bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Analysis of Long-Term Experiments
Authors: Loughin Thomas M. , Roediger Mollie Poehlman , Milliken George A. , Schmidt John P. 
Published: July 2006

SummaryLong-term experiments are commonly used tools in agronomy, soil science and other disciplines for comparing the effects of different treatment regimes over an extended length of time. Periodic measurements, typically annual, are taken on experimental units and are often analysed by using customary tools and models for repeated measures. These models contain nothing that accounts for the random environmental variations that typically affect all experimental units simultaneously and can alter treatment effects. This added variability can dominate that from all other sources and can adversely influence the results of a statistical analysis and interfere with its interpretation. The effect that this has on the standard repeated measures analysis is quantified by using an alternative model that allows for random variations over time. This model, however, is not useful for analysis because the random effects are confounded with fixed effects that are already in the repeated measures model. Possible solutions are reviewed and recommendations are made for improving statistical analysis and interpretation in the presence of these extra random variations.
Multiple Randomizations
Authors: Brien C. J. , Bailey R. A. 
Published: July 2006

SummaryMultitiered experiments are characterized by involving multiple randomizations, in a sense that we make explicit. We compare and contrast six types of multiple randomizations, using a wide range of examples, and discuss their use in designing experiments. We outline a system of describing the randomizations in terms of sets of objects, their associated tiers and the factor nesting, using randomization diagrams, which give a convenient and readily assimilated summary of an experiment's randomization. We also indicate how to formulate a randomization-based mixed model for the analysis of data from such experiments.
Free-Knot Spline Smoothing for Functional Data
Authors: Gervini Daniel 
Published: July 2006

SummaryThe paper introduces free-knot regression spline estimators for the mean and the variance components of a sample of curves. The asymptotic distribution of the mean estimator is derived, and asymptotic confidence bands are constructed. A comparative simulation study shows that free-knot splines estimate salient features of the functions (such as sharp peaks) more accurately than smoothing splines. This adaptive behaviour is also illustrated by an analysis of weather data.
Flexible Modelling of Neuron Firing Rates Across Different Experimental Conditions: An Application to Neural Activity in the Prefrontal Cortex During a Discrimination Task
Authors: Cadarso-Suárez Carmen , Roca-Pardiñas Javier , Molenberghs Geert , Faes Christel , Nácher Verónica , Ojeda Sabiela , Acuña Carlos 
Published: July 2006

SummaryIn many electrophysiological experiments the main objectives include estimation of the firing rate of a single neuron, as well as a comparison of its temporal evolution across different experimental conditions. To accomplish these two goals, we propose a flexible approach based on the logistic generalized additive model including condition-by-time interactions. If an interaction of this type is detected in the model, we then establish that the use of the temporal odds ratio curves is very useful in discriminating between the conditions under which the firing probability is higher. Bootstrap techniques are used for testing for interactions and constructing pointwise confidence bands for the true odds ratio curves. Finally, we apply the new methodology to assessing relationships between neural response and decision-making in movement-selective neurons in the prefrontal cortex of behaving monkeys.
High Dimensional Multivariate Mixed Models for Binary Questionnaire Data
Authors: Fieuws Steffen , Verbeke Geert , Boen Filip , Delecluse Christophe 
Published: July 2006

SummaryQuestionnaires that are used to measure the effect of an intervention often consist of different sets of items, each set possibly measuring another concept. Mixed models with set-specific random effects are a flexible tool to model the different sets of items jointly. However, computational problems typically arise as the number of sets increases. This is especially true when the random-effects distribution cannot be integrated out analytically, as with mixed models for binary data. A pairwise modelling strategy, in which all possible bivariate mixed models are fitted and where inference follows from pseudolikelihood theory, has been proposed as a solution. This approach has been applied to assess the effect of physical activity on psychocognitive functioning, the latter measured by a battery of questionnaires.
A Generalized Estimating Equation Method for Fitting Autocorrelated Ordinal Score Data with an Application in Horticultural Research
Authors: Parsons N. R. , Edmondson R. N. , Gilmour S. G. 
Published: July 2006

SummaryGeneralized estimating equations for correlated repeated ordinal score data are developed assuming a proportional odds model and a working correlation structure based on a first-order autoregressive process. Repeated ordinal scores on the same experimental units, not necessarily with equally spaced time intervals, are assumed and a new algorithm for the joint estimation of the model regression parameters and the correlation coefficient is developed. Approximate standard errors for the estimated correlation coefficient are developed and a simulation study is used to compare the new methodology with existing methodology. The work was part of a project on post-harvest quality of pot-plants and the generalized estimating equation model is used to analyse data on poinsettia and begonia pot-plant quality deterioration over time. The relationship between the key attributes of plant quality and the quality and longevity of ornamental pot-plants during shelf and after-sales life is explored.
Ethnic differences in allopregnanolone concentrations in women during rest and following mental stress
Authors: Girdler Susan S. , Beth Mechlin M. , Light Kathleen C. , Leslie Morrow A. 
Published: July 2006

AbstractThe neuroactive steroid allopregnanolone (ALLO) is stress sensitive, negatively modulates the HPA axis, and has been implicated in mood disorders. We examined ethnic differences in plasma ALLO at rest and following mental stress in African American (AA) men (n=21) and women (n=24) and non‐Hispanic White men (n=24) and women (n=25). Overall, AA women had lower ALLO concentrations than non‐Hispanic White women (p<.05), especially following mental stress (p<.01). Only 20% of AA women showed the expected stress‐induced increase in ALLO compared with 59% of non‐Hispanic White women (p<.01). No ethnic differences were seen in men. For both ethnic groups, poststress ALLO was negatively correlated with poststress cortisol (p<.05). Results are interpreted to reflect dysregulation in ALLO mechanisms in AA women and may have implications for ethnic differences in mood disorders.
Responses to the Trier Social Stress Test (TSST) in single versus grouped participants
Authors: Childs Emma , Vicini Lisa Marie , De Wit Harriet 
Published: July 2006

AbstractPsychological stress plays an important role in psychopathologies. Laboratory methods have been designed to study stress responses in health and disease. The Trier Social Stress Test is a procedure designed to induce psychosocial stress, but the method is costly in terms of time and personnel requirements. We investigated whether conducting the task with multiple participants influenced cortisol, heart rate, and subjective responses and improved efficiency. Healthy male and female volunteers (N=32) performed the task individually or in groups. Salivary cortisol, anxiety, and jitteriness increased and calmness decreased similarly in both conditions. Grouped participants exhibited greater peak increases in heart rate than those who performed individually. The findings suggest that the TSST may be conducted with multiple participants without significantly affecting subjective and cortisol responses to the task.
The impact of emotions on the sensory and affective dimension of perceived dyspnea
Authors: Von Leupoldt Andreas , Mertz Corinna , Kegat Sarah , Burmester Swantje , Dahme Bernhard 
Published: July 2006

AbstractDyspnea is an impairing symptom in various diseases. Recent research has shown that the perception of dyspnea, like pain, consists of a sensory (intensity) and an affective (unpleasantness) dimension, but little is known about the specific impact of different emotions on these distinct dimensions. We therefore examined the impact of viewing affective picture series of positive, neutral, and negative valence on perceived dyspnea during resistive load breathing in healthy volunteers. Inspiratory time (Ti), breathing frequency (f), and oscillatory resistance (Ros) remained unchanged across conditions. Ratings for unpleasantness of dyspnea increased from positive to neutral to negative series, but ratings for intensity of dyspnea showed no changes. The results suggest that the affective dimension of the perception of dyspnea is particularly vulnerable to emotional influences, irrespective of objective lung function.
Attentional set mixing: Effects on target selection and selective response activation
Authors: Ruge Hannes , Stoet Gijsbert , Naumann Ewald 
Published: July 2006

AbstractPerformance is impaired under set mixing conditions that require frequent readjustments of attentional focus over an extended time period. We compared set repetitions within pure blocks (constant focus of attention) to physically identical repetitions within mixed blocks (changing focus of attention). The aim was to investigate how set mixing affects target selection, indexed by the N2pc component, and selective response activation, indexed by the lateralized readiness potential (LRP). We found that set mixing prolonged the evolution of the N2pc while leaving its onset unaffected. Impaired target selection indicated by the N2pc mixing effect also delayed the start of response planning indexed by an onset delay of the stimulus‐locked LRP, explaining one part of the behavioral mixing cost. A larger part of mixing cost could be attributed to a prolonged response planning phase, indexed by an earlier onset of the response‐locked LRP.
Trimeric Autotransporters Require Trimerization of the Passenger Domain for Stability and Adhesive Activity
Authors: Cotter Shane E. , Surana Neeraj K. , Grass Susan , St. Geme Joseph W. 
Published: July 2006

ABSTRACT

In recent years, structural studies have identified a number of bacterial, viral, and eukaryotic adhesive proteins that have a trimeric architecture. The prototype examples in bacteria are the
Haemophilus influenzae
Hia adhesin and the
Yersinia enterocolitica
YadA adhesin. Both Hia and YadA are members of the trimeric-autotransporter subfamily and are characterized by an internal passenger domain that harbors adhesive activity and a short C-terminal translocator domain that inserts into the outer membrane and facilitates delivery of the passenger domain to the bacterial surface. In this study, we examined the relationship between trimerization of the Hia and YadA passenger domains and the capacity for adhesive activity. We found that subunit-subunit interactions and stable trimerization are essential for native folding and stability and ultimately for full-level adhesive activity. These results raise the possibility that disruption of the trimeric architecture of trimeric autotransporters, and possibly other trimeric adhesins, may be an effective strategy to eliminate adhesive activity.
Control of Acetyl-Coenzyme A Synthetase (AcsA) Activity by Acetylation/Deacetylation without NAD
+
Involvement in
Bacillus subtilis
Authors: Gardner Jeffrey G. , Grundy Frank J. , Henkin Tina M. , Escalante-Semerena Jorge C. 
Published: July 2006

ABSTRACT

Posttranslational modification is an efficient mechanism for controlling the activity of structural proteins, gene expression regulators, and enzymes in response to rapidly changing physiological conditions. Here we report in vitro and in vivo evidence that the
acuABC
operon of the gram-positive soil bacterium
Bacillus subtilis
encodes a protein acetyltransferase (AcuA) and a protein deacetylase (AcuC), which may control the activity of acetyl-coenzyme A (CoA) synthetase (AMP-forming, AcsA) in this bacterium. Results from in vitro experiments using purified proteins show that AcsA is a substrate for the acetyl-CoA-dependent AcuA acetyltransferase. Mass spectrometry analysis of a tryptic digest of acetylated AcsA (AcsA
Ac
) identified residue Lys549 as the sole modification site in the protein. Unlike sirtuins, the AcuC protein did not require NAD
+
as cosubstrate to deacetylate AcsA
Ac
. The function of the putative AcuB protein remains unknown.
Characterization ofBacillus anthracis-Like Bacteria Isolated from Wild Great Apes from Côte d'Ivoire and Cameroon
Authors: Klee Silke R. , Özel Muhsin , Appel Bernd , Boesch Christophe , Ellerbrok Heinz , Jacob Daniela , Holland Gudrun , Leendertz Fabian H. , Pauli Georg , Grunow Roland , Nattermann Herbert 
Published: July 2006

ABSTRACTWe present the microbiological and molecular characterization of bacteria isolated from four chimpanzees and one gorilla thought to have died of an anthrax-like disease in Côte d'Ivoire and Cameroon. These isolates differed significantly from classicBacillus anthracisby the following criteria: motility, resistance to the gamma phage, and, for isolates from Cameroon, resistance to penicillin G. A capsule was expressed not only after induction by CO2and bicarbonate but also under normal growth conditions. Subcultivation resulted in beta-hemolytic activity and gamma phage susceptibility in some subclones, suggesting differences in gene regulation compared to classicB. anthracis. The isolates from Côte d'Ivoire and Cameroon showed slight differences in their biochemical characteristics and MICs of different antibiotics but were identical in all molecular features and sequences analyzed. PCR and Southern blot analyses confirmed the presence of both the toxin and the capsule plasmid, with sizes corresponding to theB. anthracisvirulence plasmids pXO1 and pXO2. Protective antigen was expressed and secreted into the culture supernatant. The isolates possessed variants of the Ba813 marker and the SG-749 fragment differing from that of classicB. anthracisstrains. Multilocus sequence typing revealed a close relationship of our atypical isolates with both classicB. anthracisstrains and two uncommonly virulentBacillus cereusandBacillus thuringiensisisolates. We propose that the newly discovered atypicalB. anthracisstrains share a common ancestor with classicB. anthracisor that they emerged recently by transfer of theB. anthracisplasmids to a strain of theB. cereusgroup.
The Stringent Response Is Required for
Helicobacter pylori
Survival of Stationary Phase, Exposure to Acid, and Aerobic Shock
Authors: Mouery Kyle , Rader Bethany A. , Gaynor Erin C. , Guillemin Karen 
Published: July 2006

ABSTRACT

The gastric pathogen
Helicobacter pylori
must adapt to fluctuating conditions in the harsh environment of the human stomach with the use of a minimal number of transcriptional regulators. We investigated whether
H. pylori
utilizes the stringent response, involving signaling through the alarmone (p)ppGpp, as a survival strategy during environmental stresses. We show that the
H. pylori
homologue of the bifunctional (p)ppGpp synthetase and hydrolase SpoT is responsible for all cellular (p)ppGpp production in response to starvation conditions. Furthermore, the
H. pylori spoT
gene complements the growth defect of
Escherichia coli
mutants lacking (p)ppGpp. An
H. pylori spoT
deletion mutant is impaired for stationary-phase survival and undergoes a premature transformation to a coccoid morphology. In addition, the
spoT
deletion mutant is unable to survive specific environmental stresses, including aerobic shock and acid exposure, which are likely to be encountered by this bacterium during infection and transmission.
Transcriptional Profile of
Haemophilus influenzae
: Effects of Iron and Heme
Authors: Whitby Paul W. , VanWagoner Timothy M. , Seale Thomas W. , Morton Daniel J. , Stull Terrence L. 
Published: July 2006

ABSTRACT

Haemophilus influenzae
requires either heme or a porphyrin and iron source for growth. Microarray studies of
H. influenzae
strain Rd KW20 identified 162 iron/heme-regulated genes, representing ∼10% of the genome, with ≥1.5-fold changes in transcription in response to iron/heme availability in vitro. Eighty genes were preferentially expressed under iron/heme restriction; 82 genes were preferentially expressed under iron/heme-replete conditions.
Mutational Analysis of the Promoter Recognized by
Chlamydia
and
Escherichia coli
σ
28
RNA Polymerase
Authors: Yu Hilda Hiu Yin , Di Russo Elizabeth G. , Rounds Megan A. , Tan Ming 
Published: July 2006

ABSTRACT

σ
28
RNA polymerase is an alternative RNA polymerase that has been postulated to have a role in developmental gene regulation in
Chlamydia
. Although a consensus bacterial σ
28
promoter sequence has been proposed, it is based on a relatively small number of defined promoters, and the promoter structure has not been systematically analyzed. To evaluate the sequence of the σ
28
-dependent promoter, we performed a comprehensive mutational analysis of the
Chlamydia trachomatis hctB
promoter, testing the effect of point substitutions on promoter activity. We defined a −35 element recognized by chlamydial σ
28
RNA polymerase that resembles the consensus −35 sequence. Within the −10 element, however, chlamydial σ
28
RNA polymerase showed a striking preference for a CGA sequence at positions −12 to −10 rather than the longer consensus −10 sequence. We also observed a strong preference for this CGA sequence by
Escherichia coli
σ
28
RNA polymerase, suggesting that this previously unrecognized motif is the critical component of the −10 promoter element recognized by σ
28
RNA polymerase. Although the consensus spacer length is 11 nucleotides (nt), we found that σ
28
RNA polymerase from both
Chlamydia
and
E. coli
transcribed a promoter with either an 11- or 12-nt spacer equally well. Altogether, we found very similar results for σ
28
RNA polymerase from
C. trachomatis
and
E. coli
, suggesting that promoter recognition by this alternative RNA polymerase is well conserved among bacteria. The preferred σ
28
promoter that we defined in the context of the
hctB
promoter is TAAAGwwy-n
11/12
-ryCGAwrn, where w is A or T, r is a purine, y is a pyrimidine, n is any nucleotide, and n
11/12
is a spacer of 11 or 12 nt.
Transcription of the
pst
Operon of
Clostridium acetobutylicum
Is Dependent on Phosphate Concentration and pH
Authors: Fischer Ralf-Jörg , Oehmcke Sonja , Meyer Uta , Mix Maren , Schwarz Katrin , Fiedler Tomas , Bahl Hubert 
Published: July 2006

ABSTRACT

The
pst
operon of
Clostridium acetobutylicum
ATCC 824 comprises five genes,
pstS
,
pstC
,
pstA
,
pstB
, and
phoU
, and shows a gene architecture identical to that of
Escherichia coli
. Deduced proteins are predicted to represent a high-affinity
p
hosphate-
s
pecific ABC (ATP-binding cassette)
t
ransport system (Pst) and a protein homologous to PhoU, a negative phosphate regulon regulator. We analyzed the expression patterns of the
pst
operon in P
i
-limited chemostat cultures during acid production at pH 5.8 or solvent production at pH 4.5 and in response to P
i
pulses. Specific mRNA transcripts were found only when external P
i
concentrations had dropped below 0.2 mM. Two specific transcripts were detected, a 4.7-kb polycistronic mRNA spanning the whole operon and a quantitatively dominating 1.2-kb mRNA representing the first gene,
pstS
. The mRNA levels clearly differed depending on the external pH. The amounts of the full-length mRNA detected were about two times higher at pH 5.8 than at pH 4.5. The level of
pstS
mRNA increased by a factor of at least 8 at pH 5.8 compared to pH 4.5 results. Primer extension experiments revealed only one putative transcription start point 80 nucleotides upstream of
pstS
. Thus, additional regulatory sites are proposed in the promoter region, integrating two different extracellular signals, namely, depletion of inorganic phosphate and the pH of the environment. After phosphate pulses were applied to a phosphate-limited chemostat we observed faster phosphate consumption at pH 5.8 than at pH 4.5, although higher optical densities were recorded at pH 4.5.
The FAD-Dependent Tricarballylate Dehydrogenase (TcuA) Enzyme of
Salmonella enterica
Converts Tricarballylate into
cis
-Aconitate
Authors: Lewis Jeffrey A. , Escalante-Semerena Jorge C. 
Published: July 2006

ABSTRACT

Tricarballylate is the causative agent of grass tetany, a ruminant disease characterized by acute magnesium deficiency. Tricarballylate toxicity has been attributed to its ability to chelate magnesium and to inhibit aconitase, a Krebs cycle enzyme. Neither the ruminant nor the normal rumen flora can catabolize tricarballylate to ameliorate its toxic effects. However, the gram-negative enterobacterium
Salmonella enterica
can use tricarballylate as a carbon and energy source, providing an opportunity to study the genes and enzymes required for tricarballylate catabolism. The tricarballylate utilization (
tcu
) genes are organized into two transcriptional units, i.e.,
tcuR
and
tcuABC
. Here, we report the initial biochemical analysis of TcuA. TcuA catalyzed the oxidation of tricarballylate to
cis
-aconitate. The apparent

K
m

of TcuA for tricarballylate was 3.8 ± 0.4 mM, with a
V
max
of 7.9 ± 0.3 mM min
−1
, turnover number (
k
cat
) of 6.7 × 10
−2
s
−1
, and a catalytic efficiency (
k
cat
/

K
m

) of 17.8 M
−1
s
−1
. Optimal activity was measured at pH 7.5 and 30°C. The enzyme was inactivated at 45°C. One mole of FAD was present per mole of TcuA. We propose a role for TcuB as an electron shuttle protein responsible for oxidizing FADH
2
back to FAD in TcuA.
Phase Variation and Genomic Architecture Changes inAzospirillum
Authors: Vial Ludovic , Lavire Céline , Mavingui Patrick , Blaha Didier , Haurat Jacqueline , Moënne-Loccoz Yvan , Bally René , Wisniewski-Dyé Florence 
Published: July 2006

ABSTRACTThe plant growth-promoting rhizobacteriumAzospirillum lipoferum4B generates in vitro at high frequency a stable nonswimming phase variant designated 4VI, which is distinguishable from the wild type by the differential absorption of dyes. The frequency of variants generated by arecAmutant ofA. lipoferum4B was increased up to 10-fold. The pleiotropic modifications characteristic of the phase variant are well documented, but the molecular processes involved are unknown. Here, the objective was to assess whether genomic rearrangements take place during phase variation of strain 4B. The random amplified polymorphic DNA (RAPD) profiles of strains 4B and 4VIdiffered. RAPD fragments observed only with the wild type were cloned, and three cosmids carrying the corresponding fragments were isolated. The three cosmids hybridized with a 750-kb plasmid and pulse-field gel electrophoresis analysis revealed that this replicon was missing in the 4VIgenome. The same rearrangements took place during phase variation of 4BrecA. Large-scale genomic rearrangements during phase variation were demonstrated for two additional strains. InAzospirillum brasilenseWN1, generation of stable variants was correlated with the disappearance of a replicon of 260 kb. ForAzospirillum irakenseKBC1, the variant was not stable and coincided with the formation of a new replicon, whereas the revertant recovered the parental genomic architecture. This study shows large-scale genomic rearrangements inAzospirillumstrains and correlates them with phase variation.