bluuebunny/crossref_metadata_2025_split huggingface dataset:
Second-Order Residual Analysis of Spatiotemporal Point Processes and Applications in Model Evaluation
Authors: Zhuang Jiancang 
Published: July 2006

SummaryThe paper gives first-order residual analysis for spatiotemporal point processes that is similar to the residual analysis that has been developed by Baddeley and co-workers for spatial point processes and also proposes principles for second-order residual analysis based on the viewpoint of martingales. Examples are given for both first- and second-order residuals. In particular, residual analysis can be used as a powerful tool in model improvement. Taking a spatiotemporal epidemic-type aftershock sequence model for earthquake occurrences as the base-line model, second-order residual analysis can be useful for identifying many features of the data that are not implied in the base-line model, providing us with clues about how to formulate better models.
Minimum Volume Confidence Regions for a Multivariate Normal Mean Vector
Authors: Efron Bradley 
Published: July 2006

SummarySince Stein's original proposal in 1962, a series of papers have constructed confidence regions of smaller volume than the standard spheres for the mean vector of a multivariate normal distribution. A general approach to this problem is developed here and used to calculate a lower bound on the attainable volume. Bayes and fiducial methods are involved in the calculation. Scheffé-type problems are used to show that low volume by itself does not guarantee favourable inferential properties.
Assessing the Finite Dimensionality of Functional Data
Authors: Hall Peter , Vial Céline 
Published: July 2006

SummaryIf a problem in functional data analysis is low dimensional then the methodology for its solution can often be reduced to relatively conventional techniques in multivariate analysis. Hence, there is intrinsic interest in assessing the finite dimensionality of functional data. We show that this problem has several unique features. From some viewpoints the problem is trivial, in the sense that continuously distributed functional data which are exactly finite dimensional are immediately recognizable as such, if the sample size is sufficiently large. However, in practice, functional data are almost always observed with noise, for example, resulting from rounding or experimental error. Then the problem is almost insolubly difficult. In such cases a part of the average noise variance is confounded with the true signal and is not identifiable. However, it is possible to define the unconfounded part of the noise variance. This represents the best possible lower bound to all potential values of average noise variance and is estimable in low noise settings. Moreover, bootstrap methods can be used to describe the reliability of estimates of unconfounded noise variance, under the assumption that the signal is finite dimensional. Motivated by these ideas, we suggest techniques for assessing the finiteness of dimensionality. In particular, we show how to construct a critical point V^q such that, if the distribution of our functional data has fewer than q−1 degrees of freedom, then we should be willing to assume that the average variance of the added noise is at least V^q. If this level seems too high then we must conclude that the dimension is at least q−1. We show that simpler, more conventional techniques, based on hypothesis testing, are generally not effective.
Correlograms for Non-Stationary Autoregressions
Authors: Nielsen Bent 
Published: July 2006

SummaryAnalysis of time series often involves correlograms and partial correlograms as graphical descriptions of temporal dependence. Two methods are available for computing these statistics: one based on autocorrelations and the other on scaled autocovariances. For a stationary time series the resulting plots are nearly identical. When it comes to time series exhibiting non-stationary features these methods can lead to very different results. This has two consequences: incorrect inferences can be drawn when confusing these concepts; better discrimination between stationary and non-stationarity is achieved when using autocorrelations instead of, or along with, the autocovariances which are commonly used in statistical software.
Modelling Beyond Regression Functions: An Application of Multimodal Regression to Speed–Flow Data
Authors: Einbeck Jochen , Tutz Gerhard 
Published: July 2006

SummaryFor speed–flow data, which are intensively discussed in transportation science, common nonparametric regression models of the type y = m(x)+noise turn out to be inadequate since simple functional models cannot capture the essential relationship between the predictor and response. Instead a more general setting is required, allowing for multifunctions rather than functions. The tool proposed is conditional modes estimation which, in the form of local modes, yields several branches that correspond to the local modes. A simple algorithm for computing the branches is derived. This is based on a conditional mean shift algorithm and is shown to work well in the application that is considered.
Analysis of Functional Status Transitions by Using a Semi-Markov Process Model in the Presence of Left-Censored Spells
Authors: Cai Liming , Schenker Nathaniel , Lubitz James 
Published: July 2006

SummaryTo analyse functional status transitions in the older population better, we fit a semi-Markov process model to data from the 1992–2002 Medicare Current Beneficiary Survey. We used an analogue of the stochastic EM algorithm to address the problem of left censoring of spells in longitudinal data. The iterative algorithm converged robustly under various initial values for the unobserved elapsed durations of spells in progress at base-line. Results on life expectancy and recovery from functional limitations based on the semi-Markov process model differ from those based on the traditional multistate life-table method. The proposed treatment of left-censored spells has the potential to expand the modelling capability that is available to researchers in fields where left censoring is a concern.
Spatial attention freezes during the attention blink
Authors: Dell'Acqua R. , Sessa P. , Jolicœur P. , Robitaille N. 
Published: July 2006

AbstractA variant of the rapid serial visual presentation paradigm was used to display sequentially two lateral sequences of stimuli, one to the left and one to the right of fixation, embedding two pairs of target stimuli, T1 and T2. T1 was composed of a pair of alphanumeric characters, and subjects had either to ignore T1 or to encode T1 for a delayed response. T2 was a lateral square of a prespecified color. The square had a small gap in one side, and the task for this stimulus was to report which side had the gap. When subjects were required to ignore T1, the T2‐locked ERP produced a clear N2pc, that is, a greater negativity at electrode sites contralateral to the position occupied by T2. This N2pc was followed by a sustained posterior contralateral negativity (SPCN). When subjects were required to monitor T1 in addition to T2, both the N2pc and the SPCN components amplitude depended on the difficulty of the task associated with T1. If T1 was composed of digits that had to be encoded for a delayed same/different judgment, both the N2pc and the SPCN components were entirely suppressed. Although attenuated, such components were present when T1 was composed of a pair of symbols that subjects could disregard. The results suggest that a set of mechanisms subserving the allocation of attention in the spatial domain, resulting in the N2pc, suffer significant interference from concurrent cognitive operations required to encode information into visual short‐term memory.
A reasoning bias revealed by electrodermal activity
Authors: Carbonnell Laurence , Vidal Franck , Sequeira Henrique , Caverni Jean‐Paul 
Published: July 2006

AbstractThe sufficiency of behavioral data supporting reasoning biases was challenged. Our objective was to test if physiological data could significantly support reasoning biases. Experiment 1: When performing a rule discovery task with feedback, participants sytematically gave the same response. This was not compatible with norms referring to a formal logic system, but was insufficient to conclude there was a reasoning bias. Only the knowledge of participants' expectations of feedback would merit this conclusion. Experiment 2: Participants' expectations were indexed by electrodermal activity. The results showed that when participants displayed the behavioral bias, they considered their responses to be correct and hence committed an error of logic. However, this error of logic did not prevent them from solving the task. This argues for a theory according to which human reasoning uses more economical strategies than the simple application of formal logical rules.
Agentic extraversion modulates the cardiovascular effects of the dopamine D2 agonist bromocriptine
Authors: Wacker Jan , Stemmler Gerhard 
Published: July 2006

AbstractA recent psychobiological theory postulates a dopaminergic basis for the agency facet of extraversion, leading to the prediction that this personality trait modulates the psychophysiological effects of dopaminergic drugs. A single dose of the dopamine D2 receptor agonist bromocriptine reduces blood pressure in healthy volunteers. However, it is currently unknown whether this hypotensive effect of bromocriptine is modulated by agentic extraversion. Therefore, we measured resting cardiovascular activation in groups of healthy male volunteers either high or low in agentic extraversion, either under bromocriptine (1.25 mg) or placebo. Focusing the analyses on activation components derived from 18 cardiovascular variables, we found that bromocriptine reduces alpha‐adrenergic activation in the sample as a whole, whereas the effects on beta‐adrenergic and cholinergic activation are modulated by agentic extraversion.
Molecules Involved in the Modulation of Rapid Cell Death in
Xanthomonas
Authors: Raju K. K. , Gautam Satyendra , Sharma Arun 
Published: July 2006

ABSTRACT

In earlier studies from this laboratory,
Xanthomonas campestris
pv. glycines was found to exhibit a nutrition stress-related postexponential rapid cell death (RCD). The RCD was exhibited in protein-rich media but not in starch or other minimal media. This RCD in
X. campestris
pv. glycines was found to display features similar to those of the programmed cell death (PCD) of eukaryotes. Results of the present study showed that the observed RCD in this organism is both positively and negatively regulated by small molecules. The amino acids glycine and
l
-alanine as well as the D isomers of valine, methionine, and threonine were found to induce the synthesis of an active caspase-3-like protein that was associated with the onset of RCD. Addition of pyruvate and citrate to the culture medium induced both the synthesis of active caspase-3-like protein and RCD. Higher levels of intracellular accumulation of pyruvate and citrate were also observed under conditions favoring RCD. On the other hand, dextrin and maltose, the hydrolytic products of starch, inhibited the synthesis of the caspase-3-like protein. Addition of glucose and cyclic AMP (cAMP) to the RCD-favoring medium prevented RCD. Glucose, cAMP, caffeine (a known inhibitor of a phosphodiesterase that breaks down cAMP), and forskolin (from the herb
Coleus forskholii
, known to activate the enzyme adenylate cyclase that forms cAMP) inhibited the caspase enzyme activity in vivo and consequently the RCD process. The addition of glucose and other inhibitors of RCD enhanced intracellular cAMP accumulation. This is the first report demonstrating the involvement of small molecules in the regulation of nutrition stress-related stationary-phase rapid cell death in
X. campestris
pv. glycines, which is programmed.
Identification and Characterization of anAzotobacter vinelandiiType I Secretion System Responsible for Export of the AlgE-Type Mannuronan C-5-Epimerases
Authors: Gimmestad Martin , Steigedal Magnus , Ertesvåg Helga , Moreno Soledad , Christensen Bjørn Erik , Espín Guadalupe , Valla Svein 
Published: July 2006

ABSTRACTAlginate is a linear copolymer of β-d-mannuronic acid and its C-5-epimer, α-l-guluronic acid. During biosynthesis, the polymer is first made as mannuronan, and various fractions of the monomers are then epimerized to guluronic acid by mannuronan C-5-epimerases. TheAzotobacter vinelandiigenome encodes a family of seven extracellular such epimerases (AlgE1 to AlgE7) which display motifs characteristic for proteins secreted via a type I pathway. Putative ATPase-binding cassette regions from the genome draft sequence of theA. vinelandiiOP strain and experimentally verified type I transporters from other species were compared. This analysis led to the identification of one putativeA. vinelandiitype I system (eexDEF). The corresponding genes were individually disrupted inA. vinelandiistrain E, and Western blot analysis using polyclonal antibodies against all AlgE epimerases showed that these proteins were present in wild-type culture supernatants but absent from theeexmutant supernatants. Consistent with this, the wild-type strain and theeexmutants produced alginate with about 20% guluronic acid and almost pure mannuronan (≤2% guluronic acid), respectively. TheA. vinelandiiwild type is able to enter a particular desiccation-tolerant resting stage designated cyst. At this stage, the cells are surrounded by a rigid coat in which alginate is a major constituent. Such a coat was formed by wild-type cells in a particular growth medium but was missing in theeexmutants. These mutants were also found to be unable to survive desiccation. The reason for this is probably that continuous stretches of guluronic acid residues are needed for alginate gel formation to take place.
The MgtC Virulence Factor of
Salmonella enterica
Serovar Typhimurium Activates Na
+
,K
+
-ATPase
Authors: Günzel Dorothee , Kucharski Lisa M. , Kehres David G. , Romero Michael F. , Maguire Michael E. 
Published: July 2006

ABSTRACT

The
mgtC
gene of
Salmonella enterica
serovar Typhimurium encodes a membrane protein of unknown function that is important for full virulence in the mouse. Since
mgtC
is part of an operon with
mgtB
which encodes a Mg
2+
-transporting P-type ATPase, MgtC was hypothesized to function in ion transport, possibly in Mg
2+
transport. Consequently, MgtC was expressed in
Xenopus laevis
oocytes, and its effect on ion transport was evaluated using ion selective electrodes. Oocytes expressing MgtC did not exhibit altered currents or membrane potentials in response to changes in extracellular H
+
, Mg
2+
, or Ca
2+
, thus ruling out a previously postulated function as a Mg
2+
/H
+
antiporter. However, addition of extracellular K
+
markedly hyperpolarized membrane potential instead of the expected depolarization. Addition of ouabain to block the oocyte Na
+
,K
+
-ATPase completely prevented hyperpolarization and restored the normal K
+
-induced depolarization response. These results suggested that the Na
+
,K
+
-ATPase was constitutively activated in the presence of MgtC resulting in a membrane potential largely dependent on Na
+
,K
+
-ATPase. Consistent with the involvement of Na
+
,K
+
-ATPase, oocytes expressing MgtC exhibited an increased rate of
86
Rb
+
uptake and had increased intracellular free [K
+
] and decreased free [Na
+
] and ATP. The free concentrations of Mg
2+
and Ca
2+
and cytosolic pH were unchanged, although the total intracellular Ca
2+
content was slightly elevated. These results suggest that the serovar Typhimurium MgtC protein may be involved in regulating membrane potential but does not directly transport Mg
2+
or another ion.
TheBacillus subtilisPrimosomal Protein DnaD Untwists Supercoiled DNA
Authors: Zhang Wenke , Allen Stephanie , Roberts Clive J. , Soultanas Panos 
Published: July 2006

ABSTRACTThe essentialBacillus subtilisDnaD and DnaB proteins have been implicated in the initiation of DNA replication. Recently, DNA remodeling activities associated with both proteins were discovered that could provide a link between global or local nucleoid remodeling and initiation of replication. DnaD forms scaffolds and opens up supercoiled plasmids without nicking to form open circular complexes, while DnaB acts as a lateral compaction protein. Here we show that DnaD-mediated opening of supercoiled plasmids is accompanied by significant untwisting of DNA. The net result is the conversion of writhe (Wr) into negative twist (Tw), thus maintaining the linking number (Lk) constant. These changes in supercoiling will reduce the considerable energy required to open up closed circular plectonemic DNA and may be significant in the priming of DNA replication. By comparison, DnaB does not affect significantly the supercoiling of plasmids. Binding of the DnaD C-terminal domain (Cd) to DNA is not sufficient to convert Wr into negative Tw, implying that the formation of scaffolds is essential for duplex untwisting. Overall, our data suggest that the topological effects of the two proteins on supercoiled DNA are different; DnaD opens up, untwists and converts plectonemic DNA to a more paranemic form, whereas DnaB does not affect supercoiling significantly and condenses DNA only via its lateral compaction activity. The significance of these findings in the initiation of DNA replication is discussed.
DNA Supercoiling and the Lrp Protein Determine the Directionality of
fim
Switch DNA Inversion in
Escherichia coli
K-12
Authors: Kelly Arlene , Conway Colin , Ó Cróinín Tadhg , Smith Stephen G. J. , Dorman Charles J. 
Published: July 2006

ABSTRACT

Site-specific recombinases of the integrase family usually require cofactors to impart directionality in the recombination reactions that they catalyze. The FimB integrase inverts the
Escherichia coli fim
switch (
fimS
) in the on-to-off and off-to-on directions with approximately equal efficiency. Inhibiting DNA gyrase with novobiocin caused inversion to become biased in the off-to-on direction. This directionality was not due to differential DNA topological distortion of
fimS
in the on and off phases by the activity of its resident P

fimA

promoter. Instead, the leucine-responsive regulatory (Lrp) protein was found to determine switching outcomes. Knocking out the
lrp
gene or abolishing Lrp binding sites 1 and 2 within
fimS
completely reversed the response of the switch to DNA relaxation. Inactivation of either Lrp site alone resulted in mild on-to-off bias, showing that they act together to influence the response of the switch to changes in DNA supercoiling. Thus, Lrp is not merely an architectural element organizing the
fim
invertasome, it collaborates with DNA supercoiling to determine the directionality of the DNA inversion event.
Diverse Flavonoids Stimulate NodD1 Binding tonodGene Promoters inSinorhizobium meliloti
Authors: Peck Melicent C. , Fisher Robert F. , Long Sharon R. 
Published: July 2006

ABSTRACTNodD1 is a member of the NodD family of LysR-type transcriptional regulators that mediates the expression of nodulation (nod) genes in the soil bacteriumSinorhizobium meliloti. Each species of rhizobia establishes a symbiosis with a limited set of leguminous plants. This host specificity results in part from a NodD-dependent upregulation ofnodgenes in response to a cocktail of flavonoids in the host plant's root exudates. To demonstrate that NodD is a key determinant of host specificity, we expressednodDgenes from different species of rhizobia in a strain ofS. melilotilacking endogenous NodD activity. We observed thatnodgene expression was initiated in response to distinct sets of flavonoid inducers depending on the source of NodD. To better understand the effects of flavonoids on NodD, we assayed the DNA binding activity ofS. melilotiNodD1 treated with the flavonoid inducer luteolin. In the presence of luteolin, NodD1 exhibited increased binding tonodgene promoters compared to binding in the absence of luteolin. Surprisingly, although they do not stimulatenodgene expression inS. meliloti, the flavonoids naringenin, eriodictyol, and daidzein also stimulated an increase in the DNA binding affinity of NodD1 tonodgene promoters. In vivo competition assays demonstrate that noninducing flavonoids act as competitive inhibitors of luteolin, suggesting that both inducing and noninducing flavonoids are able to directly bind to NodD1 and mediate conformational changes atnodgene promoters but that only luteolin is capable of promoting the downstream changes necessary fornodgene induction.
Crystal Structure of a Type III Pantothenate Kinase: Insight into the Mechanism of an Essential Coenzyme A Biosynthetic Enzyme Universally Distributed in Bacteria
Authors: Yang Kun , Eyobo Yvonne , Brand Leisl A. , Martynowski Dariusz , Tomchick Diana , Strauss Erick , Zhang Hong 
Published: July 2006

ABSTRACT

Pantothenate kinase (PanK) catalyzes the first step in the five-step universal pathway of coenzyme A (CoA) biosynthesis, a key transformation that generally also regulates the intracellular concentration of CoA through feedback inhibition. A novel PanK protein encoded by the gene
coaX
was recently identified that is distinct from the previously characterized type I PanK (exemplified by the
Escherichia coli coaA
-encoded PanK protein) and type II eukaryotic PanKs and is not inhibited by CoA or its thioesters. This type III PanK, or PanK-III, is widely distributed in the bacterial kingdom and accounts for the only known PanK in many pathogenic species, such as
Helicobacter pylori
,
Bordetella pertussis
, and
Pseudomonas aeruginosa
. Here we report the first crystal structure of a type III PanK, the enzyme from
Thermotoga maritima
(PanK
Tm
), solved at 2.0-Å resolution. The structure of PanK
Tm
reveals that type III PanKs belong to the acetate and sugar kinase/heat shock protein 70/actin (ASKHA) protein superfamily and that they retain the highly conserved active site motifs common to all members of this superfamily. Comparative structural analysis of the PanK
Tm
active site configuration and mutagenesis of three highly conserved active site aspartates identify these residues as critical for PanK-III catalysis. Furthermore, the analysis also provides an explanation for the lack of CoA feedback inhibition by the enzyme. Since PanK-III adopts a different structural fold from that of the
E. coli
PanK—which is a member of the “P-loop kinase”superfamily—this finding represents yet another example of convergent evolution of the same biological function from a different protein ancestor.
Similarities and Differences in Interactions of the Activity-Enhancing Chemoreceptor Pentapeptide with the Two Enzymes of Adaptational Modification
Authors: Lai Wing-Cheung , Barnakova Ludmila A. , Barnakov Alexander N. , Hazelbauer Gerald L. 
Published: July 2006

ABSTRACT

Sensory adaptation and chemotaxis by
Escherichia coli
require a specific pentapeptide at the chemoreceptor carboxyl terminus. This sequence binds the two enzymes of receptor adaptational modification, enhancing catalysis, but with different binding features and mechanisms. We investigated the relative importance of each pentapeptide side chain for the two enhancing interactions.