information

Rho GTPases play an essential role during the development of the nervous system. They induce cytoskeletal rearrangements that are critical for the regulation of axon outgrowth and guidance. It is generally accepted that Rac1 and Cdc42 are positive regulators of axon outgrowth and guidance, whereas RhoA is a negative regulator. However, spatiotemporal control of their activity can modify the function of Rho GTPases during axonal morphogenesis. Signalling downstream of the axon guidance cue netrin‐1 and its receptor deleted in colorectal cancer (DCC) triggers the activation of Rac1 and the inhibition of RhoA to promote axon outgrowth. However, our previous work also suggests that netrin‐1/DCC signalling can activate RhoA in a time‐ and region‐specific manner.

Results

Here, we visualised RhoA activation in response to netrin‐1 in live embryonic cortical neurons using fluorescence resonance energy transfer. RhoA activity oscillated in unstimulated neurons and netrin‐1 increased the amplitude of the oscillations in growth cones after 5 min of stimulation. Within this period of time, netrin‐1 transiently increased RhoA activity and modulated the pattern of RhoA oscillations. We found that the timing of netrin‐1‐induced RhoA activation was different in whole neurons, cell bodies and growth cones.

Conclusions

We conclude that netrin‐1 modulates the spatiotemporal activation of RhoA in embryonic cortical neurons.

Significance

This study demonstrates for the first time the short‐term localised activation of RhoA in neuronal growth cones by the axon guidance cue netrin‐1.
Social Reproduction and Urban Competitiveness: How Dominican Bodegueros Use the Care Economy
Authors: PINE ADAM M
Published: January 2016

Drawn from a larger project examining immigration and economic redevelopment in Philadelphia, this article examines the way bodegas (small neighborhood‐based variety stores) challenge relations of competitiveness inherent in neoliberal urban development. I argue that while the rhetoric of competition and entrepreneurialism abound in discussions of urban development, ethnographic research in urban neighborhoods suggest that the caring labor of social reproduction also plays a strong role in how immigrant communities establish themselves and neighborhoods develop. I use the experience of bodegueros to demonstrate how care operates to support families, businesses, and communities within the competitive, neoliberal city. I argue care work is often juxtaposed with neoliberalism, while in reality this is a false dichotomy. Urban neoliberalism is undergirded with care labor, and it is central to the institutionalization of bodegas within urban neighborhoods as it helps sustain neighborhoods and supports the upward mobility of families who work in bodegas.
miRNA‐30e regulates abnormal differentiation of small intestinal epithelial cells in diabetic mice by downregulating Dll4 expression
Authors: Shan Ti‐Dong , Ouyang Hui , Yu Tao , Li Jie‐Yao , Huang Can‐Ze , Yang Hong‐Sheng , Zhong Wa , Xia Zhong‐Sheng , Chen Qi‐Kui
Published: January 2016

Objectives

Depression of the Notch/Hes1 pathway has been reported to play a role in abnormal differentiation of intestinal epithelial cells (IECs) in diabetes mellitus (DM). However, the mechanism by which this pathway influences IEC differentiation has remained unclear. In this study, we have investigated the role of microRNAs (miRNAs) in regulating the Notch/Hes1 pathway in IECs of DM mice.

Materials and methods

Integrated comparative miRNA microarray technology was used to determine the expression profile of miRNAs in IECs of DM mice. After bioinformatic analysis, an miRNA with altered expression levels, miRNA‐30e, was identified as a candidate for regulating the Notch pathway in DM. A luciferase reporter assay confirmed that miRNA‐30e targeted 3′‐UTR of the Notch gene. The role of miRNA‐30e in regulating Notch signalling was then explored by up‐ and downregulating its expression in vitro and in vivo.

Results

Abnormal differentiation of IECs in DM mice was associated with reduced activity of the Dll4/NICD/Hes1 signal pathway. Based on bioinformatic analyses, increased expression of miRNA‐30e was identified as a potential candidate for regulating Notch signalling. miRNA‐30e targeted the 3′‐UTR of Dll4 and downregulated Dll4 expression in primary IECs and IEC‐6 cells. Exogenous miRNA‐30e reduced activity of the Dll4/NICD/Hes1 pathway, and induced abnormal differentiation of IECs in normal mice. Conversely, treatment with miRNA‐30e antagonist upregu‐lated activity of the Dll4/NICD/Hes1 pathway in vivo, and normalized IEC differentiation in DM mice.

Conclusions

Increased levels of miRNA‐30e downregulated activity of the Dll4/NICD/Hes1 signalling pathway by targeting the 3′‐UTR of Dll4, which contributed to abnormal differentiation in small intestinal epithelia of DM mice.
The significance of hand movement mirroring in cerebral palsy
Authors: Norton Jonathan , Sawicka Katherine
Published: January 2016

This commentary is on the original article by Klingels et al. on pages 735–742 of this issue.
Forecasting fine‐scale changes in the food‐web structure of coastal marine communities under climate change
Authors: Hattab Tarek , Leprieur Fabien , Ben Rais Lasram Frida , Gravel Dominique , Loc'h François Le , Albouy Camille
Published: January 2016

Climate change is inducing deep modifications in local communities worldwide as a consequence of individualistic species range shifts. Understanding how complex interaction networks will be reorganized under climate change represents a major challenge in the fields of ecology and biogeography. However, forecasting the potential effects of climate change on local communities, and more particularly on food‐web structure, requires the consideration of highly structuring processes, such as trophic interactions. A major breakthrough is therefore expected by combining predictive models integrating habitat selection processes, the physiological limits of marine species and their trophic interactions. In this study, we forecasted the potential impacts of climate change on the local food‐web structure of the highly threatened Gulf of Gabes ecosystem located in the south of the Mediterranean Sea. We coupled the climatic envelope and habitat models to an allometric niche food web model, hence taking into account the different processes acting at regional (climate) and local scales (habitat selection and trophic interactions). Our projections under the A2 climate change scenario showed that future food webs would be composed of smaller species with fewer links, resulting in a decrease of connectance, generality, vulnerability and mean trophic level of communities and an increase of the average path length, which may have large consequences on ecosystem functioning. The unified framework presented here, by connecting food‐web ecology, biogeography and seascape ecology, allows the exploration of spatial aspects of interspecific interactions under climate change and improves our current understanding of climate change impacts on local marine food webs.
Predictability of stream insect distributions is dependent on niche position, but not on biological traits or taxonomic relatedness of species
Authors: Heino Jani , de Mendoza Guillermo
Published: January 2016

Species distributions can be analysed under two perspectives: the niche‐based approach, which focuses on species–environment relationships; and the dispersal‐based approach, which focuses on metapopulation dynamics. The degree to which each of these two components affect species distributions may depend on habitat fragmentation, species traits and phylogenetic constraints. We analysed the distributions of 36 stream insect species across 60 stream sites in three drainage basins at high latitudes in Finland. We used binomial generalised linear models (GLMs) in which the predictor variables were environmental factors (E models), within‐basin spatial variables as defined by Moran's eigenvector maps (M models), among‐basin variability (B models), or a combination of the three (E + M + B models) sets of variables. Based on a comparative analysis, model performance was evaluated across all the species using Gaussian GLMs whereby the deviance accounted for by binomial GLMs was fitted on selected explanatory variables: niche position, niche breadth, site occupancy, biological traits and taxonomic relatedness. For each type of model, a reduced Gaussian GLM was eventually obtained after variable selection (Bayesian information criterion). We found that niche position was the only variable selected in all reduced models, implying that marginal species were better predicted than non‐marginal species. The influence of niche position was strongest in models based on environmental variables (E models) or a combination of all types of variables (E + M + B models), and weakest in spatial autocorrelation models (M models). This suggests that species–environment relationships prevail over dispersal processes in determining stream insect distributions at a regional scale. Our findings have clear implications for biodiversity conservation strategies, and they also emphasise the benefits of considering both the niche‐based and dispersal‐based approaches in species distribution modelling studies.
Biogeo: an R package for assessing and improving data quality of occurrence record datasets
Authors: Robertson Mark P. , Visser Vernon , Hui Cang
Published: January 2016

Occurrence data from museum and herbarium collections are valuable for mapping biodiversity patterns in space and time. Unfortunately these collections datasets contain many errors and suffer from several data quality issues that can influence the quality of the products derived from them. It is up to the user to identify these errors and data quality issues when using these data. Despite the large number of potential users of these datasets there are few software tools dedicated to error detection and correction of collections datasets. The R package biogeo was developed for detecting and correcting errors and for assessing of data quality of collections datasets consisting of occurrence records. Features of the package include error detection, such as mismatches between the recorded country and the country where the record is plotted, records of terrestrial species that fall into the sea and outlier detection. A key feature of the package is the ability to identify likely alternative positions for points that represent obvious errors in the dataset and functions to explore records in geographical and environmental space in order to identify possible errors in the dataset. Functions are also available for converting coordinates that are in various text formats into degrees, minutes and seconds and then into decimal degrees.
Seasonal habitat use of alligator gar in a river–floodplain ecosystem at multiple spatial scales
Authors: Kluender Edward R. , Adams Reid , Lewis Lindsey
Published: January 2016

Alligator gar (Atractosteus spatula) populations are declining throughout their range in the United States, even where considered stable. Similar declines in other riverine species are occurring worldwide due to alteration of habitat in river–floodplain systems. Most rivers in the world are highly regulated, resulting in departures from historic hydrology that provides connection to the floodplain habitats used by riverine fishes. Knowledge of the seasonal habitat requirements of alligator gar and similar riverine fishes at a watershed scale is limited, hindering management practices. We used radiotelemetry to monitor movements and habitat use of adult alligator gar (N = 32; 25.0–84.5 kg; 149–224 cm) at macro‐ and microhabitat scales during 2 years of varying hydrology. Fish showed seasonal differences in their use of main channel and floodplain macrohabitats. Floodplain tributaries and their upper reaches were especially important to reproductive ecology. Minimum distance travelled per day varied seasonally. While using the main channel Fourche LaFave River, gar selected low velocity, shallow depth and complex structure along channel margins. The Fourche LaFave River is unique in its connection to floodplain habitats on a relatively predictable basis, with frequent flooding during the spring and summer reproductive period. Our study emphasises the importance of connectivity between the main river channel and floodplain habitats to a floodplain‐obligate riverine species. An intact, heterogeneous riparian zone creates essential microhabitat for the species. Understanding habitat requirements of alligator gar at multiple spatial scales in a river–floodplain system is crucial to management of many other species and river systems.
Assembling the Austrasian Letters at Trier and Lorsch
Authors: Barrett Graham , Woudhuysen George
Published: January 2016

This article is a reconsideration of the Epistulae Austrasicae. We critique the widespread notion that the constituent letters were compiled by a courtier in the late sixth century at Metz as a book of models for use in the Austrasian chancellery. We argue instead that a monk from the monastery of Lorsch assembled the letters in the early ninth century from individual exemplars and groupings that he found in archives at Trier. We conclude by outlining some implications of this rereading for the edition and interpretation of the letters as sources for the Merovingian period, and point out some avenues for future research on their reception in the Carolingian period.
Representations of the warrior‐bishop in eleventh‐century Lotharingia
Authors: Webb J.R.
Published: January 2016

Given the legal proscriptions against clerics bearing arms, the biographers of bishops who engaged in warfare faced a difficult task when they attempted to justify their heroes' military activities. In eleventh‐century Lotharingia, they did so by styling bishops as defenders of an oppressed populace. Two such biographies from Liège reach the opposite assessment of the warrior‐bishop. Their contrasting tone reveals changes in attitudes about the relationship between the church and warfare over the course of the eleventh century, when issues of episcopal power and righteous violence dominated the discourse, not only at Liège but far beyond it.
The association between ankle−brachial index and asymptomatic cranial‐carotid stenosis: a population‐based, cross‐sectional study of 5440 Han Chinese
Authors: Qiu J. , Zhou Y. , Yang X. , Zhang Y. , Li Z. , Yan N. , Wang Y. , Ge S. , Wu S. , Zhao X. , Wang W.
Published: January 2016

Background and purpose

Routine screening for asymptomatic cranial‐carotid stenosis (ACCS) is controversial and recommendation in clinical practice is vague. The ankle−brachial index (ABI) is reported as a predictor for cardiovascular disease. However, there is a scarcity of data about the association between abnormal ABI and ACCS. A population‐based cross‐sectional study was conducted to explore the relationship between ABI and ACCS.

Methods

A sample of 5440 Chinese adults aged 40–94 years old was recruited from 2010 to 2011. The ABI was measured using a portable Doppler device and ACCS was evaluated by bilateral carotid duplex ultrasound and portable examination devices. A logistic regression model was used to analyse the association between ABI and ACCS after adjusting for potential confounding factors.

Results

A low ABI was associated with ACCS [odds ratio (OR) 1.95, 95% confidence interval (CI) 1.42–2.67] after adjusting for potential confounders. When the data were stratified by age and sex, the correlation remained statistically significant in the male (OR 2.32, 95% CI 1.60–3.37) and elderly (OR 3.07, 95% CI 1.97–4.78) subgroups compared to the female (OR 1.26, 95% CI 0.67–2.39) and middle‐aged groups (OR 1.27, 95% CI 0.77–2.12), respectively.

Conclusion

This study demonstrated that low ABI is a significant risk factor for ACCS in male and elderly Chinese adults.