bluuebunny/crossref_metadata_2025 huggingface dataset:
A Critique of Everyday International Relations: The Case of Cultural Pluralism in Singapore and Vancouver
Authors: Montsion Jean Michel
Published: October 2012

In the context of Singapore and Vancouver strategically repositioning themselves as gateway cities between Asian and North American markets, I focus on Singapore's multiracialism and Vancouver's multiculturalism to frame how people encounter ‘the international’ along racialized and cultural lines in their daily lives. Building on an emerging appetite for everyday life theory in international relations, I look at Henri Lefebvre's work on alienation to explore how cultural pluralism policies structure everyday life through what I call ‘everyday borders of the international’. This will reveal how the interrelationships between daily life, political platforms like these policies, and broader political and economic structures shape different everyday encounters of the international.
City Becoming World: Nancy, Lefebvre, and the Global—Urban Imagination
Authors: Madden David J
Published: October 2012

It is part of the self-conception of the contemporary era that the world is becoming increasingly global and urban. This paper explores the global—urban imagination in works by Jean-Luc Nancy and Henri Lefebvre. Both Nancy and Lefebvre understand globalization as a fundamentally violent and unequal process that unfolds through the uneven expansion of a particular sort of urban space. They both strive to articulate a critical stance towards this process by opposing globalization to the idea of mondialisation or world forming. While their respective approaches differ in important ways, they both provide indispensible critical tools for conceptualizing the urban planet and its political possibilities. Their positions are briefly contrasted to the conservative imagery of the urban planet as techno utopia that was produced at Expo 2010 in Shanghai, China.
Contemporary Western War and the Idea of Humanity
Authors: Zehfuss Maja
Published: October 2012

In the post-cold-war period Western military force has been deployed in the name of protecting humanity despite the obvious paradox of trying to achieve such protection through means that undermine this very aim. This has generated much debate about the merits of (humanitarian) intervention. In this paper I aim not to take a position in this debate but, rather, to examine its terms. I seek to draw out what is assumed, implied, and obscured by this debate. I explore the larger issue of how the framing of the debate in terms of protecting humanity works to exclude the apparent beneficiaries from the realm of politics and generates the demand for an urgent, violent resolution to what is produced as an ethical dilemma. I start by exploring the ways in which post-cold-war Western war has been represented as war for humanity. I then draw out how critical scholarship has brought into view the fact that the apparently universal category of humanity is marked by hierarchy, and thus undermines itself. I end by arguing that the idea of humanity provides an ethical framing which both relies on and responds to the problematic association of politics with intelligibility, leaving us with a predicament that cannot be resolved.
A taxonomic review of Triodia bunicola and T. scariosa (Poaceae: Chloridoideae), based on morphological and molecular data
Authors: Hurry Charlotte R. , Walsh Neville G. , Murphy Daniel J.
Published: October 2012

Triodia bunicola (S.W.L.Jacobs) Lazarides and T. scariosa N.T.Burb. (Poaceae: Chloridoideae) were analysed to test their status as different species. Thirty-one morphological characters were scored for multivariate analysis for both species. Nuclear (ITS) and chloroplast (rpl32–trnL) DNA data were analysed cladistically for 18 species of Triodia, with a focus on species from southern Australia to look at broader geographic patterns. Cladistic analysis and morphological ordination analysis indicated that T. bunicola should be regarded as a synonym of T. scariosa. DNA evidence also suggests that there is geographic partitioning for southern Australian species of Triodia.
Phylogenetic analysis of Australian species of Veronica (V. section Labiatoides; Plantaginaceae)
Authors: Albach Dirk C. , Briggs Barbara G.
Published: October 2012

Phylogenetic analyses of DNA-sequence data have revealed that the southern hemisphere species of Veronica are derived from within the northern hemisphere Veronica clade. Previous analyses focussed on the species in New Zealand and included at maximum 7 of 23 species of section Labiatoides from Australia. In the present study, we used nuclear ribosomal-ITS and plastid ndhF–rpl32-spacer sequence data of all species currently recognised in Australia to analyse phylogenetic patterns. Most importantly, herbaceous species from coastal calcareous sands or limestone habitats do not form a clade with those from shady, moist forest habitats, as formerly believed, but seem to be independently derived from woody species. Incongruence between results from nuclear- and plastid-DNA markers suggest hybridisation to be an important factor in the evolution of the group. Our sample of V. parnkalliana included alleles similar to V. decorosa and V. novae-hollandiae at both loci, which suggests a hybrid origin.
Fundamental limits on persistent activity in networks of noisy neurons
Authors: Burak Yoram , Fiete Ila R.
Published: October 2012

Neural noise limits the fidelity of representations in the brain. This limitation has been extensively analyzed for sensory coding. However, in short-term memory and integrator networks, where noise accumulates and can play an even more prominent role, much less is known about how neural noise interacts with neural and network parameters to determine the accuracy of the computation. Here we analytically derive how the stored memory in continuous attractor networks of probabilistically spiking neurons will degrade over time through diffusion. By combining statistical and dynamical approaches, we establish a fundamental limit on the network’s ability to maintain a persistent state: The noise-induced drift of the memory state over time within the network is strictly lower-bounded by the accuracy of estimation of the network’s instantaneous memory state by an ideal external observer. This result takes the form of an information-diffusion inequality. We derive some unexpected consequences: Despite the persistence time of short-term memory networks, it does not pay to accumulate spikes for longer than the cellular time-constant to read out their contents. For certain neural transfer functions, the conditions for optimal sensory coding coincide with those for optimal storage, implying that short-term memory may be co-localized with sensory representation.
Functional characterization of pulmonary neuroendocrine cells in lung development, injury, and tumorigenesis
Authors: Song Hai , Yao Erica , Lin Chuwen , Gacayan Rhodora , Chen Miao-Hsueh , Chuang Pao-Tien
Published: October 2012

Pulmonary neuroendocrine cells (PNECs) are proposed to be the first specialized cell type to appear in the lung, but their ontogeny remains obscure. Although studies of PNECs have suggested their involvement in a number of lung functions, neither their in vivo significance nor the molecular mechanisms underlying them have been elucidated. Importantly, PNECs have long been speculated to constitute the cells of origin of human small-cell lung cancer (SCLC) and recent mouse models support this hypothesis. However, a genetic system that permits tracing the early events of PNEC transformation has not been available. To address these key issues, we developed a genetic tool in mice by introducing a fusion protein of Cre recombinase and estrogen receptor (CreER) into the
calcitonin gene-related peptide
(
CGRP
) locus that encodes a major peptide in PNECs. The

CGRP
CreER

mouse line has enabled us to manipulate gene activity in PNECs. Lineage tracing using this tool revealed the plasticity of PNECs. PNECs can be colabeled with alveolar cells during lung development, and following lung injury, PNECs can contribute to Clara cells and ciliated cells. Contrary to the current model, we observed that elimination of PNECs has no apparent consequence on Clara cell recovery. We also created mouse models of SCLC in which CGRP
CreER
was used to ablate multiple tumor suppressors in PNECs that were simultaneously labeled for following their fate. Our findings suggest that SCLC can originate from differentiated PNECs. Together, these studies provide unique insight into PNEC lineage and function and establish the foundation of investigating how PNECs contribute to lung homeostasis, injury/repair, and tumorigenesis.
Investigation of the sodium-binding sites in the sodium-coupled betaine transporter BetP
Authors: Khafizov Kamil , Perez Camilo , Koshy Caroline , Quick Matthias , Fendler Klaus , Ziegler Christine , Forrest Lucy R.
Published: October 2012

Sodium-coupled substrate transport plays a central role in many biological processes. However, despite knowledge of the structures of several sodium-coupled transporters, the location of the sodium-binding site(s) often remains unclear. Several of these structures have the five transmembrane-helix inverted-topology repeat, LeuT-like (FIRL) fold, whose pseudosymmetry has been proposed to facilitate the alternating-access mechanism required for transport. Here, we provide biophysical, biochemical, and computational evidence for the location of the two cation-binding sites in the sodium-coupled betaine symporter BetP. A recent X-ray structure of BetP in a sodium-bound closed state revealed that one of these sites, equivalent to the Na2 site in related transporters, is located between transmembrane helices 1 and 8 of the FIRL-fold; here, we confirm the location of this site by other means. Based on the pseudosymmetry of this fold, we hypothesized that the second site is located between the equivalent helices 6 and 3. Molecular dynamics simulations of the closed-state structure suggest this second sodium site involves two threonine sidechains and a backbone carbonyl from helix 3, a phenylalanine from helix 6, and a water molecule. Mutating the residues proposed to form the two binding sites increased the apparent
K
m
and
K
d
for sodium, as measured by betaine uptake, tryptophan fluorescence, and
22
Na
+
binding, and also diminished the transient currents measured in proteoliposomes using solid supported membrane-based electrophysiology. Taken together, these results provide strong evidence for the identity of the residues forming the sodium-binding sites in BetP.
Normal glucose uptake in the brain and heart requires an endothelial cell-specific HIF-1α–dependent function
Authors: Huang Yan , Lei Li , Liu DingGang , Jovin Ion , Russell Raymond , Johnson Randall S. , Di Lorenzo Annarita , Giordano Frank J.
Published: October 2012

Although intimately positioned between metabolic substrates in the bloodstream and the tissue parenchymal cells that require these substrates, a major role of the vascular endothelium in the regulation of tissue metabolism has not been widely appreciated. We hypothesized that via control of transendothelial glucose transport and contributing paracrine mechanisms the endothelium plays a major role in regulating organ and tissue glucose metabolism. We further hypothesized that the hypoxia-inducible factor -1α (HIF-1α) plays an important role in coordinating these endothelial functions. To test these hypotheses, we generated mice with endothelial cell-specific deletion of HIF-1α. Loss of HIF in the endothelium resulted in significantly increased fasting blood glucose levels, a blunted insulin response with delayed glucose clearance from the blood after i.v. loading, and significantly decreased glucose uptake into the brain and heart. Endothelial HIF-1α knockout mice also exhibited a reduced cerebrospinal fluid/blood glucose ratio, a finding consistent with reduced transendothelial glucose transport and a diagnostic criterion for the Glut1 deficiency genetic syndrome. Endothelial cells from these mice demonstrated decreased Glut1 levels and reduced glucose uptake that was reversed by forced expression of Glut1. These data strongly support an important role of the vascular endothelium in determining whole-organ glucose metabolism and indicate that HIF-1α is a critical mediator of this function.
A CERTAIN SENSE OF EUROPE?
Authors: Sjursen Helene
Published: October 2012

This article seeks to shed light on the identity problem of the European Union by investigating EU justifications for past enlargements. What kind of understanding of the EU do enlargement decisions indicate? Given that the EU is based on more than mere pragmatic problem-solving, the question is whether decisions to enlarge reflect a value-based or a rights-based polity. Although a certain sense of distinctiveness, certain elements of European particularities, are in evidence, the pull of universal principles has proven stronger thus far. Paradoxically, this presents the European political project with an important dilemma.
POVERTY, FAMILIES AND THE INVESTMENT STATE
Authors: Nygård Mikael , Krüger Nicole
Published: October 2012

Finland and Germany are traditionally seen as members of different welfare regimes with rather different approaches to family policies. During the last decade or so, poverty concerns have received an increasingly prominent position within family policy in both countries. The objects for these concerns have been different constellations of ‘poor’ families, and the policies pursued to counteract poverty have ranged from targeted measures to investments in childcare services. It has been suggested that the motivation behind recent social policy developments in Europe is a stronger accentuation of so-called social investment ideas calling for more activation, targeting and higher future returns through investments in human capital. This article explores the impact of social investment ideas on policy discourses about family-related poverty in Finland and Germany since the late-1980s by analysing poverty constructions and anti-poverty policy recommendations in government and party programs. The findings suggest a stronger focus on social investment ideas in the German discourse in terms of higher accentuation of ideas relating to equal opportunities, activation and prevention of poverty in a life-cycle perspective, whereas targeting have become a main topic in Finnish elite discourses. Furthermore, while being conditioned by institutional factors and historical policy legacies, social investment ideas have largely been adopted in an incremental way parallel to path-dependent national policy legacies.
The relationship of supervisor and trainee gender match and gender attitude match to supervisory style and the supervisory working alliance
Authors: Rarick Susan L. , Ladany Nicholas
Published: October 2012

Background: Gender‐related events have the potential to impact the supervisory relationship. Gender events might be related to the match between supervisors and supervisees on variables such as gender or gender attitudes. Method: In this study, we sought to determine whether gender match and gender attitude match were related to supervisory style and the supervisory working alliance in 94 supervisory dyads using four instruments: the Gender Attitude Inventory; Operationalisation of Gender Match; Supervisory Styles Inventory; and the Working Alliance Inventory/Supervision. Results: Progressive dyads (in which supervisors have more liberal attitudes about societal issues and culturally defined roles for women than their supervisees) were perceived by supervisors as more task‐oriented than parallel‐high dyads (in which supervisors and supervisees both had liberal attitudes). Implications for counselling supervision are discussed.
Bayesian correlated clustering to integrate multiple datasets
Authors: Kirk Paul , Griffin Jim E. , Savage Richard S. , Ghahramani Zoubin , Wild David L.
Published: October 2012

Motivation: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct—but often complementary—information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets.

Results: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI’s performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation–chip and protein–protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques—as well as to non-integrative approaches—demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.

Availability: A Matlab implementation of MDI is available from http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/.

Contact:  D.L.Wild@warwick.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
KASpOD—a web service for highly specific and explorative oligonucleotide design
Authors: Parisot Nicolas , Denonfoux Jérémie , Dugat-Bony Eric , Peyret Pierre , Peyretaillade Eric
Published: October 2012

Summary: KASpOD is a web service dedicated to the design of signature sequences using a k-mer–based algorithm. Such highly specific and explorative oligonucleotides are then suitable for various goals, including Phylogenetic Oligonucleotide Arrays.

Availability:  http://g2im.u-clermont1.fr/kaspod.

Contact:  eric.peyretaillade@udamail.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Predicting protein residue–residue contacts using deep networks and boosting
Authors: Eickholt Jesse , Cheng Jianlin
Published: October 2012

Motivation: Protein residue–residue contacts continue to play a larger and larger role in protein tertiary structure modeling and evaluation. Yet, while the importance of contact information increases, the performance of sequence-based contact predictors has improved slowly. New approaches and methods are needed to spur further development and progress in the field.

Results: Here we present DNCON, a new sequence-based residue–residue contact predictor using deep networks and boosting techniques. Making use of graphical processing units and CUDA parallel computing technology, we are able to train large boosted ensembles of residue–residue contact predictors achieving state-of-the-art performance.

Availability: The web server of the prediction method (DNCON) is available at http://iris.rnet.missouri.edu/dncon/.

Contact:  chengji@missouri.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Real Time Metagenomics: Using k-mers to annotate metagenomes
Authors: Edwards Robert A. , Olson Robert , Disz Terry , Pusch Gordon D. , Vonstein Veronika , Stevens Rick , Overbeek Ross
Published: October 2012

Summary: Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.

Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at http://edwards.sdsu.edu/rtmg. In addition, code to access the annotation servers is available for download from http://www.theseed.org/. FIGfams and k-mers are available for download from ftp://ftp.theseed.org/FIGfams/.

Contact:  redwards@mail.sdsu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Chronic stress elevates telomerase activity in rats
Authors: Beery Annaliese K. , Lin Jue , Biddle Joshua S. , Francis Darlene D. , Blackburn Elizabeth H. , Epel Elissa S.
Published: October 2012

The enzyme telomerase lengthens telomeres—protective structures containing repetitive DNA sequences at chromosome ends. Telomere shortening is associated with diseases of ageing in mammals. Chronic stress has been related to shorter immune-cell telomeres, but telomerase activity under stress may be low, permitting telomere loss, or high, partially attenuating it. We developed an experimental model to examine the impacts of extended unpredictable stress on telomerase activity in male rats. Telomerase activity was 54 per cent higher in stressed rats than in controls, and associated with stress-related physiological and behavioural outcomes. This significant increase suggests a potential mechanism for resilience to stress-related replicative senescence.
Attending to insects: Francis Willughby and John Ray
Authors: Ogilvie Brian W.
Published: October 2012

Francis Willughby and John Ray were at the forefront of the natural history of insects in the second half of the seventeenth century. Willughby in particular had a deep interest in insects' metamorphosis, behaviour and diversity, an interest that he passed on to his friend and mentor Ray. By examining Willughby's contributions to John Wilkins's
Essay towards a Real Character
(1668) and Ray's
Methodus insectorum
(1705) and
Historia insectorum
(1710), which contained substantial material from Willughby's manuscript history of insects, one may reconstruct how the two naturalists studied insects, their innovative use of metamorphosis in insect classification, and the sheer diversity of insect forms that they described on the basis of their own collections and those of London and Oxford virtuosi. Imperfect as it was,
Historia insectorum
was recognized by contemporaries as a significant contribution to the emerging field of entomology.
Effects of exposure to pile-driving sounds on the lake sturgeon, Nile tilapia and hogchoker
Authors: Halvorsen Michele B. , Casper Brandon M. , Matthews Frazer , Carlson Thomas J. , Popper Arthur N.
Published: October 2012

Pile-driving and other impulsive sound sources have the potential to injure or kill fishes. One mechanism that produces injuries is the rapid motion of the walls of the swim bladder as it repeatedly contacts nearby tissues. To further understand the involvement of the swim bladder in tissue damage, a specially designed wave tube was used to expose three species to pile-driving sounds. Species included lake sturgeon (
Acipenser fulvescens
)—with an open (physostomous) swim bladder, Nile tilapia (
Oreochromis niloticus
)—with a closed (physoclistous) swim bladder and the hogchoker (
Trinectes maculatus
)—a flatfish without a swim bladder. There were no visible injuries in any of the exposed hogchokers, whereas a variety of injuries were observed in the lake sturgeon and Nile tilapia. At the loudest cumulative and single-strike sound exposure levels (SEL
cum
and SEL
ss
respectively), the Nile tilapia had the highest total injuries and the most severe injuries per fish. As exposure levels decreased, the number and severity of injuries were more similar between the two species. These results suggest that the presence and type of swim bladder correlated with injury at higher sound levels, while the extent of injury at lower sound levels was similar for both kinds of swim bladders.
The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils
Authors: Allentoft Morten E. , Collins Matthew , Harker David , Haile James , Oskam Charlotte L. , Hale Marie L. , Campos Paula F. , Samaniego Jose A. , Gilbert M. Thomas P. , Willerslev Eske , Zhang Guojie , Scofield R. Paul , Holdaway Richard N. , Bunce Michael
Published: October 2012

Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (
k
) of 5.50 × 10
–6
per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of
in vitro
DNA depurination at pH 5. Although best described by an exponential model (
R
2
= 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.
Sperm-related phenotypes implicated in both maintenance and breakdown of a natural species barrier in the house mouse
Authors: Albrechtová Jana , Albrecht Tomáš , Baird Stuart J. E. , Macholán Miloš , Rudolfsen Geir , Munclinger Pavel , Tucker Priscilla K. , Piálek Jaroslav
Published: October 2012

The house mouse hybrid zone (HMHZ) is a species barrier thought to be maintained by a balance between dispersal and natural selection against hybrids. While the HMHZ is characterized by frequency discontinuities for some sex chromosome markers, there is an unexpected large-scale regional introgression of a Y chromosome across the barrier, in defiance of Haldane's rule. Recent work suggests that a major force maintaining the species barrier acts through sperm traits. Here, we test whether the Y chromosome penetration of the species barrier acts through sperm traits by assessing sperm characteristics of wild-caught males directly in a field laboratory set up in a Y introgression region of the HMHZ, later calculating the hybrid index of each male using 1401 diagnostic single nucleotide polymorphisms (SNPs). We found that both sperm count (SC) and sperm velocity were significantly reduced across the natural spectrum of hybrids. However, SC was more than rescued in the presence of the invading Y. Our results imply an asymmetric advantage for Y chromosome introgression consistent with the observed large-scale introgression. We suggest that selection on sperm-related traits probably explains a large component of patterns observed in the natural hybrid zone, including the Y chromosome penetration.
Social and extra-pair mating in relation to major histocompatibility complex variation in common yellowthroats
Authors: Bollmer Jennifer L. , Dunn Peter O. , Freeman-Gallant Corey R. , Whittingham Linda A.
Published: October 2012

Females are thought to gain better-quality genes for their offspring by mating with particular males. Genes of the major histocompatibility complex (MHC) play a critical role in adaptive immunity, and several studies have examined female mate choice in relation to MHC variation. In common yellowthroats, females prefer males that have larger black facial masks, an ornament associated with MHC variation, immune function and condition. Here we also tested whether mating patterns are directly correlated with MHC diversity or similarity. Using pyrosequencing, we found that the presence of extra-pair young in the brood was not related to male MHC diversity or similarity between the female and her within-pair mate. Furthermore, extra-pair sires did not differ in overall diversity from males they cuckolded, or in their similarity to the female. MHC diversity is extremely high in this species, and it may limit the ability of females to assess MHC variation in males. Thus, mating may be based on ornaments, such as mask size, which are better indicators of overall male health and genetic quality.
Cambrian bivalved arthropod reveals origin of arthrodization
Authors: Legg David A. , Sutton Mark D. , Edgecombe Gregory D. , Caron Jean-Bernard
Published: October 2012

Extant arthropods are diverse and ubiquitous, forming a major constituent of most modern ecosystems. Evidence from early Palaeozoic Konservat Lagerstätten indicates that this has been the case since the Cambrian. Despite this, the details of arthropod origins remain obscure, although most hypotheses regard the first arthropods as benthic predators or scavengers such as the fuxianhuiids or megacheirans (‘great-appendage’ arthropods). Here, we describe a new arthropod from the Tulip Beds locality of the Burgess Shale Formation (Cambrian, series 3, stage 5) that possesses a weakly sclerotized thorax with filamentous appendages, encased in a bivalved carapace, and a strongly sclerotized, elongate abdomen and telson. A cladistic analysis resolved this taxon as the basal-most member of a paraphyletic grade of nekto-benthic forms with bivalved carapaces. This grade occurs at the base of Arthropoda (panarthropods with arthropodized trunk limbs) and suggests that arthrodization (sclerotization and jointing of the exoskeleton) evolved to facilitate swimming.Predatory and fully benthic habits evolved later in the euarthropod stem-lineage and are plesiomorphically retained in pycnogonids (sea spiders) and euchelicerates (horseshoe crabs and arachnids).
Strategies for Service Quality
Authors: Sandelands Eric
Published: October 2012

For many, quality circles have been a struggle, total quality management has been something to “get around to one day” and continuous improvement has just been another expression meaning total quality management, which, of course is something that we will “get around to one day”. Worse, the acronyms used ‐ QC, TQM, CI ‐ have joined such exotic practices as JIT (Just‐in‐Time inventory), CAD‐CAM (computer‐aided development and manufacturing) and more recently BPR (business process re‐engineering) in an alphabet soup of consultant‐led packages, available to the discerning manager ‐ at a price.
Selected international research into library management
Authors: Cornish Graham P.
Published: October 2012

The term “library management” covers many different aspects of the way that a library is operated and conjures up different concepts in the minds of different people, depending on their own interests, agendas and requirements. Research into the subject is even more difficult to define because the application of research in one field can be vital to the development of another. Some researchers would not consider their research central to library matters at all, whereas the practising librarian might well see it as casting new light on a
difficult area of understanding or development.
Anbar Abstracts Issue
Authors: Sandelands Eric
Published: October 2012

This special “Anbar Abstracts” issue of the Journal of Management in Medicine is split into six sections covering abstracts under the following headings: General Management; Personnel and Training; Quality in Health Care; Health Care Marketing; Financial Management; Information Technology.
A special issue of abstracted articles on the management of change
Authors: Sandelands Eric
Published: October 2012

This special “Anbar Abstracts” issue of the Health Manpower Management is split into five sections covering abstracts under the following headings: Management tools; Participation/roles; Types of change; Management Implementation.
A universal measure of chaotropicity and kosmotropicity
Authors: Cray Jonathan A. , Russell John T. , Timson David J. , Singhal Rekha S. , Hallsworth John E.
Published: October 2012

Diverse parameters, including chaotropicity, can limit the function of cellular systems and thereby determine the extent of Earth's biosphere. Whereas parameters such as temperature, hydrophobicity, pressure, pH, Hofmeister effects, and water activity can be quantified via standard scales of measurement, the chao‐/kosmotropic activities of environmentally ubiquitous substances have no widely accepted, universal scale. We developed an assay to determine and quantify chao‐/kosmotropicity for 97 chemically diverse substances that can be universally applied to all solutes. This scale is numerically continuous for the solutes assayed (from +361 kJ kg−1 mol−1 for chaotropes to −659 kJ kg−1 mol−1 for kosmotropes) but there are key points that delineate (i) chaotropic from kosmotropic substances (i.e. chaotropes ≥ +4; kosmotropes ≤ −4 kJ kg−1 mol−1); and (ii) chaotropic solutes that are readily water‐soluble (log P < 1.9) from hydrophobic substances that exert their chaotropic activity, by proxy, from within the hydrophobic domains of macromolecular systems (log P > 1.9). Examples of chao‐/kosmotropicity values are, for chaotropes: phenol +143, CaCl2 +92.2, MgCl2 +54.0, butanol +37.4, guanidine hydrochloride +31.9, urea +16.6, glycerol [> 6.5 M] +6.34, ethanol +5.93, fructose +4.56; for kosmotropes: proline −5.76, sucrose −6.92, dimethylsulphoxide (DMSO) −9.72, mannitol −6.69, trehalose −10.6, NaCl −11.0, glycine −14.2, ammonium sulfate −66.9, polyethylene glycol‐ (PEG‐)1000 −126; and for relatively neutral solutes: methanol, +3.12, ethylene glycol +1.66, glucose +1.19, glycerol [< 5 M] +1.06, maltose −1.43 (kJ kg−1 mol−1). The data obtained correlate with solute interactions with, and structure–function changes in, enzymes and membranes. We discuss the implications for diverse fields including microbial ecology, biotechnology and astrobiology.
Carbohydrate utilization by enterohaemorrhagic Escherichia coliO157:H7 in bovine intestinal content
Authors: Bertin Yolande , Chaucheyras‐Durand Frédérique , Robbe‐Masselot Catherine , Durand Alexandra , de la Foye Anne , Harel Josée , Cohen Paul S. , Conway Tyrell , Forano Evelyne , Martin Christine
Published: October 2012

The bovine gastrointestinal (GI) tract is the main reservoir for enterohaemorrhagic Escherichia coli (EHEC) responsible for food‐borne infections. Characterization of nutrients preferentially used by EHEC in the bovine intestine would help to develop ecological strategies to reduce EHEC carriage. However, the carbon sources that support the growth of EHEC in the bovine intestine are poorly documented. In this study, a very low concentration of glucose, the most abundant monomer included in the cattle dietary polysaccharides, was detected in bovine small intestine contents (BSIC) collected from healthy cows at the slaughterhouse. Six carbohydrates reported to be included in the mucus layer covering the enterocytes [galactose, N‐acetyl‐glucosamine (GlcNAc), N‐acetyl‐ galactosamine (GalNAc), fucose, mannose and N‐acetyl neuraminic acid (Neu5Ac)] have been quantified for the first time in BSIC and accounted for a total concentration of 4.2 mM carbohydrates. The genes required for enzymatic degradation of the six mucus‐derived carbohydrates are highly expressed during the exponential growth of the EHEC strain O157:H7 EDL933 in BSIC and are more strongly induced in EHEC than in bovine commensal E. coli. In addition, EDL933 consumed the free monosaccharides present in the BSIC more rapidly than the resident microbiota and commensal E. coli, indicating a competitive ability of EHEC to catabolize mucus‐derived carbohydrates in the bovine gut. Mutations of EDL933 genes required for the catabolism of each of these sugars have been constructed, and growth competitions of the mutants with the wild‐type strain clearly demonstrated that mannose, GlcNAc, Neu5Ac and galactose catabolism confers a high competitive growth advantage to EHEC in BSIC and probably represents an ecological niche for EHEC strains in the bovine small intestine. The utilization of these mucus‐derived monosaccharides by EDL933 is apparently required for rapid growth of EHEC in BSIC, and for maintaining a competitive growth rate as compared with that of commensal E. coli. The results suggest a strategy for O157:H7 E. coli survival in the bovine intestine, whereby EHEC rapidly consumes mucus‐derived carbohydrates that are poorly consumed by bacteria belonging to the resident intestinal microbiota, including commensal E. coli.
Volunteering: A Community Response to the Rena Oil Spill in New Zealand
Authors: Sargisson Rebecca J. , Hunt Sonya , Hanlen Patricia , Smith Kelly , Hamerton Heather
Published: October 2012

We explore the experiences of people who volunteer to help remediate the effects of non‐natural environmental disasters. Following the grounding of the Rena, volunteers were engaged to clean up the resulting oil spill on the beaches of Tauranga, New Zealand. Volunteers were later invited to respond to an online questionnaire about their experiences. More women than men responded, and respondents tended to be older, and engaged in the paid workforce or retired. Greater membership in community organizations was associated with a greater participation in clean‐up events. Respondents were positive about the experience, and were more positive when they had actually participated in a clean‐up event, with positivity remaining high even after multiple volunteer occasions. Recommendations are made for increasing volunteer participation.
Residential care: an effective response to out‐of‐home children and young people?
Authors: Carrà Elisabetta
Published: October 2012

The ever‐growing number of out‐of‐home children in Italy over the last decade has urged an assessment of the available care services. Although foster care is spreading rapidly, many young people are still housed in residential facilities. Reflection on residential care quality has intensified at both a national and an international level. This paper presents the results of a study on residential care facilities for children and young people in the region of Northern Italy (Lombardy). Four dimensions of ‘quality’ are considered: efficiency, effectiveness, participation in planning and intervention, and empowerment of children and their family relationships. The combined effects of these dimensions are defined as ‘relational quality’. The results show that residential care facilities are generally good, while Social Services resources often appear inadequate for interventions aimed at birth families (efficiency). The well‐being of children in residential care facilities is high, even if they tend to move from one facility to another, rarely returning to their birth family (effectiveness). The involvement of children and their families at different stages of the care path is limited (participative approach). Finally, the most critical element is the failure to properly involve birth families (empowerment).
Epidermotropic secondary cutaneous involvement by relapsed angioimmunoblastic T‐cell lymphoma mimicking mycosis fungoides: a case report
Authors: Ponciano Ana , de Muret Anne , Machet Laurent , Gyan Emmanuel , Monegier du Sorbier Christophe , Molinier‐Frenkel Valérie , Gaulard Philippe , Ortonne Nicolas
Published: October 2012

Angioimmunoblastic T‐cell lymphoma (AITL) is frequently associated with skin lesions, but epidermotropic cutaneous involvement has never been described. A 37‐year‐old man presented with erythematous and pruriginous plaques, clinically suggestive of mycosis fungoides, distributed all over the body, 3 weeks after the last line of a polychemotherapy, given for an AITL diagnosed 1 year earlier on a lymph node biopsy. Skin biopsy showed an epidermotropic CD4+ T‐cell lymphoma, so that a diagnosis of mycosis fungoides was first proposed. Further investigations showed that atypical lymphocytes strongly expressed CD10 and markers of follicular helper T cells (TFH) including PD1, BCL‐6 and CXCL13. The diagnosis of an unusual epidermotropic cutaneous localization of the AITL was finally made, supported by the presence of the same T‐cell clone in the initial lymph node biopsy and the skin. We therefore recommend performing markers of TFH cells in patients with unusual epidermotropic cutaneous T‐cell lymphomas, particularly if they have any clinical features suggestive of AITL.
The histopathologic spectrum of decorative tattoo complications
Authors: Shinohara Michi M. , Nguyen Jennifer , Gardner Jennifer , Rosenbach Misha , Elenitsas Rosalie
Published: October 2012

Tattooing for ornamental purposes is an ancient practice that remains popular in modern times. Tattoos are encountered by the dermatopathologist either as incidental findings on skin biopsies or because of complications specific to the tattoo. A range of neoplasms and inflammatory conditions are seen in association with tattoos, many of which may be attributed to hypersensitivity to tattoo inks. The composition of tattoo inks is highly variable, and inks can contain numerous potentially allergenic or carcinogenic compounds. Infections with bacterial, viral and fungal species can occur after tattooing, sometimes after substantial delay. Atypical mycobacterial infections in particular are increasingly reported; special stains for mycobacteria should be performed and cultures recommended particularly when dense, mixed or granulomatous infiltrates are present.
Riparian ecosystems in human cancers
Authors: Alfarouk Khalid O. , Ibrahim Muntaser E. , Gatenby Robert A. , Brown Joel S.
Published: October 2012

Intratumoral evolution produces extensive genetic heterogeneity in clinical cancers. This is generally attributed to an increased mutation rate that continually produces new genetically defined clonal lineages. Equally important are the interactions between the heritable traits of cancer cells and their microenvironment that produces natural selection favoring some clonal ‘species’ over others. That is, while mutations produce the heritable variation, environmental selection and cellular adaptation govern the strategies (and genotypes) that can proliferate within the tumor ecosystem. Here we ask: What are the dominant evolutionary forces in the cancer ecosystem? We propose that the tumor vascular network is a common and primary cause of intratumoral heterogeneity. Specifically, variations in blood flow result in variability in substrate, such as oxygen, and metabolites, such as acid, that serve as critical, but predictable, environmental selection forces. We examine the evolutionary and ecological consequences of variable blood flow by drawing an analogy to riparian habitats within desert landscapes. We propose that the phenotypic properties of cancer cells will exhibit predictable spatial variation within tumor phenotypes as a result of proximity to blood flow. Just as rivers in the desert create an abrupt shift from the lush, mesic riparian vegetation along the banks to sparser, xeric and dry‐adapted plant species in the adjacent drylands, we expect blood vessels within tumors to promote similarly distinct communities of cancer cells that change abruptly with distance from the blood vessel. We propose vascular density and blood flow within a tumor as a primary evolutionary force governing variations in the phenotypic properties of cancer cells thus providing a unifying ecological framework for understanding intratumoral heterogeneity.
Structural and dynamic determinants of type I interferon receptor assembly and their functional interpretation
Authors: Piehler Jacob , Thomas Christoph , Garcia K.Christopher , Schreiber Gideon
Published: October 2012

Type I interferons (IFNs) form a network of homologous cytokines that bind to a shared, heterodimeric cell surface receptor and engage signaling pathways that activate innate and adaptive immune responses. The ability of IFNs to mediate differential responses through the same cell surface receptor has been subject of a controversial debate and has important medical implications. During the past decade, a comprehensive insight into the structure, energetics, and dynamics of IFN recognition by its two‐receptor subunits, as well as detailed correlations with their functional properties on the level of signal activation, gene expression, and biological responses were obtained. All type I IFNs bind the two‐receptor subunits at the same sites and form structurally very similar ternary complexes. Differential IFN activities were found to be determined by different lifetimes and ligand affinities toward the receptor subunits, which dictate assembly and dynamics of the signaling complex in the plasma membrane. We present a simple model, which explains differential IFN activities based on rapid endocytosis of signaling complexes and negative feedback mechanisms interfering with ternary complex assembly. More insight into signaling pathways as well as endosomal signaling and trafficking will be required for a comprehensive understanding, which will eventually lead to therapeutic applications of IFNs with increased efficacy.
Structural basis for self‐recognition by autoimmune T‐cell receptors
Authors: Yin Yiyuan , Li Yili , Mariuzza Roy A.
Published: October 2012

T‐cell receptors (TCRs) recognize peptides presented by major histocompatibility complex molecules (pMHC) to discriminate between foreign and self‐antigens. Whereas T‐cell recognition of foreign peptides is essential for protection against microbial pathogens, recognition of self‐peptides by T cells that have escaped negative selection in the thymus can lead to autoimmune disease. Structural studies of autoimmune TCR–pMHC complexes have provided insights into the mechanisms underlying self‐recognition and escape from thymic deletion. Two broad categories of self‐reactive TCRs can be clearly distinguished: (i) TCRs with altered binding topologies to self‐pMHC and (ii) TCRs that bind self‐pMHC in the canonical diagonal orientation, but where there are structural defects or suboptimal anchors in the self‐ligand. For both categories, however, the overall stability of the autoimmune TCR–pMHC complex is markedly reduced compared to anti‐microbial complexes, allowing the autoreactive T cells to evade negative selection, yet retain the ability to be activated by self‐antigens in target organs. Additionally, the structures provide insights into TCR cross‐reactivity, which can contribute to autoimmunity by increasing the likelihood of self‐pMHC recognition. Efforts are now underway to understand the impact of structural alterations in autoimmune TCR–pMHC complexes on higher order assemblies involved in TCR signaling, as well as on immunological synapse formation.