bluuebunny/crossref_metadata_2025 huggingface dataset:
The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules
Authors: Gillespie Daniel T. , Seitaridou Effrosyni , Gillespie Carol A.
Published: December 2014

Simulating the evolution of a chemically reacting system using the bimolecular propensity function, as is done by the stochastic simulation algorithm and its reaction-diffusion extension, entails making statistically inspired guesses as to where the reactant molecules are at any given time. Those guesses will be physically justified if the system is dilute and well-mixed in the reactant molecules. Otherwise, an accurate simulation will require the extra effort and expense of keeping track of the positions of the reactant molecules as the system evolves. One molecule-tracking algorithm that pays careful attention to the physics of molecular diffusion is the enhanced Green's function reaction dynamics (eGFRD) of Takahashi, Tănase-Nicola, and ten Wolde [Proc. Natl. Acad. Sci. U.S.A. 107, 2473 (2010)]. We introduce here a molecule-tracking algorithm that has the same theoretical underpinnings and strategic aims as eGFRD, but a different implementation procedure. Called the small-voxel tracking algorithm (SVTA), it combines the well known voxel-hopping method for simulating molecular diffusion with a novel procedure for rectifying the unphysical predictions of the diffusion equation on the small spatiotemporal scale of molecular collisions. Indications are that the SVTA might be more computationally efficient than eGFRD for the problematic class of non-dilute systems. A widely applicable, user-friendly software implementation of the SVTA has yet to be developed, but we exhibit some simple examples which show that the algorithm is computationally feasible and gives plausible results.
Boundary layer modification by means of wall suction and the effect on the wake behind a rectangular forebody
Authors: Trip Renzo , Fransson Jens H. M.
Published: December 2014

The wake characteristics of a two-dimensional rectangular forebody with a smooth leading edge and a blunt trailing edge are investigated. Wall suction is applied along the forebody in order to modify the developing boundary layer. An initially laminar boundary layer subject to suction yields an asymptotic suction boundary layer at the trailing edge of the body, whereas a high enough suction coefficient relaminarizes an initially turbulent boundary layer. The critical suction velocity required to achieve this significant modification of the boundary layer properties is typically in the order of 1% of the free-stream velocity, where the critical suction coefficient depends on the Reynolds number. We show that a thinner boundary layer induces a higher vortex shedding frequency and a lower base pressure. Furthermore, the boundary layer state, laminar or turbulent, has a significant influence on the wake. For example, the Strouhal number based on the effective body thickness is being reduced by 25% from laminar to turbulent inlet conditions.
Electrostatic force microscopy and electrical isolation of etched few-layer graphene nano-domains
Authors: Hunley D. Patrick , Sundararajan Abhishek , Boland Mathias J. , Strachan Douglas R.
Published: December 2014

Nanostructured bi-layer graphene samples formed through catalytic etching are investigated with electrostatic force microscopy. The measurements and supporting computations show a variation in the microscopy signal for different nano-domains that are indicative of changes in capacitive coupling related to their small sizes. Abrupt capacitance variations detected across etch tracks indicates that the nano-domains have strong electrical isolation between them. Comparison of the measurements to a resistor-capacitor model indicates that the resistance between two bi-layer graphene regions separated by an approximately 10 nm wide etch track is greater than about 1×1012 Ω with a corresponding gap resistivity greater than about 3×1014 Ω⋅nm. This extremely large gap resistivity suggests that catalytic etch tracks within few-layer graphene samples are sufficient for providing electrical isolation between separate nano-domains that could permit their use in constructing atomically thin nanogap electrodes, interconnects, and nanoribbons.
Magneto-optical controlled transmittance alteration of PbS quantum dots by moderately applied magnetic fields at room temperature
Authors: Singh Akhilesh K. , Barik Puspendu , Ullrich Bruno
Published: December 2014

We observed changes of the transmitted monochromatic light passing through a colloidal PbS quantum dot film on glass owing to an applied moderate (smaller than 1 T) magnetic field under ambient conditions. The observed alterations show a square dependence on the magnetic field increase that cannot be achieved with bulk semiconductors. The findings point to so far not recognized application potentials of quantum dots.
Liquid-phase exfoliation of chemical vapor deposition-grown single layer graphene and its application in solution-processed transparent electrodes for flexible organic light-emitting devices
Authors: Wu Chaoxing , Li Fushan , Wu Wei , Chen Wei , Guo Tailiang
Published: December 2014

Efficient and low-cost methods for obtaining high performance flexible transparent electrodes based on chemical vapor deposition (CVD)-grown graphene are highly desirable. In this work, the graphene grown on copper foil was exfoliated into micron-size sheets through controllable ultrasonication. We developed a clean technique by blending the exfoliated single layer graphene sheets with conducting polymer to form graphene-based composite solution, which can be spin-coated on flexible substrate, forming flexible transparent conducting film with high conductivity (∼8 Ω/□), high transmittance (∼81% at 550 nm), and excellent mechanical robustness. In addition, CVD-grown-graphene-based polymer light emitting diodes with excellent bendable performances were demonstrated.
Effect of temperature on the current (capacitance and conductance)–voltage characteristics of Ti/n-GaAs diode
Authors: Ejderha K. , Duman S. , Nuhoglu C. , Urhan F. , Turut A.
Published: December 2014

In this study, Ti/n-GaAs Schottky barrier diode has been fabricated by DC magnetron sputtering. The current–voltage, capacitance–voltage, and conductance–voltage characteristics of Ti/n–GaAs diode have been investigated in the temperature range of 80–320 K. The ideality factor and barrier height values have been calculated from the forward current–voltage characteristics. The variation of the diode parameters with the sample temperature has been attributed to the presence of the lateral inhomogeneities of the barrier height. The temperature dependent capacitance–voltage characteristics have been measured to calculate the carrier concentration, diffusion potential, barrier height, and temperature coefficient of the barrier height (α = −0.65 meV K−1). The fact that the temperature coefficient of the barrier height changes from metal to metal has been ascribed to the chemical nature of the contact metal or metal electronegativity.
Phylogenetic relationships of Australian Scirtidae (Coleoptera) based on mitochondrial and nuclear sequences
Authors: Cooper Steven J. B. , Watts Christopher H. S. , Saint Kathleen M. , Leijs Remko
Published: December 2014

Scirtidae is a cosmopolitan group of beetles with aquatic or saproxylic larvae. A large diversity of species has recently been described from Australia, but their systematics is uncertain. There is evidence that current genera are polyphyletic and that Australian species were wrongly placed in northern hemisphere genera. Here we investigate the systematics of Australian Scirtidae using molecular phylogenetic analyses of combined data from the mitochondrial cytochrome c oxidase subunit 1 (COI) and nuclear gene elongation factor 1-α (EF1-α) genes. We also assess the current taxonomy of Australian Scirtidae using partial COI sequences. Bayesian phylogenetic analyses of COI and EF1-α sequence data from 81 taxa show that the Australian genera Contacyphon, Pseudomicrocara and Prionocyphon are polyphyletic. There is no close relationship between Australian and Eurasian genera, with the exception of Scirtes. Phylogenetic analyses of partial COI data from Australian Scirtidae generally support the current α taxonomy, with the exception of several species that may be associated with species complexes. Geographically a high proportion of species lineages are restricted to relict patches of wet forest suggesting that they may be relict populations. The phylogeny and sequence data presented here provide a sound basis for further systematic and biogeographical studies of the Scirtidae.
Linking genetic diversity and morphological disparity: biodiversity assessment of a highly unexplored family of harvestmen (Arachnida : Opiliones : Neopilionidae) in New Zealand
Authors: Fernández Rosa , Vélez Sebastián , Giribet Gonzalo
Published: December 2014

In Opiliones, one of the largest orders within the class Arachnida, with more than 6000 described species, sexual dimorphism can be widespread and exaggerated. This great variety of forms of gender-based dimorphism suggests that sexual selection may play an important role in the diversification of some lineages. It also impacts species identification, assignment of females to described species and biodiversity assessments. Here we use DNA-sequence-based species discovery methods (the Poisson Tree Processes model with Bayesian support values, bPTP, and the Generalized Mixed Yule–Coalescent approach, GMYC, accounting for phylogenetic uncertainty) to shed light on the morphological disparity displayed in several species of neopilionid harvestmen from New Zealand. Both species delimitation analyses recovered many clades that coincide with our prior assignment of morphospecies, based solely on males, and allowed us to assign females and juveniles to these species as well as to identify putative new species and to assign some unidentified species to genera. Several genetic species, particularly Forsteropsalis inconstans and Pantopsalis cheliceroides-listeri, showed complex morphological disparity in the size and shape of the male chelicerae, but also in the general size and coloration patterns of the males. The systematic implications of our results and a possible ecological explanation for the exaggerated traits are discussed. Following our findings, the following taxonomic action is taken: Forsteropsalis nigra is considered a junior synonym of F. inconstans (new synonymy).
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications
Authors: Mu John C. , Mohiyuddin Marghoob , Li Jian , Bani Asadi Narges , Gerstein Mark B. , Abyzov Alexej , Wong Wing H. , Lam Hugo Y.K.
Published: December 2014

Summary: VarSim is a framework for assessing alignment and variant calling accuracy in high-throughput genome sequencing through simulation or real data. In contrast to simulating a random mutation spectrum, it synthesizes diploid genomes with germline and somatic mutations based on a realistic model. This model leverages information such as previously reported mutations to make the synthetic genomes biologically relevant. VarSim simulates and validates a wide range of variants, including single nucleotide variants, small indels and large structural variants. It is an automated, comprehensive compute framework supporting parallel computation and multiple read simulators. Furthermore, we developed a novel map data structure to validate read alignments, a strategy to compare variants binned in size ranges and a lightweight, interactive, graphical report to visualize validation results with detailed statistics. Thus far, it is the most comprehensive validation tool for secondary analysis in next generation sequencing.

Availability and implementation: Code in Java and Python along with instructions to download the reads and variants is at http://bioinform.github.io/varsim.

Contact:  rd@bina.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bone and kidney toxicity induced by nucleotide analogues in patients affected by HBV-related chronic hepatitis: a longitudinal study
Authors: Maggi Paolo , Montinaro Vincenzo , Leone Armando , Fasano Massimo , Volpe Anna , Bellacosa Chiara , Grattagliano Vito , Coladonato Laura , Lapadula Giovanni , Santantonio Teresa , Angarano Gioacchino
Published: December 2014

Objectives

Nucleotide analogues may promote renal and bone toxicity. The aim of the present study was to evaluate markers of osteorenal toxicity in patients affected by hepatitis B virus-related chronic hepatitis treated with lamivudine plus adefovir who were switched to tenofovir.

Patients and methods

We evaluated 60 consecutive patients at the time of the switch of treatment and after 1, 3, 6, 9 and 12 months. The mean baseline estimated glomerular filtration rate (eGFR) was 89.3 ± 19.0 mL/min/1.73 m2.

Results

During the study period we observed a reduction in mean eGFR up to 6 months after switching to tenofovir, and this remained stable for the last two timepoints. At the end of study, the mean eGFR was 82.6 ± 21.5 mL/min/1.73 m2, a reduction of 7.5%. The mean baseline proteinuria was 202.6 ± 237.6 mg/24 h. Microhaematuria was observed in 22.6% of patients and hypophosphataemia in 18.6%. After 1 month of tenofovir, we observed a worsening of serum phosphate and parathyroid hormone levels, haemoglobinuria and 24 h proteinuria. After 3 and 12 months of tenofovir, these data tended to recover to baseline levels. A total of 92.6% of patients at baseline had hypovitaminosis D. After supplementation with cholecalciferol, this percentage decreased significantly. We observed a reduced bone mineral density (BMD) in 52.7% of patients at baseline; this increased to 77.8% after 6 months of tenofovir, but at the last timepoint the percentage of patients with a reduced BMD had fallen to a level above the baseline.

Conclusions

In conclusion, patients exposed to lamivudine plus adefovir showed relevant osteorenal damage. The switch to tenofovir provoked a slight reduction in eGFR that stabilized after 6 months. The reduced BMD at baseline did not worsen under tenofovir treatment.
Locomotion and attachment of leaf beetle larvaeGastrophysa viridula(Coleoptera, Chrysomelidae)
Authors: Zurek Daniel B. , Gorb Stanislav N. , Voigt Dagmar
Published: December 2014

While adult green dock leaf beetlesGastrophysa viridulause tarsal adhesive setae to attach to and walk on smooth vertical surfaces and ceilings, larvae apply different devices for similar purposes: pretarsal adhesive pads on thoracic legs and a retractable pygopod at the 10th abdominal segment. Both are soft smooth structures and capable of wet adhesion. We studied attachment ability of different larval instars, considering the relationship between body weight and real contact area between attachment devices and the substrate. Larval gait patterns were analysed using high-speed video recordings. Instead of the tripod gait of adults, larvae walked by swinging contralateral legs simultaneously while adhering by the pygopod. Attachment ability of larval instars was measured by centrifugation on a spinning drum, revealing that attachment force decreases relative to weight. Contributions of different attachment devices to total attachment ability were investigated by selective disabling of organs by covering them with melted wax. Despite their smaller overall contact area, tarsal pads contributed to a larger extent to total attachment ability, probably because of their distributed spacing. Furthermore, we observed different behaviour in adults and larvae when centrifuged: while adults gradually slipped outward on the centrifuge drum surface, larvae stayed at the initial position until sudden detachment.
Dyadobacter sediminis sp. nov., isolated from a subterranean sediment sample
Authors: Tian Mu , Zhang Ren-Gang , Han Lu , Zhao Xing-Min , Lv Jie
Published: December 2014

A Gram-reaction-negative, flexirubin-type-pigmented, rod-shaped, aerobic, non-motile bacterium, designated strain Z12T, was isolated from a subsurface sediment sample. In a phylogenetic tree based on 16S rRNA gene sequences, strain Z12T formed a distinct clade with the members of the genus

Dyadobacter

(<96.7 % sequence similarity). The G+C content of genomic DNA was 45.4 %. The major fatty acids of strain Z12T were iso-C15 : 0, C16 : 1ω6c and/or C16 : 1ω7c (summed feature 3) and anteiso-C17 : 1 B and/or iso-C17 : 1 I (summed feature 4). The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. On the basis of phenotypic, phylogenetic and genotypic features, strain Z12T is considered to represent a novel species, for which the name Dyadobacter sediminis sp. nov., is proposed. The type strain is Z12T ( = JCM 30073T = CGMCC 1.12895T).
Pseudomonas matsuisoli sp. nov., isolated from a soil sample
Authors: Lin Shih-Yao , Hameed Asif , Hung Mei-Hua , Liu You-Cheng , Hsu Yi-Han , Young Li-Sen , Young Chiu-Chung
Published: December 2014

An aerobic, Gram-stain-negative, rod-shaped and polar-flagellated bacterium, designated strain CC-MHH0089T, was isolated from a soil sample taken on Matsu Island (Taiwan). Strain CC-MHH0089T grew at 15–30 °C and pH 5.0–10.0 and tolerated ≤8 % (w/v) NaCl. 16S rRNA gene sequence analysis showed high pairwise sequence similarity to

Pseudomonas azotifigens

6H33bT (97.3 %) and

Pseudomonas balearica

SP1402T (96.7 %) and lower sequence similarity to other strains (<96.0 %). In DNA–DNA reassociation experiments, the relatedness of strain CC-MHH0089T to

P. azotifigens

JCM 12708T was 38.3 % (reciprocal value 19.5 %). Evolutionary trees reconstructed on the basis of 16S rRNA, gyrB and rpoB gene sequences revealed a varying phylogenetic neighbourhood of strain CC-MHH0089T with regard to the most closely related type strains. The predominant quinone system was ubiquinone 9 (Q-9) and the DNA G+C content was 63.6 mol%. The major fatty acids were C12 : 0, C16 : 0, C17 : 0, C19 : 0 cyclo ω8c and summed features 2 (C14 : 0 3-OH/iso-C16 : 1 I), 3 (C16 : 1ω7c/C16 : 1ω6c) and 8 (C18 : 1ω7c/C18 : 1ω6c). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. According to its distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-MHH0089T is proposed to represent a novel species within the genus

Pseudomonas

, for which the name Pseudomonas matsuisoli sp. nov. is proposed. The type strain is CC-MHH0089T ( = BCRC 80771T = JCM 30078T).
Lichen traits responding to aridity
Authors: Matos Paula , Pinho Pedro , Aragón Gregorio , Martínez Isabel , Nunes Alice , Soares Amadeu M. V. M. , Branquinho Cristina
Published: December 2014

Climate change is expected to cause several impacts at the global scale, and drylands will be amongst the most affected areas. Thus, investigating how these changes will affect the composition, structure and functioning of dryland ecosystems has become a priority. From an ecological indicator point of view, several works have shown that functional diversity is better than species richness to understand ecosystem functioning or response to environmental factors. However, most of these works focus on plants, while those of other organisms remain largely unknown. Lichens are amongst the ecosystem components more sensitive to climatic changes due to several physiological and ecological characteristics. Their poikilohydric nature (therefore highly dependent on the atmosphere for water supply) and their ubiquity on terrestrial ecosystems underlie their potential as indicators of climate. Nonetheless, works specifically aiming to identify lichen functional traits that respond to aridity remain poorly explored, particularly in drylands.

We proposed to identify lichen functional traits and respective functional groups responding to aridity in a Mediterranean drylands ecosystem.

Lichen diversity was sampled in open holm oak woodlands along an aridity gradient in SW Europe (Iberian Peninsula). Lichen functional traits that could be easily identified and related to water uptake were selected to be tested: type of photobiont, growth form and reproduction strategy.

Lichen species composition was related to the aridity gradient. The three traits chosen were related with the community's response to aridity, but with contrasting responses in different functional groups. More specifically crustose and fruticose lichens, isidiate species and the ones with Trentepohlia as photobiont were related to the less arid part of the gradient. Foliose species and cyanolichens, on the contrary, were associated with the most arid areas.

Synthesis. We were able to identify lichen traits responding to aridity. Type of photobiont was particularly responsive, with Trentepohlia and cyanobacteria functional groups, responding clearly in contrasting ways to aridity in this drylands ecosystem. This work emphasizes functional diversity role on understanding and assessing the response to environmental factors, namely to climate. It also highlights the potential use of lichen functional groups as ecological indicators of climate change.
Effect of partial substitution of caprine milk for ovine milk, dry salting and cured scalding on lipolysis in Urfa cheeses
Authors: Atasoy Ahmet Ferit
Published: December 2014

The objectives of this study were to determine the effect of partial substitution of caprine for ovine milk, dry salting and curd scalding on the free fatty acid (FFA) level of Urfa cheeses. At the end of storage, lauric and linoleic acids were lower in cheese made from milk where up to the 30% partial substitution of caprine milk for ovine milk was made. Dry salted cheeses had higher butyric, lauric, linoleic and linolenic acid levels, and lower palmitic acid levels than their scalded counterpart. A relative increase in short‐chain FFAs occurred during ripening. Palmitic and oleic acids were the most abundant FFAs in fresh and ripened Urfa cheeses.
Identifying Possible False Matches in Anonymized Hospital Administrative Data without Patient Identifiers
Authors: Hagger‐Johnson Gareth , Harron Katie , Gonzalez‐Izquierdo Arturo , Cortina‐Borja Mario , Dattani Nirupa , Muller‐Pebody Berit , Parslow Roger , Gilbert Ruth , Goldstein Harvey
Published: December 2014

Objective

To identify data linkage errors in the form of possible false matches, where two patients appear to share the same unique identification number.

Data Source

Hospital Episode Statistics (HES) in England, United Kingdom.

Study Design

Data on births and re‐admissions for infants (April 1, 2011 to March 31, 2012; age 0–1 year) and adolescents (April 1, 2004 to March 31, 2011; age 10–19 years).

Data Collection/Extraction Methods

Hospital records pseudo‐anonymized using an algorithm designed to link multiple records belonging to the same person. Six implausible clinical scenarios were considered possible false matches: multiple births sharing HESID, re‐admission after death, two birth episodes sharing HESID, simultaneous admission at different hospitals, infant episodes coded as deliveries, and adolescent episodes coded as births.

Principal Findings

Among 507,778 infants, possible false matches were relatively rare (n = 433, 0.1 percent). The most common scenario (simultaneous admission at two hospitals, n = 324) was more likely for infants with missing data, those born preterm, and for Asian infants. Among adolescents, this scenario (n = 320) was more common for males, younger patients, the Mixed ethnic group, and those re‐admitted more frequently.

Conclusions

Researchers can identify clinically implausible scenarios and patients affected, at the data cleaning stage, to mitigate the impact of possible linkage errors.
A Simple Method for Evaluating Within Sample Prognostic Balance Achieved by Published Comorbidity Summary Measures
Authors: Egleston Brian L. , Uzzo Robert G. , Beck J. Robert , Wong Yu‐Ning
Published: December 2014

Objective

To demonstrate how a researcher can investigate the appropriateness of a published comorbidity summary measure for use with a given sample.

Data Source

Surveillance, Epidemiology, and End Results linked to Medicare claims data.

Study Design

We examined Kaplan–Meier estimated survival curves for four diseases within strata of a comorbidity summary measure, the Charlson Comorbidity Index.

Data Collection

We identified individuals with early‐stage kidney cancer diagnosed from 1995 to 2009. We recorded comorbidities present in the year before diagnosis.

Principal Findings

The use of many comorbidity summary measures is valid under appropriate conditions. One condition is that the relationships of the comorbidities with the outcome of interest in a researcher's own population are comparable to the relationships in a published algorithm's population. The original comorbidity weights from the Charlson Comorbidity Index seemed adequate for three of the diseases in our sample. We found evidence that the Charlson Comorbidity Index might underestimate the impact of one disease in our sample.

Conclusion

Examination of survival curves within strata defined by a comorbidity summary measure can be a useful tool for determining whether a published method appropriately accounts for comorbidities. A comorbidity score is only as good as those variables included.
Antiphospholipid syndrome: 30 years and our contribution
Authors: Koike Takao
Published: December 2014

In 1983, Graham Hughes first described the concept of antiphospholipid syndrome (APS). In 1984, we described the enzyme‐linked immunosorbent assay (ELISA) system which directly detected circulating aCL in patients with systemic lupus erythematosus (SLE) who revealed biological false positive serological test for syphilis. In 1990, three groups, including our group, independently reported the necessity of a cofactor for the binding of autoimmune anticardiolipin antibodies (aCL) to the solid phase phospholipids. β2‐glycoprotein I (β2GPI) was identified as this cofactor. In 1994,the epitope for aCL was shown to develop when β2GPI is adsorbed on polyoxygenated polystyrene plates. In 2000, we described antiprothrombin antibodies bind to prothrombin exposed to immobilized phosphatidylserine and established a phosphatidylserine dependent monoclonal antiprothrombin antibody. In 2004, a novel role of nicked β2GPI was identified in the negative feedback pathway of extrinsic fibrinolysis. Nicked β2GPI was found to bind angiostatin 4.5 and to attenuate its antiangiogenic property. In 2004, we demonstrated that the p38 MAPK pathway mediates induction of the TF gene in stimulated with human monoclonal anti‐ β2GPI antibodies. Very recently, β2GPI was identified as a complement regulator. The cross‐link between complement activation and prothrombotic status in patients with APS has been drawn much attention. Genetic factors are hypothesized to play a role in the susceptibility to APS based on several family studies in patients with antiphospholipid antibodies (aPL) and/or clinical manifestations of APS. The genetics of β2GPI has been extensively studied. 247 Val/Leu polymorphism can affect the conformational change of β2‐GPI and the exposure of the epitopes for aCL. We found that 247 Val was correlated with anti‐β2‐GPI production in patients with primary APS, and 247 Val may be important for β2‐GPI antigenicity. STAT4 SNP in Japanese patients with SLE and/or APS. T allele frequencies in SLE and APS were significantly elevated compared with that in healthy controls. When analyzed only in primary APS patients, T allele frequency was further higher. BANK1, BLK and SNP in 1q25.1 region were associated with not only SLE but also APS in Japanese population. These results suggest that APS and SLE, in part, share a common genetic background.
Recent advances in systemic lupus erythematosus genetics in an Asian population
Authors: Lee Hye‐Soon , Bae Sang Cheol
Published: December 2014

Recent advances in systemic lupus erythematosus (SLE) genetics in Asian populations have been achieved by genome‐wide association studies (GWASs) and following replication studies, which expanded the genetic information about shared or population‐specific risk genes between ethnic groups. Meta‐analyses and multi‐ethnic replication studies may be possible approaches that could demonstrate stronger or more suggestive evidence for multiple variants for SLE. In addition to the susceptibility of SLE itself, several genotype‐phenotype analyses have shown that the specific phenotypes of SLE can also be influenced by genetic factors. Almost all SLE genetic loci are involved in the potential pathways of SLE pathogenesis, such as Toll‐like receptor/type I interferon signaling, nuclear factor κB signaling, immune complex clearing mechanism, immune cell (B, T cell, neutrophil and monocyte) function and signaling, cell‐cycle regulation, DNA methylation and autophagy. Further studies, including the next generation sequencing technology and the systematic strategy using bioinformatics, in addition to international collaboration among SLE genetic researchers, will give us better understanding of the genetic basis of SLE.
Expenditure Inequality in Indonesia, 2008–2010: A Spatial Decomposition Analysis and the Role of Education
Authors: Hayashi Mitsuhiro , Kataoka Mitsuhiko , Akita Takahiro
Published: December 2014

Based on the 2008–2010 Susenas panel data, this study examines expenditure inequality from spatial perspectives in Indonesia, using three decomposition methods: (i) a conventional Theil index decomposition; (ii) an alternative Theil index decomposition proposed by Elbers et al. (2008); and (iii) the Blinder−Oaxaca decomposition. Our results show that overall inequality in per capita expenditure increases between 2008 and 2010, which coincides with a rising trend in the official Gini coefficient. The contribution of inequality within urban and rural areas to total inequality is larger than that of inequality between urban and rural areas. Looking within urban and rural areas, urban inequality is significantly higher than rural inequality. Java‐Bali in particular records very high urban inequality. Overall, urban inequality increases, urban–rural inequality remains stable, rural inequality decreases, and inequality at the national level increases. Although urban–rural inequality has a relatively low share in overall inequality, the share is not small enough to ignore its impact. Furthermore, when using the alternative decomposition method, the contribution of urban–rural inequality increases substantially. The present study also found that educational differences appear to have played an important role in expenditure inequality within urban areas and between urban and rural areas.
Productivity Analysis of UK Auditing Firms
Authors: Barros Carlos Pestana , Couto Eduardo , Samagaio António
Published: December 2014

This study analyses the productivity change in the United Kingdom (UK) of auditing firms over the period 2005–2012, using a Malmquist index with a technological bias. Productivity is the rate at which goods or services are produced relative to the input. A common measure of productivity is the ratio of output per unit of labour used in the production. Productivity change is the change in the total output relative to the change in the total input and it is composed of technical efficiency change (managerial practices and scale effects) and technological change (innovation and investment in new technologies). Until 2005, the auditing profession in the UK employed a regime of self‐regulation; after a brief hiatus, the country adopted the new European Statutory Audit Directive in April 2008, changing the regulatory framework. This study analyses the productivity change among UK auditing companies both before and after the regulation change. Our results indicate that the productivity change among UK auditing companies is mixed and not dictated by regulation. Furthermore, the traditional growth accounting method, which assumes Hicks‐neutral technological change, is not appropriate for an analysis of the productivity change in auditing firms.
Prenatal Screening, Reproductive Choice, and Public Health
Authors: Wilkinson Stephen
Published: December 2014

One widely held view of prenatal screening (PNS) is that its foremost aim is, or should be, to enable reproductive choice; this is the Pure Choice view. The article critiques this position by comparing it with an alternative: Public Health Pluralism. It is argued that there are good reasons to prefer the latter, including the following. (1) Public Health Pluralism does not, as is often supposed, render PNS more vulnerable to eugenics‐objections. (2) The Pure Choice view, if followed through to its logical conclusions, may have unpalatable implications, such as extending choice well beyond health screening. (3) Any sensible version of Public Health Pluralism will be capable of taking on board the moral seriousness of abortion and will advocate, where practicable, alternative means of reducing the prevalence of disease and disability. (4) Public Health Pluralism is at least as well‐equipped as the Pure Choice model to deal with autonomy and consent issues.
A New Ethical Landscape of Prenatal Testing: Individualizing Choice to Serve Autonomy and Promote Public Health: A Radical Proposal
Authors: Munthe Christian
Published: December 2014

A new landscape of prenatal testing (PNT) is presently developing, including new techniques for risk‐reducing, non‐invasive sampling of foetal DNA and drastically enhanced possibilities of what may be rapidly and precisely analysed, surrounded by a growing commercial genetic testing industry and a general trend of individualization in healthcare policies. This article applies a set of established ethical notions from past debates on PNT for analysing PNT screening‐programmes in this new situation. While some basic challenges of PNT stay untouched, the new development supports a radical individualization of how PNT screening is organized. This reformation is, at the same time, difficult to reconcile with responsible spending of resources in a publicly funded healthcare context. Thus, while the ethical imperative of individualization holds and applies to PNT, the new landscape of PNT provides reasons to start rolling back the type of mass‐screening programmes currently established in many countries. Instead, more limited offers are suggested, based on considerations of severity of conditions and optimized to simultaneously serve reproductive autonomy and public health within an acceptable frame of priorities. The new landscape of PNT furthermore underscores the ethical importance of supporting and including people with disabilities. For the very same reason, no ban on what may be analysed using PNT in the new landscape should be applied, although private offers must, of course, conform to strict requirements of respecting reproductive autonomy and what that means in terms of counselling.
WMJ‐S‐001, a novel aliphatic hydroxamate derivative, exhibits anti‐inflammatory properties via MKP‐1 in LPS‐stimulated RAW264.7 macrophages
Authors: Chen Wei‐Chuan , Yen Chia‐Sheng , Huang Wei‐Jan , Hsu Ya‐Fen , Ou George , Hsu Ming‐Jen
Published: December 2014

Background and Purpose

Hydroxamate derivatives have attracted considerable attention because of their broad pharmacological properties. Recent studies reported their potential use in the treatment of cardiovascular diseases, arthritis and infectious diseases. However, the mechanisms of the anti‐inflammatory effects of hydroxamate derivatives remain to be elucidated. In an effort to develop a novel pharmacological agent that could suppress abnormally activated macrophages, we investigated a novel aliphatic hydroxamate derivative, WMJ‐S‐001, and explored its anti‐inflammatory mechanisms.

Experimental Approach

RAW264.7 macrophages were exposed to LPS in the absence or presence of WMJ‐S‐001. COX‐2 expression and signalling molecules activated by LPS were assessed.

Key Results

LPS‐induced COX‐2 expression was suppressed by WMJ‐S‐001. WMJ‐S‐001 inhibited p38MAPK, NF‐κB subunit p65 and CCAAT/enhancer‐binding protein (C/EBP)β phosphorylation in cells exposed to LPS. Treatment of cells with a p38MAPK inhibitor (p38MAPK inhibitor III) markedly inhibited LPS‐induced p65 and C/EBPβ phosphorylation and COX‐2 expression. LPS‐increased p65 and C/EBPβ binding to the COX‐2 promoter region was suppressed in the presence of WMJ‐S‐001. In addition, WMJ‐S‐001 suppression of p38MAPK, p65 and C/EBPβ phosphorylation, and subsequent COX‐2 expression were restored in cells transfected with a dominant‐negative (DN) mutant of MAPK phosphatase‐1 (MKP‐1). WMJ‐S‐001 also caused an increase in MKP‐1 activity in RAW264.7 macrophages.

Conclusions and Implications

WMJ‐S‐001 may activate MKP‐1, which then dephosphorylates p38MAPK, resulting in a decrease in p65 and C/EBPβ binding to the COX‐2 promoter region and COX‐2 down‐regulation in LPS‐stimulated RAW264.7 macrophages. The present study suggests that WMJ‐S‐001 may be a potential drug candidate for alleviating LPS‐associated inflammatory diseases.
Proteinases, their receptors and inflammatory signalling: the Oxford South Parks Road connection
Authors: Hollenberg M D
Published: December 2014

In keeping with the aim of the Paton Memorial Lecture to ‘facilitate the historical study of pharmacology’, this overview, which is my distinct honour to write, represents a ‘Janus‐like’ personal perspective looking both backwards and forwards at the birth and growth of ‘receptor molecular pharmacology’ with special relevance to inflammatory diseases. The overview begins in the Oxford Department of Pharmacology in the mid‐1960s and then goes on to provide a current perspective of signalling by proteinases. Looking backwards, the synopsis describes the fruitful Oxford Pharmacology Department infrastructure that Bill Paton generated in keeping with the blueprint begun by his predecessor, J H Burn. Looking forwards, the overview illustrates the legacy of that environment in generating some of the first receptor ligand‐binding data and providing the inspiration and vision for those like me who were training in the department at the same time. With apologies, I mention only in passing a number of individuals who benefitted from the ‘South Parks Road connection’ using myself as one of the ‘outcome study’ examples. It is also by looking forward that I can meet the complementary aim of summarizing the lecture presented at a ‘BPS 2014 Focused Meeting on Cell Signalling’ to provide an overview of the role of proteinases and their signalling mechanisms in the setting of inflammation.

Linked Articles

This article is part of a themed section on 5th BPS Focused Meeting on Cell Signalling. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue‐13
The Enduring Predictive Significance of Early Maternal Sensitivity: Social and Academic Competence Through Age 32 Years
Authors: Raby K. Lee , Roisman Glenn I. , Fraley R. Chris , Simpson Jeffry A.
Published: December 2014

This study leveraged data from the Minnesota Longitudinal Study of Risk and Adaptation (N = 243) to investigate the predictive significance of maternal sensitivity during the first 3 years of life for social and academic competence through age 32 years. Structural model comparisons replicated previous findings that early maternal sensitivity predicts social skills and academic achievement through midadolescence in a manner consistent with an enduring effects model of development and extended these findings using heterotypic indicators of social competence (effectiveness of romantic engagement) and academic competence (educational attainment) during adulthood. Although early socioeconomic factors and child gender accounted for the predictive significance of maternal sensitivity for social competence, covariates did not fully account for associations between early sensitivity and academic outcomes.
Physical and cardiovascular performance in cases with acromegaly after regular short‐term exercise
Authors: Hatipoglu Esra , Topsakal Nuri , Erkut Atilgan Oya , Camliguney Asiye Filiz , Ikitimur Baris , Ugurlu Serdal , Niyazoglu Mutlu , Cotuk Hasan Birol , Kadioglu Pinar
Published: December 2014

Objective

Impaired physical performance is a disturbing complication of acromegaly. We aimed to evaluate the role of regular exercise in amelioration of the impaired physical performance in acromegaly.

Methods

Patients with acromegaly were divided into two groups according to their participation in a prescheduled programme of exercise. Participants in the study group were exercised 3 days a week for 3 consecutive months. Exercise tolerance was evaluated by maximal oxygen consumption (VO2max) and time (T) taken to complete the Bruce protocol, muscle flexibility by the sit and reach test (SRT) and muscle strength by the hand grip strength test (HGST). Concomitantly, anthropometric assessment was performed using body mass index (BMI), waist‐to‐hip ratio (WHR), skinfold measurements from 8 points, percentage body fat (PBF), fat mass (FM) and lean body mass (LBM).

Results

After 3 months of exercise, VO2max and T were higher in cases that exercised than in cases that did not (P = 0·004 and P = 0·001). Over 3 months, within the exercise group, VO2max and T of the Bruce protocol increased (P = 0·003 and P = 0·004) and heart rate during warming decreased (P = 0·04). SRT increased within the exercise group after 3 months (P = 0·004). HGSRT did not change significantly (right P = 0·06 and left P = 0·2). The sum of skinfolds, BMI, WHR and LBM remained stable over the study period (P = 0·1, P = 0·08, P = 0·3 and P = 0·09). PBF decreased slightly and FM decreased significantly over 3 months (P = 0·05 and P = 0·03).

Conclusion

Even short‐term exercise may improve impaired physical performance, muscle activity and disturbed body fat composition in acromegaly.
A prospective cohort study investigating gross motor function, pain, and health‐related quality of life 17 years after selective dorsal rhizotomy in cerebral palsy
Authors: Tedroff Kristina , Löwing Kristina , Åström Eva
Published: December 2014

Aim

The aim of this study is to evaluate the long‐term effects of selective dorsal rhizotomy (SDR), 15 to 20 years after surgery in patients with cerebral palsy.

Method

Eighteen children (four females, 14 males; mean age at SDR 4y 7mo, SD 1y 7mo) with bilateral spastic cerebral palsy (CP), were prospectively assessed after SDR. This study focuses on the outcome 15 to 20 years after the procedure. The assessments include the Modified Ashworth Scale for spasticity, the Gross Motor Function Measure (GMFM‐88), the Wilson Mobility Scale, The Health‐Related Quality of Life Health Survey, SF‐36v2, and the Brief Pain Inventory.

Results

The effect of normalized muscle tone in lower extremities after SDR was sustained after a median of 17 years. The best gross motor function capacity, according to the GMFM score, was seen at the 3‐year follow‐up, thereafter a gradual decline followed. Half of the individuals reported low intensity pain and interference. Compared to a norm sample the physical health component of SF‐36v2 was slightly lower and the mental health component slightly higher.

Interpretation

The spasticity‐reducing effect of SDR does not improve long‐term functioning, nor prevent contractures, but it can possibly reduce the pain often experienced by individuals with CP.
Validity of laryngeal ultrasonography in reference to endoscopy at rest and during exercise in Warmblood horses
Authors: Karlheim B. , Barton A. K. , Rohn K. , Ohnesorge B.
Published: December 2014

In this study, 59 Warmblood horses were examined endoscopically at rest, during overground endoscopy and by laryngeal ultrasonography to evaluate the validity of ultrasonography as an additional diagnostic tool for left recurrent laryngeal neuropathy in Warmblood horses. Left laryngeal function during endoscopy at rest and overground exercise was scored by 3 blinded examiners. A new semiquantitative subjective‐descriptive score was used for evaluation of ultrasonographic images. Sensitivity and specificity as well as positive and negative predictive values of ultrasonographic images for longitudinal and transverse planes were calculated in reference to endoscopic scoring results. Laryngeal ultrasonography with semiquantitative grading proved to be a very sensitive and specific technique for evaluation of recurrent laryngeal neuropathy in Warmblood horses.
Individual‐Oriented Relationship Education: An Evaluation Study in Community‐Based Settings
Authors: Visvanathan Pallavi D. , Richmond Melissa , Winder Chandra , Koenck Cynthia Hoskins
Published: December 2014

The effects of relationship education aimed at individuals, rather than couples, have not yet been widely investigated. However, increasingly, relationship education is provided to large and diverse groups of individuals who may be in varying stages of relationships. Several programs have been developed to strengthen relationship competencies among single individuals as well as among partnered individuals who, for a variety of reasons, seek relationship education without their partners. The current study is an exploratory evaluation study that examined self‐reported outcomes for 706 single and partnered individuals who attended Within My Reach classes delivered in community‐based agencies. Participants were from diverse backgrounds and exhibited many of the risk factors for poor relationship outcomes including unemployment, low income, and childhood experience of abuse or neglect. Pre‐post analyses indicated that the program was beneficial for both singles and partnered individuals. Singles reported increased belief in ability to obtain healthy relationships. Partnered individuals reported increased relationship quality, relationship confidence, and reduced conflict. Regardless of relationship status, participants also reported improvement in general relationship and communication skill. Results support the utility of individual‐oriented relationship education for singles and partnered individuals with diverse background characteristics.
A Video Recall Study of In‐session Changes in Sentiment Override
Authors: Johnson Lee N. , Tambling Rachel B. , Anderson Shayne R.
Published: December 2014

This study examines in‐session changes in sentiment override over the first three sessions of couple therapy. Couples viewed a video recording of therapy sessions immediately after each of the first three sessions and continuously rated their level of sentiment override. Ninety‐eight changes were randomly chosen for analysis. Three talk turns prior to each change was coded using the Family Relational Communication Control Coding System. Results show that changes in sentiment override occur frequently. Repeated incidents of communication control were related to negative change in sentiment override for females. Repeated incidents of being left out of the conversation were related to negative changes in sentiment override for females and positive changes for males.
Contextual Influences on Political Behavior in Cities: Toward Urban Electoral Geography
Authors: Weaver Russell
Published: December 2014

While there is now appreciable support among electoral geographers and political scientists for the idea that neighborhood context influences political behavior, there remains no consensus on the appropriate scale—i.e., the “true causally relevant” geographic extent—at which to analyze these effects. Importantly, this “uncertain geographic context problem” is not unique to electoral geography. Rather, it arises wherever researchers attempt to analyze contextual influences on individual or group behavior. This article suggests that electoral geographers might find value in the streams of urban studies literature (from outside of political science) that regularly engages in such activities. It accordingly surveys and synthesizes selected research on neighborhoods and neighborhood effects from both bodies of work, with the aim of establishing a research program in urban electoral geography. Advances in open data platforms and geographic information systems technologies are highlighted for their abilities to support empirical investigations into the proposed area of inquiry.