bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positive Selection on Transposase Genes of Insertion Sequences in the
Crocosphaera watsonii
Genome
Authors: Mes Ted H. M. , Doeleman Marije 
Published: October 2006

ABSTRACT

Insertion sequences (ISs) are mobile elements that are commonly found in bacterial genomes. Here, the structural and functional diversity of these mobile elements in the genome of the cyanobacterium
Crocosphaera watsonii
WH8501 is analyzed. The number, distribution, and diversity of nucleotide and amino acid stretches with similarity to the transposase gene of this IS family suggested that this genome harbors many functional as well as truncated IS fragments. The selection pressure acting on full-length transposase open reading frames of these ISs suggested (i) the occurrence of positive selection and (ii) the presence of one or more positively selected codons. These results were obtained using three data sets of transposase genes from the same IS family that were collected based on the level of amino acid similarity, the presence of an inverted repeat, and the number of sequences in the data sets. Neither recombination nor ribosomal frameshifting, which may interfere with the selection analyses, appeared to be important forces in the transposase gene family. Some positively selected codons were located in a conserved domain, suggesting that these residues are functionally important. The finding that this type of selection acts on IS-carried genes is intriguing, because although ISs have been associated with the adaptation of the bacterial host to new environments, this has typically been attributed to transposition or transformation, thus involving different genomic locations. Intragenic adaptation of IS-carried genes identified here may constitute a novel mechanism associated with bacterial diversification and adaptation.
The “Special Effect” of Case Mixing on Word Identification: Neuropsychological and Transcranial Magnetic Stimulation Studies Dissociating Case Mixing from Contrast Reduction
Authors: Braet Wouter , Humphreys Glyn 
Published: October 2006

Abstract
We present neuropsychological and transcranial magnetic stimulation (TMS) evidence with normal readers, that the effects of case mixing and contrast reduction on word identification are qualitatively different. Lesions and TMS applied to the right parietal lobe selectively disrupted the identification of mixed relative to single-case stimuli. Bilateral lesions and TMS applied to the occipital cortex selectively disrupted the identification of low-contrast words. These data suggest that different visual distortions (case mixing, contrast reduction) exert different effects on reading, modulated by contrasting brain regions. Case mixing is a “special” distortion and involves the recruitment of processes that are functionally distinct, and dependent on different regions in the brain, from those required to deal with contrast reduction.
Auditory Language Comprehension in Children with Developmental Dyslexia: Evidence from Event-related Brain Potentials
Authors: Sabisch B. , Hahne A. , Glass E. , von Suchodoletz W. , Friederici A. D. 
Published: October 2006

AbstractIn the present study, event-related brain potentials (ERPs) were used to compare auditory sentence comprehension in 16 children with developmental dyslexia (age 9–12 years) and unimpaired controls matched on age, sex, and nonverbal intelligence. Passive sentences were presented, which were either correct or contained a syntactic violation (phrase structure) or a semantic violation (selectional restriction). In an overall sentence correctness judgment task, both control and dyslexic children performed well. In the ERPs, control children and dyslexic children demonstrated a similar N400 component for the semantic violation. For the syntactic violation, control children demonstrated a combined pattern, consisting of an early starting bilaterally distributed anterior negativity and a late centro-parietal positivity (P600). Dyslexic children showed a different pattern that is characterized by a delayed left lateralized anterior negativity, followed by a P600. These data indicate that dyslexic children do not differ from unimpaired controls with respect to semantic integration processes (N400) or controlled processes of syntactic reanalyses (P600) during auditory sentence comprehension. However, early and presumably highly automatic processes of phrase structure building reflected in the anterior negativity are delayed in dyslexic children. Moreover, the differences in hemispheric distribution of the syntactic negativity indicate different underlying processes in dyslexic children and controls. The bilateral distribution in controls suggests an involvement of right hemispherically established prosodic processes in addition to the left hemispherically localized syntactic processes, supporting the view that prosodic information may be used to facilitate syntactic processing during normal comprehension. The left hemispheric distribution observed for dyslexic children, in contrast, suggests that these children do not rely on information about the prosodic contour during auditory sentence comprehension as much as controls do. This finding points toward a phonological impairment in dyslexic children that might hamper the development of syntactic processes.
Repetitive Transcranial Magnetic Stimulation Dissociates Working Memory Manipulation from Retention Functions in the Prefrontal, but not Posterior Parietal, Cortex
Authors: Postle Bradley R. , Ferrarelli Fabio , Hamidi Massihullah , Feredoes Eva , Massimini Marcello , Peterson Michael , Alexander Andrew , Tononi Giulio 
Published: October 2006

Abstract
Understanding the contributions of the prefrontal cortex (PFC) to working memory is central to understanding the neural bases of high-level cognition. One question that remains controversial is whether the same areas of the dorsolateral PFC (dlPFC) that participate in the manipulation of information in working memory also contribute to its short-term retention (STR). We evaluated this question by first identifying, with functional magnetic resonance imaging (fMRI), brain areas involved in manipulation. Next, these areas were targeted with repetitive transcranial magnetic stimulation (rTMS) while subjects performed tasks requiring only the STR or the STR plus manipulation of information in working memory. fMRI indicated that manipulation-related activity was independent of retention-related activity in both the PFC and superior parietal lobule (SPL). rTMS, however, yielded a different pattern of results. Although rTMS of the dlPFC selectively disrupted manipulation, rTMS of the SPL disrupted manipulation and STR to the same extent. rTMS of the postcentral gyrus (a control region) had no effect on performance. The implications of these results are twofold. In the PFC, they are consistent with the view that this region contributes more importantly to the control of information in working memory than to its STR. In the SPL, they illustrate the importance of supplementing the fundamentally correlational data from neuroimaging with a disruptive method, which affords stronger inference about structure-function relations.
Transverse Patterning and Human Amnesia
Authors: Rickard Timothy C. , Verfaellie Mieke , Grafman Jordan 
Published: October 2006

AbstractThe transverse patterning (TP) task (A+ B−, B+ C−, C+ A−) has played a central role in testing the hypothesis that medial-temporal (and, in particular, hippocampal) brain damage selectively impairs learning on at least some classes of configural (i.e., nonlinear) learning tasks. Results in the animal and human literature generally support that hypothesis. Reed and Squire [Impaired transverse patterning in human amnesia is a special case of impaired memory for two-choice discrimination tasks. Behavioral Neuroscience, 113, 3–9, 1999], however, advanced an alternative account in which impaired TP performance in amnesia reflects a generic scaling artifact arising from the greater difficulty of the TP task compared to the elemental (i.e., linear) control task that is typically used. We begin with a critique of Reed and Squire, countering their conceptual arguments and showing that their results, when analyzed appropriately, support the configural deficit hypothesis. We then report results from eight new amnesic patients and controls on an improved version of the TP task. Despite substantial practice, accuracy of patients with bilateral hippocampal damage due to anoxia reached and maintained an asymptote of only 54% correct, well below the maximum accuracy obtainable (67%) in the absence of configural learning. A patient with selective bilateral damage to the anterior thalamic nuclei exhibited a TP accuracy asymptote that was near 67%, a pattern of two out of three correct consecutive trials, and a pattern of nearly always answering correctly for two of the three TP item pairs. These results are consistent with a set of unique and parameter-free predictions of the configural deficit hypothesis.
Formal Leadership in Multilateral Negotiations: A Rational Institutionalist Theory
Authors: Tallberg Jonas 
Published: October 2006

AbstractThe exercise of leadership by the chairs of multilateral negotiations has so far received limited systematic attention in scholarship on international cooperation. This article addresses this gap by presenting a rational institutionalist theory of formal leadership that provides answers to three central questions: Why do states delegate powers of process control to the chairmanship of international negotiations? What are the power resources of formal leaders? And when, why and how do negotiation chairs wield influence over the outcomes of multilateral bargaining? The theory suggests that chairmanships are empowered to fulfil functions of agenda management, brokerage, and representation in international bargaining; identifies procedural control and privileged information as essential power resources of negotiation chairs; and isolates the conditions under which formal leaders shape the efficiency and distributional implications of multilateral bargaining. The article ends by outlining an alternative theoretical approach to formal leadership, drawn from sociological institutionalism.
The Presidency: The Role(s) of the Chair in European Union Negotiations
Authors: Elgström Ole 
Published: October 2006

AbstractUsing role theory as its analytical basis, this article delineates and analyses the specific characteristics of the Chair in the European Union (EU). The focus is thus on the EU Council Presidency and on how expectations surrounding the office impact upon its performance as administrator, agenda manager, broker, leader and representative. The EU's institutional design is marked by a rotating Presidency, by relatively short Presidency periods and by a mix of unanimity and majority voting. These traits influence the ways in which the Chair performs its role. The major argument is, however, that existing structurally based expectations of the Presidency's role (that is, expectations of neutrality and impartiality, of effectiveness and of consensus-seeking) interact with the particular role conceptions that are brought to the office by individual member states to produce both common features and variety in role performance. Empirical illustrations are taken from recent EU Presidencies to highlight continuity and fluctuation in Presidency performances.
Parameters of the Chairmanship's Effectiveness: The Case of the UN Security Council
Authors: Blavoukos Spyros , Tsakonas Panayotis , Bourantonis Dimitris 
Published: October 2006

AbstractThe article discusses the parameters conditioning the chair's effectiveness in international multilateral negotiations. Building on existing accounts of Presidential functions, an analytical typology of these parameters is provided, elaborating on the direction and magnitude of their impact. Conditioning parameters are clustered into three categories: the broader international environment in which the chair operates and the issues with which (s)he is called to deal; organization-specific features of an institutional and political nature; and the chair's personal skills and country-of-origin attributes. The potential for effect of these parameters is illustrated by reference to the chairmanship of the UN Security Council (SC). The origins, institutional features and main tasks of the Council are discussed, as well as the role of its chair as an agenda manager and broker. It is argued that the SC President's role well exceeds the formal tasks that are stipulated in the Rules of Procedure. Although mainly procedural in nature, these tasks may have important political implications, stressing the informal component of Presidential intervention. The conditioning parameters identified have a catalytic impact upon and account for the great variance in SC chair performance and the effectiveness of the chair's intervention.
Diagnosis of Variability and Trends in a Global Precipitation Dataset Using a Physically Motivated Statistical Model
Authors: Sapiano M. R. P. , Stephenson D. B. , Grubb H. J. , Arkin P. A. 
Published: October 2006

AbstractA physically motivated statistical model is used to diagnose variability and trends in wintertime (October–March) Global Precipitation Climatology Project (GPCP) pentad (5-day mean) precipitation. Quasigeostrophic theory suggests that extratropical precipitation amounts should depend multiplicatively on the pressure gradient, saturation specific humidity, and the meridional temperature gradient. This physical insight has been used to guide the development of a suitable statistical model for precipitation using a mixture of generalized linear models: a logistic model for the binary occurrence of precipitation and a Gamma distribution model for the wet day precipitation amount.The statistical model allows for the investigation of the role of each factor in determining variations and long-term trends. Saturation specific humidity qs has a generally negative effect on global precipitation occurrence and with the tropical wet pentad precipitation amount, but has a positive relationship with the pentad precipitation amount at mid- and high latitudes. The North Atlantic Oscillation, a proxy for the meridional temperature gradient, is also found to have a statistically significant positive effect on precipitation over much of the Atlantic region. Residual time trends in wet pentad precipitation are extremely sensitive to the choice of the wet pentad threshold because of increasing trends in low-amplitude precipitation pentads; too low a choice of threshold can lead to a spurious decreasing trend in wet pentad precipitation amounts. However, for not too small thresholds, it is found that the meridional temperature gradient is an important factor for explaining part of the long-term trend in Atlantic precipitation.
Is the Recent Increasing Trend of Rainfall over Northeast Brazil Related to Sub-Saharan Drought?
Authors: Rao V. Brahmananda , Giarolla Emanuel , Kayano Mary T. , Franchito Sergio H. 
Published: October 2006

Abstract
In recent years, there has been an increase in rainfall over northeast Brazil (Nordeste), while over the sub-Saharan region there has been a drought. The correlation coefficients between the 11-yr running means of the rainfall series over the two regions are significant (at the 95% confidence level by a two-sided t test), suggesting that both trends are related. The rainfall variations over the two regions are connected to the position of the intertropical convergence zone (ITCZ) over the Atlantic. A more southward (northward) position of the ITCZ is favorable for higher than normal rainfall over Nordeste (sub-Sahara). The correlation coefficient between the position of the ITCZ over the Atlantic and the rainfall over Nordeste (sub-Sahara) is negative (positive) and highly significant, reaching values over 0.9. Thus, this study suggests that a more southward than normal location of the ITCZ in the Atlantic may be the cause for the recent increasing (decreasing) trend of rainfall over Nordeste (sub-Sahara).
Constraining Climate Sensitivity from the Seasonal Cycle in Surface Temperature
Authors: Knutti Reto , Meehl Gerald A. , Allen Myles R. , Stainforth David A. 
Published: October 2006

Abstract
The estimated range of climate sensitivity has remained unchanged for decades, resulting in large uncertainties in long-term projections of future climate under increased greenhouse gas concentrations. Here the multi-thousand-member ensemble of climate model simulations from the climateprediction.net project and a neural network are used to establish a relation between climate sensitivity and the amplitude of the seasonal cycle in regional temperature. Most models with high sensitivities are found to overestimate the seasonal cycle compared to observations. A probability density function for climate sensitivity is then calculated from the present-day seasonal cycle in reanalysis and instrumental datasets. Subject to a number of assumptions on the models and datasets used, it is found that climate sensitivity is very unlikely (5% probability) to be either below 1.5–2 K or above about 5–6.5 K, with the best agreement found for sensitivities between 3 and 3.5 K. This range is narrower than most probabilistic estimates derived from the observed twentieth-century warming. The current generation of general circulation models are within that range but do not sample the highest values.
Robustness of Tropospheric Temperature Trends from MSU Channels 2 and 4
Authors: Johanson Celeste M. , Fu Qiang 
Published: October 2006

Abstract
Tropospheric temperature trends based on Microwave Sounding Unit (MSU) channel 2 data are susceptible to contamination from strong stratospheric cooling. Recently, Fu et al. devised a method of removing the stratospheric contamination by linearly combining data from MSU channels 2 and 4. In this study the sensitivity of the weights of the two channels in the retrieval algorithm for the tropospheric temperatures to the choice of period of record used in the analysis and to the choice of training dataset is examined. The weights derived using monthly temperature anomalies are within about 10% of those obtained by Fu et al. irrespective of the choice of analysis period or training dataset. The trend errors in the retrieved global-mean tropospheric temperatures tested using two independent radiosonde datasets are less than about 0.01 K decade−1 for all time periods of 25 yr or longer with different starting and ending years during 1958–2004. It is found that the retrievals are more robust if they are interpreted in terms of the layer-mean temperature for the entire troposphere, rather than the mean of the 850–300-hPa layer. Because large spurious jumps remain in the reanalyses, especially prior to 1979, one should be cautious when using them as training datasets and in testing the trend errors.
Changes in Spread and Predictability Associated with ENSO in an Ensemble Coupled GCM
Authors: Wu Renguang , Kirtman Ben P. 
Published: October 2006

Abstract
The present study documents the influence of El Niño and La Niña events on the spread and predictability of rainfall, surface pressure, and 500-hPa geopotential height, and contrasts the relative contribution of signal and noise changes to the predictability change based on a long-term integration of an interactive ensemble coupled general circulation model. It is found that the pattern of the El Niño–Southern Oscillation (ENSO)-induced noise change for rainfall follows closely that of the corresponding signal change in most of the tropical regions. The noise for tropical Pacific surface pressure is larger (smaller) in regions of lower (higher) mean pressure. The ENSO-induced noise change for 500-hPa height displays smaller spatial scales compared to and has no systematic relationship with the signal change.
The predictability for tropical rainfall and surface pressure displays obvious contrasts between the summer and winter over the Bay of Bengal, the western North Pacific, and the tropical southwestern Indian Ocean. The predictability for tropical 500-hPa height is higher in boreal summer than in boreal winter. In the equatorial central Pacific, the predictability for rainfall is much higher in La Niña years than in El Niño years. This occurs because of a larger percent reduction in the amplitude of noise compared to the percent decrease in the magnitude of signal from El Niño to La Niña years. A consistent change is seen in the predictability for surface pressure near the date line. In the western North and South Pacific, the predictability for boreal winter rainfall is higher in El Niño years than in La Niña years. This is mainly due to a stronger signal in El Niño years compared to La Niña years. The predictability for 500-hPa height increases over most of the Tropics in El Niño years. Over western tropical Pacific–Australia and East Asia, the predictability for boreal winter surface pressure and 500-hPa height is higher in El Niño years than in La Niña years. The predictability change for 500-hPa height is primarily due to the signal change.
Relationship between Shortwave Cloud Radiative Forcing and Local Meteorological Variables Compared in Observations and Several Global Climate Models
Authors: Stowasser Markus , Hamilton Kevin 
Published: October 2006

Abstract
The relations between local monthly mean shortwave cloud radiative forcing and aspects of the resolved-scale meteorological fields are investigated in hindcast simulations performed with 12 of the global coupled models included in the model intercomparison conducted as part of the preparation for Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4). In particular, the connection of the cloud forcing over tropical and subtropical ocean areas with resolved midtropospheric vertical velocity and with lower-level relative humidity are investigated and compared among the models. The model results are also compared with observational determinations of the same relationships using satellite data for the cloud forcing and global reanalysis products for the vertical velocity and humidity fields. In the analysis the geographical variability in the long-term mean among all grid points and the interannual variability of the monthly mean at each grid point are considered separately. The shortwave cloud radiative feedback (SWCRF) plays a crucial role in determining the predicted response to large-scale climate forcing (such as from increased greenhouse gas concentrations), and it is thus important to test how the cloud representations in current climate models respond to unforced variability.
Overall there is considerable variation among the results for the various models, and all models show some substantial differences from the comparable observed results. The most notable deficiency is a weak representation of the cloud radiative response to variations in vertical velocity in cases of strong ascending or strong descending motions. While the models generally perform better in regimes with only modest upward or downward motions, even in these regimes there is considerable variation among the models in the dependence of SWCRF on vertical velocity. The largest differences between models and observations when SWCRF values are stratified by relative humidity are found in either very moist or very dry regimes. Thus, the largest errors in the model simulations of cloud forcing are prone to be in the western Pacific warm pool area, which is characterized by very moist strong upward currents, and in the rather dry regions where the flow is dominated by descending mean motions.