bluuebunny/crossref_metadata_2025 huggingface dataset:
FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking
Authors: Xu Dong , Jaroszewski Lukasz , Li Zhanwen , Godzik Adam
Published: October 2013

Motivation: Homology detection enables grouping proteins into families and prediction of their structure and function. The range of application of homology-based predictions can be significantly extended by using sequence profiles and incorporation of local structural features. However, incorporation of the latter terms varies a lot between existing methods, and together with many examples of distant relations not recognized even by the best methods, suggests that further improvements are still possible.

Results: Here we describe recent improvements to the fold and function assignment system (FFAS) method, including adding optimized structural features (experimental or predicted), ‘symmetrical’ Z-score calculation and re-ranking the templates with a neural network. The alignment accuracy in the new FFAS-3D is now 11% higher than the original and comparable with the most accurate template-based structure prediction algorithms. At the same time, FFAS-3D has high success rate at the Structural Classification of Proteins (SCOP) family, superfamily and fold levels. Importantly, FFAS-3D results are not highly correlated with other programs suggesting that it may significantly improve meta-predictions. FFAS-3D does not require 3D structures of the templates, as using predicted features instead of structure-derived does not lead to the decrease of accuracy. Because of that, FFAS-3D can be used for databases other than Protein Data Bank (PDB) such as Protein families database or Clusters of orthologous groups thus extending its applications to functional annotations of genomes and protein families.

Availability and implementation: FFAS-3D is available at http://ffas.godziklab.org.

Contact:  adam@godziklab.org

Supplementary Information: Supplementary data are available at Bioinformatics online.
Comment on ‘Bayesian parentage analysis with systematic accountability of genotyping error, missing data and false matching’
Authors: Anderson Eric C. , Ng Thomas C.
Published: October 2013

Summary: We show the software SOLOMON is improved by using the likelihood ratio instead of an ad hoc statistic.

Code: github.com/eriqande/solidmon/releases/tag/v0.1-bioinformatics

Contact: eric.anderson@noaa.gov
The Top-Down Revitalization of Corsican: Considering the Reversal of a Language Shift in the Linguistic and Semiotic Landscapes of Ajaccio
Authors: Blackwood Robert
Published: October 2013

The Linguistic Landscape (LL) is being used creatively in different ways to examine language practices in multilingual communities, and a sister subdiscipline, semiotic landscapes, is emerging to include non-language elements to help better understand attitudes towards languages where two or more varieties are in competition. This article seeks to establish the extent to which the LL contributes to ‘top-down’ language revitalization, a perspective normally overlooked in favour of ‘bottom-up’ language activism. Assessing the presence and absence of the Italo-Romance language of Corsican in the French town of Ajaccio, the regional capital of Corsica, I exploit recent developments in LL studies, as well as research on language commodification, to evaluate the extent to which top-down agents revitalize a minorized language by placing it in the LL.
Hamiltonian inclusive fitness: a fitter fitness concept
Authors: Costa James T.
Published: October 2013

In 1963–1964 W. D. Hamilton introduced the concept of inclusive fitness, the only significant elaboration of Darwinian fitness since the nineteenth century. I discuss the origin of the modern fitness concept, providing context for Hamilton's discovery of inclusive fitness in relation to the puzzle of altruism. While fitness conceptually originates with Darwin, the term itself stems from Spencer and crystallized quantitatively in the early twentieth century. Hamiltonian inclusive fitness, with Price's reformulation, provided the solution to Darwin's ‘special difficulty’—the evolution of caste polymorphism and sterility in social insects. Hamilton further explored the roles of inclusive fitness and reciprocation to tackle Darwin's other difficulty, the evolution of human altruism. The heuristically powerful inclusive fitness concept ramified over the past 50 years: the number and diversity of ‘offspring ideas’ that it has engendered render it a fitter fitness concept, one that Darwin would have appreciated.
The veil of ignorance can favour biological cooperation
Authors: Queller David C. , Strassmann Joan E.
Published: October 2013

Lack of information is a constraint but ignorance can sometimes assist the evolution of cooperation by constraining selfishness. We discuss examples involving both ignorance of role or pay-off and ignorance of relatedness. Ignorance can favour cooperative traits like grouping and warning coloration and reduce conflicts from meiotic drive, imprinting, greenbeards and various forms of nepotism.
Parasites and altruism: converging roads
Authors: Zuk Marlene , Borrello Mark E.
Published: October 2013

W.D. Hamilton was most known for his work on two topics: social evolution and parasites. Although at first glance these seem to be disparate interests, they share many attributes and have logical connections within evolutionary biology. Nevertheless, Hamilton's contributions in these areas met with very different receptions, with his place in the field of social evolution assured, but his work on the role of parasites perceived as more specialized. We take an historical approach to examine the reasons for this difference.
Genes underlying altruism
Authors: Thompson Graham J. , Hurd Peter L. , Crespi Bernard J.
Published: October 2013

William D. Hamilton postulated the existence of ‘genes underlying altruism’, under the rubric of inclusive fitness theory, a half-century ago. Such genes are now poised for discovery. In this article, we develop a set of intuitive criteria for the recognition and analysis of genes for altruism and describe the first candidate genes affecting altruism from social insects and humans. We also provide evidence from a human population for genetically based trade-offs, underlain by oxytocin-system polymorphisms, between alleles for altruism and alleles for non-social cognition. Such trade-offs between self-oriented and altruistic behaviour may influence the evolution of phenotypic diversity across all social animals.
Kin selection, species richness and community
Authors: Tsuji Kazuki
Published: October 2013

Can evolutionary and ecological dynamics operating at one level of the biological hierarchy affect the dynamics and structure at other levels? In social insects, strong hostility towards unrelated individuals can evolve as a kin-selected counter-adaptation to intraspecific social parasitism. This aggression in turn might cause intraspecific competition to predominate over interspecific competition, permitting coexistence with other social insect species. In other words, kin selection—a form of intra-population dynamics—might enhance the species richness of the community, a higher-level structure. The converse effect, from higher to lower levels, might also operate, whereby strong interspecific competition may limit the evolution of selfish individual traits. If the latter effect were to prove more important, it would challenge the common view that intra-population dynamics (via individual or gene selection) is the main driver of evolution.
Size and accumulation of fuel reserves at stopover predict nocturnal restlessness in a migratory bird
Authors: Eikenaar Cas , Schläfke Jan Laszlo
Published: October 2013

Early arrival at the breeding site positively affects the breeding success of migratory birds. During migration, birds spend most of their time at stopovers. Therefore, determining which factors shape stopover duration is essential to our understanding of avian migration. Because the main purpose of stopover is to accumulate fat as fuel for the next flight bout, fuel reserves at arrival and the accumulation of fuel are both expected to affect stopover departure decisions. Here, we determined whether fuel reserves and fuel accumulation predict a bird's motivation to depart, as quantified by nocturnal migratory restlessness (Zugunruhe), using northern wheatears (
Oenanthe oenanthe
) that were captured and temporarily contained at spring stopover. We found that fuel reserves at capture were positively correlated with Zugunruhe, and negatively correlated with fuel accumulation. This indicates that fat birds were motivated to depart, whereas lean birds were set on staying and accumulating fuel. Moreover, the change in fuel reserves was positively correlated with the concurrent change in Zugunruhe, providing the first empirical evidence for a direct link between fuel accumulation and Zugunruhe during stopover. Our study indicates that, together with innate rhythms and weather, the size and accumulation of fuel reserves shape stopover duration, and hence overall migration time.
To call or not to call: parents assess the vulnerability of their young before warning them about predators
Authors: Haff Tonya M. , Magrath Robert D.
Published: October 2013

Communication about predators can reveal the effects of both conspecific and heterospecific audiences on signalling strategy, providing insight into signal function and animal cognition. In species that alarm call to their young, parents face a fundamental dilemma: calling can silence noisy offspring and so make them less likely to be overheard, but can also alert predators that young are nearby. Parents could resolve this dilemma by being sensitive to the current vulnerability of offspring, and calling only when young are most at risk. Testing whether offspring vulnerability affects parental strategy has proved difficult, however, because more vulnerable broods are often also more valuable. We tested experimentally whether parent white-browed scrubwren,
Sericornis frontalis
, assessed brood noisiness when alarm calling near nests
.
When a model predator was nearby, parents gave more alarm calls when playbacks simulated noisy broods, yet brood noisiness did not affect adult calling when only a control model was present. Parents were therefore sensitive to the tradeoff between silencing young and alerting predators to the presence of nests. Our study demonstrates that receiver vulnerability can affect signalling decisions in species other than primates.
Intimal hyperplasia following implantation of helical-centreline and straight-centreline stents in common carotid arteries in healthy pigs: influence of intraluminal flow
†
Authors: Caro Colin Gerald , Seneviratne Anusha , Heraty Kevin B. , Monaco Claudia , Burke Martin G. , Krams Rob , Chang Carlos C. , Coppola Gianfilippo , Gilson Paul
Published: October 2013

Intimal hyperplasia (IH) is a leading cause of obstruction of vascular interventions, including arterial stents, bypass grafts and arteriovenous grafts and fistulae. Proposals to account for arterial stent-associated IH include wall damage, low wall shear stress (WSS), disturbed flow and, although not widely recognized, wall hypoxia. The common non-planarity of arterial geometry and flow, led us to develop a bare-metal, nitinol, self-expanding stent with three-dimensional helical-centreline geometry. This was deployed in one common carotid artery of healthy pigs, with a straight-centreline, but otherwise identical (conventional) stent deployed contralaterally. Both stent types deformed the arteries, but the helical-centreline device additionally deformed them helically and caused swirling of intraluminal flow. At sacrifice, one month post stent deployment, histology revealed significantly less IH in the helical-centreline than straight-centreline stented vessels. Medial cross-sectional area was not significantly different in helical-centreline than straight-centreline stented vessels. By contrast, luminal cross-sectional area was significantly larger in helical-centreline than straight-centreline stented vessels. Mechanisms considered to account for those results include enhanced intraluminal WSS and enhanced intraluminal blood–vessel wall mass transport, including of oxygen, in the helical-centreline stented vessels. Consistent with the latter proposal, adventitial microvessel density was lower in the helical-centreline stented than straight-centreline stented vessels.
Impacts of light shading and nutrient enrichment geo-engineering approaches on the productivity of a stratified, oligotrophic ocean ecosystem
Authors: Hardman-Mountford Nick J. , Polimene Luca , Hirata Takafumi , Brewin Robert J. W. , Aiken Jim
Published: October 2013

Geo-engineering proposals to mitigate global warming have focused either on methods of carbon dioxide removal, particularly nutrient fertilization of plant growth, or on cooling the Earth's surface by reducing incoming solar radiation (shading). Marine phytoplankton contribute half the Earth's biological carbon fixation and carbon export in the ocean is modulated by the actions of microbes and grazing communities in recycling nutrients. Both nutrients and light are essential for photosynthesis, so understanding the relative influence of both these geo-engineering approaches on ocean ecosystem production and processes is critical to the evaluation of their effectiveness. In this paper, we investigate the relationship between light and nutrient availability on productivity in a stratified, oligotrophic subtropical ocean ecosystem using a one-dimensional water column model coupled to a multi-plankton ecosystem model, with the goal of elucidating potential impacts of these geo-engineering approaches on ecosystem production. We find that solar shading approaches can redistribute productivity in the water column but do not change total production. Macronutrient enrichment is able to enhance the export of carbon, although heterotrophic recycling reduces the efficiency of carbon export substantially over time. Our results highlight the requirement for a fuller consideration of marine ecosystem interactions and feedbacks, beyond simply the stimulation of surface blooms, in the evaluation of putative geo-engineering approaches.
Wing and body motion and aerodynamic and leg forces during take-off in droneflies
Authors: Chen Mao Wei , Zhang Yan Lai , Sun Mao
Published: October 2013

Here, we present a detailed analysis of the take-off mechanics in droneflies performing voluntary take-offs. Wing and body kinematics of the insects during take-off were measured using high-speed video techniques. Based on the measured data, the inertia force acting on the insect was computed and the aerodynamic force of the wings was calculated by the method of computational fluid dynamics. Subtracting the aerodynamic force and the weight from the inertia force gave the leg force. In take-off, a dronefly increases its stroke amplitude gradually in the first 10–14 wingbeats and becomes airborne at about the 12th wingbeat. The aerodynamic force increases monotonously from zero to a value a little larger than its weight, and the leg force decreases monotonously from a value equal to its weight to zero, showing that the droneflies do not jump and only use aerodynamic force of flapping wings to lift themselves into the air. Compared with take-offs in insects in previous studies, in which a very large force (5–10 times of the weight) generated either by jumping legs (locusts, milkweed bugs and fruit flies) or by the ‘fling’ mechanism of the wing pair (butterflies) is used in a short time, the take-off in the droneflies is relatively slow but smoother.
Domain wall motion in magnetic nanowires: an asymptotic approach
Authors: Goussev Arseni , Lund Ross G. , Robbins J. M. , Slastikov Valeriy , Sonnenberg Charles
Published: October 2013

We develop a systematic asymptotic description for domain wall motion in one-dimensional magnetic nanowires under the influence of small applied magnetic fields and currents and small material anisotropy. The magnetization dynamics, as governed by the Landau–Lifshitz–Gilbert equation, is investigated via a perturbation expansion. We compute leading-order behaviour, propagation velocities and first-order corrections of both travelling waves and oscillatory solutions, and find bifurcations between these two types of solutions. This treatment provides a sound mathematical foundation for numerous results in the literature obtained through more
ad hoc
arguments.
Control of the separated flow downstream of a backward-facing step using visual feedback
Authors: Gautier N. , Aider J.-L.
Published: October 2013

The separated flow downstream of a backward-facing step is controlled using visual information for feedback. This is done when looking at the flow from two vantage points. Flow velocity fields are computed in real time and used to yield inputs to a control loop. This approach to flow control is shown to be able to control the detached flow in the same way as has been done before by using the area of the recirculation region downstream of the step as the input for a gradient descent optimization scheme. Visual feedback using real-time computations of two-dimensional velocity fields also allows for novel inputs in the feedback scheme. As a proof of concept, the spatially averaged value of the swirling strength
λ

Ci

is successfully used as the input for an automatically tuned proportional–integral–derivative controller.
Nonlinear elastic inclusions in isotropic solids
Authors: Yavari Arash , Goriely Alain
Published: October 2013

We introduce a geometric framework to calculate the residual stress fields and deformations of nonlinear solids with inclusions and eigenstrains. Inclusions are regions in a body with different reference configurations from the body itself and can be described by distributed eigenstrains. Geometrically, the eigenstrains define a Riemannian 3-manifold in which the body is stress-free by construction. The problem of residual stress calculation is then reduced to finding a mapping from the Riemannian material manifold to the ambient Euclidean space. Using this construction, we find the residual stress fields of three model systems with spherical and cylindrical symmetries in both incompressible and compressible isotropic elastic solids. In particular, we consider a finite spherical ball with a spherical inclusion with uniform pure dilatational eigenstrain and we show that the stress in the inclusion is uniform and hydrostatic. We also show how singularities in the stress distribution emerge as a consequence of a mismatch between radial and circumferential eigenstrains at the centre of a sphere or the axis of a cylinder.
Evolution of growth by genetic accommodation in Icelandic freshwater stickleback
Authors: Robinson Beren W.
Published: October 2013

Classical Darwinian adaptation to a change in environment can ensue when selection favours beneficial genetic variation. How plastic trait responses to new conditions affect this process depends on how plasticity reveals to selection the influence of genotype on phenotype. Genetic accommodation theory predicts that evolutionary rate may sharply increase when a new environment induces plastic responses and selects on sufficient genetic variation in those responses to produce an immediate evolutionary response, but natural examples are rare. In Iceland, marine threespine stickleback that have colonized freshwater habitats have evolved more rapid individual growth. Heritable variation in growth is greater for marine full-siblings reared at low versus high salinity, and genetic variation exists in plastic growth responses to low salinity. In fish from recently founded freshwater populations reared at low salinity, the plastic response was strongly correlated with growth. Plasticity and growth were not correlated in full-siblings reared at high salinity nor in marine fish at either salinity. In well-adapted lake populations, rapid growth evolved jointly with stronger plastic responses to low salinity and the persistence of strong plastic responses indicates that growth is not genetically assimilated. Thus, beneficial plastic growth responses to low salinity have both guided and evolved along with rapid growth as stickleback adapted to freshwater.
Functional morphology and biomechanics of branch–stem junctions in columnar cacti
Authors: Schwager Hannes , Masselter Tom , Speck Thomas , Neinhuis Christoph
Published: October 2013

Branching in columnar cacti features morphological and anatomical characteristics specific to the subfamily Cactoideae. The most conspicuous features are the pronounced constrictions at the branch–stem junctions, which are also present in the lignified vascular structures within the succulent cortex. Based on finite-element analyses of ramification models, we demonstrate that these indentations in the region of high flexural and torsional stresses are not regions of structural weakness (e.g. allowing vegetative propagation). On the contrary, they can be regarded as anatomical adaptations to increase the stability by fine-tuning the stress state and stress directions in the junction along prevalent fibre directions. Biomimetic adaptations improving the functionality of ramifications in technical components, inspired, in particular, by the fine-tuned geometrical shape and arrangement of lignified strengthening tissues of biological role models, might contribute to the development of alternative concepts for branched fibre-reinforced composite structures within a limited design space.
Evolutionary routes to non-kin cooperative breeding in birds
Authors: Riehl Christina
Published: October 2013

Cooperatively breeding animals live in social groups in which some individuals help to raise the offspring of others, often at the expense of their own reproduction. Kin selection—when individuals increase their inclusive fitness by aiding genetic relatives—is a powerful explanation for the evolution of cooperative breeding, particularly because most groups consist of family members. However, recent molecular studies have revealed that many cooperative groups also contain unrelated immigrants, and the processes responsible for the formation and maintenance of non-kin coalitions are receiving increasing attention. Here, I provide the first systematic review of group structure for all 213 species of cooperatively breeding birds for which data are available. Although the majority of species (55%) nest in nuclear family groups, cooperative breeding by unrelated individuals is more common than previously recognized: 30% nest in mixed groups of relatives and non-relatives, and 15% nest primarily with non-relatives. Obligate cooperative breeders are far more likely to breed with non-kin than are facultative cooperators, indicating that when constraints on independent breeding are sufficiently severe, the direct benefits of group membership can substitute for potential kin-selected benefits. I review three patterns of dispersal that give rise to social groups with low genetic relatedness, and I discuss the selective pressures that favour the formation of such groups. Although kin selection has undoubtedly been crucial to the origin of most avian social systems, direct benefits have subsequently come to play a predominant role in some societies, allowing cooperation to persist despite low genetic relatedness.
Hippocampal structural plasticity accompanies the resulting contextual fear memory following stress and fear conditioning
Authors: Giachero Marcelo , Calfa Gaston D. , Molina Victor A.
Published: October 2013

The present research investigated the resulting contextual fear memory and structural plasticity changes in the dorsal hippocampus (DH) following stress and fear conditioning. This combination enhanced fear retention and increased the number of total and mature dendritic spines in DH. Intra-basolateral amygdala (BLA) infusion of midazolam prior to stress prevented both the enhancement of fear retention and an increase in the density of total and mature dendritic spines in DH. These findings emphasize the role of the stress-induced attenuation of GABAergic neurotransmission in BLA in the promoting influence of stress on fear memory and on synaptic remodeling in DH. In conclusion, the structural remodeling in DH accompanied the facilitated fear memory following a combination of fear conditioning and stressful stimulation.
Dopamine D1 sensitivity in the prefrontal cortex predicts general cognitive abilities and is modulated by working memory training
Authors: Wass Christopher , Pizzo Alessandro , Sauce Bruno , Kawasumi Yushi , Sturzoiu Tudor , Ree Fred , Otto Tim , Matzel Louis D.
Published: October 2013

A common source of variance (i.e., “general intelligence”) underlies an individual's performance across diverse tests of cognitive ability, and evidence indicates that the processing efficacy of working memory may serve as one such source of common variance. One component of working memory, selective attention, has been reported to co-vary with general intelligence, and dopamine D1 signaling in prefrontal cortex can modulate attentional abilities. Based on their aggregate performance across five diverse tests of learning, here we characterized the general cognitive ability (GCA) of CD-1 outbred mice. In response to a D1 agonist (SKF82958, 1 mg/kg), we then assessed the relationship between GCA and activation of D1 receptor (D1R)-containing neurons in the prelimbic region of the medial prefrontal cortex, the agranular insular cortex, and the dorsomedial striatum. Increased activation of D1R-containing neurons in the prelimbic cortex (but not the agranular insular cortex or dorsomedial striatum) was observed in animals of high GCA relative to those of low GCA (quantified by c-Fos activation in response to the D1 agonist). However, a Western blot analysis revealed no differences in the density of D1Rs in the prelimbic cortex between animals of high and low GCA. Last, it was observed that working memory training promoted an increase in animals’ GCA and enhanced D1R-mediated neuronal activation in the prelimbic cortex. These results suggest that the sensitivity (but not density) of D1Rs in the prelimbic cortex may both regulate GCA and be a target for working memory training.
Deciphering the Responses of Root Border-Like Cells of Arabidopsis and Flax to Pathogen-Derived Elicitors
Authors: Plancot Barbara , Santaella Catherine , Jaber Rim , Kiefer-Meyer Marie Christine , Follet-Gueye Marie-Laure , Leprince Jérôme , Gattin Isabelle , Souc Céline , Driouich Azeddine , Vicré-Gibouin Maïté
Published: October 2013

Plant pathogens including fungi and bacteria cause many of the most serious crop diseases. The plant innate immune response is triggered upon recognition of microbe-associated molecular patterns (MAMPs) such as flagellin22 and peptidoglycan. To date, very little is known of MAMP-mediated responses in roots. Root border cells are cells that originate from root caps and are released individually into the rhizosphere. Root tips of Arabidopsis (Arabidopsis thaliana) and flax (Linum usitatissimum) release cells known as “border-like cells.” Whereas root border cells of pea (Pisum sativum) are clearly involved in defense against fungal pathogens, the function of border-like cells remains to be established. In this study, we have investigated the responses of root border-like cells of Arabidopsis and flax to flagellin22 and peptidoglycan. We found that both MAMPs triggered a rapid oxidative burst in root border-like cells of both species. The production of reactive oxygen species was accompanied by modifications in the cell wall distribution of extensin epitopes. Extensins are hydroxyproline-rich glycoproteins that can be cross linked by hydrogen peroxide to enhance the mechanical strength of the cell wall. In addition, both MAMPs also caused deposition of callose, a well-known marker of MAMP-elicited defense. Furthermore, flagellin22 induced the overexpression of genes involved in the plant immune response in root border-like cells of Arabidopsis. Our findings demonstrate that root border-like cells of flax and Arabidopsis are able to perceive an elicitation and activate defense responses. We also show that cell wall extensin is involved in the innate immunity response of root border-like cells.
Proteome Analysis of Peroxisomes from Etiolated Arabidopsis Seedlings Identifies a Peroxisomal Protease Involved in β-Oxidation and Development
Authors: Quan Sheng , Yang Pingfang , Cassin-Ross Gaëlle , Kaur Navneet , Switzenberg Robert , Aung Kyaw , Li Jiying , Hu Jianping
Published: October 2013

Plant peroxisomes are highly dynamic organelles that mediate a suite of metabolic processes crucial to development. Peroxisomes in seeds/dark-grown seedlings and in photosynthetic tissues constitute two major subtypes of plant peroxisomes, which had been postulated to contain distinct primary biochemical properties. Multiple in-depth proteomic analyses had been performed on leaf peroxisomes, yet the major makeup of peroxisomes in seeds or dark-grown seedlings remained unclear. To compare the metabolic pathways of the two dominant plant peroxisomal subtypes and discover new peroxisomal proteins that function specifically during seed germination, we performed proteomic analysis of peroxisomes from etiolated Arabidopsis (Arabidopsis thaliana) seedlings. The detection of 77 peroxisomal proteins allowed us to perform comparative analysis with the peroxisomal proteome of green leaves, which revealed a large overlap between these two primary peroxisomal variants. Subcellular targeting analysis by fluorescence microscopy validated around 10 new peroxisomal proteins in Arabidopsis. Mutant analysis suggested the role of the cysteine protease RESPONSE TO DROUGHT21A-LIKE1 in β-oxidation, seed germination, and growth. This work provides a much-needed road map of a major type of plant peroxisome and has established a basis for future investigations of peroxisomal proteolytic processes to understand their roles in development and in plant interaction with the environment.
Endoscopic submucosal dissection for gastric cancer in elderly Japanese patients: An observational study of financial costs of treatment based on a national administrative database
Authors: Murata Atsuhiko , Muramatsu Keiji , Ichimiya Yukako , Kubo Tatsuhiko , Fujino Yoshihisa , Matsuda Shinya
Published: October 2013

Objective

There is currently little information on the medical economic outcomes of endoscopic submucosal dissection (ESD) for gastric cancer (GC) in elderly patients. This study therefore aimed to investigate the medical economic outcomes of ESD in elderly patients with GC using a national administrative database.

Methods

A total of 27 385 patients treated with ESD for GC were referred to 867 hospitals in Japan from 2009 to 2011. We collected data from the national administrative database and divided them into two groups according to age: elderly patients (≥80 years; n = 5525) and non‐elderly patients (<80 years; n = 21 860). We compared ESD‐related complications, risk‐adjusted length of stay (LOS) and medical costs during hospitalization between elderly and non‐elderly patients.

Results

There was no significant difference in ESD‐related complications between elderly and non‐elderly patients (4.3% vs 3.9%, P = 0.152). However, significant differences were observed in mean LOS and medical costs during hospitalization between the two groups (P < 0.001). Multiple linear regression analysis showed that elderly patients experienced a significantly longer LOS and higher medical costs. The unstandardized coefficient for LOS in elderly patients was 2.71 days (95% confidence interval [CI] 2.59–2.84, P < 0.001), while that for medical costs during hospitalization was USD952.1 (95% CI 847.7–1056.5, P < 0.001).

Conclusions

LOS and medical costs during hospitalization were significantly higher in elderly patients undergoing ESD for GC than in non‐elderly patients, although there was no difference in the incidence of ESD‐related complications.
A retrospective chart review of the use of rituximab for the treatment of rheumatoid arthritis in Australian rheumatology practice
Authors: Nicholls Dave , Zochling Jane , Boers Anthony , Champion Gary , Mathers David , Riordan John , Youssef Peter , Scott James , Griffiths Hedley
Published: October 2013

Aim

Rituximab is one of nine biologic agents approved for the treatment of rheumatoid arthritis (RA) in Australia. The primary study objective was to analyze the factors that lead to the therapeutic decision to use rituximab in RA.

Method

A cross‐sectional, retrospective chart review was conducted to identify patients who were treated with rituximab and to evaluate their response to treatment.

Results

Factors influencing the prescription of rituximab were identified. The most commonly reported reason for prescribing rituximab was the presence of comorbidities and the presence of seropositive disease. Median rituximab treatment duration was 32.5 months and mean number of treatment cycles was 4.1. Disease activity scores showed significant improvement from baseline to most recent visit. Rituximab treatment was well‐tolerated in this group of RA patients.

Conclusions

Rituximab was effective in a refractory group of RA patients and appears to be safe in a population with a high prevalence of comorbidities, including malignancy and recurrent infections/bronchiectasis. This study may assist rheumatologists in selecting appropriately targeted therapy in RA.
Risk of tuberculosis with anti‐tumor necrosis factor‐α therapy: substantially higher number of patients at risk in Asia
Authors: Navarra Sandra V. , Tang Boxiong , Lu Liangjing , Lin Hsiao‐Yi , Mok Chi Chiu , Asavatanabodee Paijit , Suwannalai Parawee , Hussein Heselynn , Rahman Mahboob U.
Published: October 2013

Aim

To assess the potential risk of tuberculosis (TB) in patients treated with anti‐tumor necrosis factor‐alpha (TNF‐α) agents in Asia.

Methods

Absolute risk increase (ARI) of TB was estimated for three widely used anti‐TNF‐α therapies using published standardized incidence ratios (SIR) from the French Research Axed on Tolerance of bIOtherapies registry and incidence (absolute risk [AR]) of TB in Asia. Assuming an association of increased TB risk with anti‐TNF‐α therapy and country TB AR (incidence), the ARI of TB by country was calculated by multiplying the SIR of the anti‐TNF‐α therapy by the country's TB AR. The numbers needed to harm (NNH) for each anti‐TNF‐α agent and numbers needed to treat (NNT) to reduce one TB event using etanercept therapy instead of adalimumab or infliximab were also calculated for each country.

Results

The ARI of TB with anti‐TNF‐α therapies in Asian countries is substantially higher than Western Europe and North America and the difference between etanercept versus the monoclonal antibodies becomes more evident. The NNH for Asian countries ranged from 8 to 163 for adalimumab, 126 to 2646 for etanercept and 12 to 256 for infliximab. The NNT to reduce one TB event using etanercept instead of adalimumab therapy ranged from 8 to 173, and using etanercept instead of infliximab therapy the NNT ranged from 13 to 283.

Conclusion

Higher numbers of patients are at risk of developing TB with anti‐TNF‐α therapy in Asia compared with Western Europe and North America. The relative lower risk of TB with etanercept may be particularly relevant for Asia, an endemic area for TB.
Estimating multispecies abundance using automated detection systems: ice‐associated seals in the Bering Sea
Authors: Conn Paul B. , Ver Hoef Jay M. , McClintock Brett T. , Moreland Erin E. , London Josh M. , Cameron Michael F. , Dahle Shawn P. , Boveng Peter L.
Published: October 2013

Automated detection systems employing advanced technology (e.g. infrared imagery, auditory recording systems, pattern recognition software) are compelling tools for gathering animal abundance and distribution data since investigators can often collect data more efficiently and reduce animal disturbance relative to surveys using human observers.

Even with these improvements, analysing animal abundance with advanced technology can be challenging because of potential for incomplete detection, false positives and species misidentification. We argue that double sampling with an independent sampling method can provide the critical information needed to account for such errors.

We present a hierarchical modelling framework for jointly analysing automated detection and double sampling data obtained during animal population surveys. Under our framework, observed counts in different sampling units are conceptualized as having arisen from a thinned log‐Gaussian Cox process subject to spatial autocorrelation (where thinning accounts for incomplete detection). For multispecies surveys, our approach handles incomplete species observations owing to (i) structural uncertainties (e.g. in cases where the automatic detection data do not provide species observations) and (ii) species misclassification; the latter requires auxiliary information on the misclassification process.

As an example of combining an automated detection system and a double sampling procedure, we consider the problem of estimating animal abundance from aerial surveys that use infrared imagery to detect animals, and independent, high‐resolution digital photography to provide information on species composition and thermal detection accuracy. We illustrate our approach by analysing simulated data and data from a survey of four ice‐associated seal species in the eastern Bering Sea.

Our analysis indicated reasonable performance of our hierarchical modelling approach, but suggested a need to balance model complexity with the richness of the data set. For example, highly parameterized models can lead to spuriously high predictions of abundance in areas that are not sampled, especially when there are large gaps in spatial coverage.

We recommend that ecologists employ double sampling when enumerating animal populations with automated detection systems to estimate and correct for detection errors. Combining multiple data sets within a hierarchical modelling framework provides a powerful approach for analysing animal abundance over large spatial domains.
Non–Emergency Department Interventions to Reduce ED Utilization: A Systematic Review
Authors: Morgan Sofie Rahman , Chang Anna Marie , Alqatari Mahfood , Pines Jesse M.
Published: October 2013

Objectives

Recent health policy changes have focused efforts on reducing emergency department (ED) visits as a way to reduce costs and improve quality of care. This was a systematic review of interventions based outside the ED aimed at reducing ED use.

Methods

This study was designed as a systematic review. We reviewed the literature on interventions in five categories: patient education, creation of additional non‐ED capacity, managed care, prehospital diversion, and patient financial incentives. Studies written in English, with interventions administered outside of the ED, and a comparison group where ED use was an outcome, were included. Two independent reviewers screened search results using MEDLINE, Cochrane, OAIster, or Scopus. The following data were abstracted from included studies: type of intervention, study design, population, details of intervention, effect on ED use, effect on non‐ED health care use, and other health and financial outcomes. Quality of individual articles was assessed using Grading of Recommendations Assessment, Development, and Evaluation (GRADE) guidelines.

Results

Of 39 included studies, 34 were observational and five were randomized controlled trials. Two of five studies on patient education found reductions in ED use ranging from 21% to 80%. Out of 10 studies of additional non‐ED capacity, four showed decreases of 9% to 54%, and one a 21% increase. Both studies on prehospital diversion found reductions of 3% to 7%. Of 12 studies on managed care, 10 had decreases ranging from 1% to 46%. Nine out of 10 studies on patient financial incentives found decreases of 3% to 50%, and one a 34% increase. Nineteen studies reported effect on non‐ED use with mixed results. Seventeen studies included data on health outcomes, but 13 of these only included data on hospitalizations rather than morbidity and mortality. Seven studies included data on cost outcomes. According to the GRADE guidelines, all studies had at least some risk of bias, with four moderate quality, one low quality, and 34 very low quality studies.

Conclusions

Many studies have explored interventions based outside the ED to reduce ED use in various populations, with mixed evidence. Approximately two‐thirds identified here showed reductions in ED use. The interventions with the greatest number of studies showing reductions in ED use include patient financial incentives and managed care, while the greatest magnitude of reductions were found in patient education. These findings have implications for insurers and policymakers seeking to reduce ED use.
Investors' Herd Behavior: Rational or Irrational?
Authors: Lin William T. , Tsai Shih‐Chuan , Lung Pei‐Yau
Published: October 2013

This study examines the relationships between the herding of various investor groups and trading noise in the Taiwan stock market to determine whether any of the investor groups tend to herd rationally. The study uses a unique and comprehensive data set on intraday transactions and limit order books of the Taiwan Stock Exchange (TWSE). We calculate the high‐frequency herding measures and trading noise in a call auction market. We find that institutional investors are likely to be informed traders and herd rationally based on superior information. Institutional investors' herding has a negative impact on trading noise. Their buy (sell) herding predicts positive (negative) future market returns. By contrast, the herding of individual investors tends to contain limited information, as it increases trading noise; the buy (sell) herding of individuals is negatively correlated with future market returns. These findings are more significant for stocks with higher turnover.
Maternal and Fetal Alternative Complement Pathway Activation in Early Severe Preeclampsia
Authors: Hoffman M. Camille , Rumer Kristen K. , Kramer Anita , Lynch Anne M. , Winn Virginia D.
Published: October 2013

Problem

We sought to determine whether alternative complement activation fragment Bb (Bb) levels are elevated in the maternal, fetal, and placental blood in cases of severe preeclampsia (PE) compared with normotensive controls.

Method of study

This was a cross‐sectional study of women admitted at ≥24 weeks gestation with or without severe PE. Maternal plasma was collected at the time of enrollment. Umbilical venous cord and intervillous space blood were collected at delivery. Plasma Bb levels were assessed using ELISA. Bb levels were compared between cases and controls.

Results

Median Bb levels were higher in the maternal plasma of severe PE subjects (n = 24) than in controls (n = 20), 1.45 ± 1.03 versus 0.65 ± 0.23 μg/mL, P < 0.001. In umbilical venous plasma, Bb levels were higher in severe PE subjects (n = 15) compared with controls (n = 15), 2.48 ± 1.40 versus 1.01 ± 0.57 μg/mL, P = 0.01.

Conclusion

Activation fragment Bb is increased in the maternal and umbilical venous blood of cases of severe PE when compared with normotensive controls. These data provide support for alternative complement pathway involvement in the pathogenesis of severe PE and demonstrate that alternative complement activation occurs not only in the maternal but also in the fetal compartment.
Progesterone Elicits an Inhibitory Effect upon LPS‐Induced Innate Immune Response in Pre‐Labor Human Amniotic Epithelium
Authors: Flores‐Espinosa Pilar , Pineda‐Torres Montzerrat , Vega‐Sánchez Rodrigo , Estrada‐Gutiérrez Guadalupe , Espejel‐Nuñez Aurora , Flores‐Pliego Arturo , Maida‐Claros Rolando , Paredes‐Vivas Yuriria , Morales‐Méndez Iyari , Sosa‐González Irma , Chávez‐Mendoza Angel , Zaga‐Clavellina Verónica
Published: October 2013

Problem

Infection of human fetal membranes elicits secretion of pro‐inflammatory modulators through its innate immune capacities. We investigated the effect of lipopolysacharide (LPS) and progesterone (P4) upon expression of TLR‐4/MyD88, TNFα, IL‐6, IL‐8, IL‐10, and HBD2 on the human amniotic epithelium.

Method of study

Explants of the human amniotic epithelium were pre‐treated with 0.01, 0.1, and 1.0 μm of P4; then cotreated with 1000 ng/mL LPS. TLR‐4 was immuno‐detected, and concentrations of MyD88, TNFα, IL‐6, IL‐8, IL‐10, and HBD2 were quantified by ELISA.

Results

P4 significantly reduced the expression of LPS‐induced TLR‐4/MyD88. LPS increased the concentrations of TNFα, IL‐6, IL‐8, IL‐10, and HBD2 by factors of 30‐, eight, three, three, and fivefold, respectively. P4 at 1.0 μm was the most effective dose to blunt the secretion of TNFα, IL‐6, and HBD‐2. RU‐486 blocks the effect of P4.

Conclusion

P4 inhibited LPS‐induced TLR‐4/MyD88 and pro‐inflammatory factors in the human amniotic epithelium. These results could explain partially how P4 can protect the amniotic region of fetal membranes and generate a compensatory mechanism that limits the secretion of pro‐inflammatory modulators, which could jeopardize the immune privilege during pregnancy.
Influencing the Bureaucracy: The Irony of Congressional Oversight
Authors: Clinton Joshua D. , Lewis David E. , Selin Jennifer L.
Published: October 2013

Does the president or Congress have more influence over policymaking by the bureaucracy? Despite a wealth of theoretical guidance, progress on this important question has proven elusive due to competing theoretical predictions and severe difficulties in measuring agency influence and oversight. We use a survey of federal executives to assess political influence, congressional oversight, and the policy preferences of agencies, committees, and the president on a comparable scale. Analyzing variation in political influence across and within agencies reveals that Congress is less influential relative to the White House when more committees are involved. While increasing the number of involved committees may maximize the electoral benefits for members, it may also undercut the ability of Congress as an institution to collectively respond to the actions of the presidency or the bureaucracy.
Ethnic Politics and Women's Empowerment in Africa: Ministerial Appointments to Executive Cabinets
Authors: Arriola Leonardo R. , Johnson Martha C.
Published: October 2013

Under what conditions do women participate in executive power in multiethnic societies? Previous research has examined how political institutions, socioeconomic factors, and cultural norms affect the appointment of women as cabinet ministers. However, no study has assessed the extent to which the politicization of ethnicity—a cleavage that shapes political life in many countries—affects women's cabinet appointments. Focusing on sub‐Saharan Africa, we argue that women are less likely to become cabinet ministers where incumbents use such appointments to build patronage‐based alliances with politicians who act as advocates for ethnic constituencies. Using an original dataset on the composition of cabinets in 34 African countries from 1980 to 2005, we show that women's share of cabinet appointments is significantly lower in countries where leaders must accommodate a larger number of politicized ethnic groups, but it rises with higher levels of democracy and greater representation of women in parliament.