bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure of an early native‐like intermediate of β2‐microglobulin amyloidogenesis
Authors: Vanderhaegen Saskia , Fislage Marcus , Domanska Katarzyna , Versées Wim , Pardon Els , Bellotti Vittorio , Steyaert Jan
Published: July 2013

To investigate early intermediates of β2‐microglobulin (β2m) amyloidogenesis, we solved the structure of β2m containing the amyloidogenic Pro32Gly mutation by X‐ray crystallography. One nanobody (Nb24) that efficiently blocks fibril elongation was used as a chaperone to co‐crystallize the Pro32Gly β2m monomer under physiological conditions. The complex of P32G β2m with Nb24 reveals a trans peptide bond at position 32 of this amyloidogenic variant, whereas Pro32 adopts the cis conformation in the wild‐type monomer, indicating that the cis to trans isomerization at Pro32 plays a critical role in the early onset of β2m amyloid formation.
A Markov‐chain model description of binding funnels to enhance the ranking of docked solutions
Authors: Torchala Mieczyslaw , Moal Iain H. , Chaleil Raphael A. G. , Agius Rudi , Bates Paul A.
Published: July 2013

Within the crowded, seemingly chaotic environment of the cell, proteins are still able to find their binding partners. This is achieved via an ensemble of trajectories, which funnel them towards their functional binding sites, the binding funnel. Here, we characterize funnel‐like energy structures on the global energy landscape using time‐homogeneous finite state Markov chain models. These models are based on the idea that transitions can occur between structurally similar docking solutions, with transition probabilities determined by their difference in binding energy. Funnel‐like energy structures are those containing solutions with very high equilibrium populations. Although these are found surrounding both near‐native and false positive binding sites, we show that the removal of nonfunnel‐like energy structures, by filtering away solutions with low maximum equilibrium population, can significantly improve the ranking of docked poses. Proteins 2013; 81:2143–2149. © 2013 Wiley Periodicals, Inc.
Silicon doping effect on the crystallization behavior of Ge2Sb2Te5 film
Authors: Jiang Yifan , Xu Ling , Chen Jing , Zhang Rui , Su Weining , Yu Yao , Ma Zhongyuan , Xu Jun
Published: July 2013

Pure Ge2Sb2Te5 thin films and Si‐doped Ge2Sb2Te5 thin films were deposited by electron beam evaporation method. The property of Si‐doped Ge2Sb2Te5 films are compared with that of pure Ge2Sb2Te5 films. Through in situ resistance measurement and I–V characteristic tests, an improvement of amorphous stability and an increase of crystalline resistivity are observed. The phase‐separation phenomenon is observed in TEM pictures and a distinct decrease of crystal grain size in Si‐doped Ge2Sb2Te5 thin film can be seen in HRTEM pictures. A blueshift and broadening of peaks after Si doping in Raman spectra are found and from absorption spectra, the broadening of crystalline optical bandgap in Si‐doped Ge2Sb2Te5 thin film is proved. Finally, the behavior of doped Si atoms is proposed to explain the effect of Si doping in Ge2Sb2Te5 thin film.
Influence of crystal polarity on Mg incorporation in ZnO
Authors: Adachi Yutaka , Ohashi Naoki , Sakaguchi Isao , Haneda Hajime
Published: July 2013

In this study, we investigated the influence of polarity on Mg incorporation in ZnO films grown using pulsed laser deposition. The photoluminescence (PL) measurements of (Zn,Mg)O films grown on the c(+) and c(−) faces of ZnO revealed that the peak position of the near‐band‐edge emission for the films on the c(−)‐face was at a shorter wavelength than that for the films on the c(+)‐face. This result indicates that the Mg content in the films on the c(−)‐face is higher than that for the films on the c(+)‐face regardless of the same growth conditions used, except for the polarity of the substrates. This difference in the Mg content in the c(+)‐ and c(−)‐polar films can result from the difference in the value of the sticking coefficients for Zn atoms on the c(+)‐ and c(−)‐faces. We also demonstrated that polarity determination can be possible by (Zn,Mg)O film deposition followed by PL mapping measurement.
Control Charts monitoring Product's Loss to Society
Authors: Celano G. , Faraz A. , Saniga E.
Published: July 2013

Taguchi introduced a new philosophy in quality control that accounts for the economic loss associated to process variation measured by deviations from the target value of a product quality characteristic. The Taguchi loss function has been considered in the design of control charts only for the computation of costs associated with nonconformities. This paper considers sample statistics based on the Taguchi loss function as a means to implement Shewhart control charts monitoring both the deviation from the target and dispersion of normally distributed quality characteristics. The aim of this proposed control chart is to perform on‐line quality control of a process by monitoring its quality loss cost performance over time. To compute the quality loss performance, we consider a nominal‐the‐best quality characteristic. The statistical performance of the proposed control charts has been evaluated and compared with that of widely used control charts. Implementing target costing philosophy by means of one of the proposed charts is also discussed. An example illustrates the Taguchi control chart in a practical implementation. Copyright © 2013 John Wiley & Sons, Ltd.
Multi‐allergen quantification of fining‐related egg and milk proteins in white wines by high‐resolution mass spectrometry
Authors: Monaci Linda , Losito Ilario , De Angelis Elisabetta , Pilolli Rosa , Visconti Angelo
Published: July 2013

RATIONALE

A method based on High‐Resolution Mass Spectrometry was developed for the simultaneous determination of fining agents containing potentially allergenic milk (casein) and egg‐white (lysozyme and ovalbumin) proteins, added to commercial white wines at sub‐ppm levels. Selected tryptic peptides were used as quantitative markers. An evaluation of protein digestion yields was also performed by implementing the 15 N‐valine‐labelled analogues of the best peptide markers identified for αS1‐casein and ovalbumin.

METHODS

The method was based on the combination of ultrafiltration (UF) of protein‐containing wines, tryptic digestion of the dialyzed wine extracts and liquid chromatography/high resolution mass spectrometry (LC/HRMS) analysis of tryptic digests. Peptides providing the most intense electrospray ionization (ESI)‐MS response were chosen as quantitative markers of the proteins under investigation.

RESULTS

Six‐point calibrations were performed by adding caseinate and egg‐white powder in the concentration range between 0.25 and 10 µg/mL, to an allergen‐free white wine. The following three peptide markers, LTEWTSSNVMEER, GGLEPINFQTAADQAR and ELINSWVESQTNGIIR, were highlighted as best markers for ovalbumin, while GTDVQAWIR and NTDGSTDYGILQINSR for lysozyme and YLGYLEQLLR, GPFPIIV and FFVAPFPEVFGK for caseinate. Limits of detection (LODs) ranged from 0.4 to 1.1 µg/mL.

CONCLUSIONS

The developed method is suited for assessing the contemporary presence of allergenic milk and egg proteins characterizing egg white and caseinate, fining agents typically employed for wine clarification. The LODs of the method enable the detection of sub‐ppm concentrations of residual fining agents, that could represent a potential risk for allergic consumers. Copyright © 2013 John Wiley & Sons, Ltd.
Accounting for baseline differences and measurement error in the analysis of change over time
Authors: Braun Julia , Held Leonhard , Ledergerber Bruno , Study the Swiss HIV Cohort
Published: July 2013

If change over time is compared in several groups, it is important to take into account baseline values so that the comparison is carried out under the same preconditions. As the observed baseline measurements are distorted by measurement error, it may not be sufficient to include them as covariate. By fitting a longitudinal mixed‐effects model to all data including the baseline observations and subsequently calculating the expected change conditional on the underlying baseline value, a solution to this problem has been provided recently so that groups with the same baseline characteristics can be compared. In this article, we present an extended approach where a broader set of models can be used. Specifically, it is possible to include any desired set of interactions between the time variable and the other covariates, and also, time‐dependent covariates can be included. Additionally, we extend the method to adjust for baseline measurement error of other time‐varying covariates. We apply the methodology to data from the Swiss HIV Cohort Study to address the question if a joint infection with HIV‐1 and hepatitis C virus leads to a slower increase of CD4 lymphocyte counts over time after the start of antiretroviral therapy. Copyright © 2013 John Wiley & Sons, Ltd.
pFDR and pFNR estimation for brain networks construction
Authors: Sala Sara , Quatto Piero , Valsasina Paola , Agosta Federica , Filippi Massimo
Published: July 2013

Recent developments in the study of brain functional connectivity are widely based on graph theory. In the current analysis of brain networks, there is no unique way to derive the adjacency matrix, which is a useful representation for a graph. Its entries, containing information about the existence of links, are identified by thresholding the correlation between the time series that characterized the dynamic behavior of the nodes. In this work, we put forward a strategy to choose a suitable threshold on the correlation matrix considering the problem of multiple comparisons in order to control the error rates. In this context we propose to control the positive false discovery rate (pFDR) and a similar measure involving false negatives, called the positive false nondiscovery rate (pFNR). In particular, we provide point and interval estimators for pFNR and a method for balancing the two types of error, demonstrating it by using functional magnetic resonance imaging data and Monte Carlo simulations. Copyright © 2013 John Wiley & Sons, Ltd.
Yield Point Elongation and Localized Deformation Bands in 22MnB5 Steel at Room Temperature
Authors: Min Junying , Lin Jianping
Published: July 2013

22MnB5 steel shows a yield point elongation (YPE) of ∼0.5% at room temperature. Uniaxial tensile tests of 22MnB5 steel specimens were performed in a quasi‐static strain rate range from 3.33 × 10−5 s−1 to 3.33 × 10−3 s−1 with the aid of digital image correlation (DIC) technique to investigate the deformation behavior of 22MnB5 steel in a small strain range from 0 to ∼0.02. The evolutions of full fields of strain and strain rate on the 22MnB5 steel specimens were obtained. Discontinuously propagating localized deformation bands (LDBs) were observed before, during and beyond YPE, which are known as Type B Portevin‐Le Chatelier (PLC) bands resulting in serrations on stress strain curves and they are not Luders bands unexpectedly. The peak strain rates in the LDBs before the YPE is relatively small, and during the YPE, the strain rate in the LDBs increases to ∼2 times of the applied nominal strain rate, which is explained by micro‐ and macro‐plastic deformation mechanism.
A novel neutral xylanase with high SDS resistance fromVolvariella volvacea: characterization and its synergistic hydrolysis of wheat bran with acetyl xylan esterase
Authors: Zheng Fei , Huang Jingxuan , Yin Yuhao , Ding Shaojun
Published: July 2013

A neutral xylanase (XynII) from Volvariella volvacea was identified and characterized. Unlike other modular xylanases, it consists of only a single GH10 catalytic domain with a unique C-terminal sequence (W-R-W-F) and a phenylalanine and proline-rich motif (T-P-F-P-P-F) at N-terminus, indicating that it is a novel GH10 xylanase. XynII exhibited optimal activity at pH 7 and 60 °C and stability over a broad range of pH 4.0–10.0. XynII displayed extreme highly SDS resistance retaining 101.98, 92.99, and 69.84 % activity at the presence of 300 mM SDS on birchwood, soluble oat spelt, and beechwood xylan, respectively. It remained largely intact after 24 h of incubation with proteinase K at a protease to protein ratio of 1:50 at 37 °C. The kinetic constants K  m value towards beechwood xylan was 0.548 mg ml−1, and the k  cat/K  m ratio, reflecting the catalytic efficiency of the enzyme, was 126.42 ml mg−1 s−1 at 60 °C. XynII was a true endo-acting xylanase lacking cellulase activity. It has weak activity towards xylotriose but efficiently hydrolyzed xylans and xylooligosaccharides larger than xylotriose mainly to xylobiose. Synergistic action with acetyl xylan esterase (AXEI) from V. volvacea was observed for de-starched wheat bran. The highest degree of synergy (DS 1.42) was obtained in sequential reactions with AXEI digestion preceding XynII. The high SDS resistance and intrinsic stability suggested XynII may have potential applications in various industrial processes especially for the detergent and textile industries and animal feed industries.
Extending the Lee-Carter Method to Model the Rotation of Age Patterns of Mortality Decline for Long-Term Projections
Authors: Li Nan , Lee Ronald , Gerland Patrick
Published: July 2013

In developed countries, mortality decline is decelerating at younger ages and accelerating at old ages, a phenomenon we call “rotation.” We expect that this rotation will also occur in developing countries as they attain high life expectancies. But the rotation is subtle and has proved difficult to handle in mortality models that include all age groups. Without taking it into account, however, long-term mortality projections will produce questionable results. We simplify the problem by focusing on the relative magnitude of death rates at two ages (0 and 15–19) while making assumptions about changes in rates of decline at other ages. We extend the Lee-Carter method to incorporate this subtle rotation in projection. We suggest that the extended Lee-Carter method could provide plausible projections of the age pattern of mortality for populations, including those that currently have very high life expectancies. Detailed examples are given using data from Japan and the United States.
Migration and Pacific Mortality: Estimating Migration Effects on Pacific Mortality Rates Using Bayesian Models
Authors: Richardson Ken , Jatrana Santosh , Tobias Martin , Blakely Tony
Published: July 2013

Pacific people living in New Zealand have higher mortality rates than New Zealand residents of European/Other ethnicity. The aim of this paper is to see whether Pacific mortality rates vary by natality and duration of residence. We used linked census-mortality information for 25- to 74-year-olds in the 2001 census followed for up to three years. Hierarchical Bayesian modeling provided a means of handling sparse data. Posterior mortality rates were directly age-standardized. We found little evidence of mortality differences between the overseas-born and the New Zealand–born for all-cause, cancer, and cardiovascular disease (CVD) mortality. However, we found evidence for lower all-cause (and possibly cancer and CVD) mortality rates for Pacific migrants resident in New Zealand for less than 25 years relative to those resident for more than 25 years. This result may arise from a combination of processes operating over time, including health selection effects from variations in New Zealand’s immigration policy, the location of Pacific migrants within the social, political, and cultural environment of the host community, and health impacts of the host culture. We could not determine the relative importance of these processes, but identifying the (modifiable) drivers of the inferred long-term decline in health of the overseas-born Pacific population relative to more-recent Pacific migrants is important to Pacific communities and from a national health and policy perspective.
Allosteric inhibitor specificity of Thermotoga maritima 3‐deoxy‐d‐arabino‐heptulosonate 7‐phosphate synthase
Authors: Cross Penelope J. , Parker Emily J.
Published: July 2013

3‐Deoxy‐d‐arabino‐heptulosonate 7‐phosphate synthase (DAH7PS) catalyses the first step of the shikimate pathway for the biosynthesis of aromatic amino acids. Allosteric regulation of Thermotoga maritima DAH7PS is mediated by l‐Tyr binding to a discrete ACT regulatory domain appended to a core catalytic (β/α)8 barrel. Variants of T. maritima DAH7PS (TmaDAH7PS) were created to probe the role of key residues in inhibitor selection. Substitution Ser31Gly severely reduced inhibition by l‐Tyr. In contrast both l‐Tyr and l‐Phe inhibited the TmaHis29Ala variant, while the variant where Ser31 and His29 were interchanged (His29Ser/Ser31His), was inhibited to a greater extent by l‐Phe than l‐Tyr. These studies highlight the role and importance of His29 and Ser31 for determining both inhibitory ligand selectivity and the potency of allosteric response by TmaDAH7PS.
The “Violence” of the Canon: Revisiting Contemporary Notions of Canonical Forms
Authors: Dickinson Colby
Published: July 2013

The historical conditions surrounding the processes of forming a canon are rarely examined directly, yet it is these processes that govern the realm of religious representations and identity constructions. In light of recent critical scholarship, it is imperative to address theologically the role that the canon plays within a religious tradition. This article demonstrates the cultural necessity of canonical forms despite their “monotheistic tendency” to subdivide the world into binary oppositions. By utilizing a scale of violence to determine the impact of the canonical form on culture, this article offers an account of canons and their role in forming religious identities over and beyond the violence they are said to provoke. Through this clarification, an alternative perspective on canons can emerge that reveals the violence at the core of cultural-canonical norms, thus identifying a valuable distinction between differing (violence-concealingor violence-revealing) canonical forms.
BEING ‘CHAGGA’: NATURAL RESOURCES, POLITICAL ACTIVISM, AND IDENTITY ON KILIMANJARO
Authors: Bender Matthew V.
Published: July 2013

This article argues that the emergence of Chagga political identity on Mount Kilimanjaro in the 1940s and 1950s can best be understood as a product of intensive debates over the control of natural resources and the nature of chiefly authority. As a result of perceived threats to the land and water resources of the mountain and resentment of the role of the chiefs in these issues, grassroots activists adopted a language of unity using the ethnic term ‘Chagga’ – a moniker long used by the colonial state but eschewed by the general population. With the rise of a paramount chieftaincy in 1951, the term shifted from being a symbol of colonial rule to one of common identity and resistance against the encroachment of the colonial state in local affairs.
VIOLENCE AND REGULATION IN THE DARFUR-CHAD BORDERLANDc. 1909–56: POLICING A COLONIAL BOUNDARY
Authors: Vaughan Christopher
Published: July 2013

Recent literature has emphasised the political and economic opportunities afforded to peoples living in African borderlands by the existence of permeable inter-state boundaries. This article examines the history of the Darfur-Chad borderland under colonial rule and finds that serious risks existed for those attempting to circumvent state authority in order to take advantage of such opportunities. State-led attempts to control these borders, though always incomplete, were often characterised by considerable violence. The limits of state power did not therefore straightforwardly translate into an accommodation with border societies. That said, this was also a border zone characterised by complex interaction and negotiation between state and local forms of regulation, and by multiple forms of sovereignty. This led to the emergence of plural and hybrid forms of authority, now repeatedly observed in studies of contemporary African borderlands, but rarely fully historicised.
PAWNS ON THE GOLD COAST: THE RISE OF ASANTE AND SHIFTS IN SECURITY FOR DEBT, 1680–1750
Authors: SPICKSLEY JUDITH
Published: July 2013

In the seventeenth century, Europeans on the Gold Coast took gold pawns as security for debt, but from the early eighteenth century, they turned increasingly toward the use of human pawns. This shift was the result of a transformation in levels of demand for gold amongst African sellers, most notably the Asante, who began to secure control over local gold sources fromc. 1700. The change in demand for gold was accompanied by a rise in slave prices on the West African coast, but it was the indigenous system of debt recovery that proved crucial to the success of European trade.
Domestic Courts as Agents of Development of International Immunity Rules
Authors: VAN ALEBEEK ROSANNE
Published: July 2013

This paper explores the role of domestic courts in the development of international immunity rules. It assesses how domestic immunity decisions take meaning in the process of law formation and law determination, and examines whether the distinct influence of domestic-court decisions (as compared to international-court decisions) in that process results in a different role, and concomitant different rules, in the process of interpretation of rules of international law. The paper argues that while domestic courts are as a matter of international law bound by the same rules of interpretation as international courts, they are particularly well placed to address access to court concerns raised by immunity rules and may play a prominent role in the development of international law in this field in the years to come.
Discussion of T. H. Cheng's Monograph When International Law Works, and in Particular a Defence of the Nicaragua Judgment of the ICJ
Authors: KOLB ROBERT
Published: July 2013

In this monograph Professor Tai-Heng Cheng purports to set up a global perspective on the role of international law in international relations, and in particular on the conditions and ways through which it can be effective. The perspective is the one of the ‘rational’ decision-maker, in the best vein of the New Haven school, whose theoretical framework the author espouses completely and thoroughly. The book is a valuable contribution to international legal theory; it is not written in abstract and hollow words, but on the basis of a practical enquiry based on many examples. By adopting this perspective, it provides the reader with many interesting insights. In particular, it is enriching for the European reader, who is not used to this genuinely ‘US–American’ perspective. The various chapters of the book are as follows: ‘Confronting Anxieties about International Law’; ‘The Politics of Theorizing’; ‘Legalism and Morality’; ‘Judges’; ‘Arbitrators’; ‘Regulators’; ‘Legal Advisors’; ‘Officials’; and ‘Law beyond Cases’. The purpose of these lines is not to give a full account of that book. Nor is it to portray the numerous thought-provoking and fruitful aspects of the developments contained therein; nor, by the way, is it to criticize some points on which the ‘Europeans’ will easily disagree with the author, as on what is permitted to the US officials in Guantánamo (p. 227 ff.). The point is rather to spell out some cardinal aspects, which seem to the present author to be weaknesses of the general approach or inadequacies of particular points. The critical approach, which will here be put forward, should not lead the reader to believe that the book presently criticized is devoid of merit. On the contrary, the author of these lines would not have ventured into the exercise of writing an essay on it if he had believed that such was the case.
Nano-structured smart hydrogels with rapid response and high elasticity
Authors: Xia Lie-Wen , Xie Rui , Ju Xiao-Jie , Wang Wei , Chen Qianming , Chu Liang-Yin
Published: July 2013

Smart hydrogels, or stimuli-responsive hydrogels, are three-dimensional networks composed of crosslinked hydrophilic polymer chains that are able to dramatically change their volume and other properties in response to environmental stimuli such as temperature, pH and certain chemicals. Rapid and significant response to environmental stimuli and high elasticity are critical for the versatility of such smart hydrogels. Here we report the synthesis of smart hydrogels which are rapidly responsive, highly swellable and stretchable, by constructing a nano-structured architecture with activated nanogels as nano-crosslinkers. The nano-structured smart hydrogels show very significant and rapid stimuli-responsive characteristics, as well as highly elastic properties to sustain high compressions, resist slicing and withstand high level of deformation, such as bending, twisting and extensive stretching. Because of the concurrent rapid and significant stimuli-response and high elasticity, these nano-structured smart hydrogels may expand the scope of hydrogel applications, and provide enhanced performance in their applications.
Force produced after stretch in sarcomeres and half-sarcomeres isolated from skeletal muscles
Authors: Minozzo Fábio C. , Baroni Bruno M. , Correa José A. , Vaz Marco A. , Rassier Dilson E.
Published: July 2013

The goal of this study was to evaluate if isolated sarcomeres and half-sarcomeres produce a long-lasting increase in force after a stretch is imposed during activation. Single and half-sarcomeres were isolated from myofibrils using micro-needles, which were also used for force measurements. After full force development, both preparations were stretched by different magnitudes. The sarcomere length (SL) or half-sarcomere length variations (HSL) were extracted by measuring the initial and final distances from the Z-line to the adjacent Z-line or to a region externally adjacent to the M-line of the sarcomere, respectively. Half-sarcomeres generated approximately the same amount of isometric force (29.0 ± SD 15.5 nN·μm−2) as single sarcomeres (32.1 ± SD 15.3 nN·μm−2) when activated. In both cases, the steady-state forces after stretch were higher than the forces during isometric contractions at similar conditions. The results suggest that stretch-induced force enhancement is partly caused by proteins within the half-sarcomere.
African American English–Speaking Students: A Longitudinal Examination of Style Shifting From Kindergarten Through Second Grade
Authors: Craig Holly K. , Kolenic Giselle E. , Hensel Stephanie L.
Published: July 2013

Purpose

The purpose of this longitudinal study was twofold: to examine shifting from African American English (AAE) to mainstream American English (MAE) across the early elementary grades, when students are first exposed to formal instruction in reading; and to examine how metalinguistic and cognitive variables influenced the students' dialectal adaptations from AAE to MAE in a literacy context with higher expectations for MAE.

Method

Participants were 102 typically developing AAE-speaking students enrolled in public schools in the northern Midwest. They were enrolled in the project at kindergarten and tested 3 times a year, for 3 years. Approximately half were male and half female, and two-thirds were from low socioeconomic status homes.

Results

A style shifting coefficient (SSC) was created to measure amounts of dialect change between contexts and over time by individuals. Some students shifted to MAE in literacy contexts, and shifting was not related to grade. Metalinguistic skills and SSC predicted reading, and metalinguistic skills predicted the SSC at 2nd grade. The findings indicated that cognitive executive functions may contribute to the SSC.

Conclusions

The results provide strong support for the dialect shifting–reading achievement hypothesis and indicated that metalinguistic and perhaps executive functioning are important influences on this linguistic adaptation.
The Ethico-Aesthetics of Life: Guattari and the Problem of Bioethics
Authors: Hynes Maria
Published: July 2013

The work of Deleuze and Guattari has inspired social scientists for some decades, yet it is only of late that Guattari's sole-authored work has emerged as a unique force in its own right. This paper explores what Guattari's work has to offer to the analysis of the problematic of ‘life’ and, more specifically, to the idea of bioethics. While much of the critical discourse on biopower in recent years has worked from the perspective of reflecting on the truth claims of the life sciences, Guattari's schematisation of ‘assemblages of enunciation’ in Chaosmosis offers an opening to the more ethico-aesthetic potentials of this thing we call life. I argue that the discourse of bioethics can begin to work productively once it is taken outside the scientific paradigm to which it currently remains bound. Rather than seeking to reflect on its object—life—bioethical thinking might aspire to become more experimental as a mode of thinking more sensitive to life's creative evolution.
Wishful Thinking and the Abandonment of Moving Desires over the Life Course
Authors: Coulter Rory
Published: July 2013

Many longitudinal analyses of residential mobility decision making use two or three waves of panel survey data to investigate who fulfils their moving desires. Few studies have, however, focused upon individuals who desire to move but who remain residentially immobile, either because it takes them a long time to relocate or because they abandon their moving desire. This is problematic, as undesired residential immobility could have negative consequences for individual well-being and prosperity. To address this research gap, this study uses 1991–2008 British Household Panel Survey data to analyse the duration and abandonment of moving desires. Importantly, the results show that the risk of abandoning a desire to move rises dramatically with age, suggesting that the well-documented residential rootedness of older people is not solely volitional. Event-history analysis shows that these patterns are partly due to changing levels of ties and commitments over the life course. By demonstrating that ethnicity and income are also linked to the fulfilment of moving desires, the findings contribute to our understanding of the processes producing both social inequality and neighbourhood stratification.
Cultivating Compliance: Governance of North Indian Organic Basmati Smallholders in a Global Value Chain
Authors: Arora Saurabh , Hofman Naomi Baan , Koshti Vinod , Ciarli Tommaso
Published: July 2013

Focusing on a global value chain (GVC) for organic basmati rice, we study how farmers' practices are governed through product and process standards, organic certification protocols, and contracts with buyer firms. We analyze how farmers' entry into the GVC reconfigures their agencements (defined as heterogeneous arrangements of human and nonhuman agencies which are associated with each other). These reconfigurations entail the severance of some associations among procedural and material elements of the agencements and the formation of new associations, in order to produce cultivation practices that are accurately described by the GVC's standards and protocols. Based on ethnography of two farmers in Uttarakhand, North India, we find that the same standards were enacted differently on the two farmers' fields, producing variable degrees of (selective) compliance with the ‘official’ GVC standards. We argue that the disjuncture between the ‘official’ scripts of the standards and actual cultivation practices must be nurtured to allow farmers' agencements to align their practices with local sociotechnical relations and farm ecology. Furthermore, we find that compliance and disjuncture were facilitated by many practices and associations that were officially ungoverned by the GVC.
If We Build it, Will They Pay? Predicting Property Price Effects of Transport Innovations
Authors: Ahlfeldt Gabriel M
Published: July 2013

In this study I apply a gravity-type labor-market accessibility model to the Greater London Area to investigate house price capitalization effects. The spatial scope of labor-market effects is found to be about 60 minutes. Doubling accessibility increases the utility of an average household by about 12%. I combine the gravity approach with a transport decision model that takes into account the urban rail network architecture, allows for mode switching, and thus accounts for the effective accessibility offered by a station, to predict the property price effects of the 1999 Jubilee Line and DLR extension. A considerable degree of heterogeneity is predicted both in terms of the magnitude as well as the spatial extent of price effects around new stations. A quasi-experimental property price analysis reveals that the model performs well in predicting the effective capitalization effects, suggesting that the approach might be a viable ingredient in transport planning.
From Designed Spaces to Designer Savvy Societies: The Potential of Ideas Competitions in Willing Participation
Authors: Picken Felicity
Published: July 2013

The design of public space has gained importance as cities are increasingly positioned in global flows of people, capital, and ideas. These spaces speak to the culture of a place as much as to the quality of its design, but the implementation of design as an inclusive process is fraught with difficulty. This is particularly pertinent in discussions about better ways of engaging people with urban design, where there is often a language barrier between those who specialise in spatial manipulation and the broader ‘society’ that uses this space. This paper gives an empirical account of how a spatial consciousness can be translated to society through an international design competition. The competition method of urban design relies upon promotion and ‘eventfulness’, both of which interpolate the public and contribute towards the generation of a deeper interest in the spatial imaginary of city planning. The creation of ‘urban design consumers' through the visual consumption of the designs themselves offers an alternative way to gain public interest to the established traditions of public notices and formal public meetings. In this case, the competition extended the activity of urban designers beyond the mechanics of ‘space production’ to include ‘consumer production’ where a more intimate relationship between city planning and the people began to emerge.
Structural basis of Vps33A recruitment to the human HOPS complex by Vps16
Authors: Graham Stephen C. , Wartosch Lena , Gray Sally R. , Scourfield Edward J. , Deane Janet E. , Luzio J. Paul , Owen David J.
Published: July 2013

The multisubunit homotypic fusion and vacuole protein sorting (HOPS) membrane-tethering complex is required for late endosome-lysosome and autophagosome-lysosome fusion in mammals. We have determined the crystal structure of the human HOPS subunit Vps33A, confirming its identity as a Sec1/Munc18 family member. We show that HOPS subunit Vps16 recruits Vps33A to the human HOPS complex and that residues 642–736 are necessary and sufficient for this interaction, and we present the crystal structure of Vps33A in complex with Vps16(642–736). Mutations at the binding interface disrupt the Vps33A–Vps16 interaction both in vitro and in cells, preventing recruitment of Vps33A to the HOPS complex. The Vps33A–Vps16 complex provides a structural framework for studying the association between Sec1/Munc18 proteins and tethering complexes.
COPI buds 60-nm lipid droplets from reconstituted water–phospholipid–triacylglyceride interfaces, suggesting a tension clamp function
Authors: Thiam Abdou Rachid , Antonny Bruno , Wang Jing , Delacotte Jérôme , Wilfling Florian , Walther Tobias C. , Beck Rainer , Rothman James E. , Pincet Frédéric
Published: July 2013

Intracellular trafficking between organelles is achieved by coat protein complexes, coat protomers, that bud vesicles from bilayer membranes. Lipid droplets are protected by a monolayer and thus seem unsuitable targets for coatomers. Unexpectedly, coat protein complex I (COPI) is required for lipid droplet targeting of some proteins, suggesting a possible direct interaction between COPI and lipid droplets. Here, we find that COPI coat components can bud 60-nm triacylglycerol nanodroplets from artificial lipid droplet (LD) interfaces. This budding decreases phospholipid packing of the monolayer decorating the mother LD. As a result, hydrophobic triacylglycerol molecules become more exposed to the aqueous environment, increasing LD surface tension. In vivo, this surface tension increase may prime lipid droplets for reactions with neighboring proteins or membranes. It provides a mechanism fundamentally different from transport vesicle formation by COPI, likely responsible for the diverse lipid droplet phenotypes associated with depletion of COPI subunits.
How hydrophobic drying forces impact the kinetics of molecular recognition
Authors: Mondal Jagannath , Morrone Joseph A. , Berne B. J.
Published: July 2013

A model of protein–ligand binding kinetics, in which slow solvent dynamics results from hydrophobic drying transitions, is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry states with lifetimes in each state that are long enough for the extraction of a separable potential of mean force and wet-to-dry transitions. We present a diffusive surface hopping model that is represented by a 2D Markovian master equation. One dimension is the standard reaction coordinate, the ligand–pocket separation, and the other is the solvent state in the region between ligand and binding pocket which specifies whether it is wet or dry. In our model, the ligand diffuses on a dynamic free-energy surface which undergoes kinetic transitions between the wet and dry states. The model yields good agreement with results from explicit solvent molecular dynamics simulation and an improved description of the kinetics of hydrophobic assembly. Furthermore, it is consistent with a “non-Markovian Brownian theory” for the ligand–pocket separation coordinate alone.
Near-optimal experimental design for model selection in systems biology
Authors: Busetto Alberto Giovanni , Hauser Alain , Krummenacher Gabriel , Sunnåker Mikael , Dimopoulos Sotiris , Ong Cheng Soon , Stelling Jörg , Buhmann Joachim M.
Published: July 2013

Motivation: Biological systems are understood through iterations of modeling and experimentation. Not all experiments, however, are equally valuable for predictive modeling. This study introduces an efficient method for experimental design aimed at selecting dynamical models from data. Motivated by biological applications, the method enables the design of crucial experiments: it determines a highly informative selection of measurement readouts and time points.

Results: We demonstrate formal guarantees of design efficiency on the basis of previous results. By reducing our task to the setting of graphical models, we prove that the method finds a near-optimal design selection with a polynomial number of evaluations. Moreover, the method exhibits the best polynomial-complexity constant approximation factor, unless P = NP. We measure the performance of the method in comparison with established alternatives, such as ensemble non-centrality, on example models of different complexity. Efficient design accelerates the loop between modeling and experimentation: it enables the inference of complex mechanisms, such as those controlling central metabolic operation.

Availability: Toolbox ‘NearOED’ available with source code under GPL on the Machine Learning Open Source Software Web site (mloss.org).

Contact: busettoa@inf.ethz.ch

Supplementary information: Supplementary data are available at Bioinformatics online.
Sensitivities of Baseline Isolates and Boscalid-Resistant Mutants of Alternaria alternata from Pistachio to Fluopyram, Penthiopyrad, and Fluxapyroxad
Authors: Avenot H. F. , van den Biggelaar H. , Morgan D. P. , Moral J. , Joosten M. , Michailides T. J.
Published: July 2013

Resistance of Alternaria alternata to boscalid, the first succinate dehydrogenase inhibitor (SDHI) fungicide labeled on pistachio, has become a common occurrence in California pistachio orchards and affects the performance of this fungicide. In this study, we established the baseline sensitivities of A. alternata to the new SDHIs fluopyram, fluxapyroxad, and penthiopyrad and assessed their cross resistance patterns with boscalid. Examination of the effective fungicide concentration that inhibits mycelial growth to 50% relative to the control (EC50) for 50 baseline isolates revealed that the majority were sensitive to boscalid, penthiopyrad, fluopyram, and fluxapyroxad. Analysis of EC50 values for boscalid for 117 A. alternata isolates originating from boscalid-exposed orchards showed that 44, 3, 1, and 69 isolates had sensitive, reduced sensitivity, moderately resistant, and highly resistant boscalid phenotypes, respectively. Molecular investigation of the occurrence of known SDH mutations showed that, among the 69 isolates highly resistant to boscalid, 44, 2, 14, and 1 isolates possessed the mutations leading to the H277Y, H277R, H134R, and H133R amino acid substitutions in AaSDHB, AaSDHB, AaSDHC, and AaSDHD subunits, respectively. Some SDHB or SDHC mutants displayed highly sensitive, sensitive, or reduced sensitivity phenotypes toward penthiopyrad or fluxapyroxad, whereas other had low, moderate, or high levels of resistance to these fungicides. In contrast, all the SDHB mutants were sensitive to fluopyram, while 10, 5, and 1 SDHC mutants had sensitive, reduced sensitivity, and moderately resistant fluopyram phenotypes, respectively. The SDHD mutant had reduced sensitivity to fluopyram and penthiopyrad but was highly resistant to fluxapyroxad. The discrepancies of cross-resistance patterns between SDHIs suggest that their binding sites in complex II may differ slightly and that additional mechanisms of resistance to these compounds are likely involved. Ultimately, the findings of this study should lead to the rational and sustained deployment of new SDHIs in Alternaria late blight spray programs.
Foliar Application of Biofilm Formation–Inhibiting Compounds Enhances Control of Citrus Canker Caused by Xanthomonas citri subsp. citri
Authors: Li Jinyun , Wang Nian
Published: July 2013

Citrus canker caused by the bacterium Xanthomonas citri subsp. citri is an economically important disease of citrus worldwide. Biofilm formation plays an important role in early infection of X. citri subsp. citri on host leaves. In this study, we assessed the hypothesis that small molecules inhibiting biofilm formation reduce X. citri subsp. citri infection and enhance the control of citrus canker disease. D-leucine and 3-indolylacetonitrile (IAN) were found to prevent biofilm formation by X. citri subsp. citri on different abiotic surfaces and host leaves at a concentration lower than the minimum inhibitory concentration (MIC). Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis indicated that IAN repressed expression of chemotaxis/motility-related genes in X. citri subsp. citri. In laboratory experiments, planktonic and biofilm cells of X. citri subsp. citri treated with D-leucine and IAN, either alone or in combination, were more susceptible to copper (CuSO4) than those untreated. In greenhouse assays, D-leucine and IAN applied alone or combined with copper reduced both the number of canker lesions and bacterial populations of X. citri subsp. citri on citrus host leaves. This study provides the basis for the use of foliar-applied biofilm inhibitors for the control of citrus canker alone or combined with copper-based bactericides.
Building the Evidence on Simulation Validity
Authors: Weller Jennifer , Henderson Robert , Webster Craig S. , Shulruf Boaz , Torrie Jane , Davies Elaine , Henderson Kaylene , Frampton Chris , Merry Alan F.
Published: July 2013

Background:

Effective teamwork is important for patient safety, and verbal communication underpins many dimensions of teamwork. The validity of the simulated environment would be supported if it elicited similar verbal communications to the real setting. The authors hypothesized that anesthesiologists would exhibit similar verbal communication patterns in routine operating room (OR) cases and routine simulated cases. The authors further hypothesized that anesthesiologists would exhibit different communication patterns in routine cases (real or simulated) and simulated cases involving a crisis.

Methods:

Key communications relevant to teamwork were coded from video recordings of anesthesiologists in the OR, routine simulation and crisis simulation and percentages were compared.

Results:

The authors recorded comparable videos of 20 anesthesiologists in the two simulations, and 17 of these anesthesiologists in the OR, generating 400 coded events in the OR, 683 in the routine simulation, and 1,419 in the crisis simulation. The authors found no significant differences in communication patterns in the OR and the routine simulations. The authors did find significant differences in communication patterns between the crisis simulation and both the OR and the routine simulations. Participants rated team communication as realistic and considered their communications occurred with a similar frequency in the simulations as in comparable cases in the OR.

Conclusion:

The similarity of teamwork-related communications elicited from anesthesiologists in simulated cases and the real setting lends support for the ecological validity of the simulation environment and its value in teamwork training. Different communication patterns and frequencies under the challenge of a crisis support the use of simulation to assess crisis management skills.
Honest signalling with costly gambles
Authors: Meacham Frazer , Perlmutter Aaron , Bergstrom Carl T.
Published: July 2013

Costly signalling theory is commonly invoked as an explanation for how honest communication can be stable when interests conflict. However, the signal costs predicted by costly signalling models often turn out to be unrealistically high. These models generally assume that signal cost is determinate. Here, we consider the case where signal cost is instead stochastic. We examine both discrete and continuous signalling games and show that, under reasonable assumptions, stochasticity in signal costs can decrease the average cost at equilibrium for all individuals. This effect of stochasticity for decreasing signal costs is a fundamental mechanism that probably acts in a wide variety of circumstances.
Do small swarms have an advantage when house hunting? The effect of swarm size on nest-site selection by
Apis mellifera
Authors: Schaerf T. M. , Makinson J. C. , Myerscough M. R. , Beekman M.
Published: July 2013

Reproductive swarms of honeybees are faced with the problem of finding a good site to establish a new colony. We examined the potential effects of swarm size on the quality of nest-site choice through a combination of modelling and field experiments. We used an individual-based model to examine the effects of swarm size on decision accuracy under the assumption that the number of bees actively involved in the decision-making process (scouts) is an increasing function of swarm size. We found that the ability of a swarm to choose the best of two nest sites decreases as swarm size increases when there is some time-lag between discovering the sites, consistent with Janson & Beekman (Janson & Beekman 2007
Proceedings of European Conference on Complex Systems
, pp. 204–211.). However, when simulated swarms were faced with a realistic problem of choosing between many nest sites discoverable at all times, larger swarms were more accurate in their decisions than smaller swarms owing to their ability to discover nest sites more rapidly. Our experimental fieldwork showed that large swarms invest a larger number of scouts into the decision-making process than smaller swarms. Preliminary analysis of waggle dances from experimental swarms also suggested that large swarms could indeed discover and advertise nest sites at a faster rate than small swarms.