bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Role of Length of Stay in Healthcare-Associated Bloodstream Infection
Authors: Jeon Christie Y. , Neidell Matthew , Jia Haomiao , Sinisi Matt , Larson Elaine 
Published: October 2012

Design.We conducted a retrospective cohort study to examine the role played by length of hospital stay in the risk of healthcare-associated bloodstream infection (BSI), independent of demographic and clinical risk factors for BSI.Patients.We employed data from 113,893 admissions from inpatients discharged between 2006 and 2008.Setting.Large tertiary healthcare center in New York City.Methods.We estimated the crude and adjusted hazard of BSI by conducting logistic regression using a person-day data structure. The covariates included in the fully adjusted model included age, sex, Charlson score of comorbidity, renal failure, and malignancy as static variables and central venous catheterization, mechanical ventilation, and intensive care unit stay as time-varying variables.Results.In the crude model, we observed a nonlinear increasing hazard of BSI with increasing hospital stay. This trend was reduced to a constant hazard when fully adjusted for demographic and clinical risk factors for BSI.Conclusion.The association between longer length of hospital stay and increased risk of infection can largely be explained by the increased duration of stay among those who have underlying morbidity and require invasive procedures. We should take caution in attributing the association between length of stay and BSI to a direct negative impact of the healthcare environment.
Lengthening of 3′UTR increases with morphological complexity in animal evolution
Authors: Chen Cho-Yi , Chen Shui-Tein , Juan Hsueh-Fen , Huang Hsuan-Cheng 
Published: October 2012

Abstract
Motivation: Evolutionary expansion of gene regulatory circuits seems to boost morphological complexity. However, the expansion patterns and the quantification relationships have not yet been identified. In this study, we focus on the regulatory circuits at the post-transcriptional level, investigating whether and how this principle may apply.
Results: By analysing the structure of mRNA transcripts in multiple metazoan species, we observed a striking exponential correlation between the length of 3′ untranslated regions (3′UTR) and morphological complexity as measured by the number of cell types in each organism. Cellular diversity was similarly associated with the accumulation of microRNA genes and their putative targets. We propose that the lengthening of 3′UTRs together with a commensurate exponential expansion in post-transcriptional regulatory circuits can contribute to the emergence of new cell types during animal evolution.
Contact: yukijuan@ntu.edu.tw or hsuancheng@ym.edu.tw.
Supplementary information: Supplementary data are available at Bioinformatics online.
In situ target strength estimates of visually verified orange roughy
Authors: Macaulay Gavin J. , Kloser Rudy J. , Ryan Tim E. 
Published: October 2012

Abstract
Macaulay, G. J., Kloser, R. J., and Ryan, T. E. 2013. In situ target strength estimates of visually verified orange roughy. – ICES Journal of Marine Science, 70:215–222. The first estimates of orange roughy (Hoplostethus atlanticus) target strength at 38 and 120 kHz with visual verification were obtained from a self-contained echosounder and video camera system affixed to a demersal trawl towed through dense aggregations of spawning orange roughy. Mean target strength estimates were obtained from 24 tracks of orange roughy containing 83 echoes. The mean target strength at 38 kHz was –52.0 dB with a 95% confidence interval of –53.3 to –50.9 dB for fish with a mean length of 33.9 cm. At 120 kHz the mean target strength was –47.9 dB (confidence interval of –48.8 to –46.4 dB). This work makes two significant advances: in situ TS measurements have been made that can be confidently attributed to orange roughy, and using a trawl to herd orange roughy past the system resolved the previously intractable problem of fish avoidance.
Computational simulation methodologies for mechanobiological modelling: a cell-centred approach to neointima development in stents
Authors: Boyle C. J. , Lennon A. B. , Early M. , Kelly D. J. , Lally C. , Prendergast P. J. 
Published: October 2012

The design of medical devices could be very much improved if robust tools were available for computational simulation of tissue response to the presence of the implant. Such tools require algorithms to simulate the response of tissues to mechanical and chemical stimuli. Available methodologies include those based on the principle of mechanical homeostasis, those which use continuum models to simulate biological constituents, and the cell-centred approach, which models cells as autonomous agents. In the latter approach, cell behaviour is governed by rules based on the state of the local environment around the cell; and informed by experiment. Tissue growth and differentiation requires simulating many of these cells together. In this paper, the methodology and applications of cell-centred techniques—with particular application to mechanobiology—are reviewed, and a cell-centred model of tissue formation in the lumen of an artery in response to the deployment of a stent is presented. The method is capable of capturing some of the most important aspects of restenosis, including nonlinear lesion growth with time. The approach taken in this paper provides a framework for simulating restenosis; the next step will be to couple it with more patient-specific geometries and quantitative parameter data.
Cellular modelling: experiments and simulation to develop a physiological model of G-protein control of muscarinic K
+
channels in mammalian atrial cells
Authors: Murakami Shingo , Suzuki Shingo , Ishii Masaru , Inanobe Atsushi , Kurachi Yoshihisa 
Published: October 2012

The first model of G-protein–K
ACh
channel interaction was developed 14 years ago and then expanded to include both the receptor–G-protein cycle and G-protein–K
ACh
channel interaction. The G-protein–K
ACh
channel interaction used the Monod–Wyman–Changeux allosteric model with the idea that one K
ACh
channel is composed of four subunits, each of which binds one active G-protein subunit (G
βγ
). The receptor–G-protein cycle used a previous model to account for the steady-state relationship between K
ACh
current and intracellular guanosine-5-triphosphate at various extracellular concentrations of acetylcholine (ACh). However, simulations of the activation and deactivation of K
ACh
current upon ACh application or removal were much slower than experimental results. This clearly indicates some essential elements were absent from the model. We recently found that regulators of G-protein signalling are involved in the control of K
ACh
channel activity. They are responsible for the voltage-dependent relaxation behaviour of K
ACh
channels. Based on this finding, we have improved the receptor–G-protein cycle model to reproduce the relaxation behaviour. With this modification, the activation and deactivation of K
ACh
current in the model are much faster and now fall within physiological ranges.
Medicago truncatula ERN Transcription Factors: Regulatory Interplay with NSP1/NSP2 GRAS Factors and Expression Dynamics throughout Rhizobial Infection
Authors: Cerri Marion R. , Frances Lisa , Laloum Tom , Auriac Marie-Christine , Niebel Andreas , Oldroyd Giles E.D. , Barker David G. , Fournier Joëlle , de Carvalho-Niebel Fernanda 
Published: October 2012

Abstract
Rhizobial nodulation factors (NFs) activate a specific signaling pathway in Medicago truncatula root hairs that involves the complex interplay of Nodulation Signaling Pathway1 (NSP1)/NSP2 GRAS and Ethylene Response Factor Required for Nodulation1 (ERN1) transcription factors (TFs) to achieve full ENOD11 transcription. ERN1 acts as a direct transcriptional regulator of ENOD11 through the activation of the NF-responsive “NF box.” Here, we show that NSP1, when combined with NSP2, can act as a strong positive regulator of ERN1 and ENOD11 transcription. Although ERN1 and NSP1/NSP2 both activate ENOD11, two separate promoter regions are involved that regulate expression during consecutive symbiotic stages. Our findings indicate that ERN1 is required to activate NF-elicited ENOD11 expression exclusively during early preinfection, while NSP1/NSP2 mediates ENOD11 expression during subsequent rhizobial infection. The relative contributions of ERN1 and the closely related ERN2 to the rhizobial symbiosis were then evaluated by comparing their regulation and in vivo dynamics. ERN1 and ERN2 exhibit expression profiles compatible with roles during NF signaling and subsequent infection. However, differences in expression levels and spatiotemporal profiles suggest specialized functions for these two TFs, ERN1 being involved in stages preceding and accompanying infection thread progression while ERN2 is only involved in certain stages of infection. By cross complementation, we show that ERN2, when expressed under the control of the ERN1 promoter, can restore both NF-elicited ENOD11 expression and nodule formation in an ern1 mutant background. This indicates that ERN1 and ERN2 possess similar biological activities and that functional diversification of these closely related TFs relies primarily on changes in tissue-specific expression patterns.
Presidential election scenarios
Authors: Marren Patrick 
Published: October 2012

PurposeThe aim is to demonstrate the necessity of a scenario approach to decision making where non‐experts are forced to choose between expert opinions about which they cannot possibly form their own expert opinion.Design/methodology/approachThis is an opinion column.FindingsThe 2012 presidential election is almost sure to result in more of an austerity approach to the economy – and the level of that austerity may actually be greater under a re‐elected Obama than under a new President Romney.Practical implicationsDecision makers and strategists should be prepared for more of an austerity approach to economic policy, no matter who is elected in November.Social implicationsFew people are thinking through the actual implications of this election. A scenario analysis makes it fairly clear that the range of plausible policy outcomes is far narrower than is commonly believed.OriginalityThe article gives a possibly unique outlook on the 2012 presidential election.
Effect of incorporating whey protein concentrate into stevia‐sweetened Kulfi on physicochemical and sensory properties
Authors: Giri Apurba , Rao H G Ramachandra , V Ramesh 
Published: October 2012

In 50% sugar replaced with 0.05% stevia‐added Kulfi, whey protein concentrate (WPC) at 0, 2, 3 and 4% levels were separately incorporated. Increase in WPC level resulted in significant (P < 0.05) decrease in freezing point, melting rate, hardness and moisture percentage and significant (P < 0.05) increase in specific gravity, protein percentage and total calorie content in the product. Among 0, 2, 3 and 4% WPC‐added Kulfi, 3% WPC‐added Kulfi was adjudged as best by a panel of judges. Above 3% WPC addition, the product was very soft and possessed undesirable whey flavour.
Purifying and Concentrating Genomic DNA from Mock Forensic Samples Using Millipore Amicon Filters
Authors: Garvin Alex M. , Fritsch Anja 
Published: October 2012

AbstractRegenerated cellulose filters are used for concentrating and purifying genomic DNA from casework samples, due to the high yields and low retentate volumes that these filters provide. The Millipore Ultracel YM‐100 is an example of this filter type and has been available to the forensics community for this application since 1990. In 2002, Millipore introduced the Amicon line of vertical filters that provide a larger area for filtration and have a dead space to prevent spinning to dryness. In the present study, Amicon filters were optimized in terms of g force and spin times for their ability to concentrate and purify genomic DNA. The Amicon Ultra 0.5 mL 30 K was used with mock forensic samples containing as little as 160 buccal cells, 20 nL of blood, or 8 nL of semen. In conclusion, the Amicon line of filters can be used to purify genomic DNA from small numbers of cells.
A Collation of Recently Published Western European Formulae for Age Estimation of Subadult Skeletal Remains: Recommendations for Forensic Anthropology and Osteoarchaeology
Authors: Rissech Carme , Márquez‐Grant Nicholas , Turbón Daniel 
Published: October 2012

AbstractThe aim of this study is to provide an effective and quick reference guide based on the most useful European formulae recently published for subadult age estimation. All of these formulae derive from studies on postnatal growth of the scapula, innominate, femur, and tibia, based on modern skeletal data (173 ♂, 173 ♀) from five documented collections from Spain, Portugal, and Britain. The formulae were calculated from Inverse Regression. For this reason, these formulae are especially useful for modern samples from Western Europe and in particular on 20th century human remains from the Iberian Peninsula. Eleven formulae were selected as the most useful because they can be applied to individuals from within a wide age range and in individuals of unknown sex. Due to their high reliability and because they derive from documented European skeletal samples, we recommend these formulae be used on individuals of Caucasoid ancestry from Western Europe.
Proteomic Analysis of Bovine Axonemes Exposed to Acute Alcohol: Role of Endothelial Nitric Oxide Synthase and Heat Shock Protein 90 in Cilia Stimulation
Authors: Simet Samantha M. , Pavlik Jacqueline A. , Sisson Joseph H. 
Published: October 2012

BackgroundCilia are finger‐like motor‐driven organelles, which propel inhaled particles and mucus from the lung and airways. We have previously shown that brief alcohol exposure stimulates ciliary motility through an endothelial nitric oxide synthase (eNOS)‐dependent pathway localized in the ciliary metabolon. However, the signaling molecules of the ciliary metabolon involved in alcohol‐triggered ciliary beat frequency (CBF) stimulation upstream of eNOS activation remain unknown.MethodsWe hypothesized that brief alcohol exposure alters threonine and serine phosphorylation of proteins involved in stimulating CBF. Two‐dimensional electrophoresis indicated both increases and decreases in the serine and threonine phosphorylation states of several proteins. One of the proteins identified was heat shock protein 90 (HSP90), which undergoes increased threonine phosphorylation after brief alcohol exposure. Because HSP90 has been shown to associate with eNOS in lung tissue, we hypothesized that HSP90 is a key component in alcohol‐triggered eNOS activation and that these 2 proteins co‐localize within the ciliary metabolon.ResultsImmunofluorescence experiments demonstrate that eNOS and HSP90 co‐localize within basal bodies of the ciliary metabolon and partially translocate to the axoneme upon brief alcohol exposure. Pretreatment with geldanamycin, which disrupts HSP90 chaperone functions, prevented eNOS‐HSP90 association and prevented the translocation of eNOS from the ciliary metabolon to the axoneme. Functional cilia motility studies revealed that geldanamycin blocked alcohol‐stimulated ciliary motility in bovine bronchial epithelial cells and mouse tracheal rings.ConclusionsOn the basis of the HSP90 localization with eNOS, alcohol activation of HSP90 phosphorylation, and geldanamycin's ability to inhibit HSP90‐eNOS association, prevent eNOS translocation to the axoneme, and block alcohol‐stimulated ciliary motility, we conclude that alcohol‐induced cilia stimulation occurs through the increased association of HSP90 with eNOS. These data help further elucidate the mechanism through which brief alcohol exposure stimulates CBF.
A novel evaluation method for optical integration of Class IV composite restorations
Authors: Dietschi D , Abdelaziz M , Krejci I , Di Bella E , Ardu S 
Published: October 2012

AbstractBackground:  This aim of this study was to compare traditional visual appreciation with spectrophotometry to evaluate the optical integration of anterior composite restorations.Methods:  Eleven restorations were evaluated in eight patients receiving dental treatment at fourth and fifth year student clinics at the dental school of the University of Geneva, Switzerland. Colour integration of completed restorations was assessed by visual observation according to USPHS criteria and spectrophotometric analysis; both methods were then compared.Results:  A mean ΔE of 1.1 (range 0.7 to 1.7) corresponded to an optimal visual integration between natural tooth and restoration (alpha score) while a mean ΔE of 3.3 (range 2.6 to 3.8) corresponded to clinically ‘non‐acceptable’ visual integration (charlie score). Restorations scored as ‘bravo’, corresponded to a suboptimal but not disturbing visual integration, had a mean ΔE of 2. L* and b* values present at the bevel area and into the composite bulk tended to be lower than that of the natural tooth while a* composite values were slightly higher.Conclusions:  The spectrophotometric method employed in this pilot study has confirmed the published range of ΔE (global difference of L*a*b* values) corresponding to clinically ‘optimal’, ‘acceptable’ and ‘unacceptable’ colour integration.
Do antibacterial mouthrinses affect bacteraemia in third molar surgery? A pilot study
Authors: Tuna A , Delilbasi C , Arslan A , Gurol Y , Tazegun Tekkanat Z 
Published: October 2012

AbstractBackground:  The aim of this pilot study was to evaluate the effects of mouthrinses containing 7.5% povidone iodine and 0.2% chlorhexidine on bacteraemia following impacted third molar surgery.Methods:  Thirty‐four patients were enrolled in this study. Patients in the first group were asked to rinse their mouth with the mouthrinse containing 7.5% povidone iodine, patients in the second group were asked to rinse with the mouthrinse containing 0.2% chlorhexidine and patients in the third group were asked to rinse with 0.9% NaCl (sterile saline) solution. All rinses were used for one minute preoperatively. Peripheral venous blood samples were collected at baseline (preoperatively), 1 and 15 minutes after the completion of surgical tooth removal. Each blood sample was divided in two, placed in aerobic and anaerobic culture bottles and processed for microbiological examination.Results:  Bactaeremia was detected in 33% of the povidone iodine group, 33% of the chlorhexidine group and 50% of the control group. Isolated bacteria were 58% anaerobes and predominantly 92%Streptococcus species. Incidence of bacteraemia was reduced with chlorhexidine and povidone iodine mouthrinses in third molar surgery, although the difference was not statistically significant (p > 0.05).Conclusions:  Bacteraemia was reduced with antibacterial mouthrinses in third molar surgery. The results of this study should be confirmed with further studies conducted on a larger patient population and with different antibacterial mouthrinses.
Evolution of Helicobacter pylori susceptibility to antibiotics during a 10‐year period in Lithuania
Authors: Kupcinskas Limas , Rasmussen Lone , Jonaitis Laimas , Kiudelis Gediminas , Jørgensen Marianne , Urbonaviciene Neringa , Tamosiunas Vytas , Kupcinskas Juozas , Miciuleviciene Jolanta , Kadusevicius Edmundas , Berg Douglas , Andersen Leif P. 
Published: October 2012

The study evaluated the changes in the prevalence of Helicobacter pylori strains with primary resistance to antibiotics during the last 10 years in Lithuania. H. pylori susceptibilities to antibiotics were tested in 89 patients in 1998, in 81 patients in 2001 and in 90 patients in 2007/2008. Susceptibility to metronidazole, clarithromycin, amoxicillin and tetracycline was tested using E‐test or agar dilution method. Susceptibility to ciprofloxacin was only tested in 2007/2008. Data about utilization of all authorized and available on market macrolides and clindamycin in Lithuania during 2003–2007 were evaluated using WHO ATC/DDD methodology. A total of 260 H. pylori strains cultured from untreated adult patients were investigated. Primary resistance rates (1998, 2001 and 2007/2008) for metronidazole were 24.7%, 33.3%, and 35.6%, for clarithromycin 1.1%, 3.7%, and 3.3% and for tetracycline 0%, 2.5% and 0% respectively. No cases of amoxicillin resistance have been detected. The resistance rate for ciprofloxacin was 5.6% in 2007/2008. Data of total macrolides and clarithromycin utilization in Lithuania revealed that despite an increase of consumption of these drugs in Lithuania during 2003–2007 in 1.5 times, the total macrolide consumption remains one of the lowest in Europe. We have not observed any significant changes in the susceptibility of H. pylori to the most widely used antibiotics during the recent 10‐year period. The low resistance rate to clarithromycin might be related to the policy to avoid use of macrolides as first‐line treatment for pulmonary and other infections.
Methanogenic archaea in subgingival sites: a review
Authors: Nguyen‐Hieu Tung , Khelaifia Saber , Aboudharam Gerard , Drancourt Michel 
Published: October 2012

Archaea are non‐bacterial prokaryotes associated with oral microbiota in humans, but their roles in oral pathologies remain controversial. Several studies reported the molecular detection of methanogenic archaea from periodontitis, but the significance of this association has not been confirmed yet. An electronic search was therefore conducted in MEDLINE‐Pubmed to identify all papers published in English connecting archaea and periodontal infections. Data analysis of the selected studies showed that five genera of methanogenic archaea have been detected in the subgingival microbiota, Methanobrevibacter oralis being the most frequently detected species in 41% of periodontitis patients and 55% of periodontal pockets compared to 6% of healthy subjects and 5% of periodontally‐healthy sites (p < 10−5, Chi‐squared test). Based on the five determination‐criteria proposed by Socransky (association with disease, elimination of the organism, host response, animal pathogenicity and mechanisms of pathogenicity), M. oralis is a periodontal pathogen. The methanogenic archaea load correlating with periodontitis severity further supports the pathogenic role of methanogenic archaea in periodontitis. Therefore, detection and quantification of M. oralis in periodontal pockets could help the laboratory diagnosis and follow‐up of periodontitis. Determining the origin, diversity and pathogenesis of archaea in periodontal infections warrants further investigations.