bluuebunny/crossref_metadata_2025 huggingface dataset:
Decrease in topoisomerase I is responsible for activation-induced cytidine deaminase (AID)-dependent somatic hypermutation
Authors: Kobayashi Maki , Sabouri Zahra , Sabouri Somayeh , Kitawaki Yoko , Pommier Yves , Abe Takaya , Kiyonari Hiroshi , Honjo Tasuku
Published: November 2011

Somatic hypermutation (SHM) and class-switch recombination (CSR) of the Ig gene require both the transcription of the locus and the expression of activation-induced cytidine deaminase (AID). During CSR, AID decreases the amount of topoisomerase I (Top1); this decrease alters the DNA structure and induces cleavage in the S region. Similarly, Top1 is involved in transcription-associated mutation at dinucleotide repeats in yeast and in triplet-repeat contraction in mammals. Here, we report that the AID-induced decrease in Top1 is critical for SHM. Top1 knockdown or haploinsufficiency enhanced SHM, whereas Top1 overexpression down-regulated it. A specific Top1 inhibitor, camptothecin, suppressed SHM, indicating that Top1's activity is required for DNA cleavage. Nonetheless, suppression of transcription abolished SHM, even in cells with Top1 knockdown, suggesting that transcription is critical. These results are consistent with a model proposed for CSR and triplet instability, in which transcription-induced non-B structure formation is enhanced by Top1 reduction and provides the target for irreversible cleavage by Top1. We speculate that the mechanism for transcription-coupled genome instability was adopted to generate immune diversity when AID evolved.
Multifunctional proteins revealed by overlapping clustering in protein interaction network
Authors: Becker Emmanuelle , Robisson Benoît , Chapple Charles E. , Guénoche Alain , Brun Christine
Published: November 2011

Motivation: Multifunctional proteins perform several functions. They are expected to interact specifically with distinct sets of partners, simultaneously or not, depending on the function performed. Current graph clustering methods usually allow a protein to belong to only one cluster, therefore impeding a realistic assignment of multifunctional proteins to clusters.

Results: Here, we present Overlapping Cluster Generator (OCG), a novel clustering method which decomposes a network into overlapping clusters and which is, therefore, capable of correct assignment of multifunctional proteins. The principle of OCG is to cover the graph with initial overlapping classes that are iteratively fused into a hierarchy according to an extension of Newman's modularity function. By applying OCG to a human protein–protein interaction network, we show that multifunctional proteins are revealed at the intersection of clusters and demonstrate that the method outperforms other existing methods on simulated graphs and PPI networks.

Availability: This software can be downloaded from http://tagc.univ-mrs.fr/welcome/spip.php?rubrique197

Contact:  brun@tagc.univ-mrs.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
BadiRate: estimating family turnover rates by likelihood-based methods
Authors: Librado P. , Vieira F. G. , Rozas J.
Published: November 2011

Motivation: The comparative analysis of gene gain and loss rates is critical for understanding the role of natural selection and adaptation in shaping gene family sizes. Studying complete genome data from closely related species allows accurate estimation of gene family turnover rates. Current methods and software tools, however, are not well designed for dealing with certain kinds of functional elements, such as microRNAs or transcription factor binding sites.

Results: Here, we describe BadiRate, a new software tool to estimate family turnover rates, as well as the number of elements in internal phylogenetic nodes, by likelihood-based methods and parsimony. It implements two stochastic population models, which provide the appropriate statistical framework for testing hypothesis, such as lineage-specific gene family expansions or contractions. We have assessed the accuracy of BadiRate by computer simulations, and have also illustrated its functionality by analyzing a representative empirical dataset.

Availability: BadiRate software and documentation is available from http://www.ub.edu/softevol/badirate.

Contact:  jrozas@ub.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Potato Snakin-1 Gene Silencing Affects Cell Division, Primary Metabolism, and Cell Wall Composition
Authors: Nahirñak Vanesa , Almasia Natalia Inés , Fernandez Paula Virginia , Hopp Horacio Esteban , Estevez José Manuel , Carrari Fernando , Vazquez-Rovere Cecilia
Published: November 2011

Snakin-1 (SN1) is an antimicrobial cysteine-rich peptide isolated from potato (Solanum tuberosum) that was classified as a member of the Snakin/Gibberellic Acid Stimulated in Arabidopsis protein family. In this work, a transgenic approach was used to study the role of SN1 in planta. Even when overexpressing SN1, potato lines did not show remarkable morphological differences from the wild type; SN1 silencing resulted in reduced height, which was accompanied by an overall reduction in leaf size and severe alterations of leaf shape. Analysis of the adaxial epidermis of mature leaves revealed that silenced lines had 70% to 90% increases in mean cell size with respect to wild-type leaves. Consequently, the number of epidermal cells was significantly reduced in these lines. Confocal microscopy analysis after agroinfiltration of Nicotiana  benthamiana leaves showed that SN1-green fluorescent protein fusion protein was localized in plasma membrane, and bimolecular fluorescence complementation assays revealed that SN1 self-interacted in vivo. We further focused our study on leaf metabolism by applying a combination of gas chromatography coupled to mass spectrometry, Fourier transform infrared spectroscopy, and spectrophotometric techniques. These targeted analyses allowed a detailed examination of the changes occurring in 46 intermediate compounds from primary metabolic pathways and in seven cell wall constituents. We demonstrated that SN1 silencing affects cell division, leaf primary metabolism, and cell wall composition in potato plants, suggesting that SN1 has additional roles in growth and development beyond its previously assigned role in plant defense.
Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription
Authors: Wu Yufeng , Kikuchi Shinji , Yan Huihuang , Zhang Wenli , Rosenbaum Heidi , Iniguez A. Leonardo , Jiang Jiming
Published: November 2011

The presence of the centromere-specific histone H3 variant, CENH3, defines centromeric (CEN) chromatin, but poorly understood epigenetic mechanisms determine its establishment and maintenance. CEN chromatin is embedded within pericentromeric heterochromatin in most higher eukaryotes, but, interestingly, it can show euchromatic characteristics; for example, the euchromatic histone modification mark dimethylated H3 Lys 4 (H3K4me2) is uniquely associated with animal centromeres. To examine the histone marks and chromatin properties of plant centromeres, we developed a genomic tiling array for four fully sequenced rice (Oryza sativa) centromeres and used chromatin immunoprecipitation–chip to study the patterns of four euchromatic histone modification marks: H3K4me2, trimethylated H3 Lys 4, trimethylated H3 Lys 36, and acetylated H3 Lys 4, 9. The vast majority of the four histone marks were associated with genes located in the H3 subdomains within the centromere cores. We demonstrate that H3K4me2 is not a ubiquitous component of rice CEN chromatin, and the euchromatic characteristics of rice CEN chromatin are hallmarks of the transcribed sequences embedded in the centromeric H3 subdomains. We propose that the transcribed sequences located in rice centromeres may provide a barrier preventing loading of CENH3 into the H3 subdomains. The separation of CENH3 and H3 subdomains in the centromere core may be favorable for the formation of three-dimensional centromere structure and for rice centromere function.
Synthesis and evaluation of new antioxidants for styrene butadiene rubber
Authors: Nawwar Galal , Yakout Sayed , El‐Sadiek M.S.A , El‐Sabbagh Salwa
Published: November 2011

Purpose

The purpose of this paper is to study the effect of new heterocyclic compounds on styrene butadiene rubber (SBR) mixes.

Design/methodology/approach

It has been found that the starting material 1 could react with cyromazine (2) and/or 4‐aminoantipyriene (4) as amino compounds in the presence of triethylorthoformate and in the boiling dioxane to yield triazine‐3 and/or pyrazolo 5 derivatives, respectively. The chemical structures of the new products 3 and 5 have been established by their elemental analyses spectroscopic data IR, Ms and 1H, 13C NMR. These two compounds were evaluated as antioxidants in SBR, and this evaluation was confirmed by physico‐mechanical properties of vulcanizates, IR spectra and scanning electron microscope.

Findings

The difference between maximum torque MH and minimum torque ML (ΔM), tensile strength, modulus and elongation at break increases in the presence of prepared antioxidants while the equilibrium swelling decreased. The rubber vulcanizates were subjected to thermal oxidative aging at 90°C for up to seven days. It has been found that new compounds 3 and 5 can protect SBR vulcanizates against oxidative deterioration.

Research limitations/implications

The solubility of the prepared compounds 3 and 5 is very poor and they are only soluble in dimethyl formamide (DMF) or dimethyl sulphoxide (DMSO) which have high boiling points. Also, new compounds 3 and 5 have melting points (above 300°C).

Practical implications

Triazine and antipyrine derivatives have many medical and industrial applications.

Originality/value

The new synthesized compounds revealed excellent antioxidant behaviour in comparison with the commercial antioxidant phenyl‐β‐naphthyl amine (PβN) which is used in industry.
Finite element study of residual stresses and distortions in arc welding with a trailing liquid nitrogen heat sink
Authors: Sudheesh R.S. , Siva Prasad N.
Published: November 2011

Purpose

The purpose of this paper is to study the effect of trailing liquid nitrogen (LN2) heat sink on arc welding of mild steel plates. The effect on temperature field, stress and distortions are studied using experimental and numerical methods.

Design/methodology/approach

The methodology consists of experimental and numerical methods. The temperature measured at a point near the arc is used to estimate the cooling capacity of the heat sink using inverse heat transfer (IHT) method. The estimated cooling flux is applied to the finite element model to study the stress and distortions using LN2 heat sink. The stresses are measured using X‐ray diffraction technique and the distortions using dial gauges.

Findings

IHT method has been employed in estimating the cooling capacity of the LN2 jet. This has been applied to welding to study the effect on weld induced stresses and distortions. The method can be extended to calculate the heat removal rate in various manufacturing processes where cooling is employed.

Research limitations/implications

The lack of temperature dependent material properties resulted in deviation of stresses between analytical results and experiment values.

Originality/value

IHT method developed for heat removal capacity of trailing heat sink is a contribution. The estimated heat flux shows good agreement in analytical and experimental temperature values. These temperatures have been extended to calculate stresses and out of plane distortions in welding and there is a reasonable agreement between finite element analysis and experimental results.
Teaching knowledge management by combining wikis and screen capture videos
Authors: Makkonen Pekka , Siakas Kerstin , Vaidya Shakespeare
Published: November 2011

Purpose

This paper aims to report on the design and creation of a knowledge management course aimed at facilitating student creation and use of social interactive learning tools for enhanced learning.

Design/methodology/approach

The era of social media and web 2.0 has enabled a bottom‐up collaborative approach and new ways to publish work on the web, promoted by tools such as YouTube video service. In this spirit a knowledge management course was designed aiming to facilitate university students to compose videos on different difficult concepts in the theory part of the course by searching for explanations on the web and by creating a Windows Media Player video focusing on the self‐defined problems. The videos created by the students were published on a wiki (Wetpaint) and the students were encouraged to actively share knowledge and learn from one another by familiarising themselves with the videos of the other students. In order to utilise cognitive and social constructivism, as well as problem‐based learning, the principles of the Jigsaw method were used to enable different students to create videos on different themes.

Findings

Based on the authors' experiences it is suggested that curriculum and syllabus planning should be transformed toward a more student‐centred approach. This is the most natural in the context of knowledge management, which emphasizes the meaning of participation and knowledge sharing. The social constructivist learning theory emphasizes the meaning of interaction in successful learning. By publishing videos created by the students themselves, by commenting on videos created by other students and by reading comments expressed by others the approach proved to be beneficial for learning in many ways.

Research limitations/implications

The research limitation lies in the differences of quality, format and sizes of these videos produced and the efforts and time requirements for editing and use.

Practical implications

The present finding and report implies more of these resources could be generated by students in other courses in other study areas encouraging use of these types of resources, engaging students with the curriculum, and encouraging interaction amongst students promoting deeper understanding, more positive learning experiences and the generation of curriculum teaching materials by students for class work, making learning more student focused.

Originality/value

The paper focuses on a unique process that allows the use of social technology by students for the generation of materials for use in learning.
Wireless hazard communication system
Authors: Bhattacharya Devanjan , Ghosh Jayanta Kumar , Boccardo Piero , Samadhiya N.K.
Published: November 2011

Purpose

Communication of an impending hazard to people in near real time is critical. The purpose of this paper is to develop an internet‐SMS based geo‐hazard warning communication system.

Design/methodology/approach

A warning system based on an internet‐resident concept and the available cellular mobile infrastructure is proposed in this study. The functionality of the system is modular in architecture.

Findings

The messages have been transmitted in a set of 20 SMSs six times, to locally‐owned mobile numbers, resulting in a total number of 120. It has been found that 58 messages got delivered within ten seconds, the rest within 40 more seconds. The threat messages reached the impending threat areas within acceptable time delay.

Originality/value

The paper describes the implementation of a novel and stand‐alone system for dynamic hazard warning. Cellular or mobile phone, a gadget used by common man, is expected to be the best proposition to effectively warn people individually and to propagate hazard messages to users in large regions ubiquitously. The concept allows pervasiveness and redundancy, important to withstanding hazards and bringing several original elements through the development of this “fast warning system”, as current warning strategies do not include such solutions.
An examination of the information content of S&P 500 index changes
Authors: Geppert John M. , Ivanov Stoyu I. , Karels Gordon V.
Published: November 2011

Purpose

The purpose of this paper is to examine the shocks to firm's beta around the event of addition or deletion from the S&P 500 index.

Design/methodology/approach

The total derivative of beta and Campbell and Vuolteenaho decomposition of beta methodologies are used, on monthly and daily basis, to examine the behavior of beta around the event.

Findings

Results show a significant increase in correlations of the event firms' returns and the market proxy returns and cash‐flow betas, and decrease in discount‐rate betas for added firms and the opposite effects for deleted firms. Robustness tests indicate that the total derivative changes effects are typical for the event firms industry but that the cash‐flow correlation changes are specific to the firm. These findings suggest that addition or deletion from the S&P 500 index is not an information free event.

Research limitations/implications

The Campbell and Vuolteenaho methodology has limitations – it is conditional on the selection of state variables. In future research it would be beneficial to use different state variables in the beta decomposition framework. Another relevant question for a future research is: what are the effects of the event on the Fama‐French factor model loadings?

Originality/value

The paper's findings contribute to the ongoing debate in the literature of the information hypothesis for addition or deletion from the S&P 500 index.
US macroeconomic news spillover effects on Vietnamese stock market
Authors: Nguyen Tho
Published: November 2011

Purpose

The purpose of this paper is to investigate the spillover effect of the US macroeconomic news on the first two moments of the Vietnamese stock market returns.

Design/methodology/approach

The author collected market expectation and actual announcements data for 12 key US macroeconomic announcements for the period from August 2000 to September 2009 from Bloomberg. The dataset consists of monthly Non‐farm payroll (NFPM), Unemployment level (UNEMP), Gross Domestic Product percentage level (GDP), Housing statistics (HOMEST), Industrial production (INDP), Leading Indicator (LEAD), Retail Sales (SALES), Consumer Price Index (CPI), Producer Index (PPI), Current Account (CA, quarterly), Trade Balance (BOT), and the Federal Reserve's target rates (FOMC, 8 times a year and ad hoc meetings if needed). The MA‐EGARCH (1,1) model is used for the empirical test of the US macroeconomic news spillover effects on the VNI index.

Findings

In general, the US real economic news has the strongest effect on the first two moments of the Vietnamese stock returns. This can be interpreted as evidence that Vietnamese market participants believe that the USA is targeting real economic activities other than other variables. It is also shown that even though the US stock market (proxied by S&P500 index) significantly affects the Vietnamese stock market returns, the spillover effect of the US macroeconomic news is still significant.

Research limitations/implications

The author does not explore further on the transmission channels of the spillover effects of the US news on the Vietnamese stock market, reserving this task for future research.

Originality/value

The paper contributes to the extant literature in several ways. First, to the author's knowledge, the current literature lacks empirical evidence for the impact of the US macroeconomic news on the first two moments of the Vietnamese stock markets. Given the growing integration between the two economies, evidenced by the fact that the USA is Vietnam's largest foreign direct investor and importer, the US macroeconomic news is very important, not only for Vietnamese policy makers but also for market participants. Furthermore, the choice of a small and open market with increasing exposure to the world economy and vulnerable to the US news (i.e. Vietnam) would help in reducing the problem of endogeneity bias in previous studies employing large economy pairs, as the US news might affect the Vietnamese stock market but not the reverse. Finally, previous studies tend to investigate the impact of macro news only on conditional returns. In this study, both conditional returns and the conditional variance of returns are modelled simultaneously in a time‐varying framework (MA‐GARCH) to better capture the impact of macroeconomic news on stock returns and stock market volatility.
Modelling activity‐based costing in restaurants
Authors: Kostakis Hara , Boskou George , Palisidis George
Published: November 2011

Purpose

This paper seeks to demonstrate an application of a methodology, which is based on the integration of three techniques, with the purpose of modelling activity‐based costing (ABC) in restaurants. The proposed methodology serves as a tool for effectively computing values of cost drivers in the restaurant industry, as well as making accurate cost estimations.

Design/methodology/approach

The methodology is based on the integration of three techniques: simulation modelling, association rule mining (ARM) and ABC. Simulation modelling is used to model process variability and produce a range of cost values, instead of a point estimate of the cost, by generating a range of values for the simulated cost drivers. The advantage of the proposed methodology lies on the effective utilization of ARM in the ABC model; it extracts dependencies between a cost driver, whose estimation is time‐consuming, with another cost driver, which can easily be calculated. These associations can assist the estimation of the empirical distributions of those cost drivers, which were difficult to calculate.

Findings

The extracted associations verify the hypothetical relations between the cost drivers. The output produced is more precise values of the cost drivers that are included in an ABC model and were difficult to estimate. More accurate cost estimate means better pricing decisions for the restaurant managers.

Originality/value

The proposed methodology is an innovative technique that provides more accurate accounting information in the restaurant industry.
Modeling a causality network for tourism development: an empirical analysis
Authors: Assaker Guy , Esposito Vinzi Vincenzo , O'Connor Peter
Published: November 2011

Purpose

The purpose of this paper is to capture the causal relationships between the primary constituents of the tourism destination paradigm – namely, the economy, society, and the natural and infrastructural environments – and demand for tourism at that destination.

Design/methodology/approach

Inspired by prior tourism literature, the study uses structural equation modeling (SEM) methodologies with a cross‐sectional data sample from 162 countries, to evaluate a priori proposed measurement and structural models for relationships among the economy, society, environment constructs, and tourism.

Findings

The results indicate that although the economy construct was found to have no direct influence on tourism, it does have a mediating, positive impact on tourism through the society and environment constructs, with the society construct paralleling the condition of the infrastructure. Moreover, society and environment were found to have a direct, positive impact on generating tourism activities, and revenues.

Research limitations/implications

This study contributes to the literature on tourism demand modeling by verifying causal relationships between tourism constructs and supply variables at the “country” level. In other words, it examines whether relationships among tourism constructs and variables exist and, as such, asks if they are responsible for a destination's success.

Practical implications

This study's results provide destination managers with information to help them understand how individual variables affect the economy, society, and tourism industry aggregately, and as such what actions or investments can help to develop a country's tourism industry effectively.

Originality/value

By integrating several supply‐side factors related to the destination, this paper provides more comprehensive results compared to previous applications of SEM that used a limited number of destination variables and subsequently provided only limited results.
Virtual agents in e‐commerce: representational characteristics for seniors
Authors: Chattaraman Veena , Kwon Wi‐Suk , Gilbert Juan E. , In Shim Soo
Published: November 2011

Purpose

The purpose of this paper is two‐fold: to investigate virtual agent representational characteristics (modality, interaction style, animation, realism, embodiment, and gender) employed by agent software providers in developing commercial and non‐commercial web sites; and to examine older consumers' preferences in these agent characteristics.

Design/methodology/approach

Study 1 involves a content analysis of 64 sample web sites of agent providers, and study 2 consists of four focus group interviews conducted with 25 older consumers in the age group of 65‐82 years.

Findings

Findings from both studies reveal some important disconnects between agent characteristics (modality, realism, animation, and gender) offered by virtual agent software providers and those preferred by older consumers. As a result, important recommendations are provided for the development of virtual agents for e‐commerce applications to enhance accessibility for older users.

Originality/value

No previous studies have investigated which agent characteristics enhance web accessibility and are most preferred by older users in the context of e‐commerce applications.
Locating women board members in gendered director networks
Authors: Hawarden Rosanne Jane , Marsland Stephen
Published: November 2011

Purpose

Despite the extensive study of director interlocks very little is known about gendered director networks. Boards of directors are primarily male; globally, only 5‐20 per cent of directors are women and change is described as glacially slow. The extent to which women directors are central to the network, or pushed to the margins, is unknown. Using the tools of social network analysis we extract the components of three director networks, a global and two national networks and locate the women directors. The paper aims to examine the persistence of director networks over time to determine whether gender related differences – apart from size – contribute to the apparent resistance to change.

Design/methodology/approach

The paper uses a longitudinal approach, comparing director networks on a global network scale (2004 and 2007FortuneGlobal 200) and a national one (2004 and 2007 New Zealand Stock Exchange) with the iconic 1999FortuneUS 1000 dataset. After extracting the largest connected component, the female directors are separated out. From the 2004 and 2007 data director turnover is calculated to determine the stability of the networks.

Findings

Female directors are more likely to be found in the largest connected component of the mixed gender network, indicating that they are not marginalised. Despite high turnover rates, director networks are stable over time which may manifest as resistance to change.

Originality/value

The structure of gendered director networks is unknown and the location of women directors in the network components has not been considered in board diversity research. The results point to an underlying gender equity in all director networks. A new theoretical approach, glass network theory, has implications for boardroom diversity interventions.
Feminist attributes and entrepreneurial identity
Authors: Orser Barbara J. , Elliott Catherine , Leck Joanne
Published: November 2011

Purpose

The purpose of this study is to examine how feminist attributes are expressed within entrepreneurial identity.

Design/methodology/approach

The study employed a purposive sampling technique to recruit 15 self‐identified “feminist entrepreneurs”. This included retailers, manufacturers, exploration operators, consultants, and professionals. Qualitative data were subject to content analysis.

Findings

Contrary to a feminine archetype portrayed as caring and nurturing, respondents do not describe themselves as typically portrayed in the feminist literature. Prevalent themes included participative leadership, action‐oriented, and creative thinker/or problem solver.

Research limitations/implications

Researchers should use caution in assuming feminist discourse has direct application to characterizing or stereotyping “feminist” entrepreneurs. The applicability and reliability of “off the shelf” psychometrics to describe contemporary gender roles across the myriads of processes associated with venture creation must also be questioned. Limitations: the purposive and small‐sample limits the generalizability of findings to the diverse community of female entrepreneurs. Testing of the applicability, validity, and reliability of the nomenclature used to describe self‐identity is warranted across international samples of feminist entrepreneurs.

Practical implications

The current study provides an inventory of feminist entrepreneurs' self‐described leadership attributes. The nomenclature can be used by women‐focused trainers to help clients to recognize their entrepreneurial attributes.

Social implications

The study may assist women in recognizing identity synergies and conflicts (e.g. within themselves and among family, employees, clients, etc.).

Originality/value

This is the first study that documents feminist entrepreneurs' leadership attributes. As such, the work is a step in seeking to reconcile feminist theory and entrepreneurial practice.
Migrant women in Austria: difficulties with access to health care services
Authors: Habersack Marion , Gerlich Irmina‐Anna , Mandl Manuela
Published: November 2011

Purpose

The objectives of the study, which focuses on reproductive health care services, are to identify factors that impede adequate access to care for migrant women and to identify possible solutions.

Design/methodology/approach

In this case study, problem‐based, semi‐structured individual interviews were conducted with 12 migrant women, eight staff members of non‐governmental organizations (NGOs), and eight staff members of a public hospital (physicians, nurses). The transcripts were analyzed using a grounded thematic approach.

Findings

Problems in access to services were identified in four areas: accessibility/information; institutional infrastructure; language barriers; and cultural competences.

Social implications

There is a need to develop culture‐specific understanding of health amongst service providers working in public hospitals. It is also necessary to raise awareness of traditional beliefs and behavior of migrant women to maximize good quality care. A closer collaboration of hospitals and NGOs is recommended, not least in order to ensure the demand‐ and needs‐orientation, appropriateness, effectiveness, and efficiency of health care for migrant women. Migrant women mentioned different approaches to delivering care – these solutions should, where possible, be applied in practice.

Originality/value

The study correlates and supports knowledge from existing literature regarding possible barriers to the use of health care services by women with migrant backgrounds. Recommendations for overcoming existing barriers are also identified by research participants.
Exploring criminogenic need through victim apology letters II: an IPA analysis of post‐treatment accounts of offending against children
Authors: Duff Simon
Published: November 2011

Purpose

Building on previous work, concerned with analysis of pre‐treatment apology letters of men who have offended against children, the current research focuses on post‐treatment apology letters of the same group of men.

Design/methodology/approach

A total of 26 post‐treatment apology letters of men who attended a community‐based introductory sex offender treatment programme were analysed using interpretative phenomenological analysis (IPA) to explore how the men conceptualise and understand themselves, their behaviour and their victims after treatment.

Findings

The data suggest that the men express themselves in terms of need, however, primarily this is in terms of pro‐social needs, such as a need for forgiveness, rather than in terms of criminogenic need. The one theme identifiable as a criminogenic need is concerned with sexual needs and very little detail is provided that might explain if the need is not otherwise being met; if there is a sexual preference for children, etc. Thus, from these data, it is not possible to identify a specific target need for treatment related to sexual behaviour.

Originality/value

The results raise the question as to whether criminogenic need is the correct level of analysis for thinking about sexual offending and if treatment programmes that use the language of criminogenic need are an appropriate conceptual fit. The identification of pro‐social needs suggests that interventions may need to include work on what Ward and colleagues have referred to as “personal strivings” in order to have a greater impact on victim empathy.
Predicting the potential demographic impact of predators on their prey: a comparative analysis of two carnivore–ungulate systems in Scandinavia
Authors: Gervasi Vincenzo , Nilsen Erlend B. , Sand Håkan , Panzacchi Manuela , Rauset Geir R. , Pedersen Hans C. , Kindberg Jonas , Wabakken Petter , Zimmermann Barbara , Odden John , Liberg Olof , Swenson Jon E. , Linnell John D. C.
Published: November 2011

1. Understanding the role of predation in shaping the dynamics of animal communities is a fundamental issue in ecological research. Nevertheless, the complex nature of predator–prey interactions often prevents researchers from modelling them explicitly.

2. By using periodic Leslie–Usher matrices and a simulation approach together with parameters obtained from long‐term field projects, we reconstructed the underlying mechanisms of predator–prey demographic interactions and compared the dynamics of the roe deer–red fox–Eurasian lynx–human harvest system with those of the moose–brown bear–gray wolf–human harvest system in the boreal forest ecosystem of the southern Scandinavian Peninsula.

3. The functional relationship of both roe deer and moose λ to changes in predation rates from the four predators was remarkably different. Lynx had the strongest impact among the four predators, whereas predation rates by wolves, red foxes, or brown bears generated minor variations in prey population λ. Elasticity values of lynx, wolf, fox and bear predation rates were −0·157, −0·056, −0·031 and −0·006, respectively, but varied with both predator and prey densities.

4. Differences in predation impact were only partially related to differences in kill or predation rates, but were rather a result of different distribution of predation events among prey age classes. Therefore, the age composition of killed individuals emerged as the main underlying factor determining the overall per capita impact of predation.

5. Our results confirm the complex nature of predator–prey interactions in large terrestrial mammals, by showing that different carnivores preying on the same prey species can exert a dramatically different demographic impact, even in the same ecological context, as a direct consequence of their predation patterns. Similar applications of this analytical framework in other geographical and ecological contexts are needed, but a more general evaluation of the subject is also required, aimed to assess, on a broader systematic and ecological range, what specific traits of a carnivore are most related to its potential impact on prey species.
Associations between serum homocysteine, holotranscobalamin, folate and cognition in the elderly: a longitudinal study
Authors: Hooshmand B. , Solomon A. , Kåreholt I. , Rusanen M. , Hänninen T. , Leiviskä J. , Winblad B. , Laatikainen T. , Soininen H. , Kivipelto M.
Published: November 2011

Abstract.  Hooshmand B, Solomon A, Kåreholt I, Rusanen M, Hänninen T, Leiviskä J, Winblad B, Laatikainen T, Soininen H & Kivipelto M (Aging Research Center, Karolinska Institutet, Stockholm, Sweden; KI Alzheimer’s Disease Research Center (KI‐ADRC), Karolinska Institutet, Stockholm, Sweden; National Institute for Health and Welfare (THL), Helsinki, Finland; University of Eastern Finland, Institute of Clinical Medicine, and University Hospital, Kuopio, Finland). Associations between serum homocysteine, holotranscobalamin, folate and cognition in the elderly: a longitudinal study. J Intern Med 2012; 271: 204–212.

Objectives.  To examine the associations between serum homocysteine (tHcy), holotranscobalamin (holoTC, the biologically active fraction of vitamin B12) and folate and cognitive functioning in a longitudinal population‐based study of Finnish elderly subjects.

Subjects and design.  tHcy, holoTC and folate were measured at baseline in 274 dementia‐free subjects aged 65–79 years from the Cardiovascular Risk Factors, Aging and Dementia study. Subjects were re‐examined 7 years later, and global cognition, episodic memory, executive functioning, verbal expression and psychomotor speed were assessed.

Results.  Higher baseline tHcy levels were associated with poorer performance in global cognition, relative difference: 0.90 [95% confidence interval (CI) 0.81–0.99]; episodic memory: 0.87 (95% CI 0.77–0.99); executive functions: 0.86 (95% CI 0.75–0.98); and verbal expression: 0.89 (95% CI 0.81–0.97) at follow‐up. Increased holoTC levels were related to better performance on global cognition: 1.09 (95% CI 1.00–1.19); executive functions: 1.11 (95% CI 1.01–1.21); and psychomotor speed: 1.13 (95% CI 1.01–1.26). After excluding 20 cases of incident dementia, increased tHcy remained associated with poorer performance in episodic memory, execution functions and verbal expression. Higher holoTC levels tended to be related to better performance in executive functions and psychomotor speed, while elevated serum folate concentrations were significantly related to higher scores in global cognition and verbal expression tests.

Conclusions.  tHcy, holoTC and folate levels are related to cognitive performance 7 years later even in nondemented elderly subjects. Randomized trials are needed to determine the impact of vitamin B12 and folate supplementation on preventing cognitive decline in the elderly.
Climate‐induced changes to the ancestral population size of two Patagonian galaxiids: the influence of glacial cycling
Authors: ZEMLAK TYLER S. , WALDE SANDRA J. , HABIT EVELYN M. , RUZZANTE DANIEL E.
Published: November 2011

Patagonia is one of the few areas in the Southern Hemisphere to have been directly influenced by Quaternary glaciers. In this study, we evaluate the influence that Quaternary glacial ice had on the genetic diversity of two congeneric fish species, the diadromous Galaxias maculatus and the nondiadromous Galaxias platei, using multilocus estimates of effective population size through time. Mid‐Quaternary glaciations had far‐reaching consequences for both species. Galaxias maculatus and G. platei each experienced severe genetic bottlenecks during the period when Patagonia ice sheet advance reached its maximum positions c. 1.1–0.6 Ma. Concordant drops in effective size during this time suggest that range sizes were under similar constraints. It is therefore unlikely that coastal (brackish/marine) environments served as a significant refuge for G. maculatus during glacial periods. An earlier onset of population declines for G. platei suggests that this species was vulnerable to modest glacial advances. Declines in effective sizes were continuous for both species and lasted into the late‐Pleistocene. However, G. maculatus exhibited a strong population recovery during the late‐Quaternary (c. 400 000 bp). Unusually long and warm interglacials associated with the late‐Quaternary may have helped to facilitate a strong population rebound in this primarily coastal species.
The half‐size ABC transporters STR1 and STR2 are indispensable for mycorrhizal arbuscule formation in rice
Authors: Gutjahr Caroline , Radovanovic Dragica , Geoffroy Jessika , Zhang Quan , Siegler Heike , Chiapello Marco , Casieri Leonardo , An Kyungsook , An Gynheung , Guiderdoni Emmanuel , Kumar Chellian Santhosh , Sundaresan Venkatesan , Harrison Maria J. , Paszkowski Uta
Published: November 2011

The central structure of the symbiotic association between plants and arbuscular mycorrhizal (AM) fungi is the fungal arbuscule that delivers minerals to the plant. Our earlier transcriptome analyses identified two half‐size ABCG transporters that displayed enhanced mRNA levels in mycorrhizal roots. We now show specific transcript accumulation in arbusculated cells of both genes during symbiosis. Presently, arbuscule‐relevant factors from monocotyledons have not been reported. Mutation of either of theOryza sativa(rice) ABCG transporters blocked arbuscule growth of different AM fungi at a small and stunted stage, recapitulating the phenotype ofMedicago truncatula stunted arbuscule 1and2(str1andstr2) mutants that are deficient in homologous ABCG genes. This phenotypic resemblance and phylogenetic analysis suggest functional conservation of STR1 and STR2 across the angiosperms. Malnutrition of the fungus underlying limited arbuscular growth was excluded by the absence of complementation of thestr1phenotype by wild‐type nurse plants. Furthermore, plant AM signaling was found to be intact, as arbuscule‐induced marker transcript accumulation was not affected instr1mutants. Strigolactones have previously been hypothesized to operate as intracellular hyphal branching signals and possible substrates of STR1 and STR2. However, full arbuscule development in the strigolactone biosynthesis mutantsd10andd17suggested strigolactones to be unlikely substrates of STR1/STR2. Interestingly, rice STR1 is associated with acis‐natural antisense transcript (antiSTR1). Analogous toSTR1andSTR2, at the root cortex level, theantiSTR1transcript is specifically detected in arbusculated cells, suggesting unexpected modes of STR1 regulation in rice.
A primer for biomedical scientists on how to execute Model II linear regression analysis
Authors: Ludbrook John
Published: November 2011

1. There are two very different ways of executing linear regression analysis. One is Model I, when the x‐values are fixed by the experimenter. The other is Model II, in which the x‐values are free to vary and are subject to error.

2. I have received numerous complaints from biomedical scientists that they have great difficulty in executing Model II linear regression analysis. This may explain the results of a Google Scholar search, which showed that the authors of articles in journals of physiology, pharmacology and biochemistry rarely use Model II regression analysis.

3. I repeat my previous arguments in favour of using least products linear regression analysis for Model II regressions. I review three methods for executing ordinary least products (OLP) and weighted least products (WLP) regression analysis: (i) scientific calculator and/or computer spreadsheet; (ii) specific purpose computer programs; and (iii) general purpose computer programs.

4. Using a scientific calculator and/or computer spreadsheet, it is easy to obtain correct values for OLP slope and intercept, but the corresponding 95% confidence intervals (CI) are inaccurate.

5. Using specific purpose computer programs, the freeware computer program smatr gives the correct OLP regression coefficients and obtains 95% CI by bootstrapping. In addition, smatr can be used to compare the slopes of OLP lines.

6. When using general purpose computer programs, I recommend the commercial programs systat and Statistica for those who regularly undertake linear regression analysis and I give step‐by‐step instructions in the Supplementary Information as to how to use loss functions.
Estimating updraft velocity components over large spatial scales: contrasting migration strategies of golden eagles and turkey vultures
Authors: Bohrer Gil , Brandes David , Mandel James T. , Bildstein Keith L. , Miller Tricia A. , Lanzone Michael , Katzner Todd , Maisonneuve Charles , Tremblay Junior A.
Published: November 2011

Ecology Letters (2011)

Soaring birds migrate in massive numbers worldwide. These migrations are complex and dynamic phenomena, strongly influenced by meteorological conditions that produce thermal and orographic uplift as the birds traverse the landscape. Herein we report on how methods were developed to estimate the strength of thermal and orographic uplift using publicly available digital weather and topography datasets at continental scale. We apply these methods to contrast flight strategies of two morphologically similar but behaviourally different species: golden eagle, Aquila chrysaetos, and turkey vulture, Cathartes aura, during autumn migration across eastern North America tracked using GPS tags. We show that turkey vultures nearly exclusively used thermal lift, whereas golden eagles primarily use orographic lift during migration. It has not been shown previously that migration tracks are affected by species‐specific specialisation to a particular uplift mode. The methods introduced herein to estimate uplift components and test for differences in weather use can be applied to study movement of any soaring species.
Effect of oral phytoestrogen on androgenicity and insulin sensitivity in postmenopausal women
Authors: Lee C. C. , Bloem C. J. , Kasa‐Vubu J. Z. , Liang L.‐J.
Published: November 2011

Aim: The aim of this study was to determine and compare the effect of treatment with transdermal oestrogen and phytoestrogen on insulin sensitivity and sex hormone‐binding globulin (SHBG) levels in healthy postmenopausal women.

Methods: Forty‐three healthy postmenopausal women aged 68 ± 7 (mean ± SD) years who were not receiving hormonal replacement therapy completed a 3 month randomized drug therapy study. The participants were randomized to one of four groups: 0.05 mg or 0.1 mg transdermal oestrogen/day, or 40 or 80 mg oral phytoestrogen (Promensil)/day insulin sensitivity was indirectly measured using the quantitative insulin sensitivity check index (QUICKI). SHBG, total testosterone, oestradiol, and fasting glucose and insulin levels for calculation of insulin sensitivity were obtained at baseline and at monthly intervals during the 3 months of therapy.

Results: In healthy nondiabetic postmenopausal women, the rate of change in QUICKI was significantly different between the red clover based phytoestrogen and transdermal oestrogen groups, so that after three months of therapy, QUICKI with red clover based phytoestrogen therapy was lower than that in the transdermal oestrogen group, p = 0.01. Red clover based phytoestrogen therapy was not associated with any changes in SHBG levels whereas transdermal estrogen therapy significantly increased SHBG levels, p = 0.05.

Conclusions: In contrast to transdermal oestrogen therapy, oral phytoestrogen therapy does not decrease androgenicity and is associated with a decrease in insulin sensitivity. These effects are similar to those of raloxifene and consistent with phytoestrogen's selective oestrogen receptor modulator properties.