bluuebunny/crossref_metadata_2025 huggingface dataset:
Inorganic carbon acquisition in potentially toxic and non‐toxic diatoms: the effect of pH‐induced changes in seawater carbonate chemistry
Authors: Trimborn Scarlett , Lundholm Nina , Thoms Silke , Richter Klaus‐Uwe , Krock Bernd , Hansen Per Juel , Rost Björn
Published: April 2008

The effects of pH‐induced changes in seawater carbonate chemistry on inorganic carbon (Ci) acquisition and domoic acid (DA) production were studied in two potentially toxic diatom species, Pseudo‐nitzschia multiseries and Nitzschia navis‐varingica, and the non‐toxic Stellarima stellaris. In vivo activities of carbonic anhydrase (CA), photosynthetic O2 evolution and CO2 and HCO3− uptake rates were measured by membrane inlet MS in cells acclimated to low (7.9) and high pH (8.4 or 8.9). Species‐specific differences in the mode of carbon acquisition were found. While extracellular carbonic anhydrase (eCA) activities increased with pH in P. multiseries and S. stellaris, N. navis‐varingica exhibited low eCA activities independent of pH. Half‐saturation concentrations (K1/2) for photosynthetic O2 evolution, which were highest in S. stellaris and lowest in P. multiseries, generally decreased with increasing pH. In terms of carbon source, all species took up both CO2 and HCO3−. K1/2 values for inorganic carbon uptake decreased with increasing pH in two species, while in N. navis‐varingica apparent affinities did not change. While the contribution of HCO3− to net fixation was more than 85% in S. stellaris, it was about 55% in P. multiseries and only approximately 30% in N. navis‐varingica. The intracellular content of DA increased in P. multiseries and N. navis‐varingica with increasing pH. Based on our data, we propose a novel role for eCA acting as Ci‐recycling mechanism. With regard to pH‐dependence of growth, the ‘HCO3− user’S. stellaris was as sensitive as the ‘CO2 user’N. navis‐varingica. The suggested relationship between DA and carbon acquisition/Ci limitation could not be confirmed.
Identification and characterization of two closely related β‐carbonic anhydrases from Chlamydomonas reinhardtii
Authors: Ynalvez Ruby A. , Xiao Ying , Ward Ayana S. , Cunnusamy Khrishen , Moroney James V.
Published: April 2008

Aquatic photosynthetic organisms such as the green alga Chlamydomonas reinhardtii respond to low‐CO2 conditions by inducing a CO2 concentrating mechanism (CCM). Important components of the CCM are the carbonic anhydrases (CAs), zinc metalloenzymes that catalyze the interconversion of CO2 and HCO−3. Six CAs have previously been identified in C. reinhardtii. Here, we identify and characterize two additional β‐type CAs. These two CAs are closely related β‐type CAs and have been designated as CAH7 and CAH8.Conceptual translation shows that CAH7 and CAH8 encode proteins of 399 and 333 amino acids, respectively, and they contain targeting sequences. An unusual characteristic of these two CAs is that they have carboxy‐terminal extensions containing a hydrophobic sequence. Both these CAs are constitutively expressed at the transcript and protein level. The CAH7 and CAH8 open reading frames were cloned in the overexpression vector pMal‐c2x and expressed as recombinant proteins. Activity assays showed that CAH7 and CAH8 are both active CAs. Antibodies were raised against both CAH7 and CAH8, and immunolocalization studies showed that CAH8 was localized in the periplasmic space. A possible role for CAH8 in the inorganic carbon acquisition by C. reinhardtii is discussed.
Adaptation and validation of the Spanish version of the Mood Disorder Questionnaire for the detection of bipolar disorder
Authors: Sanchez‐Moreno J , Villagran JM , Gutierrez JR , Camacho M , Ocio S , Palao D , Querejeta I , Gascon J , Sanchez G , Vieta E ,   for the EDHIPO (Hypomania Detection Study) Group
Published: April 2008

Objective:  The Mood Disorder Questionnaire (MDQ) is an instrument for the detection of patients with bipolar disorder (BD). The original English version is validated in both the psychiatric and the general population, but a validated Spanish version is not yet available. Psychometric properties of the Spanish adaptation of the MDQ in psychiatry are described.

Methods:  The MDQ is a self‐administered questionnaire comprising a list of 13 hypomanic symptoms and two questions about concurrence of symptoms and functional impairment caused by the symptoms. We selected patients from 15 psychiatric outpatient departments, diagnosed with BD type I and II (BDI and BDII) and major depression (MD) according to DSM‐IV‐TR criteria (concurrent validity instrument). A control group of healthy subjects (HS) was selected. The patient‐selection criteria included stability of the disorder and pharmacological treatment. The MDQ was administered to 236 subjects, distributed among the four groups, on two occasions, four weeks apart. We analysed the internal consistency, test–retest reliability, and discriminative capacity of the MDQ for the detection of patients with BD.

Results:  Concurrent validity based on diagnosis according to DSM‐IV‐TR was 0.83. The internal consistency, evaluated by Cronbach’s α, was 0.90. The mean (SD) number of affirmative responses by group was: 9.8 (2.4) for BDI, 8.5 (2.8) for BDII, 2.7 (2.2) for MD, and 1.02 (1.9) for HS. Statistically significant differences between all the groups were found (Kruskal–Wallis test, p < 0.001). Concurrent validity using the diagnostic variable was 0.83. Test–retest reliability was 0.92. We analysed the scale’s discriminative capacity, revealing a sensitivity value of 0.60 [95% confidence interval (CI) = 0.51–0.69] and a specificity value of 0.98 (95% CI = 0.94–0.99) in the detection of BD. The positive and negative probability ratios were 35.5 and 2.4, respectively. If we consider only seven positive responses as the discriminative criterion, sensitivity increases to 0.81 (95% CI = 0.73–0.88), the specificity value is 0.95 (95% CI = 0.89–0.98) and the positive and negative probability quotients are 16 and 5.3.

Conclusions:  The psychometric characteristics of the Spanish version are similar to those of the original version. In the Spanish adaptation of the MDQ, seven positive responses to hypomanic symptoms show a good discriminative capacity for BD in patients attending psychiatric outpatient facilities; therefore, this cut‐off score is proposed for the detection of BD in psychiatric outpatients.
A preliminary functional magnetic resonance imaging study of prefrontal‐amygdalar activation changes in adolescents with bipolar depression treated with lamotrigine
Authors: Chang Kiki D , Wagner Christopher , Garrett Amy , Howe Meghan , Reiss Allan
Published: April 2008

Objectives:  Hypotheses regarding mood dysregulation in bipolar disorder (BD) have centered on limbic overactivity with relative prefrontal underactivity during mood episodes. Therefore, we hypothesized that adolescents with bipolar depression successfully treated with lamotrigine would show decreases in amygdalar activation, and increases in prefrontal activation.

Methods:  Eight adolescents with BD underwent functional magnetic resonance imaging (fMRI) at baseline and after eight weeks of lamotrigine treatment. Blocks of negatively and neutrally valenced emotional pictures were presented during scanning, and subjects were asked to rate how each picture made them feel. Activation in bilateral amygdalae and dorsolateral prefrontal cortices (DLPFC) for negative minus neutral pictures was correlated with Children’s Depression Rating Scale (CDRS) scores.

Results:  Mean (SD) CDRS scores decreased significantly, from 53.0 (10.6) at baseline to 26.3 (5.3) at Week 8. This clinical improvement was correlated with decreased right amygdalar activation (r = 0.91, p = 0.002). At Week 8, but not baseline, CDRS score was positively correlated with bilateral amygdalar activation (r = 0.85, p = 0.007). DLPFC activation was not correlated with change in CDRS score.

Conclusions:  These preliminary results indicate that adolescents with BD treated with lamotrigine demonstrated less amygdalar activation when viewing negative stimuli as depressive symptoms improved. Larger controlled studies are needed to confirm these findings.
Genetic parameters for carcass and meat quality traits and their relationships to liveweight and wool production in hogget Merino rams
Authors: Greeff J.C. , Safari E. , Fogarty N.M. , Hopkins D.L. , Brien F.D. , Atkins K.D. , Mortimer S.I. , Van Der Werf J.H.J.
Published: April 2008

Genetic parameters for carcass and meat quality traits of about 18‐month‐old Merino rams (n = 5870), the progeny of 543 sires from three research resource flocks, were estimated. The estimates of heritability for hot carcass weight (HCW) and the various fat and muscle dimension measurements were moderate and ranged from 0.20 to 0.37. The brightness of meat (colour L*, 0.18 ± 0.03 standard error) and meat pH (0.22 ± 0.03) also had moderate estimates of heritability, although meat relative redness (colour a*, 0.10 ± 0.03) and relative yellowness (colour b*, 0.10 ± 0.03) were lower. Heritability estimates for live weights were moderate and ranged from 0.29 to 0.41 with significant permanent maternal environmental effects (0.13 to 0.10). The heritability estimates for the hogget wool traits were moderate to high and ranged from 0.27 to 0.60. The ultrasound measurements of fat depth (FATUS) and eye muscle depth (EMDUS) on live animals were highly genetically correlated with the corresponding carcass measurements (0.69 ± 0.09 FATC and 0.77 ± 0.07 EMD). Carcass tissue depth (FATGR) had moderate to low genetic correlations with carcass muscle measurements [0.18 ± 0.10 EMD and 0.05 ± 0.10 eye muscle area (EMA)], while those with FATC were negative. The genetic correlation between EMD and eye muscle width (EMW) was 0.41 ± 0.08, while EMA was highly correlated with EMD (0.89 ± 0.0) and EMW (0.78 ± 0.04). The genetic correlations for muscle colour with muscle measurements were moderately negative, while those with fat measurements were close to zero. Meat pH was positively correlated with muscle measurements (0.14 to 0.17) and negatively correlated with fat measurements (−0.06 to −0.18). EMDUS also showed a similar pattern of correlations to EMD with meat quality indicator traits, although FATUS had positive correlations with these traits which were generally smaller than their standard error. The genetic correlations among the meat colour traits were high and positive while those with meat pH were high and negative, which were all in the favourable direction. Generally, phenotypic correlations were similar or slightly lower than the corresponding genetic correlations. There were generally small to moderate negative genetic correlations between clean fleece weight (CFW) and carcass fat traits while those with muscle traits were close to zero. As the Merino is already a relatively lean breed, this implies that particular attention should be given to this relationship in Merino breeding programmes to prevent the reduction of fat reserves as a correlated response to selection for increased fleece weight. The ultrasound scan traits generally showed a similar pattern to the corresponding carcass fat and muscle traits. There was a small unfavourable genetic correlation between CFW and meat pH (0.19 ± 0.07).
Molecular Genotyping of Macrophomina phaseolina Isolates: Comparison of Microsatellite Primed PCR and Repetitive Element Sequence‐based PCR
Authors: Purkayastha S. , Kaur B. , Arora P. , Bisyer I. , Dilbaghi N. , Chaudhury A.
Published: April 2008

Seventy isolates of Macrophomina phaseolina recovered from different host plants were assessed for DNA polymorphism using two molecular techniques: microsatellite primed polymerase chain reaction (MSP‐PCR) under both touchdown (T) and non‐touchdown (NT) PCR conditions and primers corresponding to disperse repetitive sequence‐based polymerase chain reaction (rep‐PCR). Fingerprints obtained by rep‐PCR were compared with those of MSP‐PCR. Even though these methods yielded intraspecific polymorphisms, yet different levels of discrimination could be obtained. A partial correlation was apparent between the molecular techniques used. Some of the genetic groups/genotypes were supported by both the molecular markers employed in the study, thus confirming their relationship. Thirty nine MSP (T), 55 MSP (NT) and 53 rep‐PCR genotypes were identified with discrimination indices of 0.962, 0.993 and 0.99, respectively. Our results have shown that rep‐PCR is a rapid, inexpensive technique that is highly reproducible and almost as discriminatory as MSP‐PCR for genotyping M. phaseolina isolates and is highly suitable for understanding disease epidemiology at molecular level. Suggesting, thereby, that it is a robust technique employed for genotypical and phylogenetic studies for determining taxonomical diversity and phylogenetic structure of the economically important fungal pathogen of cluster bean. The data presented here will help researchers to design effective strategies for deployment of resistant germplasm in cluster bean (Cymopsis tetragonoloba) growing regions in the country and worldwide.
Assessing the Movement of Cucurbit yellow stunting disorder virus in Susceptible and Tolerant Cucumber Germplasms Using Serological and Nucleic Acid‐based Methods
Authors: Abou‐Jawdah Y. , Eid S. G. , Atamian H. S. , Havey M.
Published: April 2008

Cucurbit yellow stunting disorder virus (CYSDV) is an emerging virus causing significant yield losses in cucurbits. Simple but reliable detection and quantification methods are important tools for disease management. In susceptible germplasm, CYSDV was detected 5 days postinoculation (dpi) by reverse transcriptase polymerase chain reaction (RT‐PCR) or by tissue blot immunoassay (TBIA), and 8–9 dpi by dot blot immunoassay (DBIA) or enzyme‐linked immunosorbent assay (ELISA). For CYSDV quantification, real‐time RT‐PCR was the most sensitive method and gave the best linear range of detection, over four orders of magnitude as compared to approximately two orders of magnitude for DBIA and nucleic acid hybridization. DBIA was more sensitive than ELISA and equally sensitive to nucleic acid hybridization with a non‐radioactively labelled cDNA probe. Time course studies at 3, 5, 8 and 14 dpi using TBIA revealed that tolerance to CYSDV in three tolerant cucumber germplasms was not correlated with restricted or delayed virus movement.
Detection and Molecular Characterization of Squash leaf curl virus (SLCV) in Jordan
Authors: Al‐Musa A. , Anfoka G. , Misbeh S. , Abhary M. , Ahmad F. H.
Published: April 2008

Squash leaf curl virus (SLCV) was detected for the first time in Jordan using degenerated oligonucleotide primers. Two isolates of the virus, SLCV‐E and SLCV‐R, were detected using specific oligonucleotide primers in symptomatic Cucurbita pepo. SLCV was also found to occur naturally in Malva parviflora, which showed severe leaf curling, yellowing and stunting of the whole plants. The full‐length genomes of Squash leaf curl virus‐Malva (SLCV‐Malva) isolate were amplified using the bacteriophage Φ DNA polymerase enzyme. Nucleotide sequence analysis showed that SLCV‐Malva shared high nucleotide identity (98% and 97%) with SLCV‐EG and SLCV‐E from Egypt and USA, respectively. A survey using dot‐blot hybridization indicated that squash leaf curl disease occurred in all surveyed areas. The highest disease incidence (95%) was recorded in Dir Alla area, whereas disease incidence did not exceed 69% in squash samples collected from North Ghor.
The Potential Use of a Silicon Source as a Component of an Ecological Management of Coffee Plants
Authors: Martinati J. C. , Harakava R. , Guzzo S. D. , Tsai S. M.
Published: April 2008

Coffee is one of the most important agricultural export commodities in the world and it represents the main export from some developing countries. Therefore, the development of new methods of coffee management that improves production without causing any damage to the environment is an attractive alternative for producers. Much effort has been invested towards understanding the mode of action of compounds that can induce resistance against several pathogens without injuring the environment. Many researches have considered silicon efficient in avoiding plant pathogen penetration and development. Our aim was to verify the effect of potassium silicate and calcium/magnesium silicate in the development of coffee seedlings (Coffea arabica cv. Mundo Novo) as well as to evaluate the incidence of coffee leaf rust development under greenhouse conditions. The experiment was a completely randomized design with 12 treatments with 10 plants per treatment. The treatments were 0, 0.25, 1.25, 2.5, 4 and 5 μm of Si for each source of silicon incorporated into the soil. The seedlings were inoculated with a urediniospores suspension of Hemileia vastatrix (2 mg/ml) at the seventh month after planting (six pair of leaves). Evaluations were performed by counting the number of lesions per leaf. The statistical analysis showed that the number of lesions reduced by up to 66% at the highest silicon dose when compared to the number of lesions in control plants. Infected plants were found to have a linear decrease of lesions with the increase of silicate concentration. The lowest number of lesions per leaf area was observed in plants that received 5 μm of Si from potassium silicate. This result indicates the use of silicon as an alternative for an ecological management system for coffee disease protection.
New predictive equations for spirometric reference values and comparison with Morris equation in a Korean population
Authors: LEE Chang‐Hoon , LEE Ju‐Young , JANG Eun‐Jung , PARK Keun‐Yong , HAN Hyun‐Woo
Published: April 2008

Background and objective:  The clinical importance of the differences between actual and predicted spirometric indices in non‐Western populations is poorly defined. This study evaluated the differences between the spirometric values derived from Morris equation, traditionally used in South Korea, and the actual values, in the classification and detection of patients with respiratory diseases, and developed new predictive equations for the calculation of reference spirometric values for healthy Koreans.

Methods:  Data derived from a subset of the population who completed the initial baseline survey of the Korean Health and Genome Study were used to develop new predictive equations for spirometric reference values, using multiple linear regression. The effects of the new equations relative to those of Morris on the detection and classification of patients with respiratory diseases were then evaluated.

Results:  In total, 9999 people completed the baseline survey; a subgroup of 1314 met the study inclusion criteria and were used to develop the new predictive equations. Morris equation are 53.8% less accurate in detecting people with restrictive disorders and 15.8% less accurate in estimating the severity of COPD than the newly derived equations, although the differences between values derived from the traditional equations and values from the new equations were as small as 3.3–7.6%.

Conclusions:  The use of spirometric reference values that underestimate the actual parameters, despite the small differences, may have a significant influence on the detection of patients with restrictive disorders and the staging of COPD.
Clinically occult subpleural fibrosis and acute interstitial pneumonia a precursor to idiopathic pulmonary fibrosis?
Authors: ARAYA Jun , KAWABATA Yoshinori , JINHO Park , UCHIYAMA Takashi , OGATA Hideo , SUGITA Yutaka
Published: April 2008

Background and objective:  The clinical features and acute component of the pathological findings in patients with acute exacerbation of IPF are similar to those of acute interstitial pneumonia (AIP). A growing body of research suggests that acute exacerbation of subclinical IPF is similar to AIP. This study tested the hypothesis that subpleural fibrosis (resembling localized usual interstitial pneumonia) in patients with diffuse alveolar damage can mimic patients with AIP alone.

Methods:  The clinical, radiological and histopathological characteristics of patients with AIP with or without subpleural fibrosis, as identified at post‐mortem examination, were assessed.

Results:  Fourteen patients with AIP met the inclusion criteria. These comprised nine men and five women ranging in age from 65 to 90 years. The mean duration from onset of symptoms to admission was 12.3 days, and from admission to death was 50.5 days. All patients presented with severe respiratory failure with bilateral pulmonary infiltrates on CXR. CT scans revealed bilateral ground glass opacity (100.0%), air space consolidation (69.2%) and no honeycombing. In seven patients (50.0%) histological examination showed subpleural fibrosis. There were no differences in the clinicopathological or CT scan findings between patients with AIP only compared with those with AIP and subpleural fibrosis.

Conclusions:  Subpleural fibrosis resembling localized usual interstitial pneumonia is often present in patients diagnosed as having AIP. These patients were not distinguishable from those with AIP only, based on the clinicopathological and radiological findings.
Sources for sedimentary bacteriohopanepolyols as revealed by 16S rDNA stratigraphy
Authors: Coolen Marco J. L. , Talbot Helen M. , Abbas Ben A. , Ward Christopher , Schouten Stefan , Volkman John K. , Damsté Jaap S. Sinninghe
Published: April 2008

Bacteriohopanoids are widespread lipid biomarkers in the sedimentary record. Many aerobic and anaerobic bacteria are potential sources of these lipids which sometimes complicates the use of these biomarkers as proxies for ecological and environmental changes. Therefore, we applied preserved 16S ribosomal RNA genes to identify likely Holocene biological sources of bacteriohopanepolyols (BHPs) in the sulfidic sediments of the permanently stratified postglacial Ace Lake, Antarctica. A suite of intact BHPs were identified, which revealed a variety of structural forms whose composition differed through the sediment core reflecting changes in bacterial populations induced by large changes in lake salinity. Stable isotopic compositions of the hopanols formed from periodic acid‐cleaved BHPs, showed that some were substantially depleted in 13C, indicative of their methanotrophic origin. Using sensitive molecular tools, we found that Type I and II methanotrophic bacteria (respectively Methylomonas and Methylocystis) were unique to the oldest lacustrine sediments (> 9400 years BP), but quantification of fossil DNA revealed that the Type I methanotrophs, including methanotrophs related to methanotrophic gill symbionts of deep‐sea cold‐seep mussels, were the main precursors of the 35‐amino BHPs (i.e. aminopentol, ‐tetrol and ‐triols). After isolation of the lake ∼3000 years ago, one Type I methanotroph of the ‘methanotrophic gill symbionts cluster’ remained the most obvious source of aminotetrol and ‐triol. We, furthermore, identified a Synechococcus phylotype related to pelagic freshwater strains in the oldest lacustrine sediments as a putative source of 2‐methylbacteriohopanetetrol (2‐Me BHT). This combined application of advanced geochemical and paleogenomical tools further refined our knowledge about Holocene biogeochemical processes in Ace Lake.
Changes in the photosynthetic reaction centre II in the diatom Phaeodactylum tricornutum result in non‐photochemical fluorescence quenching
Authors: Eisenstadt Doron , Ohad Itzhak , Keren Nir , Kaplan Aaron
Published: April 2008

Diatoms are an important group of primary producers in the aquatic environment. They are able to acclimate to fast changes in the light intensity by various mechanisms including a rise in non‐photochemical fluorescence quenching (NPQ). The latter has been attributed to the xanthophyll cycle (XC) following activation of diadinoxanthin de‐epoxidase by the acidification of the thylakoid lumen. To examine whether fluorescence quenching in the diatom Phaeodactylum tricornutum depends on the ΔpH generated by the photosynthetic electron transport, we arrested the latter by 3‐(3′,4′‐dichlorophenyl)‐1,1‐dimethylurea (DCMU). This treatment hardly affected the NPQ or XC, even when methylviologen was present. Dissipation of the ΔpH by 2,4‐dinitrophenol inhibited the XC but did not alter NPQ. Similar results, i.e. inhibition of the XC but normal fluorescence quenching, were observed when the experiments were performed at 3°C. Measurements of thermoluminescence showed that excess light treatment caused a marked decline in the signals obtained as a result of recombination of QB‐ with the S3 state of the Mn cluster; this was also observed in cells treated with DCMU (recombination of QA‐ with S2). Light treatment also diminished the QA‐ re‐oxidation signals. The data suggest that changes in PSII core centre itself due to exposure to excess light conditions play an important part in the acclimation of P. tricornutum to the changing light conditions.
Transanal endoscopic microsurgery in early rectal cancer: time for a trial?
Authors: Suppiah A. , Maslekar S. , Alabi A. , Hartley J. E. , Monson J. R. T.
Published: April 2008

Objective  The optimal aim of oncological surgery is to balance cancer outcomes with preservation of function and quality of life. Radical resection (RR) offers the best curative procedure in colorectal cancer but at significant morbidity. Transanal endoscopic microsurgery (TEM) offers an alternative with less morbidity and better function. Its role remains unclear and needs to be established in the light of new emerging trends in rectal cancer. This review aims to evaluate the use of TEM and its limitations.

Method  PubMed and MEDLINE search was performed.

Results  Strongest level of evidence (Level II) favoured TEM over RR and laparoscopic resection in term of mortality and morbidity. There was no difference in recurrence at follow‐up of 41 and 56 months but neither study was adequately powered to detect a difference in recurrence/survival. Three retrospective case comparisons (Level III) also favoured TEM over RR but were subject to selection bias. Twenty eight published case series (Level IV) reported varying results due to different cancer stages, study population, full excision, adjuvant therapy and treatment indication. The oncological outcomes in TEM are similar to RR in highly selected cases but with far less mortality (near 0%), morbidity, blood loss, hospital stay and genitourinary/gastrointestinal dysfunction. TEM alone (+/− adjuvant therapy) appears sufficient for ‘favourable’ T1 tumours. ‘Unfavourable’ T1 or T2 tumours require adjuvant treatment. TEM should only be used for palliation in T3+ cancers. Seven functional studies reported significant transient dysfunction following TEM with full clinical recovery within a year. TEM is cost‐effective providing sufficient cases are performed.

Conclusion  Significant heterogeneity limits conclusions from current literature. A trial is required. Alternate end‐points to local recurrence may be required in assessing the optimal surgical approach, which balances disease control with quality of life, and probability of noncancer related death.
What controls liana success in Neotropical forests?
Authors: Van Der Heijden Geertje M. F. , Phillips Oliver L.
Published: April 2008

Aim  We seek to determine the factors which control the success of lianas across macroecological gradients. Lianas have a strong impact on the growth, mortality and biomass of tropical trees, and are reported to be increasing in dominance, so understanding their behaviour is important from the perspectives of both ecological and global change.

Location  Lowland and montane Neotropical forests.

Methods  Using 65 standardized samples of lianas (≥ 2.5 cm diameter) from across the Neotropics, we attempted to account for characteristics of both the environment and the forest in explaining macroecological variation in liana success in Neotropical forests, using regression analyses and structural equation modelling.

Results  We found that both liana density and basal area were unrelated to mean annual precipitation, dry season length or soil variables, except for a weak effect of mean annual precipitation on liana basal area. Structural characteristics of the forest explained more of the variation in liana density and basal area than the physical environment. More disturbed forests generally tended to have a higher liana density. Liana basal area, however, was highest in undisturbed forests.

Main conclusions  The availability of host trees and their characteristics may be more important than the direct effects of the physical environment in controlling the success of lianas in Neotropical forests. Changes to the tropical climate in the coming century may not strongly affect lianas directly, but could have very substantial indirect effects via changes in tree community structure and dynamics.
How general are global trends in biotic homogenization? Floristic tracking in Chile, South America
Authors: Castro Sergio A. , Jaksic Fabian M.
Published: April 2008

Aim  To quantify the occurrence of floristic change in the vascular flora of Chile. We test whether continental areas have experienced floristic modification leading to either homogenization, differentiation or tracking.

Location  Continental Chile.

Methods  On the basis of the geographical distribution of native (1806 species) and naturalized plants (552 species) in continental Chile, we quantified change between two floristic stages: (1) pre‐European flora, including native extant and extinct species; and (2) current flora, including native and naturalized species, but excluding extinct plants. We compared changes in compositional similarity (calculated by Jaccard's index, ΔJ) between pairs of regions, and similarity decay with respect to geographical distance. Additionally, by means of Whittaker's index, we examined species turnover, distinguishing between native and naturalized plants.

Results  Between floristic stages (pre‐European vs. current flora) no significant changes in floristic similarity were noted at national or regional scales. Similarity decay showed no statistical differences between pre‐European and current flora. Analysing patterns of geographical turnover, we found that species turnover of naturalized plants over their geographical range is similar to that of native plants.

Conclusions  The composition of the continental flora of Chile does not show significant modifications in similarity patterns after considering naturalized species, thus indicating floristic tracking. The causes of this phenomenon may be related to the current geographical distribution of naturalized plants, which closely parallels that of native plants. Our results differ from those obtained in Northern Hemisphere continents, thus indicating that trends of biotic change may differ between hemispheres.
How does habitat diversity affect the species–area relationship?
Authors: Kallimanis Athanasios S. , Mazaris Antonis D. , Tzanopoulos Joseph , Halley John M. , Pantis John D. , Sgardelis Stefanos P.
Published: April 2008

Aim  To examine the way in which ‘area’ and ‘habitat diversity’ interact in shaping species richness and to find a simple and valid way to express this interaction.

Location  The Natura 2000 network of terrestrial protected areas in Greece, covering approximately 16% of the national territory.

Methods  We used the Natura 2000 framework, which provides a classification scheme for natural habitat types, to quantify habitat heterogeneity. We analysed data for the plant species composition in 16,143 quadrats in which 5044 species and subspecies of higher plants were recorded. We built a simple mathematical model that incorporates the effect of habitat diversity on the species–area relationship (SAR).

Results  Our analysis showed that habitat diversity was correlated with area. However, keeping habitat diversity constant, species richness was related to area; while keeping area constant, species richness was related to habitat diversity. Comparing the SAR of the 237 sites we found that the slope of the species–area curve was related to habitat diversity.

Main conclusions  Discussion of the causes of the SAR has often focused on the primacy of area per se versus habitat heterogeneity, even though the two mechanisms are not mutually exclusive and should be considered jointly. We find that increasing habitat diversity affects the SAR in different ways, but the dominant effect is to increase the slope of the SAR. While a full model fit typically includes a variety of terms involving both area and habitat richness, we find that the effect of habitat diversity can be reduced to a linear perturbation of the slope of the species accumulation curve.
Implementable Ramsey‐Boiteux Pricing in Agricultural and Environmental Policy
Authors: Bourgeon Jean-Marc , Chambers Robert G.
Published: April 2008

Agricultural producers frequently face price discrimination that is based either on characteristics of their products, or on the physical manner in which the product is produced. We consider how to set such discriminatory prices optimally and show that for a very broad range of production technologies, the first‐best voluntary policy, which involves a modified version of Ramsey‐Boiteux pricing, is implementable even in the presence of hidden knowledge by farmers about their types.
Neuroimaging as a New Tool in the Toolbox of Psychological Science
Authors: Cacioppo John T. , Berntson Gary G. , Nusbaum Howard C.
Published: April 2008

During the past quarter century, advances in imaging technology have helped transform scientific fields. As important as the data made available by these new technologies have been, equally important have been the guides provided by existing theories and the converging evidence provided by other methodologies. The field of psychological science is no exception. Neuroimaging is an important new tool in the toolbox of psychological science, but it is most productive when its use is guided by psychological theories and complemented by converging methodologies including (but not limited to) lesion, electrophysiological, computational, and behavioral studies. Based on this approach, the articles in this special issue specify neural mechanisms involved in perception, attention, categorization, memory, recognition, attitudes, social cognition, language, motor coordination, emotional regulation, executive function, decision making, and depression. Understanding the contributions of individual and functionally connected brain regions to these processes benefits psychological theory by suggesting functional representations and processes, constraining these processes, producing means of falsifying hypotheses, and generating new hypotheses. From this work, a view is emerging in which psychological processes represent emergent properties of a widely distributed set of component processes.
Computational Cognitive Neuroscience of the Visual System
Authors: Engel Stephen A.
Published: April 2008

Should psychologists care about functional magnetic resonance imaging (fMRI)? Within the field of visual perception, the answer to this question is an emphatic “yes.” There is a long history of close interactions between psychology and neuroscience in the study of vision. In the 1980s, vision researchers developed a general framework for combining the two fields, and that framework still supports much current research. This article will briefly cover this general approach and then will illustrate how neuroimaging allows the framework to be applied to human perception. In short, fMRI can measure how information is represented in sequential stages of processing. These same representations can also be measured behaviorally. Theories of vision specify how the sequential representations participate in well-defined computations that underlie perception.
Speech Perception
Authors: Poeppel David , Monahan Philip J.
Published: April 2008

Speech perception includes, minimally, the set of computations that transform continuously varying acoustic signals into linguistic representations that can be used for subsequent processing. The auditory and motor subroutines of this complex perceptual process are executed in a network of brain areas organized in ventral and dorsal parallel pathways, performing sound-to-meaning and sound-to-motor mappings, respectively. Research on speech using neurobiological techniques argues against narrow motor or auditory theories. To account for the range of cognitive and neural attributes, integrative computational models seem promising.
Neuroscientific Evidence About the Distinction Between Short- and Long-Term Memory
Authors: Nee Derek Evan , Berman Marc G. , Moore Katherine Sledge , Jonides John
Published: April 2008

What have neuroscientific techniques contributed to the development of psychological theory about short- and long-term memory? We argue that the contributions have been varied: In some cases, data about brain mechanisms have been vital to the advancement of psychological theory; in other cases, neuroscientific data and behavioral data from normal participants have made equal contributions; and in yet other cases, the data from neuroscientific approaches have actually led psychological theory astray. We illustrate these various contributions by focusing on the relationship of short- to long-term memory.
Neural Representations of Nondeclarative Memories
Authors: Knowlton Barbara J. , Foerde Karin
Published: April 2008

Nondeclarative learning refers to abilities characterized by a lack of awareness of what has been learned and an independence from medial temporal lobe structures that support conscious memories of facts and events. Neuroimaging approaches have been used extensively in two domains of nondeclarative learning—priming and skill learning—to investigate the neural substrates supporting performance. Recent neuroimaging studies have attempted to understand what is being learned in different tasks in order to inform psychological theories of nondeclarative memory. For example, priming may be considered a form of perceptual learning or a form of stimulus–response learning, and correlations between performance and activation patterns in different regions may suggest the nature of the brain changes that support behavior. The attainment of expertise in a skill has been characterized as greater efficiency of processing in the same neural structures that support novice performance or, alternatively, as the recruitment of additional regions. Current research suggests that, within the domains of priming and skill learning, there is much heterogeneity in the underlying brain representations and psychological theories will need to account for these variations.
The Representation of Action
Authors: Oliveira Flavio T.P. , Ivry Richard B.
Published: April 2008

The motor-program concept, emphasizing how actions are represented in the brain, helped bring the study of motor control into the realm of cognitive psychology. However, interest in representational issues was in limbo for much of the past 30 years, during which time the focus was on biomechanical and abstract accounts of the constraints underlying coordinated movement. We review recent behavioral and neuroscientific evidence that highlights multiple levels of constraints in bimanual coordination, with an emphasis on work demonstrating that a primary source of constraint arises from the manner in which action goals are represented.
Contributions of Functional Neuroimaging to the Study of Social Cognition
Authors: Mitchell Jason P.
Published: April 2008

Increasingly, researchers have been applying the methods of cognitive neuroscience—especially functional neuroimaging—to address questions about how humans make inferences about the mental states of others. At the same time, a number of critics have warned against the use of these new techniques by suggesting that functional neuroimaging has been unable to provide novel insights into the nature of social cognition. Addressing these critiques, this article briefly describes some of the ways in which functional neuroimaging has indeed redirected the study of the social mind, reviewing not only the novel data these techniques have provided but also the ways in which cognitive neuroscience has prompted researchers to consider entirely new questions about the organization of human social cognition. Such questions include whether or not there are cognitive processes dedicated for social thought; what the constituent parts of our social-cognitive system might be; how social cognition overlaps with other mental processes in previously unanticipated ways; and whether social cognition might play a privileged role in the human cognitive repertoire.
The Neural Basis of Implicit Attitudes
Authors: Stanley Damian , Phelps Elizabeth , Banaji Mahzarin
Published: April 2008

Evidence that human preferences, beliefs, and behavior are influenced by sources that are outside the reach of conscious awareness, control, intention, and self-reflection is incontrovertible. Recent advances in neuroscience have enabled researchers to investigate the neural basis of these implicit attitudes, particularly attitudes involving social groups. From this research, a model with three identified neural components related to the automatic activation and regulation of implicit attitudes is beginning to emerge. The amygdala is implicated in the automatic evaluation of socially relevant stimuli, while the anterior cingulate and dorsolateral prefrontal cortices are involved in the detection and regulation, respectively, of implicit attitudes. Further support for this model comes from the inclusion of these regions in current models concerning the cognitive regulation of emotion and the detection of conflict. The identification of a putative neural substrate for implicit attitudes has had a direct impact on psychological research into their nature and operational characteristics. We discuss how this emerging neural model has influenced current research on implicit attitudes and describe the importance of such models for directing future research.
The Governance of Networks: Heuristic or Formal Analysis? A Reply to Rachel Parker
Authors: Christopoulos Dimitrios C.
Published: April 2008

Rachel Parker, in her article ‘Networked Governance or Just Networks?’ in this journal, has dealt with a very challenging question on the relevance of network interaction to governance outcomes. Her use of network concepts, however, appears to employ networks as a heuristic device. Her article employs terms that describe social network properties that are best contextualised with reference to the theoretical insights offered by formal Social Network Analysis (SNA). My suggestion in this brief review is that some of the theoretical assumptions made about concepts such as fluidity, density or trust imply specific network properties that cannot be ignored when attempting an analysis of policy outcomes.
Language shift and the family: Questions from the Sri Lankan Tamil diaspora1
Authors: Canagarajah A. Suresh
Published: April 2008

Fishman's Graded Intergenerational Disruption Scale (GIDS) emphasizes the family in maintaining the heritage languages of immigrant communities. This study uses interview data from Sri Lankan Tamil communities in the U.S.A., U.K., and Canada to explain how families account for the rapid loss of Tamil in the diaspora. It shows how the positive valuation of English since British colonization, the need to make up for past deprivations because of caste, religious, and gender inequality, the pressure for migrants to join the social mainstream, and the need to resolve intergenerational tensions influence the family to forego language maintenance goals. The findings encourage us to situate the family in macro‐social institutions, power, and history in order to understand the prospects for language maintenance. The article provides an inside view of the Sri Lankan Tamil migrant families to explain how they resolve the tensions of valuing cultural identity and yet disregarding heritage language proficiency.
Fast Stable Direct Fitting and Smoothness Selection for Generalized Additive Models
Authors: Wood Simon N.
Published: April 2008

Existing computationally efficient methods for penalized likelihood generalized additive model fitting employ iterative smoothness selection on working linear models (or working mixed models). Such schemes fail to converge for a non-negligible proportion of models, with failure being particularly frequent in the presence of concurvity. If smoothness selection is performed by optimizing ‘whole model’ criteria these problems disappear, but until now attempts to do this have employed finite-difference-based optimization schemes which are computationally inefficient and can suffer from false convergence. The paper develops the first computationally efficient method for direct generalized additive model smoothness selection. It is highly stable, but by careful structuring achieves a computational efficiency that leads, in simulations, to lower mean computation times than the schemes that are based on working model smoothness selection. The method also offers a reliable way of fitting generalized additive mixed models.
Dated Ancestral Trees from Binary Trait Data and Their Application to the Diversification of Languages
Authors: Nicholls Geoff K. , Gray Russell D.
Published: April 2008

Binary trait data record the presence or absence of distinguishing traits in individuals. We treat the problem of estimating ancestral trees with time depth from binary trait data. Simple analysis of such data is problematic. Each homology class of traits has a unique birth event on the tree, and the birth event of a trait that is visible at the leaves is biased towards the leaves. We propose a model-based analysis of such data and present a Markov chain Monte Carlo algorithm that can sample from the resulting posterior distribution. Our model is based on using a birth–death process for the evolution of the elements of sets of traits. Our analysis correctly accounts for the removal of singleton traits, which are commonly discarded in real data sets. We illustrate Bayesian inference for two binary trait data sets which arise in historical linguistics. The Bayesian approach allows for the incorporation of information from ancestral languages. The marginal prior distribution of the root time is uniform. We present a thorough analysis of the robustness of our results to model misspecification, through analysis of predictive distributions for external data, and fitting data that are simulated under alternative observation models. The reconstructed ages of tree nodes are relatively robust, whereas posterior probabilities for topology are not reliable.
The Role of Task‐Induced Involvement and Learner Proficiency in L2 Vocabulary Acquisition
Authors: Kim YouJin
Published: April 2008

Hulstijn and Laufer (2001) proposed a motivational‐cognitive construct of task‐induced involvement to account for variation in effectiveness among different vocabulary learning tasks. Building upon their original research, this study consisted of two experiments investigating the involvement load hypothesis in vocabulary learning. Experiment 1 compared the performance of 64 adult English as a second language (ESL) learners from a range of countries at two different proficiency levels (i.e., matriculated undergraduate students vs. students in an Intensive English Program) to ascertain the effectiveness of three vocabulary tasks with different levels of task‐induced involvement. Experiment 2 investigated whether two tasks hypothesized to represent the same level of task‐induced involvement would result in equivalent initial learning and retention of target words by 20 adult ESL learners at two different levels of proficiency. The results of Experiment 1 showed that a higher level of learner involvement during the task promoted more effective initial vocabulary learning and better retention of the new words. The findings of Experiment 2 indicated that when different tasks had the same involvement load, they resulted in similar amounts of initial vocabulary learning and retention of new words. The results of the two experiments are discussed in light of the involvement load hypothesis.