bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of El Niño–Southern Oscillation on the Climate, Water Balance, and Streamflow of the Mississippi River Basin
Authors: Twine Tracy E. , Kucharik Christopher J. , Foley Jonathan A. 
Published: December 2005

Abstract
Climatic and hydrologic observations and results from a terrestrial ecosystem model coupled to a regional-scale river-routing algorithm are used to document the associations between the El Niño–Southern Oscillation (ENSO) phenomenon and anomalies in climate, surface water balance, and river hydrology within the Mississippi River basin. While no ENSO signal is found in streamflow at the outlet of the basin in Vicksburg, Mississippi, significant anomalies in all water balance components are found in certain regions within the basin. ENSO is mainly associated with positive winter temperature anomalies, but hydrologic patterns vary with season, location, and ENSO phase. El Niño precipitation anomalies tend to affect evapotranspiration (ET) in the western half of the basin and runoff in the eastern half. La Niña events are associated with ET anomalies in the central portion of the basin and runoff anomalies in the southern and eastern portions of the basin. Both ENSO phases are associated with decreased snow depth. Anomalous soil moisture patterns occur at seasonal time scales and filter noisier spatial patterns of precipitation anomalies into coherent patterns with larger field significance; however, for all water budget components, there is a large amount of variability in response within a particular ENSO phase. With anomalies that are up to 4 times those of a typical event, it is clear that improved predictability of the onset and strength of an upcoming ENSO event is important for both water resource management and disaster mitigation.
Methods for the Reconstruction of Vertical Profiles from Surface Data: Multivariate Analyses, Residual GEM, and Variable Temporal Signals in the North Pacific Ocean
Authors: Nardelli Bruno Buongiorno , Santoleri Rosalia 
Published: December 2005

AbstractDifferent methods for the extrapolation of vertical profiles from sea surface measurements have been tested on 14 yr of conductivity–temperature–depth (CTD) data collected within the Hawaii Ocean Time-series (HOT) program at A Long-Term Oligotrophic Habitat Assessment (ALOHA) station in the North Pacific Ocean. A new technique, called multivariate EOF reconstruction (mEOF-R), has been proposed. The mEOF-R technique is similar to the previously developed coupled pattern reconstruction (CPR) technique and relies on the availability of surface measurements and historical profiles of salinity, temperature, and steric heights. The method is based on the multivariate EOF analysis of the vertical profiles of the three parameters and on the assumption that only a few modes are needed to explain most of the variance/covariance of the fields. The performances of CPR, single EOF reconstruction (sEOF-R), and mEOF-R have been compared with the results of residual GEM techniques and with ad hoc climatologies, stressing the potential of each method in relation to the length of the time series used to train the models and to the accuracy expected from planned satellite missions for the measurement of surface salinity, sea level, and temperature. The mEOF-R method generally produces the most reliable estimates (in the worst cases comparable to the climatologies) and seems to be slightly less susceptible to errors in the surface input. Multivariate EOF analysis of HOT data also gave by itself interesting results, being able to discriminate the three major signals driving the temporal variability in the area.
Targeted Observations with an Airborne Wind Lidar
Authors: Weissmann M. , Busen R. , Dörnbrack A. , Rahm S. , Reitebuch O. 
Published: December 2005

Abstract
This study investigates the possibilities and limitations of airborne Doppler lidar for adaptive observations over the Atlantic Ocean. For the first time, a scanning 2-μm Doppler lidar was applied for targeted measurements during the Atlantic “The Observing System Research and Predictability Experiment” (THORPEX) Regional Campaign (A-TReC) in November and December 2003. The DLR lidar system was operated for 28.5 flight hours, and measured 1612 vertical profiles of wind direction and wind speed with a horizontal and vertical resolution of 5–10 km and 100 m, respectively. On average, there were 25 reliable wind values on every profile, which cover 2500 m in the vertical (about one-third of the mean vertical extent of the profiles). A statistical comparison of 33 dropsondes and collocated lidar winds profiles allowed individual estimates of the standard deviation to be assigned to every wind value and to determine threshold values for an objective quality control of the data. The standard deviation of the difference between dropsonde and lidar winds was correlated with the derived quality indices of the lidar data and was within a range of 0.6–1.8 m s−1. Comparisons of the lidar data to the operational analysis revealed differences of up to ±15 m s−1. This emphasizes the need for more representative and higher resolved wind measurements in data-sparse regions above the Atlantic Ocean. The study constitutes the basis for the assimilation of the lidar data and impact studies at the European Centre for Medium-Range Weather Forecasts (ECMWF).
Droplet Spectra Measurements with the FSSP-100. Part I: Low Droplet Concentration Measurements
Authors: Coelho Afrâniode Araújo , Brenguier Jean-Louis , Perrin Thierry 
Published: December 2005

Abstract
Entrainment-mixing processes such as droplet spectrum broadening and its impact on the onset of precipitation are, among many others, physical phenomena whose experimental study relies on in-cloud airborne measurements. For more than 30 yr, droplet sizing has been performed mostly with the Forward Scattering Spectrometer Probe (FSSP-100). The probe performance was extensively studied and probabilistic procedures were developed for characterizing the transfer function of the probe and correcting instrumental artifacts in the measurement of both the total droplet concentration and the droplet spectral shape. These procedures are revised here with a focus on low concentration measurements and the spectral distortion that may be generated by the real-time pulse processing, when the actual droplet spectrum is broad. The transfer matrix method is extended to account for this instrumental artifact.
MMP-9, TIMP-1 and inflammatory cells in sputum from COPD patients during exacerbation
Authors: Mercer PF , Shute JK , Bhowmik A , Donaldson GC , Wedzicha JA , Warner JA 
Published: December 2005

Abstract

Background
Irreversible airflow obstruction in Chronic Obstructive Pulmonary Disease (COPD) is thought to result from airway remodelling associated with aberrant inflammation. Patients who experience frequent episodes of acute deterioration in symptoms and lung function, termed exacerbations, experience a faster decline in their lung function, and thus over time greater disease severity However the mechanisms by which these episodes may contribute to decreased lung function are poorly understood.
This study has prospectively examined changes in sputum levels of inflammatory cells, MMP-9 and TIMP-1 during exacerbations comparing with paired samples taken prior to exacerbation.

Methods
Nineteen COPD patients ((median, [IQR]) age 69 [63 to 74], forced expiratory volume in one second (FEV1) 1.0 [0.9 to1.2], FEV1% predicted 37.6 [27.3 to 46.2]) provided sputa at exacerbation. Of these, 12 were paired with a samples collected when the patient was stable, a median 4 months [2 to 8 months] beforehand.

Results
MMP-9 levels increased from 10.5 μg/g [1.2 to 21.1] prior to exacerbation to 17.1 μg/g [9.3 to 48.7] during exacerbation (P < 0.01). TIMP-1 levels decreased from 3.5 μg/g [0.6 to 7.8] to 1.5 μg/g [0.3 to 4.9] (P = 0.16). MMP-9/TIMP-1 Molar ratio significantly increased from 0.6 [0.2 to 1.1] to 3.6 [2.0 to 25.3] (P < 0.05). Neutrophil, eosinophil and lymphocyte counts all showed significant increase during exacerbation compared to before (P < 0.05). Macrophage numbers remained level. MMP-9 levels during exacerbation showed highly significant correlation with both neutrophil and lymphocyte counts (Rho = 0.7, P < 0.01).

Conclusion
During exacerbation, increased inflammatory burden coincides with an imbalance of the proteinase MMP-9 and its cognate inhibitor TIMP-1. This may suggest a pathway connecting frequent exacerbations with lung function decline.
A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
Authors: Fogolari Federico , Tosatto Silvio CE , Colombo Giorgio 
Published: December 2005

Abstract
Background
Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently evaluated by discriminating native or native-like conformations from large ensembles of so-called decoy structures.

Results
A decoy set is obtained from snapshots taken from 5 long (100 ns) molecular dynamics (MD) simulations of the thermostable subdomain from chicken villin headpiece.
An evaluation of the energy of the decoys is given using: i) a residue based contact potential supplemented by a term for the quality of dihedral angles; ii) a recently introduced combination of four statistical scoring functions for model quality estimation (FRST); iii) molecular mechanics with solvation energy estimated either according to the generalized Born surface area (GBSA) or iv) the Poisson-Boltzmann surface area (PBSA) method.

Conclusion
The decoy set presented here has the following features which make it attractive for testing energy scoring functions:
1) it covers a broad range of RMSD values (from less than 2.0 Å to more than 12 Å);
2) it has been obtained from molecular dynamics trajectories, starting from different non-native-like conformations which have diverse behaviour, with secondary structure elements correctly or incorrectly formed, and in one case folding to a native-like structure. This allows not only for scoring of static structures, but also for studying, using free energy estimators, the kinetics of folding;
3) all structures have been obtained from accurate MD simulations in explicit solvent and after molecular mechanics (MM) energy minimization using an implicit solvent method. The quality of the covalent structure therefore does not suffer from steric or covalent problems.
The statistical and physical effective energy functions tested on the set behave differently when native simulation snapshots are included or not in the set and when averaging over the trajectory is performed.
Probabilistic annotation of protein sequences based on functional classifications
Authors: Levy Emmanuel D , Ouzounis Christos A , Gilks Walter R , Audit Benjamin 
Published: December 2005

Abstract
Background
One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. This mode of protein function assignment is mostly based on the detection of sequence similarity and the premise that functional properties are conserved during evolution. Most automatic approaches developed to date rely on the identification of clusters of homologous proteins and the mapping of new proteins onto these clusters, which are expected to share functional characteristics.

Results
Here, we inverse the logic of this process, by considering the mapping of sequences directly to a functional classification instead of mapping functions to a sequence clustering. In this mode, the starting point is a database of labelled proteins according to a functional classification scheme, and the subsequent use of sequence similarity allows defining the membership of new proteins to these functional classes. In this framework, we define the Correspondence Indicators as measures of relationship between sequence and function and further formulate two Bayesian approaches to estimate the probability for a sequence of unknown function to belong to a functional class. This approach allows the parametrisation of different sequence search strategies and provides a direct measure of annotation error rates. We validate this approach with a database of enzymes labelled by their corresponding four-digit EC numbers and analyse specific cases.

Conclusion
The performance of this method is significantly higher than the simple strategy consisting in transferring the annotation from the highest scoring BLAST match and is expected to find applications in automated functional annotation pipelines.
The feasibility of whole body vibration in institutionalised elderly persons and its influence on muscle performance, balance and mobility: a randomised controlled trial [ISRCTN62535013]
Authors: Bautmans Ivan , Van Hees Ellen , Lemper Jean-Claude , Mets Tony 
Published: December 2005

Abstract

Background
Fatigue or lack of interest can reduce the feasibility of intensive physical exercise in nursing home residents. Low-volume exercise interventions with similar training effects might be an alternative. The aim of this randomised controlled trial was to investigate the feasibility of Whole Body Vibration (WBV) in institutionalised elderly, and its impact on functional capacity and muscle performance.

Methods
Twenty-four nursing home residents (15 female, 9 male; mean age 77.5 ± 11.0 years) were randomised (stratification for age, gender and ADL-category) to 6 weeks static WBV exercise (WBV+, N = 13) or control (only static exercise; N = 11). Outcome measures were exercise compliance, timed up-and-go, Tinetti-test, back scratch, chair sit-and-reach, handgrip strength and linear isokinetic leg extension.

Results
At baseline, WBV+ and control groups were similar for all outcome variables. Twenty-one participants completed the program and attended respectively 96% and 86% of the exercise sessions for the WBV+ and control groups. Training-induced changes in timed up-and-go and Tinetti-test were better for WBV+ compared to control (p = 0.029 for timed up-and-go, p = 0.001 and p = 0.002 for Tinetti body balance and total score respectively). In an alternative analysis (Worst Rank Score & Last Observation Carried Forward) the differences in change remained significant on the Tinetti body balance and total score. No other significant differences in change between both groups were observed.

Conclusion
In nursing home residents with limited functional dependency, six weeks static WBV exercise is feasible, and is beneficial for balance and mobility. The supplementary benefit of WBV on muscle performance compared to classic exercise remains to be explored further.
Prevalence and distribution of high-risk human papilloma virus (HPV) types in invasive squamous cell carcinoma of the cervix and in normal women in Andhra Pradesh, India
Authors: Sowjanya A Pavani , Jain Meenkashi , Poli Usha Rani , Padma S , Das Manik , Shah Keerti V , Rao BN , Devi Radha Rama , Gravitt Patti E , Ramakrishna Gayatri 
Published: December 2005

Abstract

Background
Despite the high incidence of cervical cancer reported from India, large scale population based studies on the HPV prevalence and genotype distribution are very few from this region. In view of the clinical trials for HPV vaccine taking place in India, it is of utmost importance to understand the prevalence of HPV genotypes in various geographical regions of India. We investigated the genotype distribution of high-risk HPV types in squamous cell carcinomas and the prevalence of high-risk HPV in cervicovaginal samples in the southern state of Andhra Pradesh (AP), India.

Methods
HPV genotyping was done in cervical cancer specimens (n = 41) obtained from women attending a regional cancer hospital in Hyderabad. HPV-DNA testing was also done in cervicovaginal samples (n = 185) collected from women enrolled in the cervical cancer screening pilot study conducted in the rural community, of Medchal Mandal, twenty kilometers away from Hyderabad.

Results
High-risk HPV types were found in 87.8% (n = 36/41) of the squamous cell carcinomas using a PCR-based line blot assay. Among the HPV positive cancers, the overall type distribution of the major high-risk HPV types was as follows: HPV 16 (66.7%), HPV 18 (19.4%), HPV 33 (5.6%), HPV 35 (5.6%), HPV 45 (5.6%), HPV 52 (2.8%), HPV 58(2.8%), HPV 59(2.8%) and HPV 73 (2.8%). Women participating in the community screening programme provided both a self-collected vaginal swab and a clinician-collected cervical swab for HPV DNA testing. Primary screening for high risk HPV was performed using the Digene Hybrid Capture 2 (hc2) assay. All hc2 positive samples by any one method of collection were further analyzed using the Roche PCR-based line blot for genotype determination. The prevalence of high risk HPV infection in this community-based screening population was 10.3% (19/185) using the clinician-collected and 7.0% (13/185) using the self-collected samples. The overall agreement between self-collected and clinician-collected samples was 92%; however among HPV-positive specimens, the HPV agreement was only moderate (39.1%). The most frequently detected HPV types in the Medchal community are HPV 52 and 16.

Conclusion
Our results suggest that the HPV type distribution in both cervical cancer tissues and in a general screening population from Andhra Pradesh is similar to that reported in India and other parts of the world. We also conclude that an effective vaccine targeting HPV 16 will reduce the cervical cancer burden in AP.
Looking for pyromania: Characteristics of a consecutive sample of Finnish male criminals with histories of recidivist fire-setting between 1973 and 1993
Authors: Lindberg Nina , Holi Matti M , Tani Pekka , Virkkunen Matti 
Published: December 2005

Abstract

Background
As pyromania is a rare diagnosis with questionable validity, we aimed to describe a forensic psychiatric population of arson recidivists.

Methods
The medical records as well as the forensic psychiatric examination statements of 90 arson recidivists referred for pretrial psychiatric assessment in Helsinki University Hospital Department of Forensic Psychiatry between 1973 and 1993 were reviewed.

Results
The most important diagnostic categories of arson recidivists were personality disorders, psychosis and mental retardation, often with comorbid alcoholism. In all, 68% of arsonists were under alcohol intoxication during the index crime. Psychotic as well as mentally retarded persons with repeated fire-setting behaviour were mostly "pure arsonists"- persons guilty only of arsons during their criminal careers. Arson recidivists with personality disorder, in contrast, often exhibited various types of criminal behaviour and arson appeared to be only one expression of a wide range of criminal activity. Comorbid alcoholism was apparently a more rarely observed phenomenon among pure arsonists than in "nonpure arsonists". We found only three subjects fulfilling the present diagnostic criteria for pyromania.

Conclusion
Using the criteria of the DSM-IV-TR, pyromania must be regarded as an extremely rare phenomenon. Especially the question of substance intoxication as an exclusion criterion for pyromania should be reconsidered.
Understanding non-compliance to colorectal cancer screening: a case control study, nested in a randomised trial [ISRCTN83029072]
Authors: Giorgi Rossi Paolo , Federici Antonio , Bartolozzi Francesco , Farchi Sara , Borgia Piero , Guasticchi Gabriella 
Published: December 2005

Abstract

Background
The major limit to colorectal cancer screening effectiveness is often low compliance. We studied the reasons for non compliance and determinants of compliance to faecal occult blood tests in Lazio, Italy.

Methods
This is a case-control study nested within a trial that tested the effect of type of test and provider on colorectal cancer screening compliance. Non compliant trial subjects were classified as cases, and compliant subjects were classified as controls. We sampled 600 cases and 600 controls matched by their general practitioner, half were invited for screening at the hospital, and the other half directly at their general practitioner's office. Cases and controls answered questions on: distance from test provider, logistical problems, perception of colorectal cancer risk, confidence in screening efficacy, fear of results, presence of colorectal cancer in the family, and gastrointestinal symptoms.

Results
About 31% of cases never received the letter offering free screening, and 17% of the sampled population had already been screened. The first reported reason for non-compliance was "lack of time" (30%); the major determinant of compliance was the distance from the test provider: odds ratio >30 minutes vs <15 minutes 0.3 (95%CI = 0.2–0.7). The odds ratio for lack of time was 0.16 (95% IC 0.1–0.26). The effect was stronger if the hospital (0.03 95%CI = 0.01–0.1) rather than the general practitioner (0.3 95%CI = 0.2–0.6) was the provider. Twenty-two percent of controls were accompanied by someone to the test.

Conclusion
To increase compliance, screening programmes must involve test providers who are geographically close to the target population.
Geostatistical analysis of disease data: estimation of cancer mortality risk from empirical frequencies using Poisson kriging
Authors: Goovaerts Pierre 
Published: December 2005

AbstractBackgroundCancer mortality maps are used by public health officials to identify areas of excess and to guide surveillance and control activities. Quality of decision-making thus relies on an accurate quantification of risks from observed rates which can be very unreliable when computed from sparsely populated geographical units or recorded for minority populations. This paper presents a geostatistical methodology that accounts for spatially varying population sizes and spatial patterns in the processing of cancer mortality data. Simulation studies are conducted to compare the performances of Poisson kriging to a few simple smoothers (i.e. population-weighted estimators and empirical Bayes smoothers) under different scenarios for the disease frequency, the population size, and the spatial pattern of risk. A public-domain executable with example datasets is provided.ResultsThe analysis of age-adjusted mortality rates for breast and cervix cancers illustrated some key features of commonly used smoothing techniques. Because of the small weight assigned to the rate observed over the entity being smoothed (kernel weight), the population-weighted average leads to risk maps that show little variability. Other techniques assign larger and similar kernel weights but they use a different piece of auxiliary information in the prediction: global or local means for global or local empirical Bayes smoothers, and spatial combination of surrounding rates for the geostatistical estimator. Simulation studies indicated that Poisson kriging outperforms other approaches for most scenarios, with a clear benefit when the risk values are spatially correlated. Global empirical Bayes smoothers provide more accurate predictions under the least frequent scenario of spatially random risk.ConclusionThe approach presented in this paper enables researchers to incorporate the pattern of spatial dependence of mortality rates into the mapping of risk values and the quantification of the associated uncertainty, while being easier to implement than a full Bayesian model. The availability of a public-domain executable makes the geostatistical analysis of health data, and its comparison to traditional smoothers, more accessible to common users. In future papers this methodology will be generalized to the simulation of the spatial distribution of risk values and the propagation of the uncertainty attached to predicted risks in local cluster analysis.