bluuebunny/crossref_metadata_2025 huggingface dataset:
Geographically structured host specificity is caused by the range expansions and host shifts of a symbiotic fungus
Authors: Wolfe Benjamin E , Pringle Anne
Published: December 2011

The inability to associate with local species may constrain the spread of mutualists arriving to new habitats, but the fates of introduced, microbial mutualists are largely unknown. The deadly poisonous ectomycorrhizal fungus Amanita phalloides (the death cap) is native to Europe and introduced to the East and West Coasts of North America. By cataloging host associations across the two continents, we record dramatic changes in specificity among the three ranges. On the East Coast, where the fungus is restricted in its distribution, it associates almost exclusively with pines, which are rarely hosts of A. phalloides in its native range. In California, where the fungus is widespread and locally abundant, it associates almost exclusively with oaks, mirroring the host associations observed in Europe. The most common host of the death cap in California is the endemic coast live oak (Quercus agrifolia), and the current distribution of A. phalloides appears constrained within the distribution of Q. agrifolia. In California, host shifts to native plants are also associated with a near doubling in the resources allocated to sexual reproduction and a prolonged fruiting period; mushrooms are twice as large as they are elsewhere and mushrooms are found throughout the year. Host and niche shifts are likely to shape the continuing range expansion of A. phalloides and other ectomycorrhizal fungi introduced across the world.
Historical temporal trends in monthly, seasonal, and annual mean, minimum, and maximum streamflows from the Okanagan River watershed in south-central British Columbia, Canada
Authors: Rayne Sierra , Forest Kaya
Published: December 2011

Historical trends in monthly, seasonal, and annual mean streamflows, as well as minimum and maximum monthly streamflows, were investigated at nine hydrometric stations in the Okanagan River watershed from south-central British Columbia, Canada. Overall, mean annual streamflows in the Okanagan River watershed are not exhibiting any significant time trends. No consistent declines in monthly minimum streamflows are evident at any point during the hydrologic year. Mean monthly and monthly maximum streamflows in tributary streams to the mainstem system appear to be significantly increasing over time during the spring snowmelt period of March and April. Any temporal changes in flow patterns at the mainstem Okanagan River stations likely reflect alterations in water management strategies over time at the respective upstream dams.
Base charge accumulation and push-out effects on nonlinearity of Type-I InP/InGaAs/InP and Type-I/II AlInP/GaAsSb/InP double heterojunction bipolar transistors
Authors: (Donald) Cheng K. Y. , Xu H. , Stuenkel M. E. , Iverson E. W. , Liao C. C. , Yang K. W. , Feng M. , (Norman) Cheng K. Y.
Published: December 2011

The influence of energy band alignment on carrier transport and signal integrity is investigated on fabricated Type-I InP/InGaAs/InP and Type-I/II AlInP/GaAsSb/InP DHBTs. The Type-I double heterojunction bipolar transistor (DHBT) requires the use of a transition region (setback and superlattice layer) in base-collector hetero-interface to minimize the conduction band discontinuity that can cause current blocking in the collector I-V characteristics. Despite the effort, Type-I DHBT exhibits gain compression and base charge accumulation at high current injection, giving a nonlinear microwave operation. In contrast, the Type-I/II DHBT has a favorable band alignment and permits hot electron injection without impedance in both emitter-base and base-collector junctions, resulting in considerable microwave linearity improvement.
Enhanced performance of hybrid solar cells using longer arms of quantum cadmium selenide tetrapods
Authors: Lee Kyu-Sung , Kim Inho , Gullapalli Sravani , Wong Michael S. , Jabbour Ghassan E.
Published: December 2011

We demonstrate that enhanced device performance of hybrid solar cells based on tetrapod (TP)-shaped cadmium selenide (CdSe) nanoparticles and conjugated polymer of poly (3-hexylthiophene) (P3HT) can be obtained by using longer armed tetrapods which aids in better spatial connectivity, thus decreasing charge hopping events which lead to better charge transport. Longer tetrapods with 10 nm arm length lead to improved power conversion efficiency of 1.12% compared to 0.80% of device having 5 nm short-armed tetrapods:P3HT photoactive blends.
Excitation of discrete and continuous spectrum for a surface conductivity model of graphene
Authors: Hanson George W. , Yakovlev Alexander B. , Mafi Arash
Published: December 2011

Excitation of the discrete (surface-wave/plasmon propagation mode) and continuous (radiation modes) spectrum by a point current source in the vicinity of graphene is examined. The graphene is represented by an infinitesimally thin, local, and isotropic two-sided conductivity surface. The dynamic electric field due to the point source is obtained by complex-plane analysis of Sommerfeld integrals, and is decomposed into physically relevant contributions. Frequencies considered are in the GHz through mid-THz range. As expected, the TM discrete surface wave (surface plasmon) can dominate the response along the graphene layer, although this depends on the source and observation point location and frequency. In particular, the TM discrete mode can provide the strongest contribution to the total electric field in the upper GHz and low THz range, where the surface conductivity is dominated by its imaginary part and the graphene acts as a reactive (inductive) sheet.
Nanostructure model of thermal conductivity for high thermoelectric performance
Authors: Poon S. J. , Limtragool K.
Published: December 2011

The effective medium theory of thermal conductivity of two-phase composites studied by Nan et al. has been extended to investigate concentrated nanocomposites. Due to the presence of inter-particle phonon scattering processes in concentrated nanocomposites, the effective lattice thermal conductivity keff varies more rapidly with the volume fraction of second-phase inclusions in the composite. Applying the new keff expressions to monolithic material systems, the results are found to capture the experimental trend of monolithic nanostructured materials. In particular, it is noted that the dimensionless figure of merit, ZT, is nearly doubled by only reducing the lattice thermal conductivity. Two-phase nanocomposites have also been evaluated, demonstrating that these latter systems are very suited for high thermoelectric performance. Present study leads to several strategies for obtaining ZT ∼ 2 or higher in nanocomposites.
Mechanical response of nanometer thick self-assembled monolayers on metallic substrates using classical nanoindentation
Authors: Costelle Leila , Jalkanen Pasi , Räisänen Minna T. , Lind Liina , Nowak Roman , Räisänen Jyrki
Published: December 2011

We report here on the mechanical response of thiolate self-assembled monolayers, a few nanometers thick, on gold and silver substrates, using ultra-low load contact probing (the limit of the nanoindentation method used) with a relatively large spherical diamond tip. Careful analysis of a large number of experimental data points enabled us to differentiate the effects stemming from the substrate, the loading rate, and the orientation and reactivity of the molecules. Three distinct patterns for the responses of the monolayers were observed, giving insight into the mechanical response of thiol modified metal surfaces.
Electronic and transport properties of achiral carbon nanotubes with di-vacancy pairs
Authors: Hu Fenglan , Zhou Jian
Published: December 2011

The transport behaviors of achiral single walled carbon nanotubes (SWNTs) with two di-vacancies have been investigated using a tight-binding model. The obtained results indicate that the number and position of the resonant conductance are related to the longitudinal inter-vacancy distance, and the conductance spectra are very different for different di-vacancy configurations. It is also found that the di-vacancy’s lateral distribution has a drastic effect on the SWNT’s transport behaviors. A 2π/n rotation invariance exists in the (10,10) armchair SWNT, and instead the 3·2π/n one for the (18,0) zigzag SWNT. Furthermore, our obtained results can give a good estimate of the transport behaviors of the metallic SWNTs with a number of di-vacancies.
Evaluating the electrical properties of silicon wafer solar cells using hyperspectral imaging of luminescence
Authors: Peloso Matthew P. , Sern Lew Jen , Trupke Thorsten , Peters Marius , Utama Roland , Aberle Armin G.
Published: December 2011

A line-imaging spectrometer is used to collect the spectrum of electroluminescence at each point of a multicrystalline silicon wafer solar cell. Characterization of the diffusion lengths of minority charge carriers is developed using a specific feature of the luminescence spectral signature. It is shown that various material and device parameters affecting the luminescence spectral signature may be determined independently. Diffusion length images derived from the proposed hyperspectral method are assessed against diffusion lengths obtained by light beam induced current measurements. Using hyperspectral imaging, diffusion lengths of minority charge carriers in a silicon wafer solar cell can be determined.
Role of copper in time dependent dielectric breakdown of porous organo-silicate glass low-k materials
Authors: Zhao Larry , Pantouvaki Marianna , Croes Kristof , Tőkei Zsolt , Barbarin Yohan , Wilson Christopher J. , Baklanov Mikhail R. , Beyer Gerald P. , Claeys Cor
Published: December 2011

The role of copper in time dependent dielectric breakdown (TDDB) of a porous low-k dielectric with TaN/Ta barrier was investigated on a metal-insulator-metal capacitor configuration where Cu ions can drift into the low-k film by applying a positive potential on the top while they are not permitted to enter the low-k dielectric if a negative potential is applied on the top. No difference in TDDB performance was observed between the positive and negative bias conditions, suggesting that Cu cannot penetrate TaN/Ta barrier to play a critical role in the TDDB of porous low-k material.
Loss of magnetization induced by doping in CeO2 films
Authors: Fernandes V. , Schio P. , de Oliveira A. J. A. , Schreiner W. H. , Varalda J. , Mosca D. H.
Published: December 2011

This work reports the effect of Mn, Fe, Co, and Cu low doping (∼3 at. %) on the ferromagnetic behavior of oxygen-defective CeO2−δ films electrodeposited on SiO2/Si(001). Our results indicate that the incorporation of a small number of 3d dopants with unoccupied outermost atomic orbitals, presumably magnetically active, strongly perturb the ferromagnetic ground-state associated with the network of electron clouds surrounding oxygen vacancies. As a consequence, a strong loss of magnetization occurs and saturation magnetization becomes uncorrelated with number of oxygen vacancies.
Slow light in one dimensional metallic-dielectric photonic crystals due to sign change of the effective dielectric constant
Authors: Shen Yun , Yu Guo Ping , Wang Guo Ping
Published: December 2011

We numerically show slow light can be achieved in one dimensional metallic-dielectric photonic crystals as a result of sign change of the effective dielectric constant. Due to the occurrence of slow light, rainbow trapping effect is realizable in chirped one dimensional metallic-dielectric photonic crystals where thicknesses of metal slabs linearly increase. The results imply the potential applications in constructing nanoscale optical buffer, memories, filter, sorter, etc. for high density integration of optical circuits.
Articulated Neoliberalism: The Specificity of Patronage, Kleptocracy, and Violence in Cambodia's Neoliberalization
Authors: Springer Simon
Published: December 2011

An exclusive focus on external forces risks the production of an overgeneralized account of a ubiquitous neoliberalism, which insufficiently accounts for the profusion of local variations that currently comprise the neoliberal project as a series of articulations with existing political economic circumstances. Although the international financial institutions initially promoted neoliberal economics in the global South, powerful elites were happy to oblige. Neoliberalism frequently reveals opportunities for well-connected officials to informally control market and material rewards, allowing them to line their own pockets. It is in this sense of the local appropriation of neoliberal ideas that scholars must go beyond conceiving of ‘neoliberalism in general’ as a singular and fully realized policy regime, ideological form, or regulatory framework, and work towards conceiving a plurality of ‘actually existing neoliberalisms' with particular characteristics arising from mutable geohistorical outcomes embedded within national, regional, and local process of market-driven sociospatial transformation. What constitutes ‘actually existing’ neoliberalism in Cambodia as distinctly Cambodian is the ways in which the patronage system has allowed local elites to co-opt, transform, and (re)articulate neoliberal reforms through a framework which asset strips public resources, thereby increasing people's exposure to corruption, coercion, and violence. It is to such an ‘articulation agenda’ that I attend to here as, in seeking to provide a more nuanced reading to recent work on neoliberalism in Cambodia by outlining some of its salient characteristics, a more empirical basis to theorizations of ‘articulated neoliberalism’ is revealed.
A Longitudinal Analysis of Moving Desires, Expectations and Actual Moving Behaviour
Authors: Coulter Rory , van Ham Maarten , Feijten Peteke
Published: December 2011

Residential mobility theory proposes that moves are often preceded by the expression of moving desires and expectations. Much research has investigated how individuals form these premove thoughts, with a largely separate literature examining actual mobility. Although a growing number of studies link premove thoughts to subsequent moving behaviour, these often do not distinguish explicitly between different types and combinations of premove thoughts. Using 1998–2006 British Household Panel Survey data, this study investigates whether moving desires and expectations are empirically distinct premove thoughts. Using multinomial regression models we demonstrate that moving desires and expectations have different meanings, and are often held in combination: the factors associated with expecting to move differ depending upon whether the move is also desired (and vice versa). Next, using panel logistic regression models, we show that different desire–expectation combinations have different effects on the probability of subsequent moving behaviour. The study identified two important groups generally overlooked in the literature: those who expect undesired moves and those who desire to move without expecting this to happen.
Network-Based Functional Regions
Authors: Farmer Carson J Q , Fotheringham A Stewart
Published: December 2011

For administration efficiency most countries subdivide their national territory into administrative regions. These regions are used to delineate areas which are internally well connected and relatively cohesive, especially compared with the links between regions. Hence, many countries seek to delineate local labour markets (LLMs): geographical regions where the majority of the local population seeks employment and from which the majority of local employers recruit labour. LLM boundaries are often based on functional regions, which represent the aggregate commuting patterns of the local population. A number of regionalisation procedures for objectivity delineating functional regions have been suggested, though many of these procedures require the use of ad hoc parameters to control the size and number of regions. Recently, a range of network-based alternatives have been developed in the literature. One of the most successful such methods is based on the concept of modularity: the extent to which there are dense connections within functional regions, but only sparse connections between functional regions. In this paper we maximise the modularity of a network of commuting flows to produce a regionalisation that exhibits less interaction than expected between regions. We demonstrate the effectiveness of this type of regionalisation procedure on a simulated geographical network, as well as using commuting data for the Republic of Ireland. We suggest that this new method has specific advantages over existing regionalisation procedures, particularly in the context of disaggregate commuting patterns of socioeconomic subgroups.
Geography, Death, and Finitude
Authors: Romanillos José Luis
Published: December 2011

Despite growing interest in the geographies of death, loss, and remembrance, comparatively little geographical research has been devoted either to the historical and cultural practices of death, or to an adequate conceptualisation of finitude. Responding to these absences, in this paper I argue for the importance of the notion of finitude within the history and philosophy of geographical thought. Situating finitude initially in the context of the work of Torsten Hägerstrand and Richard Hartshorne, the notion is argued to be both productive of a geographical ethics, and as epistemologically constitutive of phenomenological apprehensions of ‘earth’ and ‘world’. In order to better grasp the sense and genealogy of finitude, I turn to the work of Martin Heidegger, Michel Foucault, and Georges Bataille. These authors are drawn upon precisely because their writings present powerful conceptual frameworks which demonstrate the intimate relations between spatiality, death, and finitude. At the same time, their writings are critically interrogated in the light of perhaps the most important aspect of the conceptual history of finitude: the way in which it has been articulated as a site of anthropocentric distinction. I argue for a critical deconstruction of this anthropocentric basis to finitude; a deconstruction which raises a series of profound questions over the ethics, normativities, and understandings of responsibility shaping contemporary ethical geographies of the human and nonhuman. In so doing, I demonstrate the geographical importance of the notion of finitude for a variety of arenas of debate which include: phenomenological understandings of spatiality; the biopolitical boundaries drawn between human and animal; and contemporary theorisations of corporeality, materiality, and hospitality.
What distinguishes clinicians who better support patients for chronic disease self-management?
Authors: Kirby Sue E. , Dennis Sarah M. , Bazeley Pat , Harris Mark F.
Published: December 2011

Many frequent readmissions due to acute exacerbations of chronic disease could be prevented if patients self-managed. This study explored factors involved in patient activation for chronic disease self-management by qualitative analysis of interview data from hospital and community-based clinicians and patients. All clinicians reported that many frequently readmitted patients did not readily take up referral to chronic disease self-management services. This reluctance was compounded by system or access barriers. Clinicians who had a defined role in chronic disease management and patient-centred and behaviour change skills reported that although some patients were more resistant than others, patients could be persuaded to adopt self-management behaviours. Hospital clinicians and GPs were more inclined to attribute blame to clinical, social and personal patient factors, such as difficulty with support at home, social circumstances and reluctance to take responsibility. Investment in extending the skills and role of hospital clinicians and GPs to take a more supportive role in patient uptake of referrals to chronic disease self-management services would reduce hospital readmissions. Improvements in access to chronic disease self-management and GP services are also needed to address failure to take up chronic disease self-management.
Sarcomas induced in discrete subsets of prospectively isolated skeletal muscle cells
Authors: Hettmer Simone , Liu Jianing , Miller Christine M. , Lindsay Melissa C. , Sparks Cynthia A. , Guertin David A. , Bronson Roderick T. , Langenau David M. , Wagers Amy J.
Published: December 2011

Soft-tissue sarcomas are heterogeneous cancers that can present with tissue-specific differentiation markers. To examine the cellular basis for this histopathological variation and to identify sarcoma-relevant molecular pathways, we generated a chimeric mouse model in which sarcoma-associated genetic lesions can be introduced into discrete, muscle-resident myogenic and mesenchymal cell lineages. Expression of Kirsten rat sarcoma viral oncogene [Kras(G12V)] and disruption of cyclin-dependent kinase inhibitor 2A (CDKN2A;p16p19) in prospectively isolated satellite cells gave rise to pleomorphic rhabdomyosarcomas (MyoD-, Myogenin- and Desmin-positive), whereas introduction of the same oncogenetic hits in nonmyogenic progenitors induced pleomorphic sarcomas lacking myogenic features. Transcriptional profiling demonstrated that myogenic and nonmyogenicKras; p16p19nullsarcomas recapitulate gene-expression signatures of human rhabdomyosarcomas and identified a cluster of genes that is concordantly up-regulated in both mouse and human sarcomas. This cluster includes genes associated with Ras and mechanistic target of rapamycin (mTOR) signaling, a finding consistent with activation of the Ras and mTOR pathways both inKras; p16p19nullsarcomas and in 26–50% of human rhabdomyosarcomas surveyed. Moreover, chemical inhibition of Ras or mTOR signaling arrested the growth of mouseKras; p16p19nullsarcomas and of human rhabdomyosarcoma cells in vitro and in vivo. Taken together, these data demonstrate the critical importance of lineage commitment within the tumor cell-of-origin in determining sarcoma histotype and introduce an experimental platform for rapid dissection of sarcoma-relevant cellular and molecular events.
Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in
Anabaena
sp. PCC7120
Authors: Mitschke Jan , Vioque Agustín , Haas Fabian , Hess Wolfgang R. , Muro-Pastor Alicia M.
Published: December 2011

The fixation of atmospheric N
2
by cyanobacteria is a major source of nitrogen in the biosphere. In Nostocales, such as
Anabaena
, this process is spatially separated from oxygenic photosynthesis and occurs in heterocysts. Upon nitrogen step-down, these specialized cells differentiate from vegetative cells in a process controlled by two major regulators: NtcA and HetR. However, the regulon controlled by these two factors is only partially defined, and several aspects of the differentiation process have remained enigmatic. Using differential RNA-seq, we experimentally define a genome-wide map of >10,000 transcriptional start sites (TSS) of
Anabaena
sp. PCC7120, a model organism for the study of prokaryotic cell differentiation and N
2
fixation. By analyzing the adaptation to nitrogen stress, our global TSS map provides insight into the dynamic changes that modify the transcriptional organization at a critical step of the differentiation process. We identify >900 TSS with minimum fold change in response to nitrogen deficiency of eight. From these TSS, at least 209 were under control of HetR, whereas at least 158 other TSS were potentially directly controlled by NtcA. Our analysis of the promoters activated during the switch to N
2
fixation adds hundreds of protein-coding genes and noncoding transcripts to the list of potentially involved factors. These data experimentally define the NtcA regulon and the DIF
+
motif, a palindrome at or close to position −35 that seems essential for heterocyst-specific expression of certain genes.
Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan:galacturonosyltransferase complex
Authors: Atmodjo Melani A. , Sakuragi Yumiko , Zhu Xiang , Burrell Amy J. , Mohanty Sushree S. , Atwood James A. , Orlando Ron , Scheller Henrik V. , Mohnen Debra
Published: December 2011

Plant cell wall pectic polysaccharides are arguably the most complex carbohydrates in nature. Progress in understanding pectin synthesis has been slow due to its complex structure and difficulties in purifying and expressing the low-abundance, Golgi membrane-bound pectin biosynthetic enzymes.
Arabidopsis
galacturonosyltransferase (GAUT) 1 is an α-1,4-galacturonosyltransferase (GalAT) that synthesizes homogalacturonan (HG), the most abundant pectic polysaccharide. We now show that GAUT1 functions in a protein complex with the homologous GAUT7. Surprisingly, although both GAUT1 and GAUT7 are type II membrane proteins with single N-terminal transmembrane-spanning domains, the N-terminal region of GAUT1, including the transmembrane domain, is cleaved in vivo. This raises the question of how the processed GAUT1 is retained in the Golgi, the site of HG biosynthesis. We show that the anchoring of GAUT1 in the Golgi requires association with GAUT7 to form the GAUT1:GAUT7 complex. Proteomics analyses also identified 12 additional proteins that immunoprecipitate with the GAUT1:GAUT7 complex. This study provides conclusive evidence that the GAUT1:GAUT7 complex is the catalytic core of an HG:GalAT complex and that cell wall matrix polysaccharide biosynthesis occurs via protein complexes. The processing of GAUT1 to remove its N-terminal transmembrane domain and its anchoring in the Golgi by association with GAUT7 provides an example of how specific catalytic domains of plant cell wall biosynthetic glycosyltransferases could be assembled into protein complexes to enable the synthesis of the complex and developmentally and environmentally plastic plant cell wall.
Mechanistic modeling of the effects of myoferlin on tumor cell invasion
Authors: Eisenberg Marisa C. , Kim Yangjin , Li Ruth , Ackerman William E. , Kniss Douglas A. , Friedman Avner
Published: December 2011

Myoferlin (MYOF) is a member of the evolutionarily conserved ferlin family of proteins, noted for their role in a variety of membrane processes, including endocytosis, repair, and vesicular transport. Notably, ferlins are implicated in
Caenorhabditis elegans
sperm motility (Fer-1), mammalian skeletal muscle development and repair (MYOF and dysferlin), and presynaptic transmission in the auditory system (otoferlin). In this paper, we demonstrate that MYOF plays a previously unrecognized role in cancer cell invasion, using a combination of mathematical modeling and in vitro experiments. Using a real-time impedance-based invasion assay (xCELLigence), we have shown that lentiviral-based knockdown of MYOF significantly reduced invasion of MDA-MB-231 breast cancer cells in Matrigel bioassays. Based on these experimental data, we developed a partial differential equation model of MYOF effects on cancer cell invasion, which we used to generate mechanistic hypotheses. The mathematical model predictions revealed that matrix metalloproteinases (MMPs) may play a key role in modulating this invasive property, which was supported by experimental data using quantitative RT-PCR screens. These results suggest that MYOF may be a promising target for biomarkers or drug target for metastatic cancer diagnosis and therapy, perhaps mediated through MMPs.
Quantitative differences in CD45 expression unmask functions for CD45 in B-cell development, tolerance, and survival
Authors: Zikherman Julie , Doan Kristin , Parameswaran Ramya , Raschke William , Weiss Arthur
Published: December 2011

The receptor-like tyrosine phosphatase CD45 positively regulates antigen receptor signaling by dephosphorylating the inhibitory tyrosine of the src family kinases. CD45-deficient mice fail to fully unmask the role of CD45 in B cells because of the expression of a partially redundant tyrosine phosphatase, CD148. However, mice that are doubly deficient in CD45 and CD148 exhibit a very early block in B-cell development, thereby obscuring later roles for CD45. To overcome these limitations, here we take advantage of an allelic series of mice in which CD45 expression is titrated broadly (0–180%). Although high expression of CD45 inhibits T-cell receptor (TCR) signaling, we show that CD45 plays a purely positive regulatory role during B-cell receptor (BCR) signaling. In concert with exaggerated BCR signaling, increasing CD45 expression drives enhanced receptor editing in the bone marrow and profound loss of follicular and marginal zone B cells in the spleen. In the context of the IgHEL/sHEL model of B-cell tolerance, such high CD45 expression transforms anergy into deletion. Unexpectedly, elimination of the autoantigen sHEL in this model system in order to block clonal deletion fails to rescue survival of mature B cells. Rather, high CD45 expression reduces B-cell activating factor receptor (BAFFR) expression and inhibits B-cell activating factor (BAFF)–induced B-cell survival in a cell-intrinsic manner. Taken together, our findings reveal how CD45 function diverges in T cells and B cells, as well as how autoreactive B cells are censored as they transit development.
A quick fix? A retrospective analysis of the Sudan Comprehensive Peace Agreement
Authors: Rolandsen Øystein
                      H.
Published: December 2011

Critics decry the 2005 peace agreement between the government of the Sudan and the Sudan People's Liberation Movement as incomplete, a result of the desire of external actors for a quick solution that is neither truly comprehensive nor sustainable. Through a chronological analysis of the peace process between 2000 and 2005, this article demonstrates that the scope for compromise was limited and that a significantly ‘better’ deal was unlikely. The article's ambition is to present a concise and empirically grounded analysis of the peace process and to lay foundations for further investigation of a crucial, contested and complicated subject in Sudan's recent history.
The effects of government policies on cereal consumption pattern change in the Gambia
Authors: Gajigo Ousman , Saine Abdoulaye
Published: December 2011

This paper examines the effects of agricultural policies in the Gambia since independence from Great Britain in 1965. Under the two governments that have ruled the country since then, the People's Progressive Party (PPP) led by Dawda Jawara (1965–1994) and the Alliance for Patriotic Re-orientation and Construction (APRC) led by Yahya Jammeh, the country has shown little to no growth in agricultural productivity. Moreover, recent policy changes, beginning in the 1980s, resulted in marked shifts in cereal consumption patterns. Rice, which has been the staple food for the past century, but is mainly imported, has been surpassed by locally grown millet as the most heavily consumed cereal in the country as a whole. However, this change is unlikely to lead to future food security as long as the failure to implement long-term agricultural development strategies by the current APRC regime continues.
Continuous primitive accumulation in Ghana: the real-life stories of dispossessed peasants in three mining communities
Authors: Ayelazuno Jasper
Published: December 2011

The purpose of this article is to provide an opportunity for the peasants in three mining communities in Ghana to voice their experiences of primitive accumulation under contemporary global neo-liberalism. There is a plethora of literature on the exploitation of Africa, drawing on theories of new imperialism or ‘accumulation by dispossession’. However, there is not much grassroots empirical work on how different social groups experience accumulation by dispossession. It seems that NGOs and journalists do better on this than intellectuals. I seek in this article to contribute to filling this lacuna, by focusing on the hardest hit social group, namely, the peasants. I also argue that the existence of this lacuna has major theoretical and political implications for the struggle for alternatives to capitalism and ‘development’ that is distinctly anti-imperialist. The article is based on data collected through focus group discussions and in-depth personal interviews with peasants affected by surface mining activities of transnational mining corporations in three mining communities in the resource-rich Western Region of Ghana: Prestea, Dumasi and Teberebie.
SNPxGE2: a database for human SNP–coexpression associations
Authors: Wang Yupeng , Joseph Sandeep J. , Liu Xinyu , Kelley Michael , Rekaya Romdhane
Published: December 2011

Motivation: Recently, gene–coexpression relationships have been found to be often conditional and dynamic. Many studies have suggested that single nucleotide polymorphisms (SNPs) have impacts on gene expression variations in human populations.

Results: The SNPxGE2 database contains the computationally predicted human SNP–coexpression associations, i.e. the differential coexpression between two genes is associated with the genotypes of an SNP. These data were generated from a large-scale association study that was based on the HapMap phase I data, which covered 269 individuals from 4 human populations, 556 873 SNPs and 15 000 gene expression profiles. In order to reduce the computational cost, the SNP–coexpression associations were assessed using gap/substitution models, proven to have a comparable power to logistic regression models. The results, at a false discovery rate (FDR) cutoff of 0.1, consisted of 44 769 and 50 792 SNP–coexpression associations based on single and pooled populations, respectively, and can be queried in the SNPxGE2 database via either gene symbol or reference SNP ID. For each reported association, a detailed information page is provided.

Availability:  http://lambchop.ads.uga.edu/snpxge2/index.php

Contact:  wyp1125@uga.edu, rrekaya@uga.edu
Early Animal Models of Rickets and Proof of a Nutritional Deficiency Hypothesis
Authors: Chesney Russell W.
Published: December 2011

In the period between 1880 and 1930, the role of nutrition and nutritional deficiency as a cause of rickets was established based upon the results from 6 animal models of rickets. This greatly prevalent condition (60%–90% in some locales) in children of the industrialized world was an important clinical research topic. What had to be reconciled was that rickets was associated with infections, crowding, and living in northern latitudes, and cod liver oil was observed to prevent or cure the disease. Several brilliant insights opened up a new pathway to discovery using animal models of rickets. Studies in lion cubs, dogs, and rats showed the importance of cod liver oil and an antirachitic substance later termed vitamin D. They showed that fats in the diet were required, that vitamin D had a secosteroid structure and was different from vitamin A, and that ultraviolet irradiation could prevent or cure rickets. Several of these experiments had elements of serendipity in that certain dietary components and the presence or absence of sunshine or ultraviolet irradiation could critically change the course of rickets. Nonetheless, at the end of these studies, a nutritional deficiency of vitamin D resulting from a poor diet or lack of adequate sunshine was firmly established as a cause of rickets.
Hybridization to Tissues in Suspension for Whole-Mount FISH in Drosophila
Authors: Dernburg Abby F.
Published: December 2011

Hybridization to some Drosophila tissues, such as embryos or egg chambers, is easily performed in suspension. The reaction is set up in 0.5-mL polymerase chain reaction (PCR) tubes and the solutions are changed by allowing the tissue to settle to the bottom of the tube, aspirating the liquid carefully, and replacing it with 400–500 µL of a new solution. This is by far the most convenient way to perform the hybridization and requires a minimum volume for all washing steps. The denaturation step is also easy to perform consistently because the sample can be heated and annealed in a thermal cycler or conventional water bath. This protocol describes hybridization to tissues in suspension for whole-mount fluorescent in situ hybridization (FISH) in Drosophila.
Preparation of Samples for Single-Worm Tracking
Authors: Yemini Eviatar , Kerr Rex A. , Schafer William R.
Published: December 2011

Neurobiological research in genetically tractable organisms relies heavily on robust assays for behavioral phenotypes. The simple body plan of the nematode Caenorhabditis elegans makes it particularly amenable to the use of automated microscopy and image analysis to describe behavioral patterns quantitatively. This protocol first describes the preparation and use of media for growing and maintaining worms for tracking. The second part of the protocol describes how to prepare a single young adult worm for recording during video analysis. Although the protocol was developed for use in a single-worm tracker, it addresses factors important for the generation of reproducible, standardized images in all systems.
X-Ray Microtomographic Imaging of Intact Vertebrate Embryos
Authors: Metscher Brian D.
Published: December 2011

X-ray microtomography (microCT) is a highly versatile imaging method, and with appropriate contrast stains and sample mounting, it can produce high-quality images of embryos at a wide range of developmental stages. The techniques presented here provide simple and robust methods for gel embedding and microCT scanning of vertebrate embryos. The specimens are fixed by any common method, contrast-stained with phosphotungstic acid (PTA, a common reagent in histological staining), and mounted in agarose gel for scanning. The gel mounting immobilizes the sample effectively during a long scan, and holds the embryo in its liquid medium (70% ethanol), allowing nondestructive three-dimensional (3D) imaging to be followed by, for example, histological processing. An alternative procedure is given for imaging resin-embedded samples intended for transmission electron microscopy (TEM) or subsequent sectioning and ultrastructural analysis. These procedures are expected to lend themselves well to quantitative analyses of mutant and experimental phenotypes and to generating accurate 3D anatomical data for embryological atlases.
Methods for Imaging Thick Specimens: Confocal Microscopy, Deconvolution, and Structured Illumination
Authors: Murray John M.
Published: December 2011

When a thick specimen is viewed through a conventional microscope, one sees the sum of a sharp image of an in-focus region plus blurred images of all of the out-of-focus regions. High background, scattering, and aberrations are all problems when viewing thick specimens. Several methods are available to deal with these problems in living samples. These methods can be grouped into three classes: primarily optical (e.g., confocal microscopy, multiphoton microscopy), primarily computational (e.g., deconvolution techniques), and mixed (e.g., structured illumination) approaches. This article describes these techniques, which make it possible to see details within thick specimens (e.g., the interiors of cells within living tissue) by optical sectioning, without the artifacts associated with physically sectioning the specimen.
Reduction of sexual dimorphism in stream‐resident forms of three‐spined sticklebackGasterosteus aculeatus
Authors: Kitano J. , Mori S. , Peichel C. L.
Published: December 2011

Sexual dimorphism in geometric body shape and external morphology was compared between marine and stream‐resident forms of three‐spined sticklebackGasterosteus aculeatuscollected from North America and Japan. Some aspects of sexual dimorphism were shared between ecotypes: males had larger heads than females with no significant effect of ecotype on the magnitude of sexual dimorphism. By contrast, a significant sex‐by‐ecotype interaction was found for body depth. Males tended to have deeper bodies than females in both forms, but the magnitude of sexual dimorphism was reduced in stream‐resident forms. Although females were generally larger in standard length and had larger pelvic girdles, significant sexual dimorphism in these traits was not consistently found across populations or ecotypes. These results suggest that some aspects of sexual dimorphism were shared between ecotypes, while others were unique to each population. The results further suggest that ecology may influence the evolution of sexual dimorphism in some external morphological traits, such as body depth.
VEGFA and VEGFR2 genetic polymorphisms and survival in patients with diffuse large B cell lymphoma
Authors: Kim Min Kyoung , Suh Cheolwon , Chi Hyun Sook , Cho Hee Soon , Bae Young Kyung , Lee Kyung Hee , Lee Gyeong‐Won , Kim In‐Suk , Eom Hyeon‐Seok , Kong Sun‐Young , Bae Sung Hwa , Ryoo Hun Mo , Shin Im‐Hee , Mun Yeung‐Chul , Chung Hwasoon , Hyun Myung Soo
Published: December 2011

We evaluated the impact of functional polymorphisms in the vascular endothelial growth factor A (VEGFA) and vascular endothelial growth factor 2 (VEGFR2) genes on the survival of patients with diffuse large B cell lymphoma (DLBCL). Five potentially functional polymorphisms in the VEGFA (rs699947, rs2010963 and rs3025039) and VEGFR2 (rs1870377 and rs2305948) genes were assessed in 494 DLBCL patients treated with rituximab plus CHOP chemotherapy. The associations of genotype and haplotype with overall survival (OS) and progression‐free survival (PFS) were analyzed. Of the five polymorphisms, VEGFR2 rs1870377T>A was significantly associated with both OS and PFS; in the dominant model, patients with the AA + TA genotypes had significantly better OS (P = 0.002) and PFS (P = 0.004) than those with the TT genotype. The association between significantly better OS and the AA + TA genotypes was observed separately in patients with low (0–2; P = 0.035) and high (3–5; P = 0.043) International Prognostic Index scores. Multivariate analysis showed that, relative to the AA + TA genotypes, the TT genotype was an independent prognostic factor for poor OS (HR, 1.71; 95% CI, 1.21–2.43; P = 0.002) and PFS (HR, 1.57; 1.13–2.17; P = 0.004). Other independent significant predictors of survival in patients with DLBCL were International Prognostic Index score, age > 60 years, lactate dehydrogenase concentration >normal, extranodal disease >1 and presence of B symptoms. The VEGFR2 rs1870377 polymorphism might affect survival in patients with DLBCL, suggesting that angiogenesis might be related to poor survival in these patients. (Cancer Sci 2012; 103: 497–503)
Retrospective analysis of mammographic findings for Japanese women: A potential predictor for breast malignancies
Authors: Tamaki Kentaro , Ishida Takanori , Miyashita Minoru , Amari Masakazu , Ohuchi Noriaki , Uehara Kano , Kamada Yoshihiko , Tamaki Nobumitsu , Sasano Hironobu
Published: December 2011

This purpose of this study was to retrospectively stratify the risks of malignancy according to the mammographic characteristics of Japanese women. We studied the mammographic findings of 1267 Japanese women. We characterized malignant phenotypes according to mass shape, margin and mass density, and by shape and distribution of calcified foci, and to obtain possible predictors for malignancies according to age groups. Lobular and irregular mass shape, no circumscribed margin and higher density turned out to be more powerful predictors for malignancy than other radiological factors (P < 0.001, respectively). The ratio of the cases detected as a mass in those between 21 and 49 years was lower than that of other age groups. In addition, the presence of calcifications and no mammographic abnormalities were the most powerful predictors for malignancies in the young age groups (P < 0.001, respectively). The peak age of breast cancer is between 40 and 49 years in Japan. In the present study, subtle differences were found in the mammographic results for young and old women, in contrast to those of women in the USA and Europe. The results of this study might enable more accurate prediction of biological behavior of the breast lesions in Japanese women. (Cancer Sci 2012; 103: 472–476)
Therapeutic drug monitoring to adjust dosing in morbid obesity – a new use for an old methodology
Authors: Martin Jennifer H. , Saleem Mohamed , Looke David
Published: December 2011

The phenomena of hunger and need at one end of the spectrum and obesity and plenty on the other is an anomaly of the 21st century, likely to be due to a combination of distributive inequities in food, social justice, access to education and other socio‐economic factors. Both are major problems worldwide, although obesity has more media coverage due to the exponentially increasing incidence and the huge social and economic burden this is placing on Western society. For example, prevalence rates of obesity are currently exceeding 30% of adults in the USA with direct morbidity and mortality complications, in addition to the additional obesity‐related health problems and death. Obesity is also rising in children. Obese people are thus a sizable group, and as with those with altered renal or liver function, require specific consideration with respect to the appropriate dosing of medications. However guidelines for how to do this in obesity are not currently available, due to the paucity of literature and regulatory rules for new medications which usually only request the demonstration of average population effectiveness. We believe it is timely for regulatory agencies worldwide to mandate studies involving consideration of body size, particularly obesity, in approving new medications across the therapeutic spectrum. This will drive the pharmaceutical industry to consider these groups in studies and will encourage investigator‐initiated research using therapeutic drug monitoring (TDM), target concentration therapy (TCI) and pharmacogenetic (PGx) studies to optimize drug dosing.
From plots to islands: species diversity at different scales
Authors: Sfenthourakis Spyros , Panitsa Maria
Published: December 2011

Aim  To investigate how plant diversity of whole islands (‘gamma’) is related to alpha and beta diversity patterns among sampling plots within each island, thus exploring aspects of diversity patterns across scales.

Location  Nineteen islands of the Aegean Sea, Greece.

Methods  Plant species were recorded at both the whole‐island scale and in small 100 m2 plots on each island. Mean plot species richness was considered as a measure of alpha diversity, and six indices of the ‘variation’‐type beta diversity were also applied. In addition, we partitioned beta diversity into a ‘nestedness’ and a ‘replacement’ component, using the total species richness recorded in all plots of each island as a measure of ‘gamma’ diversity. We also applied 10 species–area models to predict the total observed richness of each island from accumulated plot species richness.

Results  Mean alpha diversity was not significantly correlated with the overall island species richness or island area. The range of plot species richness for each island was significantly correlated with both overall species richness and area. Alpha diversity was not correlated with most indices of beta diversity. The majority of beta diversity indices were correlated with whole‐island species richness, and this was also true for the ‘replacement’ component of beta diversity. The rational function model provided the best prediction of observed island species richness, with Monod’s and the exponential models following closely. Inaccuracy of predictions was positively correlated with the number of plots and with most indices of beta diversity.

Main conclusions  Diversity at the broader scale (whole islands) is shaped mainly by variation among small local samples (beta diversity), while local alpha diversity is not a good predictor of species diversity at broader scales. In this system, all results support the crucial role of habitat diversity in determining the species–area relationship.