bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Essential Function of Genes for a Hydratase and an Aldehyde Dehydrogenase for Growth of Pseudomonas sp. Strain Chol1 with the Steroid Compound Cholate Indicates an Aldolytic Reaction Step for Deacetylation of the Side Chain
Authors: Holert Johannes , Jagmann Nina , Philipp Bodo 
Published: May 2013

ABSTRACT

In the bacterial degradation of steroid compounds, the enzymes initiating the breakdown of the steroid rings are well known, while the reactions for degrading steroid side chains attached to C-17 are largely unknown. A recent
in vitro
analysis with
Pseudomonas
sp. strain Chol1 has shown that the degradation of the C
5
acyl side chain of the C
24
steroid compound cholate involves the C
22
intermediate 7α,12α-dihydroxy-3-oxopregna-1,4-diene-20
S
-carbaldehyde (DHOPDCA) with a terminal aldehyde group. In the present study, candidate genes with plausible functions in the formation and degradation of this aldehyde were identified. All deletion mutants were defective in growth with cholate but could transform it into dead-end metabolites. A mutant with a deletion of the
shy
gene, encoding a putative enoyl coenzyme A (CoA) hydratase, accumulated the C
24
steroid (22
E
)-7α,12α-dihydroxy-3-oxochola-1,4,22-triene-24-oate (DHOCTO). Deletion of the
sal
gene, formerly annotated as the steroid ketothiolase gene
skt
, resulted in the accumulation of 7α,12α,22-trihydroxy-3-oxochola-1,4-diene-24-oate (THOCDO). In cell extracts of strain Chol1, THOCDO was converted into DHOPDCA in a coenzyme A- and ATP-dependent reaction. A
sad
deletion mutant accumulated DHOPDCA, and expression in
Escherichia coli
revealed that
sad
encodes an aldehyde dehydrogenase for oxidizing DHOPDCA to the corresponding acid 7α,12α-dihydroxy-3-oxopregna-1,4-diene-20-carboxylate (DHOPDC) with NAD
+
as the electron acceptor. These results clearly show that the degradation of the acyl side chain of cholate proceeds via an aldolytic cleavage of an acetyl residue; they exclude a thiolytic cleavage for this reaction step. Based on these results and on sequence alignments with predicted aldolases from other bacteria, we conclude that the enzyme encoded by
sal
catalyzes this aldolytic cleavage.
Chlamydia trachomatis Transports NAD via the Npt1 ATP/ADP Translocase
Authors: Fisher Derek J. , Fernández Reinaldo E. , Maurelli Anthony T. 
Published: May 2013

ABSTRACT

Obligate intracellular bacteria comprising the order
Chlamydiales
lack the ability to synthesize nucleotides
de novo
and must acquire these essential compounds from the cytosol of the host cell. The environmental protozoan endosymbiont
Protochlamydia amoebophila
UWE25 encodes five nucleotide transporters with specificities for different nucleotide substrates, including ATP, GTP, CTP, UTP, and NAD. In contrast, the human pathogen
Chlamydia trachomatis
encodes only two nucleotide transporters, the ATP/ADP translocase
C. trachomatis
Npt1 (Npt1
Ct
) and the nucleotide uniporter Npt2
Ct
, which transports GTP, UTP, CTP, and ATP. The notable absence of a NAD transporter, coupled with the lack of alternative nucleotide transporters on the basis of bioinformatic analysis of multiple
C. trachomatis
genomes, led us to re-evaluate the previously characterized transport properties of Npt1
Ct
. Using [adenylate-
32
P]NAD, we demonstrate that Npt1
Ct
expressed in
Escherichia coli
enables the transport of NAD with an apparent

K
m

and
V
max
of 1.7 μM and 5.8 nM mg
−1
h
−1
, respectively. The

K
m

for NAD transport is comparable to the

K
m

for ATP transport of 2.2 μM, as evaluated in this study. Efflux and substrate competition assays demonstrate that NAD is a preferred substrate of Npt1
Ct
compared to ATP. These results suggest that during reductive evolution, the pathogenic chlamydiae lost individual nucleotide transporters, in contrast to their environmental endosymbiont relatives, without compromising their ability to obtain nucleotides from the host cytosol through relaxation of transport specificity. The novel properties of Npt1
Ct
and its conservation in chlamydiae make it a potential target for the development of antimicrobial compounds and a model for studying the evolution of transport specificity.
QapR (PA5506) Represses an Operon That Negatively Affects the Pseudomonas Quinolone Signal in Pseudomonas aeruginosa
Authors: Tipton Kyle A. , Coleman James P. , Pesci Everett C. 
Published: May 2013

ABSTRACT

Pseudomonas aeruginosa
is a Gram-negative, opportunistic pathogen that can cause disease in varied sites within the human body and is a significant source of morbidity and mortality in those afflicted with cystic fibrosis.
P. aeruginosa
is able to coordinate group behaviors, such as virulence factor production, through the process of cell-to-cell signaling. There are three intercellular signaling systems employed by
P. aeruginosa
, and one of these systems utilizes the small molecule 2-heptyl-3-hydroxy-4-quinolone (
Pseudomonas
quinolone signal [PQS]). PQS is required for virulence in multiple infection models and has been found in the lungs of cystic fibrosis patients colonized by
P. aeruginosa
. In this study, we have identified an RpiR family transcriptional regulator, QapR, which is an autoregulatory repressor. We found that mutation of
qapR
caused overexpression of the
qapR
operon. We characterized the
qapR
operon to show that it contains genes
qapR
, PA5507, PA5508, and PA5509 and that QapR directly controls the transcription of these genes in a negative manner. We also show that derepression of this operon greatly reduces PQS concentration in
P. aeruginosa
. Our results suggest that
qapR
affects PQS concentration by repressing an enzymatic pathway that acts on PQS or a PQS precursor to lower the PQS concentration. We believe that this operon comprises a novel mechanism to regulate PQS concentration in
P. aeruginosa
.
Role of
cis
-Acting Sites in Stimulation of the Phage λ
P
RM
Promoter by CI-Mediated Looping
Authors: Michalowski Christine B. , Little John W. 
Published: May 2013

ABSTRACT

The lysogenic state of phage λ is maintained by the CI repressor. CI binds to three operators each in the right operator (
O
R
) and left operator (
O
L
) regions, which lie 2.4 kb apart. At moderate CI levels, the predominant binding pattern is two dimers of CI bound cooperatively at each regulatory region. The resulting tetramers can then interact, forming an octamer and a loop of the intervening DNA. CI is expressed from the
P
RM
promoter, which lies in the
O
R
region and is subjected to multiple regulatory controls. Of these, the most recently discovered is stimulation by loop formation. In this work, we have investigated the mechanism by which looping stimulates
P
RM
. We find that two
cis
-acting sites lying in the
O
L
region are involved. One site, an UP element, is required for stimulation. Based on the behavior of other promoters with UP elements located upstream of the −35 region, we suggest that a subunit of RNA polymerase (RNAP) bound at
P
RM
binds to the UP element located in the
O
L
region. In addition, adjacent to the UP element lies a binding site for integration host factor (IHF); this site plays a less critical role but is required for stimulation of the weak
prm240
allele. A loop with CI at the
O
L
2 and
O
L
3 operators does not stimulate
P
RM
, while one with CI only at
O
L
2 provides some stimulation. We discuss possible mechanisms for stimulation.
Expression of the Rhizobium leguminosarum bv. trifolii
pssA
Gene, Involved in Exopolysaccharide Synthesis, Is Regulated by RosR, Phosphate, and the Carbon Source
Authors: Janczarek Monika , Urbanik-Sypniewska Teresa 
Published: May 2013

ABSTRACT

Rhizobium leguminosarum
bv. trifolii
pssA
encodes a glucosyl-isoprenylphosphate (IP)-transferase involved in the first step of exopolysaccharide (EPS) synthesis. It was found that the
pssA
gene is an important target for regulation of this biosynthetic pathway. The data of this study indicate that
pssA
transcription is a very complex and mainly positively regulated process. A detailed analysis of a 767-bp-long
pssA
upstream region revealed the presence of several sequence motifs recognized by regulatory proteins that are associated with phosphate-, carbon-, and iron-dependent regulation. In addition, numerous inverted repeats of different lengths have been identified in this region.
pssA
transcription is directed from two distal P1 and proximal P3 promoters whose sequences demonstrate a significant identity to promoters recognized by RNA polymerase sigma factor σ
70
. Among rhizobial proteins, RosR seems to be a primary regulator that positively affects
pssA
expression. This protein binds to RosR box 1 located downstream of the P1 promoter. In addition, phosphate and the carbon source strongly affect
pssA
transcription. A significantly lower level of
pssA
expression was observed in both the wild-type strain growing under phosphate-rich conditions and the
phoB
mutant. In this regulation, the PhoB protein and Pho box 2 located upstream of the P3 promoter were engaged.
pssA
transcription is also significantly affected by glucose. Transcriptional analysis of a set of
pssA-lacZ
fusions expressed in
Escherichia coli
wild-type and
cyaA
and
crp
mutants confirmed that cyclic AMP (cAMP) receptor protein (CRP) and two cAMP-CRP boxes located upstream of the P1 are required for this upregulation. Moreover, the production of EPS was totally abolished in
R. leguminosarum
bv. trifolii mutant strains 4440 and 1012 containing a Tn
5
insertion downstream of the P3 promoter and downstream of the P3 −35 hexamer, respectively.
e-Prescribing: characterisation of patient safety hazards in community pharmacies using a sociotechnical systems approach
Authors: Odukoya Olufunmilola K , Chui Michelle A 
Published: May 2013

ObjectiveTo characterise the safety hazards related to e-prescribing in community pharmacies.MethodsThe sociotechnical systems framework was used to investigate the e-prescribing technology interface in community pharmacies by taking into consideration the social, technical and environmental work elements of a user's interaction with technology. This study focused specifically on aspects of the social subsystem.Study design and settingThe study employed a cross-sectional qualitative design and was conducted in seven community pharmacies in Wisconsin. Direct observations, think aloud protocols and group interviews were conducted with 14 pharmacists and 16 technicians, and audio recorded. Recordings were transcribed and subjected to thematic content analysis guided by the sociotechnical systems’ theoretical framework.ResultsThree major themes that may increase the potential for medication errors with e-prescribing were identified and described. The three themes included: (1) increased cognitive burden on pharmacy staff, such as having to memorise parts of e-prescriptions or having to perform dosage calculations mentally; (2) interruptions during the e-prescription dispensing process; and (3) communication issues with prescribers, patients and among pharmacy staff. Pharmacy staff reported these consequences of e-prescribing increased the likelihood of medication errors.ConclusionsThis study is the first of its kind to identify patient safety risks related to e-prescribing in community pharmacies using a sociotechnical systems framework. The findings shed light on potential interventions that may enhance patient safety in pharmacies and facilitate improved e-prescribing use. Future studies should confirm patient safety hazards reported and identify ways to use e-prescribing effectively and safely in community pharmacies.
Effective prevention of thromboembolic complications in emergency surgery patients using a quality improvement approach
Authors: Kreckler Simon , Morgan Robert D , Catchpole Ken , New Steve , Handa Ashok , Collins Gary , McCulloch Peter 
Published: May 2013

ObjectiveTo assess the effectiveness of a multifaceted intervention based on industrial process improvement to identify and sustainably correct deficiencies in thromboprophylaxis delivery.Summary background dataDeep vein thrombosis and pulmonary embolism are major causes of morbidity and mortality in surgical patients, but effective prophylactic treatments are available. Ensuring reliable delivery of the intended thromboprophylaxis is, however, a long-standing problem.MethodsDelivery of thromboprophylactic treatment on an emergency general surgery admissions ward was targeted during a multidisciplinary intervention to improve process reliability using industrial quality improvement approaches. Delivery was audited against guidelines before and after 3- month intervention. Clinical outcome was evaluated by reviewing all radiological investigations for suspected Deep Vein Thrombosis (DVT) or Pulmonary Embolism (PE) from patients admitted to the unit in the 1 year immediately before and that immediately after intervention.ResultsDelivery of thromboprophylaxis according to guidelines was improved from 35% before to 87% 3 months after intervention (χ2=87.412, p<0.0001) and sustained at 86% 10 months after intervention. Radiologically identified thromboembolic events occurring up to 60 days after admission in patients admitted for over 48 h fell from 23/3075 (0.75%) before to 9/3080 (0.29%) after intervention (HR 0.39, CI 0.29 to 0.53, χ2=6.18, p=0.01292). The risk of thromboembolism in the two groups diverged during follow-up to 60 days, before converging again.ConclusionsA quality improvement process resulted in major sustainable improvements in the delivery of thromboprophylaxis associated with a 61% reduction in radiologically detected clinical episodes of thromboembolism 2 months after admission. Further study of this approach to improving care quality is warranted.
Walking and child pedestrian injury: a systematic review of built environment correlates of safe walking
Authors: Rothman Linda , Buliung Ron , Macarthur Colin , To Teresa , Howard Andrew 
Published: May 2013

BackgroundThe child active transportation literature has focused on walking, with little attention to risk associated with increased traffic exposure. This paper reviews the literature related to built environment correlates of walking and pedestrian injury in children together, to broaden the current conceptualization of walkability to include injury prevention.MethodsTwo independent searches were conducted focused on walking in children and child pedestrian injury within nine electronic databases until March, 2012. Studies were included which: 1) were quantitative 2) set in motorized countries 3) were either urban or suburban 4) investigated specific built environment risk factors 5) had outcomes of either walking in children and/or child pedestrian roadway collisions (ages 0-12). Built environment features were categorized according to those related to density, land use diversity or roadway design. Results were cross-tabulated to identify how built environment features associate with walking and injury.ResultsFifty walking and 35 child pedestrian injury studies were identified. Only traffic calming and presence of playgrounds/recreation areas were consistently associated with more walking and less pedestrian injury. Several built environment features were associated with more walking, but with increased injury. Many features had inconsistent results or had not been investigated for either outcome.ConclusionsThe findings emphasise the importance of incorporating safety into the conversation about creating more walkable cities.
The use of cost–benefit analysis in road assessments: a methodological inquiry
Authors: Vecino-Ortiz Andres I , Hyder Adnan A 
Published: May 2013

BackgroundCost–benefit analysis is a useful tool for priority setting in road safety. The value of statistical life (VOSL) is a metric used to estimate the benefits of road interventions in cost–benefit analyses. The International Road Assessment Program (iRAP), for example, created a rule-of-thumb to calculate VOSL benefits of road infrastructure when performing cost–benefit assessments in countries where data on VOSL are sparse.AimTo evaluate the rapid assessment metric developed by iRAP and provide suggestions for improvement in these methods.MethodsWe replicated iRAP calculations in order to make a critical assessment of the sources, results and conclusions.ConclusionsWe found the iRAP metric a good example for highlighting some relevant aspects that should be considered in any VOSL estimation in order to enhance its use as a guiding principle for assessing road interventions. Specifically, we recommend the explicit disclosure of the assumptions, the use of sensitivity analysis and the avoidance of omitted variables bias.
Unintentional alcohol and drug poisoning in association with substance use disorders and mood and anxiety disorders: results from the 2010 Nationwide Inpatient Sample
Authors: Yoon Young-Hee , Chen Chiung M , Yi Hsiao-Ye 
Published: May 2013

ObjectiveTo examine unintentional alcohol and drug poisoning in association with substance use disorders (SUDs) and mood and anxiety disorders.MethodInternational Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) external-cause-of-injury codes on discharge records of patients ages 12+ years from the 2010 Nationwide Inpatient Sample were examined to identify cases with unintentional alcohol poisoning (E860) and/or drug poisoning (E850–E858). ICD-9-CM diagnosis codes were examined to identify comorbid alcohol dependence, drug dependence, tobacco use disorder, and mood/anxiety disorders. Poisson regression was used to derive risk ratios to assess the associations between these comorbid conditions and alcohol/drug poisoning.ResultsEstimated numbers of hospitalisations related to unintentional alcohol and drug poisoning were, respectively, 5623 and 60 423 in men, and 3147 and 68 568 in women. For both sexes, the proportion with SUDs or mood/anxiety disorders was significantly higher among inpatients with alcohol and drug poisoning than among all inpatients. Estimated risk ratios indicated strong relationships of SUDs and mood/ anxiety disorders with unintentional poisoning from alcohol and drugs. The strongest association was between alcohol dependence and alcohol poisoning for both sexes. Significant associations also existed between drug dependence and drug poisoning, and mood/anxiety disorders and poisoning from alcohol and drugs.ConclusionsSUDs and mood/anxiety disorders are key risk factors for unintentional poisoning by alcohol and drugs among inpatients in the USA. Effective treatments of these disorders should be targeted as poisoning prevention efforts. Future studies are needed to clarify a potential bias in the data due to differential inpatient mental condition screening practices.
Cross-cultural adaptation and validation of the Portuguese version of the Parental Supervision Attributes Profile Questionnaire
Authors: Andrade Conceição , Carita Ana Isabel , Cordovil Rita , Barreiros João 
Published: May 2013

ObjectivesTo cross-culturally adapt and validate the Portuguese version of the Parental Supervision Attributes Profile Questionnaire (PSAPQ). The PSAPQ is a measure of parental supervision, which has not been translated and adapted into any language other than English.MethodsThe Portuguese version was the result of forward/backward translations, consensus panels and pretesting. Reliability and internal consistency were assessed using Cronbach's α, intraclass correlation coefficient (ICC) and confirmatory factor analysis (CFA) in adults with different educational levels. Results: Cronbach's α (α=0.70–0.79) and ICC (>0.75) were acceptable in three of four factors. The results of CFA (χ2/df=2.243; CFI=0.951; GFI=0.96; RMSEA=0.056; P(RMSEA ≤ 0.05)=0.222) suggest a good adjustment between the factors.ConclusionsThe Portuguese version of PSAPQ showed acceptable psychometric properties. This study evidenced some vulnerabilities of the fate subscale, emphasising the need for further investigation of the effects of the educational level of the parents.
Ovarian cancer symptom awareness and anticipated time to help-seeking for symptoms among UK women
Authors: Low Emma L , Waller Jo , Menon Usha , Jones Annwen , Reid Frances , Simon Alice E 
Published: May 2013

ObjectivesTo determine levels of awareness of ovarian cancer symptoms and to identify barriers to help-seeking and predictors of a longer time to help-seeking in a UK female population-based sample.MethodsA UK population-based sample of women [n=1000, including a subsample of women at higher risk due to their age (≥45 years,n=510)] completed the Ovarian Cancer Awareness Measure by telephone interview. Questions measured symptom awareness (using recall and recognition), barriers to medical help-seeking and anticipated time to help-seeking. Regression analyses identified predictors of a higher score on a scale of anticipated time to help-seeking.ResultsMost women (58% overall sample; 54% subgroup) were unable to recall any symptoms but 99% recognised at least one. Recognition was lowest for difficulty eating and persistently feeling full. In the sample overall, higher socio-economic status and higher endorsement of practical and service barriers independently predicted a longer anticipated time to help-seeking for more symptoms. White ethnicity was an additional predictor in the older subgroup.ConclusionsThis study suggests awareness of ovarian cancer symptoms is low in the UK, and varies widely between symptoms. It identifies variables that may be involved in a longer time to help-seeking for possible ovarian cancer symptoms and highlights the need for more in-depth research into the factors related to time to help-seeking in real-world situations.
Myths and misconceptions about intrauterine contraception among women seeking termination of pregnancy
Authors: Michie Lucy , Cameron Sharon T , Glasier Anna , Wellings Kaye , Loudon Joanna 
Published: May 2013

BackgroundImmediate initiation of an intrauterine device (IUD) or intrauterine system (IUS) following termination of pregnancy (TOP) is associated with a significant reduction in the risk of another TOP. In spite of its high efficacy, uptake of intrauterine contraception in the UK is low. Myths and misconceptions about the method may contribute to the low uptake.Study designAnonymous, self-administered questionnaire among women requesting a TOP in a hospital abortion service in Scotland, UK.MethodsMisconceptions about intrauterine contraception were extracted from an online social networking and micro-blogging service, and from existing research to develop a questionnaire containing 12 negative statements about intrauterine contraception. Respondents indicated their level of agreement with each statement.ResultsA total of 106/125 (85%) women requesting a TOP completed the questionnaire. The two commonest negative statements that respondents agreed with were that the IUD/IUS ‘Is painful to have inserted’ (n=36; 34%) and that ‘It can move around inside your body’ (n=25; 23.6%). The range of women who neither agreed nor disagreed with negative statements was 26.4–56.0%. Twenty-seven (25%) women indicated that the IUD/IUS was their planned method of post-TOP contraception.ConclusionsAlthough myths about intrauterine contraception persist among a small proportion of women requesting a TOP, lack of knowledge about the method is also evident. The consultation prior to TOP is an important opportunity to provide accurate and quality information to women about the IUD/IUS that may serve to increase uptake and prevent repeat abortions.