bluuebunny/crossref_metadata_2025_split huggingface dataset:
iHAP – integrated haplotype analysis pipeline for characterizing the haplotype structure of genes
Authors: Song Chun Meng , Yeo Boon Huat , Tantoso Erwin , Yang Yuchen , Lim Yun Ping , Li Kuo-Bin , Rajagopal Gunaretnam 
Published: December 2006

Abstract

Background
The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows that genotype data from the International HapMap Project have a high degree of transferability to the wider population. This implies that the design of genotyping studies on local populations may be facilitated through inferences drawn from information contained in HapMap populations.

Results
To facilitate analysis of HapMap data for characterizing the haplotype structure of genes or any chromosomal regions, we have developed an integrated web-based resource, iHAP. In addition to incorporating genotype and haplotype data from the International HapMap Project and gene information from the UCSC Genome Browser Database, iHAP also provides capabilities for inferring haplotype blocks and selecting tag SNPs that are representative of haplotype patterns. These include block partitioning algorithms, block definitions, tag SNP definitions, as well as SNPs to be "force included" as tags. Based on the parameters defined at the input stage, iHAP performs on-the-fly analysis and displays the result graphically as a webpage. To facilitate analysis, intermediate and final result files can be downloaded.

Conclusion
The iHAP resource, available at http://ihap.bii.a-star.edu.sg, provides a convenient yet flexible approach for the user community to analyze HapMap data and identify candidate targets for genotyping studies.
Analyzing the dose-dependence of the Saccharomyces cerevisiae global transcriptional response to methyl methanesulfonate and ionizing radiation
Authors: Benton Michael G , Somasundaram Swetha , Glasner Jeremy D , Palecek Sean P 
Published: December 2006

Abstract

Background
One of the most crucial tasks for a cell to ensure its long term survival is preserving the integrity of its genetic heritage via maintenance of DNA structure and sequence. While the DNA damage response in the yeast Saccharomyces cerevisiae, a model eukaryotic organism, has been extensively studied, much remains to be elucidated about how the organism senses and responds to different types and doses of DNA damage. We have measured the global transcriptional response of S. cerevisiae to multiple doses of two representative DNA damaging agents, methyl methanesulfonate (MMS) and gamma radiation.

Results
Hierarchical clustering of genes with a statistically significant change in transcription illustrated the differences in the cellular responses to MMS and gamma radiation. Overall, MMS produced a larger transcriptional response than gamma radiation, and many of the genes modulated in response to MMS are involved in protein and translational regulation. Several clusters of coregulated genes whose responses varied with DNA damaging agent dose were identified. Perhaps the most interesting cluster contained four genes exhibiting biphasic induction in response to MMS dose. All of the genes (DUN1, RNR2, RNR4, and HUG1) are involved in the Mec1p kinase pathway known to respond to MMS, presumably due to stalled DNA replication forks. The biphasic responses of these genes suggest that the pathway is induced at lower levels as MMS dose increases. The genes in this cluster with a threefold or greater transcriptional response to gamma radiation all showed an increased induction with increasing gamma radiation dosage.

Conclusion
Analyzing genome-wide transcriptional changes to multiple doses of external stresses enabled the identification of cellular responses that are modulated by magnitude of the stress, providing insights into how a cell deals with genotoxicity.
Key transmission parameters of an institutional outbreak during the 1918 influenza pandemic estimated by mathematical modelling
Authors: Sertsou Gabriel , Wilson Nick , Baker Michael , Nelson Peter , Roberts Mick G 
Published: December 2006

AbstractAimTo estimate the key transmission parameters associated with an outbreak of pandemic influenza in an institutional setting (New Zealand 1918).MethodsHistorical morbidity and mortality data were obtained from the report of the medical officer for a large military camp. A susceptible-exposed-infectious-recovered epidemiological model was solved numerically to find a range of best-fit estimates for key epidemic parameters and an incidence curve. Mortality data were subsequently modelled by performing a convolution of incidence distribution with a best-fit incidence-mortality lag distribution.ResultsBasic reproduction number (R0) values for three possible scenarios ranged between 1.3, and 3.1, and corresponding average latent period and infectious period estimates ranged between 0.7 and 1.3 days, and 0.2 and 0.3 days respectively. The mean and median best-estimate incidence-mortality lag periods were 6.9 and 6.6 days respectively. This delay is consistent with secondary bacterial pneumonia being a relatively important cause of death in this predominantly young male population.ConclusionTheseR0estimates are broadly consistent with others made for the 1918 influenza pandemic and are not particularly large relative to some other infectious diseases. This finding suggests that if a novel influenza strain of similar virulence emerged then it could potentially be controlled through the prompt use of major public health measures.
How emergency departments might alert for prehospital heat-related excess mortality?
Authors: Claessens Yann-Erick , Taupin Pierre , Kierzek Gérald , Pourriat Jean-Louis , Baud Michel , Ginsburg Christine , Jais Jean-Philippe , Jougla Eric , Riou Bruno , Dhainaut Jean-François , Landais Paul 
Published: December 2006

Abstract
Introduction
A major issue raised by the public health consequences of a heat wave is the difficulty of detecting its direct consequences on patient outcome, particularly because of the delay in obtaining definitive mortality results. Since emergency department (ED) activity reflects the global increase of patients' health problems during this period, the profile of patients referred to EDs might be a basis to detect an excess mortality in the catchment area. Our objective was to develop a real-time surveillance model based on ED data to detect excessive heat-related mortality as early as possible.

Methods
A day-to-day composite indicator was built using simple and easily obtainable variables related to patients referred to the ED during the 2003 heat-wave period. The design involved a derivation and validation study based on a real-time surveillance system of two EDs at Cochin Hospital and Hôtel-Dieu Hospital, Paris, France. The participants were 99,976 adult patients registered from 1 May to 30 September during 2001, 2002 and 2003. Among these participants, 3,297, 3,580 and 3,851 patients were referred to the EDs from 3 August to 19 August for 2001, 2002 and 2003, respectively. Variables retained for the indicator were selected using the receiver operating characteristic curve methodology and polynomial regression.

Results
The indicator was composed of only three variables: the percentage of patients older than 70 years, the percentage of patients with body temperature above 39°C, and the percentage of patients admitted to or who died in the ED. The curve of the indicator with time appropriately fitted the overall mortality that occurred in the region of interest.

Conclusion
A composite and simple index based on real-time surveillance was developed according to the profile of patients who visited the ED. It appeared suitable for determining the overall mortality in the corresponding region submitted to the 2003 heat wave. This index should help early warning of excessive mortality and monitoring the efficacy of public health interventions.
Evaluation of furosemide regimens in neonates treated with extracorporeal membrane oxygenation
Authors: van der Vorst Maria MJ , Wildschut Enno , Houmes Robbert J , Gischler Saskia J , Kist-van Holthe Joana E , Burggraaf Jacobus , van der Heijden Albert J , Tibboel Dick 
Published: December 2006

Abstract
Introduction
Loop diuretics are the most frequently used diuretics in patients treated with extracorporeal membrane oxygenation (ECMO). In patients after cardiopulmonary bypass (CPB) surgery, the use of continuous furosemide infusion is increasingly documented. Because ECMO and CPB are 'comparable' procedures, continuous furosemide infusion is used in newborns on ECMO. We report on the use of continuous intravenous furosemide in neonates treated with ECMO.

Methods
This was a retrospective observational study in neonates treated with continuous intravenous furosemide during ECMO.

Results
Thirty-one patients were included in the study. A median of 25 (9–149) hours after the start of ECMO, continuous furosemide therapy was started at a median rate of 0.08 (0.02–0.17) mg/kg per hour. The continuous furosemide dose was not changed in the individual patient. Seven patients received a furosemide bolus prior to, and five patients received additional loop diuretics during, the continuous infusion. Urine production before continuous furosemide therapy was not significantly different between patients who received a furosemide bolus prior to the infusion and those who did not receive this bolus (P = 0.2879). Although a positive effect of the 'loading' bolus was observed in urine output in the first 24 hours, there was no statistically significant difference in urine output (P = 0.0961) or in time (P = 0.1976) to reach a urine output of 6 ml/kg per hour between patients. After 24 hours, urine production remained a median of 6.2 ml/kg per hour irrespective of furosemide boluses. The forced diuresis was well tolerated as illustrated by stable haemodynamic parameters and a decrease in ECMO flow and vasopressor score over the observation period.

Conclusion
This is the first report on continuous intravenous furosemide therapy in newborns treated with ECMO. The furosemide regimens used in this study varied widely in continuous and intermittent doses. However, all regimens achieved adequate urine output. An advantage of continuous, over intermittent, intravenous furosemide could not be documented. Furosemide dosing regimens should be developed for neonates treated with ECMO. In addition, therapeutic drug-monitoring studies are required to prevent furosemide toxicity because so far no data are available on serum furosemide levels in neonates treated with ECMO.
The National Audit of Violence: in-patient care for adults of working age
Authors: Chaplin Robert , McGeorge Maureen , Lelliott Paul 
Published: December 2006

Aims and MethodWe audited 184 psychiatric wards against clinical practice guidelines for the management of violence. Staff and service users completed anonymous questionnaires. Environmental inspections were performed by two teams.ResultsThere were 4460 questionnaires returned. Nurses (78%) were significantly more likely to report the experience of violence than service users (37%). Drugs were reported by 72% of nurses and alcohol by 61% as causing problems. Other standards frequently not met included staffing levels, training, provision of activities, ward design and ambience.Clinical ImplicationsSpecific issues are identified that must be addressed by national and local action. A baseline is set against which the impact of this action can be judged. Priorities must include tackling drug and alcohol use in psychiatric wards.
Quality of referrals to old age psychiatry following introduction of the single assessment process
Authors: Ferriter Kathleen , Gangopadhyay Partha , Nilforooshan Ramin , Ardern Mark , Warner James 
Published: December 2006

Aims and MethodWe sought to identify changes in the quality of information in referrals to an old age psychiatry service before and after the introduction of the single assessment process. Referrals were compared in terms of length, legibility, information and clinical utility.ResultsCompared with letters before the introduction of the single assessment process, referrals made on the new forms took longer to read (mean 96 v. 124 s, P=0.001), had more illegible sections (P=0.011), contained less information (P=0.026) and were judged to be less clinically useful (P=0.001).Clinical ImplicationsThe introduction of the single assessment process has impaired clinical communication between general practitioners and psychiatrists, and might be prejudicial to patient care.
Simulations of optimized anguilliform swimming
Authors: Kern Stefan , Koumoutsakos Petros 
Published: December 2006

SUMMARYThe hydrodynamics of anguilliform swimming motions was investigated using three-dimensional simulations of the fluid flow past a self-propelled body. The motion of the body is not specified a priori, but is instead obtained through an evolutionary algorithm used to optimize the swimming efficiency and the burst swimming speed. The results of the present simulations support the hypothesis that anguilliform swimmers modify their kinematics according to different objectives and provide a quantitative analysis of the swimming motion and the forces experienced by the body.The kinematics of burst swimming is characterized by the large amplitude of the tail undulations while the anterior part of the body remains straight. In contrast, during efficient swimming behavior significant lateral undulation occurs along the entire length of the body. In turn, during burst swimming,the majority of the thrust is generated at the tail, whereas in the efficient swimming mode, in addition to the tail, the middle of the body contributes significantly to the thrust. The burst swimming velocity is 42% higher and the propulsive efficiency is 15% lower than the respective values during efficient swimming.The wake, for both swimming modes, consists largely of a double row of vortex rings with an axis aligned with the swimming direction. The vortex rings are responsible for producing lateral jets of fluid, which has been documented in prior experimental studies. We note that the primary wake vortices are qualitatively similar in both swimming modes except that the wake vortex rings are stronger and relatively more elongated in the fast swimming mode.The present results provide quantitative information of three-dimensional fluid-body interactions that may complement related experimental studies. In addition they enable a detailed quantitative analysis, which may be difficult to obtain experimentally, of the different swimming modes linking the kinematics of the motion with the forces acting on the self-propelled body. Finally, the optimization procedure helps to identify, in a systematic fashion, links between swimming motion and biological function.
β-1, 3-glucan modulates PKC signalling inLymnaea stagnalisdefence cells: a role for PKC in H2O2 production and downstream ERK activation
Authors: Lacchini Audrey H. , Davies Angela J. , Mackintosh David , Walker Anthony J. 
Published: December 2006

SUMMARYHaemocytes from the gastropod snail Lymnaea stagnalis (Linnaeus)were used as a model to characterize protein kinase C (PKC) signalling events in molluscan defence cells. Challenge of freshly collected haemocytes with theβ-1, 3-glucan laminarin resulted in a transient increase in the phosphorylation of haemocyte PKC, with maximal phosphorylation (represented by a 3.5-fold increase) occurring at 10 min; this effect was blocked by the PKC inhibitor, GF109203X. Moreover, extracellular signal-regulated kinase (ERK)was found to be a downstream target of molluscan PKC, operating via a MAPK/ERK kinase (MEK)-dependent mechanism. Pharmacological inhibition of PKC phosphorylation by U-73122 and ET-18-OCH3 suggested that laminarin-dependent PKC signalling was modulated via phospholipase C(PLC); however, a role for phosphatidylinositol-3-kinase (PI-3-K) is unlikely since the PI-3-K inhibitor LY294002 was without effect. Generation of H2O2 by haemocytes in response to laminarin was also investigated. H2O2 output increased in a dose- and time-dependent manner, with 10 mg ml-1 laminarin eliciting a 9.5-fold increase in H2O2 production after 30 min. H2O2 production was significantly attenuated by the PKC inhibitors, GF109203X and Gö 6976, and by the NADPH-oxidase inhibitor,apocynin. In conclusion, these data further our understanding of PKC signalling events in molluscan haemocytes and for the first time define a role for PKC in H2O2 production by these defence cells. Given that H2O2 is an important anti-pathogen molecule, and that haemocytes play a crucial role in the elimination of invading organisms,PKC signalling in these cells is likely to be crucial to the molluscan innate defence response.
Plasticity and stability in neuronal output via changes in intrinsic excitability: it's what's inside that counts
Authors: Schulz David J. 
Published: December 2006

SUMMARY
The nervous system faces an extremely difficult task. It must be flexible,both during development and in adult life, so that it can respond to a variety of environmental demands and produce adaptive behavior. At the same time the nervous system must be stable, so that the neural circuits that produce behavior function throughout the lifetime of the animal and that changes produced by learning endure. We are only beginning to understand how neural networks strike a balance between altering individual neurons in the name of plasticity, while maintaining long-term stability in neural system function. The balance of this plasticity and stability in neural networks undoubtedly plays a critical role in the normal functioning of the nervous system. While mechanisms of synaptic plasticity have garnered extensive study over the past three decades, it is only recently that more attention has been turned to plasticity of intrinsic excitability as a key player in neural network function. This review will focus on this emerging area of research that undoubtedly will contribute a great deal to our understanding of the functionality of the nervous system.
Compensation for environmental change by complementary shifts of thermal sensitivity and thermoregulatory behaviour in an ectotherm
Authors: Glanville E. J. , Seebacher F. 
Published: December 2006

SUMMARY
Thermoregulating animals are thought to have evolved a preferred body temperature at which thermally sensitive performance is optimised. Even during thermoregulation, however, many animals experience pronounced variability in body temperature, and may regulate to different body temperatures depending on environmental conditions. Here we test the hypothesis that there is a trade-off between regulating to lower body temperatures in cooler conditions and locomotory and metabolic performance. Animals (estuarine crocodiles, Crocodylus porosus) acclimated to cold (N=8) conditions had significantly lower maximum and mean daily body temperatures after 33 days than warm-acclimated animals (N=9), despite performing characteristic thermoregulatory behaviours. Concomitant with behavioural changes, maximum sustained swimming speed (Ucrit) shifted to the respective mean body temperatures during acclimation (cold=20°C, warm=29°C), but there was no difference in the maxima between acclimation groups. Mitochondrial oxygen consumption changed significantly during acclimation, and maximum respiratory control ratios coincided with mean body temperatures in liver, muscle and heart tissues. There were significant changes in the activities of regulatory metabolic enzymes (lactate dehydrogenase, citrate synthase, cytochrome c oxidase) and these were tissue specific. The extraordinary shift in behaviour and locomotory and metabolic performance shows that within individuals, behaviour and physiology covary to maximise performance in different environments.
Unusual response characteristics of pheromone-specific olfactory receptor neurons in the Asian corn borer moth,Ostrinia furnacalis
Authors: Takanashi Takuma , Ishikawa Yukio , Anderson Peter , Huang Yongping , Löfstedt Christer , Tatsuki Sadahiro , Hansson Bill S. 
Published: December 2006

SUMMARYMale moth pheromone-detecting receptor neurons are known to be highly specific and very sensitive. We investigated physiological and behavioral responses to female sex pheromone components in male Ostrinia furnacalis moths (Lepidoptera: Crambidae). Using recordings from a cut-sensillum technique, trichoid sensilla could be grouped into four physiological types (1-4), according to the response of receptor neurons to the two major pheromone components, (E)-12- and(Z)-12-tetradecenyl acetate (E12- and Z12-14:OAc). These types could subsequently be characterized as four subtypes (A-D) depending on neural responses to pheromone components from various sister species of O. furnacalis, (Z)-9-, (E)-11- and(Z)-11-tetradecenyl acetate.The peripheral pheromone detection system of O. furnacalis is different to that of other moths. A large majority of the neurons investigated responded to both of the two principal pheromone components. Dose-response and cross-adaptation studies showed that olfactory receptor neurons with large amplitude action potentials responded equally well to E12- and Z12-14:OAc in sensillum types 1-3. Field experiments showed that O. furnacalismales are sensitive to ratios of E12- and Z12-14:OAc and that(Z)-9-tetradecenyl acetate acts as a behavioral antagonist. O. furnacalis males thus display an unusual coding system for odors involved in sexual communication, mainly built on less specific neurons, but still have the ability to detect and respond to the correct female blend. We hypothesize that the pheromone detection system of O. furnacalis consists of two parts, where one is devoted to high sensitivity to Δ12 isomers of tetradecenyl acetate, E12- and Z12-14:OAc and the other to highly specific responses to the E12- or Z12-14:OAc. The unusual feature is thus that a large part of the system is devoted to sensitivity and only a minor part to selectivity. This could be explained by the fact that no other moth species are known to use E12- and/or Z12-14:OAc and that no strong selective pressure to increase selectivity between the isomers has been determined.
Mechanics of nectar feeding in the orchid beeEuglossa imperialis: pressure, viscosity and flow
Authors: Borrell Brendan J. 
Published: December 2006

SUMMARYThe orchid bee Euglossa imperialis sucks nectars through a slender proboscis. I tested how nectar properties influence this suction pressure and whether ambient air pressure sets the upper limit for suction feeding. Nectar intake rate was measured as a function of sucrose concentration (5-75% w/w),nectar viscosity (2-80 mPa s), and ambient pressure (101-40 kPa). Intake rate declines from about 1.2 μl s-1 to 0.003 μl s-1 as sucrose concentration increases from 15% to 65% sucrose. When sucrose concentration is held at 25% while viscosity increases from 2 to 80 mPa s,intake rate declines. When viscosity is held at 10.2 mPa s (the viscosity of 50% sucrose) while sucrose concentration increases from 5% to 50%, intake rate remains constant. Intake rate was limited by a reduction in ambient pressure at all nectar concentrations. Assuming a rigid proboscis, the Hagen-Poiseuille equation suggests that suction pressure increases with viscosity from 10 kPa at 5% sucrose to 45 kPa at 65% sucrose. However, because intake rate declined by the same fraction under hypobaria (40 kPa) at all sucrose concentrations,the euglossine bee proboscis may be better described as a collapsible tube:expanding or collapsing depending on the flow rate, the pressure gradient along the proboscis, and circumferential forces imposed by the proboscis walls.