bluuebunny/crossref_metadata_2025 huggingface dataset:
Stream Fragmentation Thresholds for a Reproductive Guild of Great Plains Fishes
Authors: Perkin Joshuah S , Gido Keith B
Published: December 2011

Impoundments, diversion dams, and stream dewatering have created a mosaic of large river fragments throughout the Great Plains of central North America. Coincident with these habitat changes are massive declines in the distribution and abundance of Great Plains fishes belonging to the “pelagic-spawning” reproductive guild. We analyzed longitudinal fragment lengths (measured in river kilometers, rkm) and literature accounts of population status for eight species from this guild across 60 fragments to derive thresholds in stream length associated with extirpations. Fragment length predicted population status (F2,21 = 30.14, P < 0.01), with lengths averaging 136 ± 21 rkm for extirpated, 226 ± 69 rkm for declining, and 458 ± 137 for stable populations. Fragment length explained 71% of reported extirpations and estimated thresholds in fragment length explained 67% of variation in population persistence. Our findings provide insight into appropriate spatial scales for conducting riverscape conservation approaches that address the hierarchical effects of fragmentation on stream-dwelling fishes.
Iridovirus Infections among Missouri River Sturgeon: Initial Characterization, Transmission, and Evidence for Establishment of a Carrier State
Authors: Kurobe T. , MacConnell E. , Hudson C. , McDowell T. S. , Mardones F. O. , Hedrick R. P.
Published: December 2011

Iridovirus infections of the integument were associated with disease and mortality among hatchery-reared populations of juvenile pallid sturgeon Scaphirhynchus albus and shovelnose sturgeon S. platorynchus from the Missouri River. Virus-infected cells in the integument of fins and body were greatly enlarged, possessed pleomorphic and eccentric nuclei, and exhibited an amphophilic to eosinophilic staining of the cytoplasm in hematoxylin-and-eosin-stained sections. Virus particles found in the host cell cytoplasm were composed of an outer hexagonal capsid measuring 254 nm in diameter and surrounding a dense nucleoid. Despite numerous attempts, the virus could not be propagated on routine cell lines used in fish viral diagnostics or from established cell lines from white sturgeon Acipenser transmontanus, pallid sturgeon, or shovelnose sturgeon. Bath exposures of healthy juvenile pallid sturgeon to a crude extract or a 0.45-μm-filtered extract from the fins of infected fish resulted in transmission of the virus and mortality. At water temperatures of 15°C, the first deaths occurred at approximately 1 month; mortality peaked between 50 and 60 d postexposure, after which surviving fish recovered. Presence of the virus was confirmed among dead and moribund pallid sturgeon by both histology and detection of viral DNA by polymerase chain reaction methods. Feeding of infected tissues and cohabitation with virus-infected shovelnose sturgeon also resulted in successful virus transmission to juvenile pallid sturgeon. Virus infections among experimentally exposed pallid sturgeon that recovered from clinical episodes persisted for at least 8.5 months, and these apparently healthy fish transmitted the virus and disease to juvenile pallid sturgeon by cohabitation. The newly described Missouri River sturgeon iridovirus (MRSIV) as found in pallid sturgeon and shovelnose sturgeon shares many properties with a group of iridoviruses associated with serious skin and gill infections in several species of sturgeon.

Received October 5, 2010; accepted October 26, 2010
Effects of Full-Stream Carbon Filtration on the Development of Head and Lateral Line Erosion Syndrome (HLLES) in Ocean Surgeon
Authors: Stamper M. Andrew , Kittell Michele M. , Patel Erin E. , Corwin Allison L.
Published: December 2011

Head and lateral line erosion syndrome (HLLES) is a common but very poorly understood disease of marine aquarium fish. One suspected etiology is the use of granulated activated carbon (GAC) to filter the water. Seventy-two ocean surgeons Acanthurus bahianus were distributed among three carbon-negative control systems and three GAC-treated systems such that each tank contained approximately the same total body mass. Each replicate system was made up of two 250-L circular tanks with a common filtration system (6 fish per tank, 12 fish per replicate system). The GAC-treated tanks were exposed to full-stream, extruded coconut shell activated carbon, which produced a mean total organic carbon content of 0.4 mg/L. The results of this study indicate that extruded coconut shell activated carbon filtering at full-stream rates can cause HLLES-type lesions in ocean surgeons. The HLLES developed exponentially over 15 d, beginning in the chin region. This was followed by pitting in the cheek region, which expanded until erosions coalesced. Once the carbon was discontinued, the processes reversed in a mean time of 49 d. As the lesions healed, they reverted from the coalesced to the pitted stage and then darkened before returning to normal.

Received September 2, 2010; accepted March 20, 2011
Calpains promote α2β1 integrin turnover in nonrecycling integrin pathway
Authors: Rintanen Nina , Karjalainen Mikko , Alanko Jonna , Paavolainen Lassi , Mäki Anita , Nissinen Liisa , Lehkonen Moona , Kallio Katri , Cheng R. Holland , Upla Paula , Ivaska Johanna , Marjomäki Varpu
Published: December 2011

Collagen receptor integrins recycle between the plasma membrane and endosomes and facilitate formation and turnover of focal adhesions. In contrast, clustering of α2β1 integrin with antibodies or the human pathogen echovirus 1 (EV1) causes redistribution of α2 integrin to perinuclear multivesicular bodies, α2-MVBs. We show here that the internalized clustered α2 integrin remains in α2-MVBs and is not recycled back to the plasma membrane. Instead, receptor clustering and internalization lead to an accelerated down-regulation of α2β1 integrin compared to the slow turnover of unclustered α2 integrin. EV1 infection or integrin degradation is not associated with proteasomal or autophagosomal processes and shows no significant association with lysosomal pathway. In contrast, degradation is dependent on calpains, such that it is blocked by calpain inhibitors. We show that active calpain is present in α2-MVBs, internalized clustered α2β1 integrin coprecipitates with calpain-1, and calpain enzymes can degrade α2β1 integrin. In conclusion, we identified a novel virus- and clustering-specific pathway that diverts α2β1 integrin from its normal endo/exocytic traffic to a nonrecycling, calpain-dependent degradative endosomal route.
Promiscuous targeting of polytopic membrane proteins to SecYEG or YidC by theEscherichia colisignal recognition particle
Authors: Welte Thomas , Kudva Renuka , Kuhn Patrick , Sturm Lukas , Braig David , Müller Matthias , Warscheid Bettina , Drepper Friedel , Koch Hans-Georg
Published: December 2011

Protein insertion into the bacterial inner membrane is facilitated by SecYEG or YidC. Although SecYEG most likely constitutes the major integration site, small membrane proteins have been shown to integrate via YidC. We show that YidC can also integrate multispanning membrane proteins such as mannitol permease or TatC, which had been considered to be exclusively integrated by SecYEG. Only SecA-dependent multispanning membrane proteins strictly require SecYEG for integration, which suggests that SecA can only interact with the SecYEG translocon, but not with the YidC insertase. Targeting of multispanning membrane proteins to YidC is mediated by signal recognition particle (SRP), and we show by site-directed cross-linking that the C-terminus of YidC is in contact with SRP, the SRP receptor, and ribosomal proteins. These findings indicate that SRP recognizes membrane proteins independent of the downstream integration site and that many membrane proteins can probably use either SecYEG or YidC for integration. Because protein synthesis is much slower than protein transport, the use of YidC as an additional integration site for multispanning membrane proteins may prevent a situation in which the majority of SecYEG complexes are occupied by translating ribosomes during cotranslational insertion, impeding the translocation of secretory proteins.
Identifying quantitative trait loci via group-sparse multitask regression and feature selection: an imaging genetics study of the ADNI cohort
Authors: Wang Hua , Nie Feiping , Huang Heng , Kim Sungeun , Nho Kwangsik , Risacher Shannon L. , Saykin Andrew J. , Shen Li ,   For the Alzheimer's Disease Neuroimaging Initiative
Published: December 2011

Motivation: Recent advances in high-throughput genotyping and brain imaging techniques enable new approaches to study the influence of genetic variation on brain structures and functions. Traditional association studies typically employ independent and pairwise univariate analysis, which treats single nucleotide polymorphisms (SNPs) and quantitative traits (QTs) as isolated units and ignores important underlying interacting relationships between the units. New methods are proposed here to overcome this limitation.

Results: Taking into account the interlinked structure within and between SNPs and imaging QTs, we propose a novel Group-Sparse Multi-task Regression and Feature Selection (G-SMuRFS) method to identify quantitative trait loci for multiple disease-relevant QTs and apply it to a study in mild cognitive impairment and Alzheimer's disease. Built upon regression analysis, our model uses a new form of regularization, group ℓ2,1-norm (G2,1-norm), to incorporate the biological group structures among SNPs induced from their genetic arrangement. The new G2,1-norm considers the regression coefficients of all the SNPs in each group with respect to all the QTs together and enforces sparsity at the group level. In addition, an ℓ2,1-norm regularization is utilized to couple feature selection across multiple tasks to make use of the shared underlying mechanism among different brain regions. The effectiveness of the proposed method is demonstrated by both clearly improved prediction performance in empirical evaluations and a compact set of selected SNP predictors relevant to the imaging QTs.

Availability: Software is publicly available at: http://ranger.uta.edu/%7eheng/imaging-genetics/

Contact:  heng@uta.edu; shenli@iupui.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
GenomeRunner: automating genome exploration
Authors: Dozmorov Mikhail G. , Cara Lukas R. , Giles Cory B. , Wren Jonathan D.
Published: December 2011

Motivation: One of the challenges in interpreting high-throughput genomic studies such as a genome-wide associations, microarray or ChIP-seq is their open-ended nature—once a set of experimentally identified regions is identified as statistically significant, at least two questions arise: (i) besides P-value, do any of these significant regions stand out in terms of biological implications? (ii) Does the set of significant regions, as a whole, have anything in common genome wide? These issues are difficult to address because of the growing number of annotated genomic features (e.g. single nucleotide polymorphisms, transcription factor binding sites, methylation peaks, etc.), and it is difficult to know a priori which features would be most fruitful to analyze. Our goal is to provide partial automation of this process to begin examining associations between experimental features and annotated genomic regions in a hypothesis-free, data-driven manner.

Results: We created GenomeRunner—a tool for automating annotation and enrichment of genomic features of interest (FOI) with annotated genomic features (GFs), in different organisms. Besides simple association of FOIs with known GFs GenomeRunner tests whether the enriched FOIs, as a group, are statistically associated with a large and growing set of genomic features.

Availability: GenomeRunner setup files and source code are freely available at http://sourceforge.net/projects/genomerunner.

Contact:  mikhail-dozmorov@omrf.org; Jonathan-Wren@omrf.org; jdwren@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data
Authors: Boeva Valentina , Popova Tatiana , Bleakley Kevin , Chiche Pierre , Cappo Julie , Schleiermacher Gudrun , Janoueix-Lerosey Isabelle , Delattre Olivier , Barillot Emmanuel
Published: December 2011

Summary: More and more cancer studies use next-generation sequencing (NGS) data to detect various types of genomic variation. However, even when researchers have such data at hand, single-nucleotide polymorphism arrays have been considered necessary to assess copy number alterations and especially loss of heterozygosity (LOH). Here, we present the tool Control-FREEC that enables automatic calculation of copy number and allelic content profiles from NGS data, and consequently predicts regions of genomic alteration such as gains, losses and LOH. Taking as input aligned reads, Control-FREEC constructs copy number and B-allele frequency profiles. The profiles are then normalized, segmented and analyzed in order to assign genotype status (copy number and allelic content) to each genomic region. When a matched normal sample is provided, Control-FREEC discriminates somatic from germline events. Control-FREEC is able to analyze overdiploid tumor samples and samples contaminated by normal cells. Low mappability regions can be excluded from the analysis using provided mappability tracks.

Availability: C++ source code is available at: http://bioinfo.curie.fr/projects/freec/

Contact:  freec@curie.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Increased Pancreatic Fat Fraction Is Present in Obese Adolescents With Metabolic Syndrome
Authors: Maggio Albane B.R. , Mueller Pascal , Wacker Julie , Viallon Magalie , Belli Dominique C. , Beghetti Maurice , Farpour‐Lambert Nathalie J. , McLin Valérie A.
Published: December 2011

Objectives:

Little is known about pancreatic fat accumulation and its possible associations with metabolic syndrome (MetS) and glucose metabolism. The aim of the present study was to quantify pancreatic fat fraction (PFF) in lean and obese adolescents and explore its relation to metabolic parameters.

Methods:

We recruited 25 lean and 24 obese adolescents. PFF and visceral adipose tissue (VAT) were determined using magnetic resonance imaging. We measured blood pressure, fasting glucose, insulin, liver enzymes, leptin, and lipid levels. Obese subjects underwent an oral glucose tolerance test.

Results:

PFF was significantly higher in obese than in lean subjects (4.8 ± 1.2 vs 3.6 ± 0.9; P < 0.001) and was associated with VAT, γ‐glutamyltransferase, triglycerides, high‐density lipoprotein cholesterol, leptin concentrations, and MetS (P < 0.05 for all). None of the obese subjects had glucose intolerance, but when adjusted for VAT, the following 3 parameters correlated negatively with PFF: fasting and 30‐ minute and 120‐minute insulin levels. We divided subjects into 3 groups: group I, lean without MetS; group II, obese without MetS; and group III, obese with MetS, and observed that PFF increased gradually among groups (I: 3.56% ± 0.88%; II: 4.70% ± 1.06%; III: 5.34% ± 1.49%; P < 0.001).

Conclusions:

Obese adolescents accumulate fat in the pancreas. PFF correlates with the presence of MetS. Even in the absence of glucose intolerance, pancreatic fat deposition is associated with impaired insulin response to glucose overload. This suggests that β‐cell dysfunction may already be present in nondiabetic obese adolescents, mirroring what has been shown in adults, and that pancreatic fat accumulation may participate in obesity‐associated pancreatic endocrine dysfunction.
Microbial diversity affects self-organization of the soil–microbe system with consequences for function
Authors: Crawford John W. , Deacon Lewis , Grinev Dmitri , Harris James A. , Ritz Karl , Singh Brajesh K. , Young Iain
Published: December 2011

Soils are complex ecosystems and the pore-scale physical structure regulates key processes that support terrestrial life. These include maintaining an appropriate mixture of air and water in soil, nutrient cycling and carbon sequestration. There is evidence that this structure is not random, although the organizing mechanism is not known. Using X-ray microtomography and controlled microcosms, we provide evidence that organization of pore-scale structure arises spontaneously out of the interaction between microbial activity, particle aggregation and resource flows in soil. A simple computational model shows that these interactions give rise to self-organization involving both physical particles and microbes that gives soil unique material properties. The consequence of self-organization for the functioning of soil is determined using lattice Boltzmann simulation of fluid flow through the observed structures, and predicts that the resultant micro-structural changes can significantly increase hydraulic conductivity. Manipulation of the diversity of the microbial community reveals a link between the measured change in micro-porosity and the ratio of fungal to bacterial biomass. We suggest that this behaviour may play an important role in the way that soil responds to management and climatic change, but that this capacity for self-organization has limits.
Foot-and-mouth disease virus epitope dominance in the antibody response of vaccinated animals
Authors: Mahapatra M. , Hamblin P. , Paton D. J.
Published: December 2011

Five neutralizing antigenic sites have been identified on the surface of serotype O foot-and-mouth disease virus (FMDV). A set of mAb neutralization-escape mutant viruses was used for the first time to evaluate the relative use of known binding sites by polyclonal antibodies from three target species: cattle, sheep and pigs. Antibodies to all five neutralizing antigenic sites were detected in all three species, with most antibodies directed against antigenic site 2, followed by antigenic site 1. In 76 % of cattle, 65 % of sheep and 58 % of pigs, most antibodies were directed against site 2. Antibodies specific to antigenic sites 3, 4 and 5 were found to be minor constituents in the sera of each of the target species. This implies that antigenic site 2 is a dominant neutralization immunogenic site in serotype O FMDV and may therefore be a good candidate for designing novel vaccines.
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
Authors: Hon Gary C. , Hawkins R. David , Caballero Otavia L. , Lo Christine , Lister Ryan , Pelizzola Mattia , Valsesia Armand , Ye Zhen , Kuan Samantha , Edsall Lee E. , Camargo Anamaria Aranha , Stevenson Brian J. , Ecker Joseph R. , Bafna Vineet , Strausberg Robert L. , Simpson Andrew J. , Ren Bing
Published: December 2011

While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these regions is accompanied by formation of repressive chromatin, with a significant fraction displaying allelic DNA methylation where one allele is DNA methylated while the other allele is occupied by histone modifications H3K9me3 or H3K27me3. Our results show a mutually exclusive relationship between DNA methylation and H3K9me3 or H3K27me3. These results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells.
Characterization of the genetic diversity, structure and admixture of British chicken breeds
Authors: Wilkinson S. , Wiener P. , Teverson D. , Haley C. S. , Hocking P. M.
Published: December 2011

The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average FST of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy‐Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average FIS of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual‐based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.
Overexpression of Id3 induces apoptosis of A549 human lung adenocarcinoma cells
Authors: Li X.‐J. , Zhu C.‐D. , Yu W. , Wang P. , Chen F.‐F. , Xia X.‐Y. , Luo B.
Published: December 2011

Objectives:  Inhibitor of differentiation 3 (Id3) protein has been implicated in the control of multiple cell death signalling pathways and in aetiology of numerous diseases. The aims of this study were to construct a recombinant eukaryotic expression vector (pEGFP/Id3), containing human Id3 (hId3) fused with enhanced green fluorescent protein (EGFP), and to determine effects of ectopic Id3 overexpression, on human lung adenocarcinoma cell (A549) proliferation.

Materials and methods:  Human Id3 cDNA was inserted into pEGFP‐N1 vector to yield the recombinant eukaryotic expression vector pEGFP/Id3. Cells were transfected with pEGFP or pEGFP/Id3, and proliferation of EGFP‐expressing cells was monitored by flow cytometry (FCM) and confocal fluorescence microscopy. RT‐PCR, immunoblotting and immunocytochemistry were used to assess Id3 mRNA transcription and protein expression. Apoptosis was evaluated by Annexin V/7‐AAD staining and FCM, while nuclear morphology of apoptotic cells was examined using Hoechst 33258 staining.

Results:  Over 4 days transfection with pEGFP, the proportion of EGFP‐positive A549 cells peaked at approximately 60% by 48 h and remained stable over the next 48 h. In contrast, the proportion of EGFP‐positive cells in cultures transfected with pEGFP/Id3 decreased from a peak of 60% at 48 h to <5% at 96 h, suggesting that Id3 expression inhibited cell proliferation or survival. Annexin V/7‐AAD and Hoechst 33258 staining revealed significantly higher rates of apoptosis in pEGFP/Id3‐transfected cells.

Conclusion:  Overexpression of Id3 triggered apoptosis in A549 human lung adenocarcinoma cells, implicating Id3 in negative control of tumour growth. These Id3‐induced pro‐apoptotic signalling pathways require further study, but this preliminary investigation suggests that Id3 regulation could be exploited in anti‐tumour therapies.
Transient host–parasitoid dynamics illuminate the practice of biological pest control
Authors: Mills Nicholas J.
Published: December 2011

image

[ The harlequin bug (Murgantia histrionica; top left) is a specialist herbivore on Isomeris arborea, an endemic plant species of the California coastal sage scrub ecosystem (top right). The bug's eggs (bottom center) are parasitized by two parasitoid natural enemies, Trissolcus murgantiae (bottom left) and Ooencyrtus johnsonii (bottom right). The harlequin bug and its parasitoids exhibit many attributes of pest‐enemy systems in general, and of Homopteran pest systems in particular. First, the bug is a specialist herbivore on a long‐lived host plant, similar to many Homopteran pests that attack long‐lived crop plants (e.g., citrus, olive, stone fruits), and its only natural enemies are the two specialist parasitoids. Second, the bug and parasitoids exhibit the same life history and population dynamics as Homopteran pest systems, with an invulnerable adult stage of the herbivore and a persistent host‐parasitoid interaction with host densities maintained at low levels. Third, the parasitoids engage in the same types of interactions as the natural enemies of Homopteran pests (exploitative competition and multiparasitism). Fourth, the bug is a minor pest of crucifers in the southeastern U.S. and the parasitoids are potential control agents. These attributes make this community an ideal model system for investigating the efficacy of natural enemies in pest suppression. ]

Kidd, D. & Amarasekare, P. (2012) The role of transient dynamics in biological pest control: insights from a host–parasitoid community. Journal of Animal Ecology, 81, 47–57.

Our current understanding of host–parasitoid relationships has been strongly influenced by the quest for stability and persistence, and consequently, is based on a large body of theory that has focused on the assumption of equilibrium dynamics. In an elegant analysis of a host–parasitoid model parameterized from laboratory observations, Kidd & Amarasekare broaden our understanding by contrasting the parameters that influence transient versus equilibrium dynamics. Their study highlights the importance of parasitoid handling time, competitive exclusion and intraspecific interference in the transient dynamics of a model host–parasitoid community.
Evolution of starvation resistance in Drosophila melanogaster: measurement of direct and correlated responses to artificial selection
Authors: SCHWASINGER‐SCHMIDT T. E. , KACHMAN S. D. , HARSHMAN L. G.
Published: December 2011

Laboratory selection for resistance to starvation has been conducted under relatively controlled conditions to investigate direct and correlated responses to artificial selection. With regard to starvation resistance, there are three physiological routes by which the trait can evolve: resource accumulation, energy conservation and starvation tolerance. A majority of energetic compounds and macromolecules including triglycerides, trehalose and other sugars, and soluble protein increased in abundance as a result of selection. Movement was additionally investigated with selected males moving less than control males and selected females exhibiting a similar response to selection. Results obtained from this study supported two of the possible evolutionary mechanisms for adaptation to starvation: energy compound storage and conservation. If the response to selection is based on an evolutionarily conserved pattern of genetic correlations (elevated lipid, elevated sugars and reduced movement), then the response to selection is medically relevant and the genetic architecture should be investigated in depth.
Where have all the blue flowers gone: pollinator responses and selection on flower colour in New ZealandWahlenbergia albomarginata
Authors: CAMPBELL D. R. , BISCHOFF M. , LORD J. M. , ROBERTSON A. W.
Published: December 2011

Although pollinators are thought to select on flower colour, few studies have experimentally decoupled effects of colour from correlated traits on pollinator visitation and pollen transfer. We combined selection analysis and phenotypic manipulations to measure the effect of petal colour on visitation and pollen export at two spatial scales inWahlenbergia albomarginata. This species is representative of many New Zealand alpine herbs that have secondarily evolved white or pale flowers. The major pollinators, solitary bees, exerted phenotypic selection on flower size but not colour, quantified by bee vision. When presented with manipulated flowers, bees visited flowers painted blue to resemble a congener over white flowers in large, but not small, experimental arrays. Pollen export was higher for blue flowers in large arrays. Pollinator preference does not explain the pale colouration ofW. albomarginata, as commonly hypothesized. Absence of bright blue could be driven instead by indirect selection of correlated characters.
Preliminary Study on the Mineral Apposition Rate in distal femoral epiphysis of New Zealand White Rabbit at Skeletal Maturity
Authors: Cacchioli A. , Ravanetti F. , Soliani L. , Borghetti P.
Published: December 2011

With 3 figures and 1 table

Studies investigating the effect of different factors on the skeletal system require characterization of an appropriate animal model. Rabbits are among the most commonly studied animals for medical research, being used in about 35% of musculoskeletal research studies. The present dynamic cross‐sectional histomorphometric study quantitatively determined mineral apposition rates (MARs) in the distal femoral epiphysis in four regions of interest (ROIs) in New Zealand white rabbits. ROIs included the craniolateral (CrL), caudolateral (CaL), craniomedial (CrM) and caudomedial (CaM) areas, using a reference height at different stages of skeletal maturity corresponding to experimental ages of 6, 7 and 8 months old (M6, M7 and M8). We evaluated whether a correlation exists in MARs between the times and the regions examined. Such data could be used in studies on growth of the rabbit's femur, on biomaterials for bone integration or regeneration and on growth disturbances produced by various pathologic factors. We found no interaction at the experimental times; thus, M6, M7 and M8 are considered homogeneous in terms of MARs. The velocity profiles of the MARs were statistically significantly different among the considered ROIs. For all experimental times, the CrM region had a higher MAR than the other ROIs. Both the CrM and CaM ROIs had higher MARs than the corresponding lateral ROIs. Our results indicate that bone formation is not constant within the cross‐section, but is statistically different between the ROIs considered.
Early implementation of antifungal therapy in the management of febrile neutropenia is associated with favourable outcome during induction chemotherapy for acute leukaemias
Authors: Khalafallah A. , Maiwald M. , Hannan T. , Abell S. , Staker J. , Supperamohan A.
Published: December 2011

Background:  Mortality related to induction chemotherapy during the treatment of acute leukaemias (AL) has been estimated at 5–20%, and this increases with age. Fungal infection remains one of the major causes of morbidity and mortality and is considered an obstacle to the successful management of acute leukaemias.

Methods:  We retrospectively analysed all patients treated for acute leukaemias at a single institution between July 2006 and January 2009, to assess the impact of early antifungal therapy on outcome during induction chemotherapy. There were 44 episodes of induction chemotherapy, with a median age of patients of 61 years (range 18–81), including 29 patients with acute myeloid leukaemia, 9 with acute lymphoblastic leukaemia and 6 with relapsed AL. The median age was 61 years (range 18–81), and 20 patients were over the age of 60 years.

Results:  All patients who developed febrile neutropenia received broad‐spectrum antibiotics. Early empirical antifungal treatment was commenced with voriconazole (15 patients) or caspofungin (12 patients) if the febrile neutropenia did not resolve after 72 h of antibiotic therapy, in conjunction with radiological changes consistent with possible fungal infection. None of the patients succumbed during induction chemotherapy. The 120‐day mortality rate after the induction therapy was 2.2%, without any incidence of invasive fungal disease.

Conclusion:  Our analysis shows that early empirical treatment for fungal infection with voriconazole or caspofungin is associated with a favourable outcome of induction therapy for acute leukaemias. Further studies to confirm this finding are warranted.
Predicting failure to return to work
Authors: Mills R.
Published: December 2011

Aim:  The research question is: is it possible to predict, at the time of workers' compensation claim lodgement, which workers will have a prolonged return to work (RTW) outcome? This paper illustrates how a traditional analytic approach to the analysis of an existing large database can be insufficient to answer the research question, and suggests an alternative data management and analysis approach.

Methods:  This paper retrospectively analyses 9018 workers' compensation claims from two different workers' compensation jurisdictions in Australia (two data sets) over a 4‐month period in 2007. De‐identified data, submitted at the time of claim lodgement, were compared with RTW outcomes for up to 3 months. Analysis consisted of descriptive, parametric (analysis of variance and multiple regression), survival (proportional hazards) and data mining (partitioning) analysis.

Results:  No significant associations were found on parametric analysis. Multiple associations were found between the predictor variables and RTW outcome on survival analysis, with marked differences being found between some sub‐groups on partitioning – where diagnosis was found to be the strongest discriminator (particularly neck and shoulder injuries). There was a consistent trend for female gender to be associated with a prolonged RTW outcome. The supplied data were not sufficient to enable the development of a predictive model.

Conclusion:  If we want to predict early who will have a prolonged RTW in Australia, workers' compensation claim forms should be redesigned, data management improved and specialised analytic techniques used.
Nurse education in Jordan: history and development
Authors: Zahran Z.
Published: December 2011

ZAHRAN Z. (2011) Nurse education in Jordan: history and development. International Nursing Review59, 380–386

Aim:  This paper provides a comprehensive analysis of the development of nurse education and practice in Jordan.

The problem:  Several types and levels of nurse education have been established influenced, in particular, by Northern American and British models of nurse education and practice. New colleges with new programmes are being introduced at all levels, with a continuing growth in the number of students graduating from nursing programmes, demonstrating the extent to which the status of nursing is changing in Jordan. However, the development of nurse education in Jordan is not wholly congruent with the development of nursing practice. The majority of nursing activities are embedded within a medical model of care or relate to carrying out medical orders, giving rise to task‐oriented care delivery. Jordanian nurses are faced with many challenges in terms of their education and practice.

Methods:  There are few published papers that provide a description of this development. The extant literature on nursing history in Jordan comprises descriptions by university academics, official websites of nursing's regularity body, in addition to anecdotal accounts and conference presentations.

Conclusion:  Nurse education in Jordan has evolved over a relatively short period of time. Collaboration between academics and healthcare providers is vital in order to shape the role of nurses and nursing in the future. Insights gained from this development may benefit nurses globally who are working towards restructuring their nurse education and practice.
Promoting Healthy Routes Back to Work? Boundary Spanning Health Professionals and Employability Programmes in Great Britain
Authors: Lindsay Colin , Dutton Matthew
Published: December 2011

Between 2003 and 2011, the Pathways to Work (PtW) initiative was established across Great Britain, as policymakers sought to address the ‘health‐related, personal and external barriers’ faced by people who were out of work and claiming incapacity benefits (IBs). In the first 18 districts that PtW was rolled‐out, the Public Employment Service (Jobcentre Plus) and National Health Service (NHS) organizations worked in partnership to deliver ‘condition management programmes’, which helped IB claimants to cope with health problems. Evaluation research has identified significant health benefits associated with these condition management programmes, but there has been less discussion of the role of frontline NHS professionals in ensuring that services worked effectively on the ground. This article deploys the concept of ‘boundary spanning’ to explore the role of NHS professionals within PtW. Drawing on more than 50 in‐depth interviews, the article concludes that these NHS staff played a key boundary spanning role in facilitating partnerships, based on an ability to engage with the values/practices of other partner organizations (especially Jobcentre Plus) and a willingness to challenge established professional boundaries and ways of working. The article notes that recent policy initiatives have abandoned the PtW partnership approach in favour of more familiar models of contracting out, and that NHS professionals have been excluded from the delivery of health/employability services. It is argued that these recent changes may negatively affect the quality and range of health‐related services available to people on IBs.
THEOLOGIANS OF SPIRITUAL TRANSFORMATION: A PROPOSAL FOR READING RENÉ GIRARD THROUGH THE LENSES OF HANS URS VON BALTHASAR AND JOHN CASSIAN
Authors: MONGRAIN KEVIN
Published: December 2011

This essay contends that René Girard is not a philosopher or a scientist whose ideas are open to theological appropriation. Instead, contrary to his assertions otherwise, the Girard corpus ought to be read as if it were articulating a form of theology whose primary intellectual home can ultimately be found on a theological map. As the field of Girardian theology grows, it becomes more evident that we need some theological lenses for examining the theology already lying waiting—sometimes inchoately, sometimes not—in Girard's texts, and also for examining how theologians use and misuse his texts. If we can see that he is already doing theology then a theological critique becomes plausible and valid in principle, and indeed becomes an internal critique. Applying good interpretive lenses will provide some rigorous criteria for analyzing the degree to which Girardian theologians are following the internal logic of Girard's thought in their appropriations of it. The interpretive lenses I propose using on Girard are first the theology of Hans Urs von Balthasar (d. 1988) and then the theology of John Cassian (d. circa 435). These two theologians provide us with lenses that help us see that Girard is fundamentally a Catholic theologian involved in resisting the speculative re‐writing of Christianity by proponents of “false gnosis” and that he belongs within the category of theologians who advocate spiritual transformation and “true gnosis.”
GIRARD AND THE SPACES OF APOCALYPTIC
Authors: O'REGAN CYRIL
Published: December 2011

This article examines the apocalyptic turn evident in René Girard's Battling to the End (2009), which puts an exclamation point on what has been an increasing tendency in Girard's thought. Its general aim is to describe Girard's particular form of biblical apocalyptic. Toward that end, (a) it unfolds Girard's arguments against other apocalyptic contenders, including Hegel and Heidegger; (b) it opens up a space of conversation with other forms of apocalyptic thought (e.g. Johann Baptist Metz and, more controversially, Emmanuel Levinas); and (c) in and through Girard's affirmation of Benedict XVI, raises the question of whether there is a structural symmetry between their thought, and whether both articulate a form of Augustinian apocalyptic.
Treatment fidelity in psychosocial intervention for children and adolescents with comorbid problems
Authors: McArthur Brae Anne , Riosa Priscilla Burnham , Preyde Michèle
Published: December 2011

Background:  Intervention fidelity has important implications for the interpretation of intervention outcomes. Reviews on fidelity implementation for psychosocial interventions targeting children and adolescents with comorbid mental health problems are scarce. The purpose of this study was to systematically review reported fidelity of psychosocial interventions for children with comorbid mental health conditions.

Method:  Fidelity and quality ratings were calculated based on an analysis of articles resulting from a previously reported systematic search of the literature (using PsycINFO, MEDLINE and ERIC databases between 1994 and 2009), using the Intervention Fidelity Assessment Checklist for the fidelity measure and the Cochrane Collaboration’s tool for assessing risk of bias for the quality measure.

Results:  Overall, few studies were found to have a high level of fidelity adherence. Only 1 of the 10 studies met the ‘high’ intervention fidelity cutoff.

Conclusions:  Findings suggest that current psychosocial interventions for children and adolescents with comorbid mental health disorders must be interpreted with caution, given many studies either do not measure intervention fidelity or have variable levels of fidelity adherence. Including fidelity components in future studies would aid in determining the effectiveness and generalizability of interventions targeted at children with comorbid disorders.
Minimum Nurse Staffing Legislation and the Financial Performance of California Hospitals
Authors: Reiter Kristin L. , Harless David W. , Pink George H. , Mark Barbara A.
Published: December 2011

Objective

To estimate the effect of minimum nurse staffing ratios on California acute care hospitals’ financial performance.

Data Sources/Study Setting

Secondary data from Medicare cost reports, the American Hospital Association's (AHA) Annual Survey, and the California Office of Statewide Health Planning and Development (OSHPD) are combined from 2000 to 2006 for 203 hospitals in California and 407 hospitals in 12 comparison states.

Study Design

The study employs a difference‐in‐difference analytical approach. Hospitals are grouped into quartiles based on pre‐regulation nurse staffing levels in adult medical‐surgical and pediatric units (quartile 1 = lowest staffing). Differences in operating margin, operating expenses per day, and inpatient operating expenses per discharge for California hospitals within a staffing quartile during the period of regulation are compared to differences at hospitals in comparison states during the same period.

Data Collection/Extraction Methods

Hospital data from Medicare cost reports are merged with nurse staffing measures obtained from AHA and from OSPHD.

Principal Findings

Relative to hospitals in comparison states, operating margins declined significantly for California hospitals in quartiles 2 and 3. Operating expenses increased significantly in quartiles 1, 2, and 3.

Conclusions

Implementation of minimum nurse staffing legislation in California put substantial financial pressure on some hospitals.
A Policy Impact Analysis of the Mandatory NCAA Sickle Cell Trait Screening Program
Authors: Tarini Beth A. , Brooks Margaret Alison , Bundy David G.
Published: December 2011

Objective

To estimate the impact of the mandatory National Collegiate Athletic Association (NCAA) sickle cell trait (SCT) screening policy on the identification of sickle cell carriers and prevention of sudden death.

Data Source

We used NCAA reports, population‐based SCT prevalence estimates, and published risks for exercise‐related sudden death attributable to SCT.

Study Design

We estimated the number of sickle cell carriers identified and the number of potentially preventable sudden deaths with mandatory SCT screening of NCAA Division I athletes. We calculated the number of student‐athletes with SCT using a conditional probability based upon SCT prevalence data and self‐identified race/ethnicity status. We estimated sudden deaths over 10 years based on published attributable risk of exercise‐related sudden death due to SCT.

Principal Findings

We estimate that over 2,000 NCAA Division I student‐athletes with SCT will be identified under this screening policy and that, without intervention, about seven NCAA Division I student‐athletes would die suddenly as a complication of SCT over a 10‐year period.

Conclusion

Universal sickle cell screening of NCAA Division I student‐athletes will identify a substantial number of sickle cell carriers. A successful intervention could prevent about seven deaths over a decade.
Reduction in hyperammonaemia by ornithine phenylacetate prevents lipopolysaccharide‐induced brain edema and coma in cirrhotic rats
Authors: Wright Gavin , Vairappan Balasubramaniyan , Stadlbauer Vanessa , Mookerjee Rajeshwar P. , Davies Nathan A. , Jalan Rajiv
Published: December 2011

Objective

In liver failure, inflammation synergistically exacerbates the deleterious cerebral effects of ammonia. The aims were to test whether treatment with the ammonia‐lowering agent ornithine phenylacetate (OP) and/or anti‐TNF‐α (infliximab) prevent the deleterious brain consequences of lipopolysaccharide (LPS) in cirrhotic rats.

Design

Rats 4 weeks following bile duct‐ligation (BDL), sham‐operation (sham) and/or 7 days hyperammonemic feed (HD), were randomized to receive LPS (1 mg/kg) or saline, and treatment with either 3 days intraperitoneal injections of OP (0.6 g/kg) and/or infliximab, 10 mg/kg. Animals were sacrificed at coma stages or at 3 h.

Results

In sham rats, both HD and LPS increased brain water, with an increase in ammonia in the former and brain cytokines in the latter but with no effect on consciousness. BDL + HD rats caused significantly higher plasma ammonia, TNF‐α and IL‐6 levels compared to sham. LPS significantly worsened coma stage, increased brain water and plasma and brain TNF‐α. OP significantly delayed LPS‐induced progression to coma stages (P < 0.009), reduced arterial ammonia and brain water (P < 0.001 and P < 0.01 respectively), which was associated with a significant reduction in cytokines. Infliximab significantly reduced plasma and brain cytokines, but not brain water. OP + infliximab attenuated increase in brain water and delayed occurrence of coma, which was not different to OP alone. In BDL rats, OP reduced the expression of brain iNOS and NFκB.

Conclusion

Reduction in ammonia with OP in cirrhotic rats prevents LPS‐induced brain edema and delays coma, suggesting that ammonia may prime the brain to the deleterious effect of LPS, possibly through effects on iNOS and NFκB related mechanisms.
Justices and Legal Clarity: Analyzing the Complexity of U.S. Supreme Court Opinions
Authors: Owens Ryan J. , Wedeking Justin P.
Published: December 2011

Legal clarity is important to understand and measure because of its connection to the rule of law. We provide the first systematic examination of the clarity of Supreme Court opinions and discover five important results. First, certain justices systematically craft clearer opinions than others. Justices Scalia and Breyer write the clearest opinions, while Justice Ginsburg consistently writes the most complex opinions. Second, ideology does not predict clarity in majority or concurring opinions. Third, all justices write clearer dissents than majority opinions, while minimum winning coalitions produce the clearest majority opinions. Fourth, justices across the board write clearer opinions in criminal procedure cases than in any other issue area. Finally, opinions that formally alter Court precedent render less clear law, potentially leading to a cycle of legal ambiguity.