bluuebunny/crossref_metadata_2025_split huggingface dataset:
Considerations When Using Discriminant Function Analysis of Antimicrobial Resistance Profiles To Identify Sources of Fecal Contamination of Surface Water in Michigan
Authors: Kaneene John B. , Miller RoseAnn , Sayah Raida , Johnson Yvette J. , Gilliland Dennis , Gardiner Joseph C. 
Published: March 2007

ABSTRACT

The goals of this study were to (i) identify issues that affect the ability of discriminant function analysis (DA) of antimicrobial resistance profiles to differentiate sources of fecal contamination, (ii) test the accuracy of DA from a known-source library of fecal
Escherichia coli
isolates with isolates from environmental samples, and (iii) apply this DA to classify
E. coli
from surface water. A repeated cross-sectional study was used to collect fecal and environmental samples from Michigan livestock, wild geese, and surface water for bacterial isolation, identification, and antimicrobial susceptibility testing using disk diffusion for 12 agents chosen for their importance in treating
E. coli
infections or for their use as animal feed additives. Nonparametric DA was used to classify
E. coli
by source species individually and by groups according to antimicrobial exposure. A modified backwards model-building approach was applied to create the best decision rules for isolate differentiation with the smallest number of antimicrobial agents. Decision rules were generated from fecal isolates and applied to environmental isolates to determine the effectiveness of DA for identifying sources of contamination. Principal component analysis was applied to describe differences in resistance patterns between species groups. The average rate of correct classification by DA was improved by reducing the numbers of species classifications and antimicrobial agents. DA was able to correctly classify environmental isolates when fewer than four classifications were used. Water sample isolates were classified by livestock type. An evaluation of the performance of DA must take into consideration relative contributions of random chance and the true discriminatory power of the decision rules.
Lack of Control of Nitrite Assimilation by Ammonium in an Oceanic Picocyanobacterium,
Synechococcus
sp. Strain WH 8103
Authors: Wyman Michael , Bird Clare 
Published: March 2007

ABSTRACT

In cyanobacteria, the transcriptional activator NtcA is involved in global nitrogen control and, in the absence of ammonium, regulates the expression of genes involved in the assimilation of alternative nitrogen sources. The oceanic picocyanobacterium
Synechococcus
sp. strain WH 8103 harbors a copy of
ntcA
, but in the present study, we show that unlike other marine cyanobacteria that have been investigated, this strain is capable of coassimilating nitrite when grown in the presence of ammonium. Transcript levels for the genes encoding the nitrate/nitrite-bispecific permease NrtP and nitrate reductase (NarB) were substantially down-regulated by ammonium, whereas the abundances of nitrite reductase (NirA) transcripts were similar in nitrite- and ammonium-grown cells. The growth of
Synechococcus
sp. strain WH 8103 in medium containing both ammonium and nitrite resulted in only minor changes in the expression profile in comparison to that of nitrite-grown cells with the exception that the gene encoding the high-affinity ammonium transporter Amt1 was down-regulated to the levels seen in ammonium-grown cells. Whereas the expression of
nrtP
,
narB
, and
amt1
appears to be NtcA dependent in this marine cyanobacterium, the transcription and expression of
nirA
appear not to be. The ability to coassimilate nitrite and reduced-nitrogen sources like ammonium may be an adaptive trait that enables oceanic strains like
Synechococcus
sp. strain WH 8103 to exploit the low nitrite concentrations found in oceanic surface waters that are not available to their principal and more numerous competitor,
Prochlorococcus
.
Thiols in Nitric Oxide Synthase-Containing
Nocardia
sp. Strain NRRL 5646
Authors: Lee Sungwon , Bergeron Hélène , Lau Peter C. K. , Rosazza John P. N. 
Published: March 2007

ABSTRACT

Mycothiol (MSH) [1-
d
-
myo
-inosityl-2-(
N
-acetyl-
l
-cysteinyl)amido-2-deoxy-α-
d
-glucopyranoside], isolated as the bimane derivative, was established to be the major thiol in
Nocardia
sp. strain NRRL 5646, a species most closely related to
Nocardia brasiliensis
strain DSM 43758
T
. Thiol formation and detection of MSH-dependent formaldehyde dehydrogenase activity in cell extracts are relevant to the possible modulation of nitric oxide toxicity generated by strain NRRL 5646.
HpdR Is a Transcriptional Activator of
Sinorhizobium meliloti hpdA
, Which Encodes a Herbicide-Targeted 4-Hydroxyphenylpyruvate Dioxygenase
Authors: Loprasert Suvit , Whangsuk Wirongrong , Dubbs James M. , Sallabhan Ratiboot , Somsongkul Kumpanart , Mongkolsuk Skorn 
Published: March 2007

ABSTRACT

Sinorhizobium meliloti hpdA
, which encodes the herbicide target 4-hydroxyphenylpyruvate dioxygenase, is positively regulated by HpdR. Gel mobility shift and DNase I footprinting analyses revealed that HpdR binds to a region that spans two conserved direct-repeat sequences within the
hpdR-hpdA
intergenic space. HpdR-dependent
hpdA
transcription occurs in the presence of 4-hydroxyphenylpyruvate, tyrosine, and phenylalanine, as well as during starvation.
Functional Complementation of the Essential Gene
fabG1
of
Mycobacterium tuberculosis
by
Mycobacterium smegmatis fabG
but Not
Escherichia coli fabG
Authors: Parish Tanya , Roberts Gretta , Laval Francoise , Schaeffer Merrill , Daffé Mamadou , Duncan Ken 
Published: March 2007

ABSTRACT

Mycolic acids are a key component of the mycobacterial cell wall, providing structure and forming a major permeability barrier. In
Mycobacterium tuberculosis
mycolic acids are synthesized by type I and type II fatty acid synthases. One of the enzymes of the type II system is encoded by
fabG1
. We demonstrate here that this gene can be deleted from the
M. tuberculosis
chromosome only when another functional copy is provided elsewhere, showing that under normal culture conditions
fabG1
is essential. FabG1 activity can be replaced by the corresponding enzyme from the closely related species
Mycobacterium smegmatis
but not by the enzyme from
Escherichia coli. M. tuberculosis
carrying FabG from
M. smegmatis
showed no phenotypic changes, and both the mycolic acids and cell wall permeability were unchanged. Thus,
M. tuberculosis
and
M. smegmatis
enzymes are interchangeable and do not control the lengths and types of mycolic acids synthesized.
A Pair of Highly Conserved Two-Component Systems Participates in the Regulation of the Hypervariable FIR Proteins in DifferentLegionellaSpecies
Authors: Feldman Michal , Segal Gil 
Published: March 2007

ABSTRACTLegionella pneumophilaand other pathogenicLegionellaspecies multiply inside protozoa and human macrophages by using the Icm/Dot type IV secretion system. The IcmQ protein, which possesses pore-forming activity, and IcmR, which functions as its chaperone, are two essential components of this system. It was previously shown that in 29Legionellaspecies, a large hypervariable-gene family (firgenes) is located upstream from a conservedicmQgene, but although nonhomologous, the FIR proteins were found to function similarly together with their corresponding IcmQ proteins. Alignment of the regulatory regions of 29firgenes revealed that they can be divided into three regulatory groups; the first group contains a binding site for the CpxR response regulator, which was previously shown to regulate theL. pneumophila firgene (icmR); the second group, which includes most of thefirgenes, contains the CpxR binding site and an additional regulatory element that was identified here as a PmrA binding site; and the third group contains only the PmrA binding site. Analysis of the regulatory region of twofirgenes, which included substitutions in the CpxR and PmrA consensus sequences, a controlled expression system, as well as examination of direct binding with mobility shift assays, revealed that both CpxR and PmrA positively regulate the expression of thefirgenes that contain both regulatory elements. The change in the regulation of thefirgenes that occurred during the course of evolution might be required for the adaptation of the differentLegionellaspecies to their specific environmental hosts.
In Vivo Modulation of a DnaJ Homolog, CbpA, by CbpM
Authors: Chenoweth Matthew R. , Trun Nancy , Wickner Sue 
Published: March 2007

ABSTRACTCbpA, anEscherichia coliDnaJ homolog, can function as a cochaperone for the DnaK/Hsp70 chaperone system, and its in vitro activity can be modulated by CbpM. We discovered that CbpM specifically inhibits the in vivo activity of CbpA, preventing it from functioning in cell growth and division. Furthermore, we have shown that CbpM interacts with CbpA in vivo during stationary phase, suggesting that the inhibition of activity is a result of the interaction. These results reveal that the activity of theE. coliDnaK system can be regulated in vivo by a specific inhibitor.
Elongation Factor Tu3 (EF-Tu3) from the Kirromycin Producer
Streptomyces ramocissimus
Is Resistant to Three Classes of EF-Tu-Specific Inhibitors
Authors: Olsthoorn-Tieleman Lian N. , Palstra Robert-Jan T. S. , van Wezel Gilles P. , Bibb Mervyn J. , Pleij Cornelis W. A. 
Published: March 2007

ABSTRACT

The antibiotic kirromycin inhibits prokaryotic protein synthesis by immobilizing elongation factor Tu (EF-Tu) on the elongating ribosome.
Streptomyces ramocissimus
, the producer of kirromycin, contains three
tuf
genes. While
tuf1
and
tuf2
encode kirromycin-sensitive EF-Tu species, the function of
tuf3
is unknown. Here we demonstrate that EF-Tu3, in contrast to EF-Tu1 and EF-Tu2, is resistant to three classes of EF-Tu-targeted antibiotics: kirromycin, pulvomycin, and GE2270A. A mixture of EF-Tu1 and EF-Tu3 was sensitive to kirromycin and resistant to GE2270A, in agreement with the described modes of action of these antibiotics. Transcription of
tuf3
was observed during exponential growth and ceased upon entry into stationary phase and therefore did not correlate with the appearance of kirromycin in stationary phase; thus, it is unlikely that EF-Tu3 functions as a resistant alternative for EF-Tu1. EF-Tu3 from
Streptomyces coelicolor
A3(2) was also resistant to kirromycin and GE2270A, suggesting that multiple antibiotic resistance is an intrinsic feature of EF-Tu3 species. The GE2270A-resistant character of EF-Tu3 demonstrated that this divergent elongation factor is capable of substituting for EF-Tu1 in vivo.
Problems of basing patient recruitment for primary care studies on routine laboratory submissions: Table 1
Authors: McNulty Cliodna , Thomas Michael , John Rhiannon , Lovering Andrew , Lewis Deirdre , MacGowan Alasdair 
Published: March 2007

Background:Use of routine urine submission rates for estimation of patient enrolment in primary care studies of acute urinary symptoms may overestimate patient recruitment rate.Aims:To compare the rates of submission of urines and significant bacteriuria from patients presenting with acute urinary symptoms in study general practices to routine microbiology laboratory urines.Methods:Routine laboratory urine submissions were determined by counting all mid-stream urine specimens submitted to the laboratory from 12 large general practitioner (GP) practices served by Gloucester and Southmead microbiology departments over two years (2000–02). Urine specimens were requested from all patients with acute urinary symptoms referred at research nurse practice visits over the same time period. The annual study urine submission was calculated using the ratio of the number of nurse practice visits to the annual number of possible consulting sessions. Significant bacteriuria was defined as a urine growing a single organism reported as >105colony forming units/ml. Rates per 1000 patients were calculated using practice population data.Results:The urine submission rate from study patients with acute urinary symptoms was one-third the routine urine submission rate from the same practices. The significant bacteriuria rate attained from the study was less than half the routine significant bacteriuria rate.Conclusion:Two-thirds of routine urine samples submitted by GPs are probably not for the investigation of acute urinary symptoms. Basing consultation sample size power calculations for primary care studies or sentinel practice-based surveillance in urinary tract infection on routine laboratory submissions is unreliable and will lead to significant overestimation of recruitment rate.
Simulation of the false twist textile yarn texturing process
Authors: Featherstone Anthony M. , Hearle John W. S. , Wellstead Peter E. 
Published: March 2007

The preliminary modelling of simulation steps required in the development of a generalised CAD (Computer-Aided-Design) package for textile machinery designers is presented. The false twist texturing process (FTTP) is chosen as the starting point, since it is the most important texturing process and it con tains most of the thermomechanical processes used in other tex turing processes. It also has an inherent problem associated with it; at high speed it is very difficult to analyse using conventional analytical techniques. The paper is divided into four sections: an introductory section which describes the false twist texturing process and reviews what modelling work has been done to date; this is followed by a sec tion which describes the simulation techniques employed and the mathematical models used; a results section where the simulation techniques are validated; and a conclusions section.
Computer modeling and simulation: The changing challenge
Authors: McLeod John 
Published: March 2007

The use of computers to model things, both real and imaginary, and the use of those models as surrogates for investigative and experimental purposes, constitute the art and science of simulation. Since its inception in the late nineteen forties simulation has undergone some interesting evolutionary changes. Paced by the development of rapidly improving computing and allied equip ment, the technology and methodology of simulation have faced — and to varying degrees learned to cope with - changing chal lenges as the ever-widening fields of application have multiplied. Hard limits are not in sight. However, vestiges of some original problems remain while others have been solved as simulation progresses from an art toward becoming a science.
Variations in Roving Weight Introduced by the Slubber
Authors: Enrick N.L. , Hicks W.D. 
Published: March 2007

Conventional sizing tests of slubber roving involve the cutting and weighing of 12-yd. lengths from the outside layers of bobbins. In the present study, mill produced rovings were subjected to special sizing tests, whereby each bobbin was sized to the barrel. The results showed many unusual patterns of variation, which are described here. One fre quent finding was that roving was excessively light or stretched at frame start-up. A comparison of processing methods, test results, and correlation diagrams of the data is presented, from which general conclusions may be drawn concerning the processing of roving. Since the weight variation in the sliver fed was determined, the weight varia tion introduced by the slubber could be evaluated.
A Stewart Platform- Based Manipulator: General Theory and Practical Construction
Authors: Fichter E.F. 
Published: March 2007

The Stewart Platform is one example of a parallel connection robot manipulator. This paper summarizes work that has been done at Oregon State University over the past several years on this topic. The work has fallen into two general areas: theoretical consideration of the generalized Stewart Platform and practical considerations for building a working machine. Both of these areas are covered in this paper. The theoretical part of the paper discusses the following four problems: 1. Given the position and orientation of the end effector, what are the actuator coordinates? 2. Given the velocity, position, and orientation of the end effector, what are the actuator velocities? 3. Given the forces exerted on the end effector by the external world and the accelerations of the end effèc tor, what are the forces at the actuators? 4. What are the singular configurations of the manipu lator? For the Stewart Platform, the singular configu rations are positions where the end effector gains one or more degrees of freedom. After the theoretical problems have been solved, there are still a group of practical problems to be tackled when a real machine is built. How can the general configuration be sim plified to make the solution of the equations practical? Once a configuration is decided upon, what are the construction considerations for building a real machine? What is the range of motion of the end effector? What are the necessary ranges of motion of the joints? What are the implications of the singularities of the Stewart Platform and what are some practical ways of solving the problems they cause? In the process of doing this research, three machines were built and a computer simulation was written and used. The most recent machine and the computer simulation will be described in this paper.
Sensor-Based Control of a Nine-Link Biped
Authors: Furusho J. , Sano A. 
Published: March 2007

We aimed to realize smooth 3D biped walking in a robot through control based on information obtained from various sensors. We employed a method to control walking by divid ing it into motions in the sagittal plane and in the lateral plane. We treated motion in the lateral plane as a regulator prob lem with two equilibrium states. We also used relatively low gain feedback coefficients obtained from the optimal regula tor theory. For motion in the sagittal plane, we put the body speed close to the smooth speed function given in advance by controlling the ankle torque. The effectiveness of the proposed control method was ex amined by computer simulation and proved by experiments with our BLR-G2 walking robot. The BLR-G2 is equipped with foot pressure and ankle torque sensors to provide infor mation about the condition of contact with the floor. The sole and ankle driving actuators undergo force/torgue feedback control based on the sensor information. These contributed toward realizing smooth walking with the sole firmly gripping the floor.
Product Family Manufacturing Plan Generation and Classification
Authors: Martinez M.T. , Favrel J. , Ghodous P. 
Published: March 2007

In the concurrent engineering approach, the problems related to product fabrication are taken into account as early as possi ble in design process. Manufacturing and assembly process design are decisive and expensive processes conditioning all the future steps of industrialisation and fabrication. In this paper a new method for assembly plan generation, based on the concept of meta-prod uct, is presented. This method is designed for modern production environments that are organised in product families with multiple op tions and variants. Facing the combinatory explosion problem, the method proposes an original representation of assembly sequences allowing the generation of a minimal list of non-redundant assembly plans called meta-sequences. In this method, an optimal assembly sequence class is selected. Then, for each product variant an optimal specific plan class is deduced from a simple analysis of product variant's components. An assembly reactive control system, adapting this optimal solution to the real assembly workshop conditions is also proposed. Another competitive problem is the case of production of old or short-series products. To rationalise their manufacturing, a solution consists in classifying products into classes, on the basis of similarity of required manufacturing processes. This technique called group technology (GT) helps to minimize unnecessary variety of products in a manufacturing plant by making designers aware of existing simi lar components. In this paper a new GT method is presented. It allows the classification of sequential manufacturing sequences as well as tree-like manufacturing plans. The method is based on an adapted representation of tree-like manufacturing plans, the distance adapted to this special case, efficient heuristics, and hierarchical bottom-up classification. Then, each product class can be managed in accordance to our family product generation method, or can be served as a base for reengineering process of firm's range of products.
Institutions, Economic Structure and Poverty in Pakistan
Authors: Hussain Akmal 
Published: March 2007

This paper argues that the tendencies for slow growth, high budget deficits and growing poverty, which were manifested in the eruption of an economic crisis in Pakistan during the 1990s, are rooted in the structure of Pakistan's economy. The emergence of such a structure is traced through a historical analysis, which examines the relationship between the processes of institutional decay, the policy of successive political regimes, the role of individual leaders and the architecture of the economy The paper shows how various military regimes laid the structural basis for the deterioration in both the polity and economy of Pakistan. It is also shown how the various democratically elected regimes not only sought authoritarian forms of power within formally democratic structures but also accelerated the process of economic decline. Thus, the crisis of growth and poverty is located as much in the deterioration of institutions, as it is in the failure of individual leaders to pursue public interest rather than their own.
Oxygen dynamics around buried lesser sandeelsAmmodytes tobianus(Linnaeus 1785): mode of ventilation and oxygen requirements
Authors: Behrens Jane W. , Stahl Henrik J. , Steffensen John F. , Glud Ronnie N. 
Published: March 2007

SUMMARYThe oxygen environment around buried sandeels (Ammodytes tobianus)was monitored by planar optodes. The oxygen penetration depth at the sediment interface was only a few mm. Thus fish, typically buried at 1–4 cm depth, were generally in anoxic sediment. However, they induced an advective transport through the permeable interstice and formed an inverted cone of porewater with 93% air saturation in front of the mouth. From dye experiments the mean ventilatory flow rate was estimated at 0.26±0.02 ml min–1 (86.9±7.3 ml min–1kg–1) (N=3). Expelled water from the gills induced a 1 cm circular plume with &lt;15% air saturation around the gills. During this quasi-steady ventilation mode, fish extracted 86.2±4.8% (N=7)of the oxygen from the inspired water. However, 13% of the investigated fish(2 of 15) occasionally wriggled their bodies and thereby transported almost fully air-saturated water down along the body, referred to as `plume ventilation'. Yet, within ∼30 min the oxic plume was replenished by oxygen-depleted water from the gills. The potential for cutaneous respiration by the buried fish was thus of no quantitative importance. Calculations derived by three independent methods (each with N=3) revealed that the oxygen uptake of sandeel buried for 6–7 h was 40–50% of previous estimates on resting respirometry of non-buried fish, indicating lower O2 requirements during burial on a diurnal timescale. Buried fish exposed to decreasing oxygen tensions gradually approached the sediment surface, but remained in the sediment until the inspired water reached 5–10% air saturation.