bluuebunny/crossref_metadata_2025 huggingface dataset:
Population dynamics of Dasycercus blythi (Marsupialia: Dasyuridae) in central Australia: how does the mulgara persist?
Authors: Masters Pip , Dickman Chris R.
Published: May 2013

Context
Central Australia has been a graveyard for native mammals, with many small and medium-sized species becoming extinct or persisting in reduced geographical ranges in this region since the advent of European settlement. Species in the critical weight range (35–5500 g) have been affected most dramatically.

Aims
We compared the dynamics of two geographically distant populations of a medium-sized surviving desert mammal, the brush-tailed mulgara (Dasycercus blythi, ~100 g), and tested the hypothesis that this species’ persistence can be explained by its demographic plasticity.

Methods
Paired sampling grids, each 31.5 ha, were set up in the Tanami Desert on the northern edge of the species’ geographical range and near Uluru Kata Tjuta National Park (UKTNP) on the southern boundary. Animals were live-trapped every 3 months between 1992 and 1995, and estimates made of population size, residency, reproduction, bodyweight and tail width; the latter was used as an index of condition.

Key results
The UKTNP site supported a larger population of D. blythi than did the Tanami Desert site. In both areas, the population fluctuated annually, declining during the breeding season (June to October) and increasing again following the influx of juveniles in spring. Females had one litter per year, with a median and maximum litter size of six; births in the Tanami occurred in July, at least a month earlier than they did at UKTNP. Bodyweights and tail widths peaked before breeding and then declined until spring, with animals retaining better body condition in the Tanami than at UKTNP. In both regions, individuals were resident for 1–2 years; daughters remained near their mother’s home range but males moved to other areas.

Conclusions
The results provided little support for our initial expectation that populations of D. blythi would behave differently in disparate parts of the species’ geographical range, and suggested instead that this mulgara exhibits a predictable life history, with limited demographic flexibility.

Implications
The persistence of D. blythi in central Australia is most likely a result of its striking flexibility in use of food resources, its ability to enter torpor and to tolerate large declines in bodyweight and condition, and its propensity to dig deep burrows. We suggest that these attributes buffer mulgaras from the impacts of introduced predators that have contributed to extinctions of other medium-sized marsupials, and from climatic and resource uncertainties that shape the dynamics of many smaller desert mammals.
Field evaluation of distance-estimation error during wetland-dependent bird surveys
Authors: Nadeau Christopher P. , Conway Courtney J.
Published: May 2013

Context
The most common methods to estimate detection probability during avian point-count surveys involve recording a distance between the survey point and individual birds detected during the survey period. Accurately measuring or estimating distance is an important assumption of these methods; however, this assumption is rarely tested in the context of aural avian point-count surveys.

Aims
We expand on recent bird-simulation studies to document the error associated with estimating distance to calling birds in a wetland ecosystem.

Methods
We used two approaches to estimate the error associated with five surveyor’s distance estimates between the survey point and calling birds, and to determine the factors that affect a surveyor’s ability to estimate distance.

Key results
We observed biased and imprecise distance estimates when estimating distance to simulated birds in a point-count scenario (error = –9 m, s.d.error = 47 m) and when estimating distances to real birds during field trials (error = 39 m, s.d.error = 79 m). The amount of bias and precision in distance estimates differed among surveyors; surveyors with more training and experience were less biased and more precise when estimating distance to both real and simulated birds. Three environmental factors were important in explaining the error associated with distance estimates, including the measured distance from the bird to the surveyor, the volume of the call and the species of bird. Surveyors tended to make large overestimations to birds close to the survey point, which is an especially serious error in distance sampling.

Conclusions
Our results suggest that distance-estimation error is prevalent, but surveyor training may be the easiest way to reduce distance-estimation error.

Implications
The present study has demonstrated how relatively simple field trials can be used to estimate the error associated with distance estimates used to estimate detection probability during avian point-count surveys. Evaluating distance-estimation errors will allow investigators to better evaluate the accuracy of avian density and trend estimates. Moreover, investigators who evaluate distance-estimation errors could employ recently developed models to incorporate distance-estimation error into analyses. We encourage further development of such models, including the inclusion of such models into distance-analysis software.
Fire and grazing influence food resources of an endangered rock-wallaby
Authors: Tuft Katherine D. , Crowther Mathew S. , McArthur Clare
Published: May 2013

Context
Fire and grazing have complex and interacting impacts on food resources available to endangered herbivores and can potentially be manipulated as part of conservation strategies.

Aims
We examined the interacting impacts of fire and grazing on the food resources available to a colony of endangered brush-tailed rock-wallabies (Petrogale penicillata) to test fire as a potential management tool.

Methods
We conducted two manipulative experiments using a repeated-measures split-block design. We measured the effects of grazing and strategic burning on total vegetation biomass and on particular plants selected by rock-wallabies. In the first experiment we measured the impact of rock-wallaby grazing alone. In the second experiment we measured grazing impacts by both rock-wallabies and potentially competitive sympatric macropods. Grazing was manipulated with three treatments: grazed (open), ungrazed (fenced) and procedural control (half fence).

Key results
In both experiments, burning resulted in greater above-ground biomass of plants selected by rock-wallabies. The response of different plant functional groups to fire was staggered, with forb biomass peaking early and browse biomass increasing above unburnt levels a year after burning.

Conclusions
Despite the limited grazing pressure exerted by the small colony of rock-wallabies in Experiment 1 we detected a negative grazing effect on forbs growing after fire in burnt plots. In Experiment 2, grazing pressure was much more marked due to the high densities of sympatric macropods. In this case, while burning resulted in greater biomass of plants selected by rock-wallabies, grazing (predominantly by sympatric macropods) negated this effect.

Implications
Small patchwork burning can be a useful tool to improve food resources for brush-tailed rock-wallabies, with effects sustained over more than two years. However, when rock-wallabies are sympatric with possible competitor species, the grazing impacts of sympatric macropods may cancel out any benefits to rock-wallabies.
Timing and synchrony of births in bighorn sheep: implications for reintroduction and conservation
Authors: Whiting Jericho C. , Olson Daniel D. , Shannon Justin M. , Bowyer R. Terry , Klaver Robert W. , Flinders Jerran T.
Published: May 2013

Context
Timing (mean birthdate) and synchrony (variance around that date) of births can influence survival of young and growth in ungulate populations. Some restored populations of ungulates may not adjust these life-history characteristics to environments of release sites until several years after release, which may influence success of reintroductions.

Aims
We quantified timing and synchrony of births from 2005 to 2007 in four populations of reintroduced bighorn sheep (Ovis canadensis) occupying two ecoregions (Central Basin and Range and Wasatch and Uinta Mountains) in Utah, USA, to investigate whether bighorns would adjust these life-history characteristics to environmental conditions of the two ecoregions. We also compared timing and synchrony of births for bighorns in their source herd (Antelope Island) with bighorns in an ecologically similar release site (Stansbury Mountains) during 2006 and 2007.

Methods
We relocated female bighorns to record birthdates of young, and observed groups of collared bighorns to quantify use of elevation by those ungulates. We also calculated the initiation, rate and timing of peak green-up by ecoregion, using the normalised difference vegetation index.

Key results
We quantified 274 birthdates, and although only separated by 57 km, bighorn populations occupying the Central Basin and Range Mountains gave birth an average of 29 days earlier than did those on the Wasatch and Uinta Mountains, which corresponded with the initiation of vegetation green-up. Additionally, bighorn sheep on the Stansbury Mountains (ecologically similar release site) gave birth at similar times as did bighorns on Antelope Island (source area).

Conclusions
Populations of bighorn sheep that were reintroduced into adjacent ecoregions adjusted timing of births to environments and green-up of vegetation in restoration areas. Timing and synchrony of births for reintroduced bighorn sheep in an ecologically similar release site were the same as those of their source area.

Implications
Consideration should be given to the adjustment of timing and synchrony of births when reintroducing bighorns, especially when animals are released into different ecoregions. Also, biologists should select release sites that are ecologically similar to source areas, thereby reducing potential negative effects of animals adjusting timing and synchrony of births to environmental conditions of restoration areas.
Phosphorylation of the CENP-A amino-terminus in mitotic centromeric chromatin is required for kinetochore function
Authors: Goutte-Gattat Damien , Shuaib Muhammad , Ouararhni Khalid , Gautier Thierry , Skoufias Dimitrios A. , Hamiche Ali , Dimitrov Stefan
Published: May 2013

The role of the mitotic phosphorylation of the amino (NH
2
) terminus of Centromere Protein A (CENP-A), the histone variant epigenetic centromeric marker, remains elusive. Here, we show that the NH
2
terminus of human CENP-A is essential for mitotic progression and that localization of CENP-C, another key centromeric protein, requires only phosphorylation of the CENP-A NH
2
terminus, and is independent of the CENP-A NH
2
terminus length and amino acid sequence. Mitotic CENP-A nucleosomal complexes contain CENP-C and phosphobinding 14-3-3 proteins. In contrast, mitotic nucleosomal complexes carrying nonphosphorylatable CENP-A–S7A contained only low levels of CENP-C and no detectable 14-3-3 proteins. Direct interactions between the phosphorylated form of CENP-A and 14-3-3 proteins as well as between 14-3-3 proteins and CENP-C were demonstrated. Taken together, our results reveal that 14-3-3 proteins could act as specific mitotic “bridges,” linking phosphorylated CENP-A and CENP-C, which are necessary for the platform function of CENP-A centromeric chromatin in the assembly and maintenance of active kinetochores.
Palb2
synergizes with
Trp53
to suppress mammary tumor formation in a model of inherited breast cancer
Authors: Bowman-Colin Christian , Xia Bing , Bunting Samuel , Klijn Christiaan , Drost Rinske , Bouwman Peter , Fineman Laura , Chen Xixi , Culhane Aedin C. , Cai Hong , Rodig Scott J. , Bronson Roderick T. , Jonkers Jos , Nussenzweig Andre , Kanellopoulou Chryssa , Livingston David M.
Published: May 2013

Germ-line mutations in
PALB2
lead to a familial predisposition to breast and pancreatic cancer or to Fanconi Anemia subtype N. PALB2 performs its tumor suppressor role, at least in part, by supporting homologous recombination-type double strand break repair (HR-DSBR) through physical interactions with BRCA1, BRCA2, and RAD51. To further understand the mechanisms underlying PALB2-mediated DNA repair and tumor suppression functions, we targeted
Palb2
in the mouse.
Palb2
-deficient murine ES cells recapitulated DNA damage defects caused by PALB2 depletion in human cells, and germ-line deletion of
Palb2
led to early embryonic lethality. Somatic deletion of
Palb2
driven by
K14-
Cre led to mammary tumor formation with long latency. Codeletion of both
Palb2
and Tumor protein 53 (
Trp53
) accelerated mammary tumor formation. Like
BRCA1
and
BRCA2
mutant breast cancers, these tumors were defective in RAD51 focus formation, reflecting a defect in
Palb2
HR-DSBR function, a strongly suspected contributor to
Brca1, Brca2
, and
Palb2
mammary tumor development. However, unlike the case of
Brca1
-mutant cells,
Trp53bp1
deletion failed to rescue the genomic instability of
Palb2
- or
Brca2
-mutant primary lymphocytes. Therefore,
Palb2
-driven DNA damage control is, in part, distinct from that executed by
Brca1
and more similar to that of
Brca2.
The mechanisms underlying
Palb2
mammary tumor suppression functions can now be explored genetically in vivo.
The age-specific force of natural selection and biodemographic walls of death
Authors: Wachter Kenneth W. , Evans Steven N. , Steinsaltz David
Published: May 2013

W. D. Hamilton’s celebrated formula for the age-specific force of natural selection furnishes predictions for senescent mortality due to mutation accumulation, at the price of reliance on a linear approximation. Applying to Hamilton’s setting the full nonlinear demographic model for mutation accumulation recently developed by Evans, Steinsaltz, and Wachter, we find surprising differences. Nonlinear interactions cause the collapse of Hamilton-style predictions in the most commonly studied case, refine predictions in other cases, and allow walls of death at ages before the end of reproduction. Haldane’s principle for genetic load has an exact but unfamiliar generalization.
Endomorphism algebras of admissible 𝑝-adic representations of 𝑝-adic Lie groups
Authors: Dospinescu Gabriel , Schraen Benjamin
Published: May 2013

We prove Schur’s lemma for absolutely irreducible admissible

p
p

-adic Banach space (respectively locally analytic) representations of

p
p

-adic Lie groups. We also prove finiteness results for the endomorphism algebra of an irreducible admissible representation.
Regulation of lipid droplet and membrane biogenesis by the acidic tail of the phosphatidate phosphatase Pah1p
Authors: Karanasios Eleftherios , Barbosa Antonio Daniel , Sembongi Hiroshi , Mari Muriel , Han Gil-Soo , Reggiori Fulvio , Carman George M. , Siniossoglou Symeon
Published: May 2013

Lipins are evolutionarily conserved phosphatidate phosphatases that perform key functions in phospholipid, triglyceride, and membrane biogenesis. Translocation of lipins on membranes requires their dephosphorylation by the Nem1p-Spo7p transmembrane phosphatase complex through a poorly understood mechanism. Here we identify the carboxy-terminal acidic tail of the yeast lipin Pah1p as an important regulator of this step. Deletion or mutations of the tail disrupt binding of Pah1p to the Nem1p-Spo7p complex and Pah1p membrane translocation. Overexpression of Nem1p-Spo7p drives the recruitment of Pah1p in the vicinity of lipid droplets in an acidic tail–dependent manner and induces lipid droplet biogenesis. Genetic analysis shows that the acidic tail is essential for the Nem1p-Spo7p–dependent activation of Pah1p but not for the function of Pah1p itself once it is dephosphorylated. Loss of the tail disrupts nuclear structure, INO1 gene expression, and triglyceride synthesis. Similar acidic sequences are present in the carboxy-terminal ends of all yeast lipin orthologues. We propose that acidic tail–dependent binding and dephosphorylation of Pah1p by the Nem1p-Spo7p complex is an important determinant of its function in lipid and membrane biogenesis.
Chemoattractant stimulation of TORC2 is regulated by receptor/G protein–targeted inhibitory mechanisms that function upstream and independently of an essential GEF/Ras activation pathway inDictyostelium
Authors: Liao Xin-Hua , Buggey Jonathan , Lee Yun Kyung , Kimmel Alan R.
Published: May 2013

Global stimulation of Dictyostelium with different chemoattractants elicits multiple transient signaling responses, including synthesis of cAMP and cGMP, actin polymerization, activation of kinases ERK2, TORC2, and phosphatidylinositide 3-kinase, and Ras-GTP accumulation. Mechanisms that down-regulate these responses are poorly understood. Here we examine transient activation of TORC2 in response to chemically distinct chemoattractants, cAMP and folate, and suggest that TORC2 is regulated by adaptive, desensitizing responses to stimulatory ligands that are independent of downstream, feedback, or feedforward circuits. Cells with acquired insensitivity to either folate or cAMP remain fully responsive to TORC2 activation if stimulated with the other ligand. Thus TORC2 responses to cAMP or folate are not cross-inhibitory. Using a series of signaling mutants, we show that folate and cAMP activate TORC2 through an identical GEF/Ras pathway but separate receptors and G protein couplings. Because the common GEF/Ras pathway also remains fully responsive to one chemoattractant after desensitization to the other, GEF/Ras must act downstream and independent of adaptation to persistent ligand stimulation. When initial chemoattractant concentrations are immediately diluted, cells rapidly regain full responsiveness. We suggest that ligand adaptation functions in upstream inhibitory pathways that involve chemoattractant-specific receptor/G protein complexes and regulate multiple response pathways.
A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA
Authors: Huson Daniel H. , Xie Chao
Published: May 2013

Summary: In the context of metagenomics, we introduce a new approach to protein database search called PAUDA, which runs ∼10 000 times faster than BLASTX, while achieving about one-third of the assignment rate of reads to KEGG orthology groups, and producing gene and taxon abundance profiles that are highly correlated to those obtained with BLASTX. PAUDA requires <80 CPU hours to analyze a dataset of 246 million Illumina DNA reads from permafrost soil for which a previous BLASTX analysis (on a subset of 176 million reads) reportedly required 800 000 CPU hours, leading to the same clustering of samples by functional profiles.

Availability: PAUDA is freely available from: http://ab.inf.uni-tuebingen.de/software/pauda. Also supplementary method details are available from this website.

Contact:  daniel.huson@uni-tuebingen.de or xiechao@bic.nus.edu.sg
FYPO: the fission yeast phenotype ontology
Authors: Harris Midori A. , Lock Antonia , Bähler Jürg , Oliver Stephen G. , Wood Valerie
Published: May 2013

Motivation: To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast.

Results: The fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species.

Availability: FYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/).

Contact: mah79@cam.ac.uk or vw253@cam.ac.uk
Killer Treg cells ameliorate inflammatory insulitis in non-obese diabetic mice through local and systemic immunomodulation
Authors: Kaminitz Ayelet , Yolcu Esma S. , Mizrahi Keren , Shirwan Haval , Askenasy Nadir
Published: May 2013

Treg cells endowed with enhanced killing activity through decoration with Fas-ligand (FasL) protein (killer Treg) have been effective in delay of hyperglycemia in prediabetic non-obese diabetic (NOD) mice. In this study, we assessed the therapeutic efficacy of these cells, harvested from age-matched euglycemic NOD donors, on the course of disease in new-onset diabetics. One dose of 4 × 106 killer Treg cells stabilized blood glucose associated with increased insulin levels in 5 of 9 mice and partially reversed the severity of islet inflammation, whereas naive Treg cells did not modulate the course of disease significantly. Killer Treg cells were shown to operate through induction of cell apoptosis within the pancreatic lymph nodes, resulting in reduced efficiency of adoptive disease transfer to NOD/SCID recipients. A second mechanism of action consisted of increased fractions of CD4+CD25−FoxP3+ T cells in the pancreas and all lymphoid organs. Immunomodulation with FasL rather than Treg cells enhanced the expression of CD25 and FoxP3 in the thymus, suggesting a possible contribution of thymic output to prolonged stabilization of the glucose levels. Autologous Treg cells evolve as excellent vehicles for targeted delivery of FasL as an immunomodulatory protein, which delete pathogenic cells at the site of inflammation and induce systemic dominance of suppressor subsets.
Linking the microbiota and metabolic disease with lymphotoxin
Authors: Upadhyay Vaibhav , Fu Yang-Xin
Published: May 2013

The field of lymphotoxin biology has seen many advances in the past decade. Notably, a role for lymphotoxin as a key effector cytokine has emerged to add to its foundational contribution to lymphoid organogenesis. It is now clear that lymphotoxin contributes to host defense for a wide variety of pathogens, and the lymphotoxin receptor is a defining feature of and regulatory mechanism in both innate and adaptive immunities. Specifically, lymphotoxin contributes to Th education, licensing of IL-22 production from type 3 innate lymphoid cells, and even maintains innate myeloid populations within the fully developed lymph node. Most recently, lymphotoxin has been implicated in regulation of the microbiota and metabolic disease. Early studies revealed that lymphotoxin might influence composition of the commensal microbiota through its regulation of immunological compartmentalization in the gut. Additionally, several epidemiological studies have linked polymorphisms in lymphotoxin to metabolic disease. Studies exploring the role of lymphotoxin in metabolic disease have demonstrated that lymphotoxin may influence metabolism both directly in the liver and indirectly through regulation of gut immune responses. It now appears that lymphotoxin may bridge the gap between altered composition of the commensal microbiota and metabolism.
Changes in serotype prevalence and antimicrobial resistance among invasive Streptococcus pneumoniae isolates in Korea, 1996–2008
Authors: Lee Sungkyoung , Bae Songmee , Lee Kwang-Jun , Yu Jae-Yon , Kang Yeonho
Published: May 2013

We investigated changes in serotypes and antimicrobial susceptibilities among 386 isolates of invasive Streptococcus pneumoniae collected from numerous hospitals in Korea from 1996 to 2008. Serotypes 19F (9.8 %), 23F (8.3 %), 19A (7.8 %), 6A (7.5 %), 3 (7.3 %), 9V (6.5 %), 6B (6.2 %), 14 (4.9 %), 1 (3.9 %), 11A (3.9 %) and 4 (3.1 %) represented 69.2 % of all isolates. While the overall proportion of PCV7 serotypes was stable over time, we observed modest decreases in children <5 years old and in adults ≥65 years old between 1996–1999 and 2007–2008. An increased prevalence of non-PCV7 serotypes in these age groups was primarily attributable to an increase in serotypes 3, 6A and 19A. Most invasive S. pneumoniae isolates showed high resistance rates to erythromycin (74.9 %), tetracycline (71.1 %) and clindamycin (61.7 %). Between 1996–2003 and 2004–2008, non-susceptibility rates to cefotaxime and multi-drugs (three or more classes) in PCV7 serotypes showed a declining trend, while in non-PCV7 serotypes there was an increasing trend. Non-PCV7 serotypes 6A and 19A, which mostly exhibited multidrug-resistant phenotypes (69.0 % and 76.7 % respectively), increased between 1996–2003 and 2004–2008. Although PCV7 was introduced in Korea in November 2003, pneumococcal vaccination has not been included in the national child vaccination programme. Our results provide details of serotype occurrence that will be useful when adoption of universal pneumococcal vaccination in Korea is being considered.
Ultrastructural and genomic characterization of a second banchine polydnavirus confirms the existence of shared features within this ichnovirus lineage
Authors: Djoumad Abdelmadjid , Stoltz Don , Béliveau Catherine , Boyle Brian , Kuhn Lisa , Cusson Michel
Published: May 2013

Polydnaviruses (PDVs) are symbiotic viruses carried by endoparasitic wasps and transmitted to caterpillar hosts during parasitization. Although they share several features, including a segmented dsDNA genome, a unique life cycle where replication is restricted to the wasp host, and immunodepressive/developmental effects on the caterpillar host, PDVs carried by ichneumonid and braconid wasps (referred to as ichnoviruses and bracoviruses, respectively) have different evolutionary origins. In addition, ichnoviruses (IVs) form two distinct lineages, with viral entities found in wasps belonging to the subfamilies Campopleginae and Banchinae displaying strikingly different virion morphologies and genomic features. However, the current description for banchine IVs is based on the characterization of a single species, namely that of the Glypta fumiferanae IV (GfIV). Here we provide an ultrastructural and genomic analysis of a second banchine IV isolated from the wasp Apophua simplicipes, and we show that this virus shares many features with GfIV, including a multi-nucleocapsid virion, an aggregate genome size of ~300 kb, genome segments <5 kb, an impressively high degree of genome segmentation and a very similar gene content (same gene families in both viruses). Altogether, the data presented here confirm the existence of shared characteristics within this banchine IV lineage.
Integrins modulate the infection efficiency of West Nile virus into cells
Authors: Schmidt Katja , Keller Markus , Bader Bernhard L. , Korytář Tomáš , Finke Stefan , Ziegler Ute , Groschup Martin H.
Published: May 2013

The underlying mechanisms allowingWest Nile virus(WNV) to replicate in a large variety of different arthropod, bird and mammal species are largely unknown but are believed to rely on highly conserved proteins relevant for viral entry and replication. Consistent with this, the integrin αvβ3 has been proposed lately to function as the cellular receptor for WNV. More recently published data, however, are not in line with this concept. Integrins are highly conserved among diverse taxa and are expressed by almost every cell type at high numbers. Our study was designed to clarify the involvement of integrins in WNV infection of cells. A cell culture model, based on wild-type and specific integrin knockout cell lines lacking the integrin subunits αv, β1 or β3, was used to investigate the susceptibility to WNV, and to evaluate binding and replication efficiencies of four distinct strains (New York 1999, Uganda 1937, Sarafend and Dakar). Though all cell lines were permissive, clear differences in replication efficiencies were observed. Rescue of the β3-integrin subunit resulted in enhanced WNV yields of up to 90 %, regardless of the virus strain used. Similar results were obtained for β1-expressing and non-expressing cells. Binding, however, was not affected by the expression of the integrins in question, and integrin blocking antibodies failed to have any effect. We conclude that integrins are involved in WNV infection but not at the level of binding to target cells.
Mutations in human papillomavirus type 16 L1 hypervariable surface-exposed loops affect L2 binding and DNA encapsidation
Authors: Faust Helena , Dillner Joakim
Published: May 2013

Prophylactic vaccines against human papillomavirus (HPV) based on virus-like particles (VLP) induce type-specific neutralizing antibodies against a small number of hypervariable residues positioned in surface-exposed loops of the major capsid protein L1. To investigate the importance of these residues for neutralization, cross-neutralization, L2 incorporation and genome encapsidation, ten surface-exposed amino acid residues in four hypervariable loops of L1 were mutated. VLPs containing mutated or WT L1, with or without WT L2, were produced in 293TT cells using pseudovirion expression vectors. The mutations reduced the ability to induce neutralizing antibodies and to incorporate the L2 protein in the capsid. Ability to induce cross-neutralizing antibodies and to encapsidate pseudogenomes were completely abrogated. In summary, the surface-exposed L1 loops are important for the function of the HPV particle.
HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses
Authors: Contreras-Galindo Rafael , Kaplan Mark H. , He Shirley , Contreras-Galindo Angie C. , Gonzalez-Hernandez Marta J. , Kappes Ferdinand , Dube Derek , Chan Susana M. , Robinson Dan , Meng Fan , Dai Manhong , Gitlin Scott D. , Chinnaiyan Arul M. , Omenn Gilbert S. , Markovitz David M.
Published: May 2013

Human endogenous retroviruses (HERVs) make up 8% of the human genome. The HERV-K (HML-2) family is the most recent group of these viruses to have inserted into the genome, and we have detected the activation of HERV-K (HML-2) proviruses in the blood of patients with HIV-1 infection. We report that HIV-1 infection activates expression of a novel HERV-K (HML-2) provirus, termed K111, present in multiple copies in the centromeres of chromosomes throughout the human genome yet not annotated in the most recent human genome assembly. Infection with HIV-1 or stimulation with the HIV-1 Tat protein leads to the activation of K111 proviruses. K111 is present as a single copy in the genome of the chimpanzee, yet K111 is not found in the genomes of other primates. Remarkably, K111 proviruses appear in the genomes of the extinct Neanderthal and Denisovan, while modern humans have at least 100 K111 proviruses spread across the centromeres of 15 chromosomes. Our studies suggest that the progenitor K111 integrated before the Homo-Pan divergence and expanded in copy number during the evolution of hominins, perhaps by recombination. The expansion of K111 provides sequence evidence suggesting that recombination between the centromeres of various chromosomes took place during the evolution of humans. K111 proviruses show significant sequence variations in each individual centromere, which may serve as markers in future efforts to annotate human centromere sequences. Further, this work is an example of the potential to discover previously unknown genomic sequences through the analysis of nucleic acids found in the blood of patients.
DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
Authors: Winter Deborah R. , Song Lingyun , Mukherjee Sayan , Furey Terrence S. , Crawford Gregory E.
Published: May 2013

DNase-seq is primarily used to identify nucleosome-depleted DNase I hypersensitive (DHS) sites genome-wide that correspond to active regulatory elements. However, ∼40 yr ago it was demonstrated that DNase I also digests with a ∼10-bp periodicity around nucleosomes matching the exposure of the DNA minor groove as it wraps around histones. Here, we use DNase-seq data from 49 samples representing diverse cell types to reveal this digestion pattern at individual loci and predict genomic locations where nucleosome rotational positioning, the orientation of DNA with respect to the histone surface, is stably maintained. We call these regions DNase I annotated regions of nucleosome stability (DARNS). Compared to MNase-seq experiments, we show DARNS correspond well to annotated nucleosomes. Interestingly, many DARNS are positioned over only one side of annotated nucleosomes, suggesting that the periodic digestion pattern attenuates over the nucleosome dyad. DARNS reproduce the arrangement of nucleosomes around transcription start sites and are depleted at ubiquitous DHS sites. We also generated DARNS from multiple lymphoblast cell line (LCL) samples. We found that LCL DARNS were enriched at DHS sites present in most of the original 49 samples but absent in LCLs, while multi-cell-type DARNS were enriched at LCL-specific DHS sites. This indicates that variably open DHS sites are often occupied by rotationally stable nucleosomes in cell types where the DHS site is closed. DARNS provide additional information about precise DNA orientation within individual nucleosomes not available from other nucleosome positioning assays and contribute to understanding the role of chromatin in gene regulation.
CYCLIN H;1 Regulates Drought Stress Responses and Blue Light-Induced Stomatal Opening by Inhibiting Reactive Oxygen Species Accumulation in Arabidopsis
Authors: Zhou Xiao Feng , Jin Yin Hua , Yoo Chan Yul , Lin Xiao-Li , Kim Woe-Yeon , Yun Dae-Jin , Bressan Ray A. , Hasegawa Paul M. , Jin Jing Bo
Published: May 2013

Arabidopsis (Arabidopsis thaliana) CYCLIN-DEPENDENT KINASE Ds (CDKDs) phosphorylate the C-terminal domain of the largest subunit of RNA polymerase II. Arabidopsis CYCLIN H;1 (CYCH;1) interacts with and activates CDKDs; however, the physiological function of CYCH;1 has not been determined. Here, we report that CYCH;1, which is localized to the nucleus, positively regulates blue light-induced stomatal opening. Reduced-function cych;1 RNA interference (cych;1 RNAi) plants exhibited a drought tolerance phenotype. CYCH;1 is predominantly expressed in guard cells, and its expression was substantially down-regulated by dehydration. Transpiration of intact leaves was reduced in cych;1 RNAi plants compared with the wild-type control in light but not in darkness. CYCH;1 down-regulation impaired blue light-induced stomatal opening but did not affect guard cell development or abscisic acid-mediated stomatal closure. Microarray and real-time polymerase chain reaction analyses indicated that CYCH;1 did not regulate the expression of abscisic acid-responsive genes or light-induced stomatal opening signaling determinants, such as MYB60, MYB61, Hypersensitive to red and blue1, and Protein phosphatase7. CYCH;1 down-regulation induced the expression of redox homeostasis genes, such as LIPOXYGENASE3 (LOX3), LOX4, ARABIDOPSIS GLUTATHIONE PEROXIDASE 7 (ATGPX7), EARLY LIGHT-INDUCIBLE PROTEIN1 (ELIP1), and ELIP2, and increased hydrogen peroxide production in guard cells. Furthermore, loss-of-function mutations in CDKD;2 or CDKD;3 did not affect responsiveness to drought stress, suggesting that CYCH;1 regulates the drought stress response in a CDKD-independent manner. We propose that CYCH;1 regulates blue light-mediated stomatal opening by controlling reactive oxygen species homeostasis.
Two polyoxometallate-based supramolecular compounds influenced by the ratio between the polyoxometallate anion and organic cation
Authors: Zhang Qian , Liu Jie , Lu Jing , Gong Shu-Wen
Published: May 2013

Two polyoxometallate-based compounds, tris[1,1′-(butane-1,4-diyl)bis(1H-imidazol-3-ium)] bis[tetracosa-μ2-oxido-dodecaoxido-μ12-phosphato-dodecamolybdenum(VI)], (C10H16N4)3[PMo12O40]2, (I), and 1,1′-(butane-1,4-diyl)bis(1H-imidazol-3-ium) 1-[4-(1H-imidazol-1-yl)butyl]-1H-imidazol-3-ium tetracosa-μ2-oxido-dodecaoxido-μ12-phosphato-dodecamolybdenum(VI) dihydrate, (C10H16N4)(C10H15N4)[PMo12O40]·2H2O, (II), were synthesized by hydrothermal techniques at different pH values. The stoichiometric ratio between the polyoxometallate (POM) anions and organic cations is 2:3 in (I), with one of the cations lying on an inversion centre. The doubly protonated 1,1′-(butane-1,4-diyl)diimidazole (BIM) cations are linked to the [PMo12O40]3−anions by hydrogen bonds to form a three-dimensional supramolecular network. The stoichiometric ratio of POM anions and organic cations is 1:2 in (II), and the anion is located about a centre of inversion. The partly protonated BIM cations and solvent water molecules form hydrogen bonds with the [PMo12O40]3−anions, yielding a two-dimensional supramolecular layer. The different lattice architectures of (I) and (II) may be governed by the ratio between the POM anions and organic cations, which, in turn, is determined by the pH value.
A reviewer's guide to the grounded theory methodology in logistics and supply chain management research
Authors: Manuj Ila , Pohlen Terrance L.
Published: May 2013

Purpose

The purpose of this paper is to analyze previous grounded theory articles and, based on this analysis, to provide a framework to assist reviewers in evaluating grounded theory research and increasing the rigor and credibility of this methodology in logistics and supply chain journals.

Design/methodology/approach

An analysis of existing articles appearing in the leading logistics and supply chain journals combined with an extensive review of the grounded theory method literature were used to develop a comprehensive framework for evaluating grounded theory research.

Findings

The paper finds that no standard criteria for publication of grounded theory research exists in logistics and supply chain journals. Grounded theory is routinely confused with other qualitative methodologies. Overall, this situation leads to publications that do not adequately address or report on the process for developing a grounded theory.

Research limitations/implications

Reviewers can use this paper to establish the quality of grounded theory research. Reviewers who are unfamiliar with or skeptical of the grounded theory method can use the framework to evaluate the rigor and credibility of a grounded theory study rather than rejecting such research. The checklist can be used to provide thorough and constructive reviews to authors.

Originality/value

The paper presents a framework that provides a ready reference for reviewers to assess whether the authors have taken appropriate action in selecting a grounded theory methodology, collecting and analyzing data, developing a theory grounded in the data, and for evaluating their research. Existing research is compared with the framework to identify potential shortcomings in the review process. The application of the framework to the review of future articles provides an opportunity to increase the credibility and rigor of grounded theory research in logistics and supply chain management journals.
Outsourcing strategies of the security sector through acquisition procedures
Authors: Juntunen Jouni , Juntunen Mari , Autere Vesa
Published: May 2013

Purpose

The aim of this research is to reveal the security‐related outsourcing strategies of the public sector and the military and the relevant logistics outcomes by examining buying tactics.

Design/methodology/approach

A tentative model was devised from theoretical literature of how buyers use their negotiating power and relationships to achieve improved service quality and/or unit‐cost reductions. The model was tested using survey data from 149 respondents from the Finnish Defence Forces, and the public sector and industrial firms in Finland via structural equation modelling analysis.

Findings

Contrary to the approach of classic economics, where negotiating power correlates with direct costs, the findings indicate that negotiating power and relationships do not affect direct costs in the public sector and military contexts, but rather that negotiating power and relationships correlate with an improved service level, which consequently decreases the indirect logistics costs.

Research limitations/implications

By focusing on improvement in services in terms of their logistics service purchasing, the buyers reveal that their outsourcing strategy involves vertical outsourcing. The data are collected from one country, which may cause bias. Further studies would be required to test this research proposal in other countries.

Practical implications

To obtain cost reductions, buyers of logistics services could learn from the public sector and the military on how to use negotiating power and relationships to obtain better service instead of short‐term cost reductions, as better service correlates with reduced costs in the long run.

Originality/value

This study is important to practitioners as well as academics since there is little quantitative research available regarding strategic outsourcing modes and outcomes of adopting different modes.
Organizational Learning, Innovation and Internationalization: A Complex System Model
Authors: Chiva Ricardo , Ghauri Pervez , Alegre Joaquín
Published: May 2013

Research on organizational learning, innovation and internationalization has traditionally linked these concepts through linear causality, by considering any one of them as the cause of another, an approach that might be considered contradictory and static. This paper aims to clarify these relationships and proposes a dynamic theoretical model that has mutual causality at its core and is based on ideas originating in complexity theory. The final model results from case studies of two clothing sector firms. The authors consider that the three concepts constitute a complex system and can adapt and transcend, as any alteration can take the system to the edge of chaos. Adaptability is fostered by concentration, improvement and discussion. Transcendence is fostered by attention, dialogue and inquiry. The different paces of the two case study companies led their systems to two different models: the incremental complex adaptive system model and the global complex generative system model. The incremental model is characterized by adaptive learning, incremental innovation and low internationalization; and the global system is characterized by generative learning, radical innovation and global internationalization. The paper ends with an exploration of the academic and management implications of the model.
The Future of Liberal Multiculturalism
Authors: Maciel Robert
Published: May 2013

This article considers the role and relevance of liberal multiculturalism in contemporary political theory. Liberal multiculturalism is a form of multiculturalism that emphasizes group-specific rights for minority groups within a liberal framework. Minority protections are adopted to secure basic liberal rights. The article first reviews Will Kymlicka's formulation of liberal multiculturalism; Kymlicka's work receives focus here as he provides the standard liberal multiculturalist position. The article then moves to exploring responses to the position. First I explore liberal responses and second I look at a recognition-based approach. In the final section the article provides a brief response to both of these critiques. I find that the liberal criticisms are overstated and that recognition-based approaches can help identify a possible way for liberal multiculturalism to respond better to the claims of minorities.
Group incentives and financial performance: the moderating role of innovation
Authors: Park Rhokeun , Kruse Douglas
Published: May 2013

Using a nationally representative and multisource data set, this study examines the mediating role of organisational commitment in the relationship between group incentives and financial performance. The study also investigates the moderating role of innovation in these relationships. The results demonstrate that organisational commitment partially mediates the relationship between group incentives and financial performance. The findings of this study support the hypotheses that the relationships of group incentives with organisational commitment and financial performance are stronger in more innovative companies than in less innovative companies. The results provide implications on how group incentives affect financial performance and which organisations in particular should provide their employees with group incentive practices.
Localized versus centralized nurse‐delivered telephone services for people in follow up for cancer: Opinions of cancer clinicians
Authors: Harrison James D , Durcinoska Ivana , Butow Phyllis N , White Kathryn , Solomon Michael J , Young Jane M
Published: May 2013

Aim

Telephone‐delivered supportive care interventions hold potential as a sustainable, low‐resource option to improve patients' outcomes. Such interventions may be delivered centrally or locally. There is limited information about clinicians' preferences for these alternative models of service delivery. This study investigated the views of cancer clinicians who had experience of a centralized model.

Methods

Interviews were conducted with 16 surgeons and nurses across New South Wales, Australia, who had participated in a trial of a centralized telephone‐based supportive care intervention. Content analysis was conducted. Data were analyzed inductively and responses organized into categories and then higher order themes.

Results

All clinicians valued the role of telephone follow ups as they would allow patients to ask questions and receive reassurance. Clinicians believed these services could reduce hospital presentations and provide equity and standardized care, particularly to those outside metropolitan centers.

Although clinicians accepted a centralized model of delivery would be cheaper, most (n = 15) indicated a preference for local delivery. This preference was based on the perception that local nurses would have superior knowledge of the local context. Despite the improved feasibility of a telephone‐only service, clinicians felt some face‐to‐face contact with patients was essential. Key at‐risk groups to target were identified. Clinicians acknowledged there could be overlap with cancer nurses locally requiring local decisions about implementation.

Conclusion

There was clear endorsement of additional telephone support with a preference for a local model of service delivery. The limited acceptability of centralized telephone‐based supportive care interventions may restrict their uptake.
Making decisions in emergency surgery
Authors: Campbell Graeme , Watters David A. K.
Published: May 2013

Background

Good decision making is essential in surgery. In an emergency, the time for decision making is often short, and the information available is incomplete. The way experienced surgeons make decisions is often not well understood, and therefore is difficult to teach to trainees.

Methods

This paper examines how decisions are made, based on recent literature and the experience of the authors and their colleagues.

Discussion

An accurate assessment precedes decision making, and is directed towards the patient, the personnel and environment. Studies of other high‐stakes professions have highlighted the existence of two distinct mental processing symptoms. One is fast and frugal, relying on pattern recognition or following a rule or protocol. This is often performed at a subconscious level. The other is a conscious, reasoned, analytical process. This requires adequate, available mental capacity. In reality, expert and experienced decision makers can adopt either or both approaches, and match their approach to the situation. Decisions made need to be constantly reviewed, particularly where there is mismatch between what was anticipated and what is encountered.

Conclusion

An algorithm of decision making in emergency surgery has been developed that is based on assessment, the decision required and the outcome of the decision. The decision must also consider the urgency of the situation and the likely outcome if the plan made fails.