bluuebunny/crossref_metadata_2025_split huggingface dataset:
From symbols to sounds: Visual symbolic information activates sound representations
Authors: Widmann Andreas , Kujala Teija , Tervaniemi Mari , Kujala Anu , Schröger Erich 
Published: August 2004

AbstractExpectations on forthcoming sounds can speed up responding to environmental changes and can, thus, be a basis for successful adaptation. The present study investigated event‐related brain potential (ERP) effects in situations where particular sounds were predicted on the basis of preceding visual information. Subjects had to map scorelike visual symbols to corresponding sounds. The sounds could be either congruent or occasionally incongruent with the corresponding symbol. When the auditory stimulation was incongruent with the visual information, a brain response was elicited starting as early as about 100 ms from the onset of the auditory stimulus. It had a bilateral frontal distribution and a polarity inversion at the mastoids compatible with the assumption of sources in auditory cortex. These results suggest that the auditory system can establish a representation of an expected stimulus on the basis of visual symbolic information.
A survey of the information management and technology training needs of doctors in an acute NHS trust in the United Kingdom
Authors: Devitt Nicola , Murphy Jeannette 
Published: August 2004

AbstractBackground:  Doctors need information skills to deliver health care in the 21st century. There is concern that those who trained before the ‘information age’ will be inadequately equipped for their work.Objectives:  To assess doctors’ use of computers for clinical tasks, and their knowledge and skills in health information management and technology.Design:  Questionnaire survey.Setting:  An acute NHS trust in the UK.Participants:  96 (83%) of all doctors in the trust responded.Main outcome measures:  Proportion of respondents reporting the following: use of computer‐based systems for clinical tasks, knowledge in eight health informatics topics, skills in using specific hardware and software applications. Also comparison of reported skills between senior and junior staff; proportion of doctors identifying specific training needs.Results:  All but one (1%) of the responding doctors used a computer regularly. Over three quarters of respondents reported they were semi‐skilled or fully skilled in basic office applications, though the juniors scored significantly more highly than the seniors for some applications. However, 44% of doctors reported no skills in database software, identifying this as a training need.Around half of the doctors were unaware of health informatics topics, including electronic patient records, the Caldicott report and data protection law. In each case the senior doctors were significantly more aware than the juniors of the topic in question.Conclusion:  Both junior and senior doctors have basic computer literacy, but nearly half of this population identify the use of database software as a training need. In addition, there are several health informatics topics of which a large proportion of doctors, particularly the juniors, have little knowledge, but which have not been identified as training needs. Some recommendations are made for provision of in‐house health informatics education for doctors.Key Messages Implications for Policy

Junior doctors need education about electronic health records and data protection.
Senior doctors are in a good position to include such health informatics training in regular post graduate education meetings.

Implications for Practice

Most doctors have acquired basic computer skills by self‐directed learning: there appears to be no need for catch‐up training for senior doctors who graduated before the computer age.
Clinical librarianship in the UK: temporary trend or permanent profession? Part I: a review of the role of the clinical librarian
Authors: Sargeant Sally J. E. , Harrison Janet 
Published: August 2004

AbstractBackground:  This paper is the first of a two‐part series of articles presenting the role of the clinical librarian (CL) in the UK today. It situates the CL concept historically, and specifically reports the findings from a study in 2002 (Skinner, The Role of the Clinical Librarian in the UK. MSc Dissertation. Loughborough University: Department of Information Science).Relevance:  The impetus for the 2002 study was the awareness of an increase in job advertisements within the NHS for roles seeking to enhance the practice of evidence‐based medicine, which included elements of clinical librarianship. Therefore the research was undertaken to establish whether this increase was coincidental, or the beginning of a new professional role for librarians.Methods:  A content analysis of CL job advertisements, examining job titles and duties was undertaken. Twenty‐three advertisements were scrutinized, and these results are presented here. As a complementary investigation, a postal questionnaire was sent to a sample of practising CLs in the UK.Results:  Several duties can be classified as core to the role of the CL. However there is a great diversity of duties attached to this core, reflecting an absence of nationally accepted practice.Conclusion:  Further work was necessary to assess current practice and how clinical librarianship can continue to grow at local and national levels. This is addressed in Part Two of this series.Key Messages Policy

Acceptance of diversifying role in medical information provision
Logistical considerations of CL personnel and their physical positioning within acute settings

Implications for practice

Establishing national professional guidelines for CLs
Establishing consistency in nomenclature
Evaluation of methodological search filters—a review
Authors: Jenkins Michelle 
Published: August 2004

AbstractObjectives:  The objectives of the study were: to provide an overview of approaches to methodological search filter development; to identify and critically review the stages of methodological search filter development; to devise a search filter appraisal checklist based on the review.Methods:  An iterative approach to searching was employed utilizing health and library databases, the world wide web and citation searching. Further systematic methods included hand searching of key journals in the field of search filter development, contacting known experts in the field and scanning reference lists of relevant papers to identify additional studies. Altogether, 51 potentially relevant papers were found, of which 20 met the inclusion criteria.Results:  Four stages of search filter development were identified from the literature (search term selection, identification of a gold standard, evaluation and validation). Variations in the methods used to approach these four stages were identified, most importantly in the extent to which search filters are tested and validated.Conclusion:  Awareness of the process and limitations involved in search filter development is essential to make an informed decision on the applicability and validity of search filters. The findings of this review indicate a considerable agenda for future research, in particular, to improve the quality of reporting of search filters and to inform users on their use and application. Based on the review, guidance in the appraisal process of search filters is given in the form of a checklist.Key Messages Implications for Policy

Improvements are needed in the quality of reporting of search filters
Further research is warranted investigating the methods used to develop search filters
Evaluation and impact of search filters on end‐user searching outcome is essential to establish the effectiveness of search filters

Implications for Practice

Appraisal of search filters for applicability and validity is required
Clearer guidance for end‐users (librarians, clinicians) on the use of search filters is needed
Genetic Recombination inBacillus subtilis168: Contribution of Holliday Junction Processing Functions in Chromosome Segregation
Authors: Carrasco Begoña , Cozar M. Castillo , Lurz Rudi , Alonso Juan C. , Ayora Silvia 
Published: August 2004

ABSTRACTBacillus subtilismutants classified within the ε (ruvA, ΔruvB, ΔrecU, andrecD) and η (ΔrecG) epistatic groups, in an otherwiserec+background, render cells impaired in chromosomal segregation. A less-pronounced segregation defect in ΔrecAand Δsms(ΔradA) cells was observed. The repair deficiency ofaddAB, ΔrecO, ΔrecR,recH, ΔrecS, and ΔsubAcells did not correlate with a chromosomal segregation defect. The sensitivity of ε epistatic group mutants to DNA-damaging agents correlates with ongoing DNA replication at the time of exposure to the agents. The Δsms(ΔradA) and ΔsubAmutations partially suppress the DNA repair defect inruvAandrecDcells and the segregation defect inruvAand ΔrecGcells. The Δsms(ΔradA) and ΔsubAmutations partially suppress the DNA repair defect of ΔrecUcells but do not suppress the segregation defect in these cells. The ΔrecAmutation suppresses the segregation defect but does not suppress the DNA repair defect in ΔrecUcells. These results result suggest that (i) the RuvAB and RecG branch migrating DNA helicases, the RecU Holliday junction (HJ) resolvase, and RecD bias HJ resolution towards noncrossovers and that (ii) Sms (RadA) and SubA proteins might play a role in the stabilization and or processing of HJ intermediates.
Transglutaminase-Mediated Cross-Linking of GerQ in the Coats of
Bacillus subtilis
Spores
Authors: Ragkousi Katerina , Setlow Peter 
Published: August 2004

ABSTRACT

The spores of
Bacillus subtilis
show remarkable resistance to many environmental stresses, due in part to the presence of an outer proteinaceous structure known as the spore coat. GerQ is a spore coat protein essential for the presence of CwlJ, an enzyme involved in the hydrolysis of the cortex during spore germination, in the spore coat. Here we show that GerQ is cross-linked into higher-molecular-mass forms due in large part to a transglutaminase. GerQ is the only substrate for this transglutaminase identified to date. In addition, we show that cross-linking of GerQ into high-molecular-mass forms occurs only very late in sporulation, after mother cell lysis. These findings, as well as studies of GerQ cross-linking in mutant strains where spore coat assembly is perturbed, lead us to suggest that coat proteins must assemble first and that their cross-linking follows as a final step in the spore coat formation pathway.
The LysR-Type Transcriptional Regulator VirR Is Required for Expression of the Virulence GenevapAofRhodococcus equiATCC 33701
Authors: Russell Dean A. , Byrne Gavin A. , O'Connell Enda P. , Boland Clara A. , Meijer Wim G. 
Published: August 2004

ABSTRACTThe virulence of the intracellular pathogenRhodococcus equiin foals is dependent on the presence of an 81-kb virulence plasmid encoding the virulence protein VapA. Expression of this protein is induced by exposure to oxidative stress, high temperatures, and low pHs, which reflect the conditions encountered byR. equiwhen it enters the host environment. The aim of this study was to determine whether the LysR-type transcriptional regulator VirR, which is encoded by the virulence plasmid, is required for the expression ofvapA. It was shown that thevirRgene is cotranscribed with four downstream genes, one of which encodes a two-component response regulator. The expression of VapA, as monitored by Western blotting, was completely dependent on the presence ofvirR. Maximal expression was observed whenvapAwas present together with the completevirRoperon, suggesting that at least one of the virR operon genes, in addition tovirR, is required for the expression ofvapAto wild-type levels. The transcriptional start site ofvapAwas determined to be a cytidine located 226 bp upstream from thevapAinitiation codon. His-tagged VirR protein was expressed inEscherichia coliand purified by nickel affinity chromatography. DNA binding studies showed that purified VirR binds to a DNA fragment containing thevapApromoter. We therefore conclude that VirR is required for the activation ofvapAtranscription.
Identification and Transcriptional Control of
Caulobacter crescentus
Genes Encoding Proteins Containing a Cold Shock Domain
Authors: Lang Elza A. S. , Marques Marilis V. 
Published: August 2004

ABSTRACT

The cold shock proteins are small peptides that share a conserved domain, called the cold shock domain (CSD), that is important for nucleic acid binding. The
Caulobacter crescentus
genome has four
csp
genes that encode proteins containing CSDs. Three of these (
cspA
,
cspB
, and
cspC
) encode peptides of about 7 kDa and are very similar to the cold shock proteins of other bacteria. Analysis by reverse transcription-PCR of the fourth gene (
cspD
), which was previously annotated as encoding a 7-kDa protein, revealed that the mRNA is larger and probably encodes a putative 21-kDa protein, containing two CSDs. A search in protein sequences databases revealed that this new domain arrangement has thus far only been found among deduced peptides of α-proteobacteria. Expression of each
Caulobacter csp
gene was studied both in response to cold shock and to growth phase, and we have found that only
cspA
and
cspB
are induced by cold shock, whereas
cspC
and
cspD
are induced at stationary phase, with different induction rates. The transcription start sites were determined for each gene, and a deletion mapping of the
cspD
promoter region defined a sequence required for maximal levels of expression, indicating that regulation of this gene occurs at the transcriptional level. Deletion of
cspA
, but not
cspD
, caused a reduction in viability when cells were incubated at 10°C for prolonged times, suggesting that
cspA
is important for adaptation to a low temperature.
A Regulatory Trade-Off as a Source of Strain Variation in the Species
Escherichia coli
Authors: King Thea , Ishihama Akira , Kori Ayako , Ferenci Thomas 
Published: August 2004

ABSTRACT

There are few existing indications that strain variation in prokaryotic gene regulation is common or has evolutionary advantage. In this study, we report on isolates of
Escherichia coli
with distinct ratios of sigma factors (RpoD, σ
D
, or σ
70
and RpoS or σ
S
) that affect transcription initiated by RNA polymerase. Both laboratory
E. coli
K-12 lineages and nondomesticated isolates exhibit strain-specific endogenous levels of RpoS protein. We demonstrate that variation in genome usage underpins intraspecific variability in transcription patterns, resistance to external stresses, and the choice of beneficial mutations under nutrient limitation. Most unexpectedly, RpoS also controlled strain variation with respect to the metabolic capability of bacteria with more than a dozen carbon sources. Strains with higher σ
S
levels were more resistant to external stress but metabolized fewer substrates and poorly competed for low concentrations of nutrients. On the other hand, strains with lower σ
S
levels had broader nutritional capabilities and better competitive ability with low nutrient concentrations but low resistance to external stress. In other words, RpoS influenced both
r
and
K
strategist functions of bacteria simultaneously. The evolutionary principle driving strain variation is proposed to be a conceptually novel trade-off that we term SPANC (for “self-preservation and nutritional competence”). The availability of multiple SPANC settings potentially broadens the niche occupied by a species consisting of individuals with narrow specialization and reveals an evolutionary advantage offered by polymorphic regulation. Regulatory diversity is likely to be a significant contributor to complexity in a bacterial world in which multiple sigma factors are a universal feature.
Slr1293 in
Synechocystis
sp. Strain PCC 6803 Is the C-3′,4′ Desaturase (CrtD) Involved in Myxoxanthophyll Biosynthesis
Authors: Mohamed Hatem E. , Vermaas Wim 
Published: August 2004

ABSTRACT

When grown at high light intensity, more than a quarter of the total carotenoids in the unicellular cyanobacterium
Synechocystis
consists of myxoxanthophyll, a polar carotenoid glycoside. The biosynthetic pathway of myxoxanthophyll is unknown but is presumed to involve a number of enzymes, including a C-3′,4′ desaturase required to add one double bond to generate 11 conjugated double bonds in the monocyclic myxoxanthophyll. A candidate for this desaturase is Slr1293, which was identified by genome similarity searching. To determine whether Slr1293 is a desaturase recognizing neurosporene and lycopene,
slr1293
was expressed in
Escherichia coli
strains accumulating neurosporene or lycopene. Confirming such a desaturase function for Slr1293, these
E. coli
strains accumulated 3′,4′-didehydroneurosporene and 3′,4′-didehydrolycopene, respectively. Indeed, deletion of
slr1293
in
Synechocystis
provides further evidence that Slr1293 is a desaturase recognizing neurosporene: In the
slr1293
deletion mutant, neurosporene was found to accumulate and was further processed to produce neurosporene glycoside. Neurosporene hereby becomes a primary candidate to be the branch point molecule between carotene and myxoxanthophyll biosynthesis in this cyanobacterium. The
slr1293
gene was concluded to encode a C-3′,4′ desaturase that is essential for myxoxanthophyll biosynthesis, and thus it was designated as
crtD
. Furthermore, as Slr1293 appears to recognize neurosporene and to catalyze the first committed step on the myxoxanthophyll biosynthesis pathway, Slr1293 plays a pivotal role in directing a portion of the precursor pool for carotenoid biosynthesis toward myxoxanthophyll biosynthesis in
Synechocystis
sp. strain PCC 6803.
Bacillus subtilisLmrA Is a Repressor of thelmrABandyxaGHOperons: Identification of Its Binding Site and Functional Analysis oflmrBandyxaGH
Authors: Yoshida Ken-ichi , Ohki Yo-hei , Murata Makiko , Kinehara Masaki , Matsuoka Hiroshi , Satomura Takenori , Ohki Reiko , Kumano Miyuki , Yamane Kunio , Fujita Yasutaro 
Published: August 2004

ABSTRACTTheBacillus subtilis lmrABoperon is involved in multidrug resistance. LmrA is a repressor of its own operon, while LmrB acts as a multidrug efflux transporter. LmrA was produced inEscherichia colicells and was shown to bind to thelmrpromoter region, in which an LmrA-binding site was identified. Genome-wide screening involving DNA microarray analysis allowed us to conclude that LmrA also repressedyxaGH, which was not likely to contribute to the multidrug resistance. LmrA bound to a putativeyxaGHpromoter region, in which two tandem LmrA-binding sites were identified. The LmrA regulon was thus determined to compriselmrABandyxaGH. All three LmrA-binding sites contained an 18-bp consensus sequence, TAGACCRKTCWMTATAWT, which could play an important role in LmrA binding.
Acid-Inducible Transcription of the Operon Encoding the Citrate Lyase Complex of
Lactococcus lactis
Biovar diacetylactis CRL264
Authors: Martín Mauricio G. , Sender Pablo D. , Peirú Salvador , de Mendoza Diego , Magni Christian 
Published: August 2004

ABSTRACT

Although
Lactococcus
is one of the most extensively studied lactic acid bacteria and is the paradigm for biochemical studies of citrate metabolism, little information is available on the regulation of the citrate lyase complex. In order to fill this gap, we characterized the genes encoding the subunits of the citrate lyase of
Lactococcus lactis
CRL264, which are located on an 11.4-kb chromosomal DNA region. Nucleotide sequence analysis revealed a cluster of eight genes in a new type of genetic organization. The
citM-citCDEFXG
operon (
cit
operon) is transcribed as a single polycistronic mRNA of 8.6 kb. This operon carries a gene encoding a malic enzyme (CitM, a putative oxaloacetate decarboxylase), the structural genes coding for the citrate lyase subunits (
citD
,
citE
, and
citF
), and the accessory genes required for the synthesis of an active citrate lyase complex (
citC
,
citX
, and
citG
). We have found that the
cit
operon is induced by natural acidification of the medium during cell growth or by a shift to media buffered at acidic pHs. Between the
citM
and
citC
genes is a divergent open reading frame whose expression was also increased at acidic pH, which was designated
citI
. This inducible response to acid stress takes place at the transcriptional level and correlates with increased activity of citrate lyase. It is suggested that coordinated induction of the citrate transporter, CitP, and citrate lyase by acid stress provides a mechanism to make the cells (more) resistant to the inhibitory effects of the fermentation product (lactate) that accumulates under these conditions.
Cloning and Expression of
afpA
, a Gene Encoding an Antifreeze Protein from the Arctic Plant Growth-Promoting Rhizobacterium
Pseudomonas putida
GR12-2
Authors: Muryoi Naomi , Sato Mika , Kaneko Shoji , Kawahara Hidehisa , Obata Hitoshi , Yaish Mahmoud W. F. , Griffith Marilyn , Glick Bernard R. 
Published: August 2004

ABSTRACT

The Arctic plant growth-promoting rhizobacterium
Pseudomonas putida
GR12-2 secretes an antifreeze protein (AFP) that promotes survival at subzero temperatures. The AFP is unusual in that it also exhibits a low level of ice nucleation activity. A DNA fragment with an open reading frame encoding 473 amino acids was cloned by PCR and inverse PCR using primers designed from partial amino acid sequences of the isolated AFP. The predicted gene product, AfpA, had a molecular mass of 47.3 kDa, a pI of 3.51, and no previously known function. Although AfpA is a secreted protein, it lacked an N-terminal signal peptide and was shown by sequence analysis to have two possible secretion systems: a hemolysin-like, calcium-binding secretion domain and a type V autotransporter domain found in gram-negative bacteria. Expression of
afpA
in
Escherichia coli
yielded an intracellular 72-kDa protein modified with both sugars and lipids that exhibited lower levels of antifreeze and ice nucleation activities than the native protein. The 164-kDa AFP previously purified from
P. putida
GR12-2 was a lipoglycoprotein, and the carbohydrate was required for ice nucleation activity. Therefore, the recombinant protein may not have been properly posttranslationally modified. The AfpA sequence was most similar to cell wall-associated proteins and less similar to ice nucleation proteins (INPs). Hydropathy plots revealed that the amino acid sequence of AfpA was more hydrophobic than those of the INPs in the domain that forms the ice template, thus suggesting that AFPs and INPs interact differently with ice. To our knowledge, this is the first gene encoding a protein with both antifreeze and ice nucleation activities to be isolated and characterized.