bluuebunny/crossref_metadata_2025_split huggingface dataset:
Failure of Routine Diagnostic Methods to Detect Influenza in Hospitalized Older Adults
Authors: Talbot H. Keipp , Williams John V. , Zhu Yuwei , Poehling Katherine A. , Griffin Marie R. , Edwards Kathryn M. 
Published: May 2010

Objective.To define the utility of using routine diagnostic methods to detect influenza in older, hospitalized adults.Design.Descriptive study.Setting.One academic hospital and 1 community hospital during the 2006–2007 and 2007–2008 influenza seasons.Participants.Hospitalized adults 50 years of age or older.Methods.Adults who were 50 years of age or older and hospitalized with symptoms of respiratory illness were enrolled and tested for influenza by use of reverse-transcriptase polymerase chain reaction (RT-PCR). Using RT-PCR as the gold standard, we assessed the performances of rapid antigen tests and conventional influenza culture and the diagnostic use of the clinical definition of influenza-like illness.Results.Influenza was detected by use of RT-PCR in 26 (11%) of 228 patients enrolled in our study. The sensitivity of the rapid antigen test performed at bedside by research staff members was 19.2% (95% confidence interval, 8.51%–37.9%); the sensitivity of conventional influenza culture was 34.6% (95% confidence interval, 19.4%–53.8%). The ability to detect influenza with both the rapid antigen test and culture was associated with patients with a higher viral load (P= .002 andP= .001, respectively). The ability to diagnose influenza by use of the clinical definition of influenza-like illness had a higher sensitivity (80.8%) but lacked specificity (40.6%).Conclusion.Because rapid antigen testing and viral culture have poor sensitivity (19.2% and 34.6%, respectively), neither testing method is sufficient to use to determine what type of isolation procedures to implement in a hospital setting.
Development of a Novel Electronic Surveillance System for Monitoring of Bloodstream Infections
Authors: Leal Jenine , Gregson Daniel B. , Ross Terry , Flemons Ward W. , Church Deirdre L. , Laupland Kevin B. 
Published: May 2010

Background.Electronic surveillance systems (ESSs) that utilize existing information in databases are more efficient than conventional infection surveillance methods.Objective.To develop an ESS for monitoring bloodstream infections (BSIs) and assess whether data obtained from the ESS were in agreement with data obtained by traditional manual medical-record review.Methods.An ESS was developed by linking data from regional laboratory and hospital administrative databases. Definitions for excluding BSI episodes representing contamination and duplicate episodes were developed and applied. Infections were classified as nosocomial infections, healthcare-associated community-onset infections, or community-acquired infections. For a random sample of episodes, data in the ESS were compared with data obtained by independent medical chart review.Results.From the records of the 306 patients whose infections were selected for comparative review, the ESS identified 323 episodes of BSI, of which 107 (33%) were classified as healthcare-associated community-onset infections, 108 (33%) were classified as community-acquired infections, 107 (33%) were classified as nosocomial infections, and 1 (0.3%) could not be classified. In comparison, 310 episodes were identified by use of medical chart review, of which 116 (37%) were classified as healthcare-associated community-onset infections, 95 (31%) as community-acquired infections, and 99 (32%) as nosocomial infections. For 302 episodes of BSI, there was concordance between the findings of the ESS and those of traditional manual chart review. Of the additional 21 discordant episodes that were identified by use of the ESS, 17 (81%) were classified as representing isolation of skin contaminants, by use of chart review. Of the additional 8 discordant episodes further identified by use of chart review, most were classified as repeat or polymicrobial episodes of disease. There was an overall 85% agreement between the findings of the ESS and those of chart review (K = 0.78; standard error, K = 0.04) for classification according to location of acquisition.Conclusion.Our novel ESS allows episodes of BSI to be identified and classified with a high degree of accuracy. This system requires validation in other cohorts and settings.
Visible-light photocatalytic activity of N/SiO
2–TiO
2 thin films on glass
Authors: Dung Dang Thi My , Dam Le Duy , Thang Chau Vinh , Chien Dang Mau 
Published: May 2010

Abstract
Nanocrystalline N-doped SiO
2/TiO
2 visible-light photocatalyst thin films were synthesized using the sol-gel method on glass substrates. The synthesized catalysts were then characterized using several analytical techniques like x-ray Diffraction (XRD), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), Atomic Force Microscopy (AFM), and UV–vis absorption spectroscopy (UV–vis). The experimental results revealed that the maximum optical response of the synthesized SiO
2/TiO
2 thin films shifted from the ultraviolet (UV) to the visible-light region (λ⩾420 nm). The photocatalytic activity of N-doped SiO
2–TiO
2 photocatalyst was considerably higher than that of SiO
2–TiO
2, and this result was obtained with an optimal concentration of 40 mol% of N. The enhanced photocatalytic activity was attributed to the increasing surface area and forming more hydroxyl groups in the doped catalyst.
A cryogenic heat capacity study of the crystallization process in Fe-based nanocrystalline alloys
Authors: Hoa Le Thi Mai , Ishizaki Kozo , Dang Mau Chien 
Published: May 2010

Abstract
Nanocrystalline alloys have attracted wide attention because of their excellent soft magnetic properties such as high saturation induction and permeability, low magnetostriction, coercive field and anisotropy. In this paper, the nanocrystalline material is prepared by annealing a melt-spun Fe
73.5
Si
13.5
Cu
1
B
9
Nb
3 amorphous ribbon with various annealing conditions. This annealing process produced a series of samples with different crystalline fractions. The primary crystallization stage was investigated by cryogenic heat capacity and x-ray diffraction. The x-ray diffraction results showed that the sample began to crystallize at 490 °C and nanocrystalline Fe
3
Si particles were formed in all the annealed samples. The crystalline fraction obtained by the cryogenic heat capacity measurement indicated that the crystalline volume fraction can be controlled by selecting the annealing temperature or annealing time. The crystallization process is almost complete (99.31%) when the sample is annealed at 600 °C for 60 min.
Investigation of hydrophilic modification for bubble-free operation in microfluidic systems and micropump applications
Authors: Le N B , Hsu Y C 
Published: May 2010

Abstract
This study developed a bubble-free method for microfluidic devices and micropump applications by modifying the wetting characteristic of their chamber surfaces. Two methods of hydrophilic film formation were investigated, that is, microwave plasma surface modification and TiO
2 thin film deposition. The evaluation results indicated that TiO
2 thin film deposition showed better stability and it was therefore selected to improve the surface wettability and unify the spreading behavior. Different hydrophilic strip shape and strip numbers were investigated and the results indicated that the vertical design with trisection strip gives the best result and effectively discharges the bubbles of microfluidic devices. The results were then applied to a peristaltic micropump and very good results were obtained. That is, the micropump stability and robustness are enhanced significantly. Furthermore, in the pump operation frequency range (i.e. 75 ±10 Hz), bubbles are discharged effectively. The results show that when the micropump operated at frequencies lower than 100 Hz, air bubbles became insignificant; therefore, operation frequencies lower than 100 Hz are considered to be the micropump's stable performance range. From the results it was concluded that bubble formation is also responsible for the flow rate downhill effect.
The fabrication of visible light responsive Ag-SiO
2 co-doped TiO
2 thin films by the sol–gel method
Authors: Dam Le Duy , Dung Dang Thi My , Thang Chau Vinh , Chien Dang Mau 
Published: May 2010

Abstract
In this study we have successfully deposited Ag-SiO
2 co-doped TiO
2 thin films on glass substrates by the sol–gel method. After being coated by a dip coating method, the film was transparent, smooth and had strong adhesion on the glass surface. The deposited film was characterized by x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), ultraviolet-visible spectroscopy (UV–Vis), a scanning electron microscope (SEM) and atomic force microscope (AFM) to investigate its crystallization, transmittance and surface structure. The antifogging ability is explained by the contact angle of water on the surface of the glass substrates under visible-light. The obtained results show that Ag-SiO
2 co-doped TiO
2 film has potential applications for self cleaning and anti-bacterial ceramic tiles.
Identifying duplicate content using statistically improbable phrases
Authors: Errami Mounir , Sun Zhaohui , George Angela C. , Long Tara C. , Skinner Michael A. , Wren Jonathan D. , Garner Harold R. 
Published: May 2010

Abstract
Motivation: Document similarity metrics such as PubMed's ‘Find related articles’ feature, which have been primarily used to identify studies with similar topics, can now also be used to detect duplicated or potentially plagiarized papers within literature reference databases. However, the CPU-intensive nature of document comparison has limited MEDLINE text similarity studies to the comparison of abstracts, which constitute only a small fraction of a publication's total text. Extending searches to include text archived by online search engines would drastically increase comparison ability. For large-scale studies, submitting short phrases encased in direct quotes to search engines for exact matches would be optimal for both individual queries and programmatic interfaces. We have derived a method of analyzing statistically improbable phrases (SIPs) for assistance in identifying duplicate content.
Results: When applied to MEDLINE citations, this method substantially improves upon previous algorithms in the detection of duplication citations, yielding a precision and recall of 78.9% (versus 50.3% for eTBLAST) and 99.6% (versus 99.8% for eTBLAST), respectively.
Availability: Similar citations identified by this work are freely accessible in the Déjà vu database, under the SIP discovery method category at http://dejavu.vbi.vt.edu/dejavu/
Contact: merrami@collin.edu
Classification of DNA sequences using Bloom filters
Authors: Stranneheim Henrik , Käller Max , Allander Tobias , Andersson Björn , Arvestad Lars , Lundeberg Joakim 
Published: May 2010

Abstract
Motivation: New generation sequencing technologies producing increasingly complex datasets demand new efficient and specialized sequence analysis algorithms. Often, it is only the ‘novel’ sequences in a complex dataset that are of interest and the superfluous sequences need to be removed.
Results: A novel algorithm, fast and accurate classification of sequences (FACSs), is introduced that can accurately and rapidly classify sequences as belonging or not belonging to a reference sequence. FACS was first optimized and validated using a synthetic metagenome dataset. An experimental metagenome dataset was then used to show that FACS achieves comparable accuracy as BLAT and SSAHA2 but is at least 21 times faster in classifying sequences.
Availability: Source code for FACS, Bloom filters and MetaSim dataset used is available at http://facs.biotech.kth.se. The Bloom::Faster 1.6 Perl module can be downloaded from CPAN at http://search.cpan.org/∼palvaro/Bloom-Faster-1.6/
Contacts: henrik.stranneheim@biotech.kth.se; joakiml@biotech.kth.se
Supplementary information: Supplementary data are available at Bioinformatics online.
Ligand-binding site prediction of proteins based on known fragment–fragment interactions
Authors: Kasahara Kota , Kinoshita Kengo , Takagi Toshihisa 
Published: May 2010

Abstract
Motivation: The identification of putative ligand-binding sites on proteins is important for the prediction of protein function. Knowledge-based approaches using structure databases have become interesting, because of the recent increase in structural information. Approaches using binding motif information are particularly effective. However, they can only be applied to well-known ligands that frequently appear in the structure databases.
Results: We have developed a new method for predicting the binding sites of chemically diverse ligands, by using information about the interactions between fragments. The selection of the fragment size is important. If the fragments are too small, then the patterns derived from the binding motifs cannot be used, since they are many-body interactions, while using larger fragments limits the application to well-known ligands. In our method, we used the main and side chains for proteins, and three successive atoms for ligands, as fragments. After superposition of the fragments, our method builds the conformations of ligands and predicts the binding sites. As a result, our method could accurately predict the binding sites of chemically diverse ligands, even though the Protein Data Bank currently contains a large number of nucleotides. Moreover, a further evaluation for the unbound forms of proteins revealed that our building up procedure was robust to conformational changes induced by ligand binding.
Availability: Our method, named ‘BUMBLE’, is available at http://bumble.hgc.jp/
Contact: kasahara@cb.k.u-tokyo.ac.jp
Supplementary information: Supplementary Material is available at Bioinformatics online.
Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase
Authors: Dibrova Daria V. , Galperin Michael Y. , Mulkidjanian Armen Y. 
Published: May 2010

Abstract
An analysis of the distribution of the Na+-translocating ATPases/ATP synthases among microbial genomes identified an atypical form of the F1Fo-type ATPase that is present in the archaea Methanosarcina barkeri and M.acetivorans, in a number of phylogenetically diverse marine and halotolerant bacteria and in pathogens Burkholderia spp. In complete genomes, representatives of this form (referred to here as N-ATPase) are always present as second copies, in addition to the typical proton-translocating ATP synthases. The N-ATPase is encoded by a highly conserved atpDCQRBEFAG operon and its subunits cluster separately from the equivalent subunits of the typical F-type ATPases. N-ATPase c subunits carry a full set of sodium-binding residues, indicating that most of these enzymes are Na+-translocating ATPases that likely confer on their hosts the ability to extrude Na+ ions. Other distinctive properties of the N-ATPase operons include the absence of the delta subunit from its cytoplasmic sector and the presence of two additional membrane subunits, AtpQ (formerly gene 1) and AtpR (formerly gene X). We argue that N-ATPases are an early-diverging branch of membrane ATPases that, similarly to the eukaryotic V-type ATPases, do not synthesize ATP.
Contact: galperin@ncbi.nlm.nih.gov; amulkid@uos.de
Supplementary information: Supplementary data are available at Bioinformatics online.
The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell
Authors: Junier Thomas , Zdobnov Evgeny M. 
Published: May 2010

Abstract
Summary: We present a suite of Unix shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes.
Availability: C source code, Python bindings and executables for various platforms are available from http://cegg.unige.ch/newick_utils. The distribution includes a manual and example data. The package is distributed under the BSD License.
Contact: thomas.junier@unige.ch
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
Authors: Yu Nancy Y. , Wagner James R. , Laird Matthew R. , Melli Gabor , Rey Sébastien , Lo Raymond , Dao Phuong , Sahinalp S. Cenk , Ester Martin , Foster Leonard J. , Brinkman Fiona S. L. 
Published: May 2010

Abstract
Motivation: PSORTb has remained the most precise bacterial protein subcellular localization (SCL) predictor since it was first made available in 2003. However, the recall needs to be improved and no accurate SCL predictors yet make predictions for archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell or bacterial hyperstructures/organelles. Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program.
Results: We developed PSORTb version 3.0 with improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies. It features an improved standalone program, with a new batch results delivery system complementing its web interface. We evaluated the most accurate SCL predictors using 5-fold cross validation plus we performed an independent proteomics analysis, showing that PSORTb 3.0 is the most accurate but can benefit from being complemented by Proteome Analyst predictions.
Availability: http://www.psort.org/psortb (download open source software or use the web interface).
Contact: psort-mail@sfu.ca
Supplementary Information: Supplementary data are availableat Bioinformatics online.
Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming
Authors: Ibarra Ignacio L. , Melo Francisco 
Published: May 2010

Abstract
Summary: Dynamic programming (DP) is a general optimization strategy that is successfully used across various disciplines of science. In bioinformatics, it is widely applied in calculating the optimal alignment between pairs of protein or DNA sequences. These alignments form the basis of new, verifiable biological hypothesis. Despite its importance, there are no interactive tools available for training and education on understanding the DP algorithm. Here, we introduce an interactive computer application with a graphical interface, for the purpose of educating students about DP. The program displays the DP scoring matrix and the resulting optimal alignment(s), while allowing the user to modify key parameters such as the values in the similarity matrix, the sequence alignment algorithm version and the gap opening/extension penalties.
We hope that this software will be useful to teachers and students of bioinformatics courses, as well as researchers who implement the DP algorithm for diverse applications.
Availability and Implementation: The software is freely available at: http://melolab.org/sat. The software is written in the Java computer language, thus it runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.
Contact: All inquiries or comments about this software should be directed to Francisco Melo at fmelo@bio.puc.cl
Blood Urea Nitrogen Concentrations in Low‐birth‐weight Preterm Infants During Parenteral and Enteral Nutrition
Authors: Roggero Paola , Giannì Maria Lorella , Morlacchi Laura , Piemontese Pasqua , Liotto Nadia , Taroni Francesca , Mosca Fabio 
Published: May 2010

ABSTRACTObjectives:Early amino acid administration has been recommended in preterm neonates to avoid protein catabolism. In the present work, blood urea nitrogen (BUN) was used to evaluate the quantity of protein intake in preterm infants. The aim of the study was to investigate the relation between protein intake and BUN during the entire duration of parenteral and enteral nutrition.Patients and Methods:We conducted a prospective, longitudinal, observational study. BUN was assessed in 92 preterm newborns on days 2, 5, and 15 of parenteral nutrition, on the day when infants consumed 160 mL/kg of milk, and at 36 weeks of postmenstrual infants' age. Protein intakes were calculated from the 24‐hour period preceding the time the BUN specimens were collected. The effects of gestational age and protein intakes on BUN concentrations during parenteral nutrition were ascertained by multiple regression analyses. The relation between BUN and protein intakes during enteral feeding was evaluated by a simple correlation analysis.Results:Using linear regression analyses, gestational age showed a significant negative correlation with BUN concentrations during parenteral nutrition, whereas protein intakes at 2, 5, and 15 days did not correlate with BUN. A moderately positive correlation between BUN and protein intake was found when the infants consumed 160 mL/kg of milk and at 36 weeks of postmenstrual age (r = 0.5, P = 0.001 and r = 0.49, P = 0.012, respectively).Conclusions:In the early postnatal period, high BUN could be the effect of many factors other than amino acid intolerance. In contrast, BUN may represent a useful index in monitoring the adequacy of protein intake during enteral nutrition.
Aluminum Loading in Preterm Neonates Revisited
Authors: Bohrer Denise , Oliveira Sandra MR , Garcia Solange C , Nascimento Paulo C , Carvalho Leandro M 
Published: May 2010

ABSTRACTPreterm neonates receiving parenteral nutrition are at risk of aluminum (Al) overload because of the presence of Al as a contaminant in parenteral formulations. Despite US Food and Drug Administration regulation, commercial products continue to present Al contamination. To reassess Al exposure in the premature neonatal population, the present study evaluated the Al balance (intake vs urinary excretion) in a group of preterm neonates during the period in which they stayed in the intensive care unit (NICU) under total parenteral nutrition. For the 10 patients selected, daily infusion solutions (nutrition and medication) were collected and the level of Al contamination was measured. From the urine collected daily, an aliquot was taken for Al determination. Blood was also collected for Al determination on the first and last day in the NICU. The measurements were carried out by atomic absorption spectrometry. The difference between Al administered and excreted revealed that 56.2% ± 22.7% of the Al intake was not eliminated. The mean serum Al levels from the first to the last day decreased from 41.2 ± 23.3 to 23.5 ± 11.2 μg/L. The resulting mean Al daily intake of the 10 patients was 15.2 ± 8.0 μg · kg−1 · day−1. Because Al intake was higher than that excreted and Al in serum decreased to practically half during the period in the NICU (±7.3 days), some amount of Al deposition occurred. Moreover, premature neonates were receiving, on average, 3 times the amount of 5 μg · kg−1 · day−1, considered by the Food and Drug Administration as a safe limit.