bluuebunny/crossref_metadata_2025 huggingface dataset:
Goals and Personal Resources that Contribute to the Development and Agency Attachment of Older Adult Volunteers
Authors: Gillespie Alayna A. , Gottlieb Benjamin H. , Maitland Scott B.
Published: February 2011

Nous avons examiné la contribution bénévolat (N = 100) pour développer le rôle bénévolat et l’attachement aux agences des personnes âgées. Informé par un cadre intégrant la réglementation du développement et la théorie de la selectivité socio-affective, nous avons testé une double hypothèse pour la prémisse que le développement de plus grand rôle et l’attachement à l’agence serait vécue par (1) les personnes âgées qui avaient des objectifs multiples pour le bénévolat, et (2) les personnes âgées qui ont poursuivi ces objectifs en faisant une plus grande utilisation de leurs ressources sociales par rapport à leur physique et leurs ressources cognitives. Les deux hypothèses ont été corroborées. Les personnes âgées qui ont des motifs nombreux pour le bénévolat, et qui maximisent l’utilisation de leurs compétences et de leurs comportements sociales, sont plus fortement attachées à leur organisme d’acceuil et atteindre des niveaux plus élevés de développement du rôle bénévole. Les implications pour le domaine du volontariat sont discutées.
Antibiotic adjuvants: multicomponent anti-infective strategies
Authors: Kalan Lindsay , Wright Gerard D.
Published: February 2011

The unremitting emergence of multidrug-resistant bacterial pathogens highlights a matching need for new therapeutic options. For example, new carbapenemases such as KPC (class A Klebsiella pneumoniae) and NDM-1 (New Delhi metallo-β-lactamase 1) are surfacing, resulting in almost total resistance to β-lactam antibiotics. Furthermore, resistance is quickly disseminated, not only in the healthcare sector, but also within the community at large, because many resistance determinants are carried on mobile genetic elements readily shared among pathogens. The absence of new antibiotics has led to a growing reliance on older, more toxic drugs such as colistin, but resistance to these is already arising. One approach to combat this growing problem is the use of combination drug antibiotic adjuvant therapy, which potentiates the activity of antibiotics. Here, we review the current situation and discuss potential drug combinations that may increase the potency of antibiotics in the future. Adjuvant therapies include antibiotic combinations, synergy between antibiotics and nonantibiotics, inhibition of resistance and molecules that alter the physiology of antibiotic-insensitive cells, such as those in biofilms. We provide a rationale for these multicomponent strategies, highlighting current research and important considerations for their clinical use and pharmacological properties.
Prebisch and Myrdal: development economics in the core and on the periphery
Authors: Puntigliano Andrés Rivarola , Appelqvist Örjan
Published: February 2011

The ideas on development issues of two ‘pioneers in development’, Raúl Prebisch and Gunnar Myrdal, are tracked in their formation and evolution. The central role of these two ‘defiant bureaucrats’ in the Economic Commission for Europe (ECE) and the Economic Commission for Latin America (CEPAL) are used to reflect on the interaction between intellectuals and international institutions in different historical contexts. Both men represented a liberal–universal strand in development thinking. Their divergent conclusions and assessments of the role of international institutions are compared, and are related to their different origins in core and periphery. It is argued that such roots influenced two different approaches to development problems within the UN system.
Towards global equilibrium: American foundations and Indian modernization, 1950s to 1970s
Authors: Unger Corinna R.
Published: February 2011

This article studies the activities of American philanthropic foundations in India between the 1950s and 1970s. It discusses why private institutions such as the Rockefeller Foundation and the Ford Foundation felt committed to responding to problems of hunger and population growth abroad and how they managed to establish themselves as leaders in the development aid arena. Instead of considering the foundations as handmaidens of US national strategic interests shaped by the Cold War, the article argues that they should be understood as highly flexible transnational agents who, in an ambitious combination of philanthropic motives, institutional interests, and trust in the power of science, diagnosed political problems and developed methods to overcome them in order to reduce global inequality.
Cancer as development gone awry: the case for bisphenol-A as a carcinogen
Authors: Sonnenschein C. , Wadia P. R. , Rubin B. S. , Soto A. M.
Published: February 2011

The discovery of a rare clear cell carcinoma of the vagina in young women gestationally exposed to the estrogen diethylstilbestrol (DES) lent empirical support to the hypothesis that prenatal exposure to xenoestrogens might cause cancer. This fact contradicted two well-accepted notions: (i) mammalian development was merely the unfolding of a genetic program and (ii) only mutagenic agents could cause cancer. The ecological developmental biology (eco–devo) movement revitalized the concept of developmental plasticity through the occurrence of polyphenisms whereby a single genotype produces diverse phenotypes which are determined by environmental cues. Based on the principles of eco–devo and the tissue organization field theory of carcinogenesis, we hypothesized that developmental exposure to xenoestrogens increased the propensity to develop mammary cancer during adulthood. Bisphenol-A (BPA), a ubiquitous xenoestrogen, was chosen as a model for environmental estrogen exposure. In mice, perinatal exposure to environmentally relevant BPA levels induced alterations of the mammary gland architecture which manifested during fetal morphogenesis and throughout life, including the development of pre-neoplastic lesions. In rats, gestational exposure to BPA induced pre-neoplastic lesions and carcinomain situthat manifested in adulthood in the absence of any additional treatment. Emerging epidemiological data reveal an increased incidence of breast cancer in women exposed to DES during gestation. Hence, both animal experiments and epidemiological data strengthen the hypothesis that fetal exposure to xenoestrogens may be an underlying cause of the increased incidence of breast cancer observed over the past 50 years.
IT Alignment and the Boundaries of the IT Function
Authors: Valorinta Mikko
Published: February 2011

This study applies the concept of organizational boundary to examine how outsourcing and the management of external and internal boundaries of the information technology (IT) function impact IT alignment. The article argues that by decreasing the governance costs for the less strategic IT transactions, IT outsourcing enables the IT function, and IT management particularly, to focus more on aligning the IT activities and plans with business strategies and priorities, and thereby improve IT alignment. This article also suggests that organizations may improve IT alignment by effectively transmitting knowledge and supporting collaboration between IT and business functions through boundary spanning activities and with boundary objects. The concept of organizational boundaries and boundary management has not been explicitly addressed by the existing research on IT alignment. This study also contributes to the IT outsourcing literature by linking outsourcing to improved IT alignment.
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions
Authors: Heo Muyoung , Maslov Sergei , Shakhnovich Eugene
Published: February 2011

How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous nonfunctional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are directly determined from its genome through biophysical properties of protein structures and binding interactions in a crowded cellular environment. The model cell includes three independent prototypical pathways, whose topologies of protein–protein interaction (PPI) subnetworks are different, but whose contributions to the cell fitness are equal. Model cells evolve through genotypic mutations and phenotypic protein copy number variations. We found a strong relationship between evolved physical–chemical properties of protein interactions and their abundances due to a “frustration” effect: Strengthening of functional interactions brings about hydrophobic interfaces, which make proteins prone to promiscuous binding. The balancing act is achieved by lowering concentrations of hub proteins while raising solubilities and abundances of functional monomers. On the basis of these principles we generated and analyzed a possible realization of the proteome-wide PPI network in yeast. In this simulation we found that high-throughput affinity capture–mass spectroscopy experiments can detect functional interactions with high fidelity only for high-abundance proteins while missing most interactions for low-abundance proteins.
Pulse of atmospheric oxygen during the late Cambrian
Authors: Saltzman Matthew R. , Young Seth A. , Kump Lee R. , Gill Benjamin C. , Lyons Timothy W. , Runnegar Bruce
Published: February 2011

A rise in atmospheric O
2
has been linked to the Cambrian explosion of life. For the plankton and animal radiation that began some 40 million yr later and continued through much of the Ordovician (Great Ordovician Biodiversification Event), the search for an environmental trigger(s) has remained elusive. Here we present a carbon and sulfur isotope mass balance model for the latest Cambrian time interval spanning the globally recognized Steptoean Positive Carbon Isotope Excursion (SPICE) that indicates a major increase in atmospheric O
2
. We estimate that this organic carbon and pyrite burial event added approximately 19 × 10
18
moles of O
2
to the atmosphere (i.e., equal to change from an initial starting point for O
2
between 10–18% to a peak of 20–28% O
2
) beginning at approximately 500 million years. We further report on new paired carbon isotope results from carbonate and organic matter through the SPICE in North America, Australia, and China that reveal an approximately 2‰ increase in biological fractionation, also consistent with a major increase in atmospheric O
2
. The SPICE is followed by an increase in plankton diversity that may relate to changes in macro- and micronutrient abundances in increasingly oxic marine environments, representing a critical initial step in the trophic chain. Ecologically diverse plankton groups could provide new food sources for an animal biota expanding into progressively more ventilated marine habitats during the Ordovician, ultimately establishing complex ecosystems that are a hallmark of the Great Ordovician Biodiversification Event.
Distributed and causal influence of frontal operculum in task control
Authors: Higo Takayasu , Mars Rogier B. , Boorman Erie D. , Buch Ethan R. , Rushworth Matthew F. S.
Published: February 2011

It has been suggested that the frontal operculum (fO) is a key node in a network for exerting control over cognitive processes. How it exerts this influence, however, has been unclear. Here, using the complementary approaches of functional MRI and transcranial magnetic stimulation, we have shown that the fO regulates increases and decreases of activity in multiple occipitotemporal cortical areas when task performance depended on directing attention to different classes of stimuli held in memory. Only one region, the fO, was significantly more active when subjects selectively attended to a single stimulus so that it determined task performance. The stimuli that guided task performance could belong to three categories—houses, body parts, and faces—associated with three occipitotemporal regions. On each trial, the pattern of functional correlation between the fO and the three occipitotemporal regions became either positive or negative, depending on which stimulus was to be attended and which ignored. Activation of the fO preceded both activity increases and decreases in the occipitotemporal cortex. The causal dependency of the distributed occipitotemporal pattern of activity increases and decreases on the fO was demonstrated by showing that transcranial magnetic stimulation–mediated interference of the fO diminished top-down selective attentional modulation in the occipitotemporal cortex, but it did not alter bottom-up activation of the same areas to the same stimuli when they were presented in isolation. The fO's prominence in cognitive control may stem from a role in regulating the level of activity of representations in posterior brain areas that are relevant or irrelevant, respectively, for response selection.
Responses of wind erosion to climate-induced vegetation changes on the Colorado Plateau
Authors: Munson Seth M. , Belnap Jayne , Okin Gregory S.
Published: February 2011

Projected increases in aridity throughout the southwestern United States due to anthropogenic climate change will likely cause reductions in perennial vegetation cover, which leaves soil surfaces exposed to erosion. Accelerated rates of dust emission from wind erosion have large implications for ecosystems and human well-being, yet there is poor understanding of the sources and magnitude of dust emission in a hotter and drier climate. Here we use a two-stage approach to compare the susceptibility of grasslands and three different shrublands to wind erosion on the Colorado Plateau and demonstrate how climate can indirectly moderate the magnitude of aeolian sediment flux through different responses of dominant plants in these communities. First, using results from 20 y of vegetation monitoring, we found perennial grass cover in grasslands declined with increasing mean annual temperature in the previous year, whereas shrub cover in shrublands either showed no change or declined as temperature increased, depending on the species. Second, we used these vegetation monitoring results and measurements of soil stability as inputs into a field-validated wind erosion model and found that declines in perennial vegetation cover coupled with disturbance to biological soil crust resulted in an exponential increase in modeled aeolian sediment flux. Thus the effects of increased temperature on perennial plant cover and the correlation of declining plant cover with increased aeolian flux strongly suggest that sustained drought conditions across the southwest will accelerate the likelihood of dust production in the future on disturbed soil surfaces.
C-terminal-truncated apolipoprotein (apo) E4 inefficiently clears amyloid-β (Aβ) and acts in concert with Aβ to elicit neuronal and behavioral deficits in mice
Authors: Bien-Ly Nga , Andrews-Zwilling Yaisa , Xu Qin , Bernardo Aubrey , Wang Charles , Huang Yadong
Published: February 2011

Apolipoprotein (apo) E4 is the major known genetic risk factor for Alzheimer's disease (AD). We have shown in vitro and in vivo that apoE4 preferentially undergoes aberrant cleavage in neurons, yielding neurotoxic C-terminal-truncated fragments. To study the effect of these fragments on amyloid-β (Aβ) clearance/deposition and their potential synergy with Aβ in eliciting neuronal and behavioral deficits, we cross-bred transgenic mice expressing apoE3, apoE4, or apoE4(Δ272–299) with mice expressing human amyloid protein precursor (APP) harboring familial AD mutations (hAPP
FAD
). At 6–8 mo of age, hAPP
FAD
mice expressing apoE3 or apoE4 had lower levels of hippocampal Aβ (94% and 89%, respectively) and less Aβ deposition (89% and 87%) than hAPP
FAD
mice without apoE, whereas hAPP
FAD
mice expressing mouse apoE had higher Aβ levels. Thus, human apoE stimulates Aβ clearance, but mouse apoE does not. Expression of apoE4(Δ272–299) reduced total Aβ levels by only 63% and Aβ deposition by 46% compared with hAPP
FAD
mice without apoE. Unlike apoE3 and apoE4, the C-terminal-truncated apoE4 bound poorly with Aβ peptides, leading to decreased Aβ clearance and increased Aβ deposition. Despite their lower levels of Aβ and Aβ deposition, hAPP
FAD
/apoE4(Δ272–299) mice accumulated pathogenic Aβ oligomers and displayed neuronal and behavioral deficits similar to or more severe than those in hAPP
FAD
mice. Thus, the C-terminal-truncated apoE4 fragment inefficiently clears Aβ peptides and acts in concert with low levels of Aβ to elicit neuronal and behavioral deficits in mice.
Exopolymer alteration of physical properties of sea ice and implications for ice habitability and biogeochemistry in a warmer Arctic
Authors: Krembs Christopher , Eicken Hajo , Deming Jody W.
Published: February 2011

The physical properties of Arctic sea ice determine its habitability. Whether ice-dwelling organisms can change those properties has rarely been addressed. Following discovery that sea ice contains an abundance of gelatinous extracellular polymeric substances (EPS), we examined the effects of algal EPS on the microstructure and salt retention of ice grown from saline solutions containing EPS from a culture of the sea-ice diatom,
Melosira arctica
. We also experimented with xanthan gum and with EPS from a culture of the cold-adapted bacterium
Colwellia psychrerythraea
strain 34H. Quantitative microscopic analyses of the artificial ice containing
Melosira
EPS revealed convoluted ice-pore morphologies of high fractal dimension, mimicking features found in EPS-rich coastal sea ice, whereas EPS-free (control) ice featured much simpler pore geometries. A heat-sensitive glycoprotein fraction of
Melosira
EPS accounted for complex pore morphologies. Although all tested forms of EPS increased bulk ice salinity (by 11–59%) above the controls, ice containing native
Melosira
EPS retained the most salt. EPS effects on ice and pore microstructure improve sea ice habitability, survivability, and potential for increased primary productivity, even as they may alter the persistence and biogeochemical imprint of sea ice on the surface ocean in a warming climate.
Caenorhabditis elegans aristaless/Arx
gene
alr-1
restricts variable gene expression
Authors: Topalidou Irini , van Oudenaarden Alexander , Chalfie Martin
Published: February 2011

Variable expressivity of mutant phenotypes in genetically identical individuals is a phenomenon widely reported but poorly understood. For example, mutations in the gene encoding the transcription factor ALR-1 in
Caenorhabditis elegans
result in variable touch receptor neuron (TRN) function. Using single-molecule in situ hybridization, we demonstrate that this phenotypic variability reflects enhanced variability in the expression of the selector gene
mec-3
, which is needed, together with
unc-86
, for the differentiation of the TRNs. In a yeast expression system, ALR-1 enhances MEC-3/UNC-86–dependent transcription from the
mec-3
promoter, showing that ALR-1 can enhance bulk
mec-3
expression. We show that, due to stochastic fluctuations, autoregulation of
mec-3
is not sufficient for TRN differentiation; ALR-1 provides a second positive feedback loop that increases
mec-3
expression, by restricting variability, and thus ensures TRN differentiation. Our results link fluctuations in gene expression to phenotypic variability, which is seen in many mutant strains, and provide an explicit demonstration of how variable gene expression can be curtailed in developing cells to ensure their differentiation. Because ALR-1 and similar proteins (
Drosophila
Aristaless and human ARX) are needed for the expression of other transcription factors, we propose that proteins in this family may act to ensure differentiation more generally.
Substance Use Prevalence and Screening Instrument Comparisons in Urban Primary Care
Authors: Lee Joshua D. , Delbanco Benjamin , Wu Edward , Gourevitch Marc N.
Published: February 2011

Substance use screening in a primary care setting compared the Alcohol, Smoking, and Substance Involvement Screening Test (ASSIST version 3.0), Two-Item Conjoint Screen (TICS), National Institute on Alcohol Abuse and Alcoholism (NIAAA) daily limit single item, and electronic medical record (EMR). Among 236 consecutive adults, ASSIST moderate- to high-risk substance use prevalence was tobacco, 15.3%; alcohol, 8.5%; cannabis, 5.1%; cocaine, 2.5%; and opioids, 2.5%. Compared to ASSIST, a positive TICS was 45% (95% confidence interval [CI], 27–64%) sensitive, 99% (95–100%) specific; the NIAAA single-item screen was 80% (56–94%) sensitive, 87% (82–91%) specific. The NIAAA single item correlated closely with alcohol ASSIST. TICS and EMR were less sensitive for any nontobacco substance use.
fconv: format conversion, manipulation and feature computation of molecular data
Authors: Neudert Gerd , Klebe Gerhard
Published: February 2011

Summary: fconv is a program intended for parsing and manipulating multiple aspects and properties of molecular data. Up to now, it has been developed and extensively tested for 3 years. It has become a very robust and comprehensive tool involved in a broad range of computational workflows that are currently applied in our drug design environment. Typical tasks are as follows: conversion and error correction of formats such as PDB(QT), MOL2, SDF, DLG and CIF; extracting ligands from PDB as MOL2; automatic or ligand-based cavity detection; rmsd calculation and clustering; substructure searches; alignment and structural superposition; building of crystal packings; adding hydrogens; calculation of various properties like the number of rotatable bonds; molecular weights or vdW volumes. The atom type classification is based on a consistent assignment of internal atom types, which are by far more differentiated compared with e.g. Sybyl atom types. Apart from the predefined mapping of these types onto Sybyl types, the user is able to assign own mappings by providing modified template files, thus allowing for tailor-made atom type sets.

Availability: fconv is free software available under GNU General Public License. C++ sources and precompiled executables for LINUX/UNIX, Mac OS and Windows, as well as tutorials are available on http://www.agklebe.de.

Contact:  klebe@staff.uni-marburg.de
A common layer of interoperability for biomedical ontologies based on OWL EL
Authors: Hoehndorf Robert , Dumontier Michel , Oellrich Anika , Wimalaratne Sarala , Rebholz-Schuhmann Dietrich , Schofield Paul , Gkoutos Georgios V.
Published: February 2011

Motivation: Ontologies are essential in biomedical research due to their ability to semantically integrate content from different scientific databases and resources. Their application improves capabilities for querying and mining biological knowledge. An increasing number of ontologies is being developed for this purpose, and considerable effort is invested into formally defining them in order to represent their semantics explicitly. However, current biomedical ontologies do not facilitate data integration and interoperability yet, since reasoning over these ontologies is very complex and cannot be performed efficiently or is even impossible. We propose the use of less expressive subsets of ontology representation languages to enable efficient reasoning and achieve the goal of genuine interoperability between ontologies.

Results: We present and evaluate EL Vira, a framework that transforms OWL ontologies into the OWL EL subset, thereby enabling the use of tractable reasoning. We illustrate which OWL constructs and inferences are kept and lost following the conversion and demonstrate the performance gain of reasoning indicated by the significant reduction of processing time. We applied EL Vira to the open biomedical ontologies and provide a repository of ontologies resulting from this conversion. EL Vira creates a common layer of ontological interoperability that, for the first time, enables the creation of software solutions that can employ biomedical ontologies to perform inferences and answer complex queries to support scientific analyses.

Availability and implementation: The EL Vira software is available from http://el-vira.googlecode.com and converted OBO ontologies and their mappings are available from http://bioonto.gen.cam.ac.uk/el-ont.

Contact:  rh497@cam.ac.uk
B2G-FAR, a species-centered GO annotation repository
Authors: Götz Stefan , Arnold Roland , Sebastián-León Patricia , Martín-Rodríguez Samuel , Tischler Patrick , Jehl Marc-André , Dopazo Joaquín , Rattei Thomas , Conesa Ana
Published: February 2011

Motivation: Functional genomics research has expanded enormously in the last decade thanks to the cost reduction in high-throughput technologies and the development of computational tools that generate, standardize and share information on gene and protein function such as the Gene Ontology (GO). Nevertheless, many biologists, especially working with non-model organisms, still suffer from non-existing or low-coverage functional annotation, or simply struggle retrieving, summarizing and querying these data.

Results: The Blast2GO Functional Annotation Repository (B2G-FAR) is a bioinformatics resource envisaged to provide functional information for otherwise uncharacterized sequence data and offers data mining tools to analyze a larger repertoire of species than currently available. This new annotation resource has been created by applying the Blast2GO functional annotation engine in a strongly high-throughput manner to the entire space of public available sequences. The resulting repository contains GO term predictions for over 13.2 million non-redundant protein sequences based on BLAST search alignments from the SIMAP database. We generated GO annotation for approximately 150 000 different taxa making available 2000 species with the highest coverage through B2G-FAR. A second section within B2G-FAR holds functional annotations for 17 non-model organism Affymetrix GeneChips.

Conclusions: B2G-FAR provides easy access to exhaustive functional annotation for 2000 species offering a good balance between quality and quantity, thereby supporting functional genomics research especially in the case of non-model organisms.

Availability: The annotation resource is available at http://www.b2gfar.org.

Contact:  aconesa@cipf.es; sgoetz@cipf.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Criteria for convective versus absolute string instability in car-following models
Authors: Ward Jonathan A. , Wilson R. Eddie
Published: February 2011

The linear stability properties of car-following models of highway traffic are analysed. A general family of models is introduced and the subsequent analysis developed in terms of its partial derivatives. Two measures of wave propagation, namely (i) the group velocity and (ii) the signal velocity, are introduced and computed. These measures are used to classify how instability propagates disturbances, measured relative to the frame of the road along which the vehicles drive. Detector data suggest that disturbances should propagate only in an upstream direction (convective upstream instability), and it is shown how to parametrize models to agree with data and avoid unrealistic downstream propagation (absolute and convective downstream instability).
A mechanism for enhanced static sliding resistance owing to surface waviness
Authors: Waters J. F. , Guduru P. R.
Published: February 2011

This paper presents an analysis of static sliding resistance of a rigid sphere on a soft elastic material with axisymmetric waviness. When the sphere is loaded laterally under a fixed normal force, the contact area is subjected to mixed-mode loading. It is shown that, as the lateral loading increases, the decrease in contact area involves unstable jumps; and each unstable jump dissipates mechanical energy. The additional energy dissipation increases the peak force required for gross sliding of the interface compared with that of a flat surface. Thus, a mechanism is proposed for enhanced static sliding resistance on the surface of a soft material owing to surface waviness-induced instabilities. Such an increase in sliding resistance is analogous to a similar increase in the detachment force between a sphere and a wavy surface during normal separation, which was reported elsewhere. The influence of mode-mixity-dependent work of adhesion on the static sliding resistance of a wavy surface is also considered.
The Chloroplast Permease PIC1 Regulates Plant Growth and Development by Directing Homeostasis and Transport of Iron
Authors: Duy Daniela , Stübe Roland , Wanner Gerhard , Philippar Katrin
Published: February 2011

The membrane-spanning protein PIC1 (for permease in chloroplasts 1) in Arabidopsis (Arabidopsis thaliana) was previously described to mediate iron transport across the inner envelope membrane of chloroplasts. The albino phenotype of pic1 knockout mutants was reminiscent of iron-deficiency symptoms and characterized by severely impaired plastid development and plant growth. In addition, plants lacking PIC1 showed a striking increase in chloroplast ferritin clusters, which function in protection from oxidative stress by sequestering highly reactive free iron in their spherical protein shell. In contrast, PIC1-overexpressing lines (PIC1ox) in this study rather resembled ferritin loss-of-function plants. PIC1ox plants suffered from oxidative stress and leaf chlorosis, most likely originating from iron overload in chloroplasts. Later during growth, plants were characterized by reduced biomass as well as severely defective flower and seed development. As a result of PIC1 protein increase in the inner envelope membrane of plastids, flower tissue showed elevated levels of iron, while the content of other transition metals (copper, zinc, manganese) remained unchanged. Seeds, however, specifically revealed iron deficiency, suggesting that PIC1 overexpression sequestered iron in flower plastids, thereby becoming unavailable for seed iron loading. In addition, expression of genes associated with metal transport and homeostasis as well as photosynthesis was deregulated in PIC1ox plants. Thus, PIC1 function in plastid iron transport is closely linked to ferritin and plastid iron homeostasis. In consequence, PIC1 is crucial for balancing plant iron metabolism in general, thereby regulating plant growth and in particular fruit development.
Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis
Authors: Kerwin Rachel E. , Jimenez-Gomez Jose M. , Fulop Daniel , Harmer Stacey L. , Maloof Julin N. , Kliebenstein Daniel J.
Published: February 2011

Modern systems biology permits the study of complex networks, such as circadian clocks, and the use of complex methodologies, such as quantitative genetics. However, it is difficult to combine these approaches due to factorial expansion in experiments when networks are examined using complex methods. We developed a genomic quantitative genetic approach to overcome this problem, allowing us to examine the function(s) of the plant circadian clock in different populations derived from natural accessions. Using existing microarray data, we defined 24 circadian time phase groups (i.e., groups of genes with peak phases of expression at particular times of day). These groups were used to examine natural variation in circadian clock function using existing single time point microarray experiments from a recombinant inbred line population. We identified naturally variable loci that altered circadian clock outputs and linked these circadian quantitative trait loci to preexisting metabolomics quantitative trait loci, thereby identifying possible links between clock function and metabolism. Using single-gene isogenic lines, we found that circadian clock output was altered by natural variation in Arabidopsis thaliana secondary metabolism. Specifically, genetic manipulation of a secondary metabolic enzyme led to altered free-running rhythms. This represents a unique and valuable approach to the study of complex networks using quantitative genetics.
Boys Meet Girls’ Rights: Bolivian Adolescent Males’ Claims of Commitment to Gender Equality
Authors: Gervais Christine
Published: February 2011

This article describes a qualitative study exploring the effects of community‐based human rights and pro‐equality education on Bolivian adolescent boys. By privileging the boys’ own voices, the study examines how the boys’ sense of solidarity toward others, derived from the citizenship duties and collegiality emphasised in non‐governmental workshops, impacted their commitment to gender equality. Research implications include the importance of educating young males on females’ rights and listening to the boys’ views on the resulting progress and remaining challenges regarding the attainment of sustainable gender equality in social spheres and public policies.
Animal models of toxic epidermal necrolysis
Authors: AZUKIZAWA Hiroaki
Published: February 2011

Stevens–Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are severe acute exfoliative skin diseases developing extensive epidermal detachment and mucosal damage. Although SJS and TEN are mostly caused by drugs, an animal model of TEN using drugs has not been established yet. We have established an autoimmune skin disease model mouse reproducing the devastating skin damage of TEN by a combination of transgenic mice expressing an epidermal model antigen and its specific CD8+ T‐cell receptor. In this model mouse, we found that the thymus‐derived CD4+CD25+ regulatory T cell (Treg) is a critical regulator of cytotoxic T lymphocytes (CTL) causing TEN. Indeed, loss of Treg function was recently demonstrated by human studies of TEN patients. Although how drug‐reactive CTL is activated in vivo is still unknown, this model elucidated the immunological pathomechanism of TEN after CTL obtained cytotoxicity against epidermal keratinocyte. In this review, roles of CTL, Treg, cytotoxic granules and antigen‐presenting cells were discussed on pathogenesis of TEN.
Nucleotide‐binding and oligomerization domain‐like receptors and retinoic acid inducible gene‐like receptors in human tonsillar T lymphocytes
Authors: Petterson Terese , Månsson Anne , Riesbeck Kristian , Cardell Lars O.
Published: February 2011

Nucleotide‐binding and oligomerization domain (NOD) ‐like receptors (NLRs) and retinoic acid‐inducible gene (RIG) ‐like receptors (RLRs) are recently discovered cytosolic pattern‐recognition receptors sensing mainly bacterial components and viral RNA, respectively. Their importance in various cells and disorders is becoming better understood, but their role in human tonsil‐derived T lymphocytes remains to be elucidated. In this study, we evaluated expression and functional relevance of NLRs and RLRs in human tonsillar CD3+ T lymphocytes. Immunohistochemistry, real‐time RT‐PCR and flow cytometry revealed expression of NOD1, NOD2, NALP1, NALP3, NAIP, IPAF, RIG‐1, MDA‐5 and LGP‐2 at mRNA and protein levels. Because of the limited number of ligands (iE‐DAP, MDP, Alum, Poly(I:C)/LyoVec), functional evaluation was restricted to NOD1, NOD2, NALP3 and RIG‐1/MDA‐5, respectively. Stimulation with the agonists alone was not enough to induce activation but upon triggering via CD3 and CD28, a profound induction of proliferation was seen in purified CD3+ T cells. However, the proliferative response was not further enhanced by the cognate ligands. Nonetheless, in tonsillar mononuclear cells iE‐DAP, MDP and Poly(I:C)/LyoVec were found to augment the CD3/CD28‐induced proliferation of tonsillar mononuclear cells. Also, iE‐DAP and MDP were found to promote secretion of interleukins 2 and 10 as well as to up‐regulate CD69. This study demonstrates for the first time a broad range of NLRs and RLRs in human tonsillar T cells and that NOD1, NOD2 and RIG‐1/MDA‐5 act synergistically with αCD3 and αCD28 to induce proliferation of human T cells. Hence, these results suggest that these receptors have a role in T‐cell activation.
The effect of music therapy on physiological signs of anxiety in patients receiving mechanical ventilatory support
Authors: Korhan Esra Akin , Khorshid Leyla , Uyar Mehmet
Published: February 2011

Aims.  The aim of this study was to investigate if relaxing music is an effective method of reducing the physiological signs of anxiety in patients receiving mechanical ventilatory support.

Background.  Few studies have focused on the effect of music on physiological signs of anxiety in patients receiving mechanical ventilatory support.

Design.  A study–case–control, experimental repeated measures design was used.

Method.  Sixty patients aged 18–70 years, receiving mechanical ventilatory support and hospitalised in the intensive care unit, were taken as a convenience sample. Participants were randomised to a control group or intervention group, who received 60 minutes of music therapy. Classical music was played to patients using media player (MP3) and headphones. Subjects had physiological signs taken immediately before the intervention and at the 30th, 60th and 90th minutes of the intervention. Physiological signs of anxiety assessed in this study were mean systolic and diastolic blood pressure, pulse rate, respiratory rate and oxygen saturation in blood measured by pulse oxymetry. Data were collected over eight months in 2006–2007.

Results.  The music group had significantly lower respiratory rates, and systolic and diastolic blood pressure, than the control group. This decrease improved progressively in the 30th, 60th and 90th minutes of the intervention, indicating a cumulative dose effect.

Conclusion.  Music can provide an effective method of reducing potentially harmful physiological responses arising from anxiety.

Relevance to clinical practice.  As indicated by the results of this study, music therapy can be supplied to allay anxiety in patients receiving mechanical ventilation. Nurses may include music therapy in the routine care of patients receiving mechanical ventilation.
Evolution and molecular mechanisms of adaptive developmental plasticity
Authors: BELDADE PATRÍCIA , MATEUS ANA RITA A. , KELLER ROBERTO A.
Published: February 2011

Aside from its selective role in filtering inter‐individual variation during evolution by natural selection, the environment also plays an instructive role in producing variation during development. External environmental cues can influence developmental rates and/or trajectories and lead to the production of distinct phenotypes from the same genotype. This can result in a better match between adult phenotype and selective environment and thus represents a potential solution to problems posed by environmental fluctuation. The phenomenon is called adaptive developmental plasticity. The study of developmental plasticity integrates different disciplines (notably ecology and developmental biology) and analyses at all levels of biological organization, from the molecular regulation of changes in organismal development to variation in phenotypes and fitness in natural populations. Here, we focus on recent advances and examples from morphological traits in animals to provide a broad overview covering (i) the evolution of developmental plasticity, as well as its relevance to adaptive evolution, (ii) the ecological significance of alternative environmentally induced phenotypes, and the way the external environment can affect development to produce them, (iii) the molecular mechanisms underlying developmental plasticity, with emphasis on the contribution of genetic, physiological and epigenetic factors, and (iv) current challenges and trends, including the relevance of the environmental sensitivity of development to studies in ecological developmental biology, biomedicine and conservation biology.
Nappe structure revealed by thermal constraints in the Taiwan metamorphic belt
Authors: Chen Chih‐Tung , Chan Yu‐Chang , Lu Chia‐Yu , Simoes Martine , Beyssac Olivier
Published: February 2011

Terra Nova, 23, 85–91, 2011

Vitrinite reflectance and Raman spectroscopy of carbonaceous material data are used to better resolve the thermal history of the Hsuehshan Range, which is accreted between the foreland fold–thrust belt and bulldozer hinterland units in the Taiwan mountain belt. The observed thermal data indicate that the strata in the northern Hsuehshan Range underwent dynamic metamorphism during the Neogene orogeny, while the strata in the southern Hsuehshan Range may have predominantly experienced burial metamorphism during Palaeogene sedimentation. Based on the thermal constraints, the Hsuehshan Range is interpreted to consist of nappe stacks, originating from the rifted Eurasian continental margin. This interpretation is consistent with well‐documented cases in the European Alps and the Himalayas and is also shown in physical modelling and thermo‐kinematic studies invoking underplating and erosion processes.
The problem of glaucony from the Shannon Sandstone (Campanian, Wyoming)
Authors: Amorosi Alessandro
Published: February 2011

Terra Nova, 23, 100–107, 2011

The Shannon Sandstone, one of the most controversial units in the field of stratigraphy, was first interpreted as a shelf sand‐ridge deposit, but subsequent studies have furnished different interpretations, from lowstand‐shoreface to incised‐valley models. Despite a general consensus among previous workers about the significance of glaucony for Shannon interpretation, mineralogical characterization of the green grains has never been undertaken: identification of glaucony has been restricted to visual inspection. Accurate characterization of ‘highly glauconitic’ deposits from the Shannon Sandstone (Powder River Basin of Wyoming, Section W3) reveals that sedimentological interpretation of the greensands relies mostly upon mistaken mineral identity. Glaucony appears as a minor component of the rock and proves to be poorly mature and significantly less abundant (0–6%) than previously inferred (up to 85%). Characterization of the glauconitic minerals, however, provides data that contribute to Shannon interpretation.
Insights on the spreading of the Tyrrhenian Sea from the magnetic anomaly pattern
Authors: Florio Giovanni , Fedi Maurizio , Cella Federico
Published: February 2011

Terra Nova, 23, 127–133, 2011

We analyse the pattern of magnetic anomalies in the Tyrrhenian back‐arc basin by a simple and objective method that is able to simplify the readability of the maps and to safely identify reversely magnetized sources. This analysis is useful to better understand the reliability of recent studies indicating the presence of striped, ‘mid‐ocean like’, magnetic anomalies in this small basin, from which spreading velocities have been calculated. Our results show that in the Vavilov and Marsili sub‐basins reversely magnetized bodies are actually present, but their areal distribution is rather irregular. The resulting pattern of normally and reversely magnetized bodies does not fit with an ocean‐like central expansion model. Instead, the distribution of magnetic sources may suggest that the crustal tearing induced by extension processes is not concentrated only beneath the seamounts, but may have in different times involved different areas of these sub‐basins.
Incidence of endophyte Neotyphodium occultans in Lolium rigidum from Australia
Authors: KIRKBY K A , PRATLEY J E , HUME D E , FAVILLE M J , AN M , WU H
Published: February 2011

Kirkby KA, Pratley JE, Hume DE, Faville MJ, An M & Wu H (2011). Incidence of endophyte Neotyphodium occultans in Lolium rigidum from Australia. Weed Research51, 261–272.

Lolium rigidum (annual ryegrass), a widespread weed of southern Australian cereal crops, has frequently evolved herbicide resistance. It is commonly found associated with the mutualistic, endophytic fungus, Neotyphodium occultans. The objectives of this study were as follows: (i) determine the occurrence of N. occultans in L. rigidum populations across southern Australia, (ii) evaluate potential associations between infection frequency and herbicide resistance, climatic and topographic variables and (iii) examine genetic diversity of N. occultans from this national collection of L. rigidum using simple sequence repeat markers. By microscopic assessment of seed, we found all seed lots were infected with N. occultans, with highly variable frequencies, ranging from 4% to 98%. Frequencies were higher in New South Wales, South Australia and Victoria (54–62%) than in Western Australia (43%) or Tasmania (17%). A negative association existed between elevation and mean rainfall, and infection frequency. Significant interactions were as follows: mean rainfall (growing season) and state and mean rainfall (growing season) and elevation. Significant associations were found between infection frequency and herbicide mode of action. Infection was lower in seed lots resistant to group B (sulfonylurea and imidazolinone) and higher in seed lots resistant to group D (dinitroaniline) herbicides. Higher infection frequencies were observed in seed lots from earlier years, with the lowest in seed lots recently collected. No significant associations were found with long‐term mean temperature or rainfall. Little genetic diversity was observed for N. occultans endophyte in Australian plants. These results provide a benchmark of the relationship of N. occultans with L. rigidum and suggest further research on the role this endophyte has in determining the fitness of L. rigidum under varying conditions of herbicide resistance, rainfall and elevation that may aid in the management of this grass.
Endogenous ochronosis: case report and a systematic review of the literature
Authors: Khaled Aida , Kerkeni Nadia , Hawilo Abdelmoti , Fazaa Becima , Kamoun Mohamed Ridha
Published: February 2011

Background  Endogenous ochronosis (EO) is a rare autosomal recessive disorder due to accumulation of oxidized and polymerized forms of homogentisic acid (HGA) in connective tissues, giving them a deep dark blue pigmentation.

Aim  Through a new Tunisian case of EO and a review of the literature, we aimed to define the epidemioclinical features of EO, its diagnostic criteria, and evolution.

Methods  Three hundred and forty patients were enrolled through 54 articles and four abstracts.

Case report  A 35‐year‐old woman, born in consanguineous parents, presented with blue‐grey patches of fingernails, first interdigital spaces, and ears with brown conjunctival pigmentation. Urine specimen turned dark on standing overnight. The diagnosis of EO was confirmed by urinary high levels of HGA. Investigations revealed radiologic signs of ochronotic arthropathy.

Review of the literature  EO is ubiquitary. Its prevalence was estimated at almost 6.5 cases/year. The mean age at diagnosis was 55.9 years (M/F: 1.85). Onset symptoms mainly consisted in cutaneous signs. Ochronotic arthropathy was the most frequently reported manifestation. Treatment was mainly symptomatic.

Discussion  EO is often revealed in adulthood mainly after the fourth decade. Urinary darkening is the first sign of the disease but is rarely reported as an onset sign. Skin signs are the alerting features. Ochronotic arthropathy is insidious but may be debilitating. No specific medical treatment of EO is available.

Conclusion  Cutaneous manifestations are the hallmarks of OE. As vital organ involvement has been reported, close monitoring and continuous surveillance is warranted.