bluuebunny/crossref_metadata_2025 huggingface dataset:
Applications of Codon and Rate Variation Models in Molecular Phylogeny
Authors: Schadt Eric E. , Sinsheimer Janet S. , Lange Kenneth
Published: January 2012

The current article illustrates the practical advantages of some new models and statistical algorithms for codon substitution and spatial rate variation in molecular phylogeny. Our companion paper in this issue discusses at length the mathematical properties of these models for nucleotide and codon substitution, for site-to-site and branch-to-branch heterogeneity in rates of evolution, and for spatial correlation in the assignment of rates. In this study we summarize the theoretical background and apply the models and algorithms to data on β-globin, the complete HIV genome, and the mitochondrial genome. Our complex but realistic models enhance biological interpretation of sequence data and show substantial improvements in model fit over existing models. All the new statistical algorithms applied are incorporated in our phylogeny software LINNAEUS, which is tuned for performance and modeling flexibility.
A Strong Effect of AT Mutational Bias on Amino Acid Usage in Buchnera is Mitigated at High-Expression Genes
Authors: Palacios Carmen , Wernegreen Jennifer J.
Published: January 2012

The advent of full genome sequences provides exceptionally rich data sets to explore molecular and evolutionary mechanisms that shape divergence among and within genomes. In this study, we use multivariate analysis to determine the processes driving genome-wide patterns of amino usage in the obligate endosymbiont Buchnera and its close free-living relative Escherichia coli. In the AT-rich Buchnera genome, the primary source of variation in amino acid usage differentiates high- and low-expression genes. Amino acids of high-expression Buchnera genes are generally less aromatic and use relatively GC-rich codons, suggesting that selection against aromatic amino acids and against amino acids with AT-rich codons is stronger in high-expression genes. Selection to maintain hydrophobic amino acids in integral membrane proteins is a primary factor driving protein evolution in E. coli but is a secondary factor in Buchnera. In E. coli, gene expression is a secondary force driving amino acid usage, and a correlation with tRNA abundance suggests that translational selection contributes to this effect. Although this and previous studies demonstrate that AT mutational bias and genetic drift influence amino acid usage in Buchnera, this genome-wide analysis argues that selection is sufficient to affect the amino acid content of proteins with different expression and hydropathy levels.
The Plastid Chromosome of Atropa belladonna and its Comparison with that of Nicotiana tabacum: The Role of RNA Editing in Generating Divergence in the Process of Plant Speciation
Authors: Schmitz-Linneweber Christian , Regel Ralph , Du Tung Gia , Hupfer Holger , Herrmann Reinhold G. , Maier Rainer M.
Published: January 2012

The nuclear and plastid genomes of the plant cell form a coevolving unit which in interspecific combinations can lead to genetic incompatibility of compartments even between closely related taxa. This phenomenon has been observed for instance in Atropa-Nicotiana cybrids. We have sequenced the plastid chromosome of Atropa belladonna (deadly nightshade), a circular DNA molecule of 156,688 bp, and compared it with the corresponding published sequence of its relative Nicotiana tabacum (tobacco) to understand how divergence at the level of this genome can contribute to nuclear-plastid incompatibilities and to speciation. It appears that (1) regulatory elements, i.e., promoters as well as translational and replicational signal elements, are well conserved between the two species; (2) genes—including introns—are even more highly conserved, with differences residing predominantly in regions of low functional importance; and (3) RNA editotypes differ between the two species, which makes this process an intriguing candidate for causing rapid reproductive isolation of populations.
The 5′ Leader of Plant PgiC has an Intron: The Leader Shows Both the Loss and Maintenance of Constraints Compared with Introns and Exons in the Coding Region
Authors: Gottlieb L. D. , Ford V. S.
Published: January 2012

PgiC, a complex gene with 23 coding exons and 22 intervening introns, encodes the cytosolic isozyme of phosphoglucose isomerase (EC 5.3.1.9) in higher plants. Here, we report RNA ligase–mediated rapid amplification of cDNA ends experiments that showed that PgiC in Clarkia (Onagraceae) and Arabidopsis thaliana has an intron in the 5′ leader. Comparison of the EMBL accessions of the cDNA and genomic sequences showed that this is also the case in rice (Oryza sativa), suggesting that a leader intron is generally present in higher plant PgiC. The intron is bounded by consensus 5′-GT and AG-3′ splice sites but showed alternative splicing in Clarkia, resulting in mature transcripts that differ by 8–19 nt in length. The intron is located 18 or 10 nt upstream of the start codon in Clarkia, 2 nt upstream in Arabidopsis, and 9 nt in rice. PgiC in Clarkia was duplicated before the divergence of the extant species, many of which have two expressed genes PgiC1 and PgiC2. Full-length transcripts of both genes identified the transcription start and made it possible to identify the leader intron and leader exon (between the transcription start and leader intron) from previously obtained genomic sequences of both genes in other Clarkia species. These data permit the comparison of evolution in the leader exon and intron with the exons and introns of the coding region, a topic that has not been studied previously. Both the leader exon and the leader intron resemble introns of the coding region in base substitution rate and accumulation of gaps. But the leader intron splice junctions are not strictly conserved in position as are those of the coding region introns. Also, in base composition, the leader intron resembles the other introns, whereas the leader exon more nearly resembles the coding exons. A difference in base composition between coding exons and flanking introns is known to be important for the recognition of splice sites. Thus, the marked difference in base composition between the leader exon and leader intron is probably maintained by selection despite a high rate of sequence divergence.
Aggregation Among Binary, Count, and Duration Models: Estimating the Same Quantities from Different Levels of Data
Authors: Alt James E. , King Gary , Signorino Curtis S.
Published: January 2012

Binary, count, and duration data all code discrete events occurring at points in time. Although a single data generation process can produce all of these three data types, the statistical literature is not very helpful in providing methods to estimate parameters of the same process from each. In fact, only a single theoretical process exists for which known statistical methods can estimate the same parameters—and it is generally used only for count and duration data. The result is that seemingly trivial decisions about which level of data to use can have important consequences for substantive interpretations. We describe the theoretical event process for which results exist, based on time independence. We also derive a set of models for a time-dependent process and compare their predictions to those of a commonly used model. Any hope of understanding and avoiding the more serious problems of aggregation bias in events data is contingent on first deriving a much wider arsenal of statistical models and theoretical processes that are not constrained by the particular forms of data that happen to be available. We discuss these issues and suggest an agenda for political methodologists interested in this very large class of aggregation problems.
Mixed Logit Models for Multiparty Elections
Authors: Glasgow Garrett
Published: January 2012

Mixed logit (MXL) is a general discrete choice model thus far unexamined in the study of multicandidate and multiparty elections. Mixed logit assumes that the unobserved portions of utility are a mixture of an IID extreme value term and another multivariate distribution selected by the researcher. This general specification allows MXL to avoid imposing the independence of irrelevant alternatives (IIA) property on the choice probabilities. Further, MXL is a flexible tool for examining heterogeneity in voter behavior through random-coefficients specifications. MXL is a more general discrete choice model than multinomial probit (MNP) in several respects, and can be applied to a wider variety of questions about voting behavior than MNP. An empirical example using data from the 1987 British General Election demonstrates the utility of MXL in the study of multicandidate and multiparty elections.
Logistic Regression in Rare Events Data
Authors: King Gary , Zeng Langche
Published: January 2012

We study rare events data, binary dependent variables with dozens to thousands of times fewer ones (events, such as wars, vetoes, cases of political activism, or epidemiological infections) than zeros (“nonevents”). In many literatures, these variables have proven difficult to explain and predict, a problem that seems to have at least two sources. First, popular statistical procedures, such as logistic regression, can sharply underestimate the probability of rare events. We recommend corrections that outperform existing methods and change the estimates of absolute and relative risks by as much as some estimated effects reported in the literature. Second, commonly used data collection strategies are grossly inefficient for rare events data. The fear of collecting data with too few events has led to data collections with huge numbers of observations but relatively few, and poorly measured, explanatory variables, such as in international conflict data with more than a quarter-million dyads, only a few of which are at war. As it turns out, more efficient sampling designs exist for making valid inferences, such as sampling all available events (e.g., wars) and a tiny fraction of nonevents (peace). This enables scholars to save as much as 99% of their (nonfixed) data collection costs or to collect much more meaningful explanatory variables. We provide methods that link these two results, enabling both types of corrections to work simultaneously, and software that implements the methods developed.
Nonseparable Preferences, Measurement Error, and Unstable Survey Responses
Authors: Lacy Dean
Published: January 2012

A person has nonseparable preferences when her preference on an issue depends on the outcome of other issues. A model of survey responses in which preferences are measured with error implies that responses will change depending on the order of questions and vary over time when respondents have nonseparable preferences. Results from two survey experiments confirm that changes in survey responses due to question order are explained by nonseparable preferences but not by the respondent's level of political information, partisanship, or ideology.
Bias in Conditional and Unconditional Fixed Effects Logit Estimation
Authors: Katz Ethan
Published: January 2012

Fixed-effects logit models can be useful in panel data analysis, whenNunits have been observed forTtime periods. There are two main estimators for such models: unconditional maximum likelihood and conditional maximum likelihood. Judged on asymptotic properties, the conditional estimator is superior. However, the unconditional estimator holds several practical advantages, and therefore I sought to determine whether its use could be justified on the basis of finite-sample properties. In a series of Monte Carlo experiments forT< 20, I found a negligible amount of bias in both estimators whenT≥ 16, suggesting that a researcher can safely use either estimator under such conditions. WhenT< 16, the conditional estimator continued to have a very small amount of bias, but the unconditional estimator developed more bias asTdecreased.
Testing for Publication Bias in Political Science
Authors: Gerber Alan S. , Green Donald P. , Nickerson David
Published: January 2012

If the publication decisions of journals are a function of the statistical significance of research findings, the published literature may suffer from “publication bias.” This paper describes a method for detecting publication bias. We point out that to achieve statistical significance, the effect size must be larger in small samples. If publications tend to be biased against statistically insignificant results, we should observe that the effect size diminishes as sample sizes increase. This proposition is tested and confirmed using the experimental literature on voter mobilization.
Indoor radon levels in buildings in the autonomous community of Extremadura (Spain)
Authors: Baeza A. , Navarro E. , Roldán C. , L. Ferrero J. , Juanes D. , A. Corbacho J. , J. Guillén F.
Published: January 2012

Indoor air samples taken in buildings throughout the provinces of Cáceres and Badajoz in the Autonomous Community of Extremadura, Spain, were analysed for airborne radon concentrations using charcoal canisters. Measurements were made during the years 1998-2000. The geometrical mean indoor concentration was 90 Bq m-3. An estimated annual effective dose of 1.6 mSv y-1 was calculated for residents, assuming an equilibrium factor of 0.4 and an occupancy factor of 0.8. the relative importance of the principal variables that condition radon concentrations inside buildings was also delimited experimentally. These were soil type, construction materials used, the height of the room above ground level, and the degree of ventilation. The temporal evolution of the radon concentration was analysed, as this aspect could be particularly important in a Continental-Mediterranean climate such as that of the two provinces of the study.
Identity economics and the brain: uncovering the mechanisms of social conflict
Authors: Huettel Scott A. , Kranton Rachel E.
Published: January 2012

Social contexts can have dramatic effects on decisions. When individuals recognize each other as coming from the same social group, they can coordinate their actions towards a common goal. Conversely, information about group differences can lead to conflicts both economic and physical. Understanding how social information shapes decision processes is now a core goal both of behavioural economics and neuroeconomics. Here, we describe the foundations for research that combines the theoretical framework from identity economics with the experimental methods of neuroscience. Research at this intersection would fill important gaps in the literature not addressed by current approaches in either of these disciplines, nor within social neuroscience, psychology or other fields. We set forth a simple taxonomy of social contexts based on the information content they provide. And, we highlight the key questions that would be addressed by a new ‘identity neuroeconomics’. Such research could serve as an important and novel link between the social and natural sciences.
Race and reputation: perceived racial group trustworthiness influences the neural correlates of trust decisions
Authors: Stanley Damian A. , Sokol-Hessner Peter , Fareri Dominic S. , Perino Michael T. , Delgado Mauricio R. , Banaji Mahzarin R. , Phelps Elizabeth A.
Published: January 2012

Decisions to trust people with whom we have no personal history can be based on their social reputation—a product of what we can observe about them (their appearance, social group membership, etc.)—and our own beliefs. The striatum and amygdala have been identified as regions of the brain involved in trust decisions and trustworthiness estimation, respectively. However, it is unknown whether social reputation based on group membership modulates the involvement of these regions during trust decisions. To investigate this, we examined blood-oxygenation-level-dependent (BOLD) activity while participants completed a series of single-shot trust game interactions with real partners of varying races. At the time of choice, baseline BOLD responses in the striatum correlated with individuals' trust bias—that is, the overall disparity in decisions to trust Black versus White partners. BOLD signal in the striatum was higher when deciding to trust partners from the race group that the individual participant considered less trustworthy overall. In contrast, activation of the amygdala showed greater BOLD responses to Black versus White partners that scaled with the amount invested. These results suggest that the amygdala may represent emotionally relevant social group information as a subset of the general detection function it serves, whereas the striatum is involved in representing race-based reputations that shape trust decisions.
Evidence of sustained populations of a small reef fish on artificial structures. Does depth affect production on artificial reefs?
Authors: Fowler A. M. , Booth D. J.
Published: January 2012

The length frequencies and age structures of resident Pseudanthias rubrizonatus (n = 407), a small protogynous serranid, were measured at four isolated artificial structures on the continental shelf of north‐western Australia between June and August 2008, to determine whether these structures supported full (complete size and age‐structured) populations of this species. The artificial structures were located in depths between 82 and 135 m, and growth rates of juveniles and adults, and body condition of adults, were compared among structures to determine the effect of depth on potential production. All life‐history stages, including recently settled juveniles, females and terminal males, of P. rubrizonatus were caught, ranging in standard length (Ls) from 16·9 to 96·5 mm. Presumed ages estimated from whole and sectioned otoliths ranged between 22 days and 5 years, and parameter ±s.e. estimates of the von Bertalanffy growth model were L∞ = 152 ± 34 mm, k = 0·15(±0·05) and t0 = −1·15(±0·15). Estimated annual growth rates were similar between shallow and deep artificial structures; however, otolith lengths and recent growth of juveniles differed among individual structures, irrespective of depth. The artificial structures therefore sustained full populations of P. rubrizonatus, from recently settled juveniles through to adults; however, confirmation of the maximum age attainable for the species is required from natural populations. Depth placement of artificial reefs may not affect the production of fish species with naturally wide depth ranges.
An elasmobranch maternity ward: female round stingrays Urobatis halleri use warm, restored estuarine habitat during gestation
Authors: Jirik K. E. , Lowe C. G.
Published: January 2012

The habitat use and movements of the round stingray Urobatis halleri were compared between shallow restored and natural habitats of the Anaheim Bay Estuary (CA, U.S.A.) in relation to water temperature. Restored habitat remained significantly warmer than natural habitat from spring through to autumn. Strong sexual segregation occurred in the restored habitat with mature female U. halleri forming large unisex aggregations in summer, during months of peak seasonal water temperatures, and males only present during spring. Most mature females collected from restored habitat during months of high abundance were determined to be pregnant using non‐invasive field ultrasonography. Tagged females typically spent <14 days in the restored habitat, using the habitat less as seasonal water temperatures decreased. Females tended to emigrate from the estuary by mid‐August, coinciding with the time of year for parturition. The elevated water temperatures of the restored habitat may confer an energetic cost to male U. halleri, but females (particularly pregnant females) may derive a thermal reproductive benefit by using warm, shallow habitats for short periods of time during months of peak water temperatures. These findings have management implications for the design of coastal habitat restoration projects and marine protected areas that incorporate thermal environments preferred by aggregating female elasmobranchs.
Percutaneous mitral valve repair in a ventilator‐dependant patient
Authors: Davis C.
Published: January 2012

I report the case of a 57‐year‐old patient admitted to the intensive care unit with severe community‐acquired pneumonia, complicated by prolonged mechanical ventilation of the lungs and intractable cardiac failure. He underwent percutaneous coronary angioplasty of the right coronary artery, but this did not improve his clinical condition. He was subsequently found to be suffering from mitral valve prolapse, that was felt to be the cause of recurrent episodes of severe pulmonary oedema. As open surgery was felt to be not feasible, the patient underwent percutaneous repair of his mitral valve using the MitraClip® device, and, after months of ventilatory support, was then weaned from the ventilator in a matter of days. While the procedure itself and the technology employed are still under evaluation, I conclude that the technique of percutaneous mitral valve repair may be considered for similar patients for whom open repair is contraindicated.
A comparison of Rapydan® patch and Ametop® gel for venous cannulation*
Authors: Ravishankar N. , Elliot S. C. , Beardow Z. , Mallick A.
Published: January 2012

Ametop® gel (4% tetracaine) is used to provide topical anaesthesia for venous cannulation. Rapydan® patch (7% lidocaine and 7% tetracaine) has been developed to provide topical anaesthesia by a different mechanism, that of heat assisted delivery. We compared the topical anaesthetic effect of these agents for venous cannulation. One hundred healthy adults undergoing day‐case surgery were randomly assigned to receive either Rapydan (n = 50) or Ametop (n = 50) before venous cannulation. Pain on insertion was scored on a visual analogue scale between 0 and 100 (where 100 = unbearable pain). Median(IQR[range]) pain scores were not different between groups with 11 (5–20 [0–72]) for Rapydan and 10 (5–24 [0–95]) for Ametop (p = 0.63). Adequate topical anaesthesia was achieved in over 90% of patients in both groups. Rapydan produces topical anaesthesia comparable with Ametop for venous cannulation.
The projected effects of climatic and vegetation changes on the distribution and diversity of Southeast Asian bats
Authors: Hughes Alice C. , Satasook Chutamas , Bates Paul J. J. , Bumrungsri Sara , Jones Gareth
Published: January 2012

Southeast‐Asia (SEA) constitutes a global biodiversity hotspot, but is exposed to extensive deforestation and faces numerous threats to its biodiversity. Climate change represents a major challenge to the survival and viability of species, and the potential consequences must be assessed to allow for mitigation. We project the effects of several climate change scenarios on bat diversity, and predict changes in range size for 171 bat species throughout SEA. We predict decreases in species richness in all areas with high species richness (>80 species) at 2050–2080, using bioclimatic IPCC scenarios A2 (a severe scenario, continuously increasing human population size, regional changes in economic growth) and B1 (the ‘greenest’ scenario, global population peaking mid‐century). We also predicted changes in species richness in scenarios that project vegetation changes in addition to climate change up to 2050. At 2050 and 2080, A2 and B1 scenarios incorporating changes in climatic factors predicted that 3–9% species would lose all currently suitable niche space. When considering total extents of species distribution in SEA (including possible range expansions), 2–6% of species may have no suitable niche space in 2050–2080. When potential vegetation and climate changes were combined only 1% of species showed no changes in their predicted ranges by 2050. Although some species are projected to expand ranges, this may be ecologically impossible due to potential barriers to dispersal, especially for species with poor dispersal ability. Only 1–13% of species showed no projected reductions in their current range under bioclimatic scenarios. An effective way to facilitate range shift for dispersal‐limited species is to improve landscape connectivity. If current trends in environmental change continue and species cannot expand their ranges into new areas, then the majority of bat species in SEA may show decreases in range size and increased extinction risk within the next century.
Consequences of declining snow accumulation for water balance of mid‐latitude dry regions
Authors: Schlaepfer Daniel R. , Lauenroth William K. , Bradford John B.
Published: January 2012

Widespread documentation of positive winter temperature anomalies, declining snowpack and earlier snow melt in the Northern Hemisphere have raised concerns about the consequences for regional water resources as well as wildfire. A topic that has not been addressed with respect to declining snowpack is effects on ecosystem water balance. Changes in water balance dynamics will be particularly pronounced at low elevations of mid‐latitude dry regions because these areas will be the first to be affected by declining snow as a result of rising temperatures. As a model system, we used simulation experiments to investigate big sagebrush ecosystems that dominate a large fraction of the semiarid western United States. Our results suggest that effects on future ecosystem water balance will increase along a climatic gradient from dry, warm and snow‐poor to wet, cold and snow‐rich. Beyond a threshold within this climatic gradient, predicted consequences for vegetation switched from no change to increasing transpiration. Responses were sensitive to uncertainties in climatic prediction; particularly, a shift of precipitation to the colder season could reduce impacts of a warmer and snow‐poorer future, depending on the degree to which ecosystem phenology tracks precipitation changes. Our results suggest that big sagebrush and other similar semiarid ecosystems could decrease in viability or disappear in dry to medium areas and likely increase only in the snow‐richest areas, i.e. higher elevations and higher latitudes. Unlike cold locations at high elevations or in the arctic, ecosystems at low elevations respond in a different and complex way to future conditions because of opposing effects of increasing water‐limitation and a longer snow‐free season. Outcomes of such nonlinear interactions for future ecosystems will likely include changes in plant composition and productivity, dynamics of water balance, and availability of water resources.
Size increase in high elevation ground squirrels over the last century
Authors: Eastman Lindsey M. , Morelli Toni Lyn , Rowe Kevin C. , Conroy Chris J. , Moritz Craig
Published: January 2012

There is increasing evidence for morphological change in response to recent environmental change, but how this relates to fluctuations in geographic range remains unclear. We measured museum specimens from two time periods (1902–1950 and 2000–2008) that vary significantly in climate to assess if and how two high elevation contracting species of ground squirrels in the Sierra Nevada of California, Belding's ground squirrel (Urocitellus beldingi) and the golden‐mantled ground squirrel (Callospermophilus lateralis), and one lower elevation, stable species, the California ground squirrel (Otospermophilus beecheyi), have responded morphologically to changes over the last century. We measured skull length (condylobasal length), an ontogenetically more labile trait highly correlated with body size, and maxillary toothrow length, a more developmentally constrained trait predictive of skull shape. C. lateralis and U. beldingi, both obligate hibernators, have increased in body size, but have not changed in shape. In contrast, O. beecheyi, which only hibernates in parts of its range, has shown no significant change in either morphometric trait. The increase in body size in the higher elevation species, hypothesized to be a plastic effect due to a longer growing season and thus prolonged food availability, opposes the expected direction of selection for decreased body size under chronic warming. Our study supports that population contraction is related to physiological rather than nutritional constraints.
Simulating devil facial tumour disease outbreaks across empirically derived contact networks
Authors: Hamede Rodrigo , Bashford Jim , Jones Menna , McCallum Hamish
Published: January 2012

1. Understanding the nature and characteristics of contact heterogeneities is crucial for predicting the epidemic behaviour of infectious diseases. Nonetheless, few studies include contact heterogeneities when modelling disease outbreaks in wildlife, which differ in their population impact from human diseases.

2. We use empirical estimates of contact heterogeneities and network metrics to simulate outbreaks of devil facial tumour disease (DFTD), an extinction‐threatening infectious cancer. We incorporate tuneable algorithms, with a range of transmission rates and latent periods of DFTD, to grow devil population networks capable of reproducing observed aspects of devil ecology, demographic and seasonal‐based mixing preferences. The outputs of the network model are compared with a stochastic mean‐field model, in which every individual is equally likely to pass or acquire infection through time.

3. Our network model predicts a lower epidemic threshold for DFTD compared with the stochastic mean‐field model. While host extinction probabilities are similar in both models, the network model predicts faster devil extinction and higher DFTD extinction probabilities, particularly for intermediate levels of transmissibility.

4. While the time taken to devil extinction increases with the longer estimate of latent period, probabilities of both, disease and devil extinction, are greater with the shorter latent period. Host–pathogen coexistence is strictly subject to the longest plausible estimate of latent period and low transmissibility.

5.
Synthesis and applications. In the particular case of DFTD, incorporating observed host network structure has only a modest effect on the outcome of the host pathogen interaction. In general, however, non‐random network structure may have major implications for the management of wildlife diseases. Our results suggest that this is particularly likely for pathogens in which the probability of transmission given a contact is intermediate. Our approach provides a template for using empirically obtained data on contact networks to develop models to explore the extent to which network structure influences R0, the probability of extinction and the mean time until extinction.
Assessing the role of competition and stress: a critique of importance indices and the development of a new approach
Authors: Rees Mark , Childs Dylan Z. , Freckleton Robert P.
Published: January 2012

1. Many studies have explored how plant interactions vary along environmental gradients, and these relationships are fundamental to the many ideas in vegetation dynamics.

2. It has been argued that studies should differentiate between the intensity (absolute effect) and importance (relative effect) of a process, and several important indices have been presented in the literature.

3. We explore the mathematical properties of one of the most popular of these indices (Cimp) and demonstrate that it is (i) insensitive to the underlying ecology, (ii) highly constrained, so making statistical analysis difficult and (iii) can have more complex behaviour than the processes it seeks to summarise.

4. We demonstrate that the positive relationship between Cimp and productivity, which has been used to support the ideas of Grime, is entirely predictable without any information on competition and how it affects plant performance.

5. The properties of three other competition indices (ACI, RCI and lnRR) in relation to habitat productivity are briefly presented. ACI is closely related to Cimp and so shares many of its properties, see Summary point 3 above.

6. An alternative method of analysing variation in plant performance on environmental gradients is then presented. This approach, which is based on a variance decomposition, is easy to implement and has a simple biological interpretation.

7. Synthesis. We strongly discourage the use of heuristic indices in ecological research. The majority of the 50 or so indices that have been used in competition studies have been developed with little or no regard to underlying theory or models. However, it is possible to make predictions about how competition varies along gradients from models that translate into both qualitative and quantitative conditions and metrics, and we encourage authors to do this.
Relationships between spatio‐temporal environmental and genetic variation reveal an important influence of exogenous selection in a pupfish hybrid zone
Authors: CARSON EVAN W. , TOBLER MICHAEL , MINCKLEY W. L. , AINSWORTH RYAN J. , DOWLING THOMAS E.
Published: January 2012

The importance of exogenous selection in a natural hybrid zone between the pupfishesCyprinodon atrorusandCyprinodon bifasciatuswas tested via spatio‐temporal analyses of environmental and genetic change over winter, spring and summer for three consecutive years. A critical influence of exogenous selection on hybrid zone regulation was demonstrated by a significant relationship between environmental (salinity and temperature) and genetic (three diagnostic nuDNA loci) variation over space and time (seasons) in the Rio Churince system, Cuatro Ciénegas, Mexico. At sites environmentally more similar to parental habitats, the genetic composition of hybrids was stable and similar to the resident parental species, whereas complex admixtures of parental and hybrid genotypic classes characterized intermediate environments, as did the greatest change in allelic and genotypic frequencies across seasons. Within hybrids across the entire Rio Churince system, seasonal changes in allelic and genotypic frequencies were consistent with results from previous reciprocal transplant experiments, which showedC. bifasciatusto suffer high mortality (75%) when exposed to the habitat ofC. atrorusin winter (extreme temperature lows and variability) and summer (abrupt salinity change and extreme temperature highs and variability). Although unconfirmed, the distributional limits ofC. atrorusandC. atrorus‐like hybrids appear to be governed by similar constraints (predation or competition). The argument favouring evolutionary significance of hybridization in animals is bolstered by the results of this study, which links the importance of exogenous selection in a contemporary hybrid zone betweenC. atrorusandC. bifasciatusto previous demonstration of the long‐term evolutionary significance of environmental variation and introgression on the phenotypic diversification Cuatro CiénegasCyprinodon.
Palaeoclimate of the Late Jurassic of Portugal: comparison with the Western United States
Authors: MYERS TIMOTHY S. , TABOR NEIL J. , JACOBS LOUIS L. , MATEUS OCTÁVIO
Published: January 2012

Investigation of the palaeoclimatic conditions associated with Upper Jurassic strata in Portugal and comparison with published palaeoclimate reconstructions of the Upper Jurassic Morrison Formation in western North America provide important insights into the conditions that allowed two of the richest terrestrial faunas of this period to flourish. Geochemical analyses and observations of palaeosol morphology in the informally named Upper Jurassic Lourinhã formation of western Portugal indicate warm and wet palaeoclimatic conditions with strongly seasonal precipitation patterns. Palaeosol profiles are dominated by carbonate accumulations and abundant shrink‐swell (vertic) features that are both indicative of seasonal variation in moisture availability. The δ18OSMOW and δDSMOW values of phyllosilicates sampled from palaeosol profiles range from +22·4‰ to +22·7‰ and −53·0‰ to −37·3‰, respectively. These isotope values correspond to temperatures of formation between 32°C and 39°C ± 3°, with an average of 36°C, which suggest surface temperatures between 27°C and 34°C (average 31°C). On average, these surface temperature estimates are 1°C higher than the highest summer temperatures modelled for Late Jurassic Iberia using general circulation models. Elemental analysis of matrix material from palaeosol B‐horizons provides proxy (chemical index of alteration minus potassium) estimates of mean annual precipitation ranging from 766 to 1394 mm/year, with an average of approximately 1100 mm/year. Palaeoclimatic conditions during deposition of the Lourinhã formation are broadly similar to those inferred for the Morrison Formation, except somewhat wetter. Seasonal variation in moisture availability does not seem to have negatively impacted the ability of these environments to support rich and relatively abundant faunas. The similar climate between these two Late Jurassic terrestrial ecosystems is probably one of the factors which explains the similarity of their vertebrate faunas.
Construction of rice mini‐chromosomes by telomere‐mediated chromosomal truncation
Authors: Xu Chunhui , Cheng Zhukuan , Yu Weichang
Published: January 2012

Telomere truncation has been shown to be an efficient technology for the creation of mini‐chromosomes that can be used as artificial chromosome platforms for genetic engineering. Artificial chromosome‐based genetic engineering is considered to be superior to the existing techniques of randomized gene integration by Agrobacterium or biolistic‐mediated genetic transformation. It organizes multiple transgenes as a unique genetic linkage block for subsequent manipulations in breeding. Telomere truncation technology relies on three components: the telomere sequence that mediates chromosomal truncation, a selection marker that allows the selection of transgenic events, and a site‐specific recombination system that can be used to accept future genes into the mini‐chromosome by gene targeting. These elements are usually pre‐assembled before transformation, a process that is both time and labor consuming. We found in this research that the three elements could be mixed to transform plant cells in a biolistic transformation, and produced efficient chromosomal truncations and mini‐chromosomes in rice. This system will allow rapid construction of mini‐chromosomes with a flexible selection of resistant markers, site‐specific recombination systems and other desirable elements. In addition, a rice telotrisomic line was used as the starting material for chromosomal truncations. Mini‐chromosomes from the truncations of both the telocentric chromosome and other chromosomes were recovered. The mini‐chromosomes remained stable during 2 years of subculture. The construction of mini‐chromosomes in rice, an economically important crop, will provide a platform for future artificial chromosome‐based genetic engineering of rice for stacking multiple genes.
Genome‐wide identification of SOC1 and SVP targets during the floral transition in Arabidopsis
Authors: Tao Zhen , Shen Lisha , Liu Chang , Liu Lu , Yan Yuanyuan , Yu Hao
Published: January 2012

Floral transition in Arabidopsis is tightly controlled by complex genetic regulatory networks in response to endogenous and environmental flowering signals. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and SHORT VEGETATIVE PHASE (SVP), two key MADS‐domain transcription factors, perceive these signals and function as antagonistic flowering regulators. To understand how these factors mediate floral transition, we mapped in vivo binding sites of SOC1 and SVP using chromatin immunoprecipitation followed by hybridization to whole‐genome tiling arrays (ChIP‐chip). Genes that encoded proteins with transcription regulator activity and transcription factor activity were the most enriched groups of genes of those bound by SOC1 and SVP, which indicates their central roles in flowering regulatory networks. In combination with gene expression microarray studies, we further identified the genes whose expression was controlled directly by SOC1 or SVP. Among the common direct targets identified, APETALA2 (AP2)‐like genes that repress FT and SOC1 expression were down‐regulated by SOC1, but up‐regulated by SVP, revealing a complex feedback regulation among the key genes that determine the integration of flowering signals. SOC1 regulatory regions were also accessed by SOC1 itself and SVP, suggesting that self‐activation and repression by SVP contribute to the control of SOC1 expression. In addition, ChIP‐chip analysis demonstrated that miR156e and miR172a, which are involved in the regulation of AP2‐like genes, were direct targets of SOC1 and SVP, respectively. Taken together, these findings revealed that feedback regulatory loops mediated by SOC1 and SVP are essential components of the gene regulatory networks that underpin the integration of flowering signals during floral transition.
The opportunity to be misled in studies of sexual selection
Authors: JENNIONS M. D. , KOKKO H. , KLUG H.
Published: January 2012

It is a challenge to measure sexual selection because both stochastic events (chance) and deterministic factors (selection) generate variation in individuals’ reproductive success. Most researchers realize that random events (‘noise’) make it difficult to detect a relationship between a trait and mating success (i.e. the presence of sexual selection). There is, however, less appreciation of the dangers that arise if stochastic events vary systematically. Systematic variation makes variance‐based approaches to measuring the role of selection problematic. This is why measuring the opportunity for sexual selection (Is and Imates) is so vulnerable to misinterpretation. Although Is does not measure actual sexual selection (because it includes stochastic variation in mating/fertilization success) it is often implicitly assumed that it will be correlated with the actual strength of sexual selection. The hidden assumption is that random noise is randomly distributed across populations, species or the sexes. Here we present a simple numerical example showing why this practice is worrisome. Specifically, we show that chance variation in mating success is higher when there are fewer potential mates per individual of the focal sex [i.e. when the operational sex ratio (OSR), is more biased]. This will lead to the OSR covarying with Is even when the strength of sexual selection is unaffected by the OSR. This can generate false confidence in identifying factors that determine variation in the strength of sexual selection. We emphasize that in nature, even when sexual selection is strong, chance variation in mating success is still inevitable because the number of mates per individual is a discrete number. We hope that our worked example will clarify a recent debate about how best to measure sexual selection.
Bericht über zwei Fälle von Unteridefer‐Osteomyelitis durch Candida albicans: Report on two Cases of Mandibular Osteomyelitis Caused by Candida albicans
Authors: Meier J.
Published: January 2012

Zusammenfassung: Es wird über zwei Fälle von Unterkieferosteomyelitis berichtet, bei denen erst nach längerem therapierefraktärem Verlauf der Nachweis von Candida albicans gelang und die unter dreimonatiger Therapie mit Miconazol bzw. Ketoconazol zur Abheilung gebracht werden konnten. Osteomyelitiden durch Candida albicans sind extreme Raritäten. Bei weiterem z. T. kritiklosem Umgang mit Antibioth müssen solche Fälle zukünftig wohl häufiger erwartet werden. Erne Pilz‐(super‐)Infektion ist differentialdiagnostisch bei allen chronischen Osteomyelitiden in Betracht zu ziehen.

Summary: Two cases of mandibular osteomyelitis caused by Candida albicans are described. In both the diagnosis was made after a long unsuccessful antibacterial and surgical therapy. Only the administration of Miconazole respectively Ketoconazole lead to healing. Osteomyelitis caused by fungi is an extremely rare disease, the partly uncritical use of antibiotics will probably provide increasing numbers of mycotic infections of bone. In all cases of chronic osteomyelitis (super‐) infection by fungi has to be considered.
Effekt von Insulin auf die Keimschlauch‐und Myzel‐Bildung von Candida albicans: Effect of Insulin on Germ Tube and Mycelial Formation of Candida albicans
Authors: Nolting S. , Hagemeier H. H. , Fegeler K.
Published: January 2012

Zusammenfassung:

 Insuli fördert den Prolineinbau in die Candida albicans‐Zelle.

 Bei konstanten Insulin‐ und Prolin‐Konzentrationen, beeinflussen verschiedene Glucose‐Spiegel die Sproßzellen‐Myzel‐Transformation wesentlich.

 Hohe Glucose‐Konzentrationen induzieren Sproßzellen‐Morphologie.

Summary:

 Insulin enhances the uptake of proline in to the Candida albicans cell.

 At constant concentrations of insulin and proline different glucose levels will influence considerably the transformation of blastospores into mycelia.

 High glucose concentrations induce the blastospore morphology.
Adsorption of Candida Albicans from Blood of Infected Rats by Coated Charcoal*
Authors: Keller F. , Hennemann H. , Barz R.
Published: January 2012

Summary: The haemoperfusion technique was found to be an improved method to detect pathogens in the circulating blood. This could be shown in animal experiments with Candida albicans. The rates of positive results in the applied diagnostic haemoperfusion system are superior to the conventional venule technique in the critical range from 105 to 107 pathogens per animal. Scan electron microscopic pictures demonstrate that microorganisms can be adsorbed form the blood circulation of infected animals when blood culture are already negative.
Etiology of Dermatophytoses in Denmark Based on a Material of 1070 Cases: Die Ätiologie der Dermatophytosen in Dänemark nach einem Material von 1070 Fällen
Authors: Foged E. K. , Nielsen T.
Published: January 2012

Summary: To illustrate the actual distribution of dermatophytes in Denmark, 1070 patients with tineal affection diagnosed 1969–80 were divided into groups showing the relations between age, sex, localization and type of dermatophyte. The results are presented in four Tables.

Compared with previous Danish investigations T. rubrum was the most frequent cause of infection (54.5%). This dermatophyte was rarely diagnosed before 1947 at which time T. mentagrophytes was the most commom cause of tineal infection. In the present material isolation of T. mentagrophytes amounted to only 19.9%.

The zoophilic dermatophyte infections comprised about ten per cent and were mainly caused by M. canis and T. verrucosum.

From a general point of view the dermatophytic flora was in accordance with the conditions in Europe apart from a few exceptions.

Zusammenfassung: Um die aktuelle Verteilung der Dermatophyten in Dänemark zu illustrieren, wurde eine Aufstellung von 1070 Patienten mit Dermatophyteninfektionen aus der Zeitperiode von 1969 bis 1980 vorgenommen, die die Relation zwischen Alter, Geschlecht, Lokalisation und Dermatophytenart zeigt. Die Ergebnisse werden in 4 Tabellen angeführt.

Im Vergleich mit früheren dänischen Untersuchungen wurde T. rubrum als häufigste Ursache der Infektion (54,3%) gefunden. Dieser Dermatophyt war vor 1947 selten, als T. mentagrophytes die häufigste Ursache der Mykose war, dessen Häufigkeit jetzt in unserem Material nur 19,9 % beträgt.

Die zoophilen Dermatophytinfektionen machten etwa 10% aus und waren hauptsächlich von M. canis und T. vemcosum venusacht.

Von einzelnen Ausnahmen abgesehen, wurde gefunden, daß die Dermatophytflora generell gesehen mit den Verhältnissen im übrigen Europa übereinstimmte.