bluuebunny/crossref_metadata_2025_split huggingface dataset:
σE‐dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay
Authors: Papenfort Kai , Pfeiffer Verena , Mika Franziska , Lucchini Sacha , Hinton Jay C. D. , Vogel Jörg 
Published: November 2006

SummaryThe bacterial envelope stress response (ESR) is triggered by the accumulation of misfolded outer membrane proteins (OMPs) upon envelope damage or excessive OMP synthesis, and is mediated by the alternative sigma factor, σE. Activation of the σE pathway causes a rapid downregulation of major omp mRNAs, which prevents further build‐up of unassembled OMPs and liberates the translocation and folding apparatus under conditions that require envelope remodelling. The factors that facilitate the rapid removal of the unusually stable omp mRNAs in the ESR were previously unknown. We report that in Salmonella the ESR relies upon two highly conserved, σE‐controlled small non‐coding RNAs, RybB and MicA. By using a transcriptomic approach and kinetic analyses of target mRNA decay in vivo, RybB was identified as the factor that selectively accelerates the decay of multiple major omp mRNAs upon induction of the ESR, while MicA is proposed to facilitate rapid decay of the single ompA mRNA. In unstressed bacterial cells, the two σE‐dependent small RNAs function within a surveillance loop to maintain envelope homeostasis and to achieve autoregulation of σE.
Obliquity‐dominated glacio‐eustatic sea level change in the early Oligocene: evidence from the shallow marine siliciclastic Rupelian stratotype (Boom Formation, Belgium)
Authors: Abels Hemmo A. , Simaeys Stefaan Van , Hilgen Frits J. , Man Ellen De , Vandenberghe Noël 
Published: November 2006

AbstractOur results prove that glacio‐eustatic sea level oscillations in the early Oligocene were dominantly obliquity controlled with additional influence of the ∼100‐ and 405‐kyr eccentricity cycles. This was derived from spectral analysis of resistivity records from an extended downhole section of the Boom Clay succession in Belgium, that reveals a prevailing obliquity control on the laterally persistent metre‐scale alternations of shallow marine silt‐ and claystones in the Rupelian historical stratotype succession. These direct measurements of sea level variations in a shallow marine setting corroborate that variations with similar frequencies in benthonic oxygen isotope records from the open ocean indeed reflect, at least partly, ice volume change. A very tentative astronomical tuning has been established for the Boom Clay succession which awaits future confirmation with the addition of more accurate age calibration points.
Efficacy of artemether–lumefantrine for the treatment of uncomplicated falciparum malaria in northwest Cambodia
Authors: Denis Mey Bouth , Tsuyuoka Reiko , Lim Pharath , Lindegardh Niklas , Yi Poravuth , Top Sophoan Narann , Socheat Duong , Fandeur Thierry , Annerberg Anna , Christophel Eva Maria , Ringwald Pascal 
Published: November 2006

SummaryObjective  To determine the efficacy of artemether–lumefantrine malaria treatment, as an alternative to artesunate + mefloquine, which is becoming ineffective in some areas of the Thai–Cambodian border.Methods  Two studies were conducted to monitor the efficacy of artemether–lumefantrine in Sampov Lun referral hospital, Battambang Province, in 2002 and 2003, and one study was conducted to assess the efficacy of mefloquine + artesunate in 2003 for comparison. The studies were performed according to the WHO standardized protocol with a follow‐up of 28 days. The therapeutic efficacy tests were complemented with in vitro tests and in 2003, with the measurement of lumefantrine plasma concentration at day 7 for the patients treated with artemether–lumefantrine.Results  A total of 190 patients were included: 55 were treated with artemether–lumefantrine in 2002 (AL2002), 80 with artemether–lumefantrine and food supplementation in 2003 (AL2003) and 55 with artesunate + mefloquine in 2003 (AM2003). With the per‐protocol analysis, the cure rate was 71.1% in study AL2002, 86.5% in study AL2003 and 92.4% in study AM2003. All the data were PCR corrected. The artemether–lumefantrine cure rate was unexpectedly low in 2002, but it increased with food supplementation in 2003. There was a significant difference (P = 0.02) in lumefantrine plasma concentrations between adequate clinical and parasitological responses and treatment failure cases. In vitro susceptibility to lumefantrine was reduced for isolates sampled from patients presenting with treatment failure, but the difference was not statistically different from isolates sampled from patients who were successfully treated.Conclusion  Treatment failure cases of artemether–lumefantrine are most probably because of low levels of lumefantrine blood concentration. Further investigations are necessary to determine whether resistance of Plasmodium falciparum isolates to lumefantrine is present in the region.
Light and GABAA receptor activation alter Period mRNA levels in the SCN of diurnal Nile grass rats
Authors: Novak Colleen M. , Ehlen J. Christopher , Paul Ketema N. , Fukuhara Chiaki , Albers H. Elliott 
Published: November 2006

AbstractWe examined Period (Per) mRNA rhythms in the suprachiasmatic nucleus (SCN) of a diurnal rodent and assessed how phase‐shifting stimuli acutely affect SCN Per mRNA using semiquantitative in situ hybridization. First, Per1 and Per2 varied rhythmically in the SCN over the course of one circadian cycle in constant darkness: Per1 mRNA was highest in the early to mid‐subjective day, while Per2 mRNA levels peaked in the late subjective day. Second, acute light exposure in the early subjective night significantly increased both Per1 and Per2 mRNA. Third, Per2 but not Per1 levels decreased 1 and 2 h after injection of the γ‐aminobutyric acid (GABA)A receptor agonist muscimol into the SCN during the subjective day. Fourth, muscimol also reduced the light‐induced Per2 in the early subjective night, but Per1 induction by light was not significantly affected. Consistent with previous studies, these data demonstrate that diurnal and nocturnal animals show very similar daily patterns of Per mRNA and light‐induced Per increases in the SCN. As with light, muscimol alters circadian phase, and daytime phase alterations induced by muscimol are associated with significant decreases in Per2 mRNA. In diurnal animals, muscimol‐induced decreases in Per are associated with phase delays rather than advances. The direction of the daytime phase shift may be determined by the relative suppression of Per1 vs. Per2 in SCN cells. As in nocturnal animals, changes in Per1 and Per2 mRNA by photic and non‐photic stimuli appear to be associated with circadian phase alteration.
Second‐by‐second measurement of acetylcholine release in prefrontal cortex
Authors: Bruno John P. , Gash Clelland , Martin Brad , Zmarowski Amy , Pomerleau Francois , Burmeister Jason , Huettl Peter , Gerhardt Greg A. 
Published: November 2006

AbstractMicrodialysis has been widely used to measure acetylcholine (ACh) release in vivo and has provided important insights into the regulation of cholinergic transmission. However, microdialysis can be constrained by limited spatial and temporal resolution. The present experiments utilize a microelectrode array (MEA) to rapidly measure ACh release and clearance in anaesthetized rats. The array electrochemically detects, on a second‐by‐second basis, changes in current selectively produced by the hydrolysis of ACh to choline (Ch) and the subsequent oxidation of choline and hydrogen peroxidase (H2O2) at the electrode surface. In vitro calibration of the microelectrode revealed linear responses to ACh (R2 = 0.9998), limit of detection of 0.08 µm, and signal‐to‐noise ratio of 3.0. The electrode was unresponsive to ascorbic acid (AA), dopamine (DA), or norepinephrine (NE) interferents. In vivo experiments were conducted in prefrontal cortex (PFC) of anaesthetized rats. Pressure ejections of ACh (10 mm; 40 nL) through an adjoining micropipette produced a rapid rise in current, reaching maximum amplitude in ∼1.0 s and cleared by 80% within 4–11 s. Endogenously released ACh, following local depolarization with KCl (70 mm; 40, 160 nL), was detected at values as low as 0.05 µm. These signals were volume‐dependent and cleared within 4–12 s. Finally, nicotine (1.0 mm, 80 nL) stimulated ACh signals. Nicotine‐induced signals reflected the hydrolysis of ACh by endogenous acetylcholinesterase (AChE) as inhibition of the enzyme following perfusion with neostigmine (10 µm) attenuated the signal (40–94%). Collectively, these data validate a novel method for rapidly measuring cholinergic transmission in vivo with a spatial and temporal resolution that far exceeds conventional microdialysis.
Topical eutectic mixture for premature ejaculation (TEMPE): a novel aerosol‐delivery form of lidocaine‐prilocaine for treating premature ejaculation
Authors: Dinsmore Wallace W. , Hackett Geoffrey , Goldmeier David , Waldinger Marcel , Dean John , Wright Patrick , Callander Michael , Wylie Kevan , Novak Claire , Keywood Charlotte , Heath Patricia , Wyllie Michael 
Published: November 2006

OBJECTIVETo evaluate, in a phase II study, the efficacy and safety of a topical eutectic mixture for premature ejaculation (TEMPE), a metered‐dose aerosol spray containing a eutectic mixture of lidocaine and prilocaine, as a treatment for PE.PATIENTS AND METHODSMen with PE (Diagnostic and Statistical Manual‐IV definition) aged 18–75 years were randomized into a double‐blind, placebo‐controlled study in the UK and the Netherlands. Efficacy variables included the mean change in intravaginal ejaculatory latency time (IELT) from baseline and the proportion of patients who achieved an IELT of ≥ 4, ≥ 3 or ≥ 2 min on two occasions, and the effect of TEMPE on the index of ejaculatory control (IEC) and sexual quality‐of‐life (SQoL) scores of patients and their partners. Safety and adverse event data were also collected.Fifty‐four patients were randomized and received study treatment.RESULTSThe observed mean change in IELT from baseline to the end of the treatment period was 3.8 min in the TEMPE group and 0.7 min in the placebo group, and when adjusted for baseline and centre was 2.4 times higher in the TEMPE than the placebo group (P < 0.01). The efficacy of TEMPE in increasing IELT was further supported by positive trends in the other efficacy endpoints. The proportion of men who had an IELT time ≥ 2, ≥ 3 or ≥ 4 min on two occasions after treatment was 11/20 (55%), 8/20 (40%) and 5/25 (20%) in the TEMPE group, and 8/23 (35%), 3/23 (13%) and 3/23 (13%) in the placebo group, respectively, although these differences were not statistically significant. Improvements in IEC and SQoL (male and female) scores also showed trends towards greater efficacy for TEMPE than placebo. In all, 35 of 42 (83%) patients considered the spray easy to use. Mild to moderate local numbness occurred in three (12%) of the TEMPE‐treated patients but did not lead to discontinuation.CONCLUSIONTopical treatment with TEMPE produced a statistically and clinically significant increase in IELT compared with placebo, and resulted in positive trends in ejaculatory control and SQoL. TEMPE was considered easy to use and was well tolerated. The data support the conduct of further large‐scale studies to establish the utility of TEMPE as a first‐line treatment for PE.
Inflammation associated with implants with different surface types
Authors: Pongnarisorn Nuchjaree J. , Gemmell Erica , Tan Albert E. S. , Henry Patrick J. , Marshall Roderick I. , Seymour Gregory J. 
Published: November 2006

AbstractObjectives: The aim of this study was to determine the nature of the inflammatory infiltrate associated with different transmucosal implant surfaces in dogs.Methods: Three experimental and one control single‐stage implants were randomly placed on each side of the jaw in eight dogs. The transmucosal portion of the test implants consisted of an acid‐etched surface (type A), a machined surface with a circumferential groove (type C) and a surface prepared by mild anodic oxidation (type D). The control was a standard machined surface (type B). In order to determine the response to the different surfaces, plaque control was carried out twice weekly following placement of the implants for the entire period of the experiment. At 6 months, gingival biopsies and plaque samples were obtained. The area of inflammatory infiltrate and the nature of the infiltrating cell types were determined using immunohistology. Real‐time polymerase chain reaction was used to identify putative periodontal pathogens.Results: Inflammatory infiltrates were associated with all implant surfaces and were commonly found subepithelially and perivascularly. T cells were the predominant infiltrating cell type in all lesions, associated with the different surfaces. In all lesions the CD4 : CD8 ratio was approximately 2 : 1. Statistical analysis showed that the type C surface (machined surface with a groove) had significantly larger inflammatory infiltrates than the type B surface (machined surface without a groove; P<0.05). No statistically significant differences were found with respect to the size of the inflammatory infiltrates or in terms of the nature of infiltrating cells. However, despite the intensive plaque control regime, plaque was present on all implant surfaces at the time of biopsy 6 months after placement. All implants had similar numbers of Tannerella forsythia, Fusobacterium nucleatum and Porphyromonas gingivalis. Actinobacillus actinomycetemcomitans, was not detected in any sample.Conclusions: These results suggest that the development of inflammation associated with implants is independent of surface type, but is nevertheless associated with the presence of plaque. The different surfaces had no influence on the nature of the infiltrate, with T cells being the predominant cell type in all lesions. Finally, the different implant surface types seemed not to influence the peri‐implant microbiota. However, the presence of the circumferential groove tended to be associated with larger infiltrates. Whether this is due to increased plaque accumulation remains to be determined.
Review article: the risks of oesophageal acid exposure ‐ from minimal mucosal changes to malignancy
Authors: HUNT R. H. 
Published: November 2006

SummaryGastro‐oesophageal reflux disease is very common and presents with a spectrum of symptoms with or without oesophageal damage. Gastro‐oesophageal reflux disease has an adverse impact on quality of life, especially in those with nocturnal symptoms.Prolonged exposure of the oesophageal mucosa to acidic gastric contents with pepsin and bile increases the risk of oesophageal mucosal injury. The frequency and severity of symptoms and oesophagitis correlate with the frequency, severity and duration of acid exposure, particularly at night‐time.This study reviews the mechanisms and evidence for acid‐induced symptoms and oesophageal injury, from superficial mucosal injury to Barrett's oesophagus and the long‐term risk of oesophageal adenocarcinoma.Optimizing the choice and dose regimen of proton‐pump inhibitor is essential for treating gastro‐oesophageal reflux disease, and nocturnal acid control is important in preventing complicated gastro‐oesophageal reflux disease.
Review article: a conceptual model for the relationship of nocturnal acidity and extra‐oesophageal manifestations of gastro‐oesophageal reflux disease ‐ where are we now?
Authors: SHAKER R. 
Published: November 2006

SummaryA number of extra‐oesophageal abnormalities ranging from otolaryngologic disorders and dysphonia to non‐cardiac chest pain and sleep disturbances have been attributed to gastro‐oesophageal reflux disease. A significant degree of uncertainty and confusion continues to exist with regard to the pathogenesis, diagnosis and treatment of these conditions.The following conceptual model could be proposed for the pathogenesis of the extra‐oesophageal manifestations of gastro‐oesophageal reflux disease and, consequently, the likely response to therapy.This model suggests that these disorders are, in fact, multifactorial and that the contributions of refluxed gastric contents comprise only part of the pathogenesis. In the case of asthma, for example, factors that influence airway resistance and symptom production include basal airway resistance, intra‐oesophageal events, such as acid reflux‐stimulating vagal afferent fibres and inducing further airway changes, and extra‐oesophageal, allergic and other pulmonary factors that can influence airway resistance. This model allows for different degrees of influence from these three main contributors. In this model, if gastro‐oesophageal reflux disease‐related events contribute minimally to the changes in airway resistance compared with other factors, treating gastro‐oesophageal acid reflux would result in minimal or no change in symptoms and vice versa.At present, as it is difficult to identify prospectively those patients in whom reflux comprises the main pathological factor, and who might therefore respond to acid suppression, a trial of empiric proton‐pump inhibitor therapy with reflux precautionary measures seems appropriate and has been suggested by some expert panels.
NONLINEAR DYNAMICS OF AIR-WATER MIXTURES IN VERTICAL PIPES: EXPERIMENTAL TRENDS
Authors: CANTELLI L. , FICHERA A. , GUGLIELMINO I. D. , PAGANO A. 
Published: November 2006

This study reports the results of the characterization of an air-water two-phase experimental apparatus and the preliminary analyses of the experimental time series. The test section of the apparatus consists of a vertical pipe equipped with an impedance void fraction sensor. The carrying frequency of the impedance sensor has been chosen in order to operate it as a resistive sensor. The calibration of the sensor has been performed through comparison of the instantaneous two-phase mixture conductivity signal and the local actual dimension of the bubble as estimated from high resolution photograph. The calibration curve allows, therefore, reliable estimation of the void fraction time series. A preliminary analysis of the time series has been performed both in time and frequency domains, evaluating also the time series autocorrelation. These analyses have pointed out the inadequacy of linear tools for the characterization of two-phase flow dynamics, which are nonetheless characterized by strong recurrence and autocorrelation, which need to be further exploited by mean of nonlinear analysis in phase space. Phase space representation of different typical flow patterns, corresponding to a succession of bifurcation, shows the high potential of nonlinear analytical tools, to be adopted in order to exploit the system dynamics.
A hierarchical Naïve Bayes Model for handling sample heterogeneity in classification problems: an application to tissue microarrays
Authors: Demichelis Francesca , Magni Paolo , Piergiorgi Paolo , Rubin Mark A , Bellazzi Riccardo 
Published: November 2006

Abstract

Background
Uncertainty often affects molecular biology experiments and data for different reasons. Heterogeneity of gene or protein expression within the same tumor tissue is an example of biological uncertainty which should be taken into account when molecular markers are used in decision making. Tissue Microarray (TMA) experiments allow for large scale profiling of tissue biopsies, investigating protein patterns characterizing specific disease states. TMA studies deal with multiple sampling of the same patient, and therefore with multiple measurements of same protein target, to account for possible biological heterogeneity. The aim of this paper is to provide and validate a classification model taking into consideration the uncertainty associated with measuring replicate samples.

Results
We propose an extension of the well-known Naïve Bayes classifier, which accounts for biological heterogeneity in a probabilistic framework, relying on Bayesian hierarchical models. The model, which can be efficiently learned from the training dataset, exploits a closed-form of classification equation, thus providing no additional computational cost with respect to the standard Naïve Bayes classifier. We validated the approach on several simulated datasets comparing its performances with the Naïve Bayes classifier. Moreover, we demonstrated that explicitly dealing with heterogeneity can improve classification accuracy on a TMA prostate cancer dataset.

Conclusion
The proposed Hierarchical Naïve Bayes classifier can be conveniently applied in problems where within sample heterogeneity must be taken into account, such as TMA experiments and biological contexts where several measurements (replicates) are available for the same biological sample. The performance of the new approach is better than the standard Naïve Bayes model, in particular when the within sample heterogeneity is different in the different classes.
Acceptability and outcomes of the Percutaneous Endoscopic Gastrostomy (PEG) tube placement- patients' and care givers' perspectives
Authors: Anis Muhammad K , Abid Shahab , Jafri Wasim , Abbas Zaigham , Shah Hasnain A , Hamid Saeed , Wasaya Rozina 
Published: November 2006

Abstract

Background
Percutaneous endoscopic gastrostomy tube has now become a preferred option for the long-term nutritional support device for patients with dysphagia. There is a considerable debate about the health issues related to the quality of life of these patients. Our aim of the study was to assess the outcome and perspectives of patients/care givers, about the acceptability of percutaneous endoscopic gastrostomy tube placement.

Methods
This descriptive analytic study conducted in patients, who have undergone percutaneous endoscopic gastrostomy tube placement during January 1998 till December 2004. Medical records of these patients were evaluated for their demographic characteristics, underlying diagnosis, indications and complications. Telephonic interviews were conducted till March 2005, on a pre-tested questionnaire to address psychological, social and physical performance status, of the health related quality of life issues.

Results
A total of 191 patients' medical records were reviewed, 120 (63%) were males, and mean age was 63 years. Early complication was infection at PEG tube site in 6 (3%) patients. In follow up over 365 ± 149 days, late complications (occurring 72 hours later) were infection at PEG tube site in 29 (15 %) patient and dislodgment/blockage of the tube in 26 (13.6%). Interviews were possible with 126 patients/caretakers. Karnofsky Performance Score of 0, 1, 2, 3 and 4 was found in 13(10%), 18(14%), 21(17%), 29(23%) and 45(36%) with p-value < 0.001. Regarding the social and psychological aspects; 76(60%) would like to have the PEG tube again if required, 105(83 %) felt ease in feeding, and 76(60%) felt that PEG-tube helped in prolonging the survival. Regarding negative opinions; 49(39 %) felt that the feeding was too frequent, 45(36 %) felt apprehensive about dependency for feeding and 62(49%) were concerned about an increase in the cost of care.

Conclusion
PEG-tube placement was found to be relatively free from serious immediate and long- term complications. Majority of caregivers and patient felt that PEG-tube helped in feeding and prolonging the survival. Studies are needed to assess the real benefit in terms of actual nutritional gain and quality of life in such patients.