bluuebunny/crossref_metadata_2025 huggingface dataset:
FORMAL: A model to identify organisms present in metagenomes using Monte Carlo Simulation
Authors: Silva Genivaldo Gueiros Z. , Dutilh Bas E. , Edwards Robert A.
Published: October 2014

One of the major goals in metagenomics is to identify organisms present in the microbial community from a huge set of unknown DNA sequences. This profiling has valuable applications in multiple important areas of medical research such as disease diagnostics. Nevertheless, it is not a simple task, and many approaches that have been developed are slow and depend on the read length of the DNA sequences. Here we introduce an innovative and agile approach which k-mer and Monte Carlo simulation to profile and report abundant organisms present in metagenomic samples and their relative abundance without sequence length dependencies. The program was tested with a simulated metagenomes, and the results show that our approach predicts the organisms in microbial communities and their relative abundance.
Introns structure patterns of variation in nucleotide composition inArabidopsis thalianaand rice protein-coding genes
Authors: Ressayre Adrienne , Glémin Sylvain , Montalent Pierre , Serre-Giardi Laurana , Dillmann Christine , Joets Johann
Published: October 2014

Plant genomes are large, intron-rich and present a wide range of variation in coding regionG+Ccontent. Concerning coding regions, a sort of syndrome can be described in plants: the increase inG+Ccontent is associated with both the increase in heterogeneity among genes within a genome and the increase in variation across genes. Taking advantage of the large number of genes composing plant genomes and the wide range of variation in gene intron number, we performed a comprehensive survey of the patterns of variation inG+Ccontent at different scales from the nucleotide level to the genome scale in two speciesArabidopsis thalianaandOryza sativa, comparing the patterns in genes with different intron numbers. In both species, we observed a pervasive effect of gene intron number and location along genes onG+Ccontent, codon and amino acid frequencies suggesting that in both species, introns have a barrier effect structuringG+Ccontent along genes. In external gene regions (located upstream first or downstream last intron), species-specific factors are shapingG+Ccontent while in internal gene regions (surrounded by introns),G+Ccontent is constrained to remain within a range common to both species. In rice, introns appear as a major determinant of geneG+Ccontent while inA. thalianaintrons have a weaker but significant effect. The structuring effect of introns in both species is susceptible to explain theG+Ccontent syndrome observed in plants.
Using phishing experiments and scenario-based surveys to understand security behaviours in practice
Authors: Rocha Flores Waldo , Holm Hannes , Svensson Gustav , Ericsson Göran
Published: October 2014

Purpose

– The purpose of the study was threefold: to understand security behaviours in practice by investigating factors that may cause an individual to comply with a request posed by a perpetrator; to investigate if adding information about the victim to an attack increases the probability of the attack being successful; and, finally, to investigate if there is a correlation between self-reported and observed behaviour.

Design/methodology/approach

– Factors for investigation were identified based on a review of existing literature. Data were collected through a scenario-based survey, phishing experiments, journals and follow-up interviews in three organisations.

Findings

– The results from the experiment revealed that the degree of target information in an attack increased the likelihood that an organisational employee falls victim to an actual attack. Further, an individual’s trust and risk behaviour significantly affected the actual behaviour during the phishing experiment. Computer experience at work, helpfulness and gender (females tend to be less susceptible to a generic attack than men), had a significant correlation with behaviour reported by respondents in the scenario-based survey. No correlation between the results from the scenario-based survey and the experiments was found.

Research limitations/implications

– One limitation is that the scenario-based survey may have been interpreted differently by the participants. Another is that controlling how the participants reacted when receiving the phishing mail, and what actually triggered each and every participant to click on the attached link, was not possible. Data were however collected to capture these aspects during and after the experiments. In conclusion, the results do not imply that one or the other method should be ruled out, as they have both advantages and disadvantages which should be considered in the context of collecting data in the critical domain of information security.

Originality/value

– Two different methods to collect data to understand security behaviours have rarely been used in previous research. Studies that add target information to understand if such information could increase the probability of attack success is sparse. This paper includes both approaches.
Exploring the blurred nature of strategic linkages across the BSC
Authors: Francioli Francesca , Cinquini Lino
Published: October 2014

Purpose

– The research aims at addressing the way in which linkages based on qualitative causality could be preferred in designing a balanced scorecard (BSC), by applying a cost-benefit judgment with respect to the complexity of defining strong, statistically reliable cause-and-effect relations among performance measures.

Design/methodology/approach

– The authors review the way in which cause-and-effect relations across the BSC have been developed based on a case study of BSC implemented in an Italian bank collecting data by in-depth interviews and company’s internal archives.

Findings

– The research reveals how the ambiguity, or “blurred nature”, of strategic linkages is recognized in the empirical setting of an bank, facing a highly uncertain and complex environment and how the orthodox tools of strategy maps and explicit cause-and-effect linkages prescribed by the theoretical literature are avoided by the human actors. Despite these omissions, the BSC is nevertheless effective. As the case shows, it generated a “democracy” where individuals and departments communicate, commit and collaborate in an effort to implement strategy. The research also shows the role of the BSC in heightening the importance and awareness of performance evaluation among the actors.

Practical implications

– The research provides practitioners with insights into how to design and manage cause-and-effect relationships in BSC. In particular, evidence is provided that finality linkages in BSC may be successful in use and predictive capabilities, according with expectations and purposes of the organization’s “climate of control”, in a context in which the cost-benefit philosophy in implementing BSC is followed.

Originality/value

– The paper addresses an issue of practical relevance in the implementation of BSC showing a discrepancy between theoretical and practical meaning of causality. Besides the research highlights, the extent to which linkages across the BSC perspectives (and related measures and variables) can only be based on individual assumptions about the means to an end and based on qualitative assertions (finality).
Reintegrating socially excluded individuals through a social enterprise intervention
Authors: Seddon Fred , Hazenberg Richard , Denny Simon
Published: October 2014

Purpose

– The aim of this research project is to reveal participant perceptions of a Social Enterprise Intervention (SEI) programme, run by a social enterprise and designed to reintegrate socially excluded individuals into society.

Design/methodology/approach

– The research participants were the social entrepreneur, staff at the social enterprise, the SEI programme attendees and a representative from an external referral agency. Participants engaged in semi-structured interviews with a researcher designed to elicit participant perceptions of the programme.

Findings

– Results of the analysis of the interviews revealed six emergent themes that were interpreted by the researchers as: “social mission focus”, “heroic social entrepreneur”, “social impact”, “recidivism”, “the programme” and “programme attendees”. Results of the analysis reveal that all research participants reported the programme helped to re-socialise the programme attendees and increased their self-confidence and self-esteem. Participants also believed programme attendees acquired important skills and qualifications in general warehouse activities and forklift truck driving, which would greatly increase their future employability. Programme attendees indicated the “real world” working environment was important to their feelings of success on the programme.

Originality/value

– This paper identifies a hybrid SEI programme based upon the “vision” of a “heroic” social entrepreneur. It also identifies the advantages of the “real” working environment in increasing the employability of socially excluded individuals whilst, at the same time, increasing their social skills.
More for less: sampling strategies of plant functional traits across local environmental gradients
Authors: Carmona Carlos P. , Rota Cristina , Azcárate Francisco M. , Peco Begoña
Published: October 2014

Ecologists use approaches based on plant functional traits to tackle several fundamental and applied questions. Although a perfect characterization of functional trait structure requires the measurement of all the individuals in communities, this is prohibitively resource‐consuming. Consequently, the general practice is to average the trait values of a reduced number of individuals per species. However, there are different alternatives regarding the number, identity and spatial location of the individuals chosen to calculate species‐averaged trait values.

In this study, we compared different strategies for sampling functional traits, using community‐weighted mean trait values (CWM) and the Rao index of functional diversity (FD). We intensively sampled the functional trait structure along a topographical gradient in a Mediterranean grassland, obtaining accurate estimations of the ‘real’ values of these indices (CWMI and FDI) for three traits (height, leaf area and specific leaf area).

We simulated three different sampling strategies differing in the spatial location of the individuals used to estimate species‐mean trait: (i) average of the whole gradient (GLO), (ii) average of the sampling unit in which the abundances of species maximize (MAX) and (iii) average of a reduced number of individuals per species and sampling unit (LOC). For each strategy, we simulated different sampling intensities (number of individuals sampled).

For each trait, we examined the ability of each strategy and sampling intensity to accurately estimate CWMI and FDI, as well as their ability to detect changes in functional trait structure along the topographical gradient.

LOC outperformed the other strategies in terms of accuracy and bias, and was much more efficient to describe changes along the gradient, regardless of the traits and indicators considered. Furthermore, LOC was the only strategy that improved consistently as sampling intensity increased, especially at low levels of intensity.

Our results indicate that the impact of considering intraspecific variability in trait values can be greater than commonly assumed. Strategies that neglect this source of variability can result in inaccurate or biased estimations of the functional trait structure of plant communities. Most importantly, we show that intraspecific variability can be taken into consideration without any increases in the total number of individuals measured.
Understanding home modifications impact on clients and their family's experience of home: A qualitative study
Authors: Aplin Tammy , de Jonge Desleigh , Gustafsson Louise
Published: October 2014

Background/aim

Home modifications aim to enhance safety and occupational performance in the home. However, given the complexity and unique meaning of the home, they can impact aspects other than function. This qualitative descriptive study aimed to explore the impact of home modifications on clients and their family's experience of home.

Methods

Home modification clients and their family and carers participated in 42 in‐depth interviews which were analysed using a template analysis.

Findings

Home modifications impacted positively and negatively on five dimensions of the home environment, the personal, occupational, physical, temporal and social dimension. The outcomes of the modifications and the home modification process were influenced by three themes, workmanship, consultation or involvement in decision‐making, and the societal dimension of the home environment.

Conclusions

The negative outcomes and poor consultation experiences suggest the need for occupational therapists to understand their client's personal experience of home and to comprehensively follow‐up and evaluate these following home modifications.
Duration of freezing necessary to damage the leaves of Fallopia japonica (Houtt.) Ronse Decraene
Authors: Baxendale Victoria J. , Tessier Jack T.
Published: October 2014

Fallopia japonica (Houtt.) Ronse Decraene is an invasive plant species that introduces economic, social, and environmental stresses. After observing frost damage to F. japonica plants in the field, we exposed leaves of F. japonica and a native species (Acer saccharum Marshall) to freezing temperatures in the laboratory and compared their net photosynthetic rate to that of fresh leaves. In both species, the net photosynthetic rate of leaves frozen for 0.5 h or for 1 h were not significantly different from each other but were both significantly less than that of fresh leaves. Fresh leaves of F. japonica had a higher net photosynthetic rate than those of A. saccharum, but the relationship was reversed in all freezing treatments. Frozen leaves of F. japonica contained microscopically visible frost lenses, which revealed the mechanism of the damage. These results quantify how quickly F. japonica is damaged by freezing conditions and suggest that minimum vernal temperatures may limit its range expansion.
Measuring the Volatility of Wheat Futures Prices on the LIFFE
Authors: Dawson P. J.
Published: October 2014

Agricultural prices rose dramatically in 2007 and have subsequently fluctuated at high levels. This paper estimates the volatility of daily wheat futures prices on the Euronext/London International Financial Futures and Options Exchange for 1996–2012 using an exponential generalised autoregressive conditional heteroscedasticity model with a constant (price) elasticity of variance (CEV) and a broken trend. Results show that volatility is highly persistent; there is a structural break in volatility in June 2007 when volatility rose by 10%; subsequently, the wheat futures price has become more volatile; and the CEV is 0.04.
Moral hazard, adverse selection, and health expenditures: A semiparametric analysis
Authors: Bajari Patrick , Dalton Christina , Hong Han , Khwaja Ahmed
Published: October 2014

Theoretical models predict asymmetric information in health insurance markets may generate inefficient outcomes due to adverse selection and moral hazard. However, previous empirical research has found it difficult to disentangle adverse selection from moral hazard in health care consumption. We propose a two‐step semiparametric estimation strategy to identify and estimate a canonical model of asymmetric information in health care markets. With this method, we can estimate a structural model of demand for health care. We illustrate this method using a claims‐level data set with confidential information from a large self‐insured employer. We find significant evidence of moral hazard and adverse selection.
Competition leverage: how the demand side affects optimal risk adjustment
Authors: Bijlsma Michiel , Boone Jan , Zwart Gijsbert
Published: October 2014

We study optimal risk adjustment in imperfectly competitive health insurance markets when high‐risk consumers are less likely to switch insurer than low‐risk consumers. Insurers then have an incentive to select even if risk adjustment perfectly corrects for cost differences. To achieve first best, risk adjustment should overcompensate insurers for serving high‐risk agents. Second, we identify a trade‐off between efficiency and consumer welfare. Reducing the difference in risk adjustment subsidies increases consumer welfare by leveraging competition from the elastic low‐risk market to the less elastic high‐risk market. Third, mandatory pooling can increase consumer surplus further, at the cost of efficiency.
User Innovation in Techniques: A Case Study Analysis in the Field of Medical Devices
Authors: Hinsch Mareike E. , Stockstrom Christoph , Lüthje Christian
Published: October 2014

Users are the primary source of new techniques, i.e. systematic activities by which a complex task is accomplished. Even though user‐generated techniques are a pervasive phenomenon which can be observed in many different contexts, existing research on user innovation has focused on product and service innovations. We focus on this important area of user innovation by studying four cases in the field of medical devices to analyse the processes by which users generate and diffuse new techniques as well as the interdependencies between user‐generated techniques and subsequent changes to product use and product innovation. Our findings suggest that user innovation in techniques triggers product innovation by users and manufacturers. Therefore, users' contributions to total innovation output are much higher than previously considered. Additionally, the diffusion of techniques differs significantly from the diffusion of new products. It can only be achieved with the involvement of diffusion agents and their interpersonal interaction and joint performance of the technique with possible adopters. As the diffusion of a technique is often a prerequisite for the diffusion of any related product, companies are forced to re‐think their marketing strategies.
Acute-phase protein α1-anti-trypsin: diverting injurious innate and adaptive immune responses from non-authentic threats
Authors: Guttman O , Baranovski B M , Schuster R , Kaner Z , Freixo-Lima G S , Bahar N , Kalay N , Mizrahi M I , Brami I , Ochayon D E , Lewis E C
Published: October 2014

One would assume that the anti-inflammatory activity of α1-anti-trypsin (AAT) is the result of inhibiting neutrophil enzymes. However, AAT exhibits tolerogenic activities that are difficult to explain by serine-protease inhibition or by reduced inflammatory parameters. Targets outside the serine-protease family have been identified, supporting the notion that elastase inhibition, the only functional factory release criteria for clinical-grade AAT, is over-emphasized. Non-obvious developments in the understanding of AAT biology disqualify it from being a straightforward anti-inflammatory agent: AAT does not block dendritic cell activities, nor does it promote viral and tumour susceptibilities, stunt B lymphocyte responses or render treated patients susceptible to infections; accordingly, outcomes of elevated AAT do not overlap those attained by immunosuppression. Aside from the acute-phase response, AAT rises during the third trimester of pregnancy and also in advanced age. At the molecular level, AAT docks onto cholesterol-rich lipid-rafts and circulating lipid particles, directly binds interleukin (IL)-8, ADAM metallopeptidase domain 17 (ADAM17) and danger-associated molecular pattern (DAMP) molecules, and its activity is lost to smoke, high glucose levels and bacterial proteases, introducing a novel entity – ‘relative AAT deficiency’. Unlike immunosuppression, AAT appears to help the immune system to distinguish between desired responses against authentic threats, and unwanted responses fuelled by a positive feedback loop perpetuated by, and at the expense of, inflamed injured innocent bystander cells. With a remarkable clinical safety record, AAT treatment is currently tested in clinical trials for its potential benefit in a variety of categorically distinct pathologies that share at least one common driving force: cell injury.
Role Asymmetry and Code Transmission in Signaling Games: An Experimental and Computational Investigation
Authors: Moreno Maggie , Baggio Giosuè
Published: October 2014

In signaling games, a sender has private access to a state of affairs and uses a signal to inform a receiver about that state. If no common association of signals and states is initially available, sender and receiver must coordinate to develop one. How do players divide coordination labor? We show experimentally that, if players switch roles at each communication round, coordination labor is shared. However, in games with fixed roles, coordination labor is divided: Receivers adjust their mappings more frequently, whereas senders maintain the initial code, which is transmitted to receivers and becomes the common code. In a series of computer simulations, player and role asymmetry as observed experimentally were accounted for by a model in which the receiver in the first signaling round has a higher chance of adjusting its code than its partner. From this basic division of labor among players, certain properties of role asymmetry, in particular correlations with game complexity, are seen to follow.
Influence of cyclic torsional preloading on cyclic fatigue resistance of nickel – titanium instruments
Authors: Pedullà E. , Lo Savio F. , Boninelli S. , Plotino G. , Grande N. M. , Rapisarda E. , La Rosa G.
Published: October 2014

Aim

To evaluate the effect of different torsional preloads on cyclic fatigue resistance of endodontic rotary instruments constructed from conventional nickel‐titanium (NiTi), M‐Wire or CM‐Wire.

Methodology

Eighty new size 25, 0.06 taper Mtwo instruments (Sweden & Martina), size 25, 0.06 taper HyFlex CM (Coltene/Whaledent, Inc) and X2 ProTaper Next (Dentsply Maillefer) were used. The Torque and distortion angles at failure of new instruments (n = 10) were measured, and 0% (n = 10), 25%, 50% and 75% (n = 20) of the mean ultimate torsional strength as preloading condition were applied according to ISO 3630‐1 for each brand. The twenty files tested for every extent of preload were subjected to 20 or 40 torsional cycles (n = 10). After torsional preloading, the number of cycles to failure was evaluated in a simulated canal with 60° angle of curvature and 5 mm of radius of curvature. Data were analysed using two‐way analysis of variance. The fracture surface of each fragment was examined with a scanning electron microscope (SEM). Data were analysed by two‐way analyses of variance.

Results

Preload repetitions did not influence the cyclic fatigue of the three brands; however, the 25%, 50% and 75% torsional preloading significantly reduced the fatigue resistance of all instruments tested (P < 0.01, P < 0.001 and P < 0.0001, respectively) except for the HyFlex CM preloaded with 25% of the maximum torsional strength (P > 0.05).

Conclusions

Torsional preloads reduced the cyclic fatigue resistance of conventional and treated (M‐wire and CM‐wire) NiTi rotary instruments except for size 25, 0.06 taper HyFlex CM instruments with a 25% of torsional preloading.
The influence of interleukin‐7 receptor α‐chain haplotypes on outcome after allogeneic hematopoietic cell transplantation
Authors: Broux B. , Shamim Z. , Wang T. , Spellman S. , Haagenson M. , Stinissen P. , Ryder L. P. , Müller K. , Hellings N.
Published: October 2014

We investigated the influence of IL‐7 receptor α‐chain (IL‐7Rα) gene haplotypes in donors on the outcome of haematopoietic cell transplantation (HCT). Unlike the association between single donor SNPs and HCT outcome found previously, only trends towards association were found here, due to ‘dilution’ of SNPs into haplotypes.
Effects of abstract and concrete simulation elements on science learning
Authors: Jaakkola T. , Veermans K.
Published: October 2014

Contemporary evidence on the effectiveness of concrete and abstract representations in science education is based solely on studies conducted in college context. There it has been found that learning with abstract representations produces predominantly better outcomes than learning with concrete representations and combining the representations can be even more productive. In the present study, 52 elementary school students used a computer simulation to discover the basic principles of electric circuits. The perceptual concreteness of simulation elements either remained concrete or switched from concrete to abstract during the learning. In order to compare the relative effectiveness of the learning conditions and assess the changes in students' conceptual understanding, the students completed a subject knowledge assessment questionnaire before and after learning with the simulation. According to the results, the students gained a better understanding of the circuits by learning with constantly concrete simulation elements than switching from concrete to abstract elements during the learning. Constantly concrete elements also enhanced the learning process by reducing the learning times. The outcomes of the study suggest that the effects of concrete and abstract representations in science education are notably different in elementary school context as compared with college contexts.
Turnover in the Council of the European Union: What It is and Why It Matters
Authors: Scherpereel John A. , Perez Lauren K.
Published: October 2014

This article analyzes personnel turnover in the Council of the European Union. It draws upon analysis of an original monthly database of ministers in EU Member States from 2004 to 2012. After surveying the literature on the negative effects of high legislative turnover, descriptive statistics are presented that demonstrate high levels of turnover in the Council as a whole and high levels of turnover across all nine sectoral Council configurations. A statistical model is then proposed that tests whether variations in levels of Council turnover affect the institution's bargaining success vis‐à‐vis other EU institutions. The finding, consistent with the broader literature's predictions, is that high levels of turnover hurt the Council vis‐à‐vis the European Parliament and the European Commission. The article concludes with general remarks about the implications of turnover for the Council system and for the EU more broadly.
Maternal protein restriction induces early‐onset glucose intolerance and alters hepatic genes expression in the peroxisome proliferator‐activated receptor pathway in offspring
Authors: Zheng Jia , Xiao Xinhua , Zhang Qian , Yu Miao , Xu Jianping , Wang Zhixin
Published: October 2014

Aims/Introduction

Maternal undernutrition during pregnancy and/or lactation can alter the offspring's response to environmental challenges, and thus increases the risk of the development of metabolic diseases at a later age. However, whether maternal protein restriction can modulate glucose metabolism in the early life of offspring is less understood. Furthermore, we explored the potential underlying mechanisms that illustrate this phenotype.

Materials and Methods

To test this hypothesis, we examined the offspring of C57BL/6J mice at weaning to determine the effects of feeding their mothers a low‐protein diet or normal chow diet throughout pregnancy and lactation. Gene array experiments and quantitative real‐time polymerase chain reaction were utilized to explore the altered hepatic genes expression.

Results

The offspring of dams fed a low‐protein diet had a lower birthweight and bodyweight, impaired glucose tolerance, decreased insulin sensitivity, and decreased serum cholesterol at weaning. Using gene array experiments, 253 differentially expressed genes were identified in the liver tissues of the offspring between the two groups. Bioinformatic analyses showed that all differentially expressed genes were mapped to 11 pathways. We focused on the ‘peroxisome proliferator‐activated receptor signaling pathway,’ because peroxisome proliferator‐activated receptors have emerged as central regulators of glucose and lipid homeostasis. Quantitative real‐time polymerase chain reaction was utilized for the validation of genes in the pathway.

Conclusions

A maternal low‐protein diet during pregnancy and lactation promotes early‐onset glucose intolerance in the offspring mice, and the altered hepatic genes expression in peroxisome proliferator‐activated receptor signaling pathway could play role in regulating this phenomenon.
Transient elastography compared to serum markers to predict liver fibrosis in a cohort of Chinese patients with chronic hepatitis B
Authors: Jia Jidong , Hou Jinlin , Ding Huiguo , Chen Guofeng , Xie Qing , Wang Yuming , Zeng Minde , Zhao Jingmin , Wang Tailing , Hu Xiqi , Schuppan D.
Published: October 2014

Background and Aim

Liver stiffness measurement (LSM) using transient elastography (FibroScan) is a useful tool to assess fibrosis in various chronic liver diseases. However, studies were mainly performed in Western countries and largely focused on chronic hepatitis C (CHC). We therefore carried out a multicenter study to validate the accuracy of LSM in the assessment of liver fibrosis in a large cohort of Chinese patients with chronic hepatitis B (CHB).

Methods

We compared LSM results to histological staging and serum fibrosis markers (five direct markers, APRI and FIB‐4) using Spearman correlation analysis and area under receiver operating characteristic (ROC) curves (AUROCs).

Results

Four hundred sixty‐nine patients were enrolled and eligible for statistical analysis. LSM in F0 to F4 was 5.5 ± 1.7, 5.8 ± 2.2, 7.6 ± 3.4, 14.5 ± 10.8, and 22.3 ± 13.6 kPa, respectively (correlation with fibrosis stage r = 0.522, P < 0.001). AUROC for LSM to correctly allocate patients to histological fibrosis stage ≥ F2, ≥ F3, and F4 was 0.82, 0.88, and 0.90, respectively. LSM outperformed serum fibrosis markers for detection of fibrosis F ≥ 2 and F4. Patients with ALT levels 1–5x and > 5x the upper limit of normal values had significantly higher stiffness values than stage‐matched patients with normal alanine aminotransferase.

Conclusion

Transient elastography is a reliable noninvasive technique to predict significant liver fibrosis in Chinese patients with CHB, being superior to current biomarker panels. However, enhanced inflammatory activity can lead to elevated stiffness values unrelated to histological fibrosis stage.
Agriculture, Land Tenure and International Migration in RuralGuatemala
Authors: Aguilar‐Støen Mariel , Taylor Matthew , Castellanos Edwin
Published: October 2014

In this paper, we ask what the effects of migration and remittances are on land tenure, agriculture and forests, based on empirical evidence from four rural communities inGuatemala. Our results suggest that remittances improve migrant families' access to agricultural land which – depending on the context – fosters more equitable local land distribution patterns or land concentration by migrant families. Changes in the political economy of the country also combine to stimulate these patterns, while remittances contribute to secure land rights held by migrant households. But even though migrant households are acquiring more land, the trend does not change the traditional pattern of land distribution in the country. Regarding forests, significant changes were not observed in two of the communities, while in one we observed forest decline and in the last, forest recovery. A trend away from reliance on the land for survival results in forest recovery.
Expression of Concern: The functions of HMGB1 depend on molecular localization and post‐translational modifications
Authors: Andersson U. , Antoine D. J. , Tracey K. J.
Published: October 2014

This Expression of Concern relates to the article “The functions of HMGB1 depend on molecular localization and post‐translational modifications” by Andersson, Antoine & Tracey (DOI: 10.1111/joim.12905).
Temporal Sweetness Profile of MNEI and Comparison with Commercial Sweeteners
Authors: Di Monaco R. , Miele N.A. , Volpe S. , Picone D. , Cavella S.
Published: October 2014

None of the current sweeteners match sucrose in terms of sweet taste quality or temporal characteristics. In fact, the sensory performance of a sweetener changes over time and it could interact with other stimuli. Time–intensity (t‐I) and temporal of dominance sensation (TDS) are both dynamic sensory methods, but they give different and complementary information: t‐I focuses on the evolution of the intensity of one attribute, whereas TDS is a descriptive multi‐attribute methodology that deals with the interactions among attributes.

The objectives of this study were to describe the sweetness temporal profile of a new protein‐based sweetener, MNEI, and to compare it with that of aspartame, saccharin and sucrose. First, equi‐sweetness values of MNEI and of three sweeteners were determined. Then, those concentrations were investigated: the intensity of sweetness over time was evaluated in aqueous solutions by the t‐I method; the interaction between sweetness and other sensory stimuli was evaluated in more complex solutions, containing flavoring and acidifying agents, by means of the TDS method. t‐I results showed that the sweetness provided by MNEI decreased later than the others, in different times, and it was not extinguished completely, whereas TDS results showed that the dominant attributes of model beverages were almost the same for all sweeteners.

Practical Applications

The structure of MNEI is completely compatible with that of natural proteins. This protein determines a sensory performance similar to that of other studied sweeteners, especially aspartame, but has been proven to be stable in heat treatment and pH changes. No off‐flavor that generally characterizes many high‐intensity sweeteners (HIS) was detected when tested by the assessors. Indeed, even if the sweetness imparted by MNEI was perceived later than the sweetness provided by sucrose, in the presence of other stimuli, no significant differences were detected. These properties could make MNEI a good choice as HIS for low‐calorie beverages and dairy products.
Can green iguanas compensate for vanishing seed dispersers in the Atlantic forest fragments of north‐east Brazil?
Authors: de A. Moura A. C. , Cavalcanti L. , Leite‐Filho E. , Mesquita D. O. , McConkey K. R.
Published: October 2014

The Atlantic forest of Brazil is a biodiversity hot spot, but is extremely fragmented. Local extinction of important seed dispersers, such as primates, threatens the maintenance of these fragments. It is important to evaluate the capacity of fragment‐tolerant species to disperse seeds and help maintain plant communities within fragments. Green iguanas Iguana iguana are large, fragment‐tolerant, canopy‐dwelling lizards and have been noted to disperse seeds. We described the seed dispersal patterns produced by green iguanas in six urban forest fragments (1.2–8 ha in size) in the Atlantic forest of north‐east Brazil, over 20 months. A total of 294 seeds were counted in 321 scats, and 12 plant species were dispersed. The largest seeds dispersed were 14.9 mm long and up to 9.2 mm wide. Iguanas deposited 86.9% of scats within latrines, which were used over a mean of at least 9 months. We show that iguanas can be effective seed dispersers and might partially replicate deposition patterns produced by howler monkeys in other studies. It is critical that we improve our understanding on the functional roles played by these cryptic, yet common, iguanas in order to determine whether they could buffer the negative effects caused by the local extinction of primates from forest fragments.
The structural basis for enhancer‐dependent assembly and activation of the AAA transcriptional activator NorR
Authors: Bush Matt , Ghosh Tamaswati , Sawicka Marta , Moal Iain H. , Bates Paul A. , Dixon Ray , Zhang Xiaodong
Published: October 2014

σ54‐dependent transcription controls a wide range of stress‐related genes in bacteria and is tightly regulated. In contrast to σ70, the σ54‐RNA polymerase holoenzyme forms a stable closed complex at the promoter site that rarely isomerises into transcriptionally competent open complexes. The conversion into open complexes requires the ATPase activity of activator proteins that bind remotely upstream of the transcriptional start site. These activators belong to the large AAA protein family and the majority of them consist of an N‐terminal regulatory domain, a central AAA domain and a C‐terminal DNA binding domain. Here we use a functional variant of the NorR activator, a dedicated NO sensor, to provide the first structural and functional characterisation of a full length AAA activator in complex with its enhancer DNA. Our data suggest an inter‐dependent and synergistic relationship of all three functional domains and provide an explanation for the dependence of NorR on enhancer DNA. Our results show that NorR readily assembles into higher order oligomers upon enhancer binding, independent of activating signals. Upon inducing signals, the N‐terminal regulatory domain relocates to the periphery of the AAA ring. Together our data provide an assembly and activation mechanism for NorR.
The diphthamide modification pathway from Saccharomyces cerevisiae – revisited
Authors: Schaffrath Raffael , Abdel‐Fattah Wael , Klassen Roland , Stark Michael J. R.
Published: October 2014

Diphthamide is a conserved modification in archaeal and eukaryal translation elongation factor 2 (EF2). Its name refers to the target function for diphtheria toxin, the disease‐causing agent that, through ADP ribosylation of diphthamide, causes irreversible inactivation of EF2 and cell death. Although this clearly emphasizes a pathobiological role for diphthamide, its physiological function is unclear, and precisely why cells need EF2 to contain diphthamide is hardly understood. Nonetheless, the conservation of diphthamide biosynthesis together with syndromes (i.e. ribosomal frame‐shifting, embryonic lethality, neurodegeneration and cancer) typical of mutant cells that cannot make it strongly suggests that diphthamide‐modified EF2 occupies an important and translation‐related role in cell proliferation and development. Whether this is structural and/or regulatory remains to be seen. However, recent progress in dissecting the diphthamide gene network (DPH1–DPH7) from the budding yeast Saccharomyces cerevisiae has significantly advanced our understanding of the mechanisms required to initiate and complete diphthamide synthesis on EF2. Here, we review recent developments in the field that not only have provided novel, previously overlooked and unexpected insights into the pathway and the biochemical players required for diphthamide synthesis but also are likely to foster innovative studies into the potential regulation of diphthamide, and importantly, its ill‐defined biological role.
Cerebrospinal Fluid Cytokines and Neurotrophic Factors in Human Chronic Pain Populations: A Comprehensive Review
Authors: Bjurstrom Martin F. , Giron Sarah E. , Griffis Charles A.
Published: October 2014

Chronic pain is a prevalent and debilitating condition, conveying immense human burden. Suffering is caused not only by painful symptoms, but also through psychopathological and detrimental physical consequences, generating enormous societal costs. The current treatment armamentarium often fails to achieve satisfying pain relief; thus, research directed toward elucidating the complex pathophysiological mechanisms underlying chronic pain syndromes is imperative. Central neuroimmune activation and neuroinflammation have emerged as driving forces in the transition from acute to chronic pain, leading to central sensitization and decreased opioid efficacy, through processes in which glia have been highlighted as key contributors. Under normal conditions, glia exert a protective role, but in different pathological states, a deleterious role is evident—directly and indirectly modulating and enhancing pain transmission properties of neurons, and shaping synaptic plasticity in a dysfunctional manner. Cytokines and neurotrophic factors have been identified as pivotal mediators involved in neuroimmune activation pathways and cascades in various preclinical chronic pain models. Research confirming these findings in humans has so far been scarce, but this comprehensive review provides coherent data supporting the clear association of a mechanistic role of altered central cytokines and neurotrophic factors in a number of chronic pain states despite varying etiologies. Given the importance of these factors in neuropathic and inflammatory chronic pain states, prospective therapeutic strategies, and directions for future research in this emerging field, are outlined.
Carbohydrate metabolism before and after dehiscence in the recalcitrant pollen of pumpkin (Cucurbita pepo L.)
Authors: Carrizo García C. , Guarnieri M. , Pacini E.
Published: October 2014

Pumpkin (Cucurbita pepo L.) pollen is starchy, sucrose‐poor and recalcitrant, features opposite to those of several model species; therefore, some differences in carbohydrate metabolism could be expected in this species. By studying pumpkin recalcitrant pollen, the objective was to provide new biochemical evidence to improve understanding of how carbohydrate metabolism might be involved in pollen functioning in advanced stages. Four stages were analysed: immature pollen from 1 day before anthesis, mature pollen, mature pollen exposed to the environment for 7 h, and pollen rehydrated in a culture medium. Pollen viability, water and carbohydrate content and activity of enzymes involved in carbohydrate metabolism were quantified in each stage. Pollen viability and water content dropped quickly after dehiscence, as expected. The slight changes in carbohydrate concentration and enzyme activity during pollen maturation contrast with major changes recorded with ageing and rehydration. Pumpkin pollen seems highly active and closely related to its surrounding environment in all the stages analysed; the latter is particularly evident among insoluble sucrolytic enzymes, mainly wall‐bound acid invertase, which would be the most relevant for sucrose cleavage. Each stage was characterised by a particular metabolic/enzymatic profile; some particular features, such as the minor changes during maturation, fast sucrolysis upon rehydration or sharp decrease in insoluble sucrolytic activity with ageing seem to be related to the lack of dormancy and recalcitrant nature of pumpkin pollen.
Incidence and aetiologies of pulmonary granulomatous inflammation: A decade of experience
Authors: Nazarullah Alia , Nilson Robert , Maselli Diego Jose , Jagirdar Jaishree
Published: October 2014

Background and objective

Granulomatous lung disease (GLD) is caused by a wide range of conditions. Often there is a need to correlate pathological findings with clinical, microbiological or radiological data to determine an aetiology. The aim of this study was to determine the different aetiologies of GLD over the past decade.

Methods

Among 2228 consecutive lung specimens from 1999 to 2011, 226 cases (10.1%) were positive for GLD. One hundred ninety patients were retrospectively reviewed and diagnoses were assigned based on availability of histological/clinical/microbiological correlation.

Results

A confident, probable and uncertain diagnosis was made in 68.4%, 13.2% and 18.4% patients. The aetiologies comprised infectious, non‐infectious and uncertain in 54.7%, 26.8% and 18.4% patients. Mycobacterial infections constituted 27% of all patients, and included atypical, tuberculous and unclassified mycobacteria in order of frequency. Acid‐fast bacilli (AFB) were visualized in tissue sections in 29% cases and cultured in 73% cases. Fungal infections comprised 27% of all cases, which included Coccidioides, Cryptococcus, Aspergillus and Histoplasma in order of frequency. Fungi were visualized in tissue sections with Gomori methenamine silver (GMS) stain in 83% patients and cultured in 52% cases. Sarcoidosis was the major non‐infectious aetiology, constituting 21% of all patients. Necrosis in granulomas was associated with the presence of infection (P < 0.001).

Conclusions

The aetiology in necrotizing GLD with negative AFB and GMS stains is most likely infectious due to atypical mycobacteria. Coccidioidomycosis was the most common fungal infection. The aetiology in non‐necrotizing GLD is most likely non‐infectious, probably sarcoidosis.
Is Kurdish Endangered in Turkey? A Comparison between the Politics of Linguicide in Ireland and Turkey
Authors: O'Driscoll Dylan
Published: October 2014

This article examines the historical process of the demise of Gaelic in Ireland due to the policies developed by England, and compares this to the process Kurdish is currently undergoing in Turkey. This comparison accentuates the threat that Kurdish is facing and demonstrates that the language is in danger of being eradicated. Through highlighting the similarities in the policies used by both England and Turkey to eradicate ethnic threats through assimilation, and the speed in which this process is happening in Turkey, this article determines that Kurdish has reached an important stage and that the actions over the next few decades will decide its future.
Measuring Drug and Alcohol Use Among College Student‐Athletes*
Authors: Druckman James N. , Gilli Mauro , Klar Samara , Robison Joshua
Published: October 2014

Objective

Few issues in athletics today receive more attention than drug and alcohol usage, especially when it comes to college athletics. We seek to address self‐report biases related to drug usage and heavy drinking.

Methods

We employ an experimental measurement technique.

Results

Our results suggest that a greater percentage of student‐athletes from a major conference knowingly engage in these two behaviors than self‐reports indicate. Specifically, we find 37 percent of respondents seem to have taken banned performance‐enhancing drugs (compared to 4.9 percent who directly admit to doing so when asked), and 46 percent seem to have consumed more than five drinks in a week (compared to about 3 percent who openly admit to doing so).

Conclusions

We provide evidence for the extent of self‐underreporting when it comes to drug and alcohol usage among college athletes. That said, future work is needed to accurately pinpoint specific substances and the frequency with which they are taken; for example, it could be the percentage of individuals using banned substances stems from consuming significant concentrations of caffeine (e.g., multiple cups of coffee).
The HLA‐A*68:23 allele in the Chilean population
Authors: Turner E. V. , Dilioglou S. , Arnold P. Y. , Palma J. , Rivera G.
Published: October 2014

HLA‐A*68:23, first described in 2002, has not been widely reported. The studies reported here were performed for support of a collaborative hematopoietic stem cell transplantation program at Luis Calvo Mackenna Hospital for which St. Jude Children's Research Hospital provided human leukocyte antigen (HLA) typing. Family studies performed between 2000 and 2011 included 197 patients and their immediate family members. In a total of 559 individuals, A*68:23 was confirmed by DNA sequencing in eight individuals with no known relationship to each other. A*68:23 positive individuals included six patients, along with one of their parents, and two parents whose children did not inherit A*68:23. The frequency of A*68:23 in this Chilean population is >0.0125. This HLA‐A allele appears to fit the description of a well‐documented allele in this population studied in Santiago, Chile.