bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three Putative Types of El Niño Revealed by Spatial Variability in Impact on Australian Wheat Yield
Authors: Potgieter A. B. , Hammer G. L. , Meinke H. , Stone R. C. , Goddard L. 
Published: June 2005

Abstract
The El Niño–Southern Oscillation (ENSO) phenomenon significantly impacts rainfall and ensuing crop yields in many parts of the world. In Australia, El Niño events are often associated with severe drought conditions. However, El Niño events differ spatially and temporally in their manifestations and impacts, reducing the relevance of ENSO-based seasonal forecasts. In this analysis, three putative types of El Niño are identified among the 24 occurrences since the beginning of the twentieth century. The three types are based on coherent spatial patterns (“footprints”) found in the El Niño impact on Australian wheat yield. This bioindicator reveals aligned spatial patterns in rainfall anomalies, indicating linkage to atmospheric drivers. Analysis of the associated ocean–atmosphere dynamics identifies three types of El Niño differing in the timing of onset and location of major ocean temperature and atmospheric pressure anomalies. Potential causal mechanisms associated with these differences in anomaly patterns need to be investigated further using the increasing capabilities of general circulation models. Any improved predictability would be extremely valuable in forecasting effects of individual El Niño events on agricultural systems.
Global Changes of the Water Cycle Intensity
Authors: Bosilovich Michael G. , Schubert Siegfried D. , Walker Gregory K. 
Published: June 2005

Abstract
In this study, numerical simulations of the twentieth-century climate are evaluated, focusing on the changes in the intensity of the global water cycle. A new model diagnostic of atmospheric water vapor cycling rate is developed and employed that relies on constituent tracers predicted at the model time step. This diagnostic is compared to a simplified traditional calculation of cycling rate, based on monthly averages of precipitation and total water content. The mean sensitivity of both diagnostics to variations in climate forcing is comparable. However, the new diagnostic produces systematically larger values with more variability.
Climate simulations were performed using SSTs of the early (1902–21) and late (1979–98) twentieth century along with the appropriate CO2 forcing. In general, the increase of global precipitation with the increases in SST that occurred between the early and late twentieth century is small. However, an increase of atmospheric temperature leads to a systematic increase in total precipitable water. As a result, the residence time of water in the atmosphere increased, indicating a reduction of the global cycling rate. This result was explored further using a number of 50-yr climate simulations from different models forced with observed SST. The anomalies and trends in the cycling rate and hydrologic variables of different GCMs are remarkably similar. The global annual anomalies of precipitation show a significant upward trend related to the upward trend of surface temperature, during the latter half of the twentieth century. While this implies an increase in the simulated hydrologic cycle intensity, a concomitant increase of total precipitable water again leads to a decrease in the calculated global cycling rate. An analysis of the land/sea differences shows that the simulated precipitation over land has a decreasing trend, while the oceanic precipitation has an upward trend consistent with previous studies and the available observations. The decreasing continental trend in precipitation is located primarily over tropical land regions, with some other regions, such as North America, experiencing an increasing trend. Precipitation trends are diagnosed further using the water tracers to delineate the precipitation that occurs because of continental evaporation, as opposed to oceanic evaporation. These model diagnostics show that over global land areas, the recycling of continental moisture is decreasing in time. However, the recycling changes are not spatially uniform so that some regions, most notably over the United States, experience continental recycling of water that increases in time.
Evaluation of Temperature Differences for Paired Stations of the U.S. Climate Reference Network
Authors: Gallo Kevin P. 
Published: June 2005

Abstract
Adjustments to data observed at pairs of climate stations have been recommended to remove the biases introduced by differences between the stations in time of observation, temperature instrumentation, latitude, and elevation. A new network of climate stations, located in rural settings, permits comparisons of temperatures for several pairs of stations without two of the biases (time of observation and instrumentation). The daily, monthly, and annual minimum, maximum, and mean temperatures were compared for five pairs of stations included in the U.S. Climate Reference Network. Significant differences were found between the paired stations in the annual minimum, maximum, and mean temperatures for all five pairs of stations. Adjustments for latitude and elevation differences contributed to greater differences in mean annual temperature for four of the five stations. Lapse rates computed from the mean annual temperature differences between station pairs differed from a constant value, whether or not latitude adjustments were made to the data. The results suggest that microclimate influences on temperatures observed at nearby (horizontally and vertically) stations are potentially much greater than influences that might be due to latitude or elevation differences between the stations.
A Debiased Ranked Probability Skill Score to Evaluate Probabilistic Ensemble Forecasts with Small Ensemble Sizes
Authors: Müller W. A. , Appenzeller C. , Doblas-Reyes F. J. , Liniger M. A. 
Published: June 2005

Abstract
The ranked probability skill score (RPSS) is a widely used measure to quantify the skill of ensemble forecasts. The underlying score is defined by the quadratic norm and is comparable to the mean squared error (mse) but it is applied in probability space. It is sensitive to the shape and the shift of the predicted probability distributions. However, the RPSS shows a negative bias for ensemble systems with small ensemble size, as recently shown. Here, two strategies are explored to tackle this flaw of the RPSS. First, the RPSS is examined for different norms L (RPSSL). It is shown that the RPSSL=1 based on the absolute rather than the squared difference between forecasted and observed cumulative probability distribution is unbiased; RPSSL defined with higher-order norms show a negative bias. However, the RPSSL=1 is not strictly proper in a statistical sense. A second approach is then investigated, which is based on the quadratic norm but with sampling errors in climatological probabilities considered in the reference forecasts. This technique is based on strictly proper scores and results in an unbiased skill score, which is denoted as the debiased ranked probability skill score (RPSSD) hereafter. Both newly defined skill scores are independent of the ensemble size, whereas the associated confidence intervals are a function of the ensemble size and the number of forecasts.
The RPSSL=1 and the RPSSD are then applied to the winter mean [December–January–February (DJF)] near-surface temperature predictions of the ECMWF Seasonal Forecast System 2. The overall structures of the RPSSL=1 and the RPSSD are more consistent and largely independent of the ensemble size, unlike the RPSSL=2. Furthermore, the minimum ensemble size required to predict a climate anomaly given a known signal-to-noise ratio is determined by employing the new skill scores. For a hypothetical setup comparable to the ECMWF hindcast system (40 members and 15 hindcast years), statistically significant skill scores were only found for a signal-to-noise ratio larger than ∼0.3.
libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny
Authors: Butt Davin , Roger Andrew J , Blouin Christian 
Published: June 2005

Abstract
Background
An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task.

Results
The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used to compute likelihoods, search tree topologies, estimate site rates, cluster sequences, manipulate tree structures and compare phylogenies for a broad selection of applications.

Conclusion
Using this library, it is possible to rapidly prototype applications that use the sophistication of phylogenetic likelihoods without getting involved in a major software engineering project. libcov is thus a potentially valuable building block to develop in-house methodologies in the field of protein phylogenetics.
Chemistry in Bioinformatics
Authors: Murray-Rust Peter , Mitchell John BO , Rzepa Henry S 
Published: June 2005

Abstract
Abstract
Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.
Which gene did you mean?
Authors: Mons Barend 
Published: June 2005

AbstractComputational Biology needs computer-readable information records. Increasingly, meta-analysed and pre-digested information is being used in the follow up of high throughput experiments and other investigations that yield massive data sets. Semantic enrichment of plain text is crucial for computer aided analysis. In general people will think about semantic tagging as just another form of text mining, and that term has quite a negative connotation in the minds of some biologists who have been disappointed by classical approaches of text mining. Efforts so far have tried to develop tools and technologies that retrospectively extract the correct information from text, which is usually full of ambiguities. Although remarkable results have been obtained in experimental circumstances, the wide spread use of information mining tools is lagging behind earlier expectations. This commentary proposes to make semantic tagging an integral process to electronic publishing.
Hypothermia in a surgical intensive care unit
Authors: Abelha Fernando J , Castro Maria A , Neves Aida M , Landeiro Nuno M , Santos Cristina C 
Published: June 2005

Abstract

Background
Inadvertent hypothermia is not uncommon in the immediate postoperative period and it is associated with impairment and abnormalities in various organs and systems that can lead to adverse outcomes. The aim of this study was to estimate the prevalence, the predictive factors and outcome of core hypothermia on admission to a surgical ICU.

Methods
All consecutive 185 adult patients who underwent scheduled or emergency noncardiac surgery admitted to a surgical ICU between April and July 2004 were admitted to the study. Tympanic membrane core temperature (Tc) was measured before surgery, on arrival at ICU and every two hours until 6 hours after admission. The following variables were also recorded: age, sex, body weight and height, ASA physical status, type of surgery, magnitude of surgical procedure, anesthesia technique, amount of intravenous fluids administered during anesthesia, use of temperature monitoring and warming techniques, duration of the anesthesia, ICU length of stay, hospital length of stay and SAPS II score. Patients were classified as either hypothermic (Tc ≤ 35°C) or normothermic (Tc> 35°C). Univariate analysis and multiple regression binary logistic with an odds ratio (OR) and its 95% Confidence Interval (95%CI) were used to compare the two groups of patients and assess the relationship between each clinical predictor and hypothermia. Outcome measured as ICU length of stay and mortality was also assessed.

Results
Prevalence of hypothermia on ICU admission was 57.8%. In univariate analysis temperature monitoring, use of warming techniques and higher previous body temperature were significant protective factors against core hypothermia. In this analysis independent predictors of hypothermia on admission to ICU were: magnitude of surgery, use of general anesthesia or combined epidural and general anesthesia, total intravenous crystalloids administrated and total packed erythrocytes administrated, anesthesia longer than 3 hours and SAPS II scores. In multiple logistic regression analysis significant predictors of hypothermia on admission to the ICU were magnitude of surgery (OR 3.9, 95% CI, 1.4–10.6, p = 0.008 for major surgery; OR 3.6, 95% CI, 1.5–9.0, p = 0.005 for medium surgery), intravenous administration of crystalloids (in litres) (OR 1.4, 95% CI, 1.1–1.7, p = 0.012) and SAPS score (OR 1.0, 95% CI 1.0–1.7, p = 0.014); higher previous temperature in ward was a significant protective factor (OR 0.3, 95% CI 0.1–0.7, p = 0.003). Hypothermia was neither a risk factor for hospital mortality nor a predictive factor for staying longer in ICU.

Conclusion
The prevalence of patient hypothermia on ICU arrival was high. Hypothermia at time of admission to the ICU was not an independent factor for mortality or for staying longer in ICU.
Physicians perceived usefulness of high-cost diagnostic imaging studies: results of a referral study in a German medical quality network
Authors: Schneider Antonius , Rosemann Thomas , Wensing Michel , Szecsenyi Joachim 
Published: June 2005

Abstract
Background
Medical and technological progress has led to increased numbers of diagnostic tests, some of them inducing high financial costs. In Germany, high-cost diagnostic imaging is performed by a medical specialist after referral by a general practitioner (GP) or specialist in primary care. The aim of this study was to evaluate the physicians' perceived usefulness of high-cost diagnostic imaging in patients with different clinical conditions.

Methods
Thirty-four GPs, one neurologist and one orthopaedic specialist in ambulatory care from a Medical Quality Network documented 234 referrals concerning 97 MRIs, 96 CTs-scan and 41 intracardiac catheters in a three month period. After having received the test results, they indicated if these were useful for diagnosis and treatment of the patient.

Results
The physicians' perceived usefulness of tests was lowest in suspected cerebral disease (40% of test results were seen as useful), cervical spine problems (64%) and unexplained abdominal complaints (67%). The perceived usefulness was highest in musculoskeletal symptoms (94%) and second best in cardiological diseases (82%).

Conclusion
The perceived usefulness of high-cost diagnostic imaging was lower in unexplained complaints than in specific diseases. Interventions to improve the effectiveness and efficiency of test ordering should focus on clinical decision making in conditions where GPs perceived low usefulness.
A conscious mouse model of gastric ileus using clinically relevant endpoints
Authors: Firpo Matthew A , Rollins Michael D , Szabo Aniko , Gull Justin D , Jackson Jeffrey D , Shao Yuanlin , Glasgow Robert E , Mulvihill Sean J 
Published: June 2005

Abstract
Background
Gastric ileus is an unsolved clinical problem and current treatment is limited to supportive measures. Models of ileus using anesthetized animals, muscle strips or isolated smooth muscle cells do not adequately reproduce the clinical situation. Thus, previous studies using these techniques have not led to a clear understanding of the pathophysiology of ileus. The feasibility of using food intake and fecal output as simple, clinically relevant endpoints for monitoring ileus in a conscious mouse model was evaluated by assessing the severity and time course of various insults known to cause ileus.

Methods
Delayed food intake and fecal output associated with ileus was monitored after intraperitoneal injection of endotoxin, laparotomy with bowel manipulation, thermal injury or cerulein induced acute pancreatitis. The correlation of decreased food intake after endotoxin injection with gastric ileus was validated by measuring gastric emptying. The effect of endotoxin on general activity level and feeding behavior was also determined. Small bowel transit was measured using a phenol red marker.

Results
Each insult resulted in a transient and comparable decrease in food intake and fecal output consistent with the clinical picture of ileus. The endpoints were highly sensitive to small changes in low doses of endotoxin, the extent of bowel manipulation, and cerulein dose. The delay in food intake directly correlated with delayed gastric emptying. Changes in general activity and feeding behavior were insufficient to explain decreased food intake. Intestinal transit remained unchanged at the times measured.

Conclusion
Food intake and fecal output are sensitive markers of gastric dysfunction in four experimental models of ileus. In the mouse, delayed gastric emptying appears to be the major cause of the anorexic effect associated with ileus. Gastric dysfunction is more important than small bowel dysfunction in this model. Recovery of stomach function appears to be simultaneous to colonic recovery.
Another explanation for the low allergy rate in the rural Alpine foothills
Authors: Wjst Matthias 
Published: June 2005

AbstractA low allergy rate in coal and wood heated homes has been described in the small villages in the Alpine foothills and subsequently found to be associated with the farming environment. This was interpreted within the framework of the hygiene hypothesis but there are also alternative explanations. Lower air pollution could be one reason, which is, however, unlikely since the differences between the Bavarian countryside and the Munich municipal area were only weak. There could be genetic differences between the urban and rural population by previous isolation or by self-selection. The potential drop-out of allergy genes, however, will also not explain the absent increase of allergies in two generations. More likely, other lifestyle factors are important. Dietary habits are different in farmers and a less frequent vitamin D supplementation of newborns (otherwise expected to be allergy promoting) has been shown recently. The underlying cause for the "non-allergic farm child" remains speculative until the transfer of any farm-associated factor is leading to a similar risk reduction in the general population.
Drug use and risk behaviours among injecting drug users: a comparison between sex workers and non-sex workers in Sydney, Australia
Authors: Roxburgh Amanda , Degenhardt Louisa , Breen Courtney 
Published: June 2005

AbstractBackgroundThis paper examines the differences in demographics, drug use patterns and self reported risk behaviours between regular injecting drug users (IDU) who report engaging in sex work for money or drugs and regular injecting drug users who do not.MethodsCross sectional data collected from regular IDU interviewed as part of the New South Wales (NSW) Illicit Drug Reporting System (IDRS) in 2003 were analysed.ResultsIDU who reported engaging in sex work were more likely to be female, and identify as being of Aboriginal and/or Torres Strait Islander descent. They initiated injecting drug use at a significantly younger age and were more likely to report injection related problems than IDU who had not engaged in sex work. There were no differences in the drug classes used, but findings suggested that the sex workers tended to be more frequent users of crystalline methamphetamine (ice) and benzodiazepines.ConclusionThe similarities between these groups were more striking than the differences. Further research, examining a larger sample is needed to clarify whether injecting drug users who are sex workers have heavier use patterns.
Introducing article-processing charges and inviting "detailed methods sections" articles
Authors: Phillips Carl V 
Published: June 2005

AbstractThis editorial introduces the use of article-processing charges at Epidemiologic Perspectives & Innovations and reviews that advantages of publishing in an Open Access journal. In addition, it introduces a new type of article the journal hopes to publish, detailed reports of study design or data analysis methods that have been used in health science research. The new type of article is intended to supplement the woefully constrained methods sections in standard research report articles, providing information that better fulfills the goals of scientific publishing.
Prospects for surviving climate change in Antarctic aquatic species
Authors: Peck Lloyd S 
Published: June 2005

Abstract
Maritime Antarctic freshwater habitats are amongst the fastest changing environments on Earth. Temperatures have risen around 1°C and ice cover has dramatically decreased in 15 years. Few animal species inhabit these sites, but the fairy shrimp Branchinecta gaini typifies those that do. This species survives up to 25°C daily temperature fluctuations in summer and passes winter as eggs at temperatures down to -25°C. Its annual temperature envelope is, therefore around 50°C. This is typical of Antarctic terrestrial species, which exhibit great physiological flexibility in coping with temperature fluctuations. The rapidly changing conditions in the Maritime Antarctic are enhancing fitness in these species by increasing the time available for feeding, growth and reproduction, as well as increasing productivity in lakes. The future problem these animals face is via displacement by alien species from lower latitudes. Such invasions are now well documented from sub-Antarctic sites.
In contrast the marine Antarctic environment has very stable temperatures. However, seasonality is intense with very short summers and long winter periods of low to no algal productivity. Marine animals grow slowly, have long generation times, low metabolic rates and low levels of activity. They also die at temperatures between +5°C and +10°C. Failure of oxygen supply mechanisms and loss of aerobic scope defines upper temperature limits. As temperature rises, their ability to perform work declines rapidly before lethal limits are reached, such that 50% of populations of clams and limpets cannot perform essential activities at 2–3°C, and all scallops are incapable of swimming at 2°C. Currently there is little evidence of temperature change in Antarctic marine sites. Models predict average global sea temperatures will rise by around 2°C by 2100. Such a rise would take many Antarctic marine animals beyond their survival limits. Animals have 3 mechanisms for coping with change: they can 1) use physiological flexibility, 2) evolve new adaptations, 3) migrate to better sites. Antarctic marine species have poor physiological scopes, long generation times and live on a continent whose coastline covers fewer degrees of latitude than all others. On all 3 counts Antarctic marine species have poorer prospects than most large faunal groups elsewhere.