bluuebunny/crossref_metadata_2025 huggingface dataset:
A proposed method to determine fumonisin exposure from maize consumption in a rural South African population using a culturally appropriate FFQ
Authors: Lombard Martani , Steyn Nelia , Burger Hester-Mari , Charlton Karen , Gelderblom Wentzel
Published: November 2012

Objective

To develop an FFQ for estimating culture-specific maize intake that can distinguish between home-grown and commercial maize. Home-grown maize is more likely to be contaminated with fumonisins, mycotoxins that are associated with increased risk of oesophageal cancer.

Design

An existing FFQ developed for use in urban Xhosa populations was used as the initial framework for the maize-specific FFQ (M-FFQ). The existing questionnaire contained 126 food items divided into ten food groups (bread, cereals, vegetables, fruit, meat, dairy, snacks, condiments, beverages and fat). The M-FFQ was developed based on additional data obtained from a literature search, 24 h recalls (n159), in-depth interviews (n4), focus group discussions (n56) and expert consultation. Food items available in local shops (n3) were compared with information obtained from focus group discussions.

Setting

Five villages in two rural isiXhosa-speaking areas of the Eastern Cape Province, known to have a high incidence of oesophageal cancer, were randomly selected.

Subjects

Women aged 18–55 years were recruited by snowball sampling and invited to participate.

Results

The final M-FFQ comprised twenty-one maize-based food items, including traditional Xhosa dishes and beverages. The questionnaire focused on maize-specific dishes and distinguished between home-grown maize and commercial maize consumption.

Conclusions

A culturally specific dietary assessment method was designed to determine maize consumption and therefore fumonisin exposure. The questionnaire will be tested against 24 h recalls and other methods to determine its validity, after which it will be used in various epidemiological studies to determine fumonisin exposure.
“The Hora Staccato in Swing!”: Jascha Heifetz's Musical Eclecticism and the Adaptation of Violin Miniatures
Authors: WALDEN JOSHUA S.
Published: November 2012

Jascha Heifetz (1901–87) promoted a modern brand of musical eclecticism, recording, performing, and editing adaptations of folk and popular songs while remaining dedicated to the standard violin repertoire and the compositions of his contemporaries. This essay examines the complex influences of his displacement from Eastern Europe and assimilation to the culture of the United States on both the hybridity of his repertoire and the critical reception he received in his new home. It takes as its case study Heifetz's composition of the virtuosic showpiece “Hora Staccato,” based on a Romany violin performance he heard in Bucharest, and his later adaptation of the music into an American swing hit he titled “Hora Swing-cato.” Finally, the essay turns to the field of popular song to consider how two of the works Heifetz performed most frequently were adapted for New York Yiddish radio as Tin Pan Alley–style songs whose lyrics narrate the early twentieth-century immigrant experience. The performance and arrangement history of many of Heifetz's miniatures reveals the multivalent ways in which works in his repertoire, and for some listeners Heifetz himself, were reinterpreted, adapted, and assimilated into American culture.
Morton Feldman's Graphic Notation:Projectionsand Trajectories
Authors: BOUTWELL BRETT
Published: November 2012

In the winter of 1950–51 Morton Feldman composed a series of pieces titledProjectionsin a new notation of his own invention. The first-known graphically scored works of the postwar era, theProjectionswere immediately championed by Feldman's friend John Cage in the language of his budding philosophy of non-intention, a framework of thought largely alien to Feldman. In later years, Feldman instead explained theProjectionsthrough the discourse of abstract-expressionist painting, substituting its model of willful creative action for Cage's Zen-inspired doctrine of aesthetic indifference. Yet the story behind his graphic notation is more tangled still, for its sources included both Edgard Varèse and Stefan Wolpe, composers whose spatialized vision of sound influenced Feldman's new conception of the creative act. An examination of the origin and reception of theProjectionsoffers insight into the forces that catalyzed experimental notation in postwar New York and the rationales that were ultimately ascribed to it.
The influence of Europarties on Central and Eastern European partner parties: a theoretical and analytical model
Authors: von dem Berge Benjamin , Poguntke Thomas
Published: November 2012

This article provides a comprehensive theoretical model for analysing the influence of European party federations (Europarties) on their Central and Eastern European (CEE) partner parties. It draws on the concepts of Europeanization and party change and is, in principle, applicable to similar processes of party enlargement elsewhere. In the process of their Eastern enlargement, Europarties have searched for suitable CEE partner parties on which they have tried to exert influence. Thus far, little is known about the precise mechanisms involved and the actual impact of these processes. We argue that Europarty influence leads to party change on the side of the CEE partners, which brings about ‘West-Europeanization’. Europarties are expected to apply a double strategy that consists of a process of political exchange based on a largely asymmetric power relationship in favour of Europarties and a socialization strategy in which Europarties try to socialize their partners and convince them of the appropriateness of change. We present the theoretical and analytical tools for the analysis of the arguably largest extension of transnational party organizations, which provides ample testing ground for more general theories on party change. Furthermore, we present preliminary empirical evidence on the two most important cases, namely the European People's Party and the Party of European Socialists, which indicates that Europarties played an important role in the development of CEE parties and party systems in general.
Street drug use during pregnancy: potential programming effects on preschool wheeze
Authors: Alton M. E. , Tough S. C. , Mandhane P. J. , Kozyrskyj A. L.
Published: November 2012

Street drug use during pregnancy is detrimental to fetal development. Although the prevalence of wheeze is high in offspring of substance-abusing mothers, nothing is known about the role of street drug use during pregnancy in its development. We investigated the impact of maternal street drug use and distress during pregnancy on the development of wheeze and allergy in preschool children. Questionnaire data were accessed from the Community Perinatal Care trial of 791 mother–child pairs in Calgary, Alberta. Using logistic regression, the association between maternal substance use and distress during pregnancy, and wheeze and allergy at age 3 years was determined in boys and girls. After adjusting for alcohol use during pregnancy, pre- and postnatal tobacco use, preterm birth, duration of exclusive breastfeeding, daycare attendance and maternal socioeconomic status, maternal street drug use during pregnancy [odds ratio (OR): 5.02, 95% confidence interval (CI): 1.30–19.4] and severe maternal distress during pregnancy (OR: 5.79, 95% CI: 1.25–26.8) were associated with wheeze in girls. In boys, an independent association was found between severe distress during pregnancy (OR: 3.85, 95% CI: 1.11–13.3) and allergies, but there was no association with maternal street drug use. In conclusion, we found an association between maternal street drug use and wheeze in preschool girls that could not be accounted for by maternal distress, smoking or alcohol use during pregnancy. Prenatal programming effects of street drugs may explain this association.
The Investigation of Simultaneous Interpreters as an Alternative Approach to Address the Signature of Multilingual Speech Processing
Authors: Elmer Stefan
Published: November 2012

In the field of cognitive neuroscience, understanding the functional, temporal, and anatomical characteristics of multilingual speech processing has previously been a topic of intense investigations. In this article, I will attempt to describe how the investigation of simultaneous interpreters can be used as a fruitful and alternative approach for better comprehending the neuronal signature of multilingual speech processing, foreign language acquisition, as well as the functional and structural adaptivity of the human brain in general. Thereby, I will primarily focus on the commonalities underlying different degrees of speech competence rather than on the differences. In this context, particular emphasis will be placed on the contribution of extra-linguistic brain functions which are necessary for accommodating cognitive and motor control mechanisms in the multilingual brain. Certainly, the framework outlined in this article will not replace the meanwhile established psycholinguistic or neuroscientific models of speech processing, but only attempts to provide a novel and alternative perspective.
Motor Training-Induced Neuroplasticity
Authors: Bezzola Ladina , Mérillat Susan , Jäncke Lutz
Published: November 2012

The present lab-review presents and discusses our previous and current research into motor training-induced neuroplasticity by classifying our work on the basis of two broad aspects: (1) the applied study design (i.e., cross-sectional vs. longitudinal) and (2) the complexity of the motor task subjected to training (i.e., elementary finger movements vs. highly complex physical activity). Together with others we demonstrate that training-induced anatomic and functional changes are evident for a wide range of motor tasks and for several age cohorts. Finally, we discuss our findings from a lifespan perspective and embed them in the context of research investigating the beneficial effect of motor training-induced neuroplasticity on brain aging.
Gender and Racial Differences for Suicide Attempters and Ideators in a High-Risk Community Corrections Population
Authors: McCullumsmith Cheryl B. , Clark C. Brendan , Perkins Adam , Fife Jessaka , Cropsey Karen L.
Published: November 2012

Background: Community corrections populations are a high-risk group who carry multiple suicide risk factors. Aims: To identify factors correlated with historical suicide attempts and ideation among African-American men, African-American women, White men, and White women in a community corrections population. Method: Self-report data from 18,753 enrollees in community corrections were analyzed. Multinomial logistic regression analyses were conducted to determine associations between historical suicidal ideation and attempts among the four demographic groups. Results: Participants with historical suicide attempts tended to be younger, White, female, be taking psychotropic medication, have a history of physical or sexual abuse, and meet criteria for dependence on alcohol, amphetamines, cocaine, opioids, or sedatives. Five variables were commonly associated with suicide attempts for all four race/gender groups: younger age, being on disability or retirement, taking psychotropic medication, history of sexual or physical abuse, and cocaine dependence. Other demographic variables had race or gender specificities as risk factors for suicide attempts. Conclusions: Participants had high rates of historical suicide attempts with unique correlates differentiating attempters from ideators among different racial and gender groups. Cocaine dependence was universal predictor of suicide attempts, while other substance dependencies show specific racial and gender profiles associated with suicide attempts.
Peer Response to Messages of Distress
Authors: Barton Alison L. , Hirsch Jameson K. , Lovejoy M. Christine
Published: November 2012

Background: Suicidal young adults often confide their distress to peers. It is unclear, however, what types of assistance a friend may offer in response to various symptoms of distress as well as whether the sex of either individual affects responses. Aims: We examined open-ended responses to e-mail vignettes from a fictitious friend exhibiting depressed, irritable, or overtly suicidal communications. Method: College student participants (n = 106) read e-mail messages from a fictitious friend, to which they composed a reply. Replies were coded to reflect the presence/absence of mention of professional help, problem-oriented (personal) help, and social support. Results: Problem-oriented help was offered the most across conditions; professional help was offered least in response to depressed or irritable vignettes. Women were more likely to offer any type of help than men. Patterns of help-giving and sex differences in help-giving varied by condition. Conclusions: Results indicate students’ preferences for solving peer problems personally rather than professionally. Campus prevention and intervention efforts should focus on enhancing students’ peer support and referral skills.
Synthesis of benthic flux components in the Patos Lagoon coastal zone, Rio Grande do Sul, Brazil
Authors: King J. N.
Published: November 2012

The primary objective of this work is to synthesize components of benthic flux in the Patos Lagoon coastal zone, Rio Grande do Sul, Brazil. Specifically, the component of benthic discharge flux forced by the terrestrial hydraulic gradient is 0.8 m3 d−1; components of benthic discharge and recharge flux associated with the groundwater tidal prism are both 2.1 m3 d−1; components of benthic discharge and recharge flux forced by surface‐gravity wave setup are both 6.3 m3 d−1; the component of benthic discharge flux that transports radium‐228 is 350 m3 d−1; and components of benthic discharge and recharge flux forced by surface‐gravity waves propagating over a porous medium are both 1400 m3 d−1. (All models are normalized per meter shoreline.) Benthic flux is a function of components forced by individual mechanisms and nonlinear interactions that exist between components. Constructive and destructive interference may enhance or diminish the contribution of benthic flux components. It may not be possible to model benthic flux by summing component magnitudes. Geochemical tracer techniques may not accurately model benthic discharge flux or submarine groundwater discharge (SGD). A conceptual model provides a framework on which to quantitatively characterize benthic discharge flux and SGD with a multifaceted approach.
Evaluation of permeability and non‐Darcy flow in vuggy macroporous limestone aquifer samples with lattice Boltzmann methods
Authors: Sukop Michael C. , Huang Haibo , Alvarez Pedro F. , Variano Evan A. , Cunningham Kevin J.
Published: November 2012

Key Points

WithCTdata, Lattice Boltzmann methods can measure extreme permeabilites

Lattice Boltzmann methods are capable of simulating non‐Darcy flows

In some aquifers, non‐Darcy flows can occur at low gradients
Terrestrial dominance of organic matter in north temperate lakes
Authors: Wilkinson Grace M. , Pace Michael L. , Cole Jonathan J.
Published: November 2012

Aquatic ecosystems are hotspots of decomposition and sources of carbon dioxide to the atmosphere that are globally significant. Carbon exported from land (allochthonous) also supplements the carbon fixed by photosynthesis in aquatic ecosystems (autochthonous), contributing to the organic matter (OM) that supports aquatic consumers. Although the presence of terrestrial compounds in aquatic OM is well known, the contribution of terrestrial versus aquatic sources to the composition of OM has been quantified for only a handful of systems. Here we use stable isotopes of hydrogen and carbon to demonstrate that the terrestrial contribution (ΦTerr) to particulate organic matter (POM) is as large or larger (mean = 54.6% terrestrial) than the algal contribution in 39 lakes of the northern highlands region of Wisconsin and Michigan. Further, the largest carbon pool, dissolved organic matter (DOM), is strongly dominated by allochthonous material (mean for the same set of lakes approximately 100% terrestrial). Among lakes, increases in terrestrial contribution to POM are significantly correlated with more acidic pH. Extrapolating this relationship using a survey of pH in 1692 lakes in the region reveals that, with the exception of eutrophic lakes, most of the OM in lakes is of terrestrial origin. These results are consistent with the growing evidence that lakes are significant conduits for returning degraded terrestrial carbon to the atmosphere.
Contribution of ocean current to the increase in N abundance in the Northwestern Pacific marginal seas
Authors: Kim Seung‐Kyu , Chang Kyung‐Il , Kim Bongguk , Cho Yang‐Ki
Published: November 2012

In the northwestern Pacific marginal seas, there has been a rapid temporal increase and spatial variability in the relative abundance of dissolved inorganic nitrogen over dissolved inorganic phosphate. The cause and mechanisms of this temporal and spatial variation is under debate. Recently, atmospheric deposition of nitrogen has been shown to be the major cause of the spatio‐temporal variation in the concentration ratio of dissolved nitrogen and phosphate. We show that the transport by ocean currents is a more crucial factor causing the spatio‐temporal variation in the ratio of dissolved nitrogen and phosphate in the study area.
Pc1–2 auroral pulsations
Authors: Roldugin V. C. , Roldugin A. V. , Pilgaev S. V.
Published: November 2012

By observations at Lovozero station (64.3 N, 114.3 E CGM coordinates), we have investigated two events of auroral pulsations of Pc1–2 type with periods in the range 2.5–7 s accompanied by similar geomagnetic pulsations. Luminous variations in different parts of the sky were found by photometric measurements of the frames of all‐sky camera, which was operated at the rate of one frame per second. The pulsations under study are associated with the diffuse aurora. For the event with 7 s period, a phase relationship between auroral and magnetic pulsations is as follows: the luminosity bursts are coincident with positive half periods in the Z component and negative ones in the D component, while positive peaks in the H component lag behind the luminous peaks by about π/2. For the event with 2.5 s period, this relationship appears different. Within one of 10‐min intervals, Pc2 pulsations observed in both magnetic field and aurora were superposed by regular Pc4 pulsations of 1‐min period. For these, the luminosity bursts corresponded to negative half periods in the Z component. A connection between auroral and magnetic pulsations is discussed.
An integration to optimally constrain the thermal structure of oceanic lithosphere
Authors: Goutorbe B. , Hillier J. K.
Published: November 2012

The evolution through time of the oceanic lithosphere is a substantial, incompletely resolved geodynamical problem. Consensus remains elusive regarding its thermal structure, physical properties, and the best model through which to unify observational constraints. We robustly reevaluate all three of these by (i) simultaneously fitting heat flow, bathymetry, and temperatures derived from a shear velocity model of the upper mantle, (ii) using the three main thermal models (half‐space, plate, and Chablis), and (iii) analyzing five depth‐age curves, wherein contrasting techniques were used to exclude anomalous features from seafloor depths. The thermal models are updated to all include a temperature‐dependent heat capacity, a temperature‐ and pressure‐dependent thermal conductivity, and an initial condition of adiabatic decompression including melting. The half‐space model, which lets the lithosphere thicken indefinitely, cannot accurately fit the subsidence curves and requires mantle potential temperatures, Tm, that are too high. On the other hand, the models including a mechanism of basal heat supply are able to simultaneously explain all observations within two standard errors, with best‐fitting parameters robust to the choice of the filtered bathymetry curve. For the plate model, which imposes a constant temperature at a fixed depth, Tm varies within 1380–1390°C, the equilibrium plate thickness a within 106–110 km, and the bulk thermal expansivity within 2.95−3.20 ⋅ 10−5 K−1. For the Chablis model, which prescribes a fixed heat flow at the base of a thickening lithosphere, the best‐fitting values are Tm = 1320−1380°C, a = 176−268 km, K−1. Driven by more accurate ocean depths, the plate model provides better joint‐fittings to the observations; however, it requires values of lower than experimentally measured, which can be explained by a reduction of the apparent expansivity due to elastic rigidity of the upper lithosphere. The Chablis model better fits the data when is set close to or above the experimental values. Although statistically consistent within two standard errors, a tendency toward incompatibility between observed depth‐age curves and seismically derived temperatures is revealed with new clarity, because the latter do not exhibit a clear steady state whereas the former flatten; further work is needed to identify the origin of this apparent discrepancy.This work opens the way to investigations fully independent of particular solutions of the heat equation.
Retrievals of vertical profiles of stratus cloud properties from combined oxygen A‐band and radar observations
Authors: Li Siwei , Min Qilong
Published: November 2012

A synergetic algorithm of retrieving vertical distribution of cloud drop effective radius (Re), liquid water content (LWC), and optical depth has been developed by combining oxygen A‐band spectral measurements with radar reflectivity. The underlying physics is to utilize the photon path length information from oxygen A‐band measurements to constrain the retrievals of cloud microphysical properties from radar reflectivity. Through a radiation closure of the rotating shadowband spectrometer (RSS) diffuse‐horizontal irradiances in the oxygen A‐band (which is sensitive to vertical distribution of the 2nd moment of particle size distribution), vertical distributions of cloud microphysical property (the 3rd moment of particle size distribution) are optimized and retrieved from Millimeter Wave Cloud Radar (MMCR) reflectivity (the 6th moment of particle size distribution). The critical issues in the synergetic cloud retrievals of combining passive and active instruments are discussed and carefully taken into account. Evaluation and validation through case studies show that the retrieved column mean values of cloud optical depth, effective radius, and liquid water path agree well with independent measurements from the microwave radiometer (MWR) and independent retrievals from a combined algorithm of multifilter rotating shadowband radiometer (MFRSR) and MWR and the column physical characterization (CPC) of MMCR. These studies demonstrate that this active‐passive synergetic retrieval algorithm is feasible and accurate for retrievals of vertical distribution of cloud Re and LWC for stratus clouds.
Lithium in the aragonite skeletons of massive Porites corals: A new tool to reconstruct tropical sea surface temperatures
Authors: Hathorne Ed C. , Felis Thomas , Suzuki Atsushi , Kawahata Hodaka , Cabioch Guy
Published: November 2012

Previous studies have demonstrated the potential for the Li content of coral aragonite to record information about environmental conditions, but no detailed study of tropical corals exists. Here we present the Li and Mg to Ca ratios at a bimonthly to monthly resolution over 25 years in two modern Porites corals, the genus most often used for paleoclimate reconstructions in the tropical Indo‐Pacific. A strong relationship exists between coral Li/Ca and locally measured SST, indicating that coral Li/Ca can be used to reconstruct tropical SST variations. However, Li/Ca ratios of the skeleton deposited during 1979–1980 do not track local SST well and are anomalously high in places. The Mg/Ca ratios of this interval are also anomalously high, and we suggest Li/Ca can be used to reconstruct tropical SST only when Mg/Ca data are used to carefully screen for relatively rare biological effects. Mg/Li or Li/Mg ratios provide little advantage over Li/Ca ratios, except that the slope of the Li/Mg temperature relationship is more similar between the two corals. The Mg/Li temperature relationship for the coral that experienced a large temperature range is similar to that found for cold water corals and aragonitic benthic foraminifera in previous studies. The comparison with data from other biogenic aragonites suggests the relationship between Li/Mg and water temperature can be described by a single exponential relationship. Despite this hint at an overarching control, it is clear that biological processes strongly influence coral Li/Ca, and more calibration work is required before widely applying the proxy.
Structural basis of ligand recognition in 5‐HT3 receptors
Authors: Kesters Divya , Thompson Andrew J , Brams Marijke , van Elk René , Spurny Radovan , Geitmann Matthis , Villalgordo Jose M , Guskov Albert , Helena Danielson U , Lummis Sarah C R , Smit August B , Ulens Chris
Published: November 2012

The 5‐HT3 receptor is a pentameric serotonin‐gated ion channel, which mediates rapid excitatory neurotransmission and is the target of a therapeutically important class of anti‐emetic drugs, such as granisetron. We report crystal structures of a binding protein engineered to recognize the agonist serotonin and the antagonist granisetron with affinities comparable to the 5‐HT3 receptor. In the serotonin‐bound structure, we observe hydrophilic interactions with loop E‐binding site residues, which might enable transitions to channel opening. In the granisetron‐bound structure, we observe a critical cation–π interaction between the indazole moiety of the ligand and a cationic centre in loop D, which is uniquely present in the 5‐HT3 receptor. We use a series of chemically tuned granisetron analogues to demonstrate the energetic contribution of this electrostatic interaction to high‐affinity ligand binding in the human 5‐HT3 receptor. Our study offers the first structural perspective on recognition of serotonin and antagonism by anti‐emetics in the 5‐HT3 receptor.
Chaperoning the synapse—NMNAT protects Bruchpilot from crashing
Authors: Lauwers Elsa , Verstreken Patrik
Published: November 2012

Maintaining active zone structure is crucial for synaptic function. In this issue of EMBO reports, NMNAT is shown to act as a chaperone that protects the active zone structural protein Bruchpilot from degradation.
Economic and Policy Aspects of Integrated Forest Biorefineries
Authors: Gan Jianbang
Published: November 2012

Integrated forest biorefineries (IFBRs) have several technological and economic advantages. As such, they are expected to play a major role in the future bioenergy industry. This chapter describes the supply chains and key economic aspects of IFBRs. A decision support model is presented that maximizes the net socioeconomic and environmental benefits of using available biomass sources to produce multiple end-products through the selection of production technology, siting and size of production facilities, and transportation mode. Barriers to IFBR development and deployment are also identified, and policies are proposed to overcome the barriers. Overall, IFBRs, especially when integrated with the supply chains of traditional forest products, have great potential and can enhance the efficiency of resource use, overall economic return, and job creation, thus contributing to the prosperity and sustainability of the forest products and bioenergy industries and forest-based communities.
Integrated Forest Biorefineries: Industrial Sustainability
Authors: Ackom Emmanuel Kofi
Published: November 2012

In the past, industrial activities and economic growth have often been associated with overexploitation of natural resources and environmental degradation. Over the last few decades, however, public pressure coupled with increasing awareness within industry on the impacts of their activities has resulted in a shift towards better environmental stewardship. Industrial sustainability offer great opportunities to improve the triple bottom line of the integrated forest biorefinery that, however, need to be explored. The work reported here analyzes the critical issues associated with industrial sustainability of integrated forest biorefinery. It showcases industrial sustainability concepts that are already in place in integrated forest biorefinery, which requires fine tuning in order to derive the maximum benefits. The chapter highlights the opportunities and barriers in integrated forest biorefinery to achieving the goals of industrial manufacturing, economic growth and environmental benefits in a socially responsible manner.  Policy interventions for reforms toward improved industrial sustainability practices in integrated forest biorefinery are provided.
Niche Position and Opportunities for Woody Biomass Conversion
Authors: Amidon Thomas E. , Bujanovic Biljana , Liu Shijie , Hasan Asif , Howard Joel R.
Published: November 2012

For centuries, humans used plant biomass as food and heat, but use of biomass for fuel and chemicals was largely displaced by fossil sources after the commercial utilization of coal, and more recently petroleum and natural gas. Fossil sources have certain advantages over biomass in terms of energy density, shipping, and storage. However, fossil fuel combustion by a rapidly expanding world population over the past century has led to sharp increases in atmospheric CO2, and may very well be linked to human-induced climate change. Moreover, petroleum is an unsustainable energy source; even the most conservative projections indicate crude oil reserves will be depleted by the year 2100 (1). Rebuilding the potential of biomass as a renewable source of materials and cleaner energy is imperative to the sustainability of human civilization. Commercial deployment of lignocellulosic-based biorefinery technology, making full use of all available forest materials, woody biomass crops, perennial grasses, and agricultural residues, is the niche opportunity pathway in woody biomass conversion for ABS Process™ Biorefinery Technology, incorporating Hot Water Extraction™ cooking to contribute toward sustainable world development. A critical factor in defining the success of this process may be integration of lignin products into the product portfolio.
Epicuticular-wax removal influences gas exchange and water relations in the leaves of an exotic and native species from a Brazilian semiarid region under induced drought stress
Authors: Figueiredo Karla V. , Oliveira Marciel T. , Oliveira Antônio Fernando M. , Silva Gabriela C. , Santos Mauro G.
Published: November 2012

The primary physiological function of the leaf cuticle is to limit water loss. Thus, in the present study, we examined the hypothesis that variation in the quality and content of the epicuticular wax between different species influences leaf gas exchange. Plants of Jatropha mollissima (Pohl) Bailon, a Brazilian semiarid native, and Jatropha curcas L. (Euphorbiaceae), an exotic species, were subjected to a water deficit in the presence or absence of epicuticular wax. Plants were grown in 10-L pots under greenhouse conditions. The relative water content, gas-exchange parameters and primary carbon metabolism were measured at 21 days after the irrigation was reduced to induce a water deficit. The well-watered plants of both species showed recovery of gas exchange days after the removal of epicuticular wax. Furthermore, under drought, a gradual increase in transpiration rates was observed only in the leaves of native species without wax, although the stomatal conductance did not differ between the species. High relative water content was maintained, except in the leaves under drought and without wax from Day 13 onward, when compared with all other treatments. The wax production was induced in both species under water shortage. Nevertheless, the native species showed a higher content of long-chain n-alkanes. In fact, the barrier to water vapour under reduced stomatal conductance was highest in the native species.
Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolution
Authors: Frankel Nicolás , Wang Shu , Stern David L.
Published: November 2012

Similar morphological, physiological, and behavioral features have evolved independently in different species, a pattern known as convergence. It is known that morphological convergence can occur through changes in orthologous genes. In some cases of convergence,
cis
-regulatory changes generate parallel modifications in the expression patterns of orthologous genes. Our understanding of how changes in
cis
-regulatory regions contribute to convergence is hampered, usually, by a limited understanding of the global
cis
-regulatory structure of the evolving genes. Here we examine the genetic causes of a case of precise phenotypic convergence between
Drosophila sechellia
and
Drosophila ezoana
, species that diverged
∼
40 Mya. Previous studies revealed that changes in multiple transcriptional enhancers of
shavenbaby
(
svb
, a transcript of the
ovo
locus) caused phenotypic evolution in the
D. sechellia
lineage. It has also been shown that the convergent phenotype of
D. ezoana
was likely caused by
cis
-regulatory evolution of
svb
. Here we show that the large-scale
cis-
regulatory architecture of
svb
is conserved between these
Drosophila
species. Furthermore, we show that the
D. ezoana
orthologs of the evolved
D. sechellia
enhancers have also evolved expression patterns that correlate precisely with the changes in the phenotype. Our results suggest that phenotypic convergence resulted from multiple noncoding changes that occurred in parallel in the
D. sechellia
and
D. ezoana
lineages.
Rab35 regulates cadherin-mediated adherens junction formation and myoblast fusion
Authors: Charrasse Sophie , Comunale Franck , De Rossi Sylvain , Echard Arnaud , Gauthier-Rouvière Cécile
Published: November 2012

Cadherins are homophilic cell–cell adhesion molecules implicated in many fundamental processes, such as morphogenesis, cell growth, and differentiation. They accumulate at cell–cell contact sites and assemble into large macromolecular complexes named adherens junctions (AJs). Cadherin targeting and function are regulated by various cellular processes, many players of which remain to be uncovered. Here we identify the small GTPase Rab35 as a new regulator of cadherin trafficking and stabilization at cell–cell contacts in C2C12 myoblasts and HeLa cells. We find that Rab35 accumulates at cell–cell contacts in a cadherin-dependent manner. Knockdown of Rab35 or expression of a dominant-negative form of Rab35 impaired N- and M-cadherin recruitment to cell–cell contacts, their stabilization at the plasma membrane, and association with p120 catenin and led to their accumulation in transferrin-, clathrin-, and AP-2–positive intracellular vesicles. We also find that Rab35 function is required for PIP5KIγ accumulation at cell–cell contacts and phosphatidyl inositol 4,5-bisphosphate production, which is involved in cadherin stabilization at contact sites. Finally, we show that Rab35 regulates myoblast fusion, a major cellular process under the control of cadherin-dependent signaling. Taken together, these results reveal that Rab35 regulates cadherin-dependent AJ formation and myoblast fusion.
A conserved regulatory mode in exocytic membrane fusion revealed by Mso1p membrane interactions
Authors: Weber-Boyvat Marion , Zhao Hongxia , Aro Nina , Yuan Qiang , Chernov Konstantin , Peränen Johan , Lappalainen Pekka , Jäntti Jussi
Published: November 2012

Sec1/Munc18 family proteins are important components of soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) complex–mediated membrane fusion processes. However, the molecular interactions and the mechanisms involved in Sec1p/Munc18 control and SNARE complex assembly are not well understood. We provide evidence that Mso1p, a Sec1p- and Sec4p-binding protein, interacts with membranes to regulate membrane fusion. We identify two membrane-binding sites on Mso1p. The N-terminal region inserts into the lipid bilayer and appears to interact with the plasma membrane, whereas the C-terminal region of the protein binds phospholipids mainly through electrostatic interactions and may associate with secretory vesicles. The Mso1p membrane interactions are essential for correct subcellular localization of Mso1p–Sec1p complexes and for membrane fusion in Saccharomyces cerevisiae. These characteristics are conserved in the phosphotyrosine-binding (PTB) domain of β-amyloid precursor protein–binding Mint1, the mammalian homologue of Mso1p. Both Mint1 PTB domain and Mso1p induce vesicle aggregation/clustering in vitro, supporting a role in a membrane-associated process. The results identify Mso1p as a novel lipid-interacting protein in the SNARE complex assembly machinery. Furthermore, our data suggest that a general mode of interaction, consisting of a lipid-binding protein, a Rab family GTPase, and a Sec1/Munc18 family protein, is important in all SNARE-mediated membrane fusion events.
PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays
Authors: Yang Shengping , Pounds Stanley , Zhang Kun , Fang Zhide
Published: November 2012

Motivation: Normalization is critical in DNA copy number analysis. We propose a new method to correctly identify two-copy probes from the genome to obtain representative references for normalization in single nucleotide polymorphism arrays. The method is based on a two-state Hidden Markov Model. Unlike most currently available methods in the literature, the proposed method does not need to assume that the percentage of two-copy state probes is dominant in the genome, as long as there do exist two-copy probes.

Results: The real data analysis and simulation study show that the proposed algorithm is successful in that (i) it performs as well as the current methods (e.g. CGHnormaliter and popLowess) for samples with dominant two-copy states and outperforms these methods for samples with less dominant two-copy states; (ii) it can identify the copy-neutral loss of heterozygosity; and (iii) it is efficient in terms of the computational time used.

Availability: R scripts are available at http://publichealth.lsuhsc.edu/PAIR.html.

Contact:  zfang@lsuhsc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fitting a non-parametric stock–recruitment model in R that is useful for deriving MSY reference points and accounting for model uncertainty
Authors: Cadigan Noel G.
Published: November 2012

Cadigan, N. G. 2013. Fitting a non-parametric stock–recruitment model in R that is useful for deriving MSY reference points and accounting for model uncertainty. – ICES Journal of Marine Science, 70:56–67. Modelling the relationship between parental stock size and subsequent recruitment of fish to a fishery is often required when deriving reference points, which are a fundamental component of fishery management. A non-parametric approach to estimate stock–recruitment relationships is illustrated using a simulated example and nine case studies. The approach preserves compensatory density dependence in which the recruitment rate monotonically decreases as stock size increases, which is a basic assumption of commonly used parametric stock–recruitment models. The implications of the non-parametric estimates on maximum sustainable yield (MSY) reference points are illustrated. The approach is used to provide non-parametric bootstrapped confidence intervals for reference points. The efficacy of the approach is investigated using simulations. The results demonstrate that the non-parametric approach can provide a more realistic estimation of the stock–recruitment relationship when informative data are available compared with common parametric models. Also, bootstrap confidence intervals for MSY reference points based on different parametric stock–recruitment models often do not overlap. The confidence intervals based on the non-parametric approach tend to be much wider, and reflect better uncertainty due to stock–recruit model choice.
iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data
Authors: Mezlini Aziz M. , Smith Eric J.M. , Fiume Marc , Buske Orion , Savich Gleb L. , Shah Sohrab , Aparicio Sam , Chiang Derek Y. , Goldenberg Anna , Brudno Michael
Published: November 2012

High-throughput RNA sequencing (RNA-seq) promises to revolutionize our understanding of genes and their role in human disease by characterizing the RNA content of tissues and cells. The realization of this promise, however, is conditional on the development of effective computational methods for the identification and quantification of transcripts from incomplete and noisy data. In this article, we introduce iReckon, a method for simultaneous determination of the isoforms and estimation of their abundances. Our probabilistic approach incorporates multiple biological and technical phenomena, including novel isoforms, intron retention, unspliced pre-mRNA, PCR amplification biases, and multimapped reads. iReckon utilizes regularized expectation-maximization to accurately estimate the abundances of known and novel isoforms. Our results on simulated and real data demonstrate a superior ability to discover novel isoforms with a significantly reduced number of false-positive predictions, and our abundance accuracy prediction outmatches that of other state-of-the-art tools. Furthermore, we have applied iReckon to two cancer transcriptome data sets, a triple-negative breast cancer patient sample and the MCF7 breast cancer cell line, and show that iReckon is able to reconstruct the complex splicing changes that were not previously identified. QT-PCR validations of the isoforms detected in the MCF7 cell line confirmed all of iReckon's predictions and also showed strong agreement (r2= 0.94) with the predicted abundances.
Moral development as a crucial treatment goal for young people in institutional care: a critical comparison between milieu therapy and cognitive behavioral therapy
Authors: Ahonen Lia , Degner Jürgen
Published: November 2012

Purpose

This article aims to analyze and discuss the role of moral development in treatment of behavior problems and, further, to describe differences and similarities between two different methods – milieu therapy (MT) and cognitive behavioral therapy (CBT) – in terms of addressing criminogenic needs and promoting moral development.

Design/methodology/approach

By performing a literature review, the study shows that even though there are both pros and cons using MT and CBT in institutional care, relationships strong enough to restructure a young person's moral reasoning require time, and involves not only the young person's parents and social network members, but also a genuine therapeutic alliance with clinical staff at the institution.

Findings

These are central factors articulated in both CBT and MT, but are more explicitly expressed in MT. The results presented in this article highlight some important practical implications: in order to redevelop moral self and societal values, an overly narrow focus on criminogenic needs might exclude other components or processes of treatment and behavioral change. Together with a treatment program that views close staff‐resident interactions as of secondary importance, this could impair the possibility to obtain positive and long‐lasting treatment results.

Originality/value

In practice, moral development itself should be considered as an overall treatment goal, integrated into the daily life at the institution, 24 hours a day. Finally, the possibility to work with moral development in institutional settings is discussed.
Balancing heat, water and nutrients under environmental change: a thermodynamic niche framework
Authors: Kearney Michael R. , Simpson Stephen J. , Raubenheimer David , Kooijman Sebastiaan A. L. M.
Published: November 2012

Models of the regulatory behaviour of organisms are fundamental to a strong physiologically‐based understanding of species' responses to global environmental change. Biophysical models of heat and water exchange in organisms (biophysical ecology) and nutritionally‐explicit models for understanding feeding behaviour and its fitness consequences (the Geometric Framework of nutrition, GF) are providing such an underpinning. However, temperature, water and nutrition interact in fundamental ways in influencing the responses of the organism to their environment, and a priority is to develop an integrated approach for conceptualising and measuring these interactions.

Ideally, such an approach would be based on a thermodynamically‐formalized energy and mass budgeting approach that is sparsely parameterised and sufficiently general to apply across a range of situations and organisms. Here we illustrate how mass‐balance aspects of Dynamic Energy Budget theory can be applied to obtain first‐principles estimates of fluxes of O2, CO2, H2O and nitrogenous waste.

Then, using an herbivorous lizard (Egernia cunninghami) as a case study, we demonstrate how these estimates can be integrated with heat/water exchange models and environmental data to provide a holistic understanding of how foraging strategy, food availability, habitat and weather interact with heat, water and nutrient/energy budgets across the life‐cycle.

The analysis shows the potential importance of the water balance in affecting the energy budgets of ‘ dry skinned’ ectotherms, especially early in ontogeny, and highlights a significant gap in our knowledge of the physiological and behavioural traits that affect water balance when compared with our knowledge of thermal traits.

In general, the modelling approach we describe can provide the thermodynamically‐constrained stage on which other evolutionary and ecological interactions play out; the ‘thermodynamic niche’. This in turn provides a solid foundation from which to tackle key questions about organismal responses to environmental change.
Effects of metformin in women with polycystic ovary syndrome treated with gonadotrophins for in vitro fertilisation and intracytoplasmic sperm injection cycles: a systematic review and meta‐analysis of randomised controlled trials
Authors: Palomba S , Falbo A , La Sala GB
Published: November 2012

Background

Metformin is widely used for treating women with polycystic ovary syndrome (PCOS), and many patients with PCOS who are infertile receive gonadotrophins while being treated with metformin.

Objectives

To assess the effects of metformin administration in infertile patients with PCOS who receive gonadotrophins for in vitro fertilisation (IVF) and intracytoplasmic sperm injection (ICSI) cycles.

Search strategy

We searched international scientific databases, websites for the registration of trials, and bibliographies of retrieved articles, books, and review articles up to August 2012.

Selection criteria

Randomised controlled trials (RCTs).

Data collection and analysis

Authors independently reviewed and extracted the data.

Main results

Ten RCTs (with a total of 845 women with PCOS) were included in the final analysis. Metformin administration in IVF/ICSI cycles had no effect on the rates of pregnancy (OR 1.20, 95% CI 0.90–1.61) and live birth (OR 1.69, 95% CI 0.85–3.34). No effect of metformin dose, metformin pretreatment duration, and stopping time of metformin administration was observed on these reproductive end points. Metformin administration reduced the risk of ovarian hyperstimulation syndrome (OHSS; OR 0.27, 95% CI 0.16–0.46) and of miscarriage (OR 0.50, 95% CI 0.30–0.83), while increased that of implantation (OR 1.42, 95% CI 1.24–2.75).

Author's conclusions

In infertile patients with PCOS treated with gonadotrophins for IVF/ICSI cycles, metformin exerts no clinical effect on rates of pregnancy or live birth, but it reduces the risk of OHSS, and improves the rates of miscarriage and implantation. Further RCTs are needed to assess the reproductive effect of metformin in young well‐selected patients with PCOS and specific phenotypes and features.