bluuebunny/crossref_metadata_2025 huggingface dataset:
Emergence of Stuttering-Like Disfluencies During Therapy: An Exploratory Study
Authors: Hall Nancy E.
Published: March 2011

Anecdotal reports exist on the emergence of stuttering-like behavior during the course of language therapy, yet there is little empirical evidence of its occurrence. The aim of the present study is to address this lack of evidence by surveying school-based speech-language pathologists on their experiences with this phenomenon. Results show nearly 50% of the 324 respondents report observing the appearance of disfluencies in the speech of previously fluent children during language therapy. Findings are discussed from the perspective of interacting processes of language formulation and speech production. Cautions on data interpretation and recommendations for future research are presented.
Medicaid 101: A Primer for Speech-Language Pathologists in Education Settings
Authors: Deppe Janet , Ireland Marie
Published: March 2011

This paper will provide the school-based speech-language pathologist (SLP) with an overview of the federal requirements for Medicaid, including provider qualifications, “under the direction of” rule, medical necessity, and covered services. Billing, documentation, and reimbursement issues at the state level will be examined. A summary of the findings of the Office of Inspector General audits of state Medicaid plans is included as well as what SLPs need to do in order to ensure that services are delivered appropriately. Emerging trends and advocacy tools will complete the primer on Medicaid services in school settings.
Tiny antennas form vast radio telescope array
Authors: Feder Toni
Published: March 2011

A grassroots telescope array is taking aim at a wide range of astronomy questions, with projects in geophysics and agriculture piggybacking on its infrastructure.
Recollision physics
Authors: Corkum Paul B.
Published: March 2011

A technique that uses light to create particle collisions that create light is poised to provide unprecedented access to the inner workings of atoms and molecules.
End of a Paradigm: The Current Crisis and the Idea of Stateless Cities
Authors: Therborn Göran
Published: March 2011

Urban studies in the social sciences have for two decades been driven by a hegemonic conception, under slightly different, competing labels: world city, global city, and world city networks. While making important cognitive contributions, it has, I argue, been fundamentally flawed in assuming nation-states and state-processed national economies to be unimportant to the world economy and to world/global cities. While in several ways enriching urban knowledge, its dominance has also impoverished urban research by reducing cities to zip codes of firms and labour markets, leaving out that cities are also places of meaningful built environments, in which people live and interact. Basic assumptions and arguments of the world/global city idea by the three most distinguished representatives of the approach—John Friedmann, Saskia Sassen, and Peter J Taylor—are critically scrutinized. The current economic crisis has demonstrated these assumptions and arguments about cities in the world economy as untenable. The economic crisis is spawning a paradigmatic crisis, which should be seen as an opportunity for wider views of cities to be opened up.
Migration and Climate Change: Towards an Integrated Assessment of Sensitivity
Authors: Black Richard , Kniveton Dominic , Schmidt-Verkerk Kerstin
Published: March 2011

This paper sets out a new approach to understanding the relationship between migration and climate change. Based on the understanding that migration is a significant, growing, but also complex phenomenon, this approach seeks to address the sensitivity of existing migration drivers in specific contexts to climate change. In contrast to existing approaches which have sought to generate global-level estimates of the numbers of ‘climate migrants’, this integrated assessment approach seeks instead to understand how and why existing flows from and to specific locations may change in the future, and provide a practical tool for climate adaptation planning. Examples of the application of this approach are provided for Ghana and Bangladesh.
Game-Theory Approach for Resident Coalitions to Allocate Green-Roof Benefits
Authors: Tsang S W , Jim C Y
Published: March 2011

Roof greening in cities provides a range of environmental, economic, and social benefits. However, the lack of motivation among property owners in high-rise buildings poses an intractable obstacle to its wide implementation in compact cities. Cooperation amongst stakeholders, from individual-building to city-block scales, could facilitate adoption of green roofing, with implications for urban sustainability. This study is an attempt to evaluate the net gain from roof greening in terms of apportioned collective costs and benefits to a group of property owners. With government tax exemption to encourage green-roof installation, a fair-allocation scheme, based on the Shapley value, is adopted to distribute the net gain in a partnership structure. A case study in Hong Kong serves to illustrate the application of the method to allocate theoretically the sharable gain of roof greening translated into monetary terms. The results verify the importance of individual owners in different coalition configurations in moulding the benefit profile. The crux of the financial incentive scheme is the enhanced rewards to optimized cooperation, and the pump-priming triggering of cooperation and action. The benefits of green roofs could be maximized by their widespread and contiguous, rather than piecemeal, installation. Green roofs could reduce both capital and recurrent public expenditures in stormwater management, healthcare, and green-space provision, the savings from which would be more than enough to fund the tax-exemption scheme. The findings yield convincing justifications for government financial incentives to promote public–private partnerships and cooperative coalitions of stakeholders in roof greening in compact urban areas.
Volatile organic compounds sources in Paris in spring 2007. Part II: source apportionment using positive matrix factorisation
Authors: Gaimoz Cécile , Sauvage Stéphane , Gros Valérie , Herrmann Frank , Williams Jonathan , Locoge Nadine , Perrussel Olivier , Bonsang Bernard , d'Argouges Odile , Sarda-Estève Roland , Sciare Jean
Published: March 2011

Environmental context
Volatile organic compounds are key compounds in atmospheric chemistry as precursors of ozone and secondary organic aerosols. To determine their impact at a megacity scale, a first important step is to characterise their sources. We present an estimate of volatile organic compound sources in Paris based on a combination of measurements and model results. The data suggest that the current emission inventory strongly overestimates the volatile organic compounds emitted from solvent industries, and thus needs to be corrected.

Abstract
A positive matrix factorisation model has been used for the determination of volatile organic compound (VOC) source contributions in Paris during an intensive campaign (May–June 2007). The major sources were traffic-related emissions (vehicle exhaust, 22% of the total mixing ratio of the measured VOCs, and fuel evaporation, 17%), with the remaining emissions from remote industrial sources (35%), natural gas and background (13%), local sources (7%), biogenic and fuel evaporation (5%) and wood-burning (2%). It was noted that the remote industrial contribution was highly dependent on the air-mass origin. During the period of oceanic influences (when only local and regional pollution was observed), this source made a relatively low contribution (<15%), whereas the source contribution linked to traffic was high (54%). During the period of continental influences (when additional continental pollution was observed), remote industrial sources played a dominant role, contributing up to 50% of measured VOCs. Finally, the positive matrix factorisation results obtained during the oceanic air mass-influenced period were compared with the local emission inventory. This comparison suggests that the VOC emission from solvent industries might be overestimated in the inventory, consistent with findings in other European cities.
Arsenic cycling in marine systems: degradation of arsenosugars to arsenate in decomposing algae, and preliminary evidence for the formation of recalcitrant arsenic
Authors: Navratilova Jana , Raber Georg , Fisher Steven J. , Francesconi Kevin A.
Published: March 2011

Environmental context
Despite high levels of complex organoarsenic compounds in marine organisms, arsenic in seawater is present almost entirely as inorganic species. We examine the arsenic products from a marine alga allowed to decompose under simulated natural coastal conditions, and demonstrate a multi-step conversion of organic arsenicals to inorganic arsenic. The results support the hypothesis that the arsenic marine cycle begins and ends with inorganic arsenic.

Abstract
Time series laboratory experiments were performed to follow the degradation of arsenic compounds naturally present in marine algae. Samples of the brown alga Ecklonia radiata, which contains three major arsenosugars, were packed into 12 tubes open to air at one end only, and allowed to naturally decompose under moist conditions. During the subsequent 25 days, single tubes were removed at intervals of 1–4 days; their contents were cut into four sections (from open to closed end) and analysed for arsenic species by HPLC/ICPMS following an aqueous methanol extraction. In the sections without direct contact with air, the original arsenosugars were degraded primarily to arsenate via two major intermediates, dimethylarsinoylethanol (DMAE) and dimethylarsinate (DMA). The section with direct contact with air degraded more slowly and significant amounts of arsenosugars remained after 25 days. We also report preliminary data suggesting that the amount of non-extractable or recalcitrant arsenic (i.e. insoluble after sequential extractions with water/methanol, acetone, and hexane) increased with time. Furthermore, we show that treatment of the pellet with 0.1-M trifluoroacetic acid at 95°C solubilises a significant amount of this recalcitrant arsenic, and that the arsenic is present mainly as a cationic species of currently unknown structure.
Nazi Germany and the Karaites in 1938–1944: between racial theory andRealpolitik
Authors: Feferman Kiril
Published: March 2011

This article explores the policies of Nazi Germany towards the Karaites, a group of Jewish ancestry which emerged during the seventh to the ninth centuries CE, when its followers rejected the mainstream Jewish interpretation of Tanakh. Karaite communities flourished in Persia, Turkey, Egypt, Crimea, and Lithuania. From 1938 to 1944, the Nazi bureaucracy and scholarship examined the question of whether the Karaites were of Jewish origin, practiced Judaism and had to be treated as Jews. Because of its proximity to Judenpolitik and later to the Muslim factor, the subject got drawn into the world of Nazi grand policy and became the instrument of internecine power struggles between various agencies in Berlin. The Muslim factor in this context is construed as German cultivation of a special relationship with the Muslim world with an eye to political dividends in the Middle East and elsewhere. Nazi views of the Karaites’ racial origin and religion played a major role in their policy towards the group. However, as the tides of the war turned against the Germans, various Nazi agencies demonstrated growing flexibility either to re-tailor the Karaites’ racial credentials or to entirely gloss over them in the name of “national interests,” i.e. a euphemism used to disguise Nazi Germany's overtures to the Muslim world.
Rewriting and remembering Romanian communism: some controversial issues
Authors: Ciobanu Monica
Published: March 2011

This article examines the dynamic relationship between the two major dimensions of memory and justice in the context of post-communist countries: truth-telling and retroactive justice. This interdependent and uneasy relationship is illustrated by recent attempts at constructing a new historical narrative of the communist past in Romania in the wake of the de-secretization of the files of both the Communist Party and the communist secret police (Securitate). A systematic analysis of the activity of institutions that have been directly involved in research and public education about the recent past – the National Archives, the National Council for the Study of Securitate's Archives, and the Institute for the Investigation of Crimes of Communism – is undertaken. The work of these three institutional actors shows a direct relationship between truth-telling in its various forms (access to archives, opening the files and exhumations) and any subsequent retroactive justice and restitution. The main argument of the paper is that while deep-seated dichotomies between former communist and anti-communists in addressing the past still persist, a more nuanced way of seeing the regime that explores the ambiguous line that divides outright repression from cooptation is emerging.
Connectedness of PPI network neighborhoods identifies regulatory hub proteins
Authors: Fox Andrew D. , Hescott Benjamin J. , Blumer Anselm C. , Slonim Donna K.
Published: March 2011

Motivation: With the growing availability of high-throughput protein–protein interaction (PPI) data, it has become possible to consider how a protein's local or global network characteristics predict its function.

Results: We introduce a graph-theoretic approach that identifies key regulatory proteins in an organism by analyzing proteins' local PPI network structure. We apply the method to the yeast genome and describe several properties of the resulting set of regulatory hubs. Finally, we demonstrate how the identified hubs and putative target gene sets can be used to identify causative, functional regulators of differential gene expression linked to human disease.

Availability: Code is available at http://bcb.cs.tufts.edu/hubcomps.

Contact:  fox.andrew.d@gmail.com; slonim@cs.tufts.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
MemLoci: predicting subcellular localization of membrane proteins in eukaryotes
Authors: Pierleoni Andrea , Martelli Pier Luigi , Casadio Rita
Published: March 2011

Motivation: Subcellular localization is a key feature in the process of functional annotation of both globular and membrane proteins. In the absence of experimental data, protein localization is inferred on the basis of annotation transfer upon sequence similarity search. However, predictive tools are necessary when the localization of homologs is not known. This is so particularly for membrane proteins. Furthermore, most of the available predictors of subcellular localization are specifically trained on globular proteins and poorly perform on membrane proteins.

Results: Here we develop MemLoci, a new support vector machine-based tool that discriminates three membrane protein localizations: plasma, internal and organelle membrane. When tested on an independent set, MemLoci outperforms existing methods, reaching an overall accuracy of 70% on predicting the location in the three membrane types, with a generalized correlation coefficient as high as 0.50.

Availability: The MemLoci server is freely available on the web at: http://mu2py.biocomp.unibo.it/memloci. Datasets described in the article can be downloaded at the same site.

Contact:  casadio@biocomp.unibo.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Diabetes Blockade of Sevoflurane Postconditioning Is Not Restored by Insulin in the Rat Heart
Authors: Drenger Benjamin , Ostrovsky Israel A. , Barak Michal , Nechemia-Arbely Yael , Ziv Ehud , Axelrod Jonathan H.
Published: March 2011

Background

The possibility of restoring sevoflurane postconditioning (sevo-postC) cardioprotection in diabetic animals is uncertain. We hypothesized that attenuation of myocardial injury by sevo-postC might be hindered by inhibition of signal transducer and activator of transcription (STAT) 3-regulated activity of phosphatidylinositol 3-kinase (PI3K) in diabetic animals. To determine whether postC cardioprotection can be restored by normoglycemia, we treated rats with insulin.

Methods

Diabetic or nondiabetic rats were randomly subjected to 30-min ischemia/reperfusion, with ischemic postC or sevo-postC, with and without mitochondrial adenosine triphosphate-dependent potassium channel blocker 5-hydroxy decanoate sodium and PI3K antagonist wortmannin. The infarct area, phosphorylated STAT3, and apoptosis were examined. Studies were repeated after insulin treatment.

Results

Ischemic postC and sevo-postC significantly reduced infarct size by 50% in the nondiabetic rats (P < 0.002), a phenomenon completely reversed by 5-hydroxy decanoate sodium and wortmannin. Diabetes mellitus blocked the protective effect of postC, and insulin treatment to achieve normoglycemia did not restore cardioprotection. Phosphorylated STAT3 nuclear retention was significantly increased after ischemia-reperfusion and was further enhanced in response to ischemic postC (P < 0.05) but was significantly reduced in diabetic rats (by 43%; P < 0.01).

Conclusions

The effective reduction in infarct size and apoptosis in the nondiabetic rat heart by postC was completely abrogated in diabetic rats. This inhibition is not relieved by insulin-induced normoglycemia. The PI3K pathway and mitochondrial adenosine triphosphate-dependent potassium channel activation are involved in the mechanism of postC. In diabetic rats, STAT3 activation was strongly reduced, as was postC cardioprotection, suggesting that the inability of insulin to restore postC may be attributed to diabetes-induced STAT3-mediated inhibition of PI3K signaling.
Flagellar phenotypic plasticity in volvocalean algae correlates with Péclet number
Authors: Solari Cristian A. , Drescher Knut , Ganguly Sujoy , Kessler John O. , Michod Richard E. , Goldstein Raymond E.
Published: March 2011

Flagella-generated fluid stirring has been suggested to enhance nutrient uptake for sufficiently large micro-organisms, and to have played a role in evolutionary transitions to multicellularity. A corollary to this predicted size-dependent benefit is a propensity for phenotypic plasticity in the flow-generating mechanism to appear in large species under nutrient deprivation. We examined four species of volvocalean algae whose radii and flow speeds differ greatly, with Péclet numbers (Pe) separated by several orders of magnitude. Populations of unicellularChlamydomonas reinhardtiiand one- to eight-celledGonium pectorale(Pe∼ 0.1–1) and multicellularVolvox carteriandVolvox barberi(Pe∼ 100) were grown in diluted and undiluted media. ForC. reinhardtiiandG. pectorale, decreasing the nutrient concentration resulted in smaller cells, but had no effect on flagellar length and propulsion force. In contrast, these conditions inducedVolvoxcolonies to grow larger and increase their flagellar length, separating the somatic cells further. Detailed studies onV. carterifound that the opposing effects of increasing beating force and flagellar spacing balance, so the fluid speed across the colony surface remains unchanged between nutrient conditions. These results lend further support to the hypothesized link between the Péclet number, nutrient uptake and the evolution of biological complexity in the Volvocales.
Social learning and evolution: the cultural intelligence hypothesis
Authors: van Schaik Carel P. , Burkart Judith M.
Published: March 2011

If social learning is more efficient than independent individual exploration, animals should learn vital cultural skills exclusively, and routine skills faster, through social learning, provided they actually use social learning preferentially. Animals with opportunities for social learning indeed do so. Moreover, more frequent opportunities for social learning should boost an individual's repertoire of learned skills. This prediction is confirmed by comparisons among wild great ape populations and by social deprivation and enculturation experiments. These findings shaped the cultural intelligence hypothesis, which complements the traditional benefit hypotheses for the evolution of intelligence by specifying the conditions in which these benefits can be reaped. The evolutionary version of the hypothesis argues that species with frequent opportunities for social learning should more readily respond to selection for a greater number of learned skills. Because improved social learning also improves asocial learning, the hypothesis predicts a positive interspecific correlation between social-learning performance and individual learning ability. Variation among primates supports this prediction. The hypothesis also predicts that more heavily cultural species should be more intelligent. Preliminary tests involving birds and mammals support this prediction too. The cultural intelligence hypothesis can also account for the unusual cognitive abilities of humans, as well as our unique mechanisms of skill transfer.
Exploring the costs and benefits of social information use: an appraisal of current experimental evidence
Authors: Rieucau Guillaume , Giraldeau Luc-Alain
Published: March 2011

Research on social learning has focused traditionally on whether animals possess the cognitive ability to learn novel motor patterns from tutors. More recently, social learning has included the use of others as sources of inadvertent social information. This type of social learning seems more taxonomically widespread and its use can more readily be approached as an economic decision. Social sampling information, however, can be tricky to use and calls for a more lucid appraisal of its costs. In this four-part review, we address these costs. Firstly, we address the possibility that only a fraction of group members are actually providing social information at any one time. Secondly, we review experimental research which shows that animals are circumspect about social information use. Thirdly, we consider the cases where social information can lead to incorrect decisions and finally, we review studies investigating the effect of social information quality. We address the possibility that using social information or not is not a binary decision and present results of a study showing that nutmeg mannikins combine both sources of information, a condition that can lead to the establishment of informational cascades. We discuss the importance of empirically investigating the economics of social information use.
Evolution, revolution or saltation scenario for the emergence of modern cultures?
Authors: d'Errico Francesco , Stringer Chris B.
Published: March 2011

Crucial questions in the debate on the origin of quintessential human behaviours are whether modern cognition and associated innovations are unique to our species and whether they emerged abruptly, gradually or as the result of a discontinuous process. Three scenarios have been proposed to account for the origin of cultural modernity. The first argues that modern cognition is unique to our species and the consequence of a genetic mutation that took place approximately 50 ka in Africa among already evolved anatomically modern humans. The second posits that cultural modernity emerged gradually in Africa starting at least 200 ka in concert with the origin of our species on that continent. The third states that innovations indicative of modern cognition are not restricted to our species and appear and disappear in Africa and Eurasia between 200 and 40 ka before becoming fully consolidated. We evaluate these scenarios in the light of new evidence from Africa, Asia and Europe and explore the mechanisms that may have led to modern cultures. Such reflections will demonstrate the need for further inquiry into the relationship between climate and demographic/cultural change in order to better understand the mechanisms of cultural transmission at work in Neanderthals and earlyHomo sapienspopulations.
The origins of stone tool technology in Africa: a historical perspective
Authors: de la Torre Ignacio
Published: March 2011

The search for the earliest stone tools is a topic that has received much attention in studies on the archaeology of human origins. New evidence could position the oldest traces of stone tool-use before 3.39 Myr, substantially earlier than previously documented. Nonetheless, the first unmistakable evidence of tool-making dates to 2.6 Ma, the period in which Oldowan assemblages first appear in the East African record. However, this is not an unchangeable time boundary, and considerations about the tempo and modo of tool-making emergence have varied through time. This paper summarizes the history of research on the origins of stone knapping in Africa and places the current evidence in a historical perspective.
Culture and cognition in the Acheulian industry: a case study from Gesher Benot Yaʿaqov
Authors: Goren-Inbar Naama
Published: March 2011

The Acheulian presence in the Dead Sea Rift and its environs is characterized by the discontinuity of its cultural manifestations. Nevertheless, the long stratigraphic sequences of the Acheulian Technocomplex provide a unique opportunity for synergetic examination along a temporal trajectory. Hominin cognitive and cultural behaviour are studied at Gesher Benot Yaʿaqov through analyses of lithic, palaeontological and palaeobotanical assemblages, as well as the Early–Middle Pleistocene environment, ecology and climate. The study attempts to reconstruct reduction sequences of some major artefact groups at the site, which include raw material acquisition, production, technology, typology, usage and discard. Experimental archaeology illustrates artefact mobility on the palaeo-landscape. Strategies of biomass-exploitation are studied in detail, with other aspects yielding additional information on hominin subsistence and adaptive responses to their environment. The cultural marker of fire and the spatial association of selected categories of finds are integrated in the general synthesis, allowing reconstruction of the cultural and cognitive realm of Acheulian hominins. The synthesis attempts to reassess the abilities, social structure, subsistence and adaptability to the changing environment of hominins in the Levantine Corridor.
What drives the evolution of hunter–gatherer subsistence technology? A reanalysis of the risk hypothesis with data from the Pacific Northwest
Authors: Collard Mark , Buchanan Briggs , Morin Jesse , Costopoulos Andre
Published: March 2011

Recent studies have suggested that the decisions that hunter–gatherers make about the diversity and complexity of their subsistence toolkits are strongly affected by risk of resource failure. However, the risk proxies and samples employed in these studies are potentially problematic. With this in mind, we retested the risk hypothesis with data from hunter–gatherer populations who lived in the northwest coast and plateau regions of the Pacific Northwest during the early contact period. We focused on these populations partly because the northwest coast and plateau differ in ways that can be expected to lead to differences in risk, and partly because of the availability of data for a wide range of risk-relevant variables. Our analyses suggest that the plateau was a more risky environment than the northwest coast. However, the predicted differences in the number and complexity of the populations' subsistence tools were not observed. The discrepancy between our results and those of previous tests of the risk hypothesis is not due to methodological differences. Rather, it seems to reflect an important but hitherto unappreciated feature of the relationship between risk and toolkit structure, namely that the impact of risk is dependent on the scale of the risk differences among populations.
Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
Authors: Yang Xiaohan , Tschaplinski Timothy J. , Hurst Gregory B. , Jawdy Sara , Abraham Paul E. , Lankford Patricia K. , Adams Rachel M. , Shah Manesh B. , Hettich Robert L. , Lindquist Erika , Kalluri Udaya C. , Gunter Lee E. , Pennacchio Christa , Tuskan Gerald A.
Published: March 2011

Small proteins (10–200 amino acids [aa] in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained ∼2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences. We identified an initial set of 12,852 sORFs encoding proteins of 10–200 aa in length. Three computational approaches were then used to enrich for bona fide protein-coding sORFs from the initial sORF set: (1) coding-potential prediction, (2) evolutionary conservation between P. deltoides and other plant species, and (3) gene family clustering within P. deltoides. As a result, a high-confidence sORF candidate set containing 1469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set. In the high-confidence sORF candidate set, known protein domains were identified in 1282 genes (higher-confidence sORF candidate set), out of which 611 genes, designated as highest-confidence candidate sORF set, were supported by proteomics data. Of the 611 highest-confidence candidate sORF genes, 56 were new to the current Populus genome annotation. This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available.
Preparation of Live Testis Squashes inDrosophila
Authors: Bonaccorsi Silvia , Giansanti Maria G. , Cenci Giovanni , Gatti Maurizio
Published: March 2011

INTRODUCTION

The easiest and fastest method for the analysis of spermatocyte growth and male meiosis is the examination of living testis squashes in aqueous solutions. These preparations allow unambiguous recognition of most cell types ofDrosophilaspermatogenesis, as well as most phases of male meiosis. Living testes squashes can be carried out successfully using a variety of aqueous solutions. This protocol describes a standard method for preparing live testes squashes and the various aqueous solutions that can be used.
Labeling Neuronal Membrane Receptors with Quantum Dots
Authors: Lévi Sabine , Dahan Maxime , Triller Antoine
Published: March 2011

INTRODUCTION

This protocol describes a highly sensitive approach for tracking the motion of membrane molecules over extended time periods with single-molecule resolution. This technique uses nanometer-sized quantum dots (QDs) linked to the extracellular part of the proteins to be followed. Single-fluorophore epifluorescence imaging then reveals the membrane diffusion of the particle of interest. Two methods are presented for labeling neurons with the primary antibody of choice along with a secondary anti-Fab antibody that is either biotinylated or directly coupled to the desired QD. The behavior of QD-labeled molecules can then be followed within the cell using epifluorescence imaging.
Microinjecting Cells Using a Pulsed-Flow Microinjection System
Authors: Dean David A. , Gasiorowski Joshua Z.
Published: March 2011

INTRODUCTION

The efficient delivery of exogenous DNA to cells for expression and function studies is an essential technique of modern cell biology, and direct delivery of genetic material by microinjection remains a reliable means of transfection. A pulsed-flow microinjection system, such as the Eppendorf InjectMan and FemtoJet systems, permits a high level of control over the microinjection parameters, ensuring reproducibility. The system is also easy to use, is rapid, and is less likely to damage cells than the constant-flow method.
Microinjecting Cells Using a Constant-Flow Microinjection System
Authors: Dean David A. , Gasiorowski Joshua Z.
Published: March 2011

INTRODUCTION

The efficient delivery of exogenous DNA to cells for expression and function studies is an essential technique of modern cell biology, and direct delivery of genetic material by microinjection remains a reliable means of transfection. In the system described here a constant flow of sample is delivered from the tip of the pipette, and the amount of sample injected into the cell is determined by how long the pipette remains in the cell. The system can be assembled at relatively low cost using commercially available components: Typically, a pressure regulator that can be adjusted for two pressures (back pressure and injection pressure), a capillary holder, and coarse and fine micromanipulators. A constant-flow system, by design, injects less reproducible cell volumes than does a pulsed-flow system. However, with practice, this difference can be made negligible.
MRI in Developmental Biology and the Construction of Developmental Atlases
Authors: Ruffins Seth W. , Jacobs Russell E.
Published: March 2011

INTRODUCTION

Microscopic magnetic resonance imaging (μMRI) is a noninvasive, nonoptical imaging modality that allows the entire volume of opaque specimens to be imaged. Because μMRI is not a destructive method, biologists are afforded anatomically unperturbed imagery of embryonic development and the ability to observe morphogenetic movements deep within optically inaccessible embryos. Compared with optical methods, μMRI data acquisition is slow, and image resolution is very low. This might suggest that μMRI is not viable for developmental studies. In this article, we discuss when μMRI is an appropriate imaging modality and how it has contributed to a richer understanding of embryonic development by allowing direct observation of dynamic processes in optically inaccessible regions of unperturbed embryos. We close the article with a discussion of μMRI for the construction of digital anatomical developmental atlases and how such atlases can be used.
Nonviral Gene Delivery
Authors: Dean David A. , Gasiorowski Joshua Z.
Published: March 2011

INTRODUCTION

Modern cell biology increasingly relies on molecular tools to facilitate the study of cellular processes. With the advent of recombinant DNA technology, reverse transcription–polymerase chain reaction (RT-PCR) to amplify almost any gene, and fluorescent proteins that can be fused to any desired target protein, the number and scope of functional studies designed to determine the roles of proteins within cells have exploded. Creating the appropriate fusion protein plasmid is a key step, but the DNA must also be delivered to the cell for expression and function studies. There are several common approaches for delivering DNA, including liposome- and polymer-mediated transfection, electroporation, and direct DNA delivery by microinjection. This article provides an overview of several of these nonviral gene delivery methods, with an emphasis on direct injection of plasmids into cells.
Integration of the life of field seismic data with the reservoir model at the Valhall Field‡
Authors: van Gestel Jean‐Paul , Best Kevin D. , Barkved Olav I. , Kommedal Jan H.
Published: March 2011

The frequent time‐lapse observations from the life of field seismic system across the Valhall field provide a wealth of information. The responses from the production and injection wells can be observed through time‐shift and amplitude changes. These observations can be compared to modelled synthetic seismic responses from a reservoir simulation model of the Valhall Field. The observed differences between the observations and the modelling are used to update and improve the history match of the reservoir model. The uncertainty of the resulting model is reduced and a more confident prediction of future reservoir performance is provided.

A workflow is presented to convert the reservoir model to a synthetic seismic response and compare the results to the observed time‐lapse responses for any time range and area of interest. Correlation based match quality factors are calculated to quantify the visual differences. This match quality factor allows us to quantitatively compare alternative reservoir models to help identify the parameters that best match the seismic observations.

Three different case studies are shown where this workflow has helped to reduce the uncertainty range associated with specific reservoir parameters. By updating various reservoir model parameters we have been able to improve the match to the observations and thereby improve the overall reservoir model predictability. The examples show positive results in a range of different reservoir modelling issues, which indicates the flexibility of this workflow and the ability to have an impact in most reservoir modelling challenges.
Wave equation least square imaging using the local angular Hessian for amplitude correction
Authors: Ren Haoran , Wu Ru‐Shan , Wang Huazhong
Published: March 2011

Local angular Hessian can be used to improve wave equation least square migration images. By decomposing the original Hessian operator into the local wavenumber domain or the local angle domain, the least square migration image is obtained as the solution of a linearized least‐squares inversion in the frequency and local angle domains. The local angular Hessian contains information about the acquisition geometry and the propagation effects based on the given velocity model. The inversion scheme based on the local angular Hessian avoids huge computation on the exact inverse Hessian matrix. To reduce the instability in the inversion, damping factors are introduced into the deconvolution filter in the local wavenumber domain and the local angle domain. The algorithms are tested using the SEG/EAGE salt2D model and the Sigsbee2A model. Results show improved image quality and amplitudes.
Maintaining northern peatland ecosystems in a changing climate: effects of soil moisture, drainage and drain blocking on craneflies
Authors: CARROLL MATTHEW J. , DENNIS PETER , PEARCE‐HIGGINS JAMES W. , THOMAS CHRIS D.
Published: March 2011

The capacity of peatlands in the northern hemisphere to provide carbon storage, maintain water quality and support northern biodiversity is threatened by a combination of climate change and inappropriate land management. Historical drainage and increasing temperatures threaten the maintenance of the high water tables required for effective peatland functioning, and there is an urgent need to develop appropriate adaptation strategies. Here we use a large‐scale replicated experimental design to test the effects of artificial drainage and drain blocking upon soil moisture and cranefly (Diptera: Tipulidae) abundance. Craneflies constitute a key component of peatland biological communities; they are important herbivores and a major prey item for breeding birds. However, they are also susceptible to drought, so are at risk from future climate change. We found that cranefly abundance increased with soil moisture, in a wedge‐shaped relationship; high soil moisture is a necessary condition for high cranefly abundance. Blocking drains increased both soil moisture (by 0.06 m3 m−3 in 2009 and 0.23 m3 m−3 in 2010) and cranefly abundance (1.3‐fold in 2009, 4.5‐fold in 2010), but the strength and significance of the effects varied between years. The benefits of restoring ecosystem moisture levels are likely to be greatest during dry years and at dry sites. This study provides some of the first evidence that adaptation management can potentially reduce some of the negative effects of climate change on vulnerable peatland systems. Management to maintain or increase soil moisture in peatlands can therefore be expected to increase populations of craneflies and their avian predators (which are of conservation and economic interest), but also increase the resilience of the ecosystem to future warming and increasingly frequent droughts, and improve carbon storage and water quality.
Impact of disability on families: grandparents' perspectives
Authors: Miller E. , Buys L. , Woodbridge S.
Published: March 2011

Background  Caring for a child with a disability can be a unique and challenging experience, with families often relying on informal networks for support. Often, grandparents are key support resources, yet little is known about their roles and experiences. Reporting on data collected in a larger Australian study, this article explores grandparents' experiences of caring for a child with a disability and the impact on their family relationships and quality of life.

Method  A qualitative purposive sampling design was utilised; semi‐structured interviews were conducted with 22 grandparents (17 women, 5 men) of children with a disability. Grandparents ranged in age from 55 to 75 years old and lived within a 90‐min drive of Brisbane, Australia. Interviews were transcribed and responses analysed using a thematic approach, identifying categories, themes and patterns.

Findings  Four key themes characterised grandparents' views about their role in the family: holding own emotions (decision to be positive), self‐sacrifice (decision to put family needs first), maintaining family relationships (being the ‘go‐between’) and quality of life for family in the future (concerns about the future).

Conclusions  Grandparents are central to family functioning and quality of life, but this contribution comes with a significant cost to their own personal well‐being. Implications for policy, practice and research are discussed, particularly grandparents' fear that their family could not cope without their support.
Mutations selected in the hepatitis C virus NS3 protease domain during sequential treatment with boceprevir with and without pegylated interferon alfa‐2b
Authors: Vermehren J. , Susser S. , Lange C. M. , Forestier N. , Karey U. , Hughes E. , Ralston R. , Tong X. , Zeuzem S. , Sarrazin C.
Published: March 2011

Summary.  Treatment with hepatitis C virus (HCV)‐NS3‐protease inhibitors lead to the selection of resistant variants. Viral kinetics and resistance profiles in patients who are re‐treated with the same protease inhibitor are unknown. Viral kinetics and NS3‐resistance mutations obtained by clonal sequencing of the NS3‐protease were analyzed in nine HCV‐genotype‐1‐infected nonresponder patients who were sequentially treated with boceprevir (400 mg t.i.d.) for 1 week, peginterferon‐alfa‐2b for 2 weeks and combination of the two for 2 weeks in varying order. In addition to predominant wild‐type isolates, previously described boceprevir‐resistant mutations (V36, T54, R155, A156, V170) were observed. Furthermore, two resistant mutations (Q41, F43) were detected for the first time in vivo. In three patients, mutations selected after initial treatment with boceprevir were re‐selected during subsequent boceprevir exposure. However, mutational patterns after the first and second exposure to boceprevir were different in five patients. In one patient, a viral variant (V55A) known to reduce susceptibility to boceprevir was the predominant variant observed at baseline and throughout treatment and was associated with a shallow viral decline. Different resistance mutations were selected during treatment with boceprevir ± peginterferon. Sequential short‐term dosing of boceprevir was not associated with accumulation of resistant variants but pre‐existing variants may impair virologic response.
Transgenic Bt maize: farmers’ perceptions, refuge compliance and reports of stem borer resistance in South Africa
Authors: Kruger M. , Van Rensburg J. B. J. , Van den Berg J.
Published: March 2011

Based on surface area, South Africa is currently ranked the eighth in planting genetically modified (GM) crops in the world. Bt maize (MON810) has been grown to control lepidopterous stem borers in South Africa since its first release during 1998. The first report of resistance of the African maize stem borer, Busseola fusca (Lepidoptera: Noctuidae) and poor compliance to refuge requirements that could have contributed to resistance development prompted this study which was done in the main maize production area of South Africa. Objectives were to evaluate farmer’s perceptions of the regulatory aspects guiding the planting of Bt maize and refugia and how it was applied between 1998 and 2010. This study involved 105 commercial farmers covering 87 778 ha of maize throughout the main maize production region on the Highveld of South Africa. A questionnaire survey was conducted and addressed signing of technical agreements upon purchasing GM seed, refuge compliance, pest management practices, perceived benefits and risks relating to Bt maize. Compliance with refugia requirements was low especially during the initial 5–7 years after release. An alarmingly high number of farmers applied insecticides as preventative sprays on Bt maize and refugia irrespective of stem borer infestation levels. A large proportion of farmers reported significant borer infestation levels on Bt maize and between 5% and 93% farmers in all districts applied insecticides to Bt maize to limit borer damage, indicating that the occurrence of resistance is more wide‐spread in the country than previously thought. This study shows irresponsible management of GM crop technology by farmers, chemical and seed companies. Concerns and perceptions of farmers in South Africa seem to differ from those in Europe. South African farmers perceived little, if any, negative impact on non‐target organisms and remain positive about the technology in spite of resistance development. Other studies indicated that European farmers were concerned about these aspects. A shared concern, however, was consumer acceptance of GM maize and marketability on the export market.
Herbivore‐induced plant volatiles enhance the ability of parasitic wasps to find hosts on a plant
Authors: Uefune M. , Kugimiya S. , Sano K. , Takabayashi J.
Published: March 2011

We previously reported that cabbage plants emitted volatiles in response to herbivory by diamondback moth (DBM) larvae and that a cocktail of four induced volatile compounds (n‐heptanal, sabinene, α‐pinene and (Z)‐3‐hexenyl acetate) attracted Cotesia vestalis, a wasp parasitoid of DBM larvae (Shiojiri et al., PLOS ONE, 2010). Here, we describe the behaviour of the wasp in response to exposure to the cocktail and a solvent (control) on crucifer plants (Brassica rapa) with DBM larvae. Wasps showed longer residence and search times on plants with the cocktail than they did on control plants. Further, both wasp–host encounters and oviposition frequencies were significantly higher on plants associated with the cocktail and the rates of parasitism on plants with the cocktail increased due to longer residence and increased searching activity by the parasitoid on the plant. These results indicate that the host‐searching activity of the parasitoid C. vestalis is enhanced on host‐infested plants by the DBM‐induced plant volatiles.