bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species richness estimators: how many species can dance on the head of a pin?
Authors: O'HARA R. B. 
Published: March 2005

Summary

Several species richness estimators (two non‐parametric, four based on rarefaction curves and two from fitting of abundance distributions) were compared by examining their performance in estimating the species richness for two moth data sets from the United Kingdom. Comparisons were also made using data simulated from the fitted abundance distributions.
The different species richness estimators gave different estimates. The non‐parametric estimates and the rarefaction estimates were similar, but were smaller than the parametric estimates. When the simulated data were used, the only methods to give estimates near the true value was the parametric method using the distribution from which the data were simulated.
At present it is impossible to decide whether any of the estimation methods will give a realistic estimate, as not enough is known about the true numbers of species in communities. Until this is rectified, the most that can be hoped for is to obtain upper and lower bounds on species richness.
An Experimental Performance Evaluation of Spatio‐Temporal Join Strategies
Authors: Jeong Seung‐Hyun , Paton Norman W. , Fernandes Alvaro A. A. , Griffiths Tony 
Published: March 2005

AbstractMany applications capture, or make use of, spatial data that changes over time. This requirement for effective and efficient spatio‐temporal data management has given rise to a range of research activities relating to spatio‐temporal data management. Such work has sought to understand, for example, the requirements of different categories of application, and the modelling facilities that are most effective for these applications. However, at present, there are few systems with fully integrated support for spatio‐temporal data, and thus developers must often construct custom solutions for their applications. Developers of both bespoke solutions and of generic spatio‐temporal platforms will often need to support the fusion of large spatio‐temporal data sets. Supporting such requests in a database setting involves the use of join operations with both spatial and temporal conditions – spatio‐temporal joins. However, there has been little work to date on spatio‐temporal join algorithms or their evaluation. This paper presents an evaluation of several approaches to the implementation of spatio‐temporal joins that build upon widely available indexing techniques. The evaluation explores how several algorithms perform for databases with different spatial and temporal characteristics, with a view to helping developers of generic infrastructures or custom solutions in the selection and development of appropriate spatio‐temporal join strategies.
Natural Conversational Interfaces to Geospatial Databases
Authors: Cai Guoray , Wang Hongmei , MacEachren Alan M. , Fuhrmann Sven 
Published: March 2005

AbstractNatural (spoken) language, combined with gestures and other human modalities, provides a promising alternative for interacting with computers, but such benefit has not been explored for interactions with geographical information systems. This paper presents a conceptual framework for enabling conversational human‐GIS interactions. Conversations with a GIS are modeled as human‐computer collaborative activities within a task domain. We adopt a mental state view of collaboration and discourse and propose a plan‐based computational model for conversational grounding and dialogue generation. At the implementation level, our approach is to introduce a dialogue agent,GeoDialogue, between a user and a geographical information server.GeoDialogueactively recognizes user's information needs, reasons about detailed cartographic and database procedures, and acts cooperatively to assist user's problem solving.GeoDialogueserves as a semantic ‘bridge’ between the human language and the formal language that a GIS understands. The behavior of such dialogue‐assisted human‐GIS interfaces is illustrated through a scenario simulating a session of emergency response during a hurricane event.
PSYCHOSOCIAL FACTORS IN PATIENTS WITH CHRONIC KIDNEY DISEASE: Health‐Related Quality of Life in Nephrology Research and Clinical Practice
Authors: Unruh Mark L. , Weisbord Steven D. , Kimmel Paul L. 
Published: March 2005

ABSTRACTPhysical, psychosocial, and lifestyle disturbances, along with physical and emotional symptoms, have been shown to impact the health‐related quality of life (HRQOL) of those dependent on renal replacement therapy. The value of HRQOL measurement as a tool to improve clinical care has been recognized by patients, clinical investigators, and health care providers. The potential importance of HRQOL assessment lies in the additional information it provides and the impact it has on the clinical decision‐making process between a patient and a physician. There remain a multitude of challenges facing renal providers who wish to incorporate HRQOL measurement to improve patient care. These challenges include the clinician's understanding of the conceptual model of HRQOL, the quality of the scientific process that contributed to the current literature on HRQOL, a willingness of the clinician to incorporate HRQOL information into clinical practice, and the logistic difficulties of collecting and applying HRQOL data in a busy practice setting. Arguably, optimizing HRQOL may be the most substantial impact the health care team will have on the person with kidney failure. In order to implement HRQOL assessment at the point of care, providers may consider using computer adaptive testing and scoring algorithms using item response theory, which will allow adequate reliability for interpretation of change among individuals. Moreover, the effective assessment and interpretation of HRQOL will be aided by continued publication of norms, outcomes of randomized controlled trials, and continued experience of investigators and clinicians.
PSYCHOSOCIAL FACTORS IN PATIENTS WITH CHRONIC KIDNEY DISEASE: Frequent Hemodialysis and Psychosocial Function
Authors: Kurella Manjula , Suri Rita S. , Chertow Glenn M. 
Published: March 2005

ABSTRACTStudies suggest that more frequent hemodialysis (HD; short daily and long nocturnal dialysis) may be associated with a variety of clinical benefits, including improvement in blood pressure, anemia, and hyperphosphatemia, regression of left ventricular hypertrophy, and reduced rates of hospitalization. Whether these clinical benefits are paralleled by improvements in health‐related quality of life (HRQOL) has been unclear. In addition, the psychosocial burden of more intensive HD schedules has not been critically evaluated. Recent reports have suggested beneficial effects of frequent HD on global HRQOL, dialysis‐related and uremic symptoms, patient satisfaction, and psychosocial burden. However, the interpretation of many of these studies is restricted by limitations in study design, follow‐up, and generalizability. This article reviews the current literature focusing on psychosocial and HRQOL effects of frequent HD and suggests future directions for research in this important area.
PSYCHOSOCIAL FACTORS IN PATIENTS WITH CHRONIC KIDNEY DISEASE: Depression and Renal Disease
Authors: Tossani Eliana , Cassano Paolo , Fava Maurizio 
Published: March 2005

ABSTRACTMajor depressive disorder (MDD) is a highly prevalent disease, frequently characterized by recurrent or chronic course, and by comorbidity with other medical illnesses. The lifetime prevalence of MDD ranges up to 17% in the general population, and it almost doubles in patients with diabetes (9–27%), stroke (22–50%), or cancer (18–39%). Moreover, MDD worsens the prognosis, quality of life, and treatment compliance of patients with comorbid medical illnesses. Similar to what is observed with other comorbid illnesses, MDD worsens the outcome of kidney disease patients by increasing both morbidity and mortality. Treatment of depressive symptoms in renal failure patients increases medication acceptability and therefore potentially improves the overall patient outcome. The issue of the safety of antidepressant treatment in subjects with renal failure is frequently counterbalanced by the risks associated with depression comorbidity, provided that antidepressants with a low volume of distribution and low protein binding are prescribed, and most important, at low initial doses. Screening for CYP isoenzyme interactions with current medications is also recommended before starting antidepressant treatment.
Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling
Authors: Freyhult Eva , Prusis Peteris , Lapinsh Maris , Wikberg Jarl ES , Moulton Vincent , Gustafsson Mats G 
Published: March 2005

Abstract
Background
Proteochemometrics is a new methodology that allows prediction of protein function directly from real interaction measurement data without the need of 3D structure information. Several reported proteochemometric models of ligand-receptor interactions have already yielded significant insights into various forms of bio-molecular interactions. The proteochemometric models are multivariate regression models that predict binding affinity for a particular combination of features of the ligand and protein. Although proteochemometric models have already offered interesting results in various studies, no detailed statistical evaluation of their average predictive power has been performed. In particular, variable subset selection performed to date has always relied on using all available examples, a situation also encountered in microarray gene expression data analysis.

Results
A methodology for an unbiased evaluation of the predictive power of proteochemometric models was implemented and results from applying it to two of the largest proteochemometric data sets yet reported are presented. A double cross-validation loop procedure is used to estimate the expected performance of a given design method. The unbiased performance estimates (P2) obtained for the data sets that we consider confirm that properly designed single proteochemometric models have useful predictive power, but that a standard design based on cross validation may yield models with quite limited performance. The results also show that different commercial software packages employed for the design of proteochemometric models may yield very different and therefore misleading performance estimates. In addition, the differences in the models obtained in the double CV loop indicate that detailed chemical interpretation of a single proteochemometric model is uncertain when data sets are small.

Conclusion
The double CV loop employed offer unbiased performance estimates about a given proteochemometric modelling procedure, making it possible to identify cases where the proteochemometric design does not result in useful predictive models. Chemical interpretations of single proteochemometric models are uncertain and should instead be based on all the models selected in the double CV loop employed here.
Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms
Authors: McKillen David J , Chen Yian A , Chen Chuming , Jenny Matthew J , Trent Harold F , Robalino Javier , McLean David C , Gross Paul S , Chapman Robert W , Warr Gregory W , Almeida Jonas S 
Published: March 2005

Abstract
Background
The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs) and gene expression microarray data for marine organisms. It provides a unique clearing-house for marine specific EST and microarray data and is currently available at http://www.marinegenomics.org.

Description
The Marine Genomics pipeline automates the processing, maintenance, storage and analysis of EST and microarray data for an increasing number of marine species. It currently contains 19 species databases (over 46,000 EST sequences) that are maintained by registered users from local and remote locations in Europe and South America in addition to the USA. A collection of analysis tools are implemented. These include a pipeline upload tool for EST FASTA file, sequence trace file and microarray data, an annotative text search, automated sequence trimming, sequence quality control (QA/QC) editing, sequence BLAST capabilities and a tool for interactive submission to GenBank. Another feature of this resource is the integration with a scientific computing analysis environment implemented by MATLAB.

Conclusion
The conglomeration of multiple marine organisms with integrated analysis tools enables users to focus on the comprehensive descriptions of transcriptomic responses to typical marine stresses. This cross species data comparison and integration enables users to contain their research within a marine-oriented data management and analysis environment.
Silhouette scores for assessment of SNP genotype clusters
Authors: Lovmar Lovisa , Ahlford Annika , Jonsson Mats , Syvänen Ann-Christine 
Published: March 2005

Abstract
Background
High-throughput genotyping of single nucleotide polymorphisms (SNPs) generates large amounts of data. In many SNP genotyping assays, the genotype assignment is based on scatter plots of signals corresponding to the two SNP alleles. In a robust assay the three clusters that define the genotypes are well separated and the distances between the data points within a cluster are short. "Silhouettes" is a graphical aid for interpretation and validation of data clusters that provides a measure of how well a data point was classified when it was assigned to a cluster. Thus "Silhouettes" can potentially be used as a quality measure for SNP genotyping results and for objective comparison of the performance of SNP assays at different circumstances.

Results
We created a program (ClusterA) for calculating "Silhouette scores", and applied it to assess the quality of SNP genotype clusters obtained by single nucleotide primer extension ("minisequencing") in the Tag-microarray format. A Silhouette score condenses the quality of the genotype assignment for each SNP assay into a single numeric value, which ranges from 1.0, when the genotype assignment is unequivocal, down to -1.0, when the genotype assignment has been arbitrary. In the present study we applied Silhouette scores to compare the performance of four DNA polymerases in our minisequencing system by analyzing 26 SNPs in both DNA polarities in 16 DNA samples. We found Silhouettes to provide a relevant measure for the quality of SNP assays at different reaction conditions, illustrated by the four DNA polymerases here. According to our result, the genotypes can be unequivocally assigned without manual inspection when the Silhouette score for a SNP assay is > 0.65. All four DNA polymerases performed satisfactorily in our Tag-array minisequencing system.

Conclusion
"Silhouette scores" for assessing the quality of SNP genotyping clusters is convenient for evaluating the quality of SNP genotype assignment, and provides an objective, numeric measure for comparing the performance of SNP assays. The program we created for calculating Silhouette scores is freely available, and can be used for quality assessment of the results from all genotyping systems, where the genotypes are assigned by cluster analysis using scatter plots.
Assessment of the paraspinal muscles of subjects presenting an idiopathic scoliosis: an EMG pilot study
Authors: Gaudreault Nathaly , Arsenault A Bertrand , Larivière Christian , DeSerres Sophie J , Rivard Charles-Hilaire 
Published: March 2005

Abstract
Background
It is known that the back muscles of scoliotic subjects present abnormalities in their fiber type composition. Some researchers have hypothesized that abnormal fiber composition can lead to paraspinal muscle dysfunction such as poor neuromuscular efficiency and muscle fatigue. EMG parameters were used to evaluate these impairments. The purpose of the present study was to examine the clinical potential of different EMG parameters such as amplitude (RMS) and median frequency (MF) of the power spectrum in order to assess the back muscles of patients presenting idiopathic scoliosis in terms of their neuromuscular efficiency and their muscular fatigue.

Methods
L5/S1 moments during isometric efforts in extension were measured in six subjects with idiopathic scoliosis and ten healthy controls. The subjects performed three 7 s ramp contractions ranging from 0 to 100% maximum voluntary contraction (MVC) and one 30 s sustained contraction at 75% MVC. Surface EMG activity was recorded bilaterally from the paraspinal muscles at L5, L3, L1 and T10. The slope of the EMG RMS/force (neuromuscular efficiency) and MF/force (muscle composition) relationships were computed during the ramp contractions while the slope of the EMG RMS/time and MF/time relationships (muscle fatigue) were computed during the sustained contraction. Comparisons were performed between the two groups and between the left and right sides for the EMG parameters.

Results
No significant group or side differences between the slopes of the different measures used were found at the level of the apex (around T10) of the major curve of the spine. However, a significant side difference was seen at a lower level (L3, p = 0.01) for the MF/time parameter.

Conclusion
The EMG parameters used in this study could not discriminate between the back muscles of scoliotic subjects and those of control subject regarding fiber type composition, neuromuscular efficiency and muscle fatigue at the level of the apex. The results of this pilot study indicate that compensatory strategies are potentially seen at lower level of the spine with these EMG parameters.
High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study
Authors: Seshasayee Aswin Sai Narain 
Published: March 2005

Abstract
Background
Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns.

Results
High-temperature unfolding molecular dynamics simulations of the Trp cage miniprotein have been carried out in explicit water using the OPLS-AA force-field incorporated in the program GROMACS. The radius of gyration (Rg) and Root Mean Square Deviation (RMSD) have been used as order parameters to follow the unfolding process. Distributions of Rg were used to identify ensembles.

Conclusion
Three ensembles could be identified. While the native-state ensemble shows an Rg distribution that is slightly skewed, the second ensemble, which is presumably the Transition State Ensemble (TSE), shows an excellent fit. The denatured ensemble shows large fluctuations, but a Gaussian curve could be fitted. This means that the unfolding process is two-state. Representative structures from each of these ensembles are presented here.
Evidence against the Hypothesis that Endothelial Endothelin B Receptor Expression Is Regulated by Relaxin and Pregnancy
Authors: Kerchner Laurie J. , Novak Jacqueline , Hanley-Yanez Karen , Doty Ketah D. , Danielson Lee A. , Conrad Kirk P. 
Published: March 2005

Abstract
The endothelial endothelin B (ETB) receptor subtype is critical for renal vasodilation induced by relaxin in nonpregnant rats and during pregnancy (the latter via endogenous circulating relaxin). Here we tested whether expression of vascular ETB receptor protein is regulated by relaxin. Small renal arteries were harvested from virgin and midterm pregnant rats as well as nonpregnant rats that were administered recombinant human relaxin (rhRLX) at 4 μg/h or vehicle for 5 d or 4–6 h. Small renal arteries dissected from additional virgin rats were incubated in vitro with rhRLX or vehicle for 3 h at 37 C. ETB expression was also evaluated in cultured human endothelial cells: aortic, coronary, umbilical vein, and dermal microvascular endothelial cells. Cells were incubated for 4, 8, or 24 h with rhRLX (5, 1, or 0.1 ng/ml) or vehicle. ETB protein expression in arteries and cells was evaluated by Western analysis. No regulation of ETB expression was observed in small renal arteries in any of the experimental protocols, nor was there an increase in the vasorelaxation response to ET-3 in small renal arteries incubated in vitro with rhRLX. rhRLX only sporadically altered ETB expression in human coronary artery endothelial cells and human umbilical vein endothelial cells at certain time points or doses, and no regulation was observed in human aortic endothelial cells or human dermal microvascular endothelial cells. These results suggest that regulation of ETB receptor protein has little or no role in relaxin stimulation of the endothelial ETB/nitric oxide vasodilatory pathway.
Super‐Efficient Exciton Funneling in Layer‐by‐Layer Semiconductor Nanocrystal Structures
Authors: Klar T. A. , Franzl T. , Rogach A. L. , Feldmann J. 
Published: March 2005

AbstractIn semiconductor nanocrystals the electronic energy gap is determined not only by the material but also by the size of the nanocrystals. This allows the construction of an energy‐gap gradient normal to multiple layers of nanocrystals where the diameters of the nanocrystals are monotonically increasing or decreasing in subsequent layers. In such devices we observe a highly efficient funneling of excitation energy from layers comprising smaller nanocrystals towards the layer with the largest nanocrystals in the center of the funnel. Most importantly, not only are excitons in radiative states transferred, but also excitons from trapped states, usually lost for luminescence, can be effectively recycled, hence increasing the overall luminescence yield.
Expression and function of the adaptor protein Gads in murine B cells
Authors: Yankee Thomas M. , Draves Kevin E. , Clark Edward A. 
Published: March 2005

AbstractNearly all hematopoietic receptors are dependent on adaptor proteins for the activation of downstream signaling pathways. The Gads adaptor protein is expressed in many hematopoietic tissues, including bone marrow, lymph node, and spleen. Using intracellular staining, we detected Gads protein in a number cells, including B cells, T cells, NK cells, monocytes, and plasmacytoid DC, but not in macrophages, neutrophils, or monocyte‐derived DC. In the B cell compartment, Gads was first expressed after immature B cells leave the bone marrow and was down‐regulated after B cell antigen receptor (BCR) ligation. Female Gads–/– mice had increased numbers of splenic B cells, as compared to female Gads+/+ mice, suggesting a role for Gads in B cell homeostasis. Although B cell production and turnover of splenic B cell subsets appeared normal in Gads–/– mice, homeostatic proliferation was significantly impaired in Gads–/– B cells. Whereas BCR ligation can induce apoptosis in wild‐type transitional stage 1 (T1) B cells, Gads–/– T1 B cells were resistant to BCR‐induced apoptosis. Gads–/– B cells also showed increased BCR‐mediated calcium mobilization. We conclude that Gads may have a negative regulatory role in signaling through survival pathways, and is necessary for normal homeostatic proliferation in B cells.