bluuebunny/crossref_metadata_2025 huggingface dataset:
Corrigendum to: Inbreeding and testicular abnormalities in a bottlenecked population of koalas (Phascolarctos cinereus)
Authors: Cristescu Romane , Cahill Valma , Sherwin William B. , Handasyde Kathrine , Carlyon Kris , Whisson Desley , Herbert Catherine A. , Carlsson Britt Louise J. , Wilton Alan N. , Cooper Des W.
Published: May 2013

Habitat destruction and fragmentation, interactions with introduced species or the relocation of animals to form new populations for conservation purposes may result in a multiplication of population bottlenecks. Examples are the translocations of koalas to French Island and its derivative Kangaroo Island population, with both populations established as insurance policies against koala extinction. In terms of population size, these conservation programs were success stories. However, the genetic story could be different. We conducted a genetic investigation of French and Kangaroo Island koalas by using 15 microsatellite markers, 11 of which are described here for the first time. The results confirm very low genetic diversity. French Island koalas have 3.8 alleles per locus and Kangaroo Island koalas 2.4. The present study found a 19% incidence of testicular abnormality in Kangaroo Island animals. Internal relatedness, an individual inbreeding coefficient, was not significantly different in koalas with testicular abnormalities from that in other males, suggesting the condition is not related to recent inbreeding. It could instead result from an unfortunate selection of founder individuals carrying alleles for testicular abnormalities, followed by a subsequent increase in these alleles' frequencies through genetic drift and small population-related inefficiency of selection. Given the low diversity and possible high prevalence of deleterious alleles, the genetic viability of the population remains uncertain, despite its exponential growth so far. This stands as a warning to other introductions for conservation reasons.
Are roads and traffic sources of physiological stress for the Florida scrub-jay?
Authors: Morgan Gina M. , Wilcoxen Travis E. , Rensel Michelle A. , Schoech Stephan J.
Published: May 2013

Context
Anthropogenic disturbances induce physiological and behavioural responses in numerous species. The negative effects of human disturbance are of special concern to threatened and endangered species.

Aims
The present study aims to compare physiological stress measures and reproductive success of Florida scrub-jays (Aphelocoma coerulescens) living near roads with jays that live away from roads. Specifically, it aims to test whether roads are stressful.

Methods
We assessed physiological measures that can serve as indicators of ‘stress’ to determine whether a highway that bisects our study site had physiological effects on adult male Florida scrub-jays. We captured male breeders from three territory types, including scrub habitat that (1) bordered a highway with a grassy shoulder that created an ‘edge’ habitat (roadside), (2) bordered human-maintained habitat (a plowed firebreak of sand with adjacent pasture) that served as a control for the edge-effect of the road (pasture) and (3) contained only natural scrub habitat (interior). We measured baseline concentrations of the stress hormone corticosterone (CORT), body mass, and a suite of longitudinal body measures to generate a body condition index in males from each territory type over three breeding seasons.

Key results
Roadside jays had greater body mass than did interior and pasture jays, although there were no differences in overall baseline CORT concentrations or body condition among territory classes. There was no difference in clutch initiation date or size and nestling and independent-young survival.

Conclusions
Our results suggest that the road through our study site has physiological effects on Florida scrub-jays; however, there is mixed evidence as to whether it acts as a chronic stressor.

Implications
Our findings provide evidence that roads and road-associated disturbance has neutral or potentially beneficial physiological effects of roads on Florida scrub-jays. Knowledge of these effects of roads and disturbance on jays will hopefully provide additional opportunities to improve conservation of this species.
Winter severity index using widely available weather information
Authors: Dawe K. L. , Boutin S.
Published: May 2013

Context
Changes in global climate and evidence of species’ responses to these changes have increased interest in relationships between climate variables and species demography and distributions. Although an important tool for many ecological questions, large-scale climate indices fail to provide the spatial resolution necessary to investigate drivers of change across small spatial scales. Climate variables that describe yearly climate variation at large spatial extents and small spatial grain are needed.

Aim
Here we develop a model for snow depth using snow water equivalent (SWE) data, which are readily available in a number of formats, to be included in a more general climate index. We use an existing winter severity index (WSI) for white-tailed deer to test the performance of the model.

Methods
We obtained data for 13 weather stations from north-western Canada, reporting both SWE and snow depth. We accumulated a snowpack from daily SWE of snowfall and then tested two methods for converting the SWE of the snowpack into the snow portion of the WSI. We then generalised the model for application to the northwest forest climate region.

Key results
Coefficients of determination (R2) relating the actual and predicted snow depth portion of the WSI ranged from 0.41 to 0.78, with only three stations being below 0.50. Coefficients of determination (R2) relating the actual and predicted WSI for the northwest climate region ranged from 0.58 to 0.88.

Conclusions
The SWE model predicts the snow portion of the WSI well for most stations and, when incorporated into the full WSI, provides a good measure of relative winter severity across space and time for most stations.

Implications
The method developed here could be applied elsewhere, where snow depth is an important factor in species ecology. The benefit of this approach is a comparatively simple method that maximises the use of widely available SWE data in place of snow-depth data.
Lagomorph and sheep effects on vegetation growth in dry and mesic grasslands in Otago, New Zealand
Authors: Scroggie Michael P. , Parkes John P. , Norbury Grant , Reddiex Ben , Heyward Richard
Published: May 2013

Context. Rabbits (Oryctolagus cuniculus) are major pests in the semiarid grasslands of eastern South Island. As the benefits of a viral biological control agent (rabbit haemorrhagic disease virus) introduced in 1997 begin to wane, landowners are again faced with the costs of controlling rabbits.
Aim. The study aimed to measure the extent of vegetation growth as rabbit and sheep densities changed to enable land managers to better justify decisions on pest and stock management.
Methods. We investigated the relationship between seasonal growth of vegetation at two replicate sites within each of three rabbit-prone areas in Otago. At these sites, the ambient densities of lagomorphs varied naturally and in response to pest-control operations, whereas the density of domestic sheep (Ovis aries) varied according to the farmers’ husbandry needs. The vegetation was highly degraded at one of the areas studied. Rabbits were present at all three sites and hares (Lepus europaeus) at two sites. At each site, we established exclosures that excluded either all herbivores or just sheep. The observed rates of vegetation growth were modelled as a function of prevailing herbivore densities, season and site. The fitted model was used to infer expected rates of change in vegetation biomass at the sites, under varying sheep and lagomorph density indices, and seasons.
Key results. In the absence of herbivores, vegetation was predicted to grow in all seasons apart from winter at the degraded sites. In the absence of sheep but in the presence of up to ~10 lagomorphs seen per kilometre of spotlight transect, accumulation of vegetation biomass follows the same seasonal pattern as in the absence of herbivores. As lagomorph counts reach 50 per kilometre, vegetation biomass accumulates only in spring and summer and only at the least degraded sites. The maximum stocking rates for sheep for which positive biomass accumulation could be maintained under varying lagomorph densities was predicted from the model.
Conclusions. At the least degraded sites some sheep could be grazed while maintaining positive pasture growth, even at high rabbit densities, except in winter if rabbit-density indices exceeded ~30 per kilometre. At the most degraded sites, a very low density of sheep could be maintained, but only in spring and only if lagomorph density indices were below ~10 per kilometre.
Monitoring indicates greater resilience for birds than for mammals in Kakadu National Park, northern Australia
Authors: Woinarski J. C. Z. , Fisher A. , Armstrong M. , Brennan K. , Griffiths A. D. , Hill B. , Choy J. Low , Milne D. , Stewart A. , Young S. , Ward S. , Winderlich S. , Ziembicki M.
Published: May 2013

Context
A previous study reported major declines for native mammal species from Kakadu National Park, over the period 2001–09. The extent to which this result may be symptomatic of more pervasive biodiversity decline was unknown.

Aims
Our primary aim was to describe trends in the abundance of birds in Kakadu over the period 2001–09. We assessed whether any change in bird abundance was related to the arrival of invading cane toads (Rhinella marina), and to fire regimes.

Methods
Birds were monitored at 136 1-ha plots in Kakadu, during the period 2001–04 and again in 2007–09. This program complemented sampling of the same plots over the same period for native mammals.

Key results
In contrast to the decline reported for native mammals, the richness and total abundance of birds increased over this period, and far more individual bird species increased than decreased. Fire history in the between-sampling period had little influence on trends for individual species. Interpretation of the overall positive trends for bird species in Kakadu over this period should be tempered by recognition that most of the threatened bird species present in Kakadu were unrecorded in this monitoring program, and the two threatened species for which there were sufficient records to assess trends – partridge pigeon (Geophaps smithii) and white-throated grass-wren (Amytornis woodwardi) – both declined significantly.

Conclusions
The current decline of the mammal fauna in this region is not reflected in trends for the region’s bird fauna. Some of the observed changes (mostly increases) in the abundance of bird species may be due to the arrival of cane toads, and some may be due to local or regional-scale climatic variation or variation in the amount of flowering. The present study provides no assurance about threatened bird species, given that most were inadequately recorded in the study (perhaps because their decline pre-dated the present study).

Implications
These contrasting trends between mammals and birds demonstrate the need for biodiversity monitoring programs to be broadly based. The declines of two threatened bird species over this period indicate the need for more management focus for these species.
Effects of large-scale high-severity fire on occupancy and abundances of an invasive large mammal in south-eastern Australia
Authors: Forsyth David M. , Gormley Andrew M. , Woodford Luke , Fitzgerald Tony
Published: May 2013

Context
Despite large mammals being an important component of many ecosystems, there is little information on the impacts of fire on large mammal populations.

Aims
We evaluated the effects of the large-scale high-severity ‘Black Saturday’ fires of 7 February 2009 on occupancy and abundances of an invasive large mammal, the sambar deer (Cervus unicolor), in south-eastern Australia.

Methods
The effects of the Black Saturday fires on the abundance of sambar deer were assessed using repeated annual counts of faecal pellets during 2007–11 in Kinglake National Park, which was burnt, and in Mount Buffalo National Park, which was not burnt. Pre-fire occupancy was modelled from data collected at 80 4-km2 cells using three survey methods. The same survey methods were used at 15 burnt (n = 9 sampled pre-fire) and 15 unburnt (n = 5 sampled pre-fire) cells 16–24 months after Black Saturday. Because multiple surveys were performed in each cell, we used a Bayesian state–space site-occupancy model to partition changes in the probability of occupancy from changes in the probability of detection.

Key results
Counts of sambar deer pellets increased linearly during 2007–11 in the unburnt Mount Buffalo National Park. Pellet counts also increased linearly in Kinglake National Park from 2007 to 2008, and then decreased (to zero) following Black Saturday; pellet counts increased again in 2010 and 2011. Sambar deer occupancy was weakly reduced (from 0.99 to 0.88) in burnt cells 16–24 months after Black Saturday, but was little changed in unburnt cells (from 0.99 to 0.98).

Conclusions
We conclude that the abundance of sambar deer was substantially reduced by the large-scale high-severity Black Saturday fires, but that most burnt habitat was reoccupied 16–24 months later.

Implications
There is concern about the negative impacts of invasive sambar deer on native biodiversity, particularly immediately post-fire. Our study suggests that it takes at least 8 months before sambar deer recolonise areas burnt by a large-scale high-severity fire; however, a risk-averse approach would be to act (e.g. by erecting fences or culling) sooner than that.
Assignment of measurable costs and benefits to wildlife conservation projects
Authors: Shwiff S. A. , Anderson A. , Cullen R. , White P. C. L. , Shwiff S. S.
Published: May 2013

Success of wildlife conservation projects is determined by a suite of biological and economic factors. Donor and public understanding of the economic factors is becoming increasingly central to the longevity of funding for conservation efforts. Unlike typical economic evaluation, many costs and benefits related to conservation efforts are realised in non-monetary terms. We identify the types of benefits and costs that arise from conservation projects and examine several well developed techniques that economists use to convert benefits and costs into monetary values so they may be compared in a common metric. Costs are typically more readily identifiable than benefits, with financial project costs reported most frequently, and opportunity and damage costs reported much less often. Most current evaluation methods rely primarily on cost-effectiveness analysis rather than cost–benefit analysis, a result of the difficultly in measuring benefits. We highlight improved methodology to measure secondary costs and benefits on a broader spatial scale, thereby promoting project efficacy and long-term success. Estimation of the secondary effects can provide a means to engage a wider audience in discussions of wildlife conservation by illuminating the relevant impacts to income and employment in local economies.
On the use of the IUCN status for the management of trophy hunting
Authors: Palazy Lucille , Bonenfant Christophe , Gaillard Jean-Michel , Courchamp Franck
Published: May 2013

Context
Whether trophy hunting is beneficial or a threat to the conservation of species is an open and hotly debated question. The International Union for Conservation of Nature (IUCN) is in charge of assessing the need for species protection at the global scale and providing a useful guide for sustainable exploitation and conservation. Consideration of the IUCN status in wildlife management and its consequences on the attractiveness of trophy-hunted species remains to be quantified.

Aims
The present study investigated the link between the IUCN status of the trophy species and its exploitation in 124 taxa. We expected that the number of trophies should be inversely correlated with the IUCN vulnerability status across species.

Methods
Using the database of the Safari Club International, one of the largest hunting associations worldwide, we investigated the effect (1) of the first status attribution and (2) of an upgrade of the IUCN status on the number of trophies recorded by the Safari Club International, by comparing the average number of trophies 5 years before and after a status change.

Key results
First, we found that the status attributed by the IUCN in a given year had no effect on the number of recorded trophies during the following 5 years. Second, upgrading the IUCN status led to an important decrease in the number of recorded trophies for most species (75%), except for the most vulnerable ones (African elephant, Loxodonta africana; banteng, Bos javanicus; lelwel hartebeest, Alcelaphus buselaphus lelwel; European bison, Bison bonasus).

Conclusions
Our results suggest that although a protective IUCN status lowers the exploitation of the moderately threatened species, hunting pressure on the most threatened one increases instead. The findings support the possibility of an anthropogenic Allee effect (AAE), i.e. a disproportionate exploitation of the rarest species.

Implications
The highly profitable exploitation of rare species could have harmful consequences, unless appropriate management actions and protection rules are enforced.
The Relationship between Language Production and Verbal Short-Term Memory: The Role of Stress Grouping
Authors: Morgan Jane L. , Edwards Stephanie , Wheeldon Linda R.
Published: May 2013

This study investigates the influence of stress grouping on verbal short-term memory (STM). English speakers show a preference to combine syllables into trochaic groups, both lexically and in continuous speech. In two serial recall experiments, auditory lists of nonsense syllables were presented with either trochaic (STRONG–weak) or iambic (weak–STRONG) stress patterns, or in monotone. The acoustic correlates that carry stress were also manipulated in order to examine the relationship between input and output processes during recall. In Experiment 1, stressed and unstressed syllables differed in intensity and pitch but were matched for spoken duration. Significantly more syllables were recalled in the trochaic stress pattern condition than in the iambic and monotone conditions, which did not differ. In Experiment 2, spoken duration and pitch were manipulated but intensity was held constant. No effects of stress grouping were observed, suggesting that intensity is a critical acoustic factor for trochaic grouping. Acoustic analyses demonstrated that speech output was not identical to the auditory input, but that participants generated correct stress patterns by manipulating acoustic correlates in the same way in both experiments. These data challenge the idea of a language-independent STM store and support the notion of separable phonological input and output processes.
When is a Cause the “Same”? Incoherent Generalization across Contexts
Authors: Barberia Itxaso , Baetu Irina , Sansa Joan , Baker A. G.
Published: May 2013

A theory or model of cause such as Cheng's power ( p) allows people to predict the effectiveness of a cause in a different causal context from the one in which they observed its actions. Liljeholm and Cheng demonstrated that people could detect differences in the effectiveness of the cause when causal power varied across contexts of different outcome base rates, but that they did not detect similar changes when only the cause–outcome contingency, ∆ p, but not power, varied. However, their procedure allowed participants to simplify the causal scenarios and consider only a subsample of observations with a base rate of zero. This confounds p, ∆ p, and the probability of an outcome (O) given a cause (C), P(O|C). Furthermore, the contingencies that they used confounded p and P(O|C) in the overall sample. Following the work of Liljeholm and Cheng, we examined whether causal induction in a wider range of situations follows the principles suggested by Cheng. Experiments 1a and 1b compared the procedure used by Liljeholm and Cheng with one that did not allow the sample of observations to be simplified. Experiments 2a and 2b compared the same two procedures using contingencies that controlled for P(O|C). The results indicated that, if the possibility of converting all contexts to a zero base rate situation was avoided, people were sensitive to changes in P(O|C), p, and ∆ p when each of these was varied. This is inconsistent with Liljeholm and Cheng's conclusion that people detect only changes in p. These results question the idea that people naturally extract the metric or model of cause from their observation of stochastic events and then, reasonably exclusively, use this theory of a causal mechanism, or for that matter any simple normative theory, to generalize their experience to alternative contexts.
ON THE DIRECT IMAGING OF TIDALLY HEATED EXOMOONS
Authors: Limbach Mary Anne , Turner Edwin L.
Published: May 2013

We demonstrate the ability of existing and planned telescopes, on the ground and in space, to directly image tidally heated exomoons orbiting gas-giant exoplanets. Tidally heated exomoons can plausibly be far more luminous than their host exoplanet and as much as 0.1% as bright as the system's stellar primary if it is a low mass star. Because emission from exomoons can be powered by tidal forces, they can shine brightly at arbitrarily large separations from the system's stellar primary with temperatures of several hundreds degrees Kelvin or even higher in extreme cases. Furthermore, these high temperatures can occur in systems that are billions of years old. Tidally heated exomoons may thus be far easier targets for direct imaging studies than giant exoplanets which must be both young and at a large projected separation (typically at least tens of AU) from their primary to be accessible to current generation direct imaging studies. For example, the (warm) Spitzer Space Telescope and the next generation of ground based instruments could detect an exomoon roughly the size of the Earth at a temperature ≈600 K and a distance ≈5 pc in the K, L, and M bands at the 5σ confidence level with a one hour exposure; in more favorable but still plausible cases, detection at distances of tens of parsecs is feasible. Future mid-infrared space telescopes, such as James Webb Space Telescope and SPICA, will be capable of directly imaging tidally heated exomoons around the nearest two dozen stars with a brightness temperature ⩾300 K and R ⩾ 1 R
⊕ orbiting at ⩾12 AU from the primary star at a 5σ confidence level in a 104 s integration. In addition it is possible that some of the exoplanets which have already been directly imaged are actually tidally heated exomoons or blends of such objects with hot young planets. If such exomoons exist and are sufficiently common (i.e., nearby), it may well be far easier to directly image an exomoon with surface conditions that allow the existence of liquid water than it will be to resolve an Earth-like planet in the classical habitable zone of its primary.
Asymptotic behavior of solutions to a class of semilinear parabolic equations with boundary degeneracy
Authors: Wang Chunpeng
Published: May 2013

This paper concerns the asymptotic behavior of solutions to a semilinear parabolic equation with boundary degeneracy. It is proved that for the problem in a bounded domain with a homogeneous boundary condition, there exist both nontrivial global and blowing-up solutions if the degeneracy is not strong, while the nontrivial solution must blow up in a finite time if the degeneracy is strong enough. For the problem in an unbounded domain, blowing-up theorems of Fujita type are established and the critical Fujita exponent is finite in the not strong degeneracy case, while infinite in the other case. Furthermore, the behavior of solutions at the degenerate point is studied, and it is shown that for the nontrivial initial datum vanishing at the degenerate point, the solution always vanishes at the degenerate point if the degeneracy is strong enough, while never if it is not.
Transforming growth factor-β1 selectively inhibits hepatocyte growth factor expression via a micro-RNA-199–dependent posttranscriptional mechanism
Authors: Mungunsukh Ognoon , Day Regina M.
Published: May 2013

Hepatocyte growth factor (HGF) is a multipotent endogenous repair factor secreted primarily by mesenchymal cells with effects on cells expressing its receptor, Met. HGF promotes normal tissue regeneration and inhibits fibrotic remodeling in part by promoting proliferation and migration of endothelial and epithelial cells and protecting these cells from apoptosis. HGF also inhibits myofibroblast proliferation. The profibrotic cytokine transforming growth factor beta 1 (TGF-β1) suppresses HGF expression but not the expression of NK2, an HGF splice variant that antagonizes HGF-induced proliferation. We investigated the mechanism for differential regulation of HGF and NK2 by TGF-β1. TGF-β1 down-regulated HGF in primary human adult pulmonary fibroblasts (HLFb) and increased the expression of miR-199a-3p, a microRNA (miRNA) associated with fibrotic remodeling. HGF and NK2 contain completely different 3′ untranslated regions (UTRs), and we determined that miR-199a-3p targeted HGF mRNA for suppression but not NK2. A pre–miR-199 mimic inhibited the expression of a luciferase reporter harboring the HGF 3′ UTR but not a pmirGLO reporter containing the NK2 3′ UTR. In contrast, an anti-miRNA inhibitor specific for miR-199a-3p prevented TGF-β1–induced reduction of both HGF mRNA and HGF protein secretion. Taken together, these findings demonstrate that HGF is distinctly regulated at the posttranscriptional level from its antagonist NK2.
PconsC: combination of direct information methods and alignments improves contact prediction
Authors: Skwark Marcin J. , Abdel-Rehim Abbi , Elofsson Arne
Published: May 2013

Summary: Recently, several new contact prediction methods have been published. They use (i) large sets of multiple aligned sequences and (ii) assume that correlations between columns in these alignments can be the results of indirect interaction. These methods are clearly superior to earlier methods when it comes to predicting contacts in proteins. Here, we demonstrate that combining predictions from two prediction methods, PSICOV and plmDCA, and two alignment methods, HHblits and jackhmmer at four different e-value cut-offs, provides a relative improvement of 20% in comparison with the best single method, exceeding 70% correct predictions for one contact prediction per residue.

Availability: The source code for PconsC along with supplementary data is freely available at http://c.pcons.net/

Contact:  arne@bioinfo.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites
Authors: Trost Brett , Arsenault Ryan , Griebel Philip , Napper Scott , Kusalik Anthony
Published: May 2013

Summary: While many experimentally characterized phosphorylation sites exist for certain organisms, such as human, rat and mouse, few sites are known for other organisms, hampering related research efforts. We have developed a software pipeline called DAPPLE that automates the process of using known phosphorylation sites from other organisms to identify putative sites in an organism of interest.

Availability: DAPPLE is available as a web server at http://saphire.usask.ca.

Contact:  brett.trost@usask.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Return of the ‘Deade Alive’: The Earl of Bristol and Dr Eglisham in the Parliament of 1626 and in Caroline Political Culture
Authors: Cogswell Thomas
Published: May 2013

Previous scholars of parliamentary history and political culture in the early seventeenth century have only paid scant attention to the earl of Bristol’s role in the 1626 Parliament and none at all to that of George Eglisham. Yet they played a dramatic role in the session. They blackened the reputation of the duke of Buckingham and even besmirched the young king. Indeed Eglisham’s accusation did more than merely follow Charles I to the grave; it helped put him there.
IL-7 production in murine lymphatic endothelial cells and induction in the setting of peripheral lymphopenia
Authors: Miller Corey N. , Hartigan-O’Connor Dennis J. , Lee Myeong Sup , Laidlaw Grace , Cornelissen Ivo P. , Matloubian Mehrdad , Coughlin Shaun R. , McDonald Donald M. , McCune Joseph M.
Published: May 2013

IL-7 is a required factor for T-cell homeostasis. Because of low expression levels and poor reagent availability, the cellular sources of IL-7 have proven challenging to characterize. In this study, we describe a reporter mouse in which enhanced GFP is expressed from the endogenous Il7 locus. We show that IL-7 is produced by lymphatic endothelial cells (LECs) distributed throughout the systemic lymphatic vasculature as well as by fibroblastic reticular cells, and that phosphorylation of STAT5 in lymphocytes is higher in lymphatics than in blood. Furthermore, in nodes depleted of lymphocytes, Il7 transcription is increased in stromal but not in myeloid subsets. These data support recent findings that lymphocyte homeostasis is influenced by access to secondary lymphoid organs and point to LECs as an important in vivo source of IL-7, bathing trafficking immune cells under both resting and lymphopenic conditions.
Aspartate Aminotransferase to Platelet Ratio Index Correlates With Hepatic Cirrhosis but Not With Fibrosis in Pediatric Patients With Intestinal Failure
Authors: Díaz Juan J. , Gura Kathleen M. , Roda Juliamna , Perez‐Atayde Antonio R. , Duggan Christopher , Jaksic Tom , Lo Clifford W.
Published: May 2013

Background and Objectives:

Patients with intestinal failure (IF) require parenteral nutrition (PN) support to obtain enough nutrients to sustain growth; long‐term PN use is associated with significant liver damage. The aim of this study was to analyze the use of a noninvasive test, the aspartate aminotransferase to platelet ratio index (APRI), in the diagnosis of liver disease in pediatric patients with IF.

Methods:

Medical records of all Boston Children's Hospital patients who received PN and underwent a liver biopsy from January 2006 until November 2010 were reviewed. Patients with IF with a clinical diagnosis were selected. APRI was calculated as (aspartate aminotransferase [U/L]/upper normal limit) × 100/platelets (109 cells/L). Presence of fibrosis and cirrhosis was estimated using the METAVIR score in liver biopsies.

Results:

Sixty‐two liver biopsies from 48 patients (22 girls) were studied. Mean APRI values in the different METAVIR categories (0–1, 2–3, 4) were 1.80, 1.17, and 4.24, respectively (analysis of variance P = 0.053; Bonferroni test for cirrhosis vs fibrosis P = 0.048). APRI could significantly predict cirrhosis (odds ratio 1.2; 95% confidence interval [CI] 1.001–1.43) but not fibrosis (METAVIR 2–3, odds ratio 1.00; 95% CI 0.86–1.18). Area under the receiver operating characteristic curve for cirrhosis was 0.67 (95% CI 0.45–0.89; P = 0.13).

Conclusions:

APRI, a noninvasive, easy‐to‐obtain bedside test, significantly predicts cirrhosis but not fibrosis in pediatric patients with IFALD. Because the clinicians need a noninvasive test to differentiate among different stages of liver fibrosis rather than differentiating cirrhosis from normal, we cannot recommend the use of this test in pediatric patients with IFALD for this purpose.
Successful substitution of fetal calf serum by human plasma for bulk cultivation of Leishmania donovani promastigotes
Authors: Mahamoud Abdelhafeiz , Osman Hussam Ali , Mansour Durria , el Harith Abdallah
Published: May 2013

The potential of human plasma (HP) or serum (HS) as a replacement for fetal calf serum (FCS) was evaluated in a liver infusion tryptose (LIT) medium for bulk cultivation ofLeishmania donovanipromastigotes. The promastigote yield with the LIT-FCS standard medium was 0.4–1.8×107ml−1, and yields of 0.5–3.4×107(P = 0.527) and 0.4–2.4×107(P = 0.062) were recorded for two LIT medium variants containing HP or HS as supplement instead of FCS. Significantly, higher promastigote yields of 1.3–4.9×107ml−1were demonstrated when LIT medium was supplemented with HP of blood group O but not A, B, AB or equally pooled ABO (P = 0.007–0.020). Matching (P = 0.56) strong positive (1 : 10 2400 to ≥1 : 262 144 00) and weak negative (1 : 5–1 : 160) direct agglutination test (DAT) titres, respectively, were demonstrated in 24 visceral leishmaniasis (VL) and 45 non-VL sera for both standard LIT-FCS and alternative LIT-HP derived antigens. Our findings indicate strong potential for sustainable production of promastigotes for important diagnostic procedures such as DAT in the VL affected areas.
NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits
Authors: Dittwald Piotr , Gambin Tomasz , Szafranski Przemyslaw , Li Jian , Amato Stephen , Divon Michael Y. , Rodríguez Rojas Lisa Ximena , Elton Lindsay E. , Scott Daryl A. , Schaaf Christian P. , Torres-Martinez Wilfredo , Stevens Abby K. , Rosenfeld Jill A. , Agadi Satish , Francis David , Kang Sung-Hae L. , Breman Amy , Lalani Seema R. , Bacino Carlos A. , Bi Weimin , Milosavljevic Aleksandar , Beaudet Arthur L. , Patel Ankita , Shaw Chad A. , Lupski James R. , Gambin Anna , Cheung Sau Wai , Stankiewicz Pawel
Published: May 2013

We delineated and analyzed directly oriented paralogous low-copy repeats (DP-LCRs) in the most recent version of the human haploid reference genome. The computationally defined DP-LCRs were cross-referenced with our chromosomal microarray analysis (CMA) database of 25,144 patients subjected to genome-wide assays. This computationally guided approach to the empirically derived large data set allowed us to investigate genomic rearrangement relative frequencies and identify new loci for recurrent nonallelic homologous recombination (NAHR)-mediated copy-number variants (CNVs). The most commonly observed recurrent CNVs were NPHP1 duplications (233), CHRNA7 duplications (175), and 22q11.21 deletions (DiGeorge/velocardiofacial syndrome, 166). In the ∼25% of CMA cases for which parental studies were available, we identified 190 de novo recurrent CNVs. In this group, the most frequently observed events were deletions of 22q11.21 (48), 16p11.2 (autism, 34), and 7q11.23 (Williams-Beuren syndrome, 11). Several features of DP-LCRs, including length, distance between NAHR substrate elements, DNA sequence identity (fraction matching), GC content, and concentration of the homologous recombination (HR) hot spot motif 5′-CCNCCNTNNCCNC-3′, correlate with the frequencies of the recurrent CNVs events. Four novel adjacent DP-LCR-flanked and NAHR-prone regions, involving 2q12.2q13, were elucidated in association with novel genomic disorders. Our study quantitates genome architectural features responsible for NAHR-mediated genomic instability and further elucidates the role of NAHR in human disease.
Deciphering Herbivory-Induced Gene-to-Metabolite Dynamics in Nicotiana attenuata Tissues Using a Multifactorial Approach
Authors: Gulati Jyotasana , Kim Sang-Gyu , Baldwin Ian T. , Gaquerel Emmanuel
Published: May 2013

In response to biotic stresses, such as herbivore attack, plants reorganize their transcriptomes and reconfigure their physiologies not only in attacked tissues but throughout the plant. These whole-organismic reconfigurations are coordinated by a poorly understood network of signal transduction cascades. To explore tissue-based interdependencies in the resistance of Nicotiana attenuata to insect attack, we conducted time-series transcriptome and metabolome profiling of herbivory-elicited source leaves and unelicited sink leaves and roots. To probe the multidimensionality of these molecular responses, we designed a novel approach of combining an extended self-organizing maps-based dimensionality reduction method with bootstrap-based nonparametric analysis of variance models to identify the onset and context of signaling and metabolic pathway activations. We illustrate the value of this analysis by revisiting dynamic changes in the expression of regulatory and structural genes of the oxylipin pathway and by studying nonlinearities in gene-metabolite associations involved in the acyclic diterpene glucoside pathway after selectively extracting modules based on their dynamic response patterns. This novel dimensionality reduction approach is broadly applicable to capture the dynamic rewiring of gene and metabolite networks in experimental design with multiple factors.
Quantification of Extracellular Carbonic Anhydrase Activity in Two Marine Diatoms and Investigation of Its Role
Authors: Hopkinson Brian M. , Meile Christof , Shen Chen
Published: May 2013

Many microalgae induce an extracellular carbonic anhydrase (eCA), associated with the cell surface, at low carbon dioxide (CO2) concentrations. This enzyme is thought to aid inorganic carbon uptake by generating CO2 at the cell surface, but alternative roles have been proposed. We developed a new approach to quantify eCA activity in which a reaction-diffusion model is fit to data on 18O removal from inorganic carbon. In contrast to previous methods, eCA activity is treated as a surface process, allowing the effects of eCA on cell boundary-layer chemistry to be assessed. Using this approach, we measured eCA activity in two marine diatoms (Thalassiosira pseudonana and Thalassiosira weissflogii), characterized the kinetics of this enzyme, and studied its regulation as a function of culture pH and CO2 concentration. In support of a role for eCA in CO2 supply, eCA activity specifically responded to low CO2 rather than to changes in pH or HCO3  −, and the rates of eCA activity are nearly optimal for maintaining cell surface CO2 concentrations near those in the bulk solution. Although the CO2 gradients abolished by eCA are small (less than 0.5 μm concentration difference between bulk and cell surface), CO2 uptake in these diatoms is a passive process driven by small concentration gradients. Analysis of the effects of short-term and long-term eCA inhibition on photosynthesis and growth indicates that eCA provides a small energetic benefit by reducing the surface-to-bulk CO2 gradient. Alternative roles for eCA in CO2 recovery as HCO3  − and surface pH regulation were investigated, but eCA was found to have minimal effects on these processes.
Poly[[tetrachlorido{μ4-tetrakis[(pyridin-4-yl)oxymethyl]methane-κ4N:N′:N′′:N′′′}dizinc(II)] dimethylformamide tetrasolvate]
Authors: Wang Ya-Qin , Xie Fa-Zhi , Du Lin
Published: May 2013

A novel metal–organic framework, {[Zn2Cl4(C25H24N4O4)]·4C3H7NO}n, has been synthesized solvothermally by assembling the semi-rigid tetrahedral ligand tetrakis[(pyridin-4-yl)oxymethyl]methane (tpom) and zinc nitrate in dimethylformamide (DMF). The crystal structure is noncentrosymmetric (P\overline{4}21c). Each ZnIIcation has a tetrahedral coordination environment (C2symmetry), which is formed by two chloride ligands and two pyridine N atoms from two tpom ligands. The tetrahedral tetradentate tpom linker has a quaternary C atom located on the crystallographic \overline{4} axis. This linker utilizes all the peripheral pyridine N atoms to connect four ZnIIcations, thereby forming a wave-like two-dimensional sheet along thecaxis. The two-dimensional layer can be topologically simplified as a typical uninodal 4-connected sql/Shubnikov net, which is represented by the Schläfli symbol {44,62}. Adjacent layers are further packed into a three-dimensional structure by C—H...Cl hydrogen bonds.
Assessment of e‐procurement auction with a balanced scorecard
Authors: Rotchanakitumnuai Siriluck
Published: May 2013

Purpose

The purpose of the paper is to assess success factors associated with e‐procurement auctions. The impacts of e‐procurement auction success factors on the four indicators of the balanced scorecard are investigated.

Design/methodology/approach

A survey approach is used to measure the constructs in the proposed model. Respondents were selected from three sectors: private, public, and government organizations using judgment sampling. Data are collected from at least two respondents from purchasing personnel in the e‐procurement user firms. At least one of the respondents is in a managerial position. The sample size is 186, representing 20.4 percent from private enterprises, 33.3 percent from public enterprises, and 46.3 percent from government agencies.

Findings

The survey results show that organizational learning of e‐procurement is influenced by service capability, good governance intention, management support policy, and organizational readiness factors. Service capability and organization learning of e‐procurement influence e‐procurement process improvement. Employee satisfaction can be determined by management support policy and e‐procurement process improvement. Employee satisfaction has the strongest positive impact on financial cost improvement. Management support policy has a negative impact on financial performance improvement. Trust in e‐procurement online intermediaries has no impact on the four measures of the balanced scorecard.

Originality/value

The study contributes to the literature by using the four balanced scorecard indicators to measure the success of e‐procurement to assist organizations to assess performance in terms of organizational learning, internal process improvement, employee satisfaction, and the financial benefit of e‐procurement.
An examination of the causes for retail stockouts
Authors: Ehrenthal Joachim C.F. , Stölzle Wolfgang
Published: May 2013

Purpose

The purpose of this paper is to increase our understanding of the causes for stockouts in retailing.

Design/methodology/approach

Mixed methods study, using instore observations, interviews with key informants in consumer goods and retailing, and a field study of stockouts and their causes in multiple wholesale stores over two years.

Findings

The results indicate that the causes for stockouts are specific to retailer, store, category and item. Improvements to store operations and the coordination of store delivery and shelf replenishment are most effective in reducing stockouts. Manual audits of stockouts and their causes benefit instore execution and provide the level of detail necessary for management to prioritize areas of improvement.

Research limitations/implications

Future research may investigate the operational and cost impact of incorporating demand seasonality in shelf replenishment that may lead to an improved coordination of replenishment and demand cycles.

Practical implications

A procedure is proposed to help store managers reduce stockouts well below the global average of 8.3 percent.

Originality/value

The paper extends the literature by providing a comprehensive set of itemized causes of retail stockouts and reflects implications for sales‐data driven research. It adds to the emergent research that applies service‐dominant logic to retail stockout research.
Democratisation as a State-Building Mechanism: A Preliminary Discussion of an Understudied Relationship
Authors: Carbone Giovanni
Published: May 2013

This review article explores the connection between two key terms in the current international development agenda, namely democratisation and state building. It does so not by looking at the establishment of well-functioning states as a necessary condition for the introduction of democracy, but rather by examining the idea that democratisation may itself play a role in favouring the consolidation of the state. Despite a recent debate on whether democracy or the state comes first, very few empirical studies have addressed the issue of the possible impact of democratic institutions and politics on state development. In the search for additional explanations and empirical evidence concerning this relationship, something more is to be learned as we turn to works that examine the effect of democratic reforms on more specific and partial dimensions, components or indicators of the state, such as violent conflict, corruption or taxation. The inclusion of the latter analyses, however, not only confirms that we still know very little about the democracy–state relationship, thus corroborating the need for new empirical research, but also highlights the conceptual and methodological flaws we must avoid when deciding what notions and measures of state and democracy are most appropriate in tackling this issue.
driftsel: an R package for detecting signals of natural selection in quantitative traits
Authors: Karhunen M. , Merilä J. , Leinonen T. , Cano J. M. , Ovaskainen O.
Published: May 2013

Approaches and tools to differentiate between natural selection and genetic drift as causes of population differentiation are of frequent demand in evolutionary biology. Based on the approach of Ovaskainen et al. (2011), we have developed an R package (driftsel) that can be used to differentiate between stabilizing selection, diversifying selection and random genetic drift as causes of population differentiation in quantitative traits when neutral marker and quantitative genetic data are available. Apart from illustrating the use of this method and the interpretation of results using simulated data, we apply the package on data from three‐spined sticklebacks (Gasterosteus aculeatus) to highlight its virtues. driftsel can also be used to perform usual quantitative genetic analyses in common‐garden study designs.
A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel
Authors: Pujolar J. M. , Jacobsen M. W. , Frydenberg J. , Als T. D. , Larsen P. F. , Maes G. E. , Zane L. , Jian J. B. , Cheng L. , Hansen M. M.
Published: May 2013

Reduced representation genome sequencing such as restriction‐site‐associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single‐nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome‐wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome‐wide set of SNP markers was available until now. The generated SNPs were widely distributed across the eel genome, aligning to 4779 different contigs and 19 703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long‐term effective population size was estimated to range between 132 000 and 1 320 000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82 425 loci and 376 918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome.