bluuebunny/crossref_metadata_2025 huggingface dataset:
PCL-R Psychopathy: Threats to Sue, Peer Review, and Potential Implications for Science and Law. A Commentary
Authors: Poythress Norman , Petrila JohnP.
Published: May 2010

Disputes among academicians are not uncommon. They are usually played out in peer review journals in the form of point-and-counterpoint articles, or rebuttals and rejoinders. Recently however, a threat of litigation was issued against the authors of an article and the editor of the scientific journal which had accepted that article for publication following peer review. In this commentary we review legal commentary on litigation (and threats of litigation) involving academic disputes and literature regarding the values that underpin the scientific peer review process. We conclude that the use of threats of litigation to suppress the publication of articles accepted for publication in scientific journals strike at the heart of the peer review process, may have a chilling effect on the values at the core of academic freedom, and may potentially impede the scientific testing of various theories, models and products.
Psychopathy, Alexithymia and Emotional Intelligence in a Forensic Hospital
Authors: Pham ThierryH. , Ducro Claire , Luminet Olivier
Published: May 2010

In this study, we compared 20 criminal psychopaths and 19 nonpsychopaths identified with the PCL-R ( Hare, 2003 ). All participants were adult males confined in a Belgian security hospital. The psychopath group and the control group were equivalent for age, IQ, and social desirability score ( Crowne & Marlowe, 1960 ). First, the two groups completed the Toronto Alexithymia Scale (TAS; Bagby et al. 1994a, b). This self report measure includes three factors: the identification of emotion states; the expression of emotion states to others, and operative thinking. Secondly, each participant completed the TEIque (Emotional Intelligence Questionnaire; Petrides & Furnam, 2003). The full version of this self-report includes 15 scales and 4 main factors. For this study, we selected six scales that were a priori supposed to be strongly involved in emotion processing: “emotional regulation” of self, “emotion management” of others, “relational aptitudes,” “emotional expression,” “emotional perception,” and “stress management.” First, psychopaths presented a lower total score on the TAS. Among the facets of psychopathy, the deficient affective component was the most negatively correlated to the TAS total score. These results disconfirmed the classical hypothesis of a perceived emotion deficit among psychopaths. Concerning the TEIque, psychopaths presented a higher score on both the “emotional perception” and “emotional regulation” scales. Again, among the facets of psychopathy, the deficient affective component was the most negatively correlated to the TEIque total score. The TAS and the TEIque total scores were negatively related ( r = .61). The overall results are discussed in light of the recent literature on affects characteristics of psychopaths ( Book, Quinsey, & Langford, 2007 ) and on their potential lifetime strategy ( Harris & Rice, 2006 ).
The Dark Side of Peer Review
Authors: Hart StephenD.
Published: May 2010

Peer review is a process often viewed as critical to the advancement of science. But, as Norman Poythress and John Petrila make clear in the lead article of this issue of the International Journal of Forensic Mental Health, it is a process that can go awry. They discuss a dispute that arose concerning publication of an article in a peer-reviewed journal, the consequences of which included, certainly, a major delay in publication of the article; probably, an extra round of reviews and required revisions that were unwarranted; and, quite possibly, a chilling effect on research in the field. In this Editorial, I reflect on Poythress and Petrila's cautionary tale and its relevance for the journal's editorial policies and procedures.
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.
Identification and Eradication of Methicillin-Resistant Staphylococcus aureus Colonization in the Neonatal Intensive Care Unit: Results of a National Survey
Authors: Milstone Aaron M. , Song Xiaoyan , Coffin Susan , Elward Alexis ,   for the Society for Healthcare Epidemiology of America's Pediatric Special Interest Group
Published: May 2010

We surveyed members of the Society for Healthcare Epidemiology of America to assess current practice with regard to identifying and eradicating methicillin-resistant Staphylococcus aureus (MRSA) colonization in the neonatal intensive care unit (NICU). Although most respondents (86%) screened patients for MRSA colonization, variation existed in the number of anatomic sites sampled and in the use of culture at NICU admission, empirical institution of isolation precautions, and MRSA decolonization therapy. Evidence-based prevention strategies for MRSA transmission and infection are needed.
Temperature effect on high-frequency magnetic properties of Fe–Co films prepared by electrodeposition
Authors: Yang Xu , Gong Luqian , Wei Jianqiang , Qiao Liang , Wang Tao , Li Fashen
Published: May 2010

Fe–Co soft magnetic films with tunable high-frequency magnetic properties were successfully electrodeposited onto ITO conductive glass substrates. A significant shift of ferromagnetic resonance frequency f
r from 1.1 to 4.2 GHz was manipulated by electrolyte temperature and an applied magnetic field. It is found that the in-plane uniaxial anisotropy field H

k
is strongly affected by the electrolyte temperature and varies from 0 to 64 Oe by increasing the electrolyte temperature from 5 to 40 °C. The resonance frequencies calculated from the in-plane uniaxial anisotropy fields are not in agreement with those from experimental measurements. According to Hoffmann's ripple theory, an additional isotropic internal field H
add is introduced to explain this discrepancy.
Heat transfer to a spherical particle in a flowing plasma
Authors: Nemchinsky Valerian
Published: May 2010

Heat flux to a sphere moving in a high-pressure plasma is considered. The sphere is electrically insulated and it is at floating potential. Numerical calculations are performed for conditions typical for plasma arc spraying: the sphere diameter is from tens to hundreds of micrometres, its velocity is on the order of hundreds of metres per second, plasma gas—argon of atmospheric pressure. It is shown that (a) the standard gas-dynamic method to calculate, Q, heat flux to a sphere Q = κRΔTNu, Nu = 2 + 0.6Re
1/2
Pr
1/3 does not describe Q correctly because it grossly overestimates heat conduction by electrons (κ is the total plasma thermal conductivity, R is the particle radius, ΔT is the temperature difference between plasma and the particle, Nu, Re and Pr are Nusselt, Reynolds and Prandtl numbers, respectively); (b) heat flux is not evenly distributed over the particle's surface: the side of the particle that faces the upstream plasma is more heated than the opposite side and (c) ionization in the particle proximity could be important under conditions typical for plasma arc spraying.
The effect of dc poling duration on space charge relaxation in virgin XLPE cable peelings
Authors: Tzimas Antonios , Rowland Simon M , Dissado Leonard A , Fu Mingli , Nilsson Ulf H
Published: May 2010

The effect of dc poling time upon the time-dependent decay of space charge in insulation peelings of cross-linked polyethylene (XLPE) cable that had not previously experienced either electrical or thermal stressing is investigated. Two dc poling durations were used, 2 h and 26 h at an electric field of 50 kV mm−1 and at ambient temperature. Space charge was measured in the two samples investigated both during space charge accumulation and throughout its subsequent decay. The results show that the length of dc poling plays an important role in the subsequent decay. Despite the fact that both samples have had the same amount of space charge by the end of both short and long poling durations the time dependence of the space charge decay is different. Most of the charge stored in the sample that had experienced the short time poling decays rapidly after voltage removal. On the other hand, the charge that is stored in the sample with the long dc poling duration decays slowly and its decay occurs in two stages. The data, which are analysed by means of the de-trapping theory of space charge decay, imply that the charge stored in the material has occupied energy states with different trap depth ranges. The two poling durations lead to different relative amounts of charge in each of the two trap depth ranges. Possible reasons for this are discussed.
Trap-free space-charge-limited electron transport in amorphous tin(IV) phthalocyanine dichloride thin film
Authors: Qiao Xianfeng , Chen Jiangshan , Ma Dongge
Published: May 2010

The morphology and electrical properties of thin films of an n-type organic semiconductor tin(IV) phthalocyanine dichloride (SnCl2Pc) are investigated. An investigation of atomic force microscopy and x-ray diffraction shows that the vacuum-deposited SnCl2Pc films on room-temperature glass substrates exhibit a homogeneous amorphous state. The temperature-dependent current–voltage characteristics of the electron-only devices show that the electron transport in SnCl2Pc thin films is bulk-limited, from the Ohmic region (J ∼ V) at low voltages to the trap-free space-charge-limited current (TFSCLC) region (J ∼ V
2) at high voltages. The linear dependence of current on voltage at low voltages yields the temperature-dependent conductivity, while the TFSCLC relationship provides a direct measurement of the free-electron mobility as a function of electric field and temperature. The zero-field electron mobility at 293 K is as high as (1.8 ± 0.3) × 10−4 cm2 V−1 s−1. It can be seen that the obtained mobility and conductivity obey well the Gaussian disorder model and the three-dimensional variable range hopping model, respectively.
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

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

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

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

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

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

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

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

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

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

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

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
The Inhibition of Lipase and Glucosidase Activities by Acacia Polyphenol
Authors: Ikarashi Nobutomo , Takeda Rumi , Ito Kiyomi , Ochiai Wataru , Sugiyama Kiyoshi
Published: May 2010

Acacia polyphenol (AP) extracted from the bark of the black wattle tree (Acacia mearnsii) is rich in unique catechin‐like flavan‐3‐ols, such as robinetinidol and fisetinidol. In an in vitro study, we measured the inhibitory activity of AP on lipase and glucosidase. In addition, we evaluated the effects of AP on absorption of orally administered olive oil, glucose, maltose, sucrose and starch solution in mice. We found that AP concentration‐dependently inhibited the activity of lipase, maltase and sucrase with an IC50 of 0.95, 0.22 and 0.60 mg ml−1, respectively. In ICR mice, olive oil was administered orally immediately after oral administration of AP solution, and plasma triglyceride concentration was measured. We found that AP significantly inhibited the rise in plasma triglyceride concentration after olive oil loading. AP also significantly inhibited the rise in plasma glucose concentration after maltose and sucrose loading, and this effect was more potent against maltose. AP also inhibited the rise in plasma glucose concentration after glucose loading and slightly inhibited it after starch loading. Our results suggest that AP inhibits lipase and glucosidase activities, which leads to a reduction in the intestinal absorption of lipids and carbohydrates.
Quercetin and Cancer Chemoprevention
Authors: Gibellini Lara , Pinti Marcello , Nasi Milena , Montagna Jonas P. , De Biasi Sara , Roat Erika , Bertoncelli Linda , Cooper Edwin L. , Cossarizza Andrea
Published: May 2010

Several molecules present in the diet, including flavonoids, can inhibit the growth of cancer cells with an ability to act as “chemopreventers”. Their cancer‐preventive effects have been attributed to various mechanisms, including the induction of cell‐cycle arrest and/or apoptosis as well as the antioxidant functions. The antioxidant activity of chemopreventers has recently received a great interest, essentially because oxidative stress participates in the initiation and progression of different pathological conditions, including cancer. Since antioxidants are capable of preventing oxidative damage, the wide use of natural food‐derived antioxidants is receiving greater attention as potential anti‐carcinogens. Among flavonoids, quercetin (Qu) is considered an excellent free‐radical scavenging antioxidant, even if such an activity strongly depends on the intracellular availability of reduced glutathione. Apart from antioxidant activity, Qu also exerts a direct, pro‐apoptotic effect in tumor cells, and can indeed block the growth of several human cancer cell lines at different phases of the cell cycle. Both these effects have been documented in a wide variety of cellular models as well as in animal models. The high toxicity exerted by Qu on cancer cells perfectly matches with the almost total absence of any damages for normal, non‐transformed cells. In this review we discuss the molecular mechanisms that are based on the biological effects of Qu, and their relevance for human health.
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

Objectives:

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

Preterm 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.
Symptoms and Subtypes in Pediatric Functional Dyspepsia: Relation to Mucosal Inflammation and Psychological Functioning
Authors: Schurman Jennifer V , Singh Meenal , Singh Vivekanand , Neilan Nancy , Friesen Craig A
Published: May 2010

Objectives:

The aim of the present study was to explore relations between antral or duodenal inflammatory cells and aspects of psychological functioning with clinical symptom presentation in children with functional dyspepsia (FD), as well as to determine whether histologic inflammation and/or psychopathology are differentially associated with FD subtypes as defined by the Rome II and Rome III criteria.

Patients and Methods:

One hundred pediatric patients with dyspepsia completed a standardized history and physical examination at initial evaluation. Patients and parents also completed a measure of psychological functioning. Subsequently, 63 of these patients underwent upper endoscopy with biopsy (4 patients excluded from analysis because of mucosal disease). Inflammatory cells in the mucosa of stomach and duodenum were enumerated. Associations between specific symptoms and FD subtypes with inflammatory cell densities and anxiety, depression, and somatization scores were examined.

Results:

Rome III subtypes were more robustly related to differences in mast cell densities and scores on psychologic subscales than was true for Rome II subtypes. At the individual symptom level, having pain wake the patient from sleep was associated with higher duodenal mast cell density. Bloating was associated with lower levels of general antral inflammation, as well as higher self‐reported levels of anxiety and somatization. Early satiety and bothersome postprandial fullness also were associated with higher levels of self‐reported anxiety and depression.

Conclusions:

The present study provides preliminary evidence for a relation between clinical presentation, specific types of inflammatory cell infiltrates, and aspects of psychological functioning in children with FD. Rome III subtyping, adopted for adult dyspepsia, may be relevant to the pediatric population.
Obesity in Pediatric Celiac Disease
Authors: Venkatasubramani Narayanan , Telega Grzegorz , Werlin Steven L
Published: May 2010

Background and Aim:

Celiac disease (CD) is a T cell–mediated chronic autoimmune enteropathy occurring in genetically susceptible individuals, and manifested by a permanent intolerance to gluten‐containing products. CD commonly presents in children as failure to thrive and malabsorption or after screening high‐risk groups such as people with diabetes. Almost half of adult patients with CD have a body mass index (BMI) >25 at diagnosis. Classic symptoms like diarrhea are less common in obese patients. Few children have been reported with CD and obesity. Because many children with newly diagnosed CD are identified by screening high‐risk groups, obesity is more common than previously suspected. The aim of the study was to estimate the prevalence of obesity at diagnosis in children with CD and to describe the clinical characteristics of this group.

Patients and Methods:

This is a retrospective study of 143 patients with CD diagnosed between 1986 and 2003 at Children's Hospital of Wisconsin. Data collected included patient's age, sex, ethnicity, presenting signs and symptoms, BMI, celiac antibody titers, small‐intestinal biopsy results, and follow‐up weight 1 year after initiating a gluten‐free diet (GFD).

Results:

Seven of the 143 (5%) patients had BMI >95th percentile. The most common presenting symptoms among obese patients were abdominal pain, diabetes, and diarrhea. Symptoms improved in all of the patients on a GFD. BMI decreased in 4 (50%), increased in 2 (25%), and was not available in 1 patient at 1 year after starting on GFD.

Conclusions:

Obesity is more common in children with CD than previously recognized. In the appropriate clinical setting, CD must be considered even in obese children.
Effects of Zinc Exposure on Zinc Transporter Expression in Human Intestinal Cells of Varying Maturity
Authors: Jou Ming‐Yu , Philipps Anthony F , Kelleher Shannon L , Lönnerdal Bo
Published: May 2010

Objectives:

Zinc (Zn) homeostasis in adults is achieved principally through a balance between intestinal absorption and excretion involving adaptive mechanisms programmed by levels of dietary Zn. Zn absorption in infants is not as tightly regulated as that in adults, which may induce potential toxicity in infants due to the relatively high capacity of Zn absorption. We hypothesized that intestinal Zn homeostasis is developmentally regulated and depends on intestinal maturation, which in turn affects Zn transporter regulation.

Materials and Methods:

Cultured human fetal (FHs 74 Int, F) and adult (Caco‐2: undifferentiated, U; differentiated, D) intestinal cells were used to determine developmental differences in Zn uptake and effects of Zn exposure on Zn transporters.

Results:

Zn uptake rates in F and U cells were higher compared with D cells (F, 9‐fold; U, 3‐fold). F cells were more intolerant to Zn exposure than were U or D cells (LD50 = 67.9 ± 5.3; 117.0 ± 5.2; 224.4 ± 3.7 μmol/L, respectively). Two mechanisms were involved in developmental regulation of Zn homeostasis: differential Zn transporter expression and differential response to Zn exposure. In F cells, zinc‐regulated transporter (ZRT)/iron‐regulated transporter (IRT)–like protein (Zip)4 expression was undetectable; Zn (50 μmol/L) increased levels of Zn transporter (ZnT)1, ZnT2, and metallothionein‐1 mRNA and ZnT1 protein. U and D cells had higher mRNA expression of ZnT1 (U: 5‐fold; D: 7‐fold, respectively) and ZnT2 (U: 2‐fold; D: 9‐fold, respectively) than F cells, and D cells also had higher Zip4 expression (3‐fold) than U cells. In U cells, Zn exposure increased Zip4 protein level, but not membrane‐associated abundance. However, in D cells, Zn exposure decreased both the Zip4 protein level and membrane‐associated abundance.

Conclusions:

Zn absorption is developmentally regulated through intestinal Zn efflux and sequestration and import mechanisms, which may be responsible for differences in Zn absorption observed between infants and adults.
Non-equilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond
Authors: Ge Hao , Qian Hong
Published: May 2010

A theory for an non-equilibrium phase transition in a driven biochemical network is presented. The theory is based on the chemical master equation (CME) formulation of mesoscopic biochemical reactions and the mathematical method of large deviations. The large deviations theory provides an analytical tool connecting the macroscopic multi-stability of an open chemical system with the multi-scale dynamics of its mesoscopic counterpart. It shows a corresponding non-equilibrium phase transition among multiple stochastic attractors. As an example, in the canonical phosphorylation–dephosphorylation system with feedback that exhibits bistability, we show that the non-equilibrium steady-state (NESS) phase transition has all the characteristics of classic equilibrium phase transition: Maxwell construction, a discontinuous first-derivative of the ‘free energy function’, Lee–Yang's zero for a generating function and a critical point that matches the cusp in nonlinear bifurcation theory. To the biochemical system, the mathematical analysis suggests three distinct timescales and needed levels of description. They are (i) molecular signalling, (ii) biochemical network nonlinear dynamics, and (iii) cellular evolution. For finite mesoscopic systems such as a cell, motions associated with (i) and (iii) are stochastic while that with (ii) is deterministic. Both (ii) and (iii) are emergent properties of a dynamic biochemical network.
Surface permeability tests: experiments and modelling for estimating effective permeability
Authors: Selvadurai A. P. S. , Selvadurai P. A.
Published: May 2010

This paper presents a technique for determining the near surface permeability of geomaterials and involves the application of a uniform flow rate to an open central region of a sealed annular patch on an otherwise unsealed flat surface. Darcy’s flow is established during attainment of a steady pressure at a constant flow rate. This paper describes the experimental configuration and its theoretical analysis via mathematical and computational techniques. The methods are applied to investigate the surface permeability characteristics of a cuboidal block of Indiana limestone measuring 508 mm. An inverse analysis procedure is used to estimate the permeability characteristics at the interior of the Indiana limestone block. The resulting spatial distribution of permeability is used to estimate theeffective permeabilityof the tested block.
A general approach to isothermal hyperelastic modelling of saturated porous media at finite strains with compressible solid constituents
Authors: Gajo Alessandro
Published: May 2010

A general approach is proposed for defining the macroscopic free-energy function of a saturated porous medium subjected to finite deformations, under isothermal conditions, in the case of compressible fluid and solid constituents. Reference is made to an elementary volume treated as an ‘open system’, moving with the solid skeleton. The strain-like variables are characterized by a suitable strain measure and the variation of fluid-mass content. Although the free energy is obtained by assembling the contributions of the single constituents, the resulting free energy is not the simple sum of the free energies of the single constituents. It is shown that the simplified approaches previously proposed in the literature are recovered as particular cases of the more general framework proposed in the present article and, in addition, new simplified constitutive frameworks are investigated. The proposed approach paves the way to the consistent hyperelastic–plastic and thermo-elastic modelling of saturated porous media with compressible fluid and solid constituents.
Laplacian image contrast in mirror electron microscopy
Authors: Kennedy S. M. , Zheng C. X. , Tang W. X. , Paganin D. M. , Jesson D. E.
Published: May 2010

We discuss an intuitive approach to interpreting mirror electron microscopy (MEM) images, whereby image contrast is primarily caused by the Laplacian of small height or potential variations across a sample surface. This variation is blurred slightly to account for the interaction of the electrons with the electrical potential away from the surface. The method is derived from the established geometrical theory of MEM contrast, and whilst it loses quantitative accuracy outside its domain of validity, it retains a simplicity that enables rapid interpretation of MEM images. A strong parallel exists between this method and out of focus contrast in transmission electron microscopy (TEM), which allows a number of extensions to be made, such as including the effects of spherical and chromatic aberration.