bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring Clustering in Clouds Using Non-Rayleigh Signal Statistics
Authors: Jameson A. R. 
Published: May 2005

Abstract
The clustering or clumping of droplets appears to be nearly ubiquitous in clouds. Clustering likely plays roles in a number of different physical processes, from the growth of hail, to snow aggregation, to the growth of raindrops, to cloud radiation, and even to what one means by a size distribution. Of more immediate concern, clustering may, at times, affect aircraft icing by introducing important fluctuations in the concentration of supercooled cloud water sufficient to alter the density of the ice collected, and hence, the aerodynamics of the wing (lift).
Yet, the intensity of clustering in clouds is spatially and temporally variable and not easy to measure. What few observations there are have been restricted to one-dimensional aircraft measurements sampling very tiny volumes. It would be useful to have a method for measuring clustering over an area and to identify regions of significant clustering that aircraft should avoid during icing conditions, for example.
A radar technique based upon a scanning procedure that uses non-Rayleigh signal statistics for quantifying clustering intensity in clouds is proposed. Such observations may enhance the safety of aircraft flying in icing conditions and may elucidate the spatial organization of clustering in clouds. Such measurements appear to be within current technological capabilities.
Coleridge and Preaching a Theological Imagination
Authors: Edmondson Stephen 
Published: May 2005

ABSTRACTThis article explores Coleridge's understanding of imagination, Scripture, the spirituality of the world, and our reality as the image of God. I begin with Coleridge's understanding of the inspiration of Scripture and the interpretive process. By locating the imagination in this interaction among writer, reader, and God, I surface Coleridge's more significant description of imaginative thinking as a spiritual act that calls us into the truth of our being and of the world's reality. Implicit in Coleridge's vision is a correlation between human imaginative creativity and the creative being of God as a dimension of our reality as the image of God. Thus, I claim that imaginative preaching, when seen through Coleridge's lens, renews that image within us, awakening us to our reality as spiritual, free beings, but only when we enact our freedom within the context of God's freedom and action which we know through our reading of Scripture.
Effect of rosuvastatin on outcomes in chronic haemodialysis patients – design and rationale of the AURORA study
Authors: Fellström Bengt , Zannad Faiez , Schmieder Roland , Holdaas Hallvard , Jardine Alan , Rose Helen , Wilpshaar Wim ,   the AURORA Study Group
Published: May 2005

AbstractBackgroundPatients with end-stage renal disease (ESRD) are at high risk of cardiovascular events. Multiple risk factors for atherosclerosis are present in ESRD and may contribute to the increased risk of cardiovascular mortality in this population. In contrast to patients with normal renal function, the benefits of modifying lipid levels on cardiovascular outcomes in patients with ESRD on haemodialysis have yet to be confirmed in large prospective randomised trials. A study to evaluate the Use of Rosuvastatin in subjects On Regular haemodialysis: an Assessment of survival and cardiovascular events (AURORA) will be the first large-scale international trial to assess the effects of statin therapy on cardiovascular morbidity and mortality in ESRD patients on chronic haemodialysis.MethodsMore than 2,750 ESRD patients who have been receiving chronic haemodialysis treatment for at least 3 months have been randomised (1:1), irrespective of baseline lipid levels, to treatment with rosuvastatin 10 mg or placebo. The primary study endpoint is the time to a major cardiovascular event (first occurrence of cardiovascular death, non-fatal myocardial infarction or non-fatal stroke). Secondary endpoints include all-cause mortality, major cardiovascular event-free survival time, time to cardiovascular death, time to non-cardiovascular death, cardiovascular interventions, tolerability of treatment and health economic costs per life-year saved. Study medication will be given until 620 subjects have experienced a major cardiovascular event.ConclusionOur hypothesis is that results from AURORA will establish the clinical efficacy and tolerability of rosuvastatin in patients with ESRD receiving chronic haemodialysis and guide the optimal management of this expanding population.
Text Detective: a rule-based system for gene annotation in biomedical texts
Authors: Tamames Javier 
Published: May 2005

Abstract

Background
The identification of mentions of gene or gene products in biomedical texts is a critical step in the development of text mining applications in biosciences. The complexity and ambiguity of gene nomenclature makes this a very difficult task.

Methods
Here we present a novel approach based on a combination of carefully designed rules and several lexicons of biological concepts, implemented in the Text Detective system. Text Detective is able to normalize the results of gene mentions found by offering the appropriate database reference.

Results
In BioCreAtIvE evaluation, Text Detective achieved results of 84% precision, 71% recall for task 1A, and 79% precision, 71% recall for mouse genes in task 1B.
Overview of BioCreAtIvE task 1B: normalized gene lists
Authors: Hirschman Lynette , Colosimo Marc , Morgan Alexander , Yeh Alexander 
Published: May 2005

Abstract

Background
Our goal in BioCreAtIve has been to assess the state of the art in text mining, with emphasis on applications that reflect real biological applications, e.g., the curation process for model organism databases. This paper summarizes the BioCreAtIvE task 1B, the "Normalized Gene List" task, which was inspired by the gene list supplied for each curated paper in a model organism database. The task was to produce the correct list of unique gene identifiers for the genes and gene products mentioned in sets of abstracts from three model organisms (Yeast, Fly, and Mouse).

Results
Eight groups fielded systems for three data sets (Yeast, Fly, and Mouse). For Yeast, the top scoring system (out of 15) achieved 0.92 F-measure (harmonic mean of precision and recall); for Mouse and Fly, the task was more difficult, due to larger numbers of genes, more ambiguity in the gene naming conventions (particularly for Fly), and complex gene names (for Mouse). For Fly, the top F-measure was 0.82 out of 11 systems and for Mouse, it was 0.79 out of 16 systems.

Conclusion
This assessment demonstrates that multiple groups were able to perform a real biological task across a range of organisms. The performance was dependent on the organism, and specifically on the naming conventions associated with each organism. These results hold out promise that the technology can provide partial automation of the curation process in the near future.
Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text
Authors: Ray Soumya , Craven Mark 
Published: May 2005

Abstract

Background
The BioCreative text mining evaluation investigated the application of text mining methods to the task of automatically extracting information from text in biomedical research articles. We participated in Task 2 of the evaluation. For this task, we built a system to automatically annotate a given protein with codes from the Gene Ontology (GO) using the text of an article from the biomedical literature as evidence.

Methods
Our system relies on simple statistical analyses of the full text article provided. We learn n-gram models for each GO code using statistical methods and use these models to hypothesize annotations. We also learn a set of Naïve Bayes models that identify textual clues of possible connections between the given protein and a hypothesized annotation. These models are used to filter and rank the predictions of the n-gram models.

Results
We report experiments evaluating the utility of various components of our system on a set of data held out during development, and experiments evaluating the utility of external data sources that we used to learn our models. Finally, we report our evaluation results from the BioCreative organizers.

Conclusion
We observe that, on the test data, our system performs quite well relative to the other systems submitted to the evaluation. From other experiments on the held-out data, we observe that (i) the Naïve Bayes models were effective in filtering and ranking the initially hypothesized annotations, and (ii) our learned models were significantly more accurate when external data sources were used during learning.
Protein annotation as term categorization in the gene ontology using word proximity networks
Authors: Verspoor Karin , Cohn Judith , Joslyn Cliff , Mniszewski Sue , Rechtsteiner Andreas , Rocha Luis M , Simas Tiago 
Published: May 2005

Abstract

Background
We participated in the BioCreAtIvE Task 2, which addressed the annotation of proteins into the Gene Ontology (GO) based on the text of a given document and the selection of evidence text from the document justifying that annotation. We approached the task utilizing several combinations of two distinct methods: an unsupervised algorithm for expanding words associated with GO nodes, and an annotation methodology which treats annotation as categorization of terms from a protein's document neighborhood into the GO.

Results
The evaluation results indicate that the method for expanding words associated with GO nodes is quite powerful; we were able to successfully select appropriate evidence text for a given annotation in 38% of Task 2.1 queries by building on this method. The term categorization methodology achieved a precision of 16% for annotation within the correct extended family in Task 2.2, though we show through subsequent analysis that this can be improved with a different parameter setting. Our architecture proved not to be very successful on the evidence text component of the task, in the configuration used to generate the submitted results.

Conclusion
The initial results show promise for both of the methods we explored, and we are planning to integrate the methods more closely to achieve better results overall.
Exploring the boundaries: gene and protein identification in biomedical text
Authors: Finkel Jenny , Dingare Shipra , Manning Christopher D , Nissim Malvina , Alex Beatrice , Grover Claire 
Published: May 2005

Abstract

Background
Good automatic information extraction tools offer hope for automatic processing of the exploding biomedical literature, and successful named entity recognition is a key component for such tools.

Methods
We present a maximum-entropy based system incorporating a diverse set of features for identifying gene and protein names in biomedical abstracts.

Results
This system was entered in the BioCreative comparative evaluation and achieved a precision of 0.83 and recall of 0.84 in the "open" evaluation and a precision of 0.78 and recall of 0.85 in the "closed" evaluation.

Conclusion
Central contributions are rich use of features derived from the training data at multiple levels of granularity, a focus on correctly identifying entity boundaries, and the innovative use of several external knowledge sources including full MEDLINE abstracts and web searches.
Recognition of protein/gene names from text using an ensemble of classifiers
Authors: Zhou GuoDong , Shen Dan , Zhang Jie , Su Jian , Tan SoonHeng 
Published: May 2005

Abstract
This paper proposes an ensemble of classifiers for biomedical name recognition in which three classifiers, one Support Vector Machine and two discriminative Hidden Markov Models, are combined effectively using a simple majority voting strategy. In addition, we incorporate three post-processing modules, including an abbreviation resolution module, a protein/gene name refinement module and a simple dictionary matching module, into the system to further improve the performance. Evaluation shows that our system achieves the best performance from among 10 systems with a balanced F-measure of 82.58 on the closed evaluation of the BioCreative protein/gene name recognitiontask (Task 1A).
Gene/protein name recognition based on support vector machine using dictionary as features
Authors: Mitsumori Tomohiro , Fation Sevrani , Murata Masaki , Doi Kouichi , Doi Hirohumi 
Published: May 2005

Abstract

Background
Automated information extraction from biomedical literature is important because a vast amount of biomedical literature has been published. Recognition of the biomedical named entities is the first step in information extraction. We developed an automated recognition system based on the SVM algorithm and evaluated it in Task 1.A of BioCreAtIvE, a competition for automated gene/protein name recognition.

Results
In the work presented here, our recognition system uses the feature set of the word, the part-of-speech (POS), the orthography, the prefix, the suffix, and the preceding class. We call these features "internal resource features", i.e., features that can be found in the training data. Additionally, we consider the features of matching against dictionaries to be external resource features. We investigated and evaluated the effect of these features as well as the effect of tuning the parameters of the SVM algorithm. We found that the dictionary matching features contributed slightly to the improvement in the performance of the f-score. We attribute this to the possibility that the dictionary matching features might overlap with other features in the current multiple feature setting.

Conclusion
During SVM learning, each feature alone had a marginally positive effect on system performance. This supports the fact that the SVM algorithm is robust on the high dimensionality of the feature vector space and means that feature selection is not required.
Do orthologous gene phylogenies really support tree-thinking?
Authors: Bapteste E , Susko E , Leigh J , MacLeod D , Charlebois RL , Doolittle WF 
Published: May 2005

AbstractBackgroundSince Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes.ResultsHeat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer.ConclusionOur phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.
An improved method for rapid generation of unmarked Pseudomonas aeruginosa deletion mutants
Authors: Choi Kyoung-Hee , Schweizer Herbert P 
Published: May 2005

AbstractBackgroundTraditional gene replacement procedures are still time-consuming. They usually necessitate cloning of the gene to be mutated, insertional inactivation of the gene with an antibiotic resistance cassette and exchange of the plasmid-borne mutant allele with the bacterial chromosome. PCR and recombinational technologies can be exploited to substantially accelerate virtually all steps involved in the gene replacement process.ResultsWe describe a method for rapid generation of unmarkedP. aeruginosadeletion mutants. Three partially overlapping DNA fragments are amplified and then spliced togetherin vitroby overlap extension PCR. The resulting DNA fragment is clonedin vitrointo the Gateway vector pDONR221 and then recombined into the Gateway-compatible gene replacement vector pEX18ApGW. The plasmid-borne deletions are next transferred to theP. aeruginosachromosome by homologous recombination. Unmarked deletion mutants are finally obtained by Flp-mediated excision of the antibiotic resistance marker. The method was applied to deletion of 25P. aeruginosagenes encoding transcriptional regulators of the GntR family.ConclusionWhile maintaining the key features of traditional gene replacement procedures, for example, suicide delivery vectors, antibiotic resistance selection and sucrose counterselection, the method described here is considerably faster due to streamlining of some of the key steps involved in the process, especially plasmid-borne mutant allele construction and its transfer into the target host. With appropriate modifications, the method should be applicable to other bacteria.
Personality disorders in substance abusers: Validation of the DIP-Q through principal components factor analysis and canonical correlation analysis
Authors: Hesse Morten 
Published: May 2005

Abstract

Background
Personality disorders are common in substance abusers. Self-report questionnaires that can aid in the assessment of personality disorders are commonly used in assessment, but are rarely validated.

Methods
The Danish DIP-Q as a measure of co-morbid personality disorders in substance abusers was validated through principal components factor analysis and canonical correlation analysis. A 4 components structure was constructed based on 238 protocols, representing antagonism, neuroticism, introversion and conscientiousness. The structure was compared with (a) a 4-factor solution from the DIP-Q in a sample of Swedish drug and alcohol abusers (N = 133), and (b) a consensus 4-components solution based on a meta-analysis of published correlation matrices of dimensional personality disorder scales.

Results
It was found that the 4-factor model of personality was congruent across the Danish and Swedish samples, and showed good congruence with the consensus model. A canonical correlation analysis was conducted on a subset of the Danish sample with staff ratings of pathology. Three factors that correlated highly between the two variable sets were found. These variables were highly similar to the three first factors from the principal components analysis, antagonism, neuroticism and introversion.

Conclusion
The findings support the validity of the DIP-Q as a measure of DSM-IV personality disorders in substance abusers.
A prospective cohort study of surgical treatment for back pain with degenerated discs; study protocol
Authors: Deyo Richard A , Mirza Sohail K , Heagerty Patrick J , Turner Judith A , Martin Brook I 
Published: May 2005

Abstract

Background
The diagnosis of discogenic back pain often leads to spinal fusion surgery and may partly explain the recent rapid increase in lumbar fusion operations in the United States. Little is known about how patients undergoing lumbar fusion compare in preoperative physical and psychological function to patients who have degenerative discs, but receive only non-surgical care.

Methods
Our group is implementing a multi-center prospective cohort study to compare patients with presumed discogenic pain who undergo lumbar fusion with those who have non-surgical care. We identify patients with predominant low back pain lasting at least six months, one or two-level disc degeneration confirmed by imaging, and a normal neurological exam. Patients are classified as surgical or non-surgical based on the treatment they receive during the six months following study enrollment.

Results
Three hundred patients discogenic low back pain will be followed in a prospective cohort study for two years. The primary outcome measure is the Modified Roland-Morris Disability Questionnaire at 24-months. We also evaluate several other dimensions of outcome, including pain, functional status, psychological distress, general well-being, and role disability.

Conclusion
The primary aim of this prospective cohort study is to better define the outcomes of lumbar fusion for discogenic back pain as it is practiced in the United States. We additionally aim to identify characteristics that result in better patient selection for surgery. Potential predictors include demographics, work and disability compensation status, initial symptom severity and duration, imaging results, functional status, and psychological distress.
Intermediate care: for better or worse? Process evaluation of an intermediate care model between a university hospital and a residential home
Authors: Plochg Thomas , Delnoij Diana MJ , van der Kruk Tineke F , Janmaat Tonnie ACM , Klazinga Niek S 
Published: May 2005

Abstract
Background
Intermediate care was developed in order to bridge acute, primary and social care, primarily for elderly persons with complex care needs. Such bridging initiatives are intended to reduce hospital stays and improve continuity of care. Although many models assume positive effects, it is often ambiguous what the benefits are and whether they can be transferred to other settings. This is due to the heterogeneity of intermediate care models and the variety of collaborating partners that set up such models. Quantitative evaluation captures only a limited series of generic structure, process and outcome parameters. More detailed information is needed to assess the dynamics of intermediate care delivery, and to find ways to improve the quality of care. Against this background, the functioning of a low intensity early discharge model of intermediate care set up in a residential home for patients released from an Amsterdam university hospital has been evaluated. The aim of this study was to produce knowledge for management to improve quality of care, and to provide more generalisable insights into the accumulated impact of such a model.

Methods
A process evaluation was carried out using quantitative and qualitative methods. Registration forms and patient questionnaires were used to quantify the patient population in the model. Statistical analysis encompassed T-tests and chi-squared test to assess significance. Semi-structured interviews were conducted with 21 staff members representing all disciplines working with the model. Interviews were transcribed and analysed using both 'open' and 'framework' approaches.

Results
Despite high expectations, there were significant problems. A heterogeneous patient population, a relatively unqualified staff and cultural differences between both collaborating partners impeded implementation and had an impact on the functioning of the model.

Conclusion
We concluded that setting up a low intensity early discharge model of intermediate care between a university hospital and a residential home is less straightforward than was originally perceived by management, and that quality of care needs careful monitoring to ensure the change is for the better.