bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Influenza Primer Design Resource: a new tool for translating influenza sequence data into effective diagnostics
Authors: Bose Michael E. , Littrell John C. , Patzer Andrew D. , Kraft Andrea J. , Metallo Jacob A. , Fan Jiang , Henrickson Kelly J. 
Published: March 2008

Background  Recent outbreaks of highly pathogenic avian influenza and multiple occurrences of zoonotic infection and deaths in humans have sparked a dramatic increase in influenza research. In order to rapidly identify and help prevent future influenza outbreaks, numerous laboratories around the world are working to develop new nucleotide‐based diagnostics for identifying and subtyping influenza viruses. While there are several databases that have been developed for manipulating the vast amount of influenza genetic data that have been produced, significant progress can still be made in developing tools for translating the genetic data into effective diagnostics.Description  The Influenza Primer Design Resource (IPDR) is the combination of a comprehensive database of influenza nucleotide sequences and a web interface that provides several important tools that aid in the development of oligonucleotides that may be used to develop better diagnostics. IPDR’s database can be searched using a variety of criteria, allowing the user to align the subset of influenza sequences that they are interested in. In addition, IPDR reports a consensus sequence for the alignment along with sequence polymorphism information, a summary of most published primers and probes that match the consensus sequence, and a Primer3 analysis of potential primers and probes that could be used for amplifying the sequence subset.Conclusions  The IPDR is a unique combination of bioinformatics tools that will greatly aid researchers in translating influenza genetic data into diagnostics, which can effectively identify and subtype influenza strains. The website is freely available at http://www.ipdr.mcw.edu.
Estimating river flow capacity in practice
Authors: Mc Gahey C. , Samuels P.G. , Knight D.W. , O'Hare M.T. 
Published: March 2008

AbstractEstimating water level underpins almost all river flood risk management (FRM) tasks from identifying routine channel maintenance actions to developing comprehensive sustainable FRM measures. Research over the past 50 years has seen considerable advances in estimating flow capacity; however, much of this knowledge has not been transferred into industry practice. This paper introduces the Conveyance and Afflux Estimation System (CES/AES) software, the primary output from two UK Environment Agency Research projects, which aim to bridge this gap between science and practice. The focus is the conveyance element, which provides a means for estimating flow capacity for a range of channel types, flow conditions and vegetation and substrate cover. An overview of the methodology and testing is given, together with a practical example of its use in decision making. The method is applied to 16 river sites from the United Kingdom, New Zealand, Argentina and Ecuador, exhibiting model performance for a wide range of channel and flow conditions. Simulations of depth‐averaged velocities at four sites are compared with observations, improving confidence in the underlying methods. The CES/AES toolset is also used in assessing flood risk versus ecological objectives for a small UK river, where vegetation is of significant conservation value but impacts flow capacity.
Functional Mapping of the
Candida albicans
Efg1 Regulator
Authors: Noffz Christine S. , Liedschulte Vanessa , Lengeler Klaus , Ernst Joachim F. 
Published: March 2008

ABSTRACT

Efg1p is a key transcriptional regulator in
Candida albicans
which controls various aspects of morphogenesis and metabolism in this organism. Efg1p contains a central basic helix-loop-helix (bHLH) domain, flanked by sequences highly conserved in fungal APSES proteins, as well as polyglutamine stretches at the N- and C-terminal ends. A systematic deletion approach to specify functional domains of Efg1p revealed that the APSES domain is essential for morphogenesis of the normal yeast and true hyphal cell forms and that bHLH flanking sequences are needed for Efg1p stability. Additional C-terminal sequences were required for hypha formation on some inducing media, and most Efg1p sequences were needed for chlamydospore morphogenesis. Overexpression of
EFG1
led to pseudohypha formation only if a functional APSES domain was present, while a switch from the opaque to the white cell type in addition depended on the presence of certain N- and C-terminal segments. Yeast two-hybrid experiments revealed that binding of Efg1p to its antagonist Czf1p required two regions outside of the APSES domain, which did not coincide with Efg1p sequences needed for its transcriptional repressor activity. Binding of the Flo8 transcription factor to Efg1p did not require the APSES domain but appeared to occur at two or more redundant domains. In contrast, DNA binding of Efg1p to an MluI cell cycle box (MCB) element solely required the APSES domain. Overall, these results suggest that functional domains of Efg1p are spread throughout most of its sequences, including the central APSES domain involved in DNA binding, as well as flanking regions required for various protein interactions and regulatory activities.
Saccharomyces cerevisiae
Phospholipase C Regulates Transcription of Msn2p-Dependent Stress-Responsive Genes
Authors: Demczuk Agnieszka , Guha Nilanjan , Nguyen Peter H. , Desai Parima , Chang Jennifer , Guzinska Katarzyna , Rollins Janet , Ghosh Chandra C. , Goodwin Leslie , Vancura Ales 
Published: March 2008

ABSTRACT

Phosphatidylinositol phosphates are involved in signal transduction, cytoskeletal organization, and membrane trafficking. Inositol polyphosphates, produced from phosphatidylinositol phosphates by the phospholipase C-dependent pathway, regulate chromatin remodeling. We used genome-wide expression analysis to further investigate the roles of Plc1p (phosphoinositide-specific phospholipase C in
Saccharomyces cerevisiae
) and inositol polyphosphates in transcriptional regulation. Plc1p contributes to the regulation of approximately 2% of yeast genes in cells grown in rich medium. Most of these genes are induced by nutrient limitation and other environmental stresses and are derepressed in
plc1
Δ cells. Surprisingly, genes regulated by Plc1p do not correlate with gene sets regulated by Swi/Snf or RSC chromatin remodeling complexes but show correlation with genes controlled by Msn2p. Our results suggest that the increased expression of stress-responsive genes in
plc1
Δ cells is mediated by decreased cyclic AMP synthesis and protein kinase A (PKA)-mediated phosphorylation of Msn2p and increased binding of Msn2p to stress-responsive promoters. Accordingly,
plc1
Δ cells display other phenotypes characteristic of cells with decreased PKA activity. Our results are consistent with a model in which Plc1p acts together with the membrane receptor Gpr1p and associated G
α
protein Gpa2p in a pathway separate from Ras1p/Ras2p and converging on PKA.
Transcriptional Regulation of the
tad
Locus in
Aggregatibacter actinomycetemcomitans
: a Termination Cascade
Authors: Kram Karin E. , Hovel-Miner Galadriel A. , Tomich Mladen , Figurski David H. 
Published: March 2008

ABSTRACT

The
tad
(
t
ight
ad
herence) locus of
Aggregatibacter actinomycetemcomitans
includes genes for the biogenesis of Flp pili, which are necessary for bacterial adhesion to surfaces, biofilm formation, and pathogenesis. Although studies have elucidated the functions of some of the Tad proteins, little is known about the regulation of the
tad
locus in
A. actinomycetemcomitans
. A promoter upstream of the
tad
locus was previously identified and shown to function in
Escherichia coli
. Using a specially constructed reporter plasmid, we show here that this promoter (
tadp
) functions in
A. actinomycetemcomitans
. To study expression of the pilin gene (
flp-1
) relative to that of
tad
secretion complex genes, we used Northern hybridization analysis and a
lacZ
reporter assay. We identified three terminators, two of which (T1 and T2) can explain
flp-1
mRNA abundance, while the third (T3) is at the end of the locus. T1 and T3 have the appearance and behavior of intrinsic terminators, while T2 has a different structure and is inhibited by bicyclomycin, indicating that T2 is probably Rho dependent. To help achieve the appropriate stoichiometry of the Tad proteins, we show that a transcriptional-termination cascade is important to the proper expression of the
tad
genes. These data indicate a previously unreported mechanism of regulation in
A. actinomycetemcomitans
and lead to a more complete understanding of its Flp pilus biogenesis.
CSF, a Species-Specific Extracellular Signaling Peptide for Communication among Strains of
Bacillus subtilis
and
Bacillus mojavensis
Authors: Pottathil Mridula , Jung April , Lazazzera Beth A. 
Published: March 2008

ABSTRACT

ComX and CSF are
Bacillus subtilis
extracellular signaling peptides. Many different strains of
B. subtilis
do not communicate due to strain-specific variation of ComX. We demonstrate that CSF is a species-specific signaling molecule that partially compensates for the lack of ComX-mediated communication between different strains of
B. subtilis
.
Repair and Antirepair DNA Helicases inHelicobacter pylori
Authors: Kang Josephine , Blaser Martin J. 
Published: March 2008

ABSTRACTOrthologs of RecG and RuvABC are highly conserved among prokaryotes; inEscherichia coli, they participate in independent pathways that branch migrate Holliday junctions during recombinational DNA repair. RecG also has been shown to directly convert stalled replication forks into Holliday junctions. The bacteriumHelicobacter pylori, with remarkably high levels of recombination, possesses RecG and RuvABC homologs, but in contrast toE. coli, H. pyloriRecG limits recombinational repair. We now show that the RuvABC pathway plays the prominent, if not exclusive, repair role. By introducing anE. coliresolvase (RusA) intoH. pylori, the repair and recombination phenotypes of theruvBmutant but not therecGmutant were improved. Our results indicate that RecG and RuvB compete for Holliday junction structures in recombinational repair, but since a classic RecG resolvase is absent fromH. pylori, deployment of the RecG pathway is lethal. We propose that evolutionary loss of theH. pyloriRecG resolvase provides an “antirepair” pathway allowing for selection of varied strains. Such competition between repair and antirepair provides a novel mechanism to maximize fitness at a bacterial population level.
Raf kinase inhibitor protein: mechanism of loss of expression and association with genomic instability
Authors: Al-Mulla F , Hagan S , Al-Ali W , Jacob S P , Behbehani A I , Bitar M S , Dallol A , Kolch W 
Published: March 2008

Aims:Raf kinase inhibitory protein (RKIP; also known as PEBP, for phosphatidylethanolamine-binding protein) is an endogenous inhibitor of the Raf– MAPK kinase (MEK)–MAP kinase pathway. It has emerged as a significant metastasis suppressor in a variety of human cancers including colorectal cancer (CRC) and was recently shown to regulate the spindle checkpoint in cultured cells. This study aims at correlating RKIP expression with chromosomal instability in colorectal cancer samples and identifies possible mechanisms of RKIP loss.Methods:Chromosomal instability was assessed using metaphase-based comparative genomic hybridisation (CGH) and loss of heterozygosity (LOH) in 65 cases with microsatellite stable CRC and correlated with RKIP expression. Methyl-specific PCR was used on DNA extracted from 82 cases with CRC to determine CpG methylation status at the RKIP promoter and the results correlated with RKIP protein expression.Results:We demonstrate for the first time that in microsatellite stable (MSS) CRC, the number of chromosomal losses is inversely proportional to RKIP expression levels. We also show that methylation of the RKIP promoter is a major mechanism by which RKIP expression is silenced in CRC.Conclusions:RKIP loss by hypermethylation of its promoter could have a significant influence on colorectal cancer aneuploidy, which might explain its association with metastatic progression.
In quest of justice? Clinical prioritisation in healthcare for the aged
Authors: Pedersen R , Nortvedt P , Nordhaug M , Slettebø Å , Grøthe K H , Kirkevold M , Brinchmann B S , Andersen B 
Published: March 2008

Background:A fair distribution of healthcare services for older patients is an important challenge, but qualitative research exploring clinicians’ consideration in daily clinical prioritisation in healthcare services for the aged is scarce.Objectives:To explore what kind of criteria, values, and other relevant considerations are important in clinical prioritisations in healthcare services for older patients.Design:A semi-structured interview-guide was used to interview 45 clinicians working with older patients. The interviews were analysed qualitatively using hermeneutical content analysis and template organising style.Participants:20 physicians and 25 nurses working in public hospitals and nursing homes in different parts of Norway.Results and interpretations:Important dilemmas relate to under-provision of community care and comprehensive approaches, and over-utilisation of certain specialised services. Overt ageism is generally not reported, but the healthcare services for the aged seem to be inadequate due to more subtle processes, for example, dominating considerations and ideals and operating conditions that do not pay sufficient attention to older patients’ needs and considerations of justice. Clinical prioritisations are described as being dominated by adapting traditional biomedical approaches to the operating conditions. Many of the clinicians indicate that there is a potential for improving end of life decisions and for reducing exaggerated use of life-prolonging treatment and hospitalisations.Conclusion:The interviews in this study indicate that considerations of justice and patients’ perspectives should be given more attention to strike a balance between specialised medical approaches and more general and comprehensive approaches in healthcare services for older patients.
Information disclosure and decision-making: the Middle East versus the Far East and the West
Authors: Mobeireek A F , Al-Kassimi F , Al-Zahrani K , Al-Shimemeri A , al-Damegh S , Al-Amoudi O , Al-Eithan S , Al-Ghamdi B , Gamal-Eldin M 
Published: March 2008

Objectives:to assess physicians’ and patients’ views in Saudi Arabia (KSA) towards involving the patient versus the family in the process of diagnosis disclosure and decision-making, and to compare them with views from the USA and Japan.Design:A self-completion questionnaire (used previously to study these issues in Japan and the USA) was translated to Arabic and validated.Participants:Physicians (n = 321) from different specialties and ranks and patients (n = 264) in a hospital or attending outpatient clinics from 6 different regions in KSA.Results:In the case of a patient with incurable cancer, 67% of doctors and 51% of patients indicated that they would inform the patient in preference to the family of the diagnosis (p = 0.001). Assuming the family already knew, 56% of doctors and 49% of patients would tell the patient even if family objected (p NS). However, in the case of HIV infection, 59% of physicians and 81% of patients would inform the family about HIV status without the patient’s consent (p = 0.001). With regards to withholding ventilatory support, about 50% of doctors and over 60% of patients supported the use of mechanical ventilation in a patient with advanced cancer, regardless of the wishes of the patient or the family. Finally, the majority of doctors and patients (>85%) were against assisted suicide.Conclusions:Although there was more recognition for a patient’s autonomy amongst physicians, most patients preferred a family centred model of care. Views towards information disclosure were midway between those of the USA and Japan. Distinctively, however, decisions regarding life prolonging therapy and assisted suicide were not influenced to a great extent by wishes of the patient or family, but more likely by religious beliefs.
Access to medical records for research purposes: varying perceptions across research ethics boards
Authors: Willison D J , Emerson C , Szala-Meneok K V , Gibson E , Schwartz L , Weisbaum K M , Fournier F , Brazil K , Coughlin M D 
Published: March 2008

Introduction:Variation across research ethics boards (REBs) in conditions placed on access to medical records for research purposes raises concerns around negative impacts on research quality and on human subject protection, including privacy.Aim:To study variation in REB consent requirements for retrospective chart review and who may have access to the medical record for data abstraction.Methods:Thirty 90-min face-to-face interviews were conducted with REB chairs and administrators affiliated with faculties of medicine in Canadian universities, using structured questions around a case study with open-ended responses. Interviews were recorded, transcribed and coded manually.Results:Fourteen sites (47%) required individual patient consent for the study to proceed as proposed. Three (10%) indicated that their response would depend on how potentially identifying variables would be managed. Eleven sites (38%) did not require consent. Two (7%) suggested a notification and opt-out process. Most stated that consent would be required if identifiable information was being abstracted from the record. Among those not requiring consent, there was substantial variation in recognising that the abstracted information could potentially indirectly re-identify individuals. Concern over access to medical records by an outside individual was also associated with requirement for consent. Eighteen sites (60%) required full committee review. Sixteen (53%) allowed an external research assistant to abstract information from the health record.Conclusions:Large variation was found across sites in the requirement for consent for research involving access to medical records. REBs need training in best practices for protecting privacy and confidentiality in health research. A forum for REB chairs to confidentially share concerns and decisions about specific studies could also reduce variation in decisions.
Influence of physicians’ life stances on attitudes to end-of-life decisions and actual end-of-life decision-making in six countries
Authors: Cohen J , van Delden J , Mortier F , Löfmark R , Norup M , Cartwright C , Faisst K , Canova C , Onwuteaka-Philipsen B , Bilsen J ,   on behalf of the Eureld Consortium
Published: March 2008

Aim:To examine how physicians’ life stances affect their attitudes to end-of-life decisions and their actual end-of-life decision-making.Methods:Practising physicians from various specialties involved in the care of dying patients in Belgium, Denmark, The Netherlands, Sweden, Switzerland and Australia received structured questionnaires on end-of-life care, which included questions about their life stance. Response rates ranged from 53% in Australia to 68% in Denmark. General attitudes, intended behaviour with respect to two hypothetical patients, and actual behaviour were compared between all large life-stance groups in each country.Results:Only small differences in life stance were found in all countries in general attitudes and intended and actual behaviour with regard to various end-of-life decisions. However, with regard to the administration of drugs explicitly intended to hasten the patient’s death (PAD), physicians with specific religious affiliations had significantly less accepting attitudes, and less willingness to perform it, than non-religious physicians. They had also actually performed PAD less often. However, in most countries, both Catholics (up to 15.7% in The Netherlands) and Protestants (up to 20.4% in The Netherlands) reported ever having made such a decision.Discussion:The results suggest that religious teachings influence to some extent end-of-life decision-making, but are certainly not blankly accepted by physicians, especially when dealing with real patients and circumstances. Physicians seem to embrace religious belief in a non-imperative way, allowing adaptation to particular situations.
A pleasure among friends: how narghile (waterpipe) smoking differs from cigarette smoking in Syria
Authors: Hammal F , Mock J , Ward K D , Eissenberg T , Maziak W 
Published: March 2008

Background:Throughout the Eastern Mediterranean region (EMR), tobacco is used primarily in two forms: cigarette smoking and waterpipe (called narghile (nar-GIL-eh) in Syria) smoking.Objective:To explore whether narghile smokers are different from cigarette smokers in how their smoking habits are embedded in their everyday lives.Methods:One-to-one interviews with 16 adult narghile smokers and 16 adult cigarette smokers about their feelings, experiences and beliefs regarding their initiation, use patterns, and attempts to quit.Findings:Narghile smokers found that narghile was a pleasurable social experience embedded in cultural rituals. By contrast, cigarette smokers saw their cigarette smoking as a mundane, oppressive, personal addiction. Narghile smokers generally started in their 20s and found that smoking narghile fostered a sense of togetherness and cultural identity, while cigarette smokers started in their early teens, males having started to becoming a “real man”. Unlike cigarette smokers who felt stigmatised, narghile smokers generally felt that smoking narghile was socially accepted. Cigarette smokers believed that cigarettes were harmful to their health and harmful to those around them, but narghile smokers believed smoking narghile was relatively harmless to themselves or to others. Unlike cigarette smokers who used cigarettes to manage stress, narghile smokers used narghile for entertainment, leisure, and escape. However, frequent narghile smokers confessed that they felt addicted in much the same way as cigarette smokers. Cigarette smokers and narghile smokers viewed quitting as a matter of will and conviction. Most cigarette smokers had tried to quit. Very few narghile smokers had ever tried to quit, and most were not interested in quitting. Disturbingly, some cigarette smokers had tried to quit cigarettes by switching to smoking narghile, but later relapsed to smoking cigarettes.Conclusions:This exploratory study suggests that Syrian narghile smokers are different from Syrian cigarette smokers in their perceptions and beliefs about their smoking, and in their smoking patterns and lived experiences with tobacco. Our findings indicate that further in-depth research is need in the EMR to understand both modes of smoking to develop effective mode-specific prevention and cessation approaches. This study also raises concerns about a possible pattern where cigarette smokers are using narghile as a method for quitting cigarettes, and then relapsing.