bluuebunny/crossref_metadata_2025 huggingface dataset:
ChEBI – an Open-access Chemistry Resource for the Life Sciences:*Facilities for On-line Submission and Curation
Authors: Hull Duncan , Josephs Zara , Owen Gareth , Turner Steve , Ennis Marcus , Adams Nico , Dekker Adriano , de Matos Paula , Hastings Janna , Steinbeck Christoph , Haug Kenneth
Published: October 2010

ChEBI (Chemical Entities of Biological Interest) is a database of ‘small’ molecular entities structured around a chemical ontology. It contains almost 600,000 entries, of which approximately 20,000 have been manually curated, as well as entries for groups (parts of molecular entities) and classes of entities. It provides a wide range of information such as chemical nomenclature, structures and related chemical values, and establishes interrelationships between entities in the ontology, in terms of both structure and role. ChEBI places a strong focus on quality, with exceptional efforts being applied to upholding IUPAC nomenclature recommendations and best IUPAC practices when drawing chemical structures.To invite the community to participate more directly in the future growth and development of ChEBI, we have developed a web-based software utility to enable direct user submissions. Users are encouraged to carry out as much of their own manual curation as possible, e.g. by adding multiple synonyms and database cross-references, and by creating multiple relationships within the ontology. The submissions are automatically validated for uniqueness (both of name and chemical structure) and correctness (such as checking that no non-allowed cycles have inadvertently been created in the ontology graph structure, and that the ontology relationships which have been specified are allowed between entities of the relevant types). Once a submission has passed the required validations, it is submitted to the ChEBI database, at which time it receives its unique ChEBI identifier. It will then become visible to the public (as a preliminary entry) as part of the monthly ChEBI release. To date, ChEBI has received over 750 such external submissions.
Fourier Descriptor Analysis and Unification of Voice Range Profile Contours: Method and Applications
Authors: Pabon Peter , Ternström Sten , Lamarche Anick
Published: October 2010

Purpose

To describe a method for unified description, statistical modeling, and comparison of voice range profile (VRP) contours, even from diverse sources.

Method

A morphologic modeling technique, which is based on Fourier descriptors (FDs), is applied to the VRP contour. The technique, which essentially involves resampling of the curve of the contour, is assessed and also is compared to density-based VRP averaging methods that use the overlap count.

Results

VRP contours can be usefully described and compared using FDs. The method also permits the visualization of the local covariation along the contour average. For example, the FD-based analysis shows that the population variance for ensembles of VRP contours is usually smallest at the upper left part of the VRP. To illustrate the method’s advantages and possible further application, graphs are given that compare the averaged contours from different authors and recording devices—for normal, trained, and untrained male and female voices as well as for child voices.

Conclusions

The proposed technique allows any VRP shape to be brought to the same uniform base. On this uniform base, VRP contours or contour elements coming from a variety of sources may be placed within the same graph for comparison and for statistical analysis.
Regional Dialect Variation in the Vowel Systems of Typically Developing Children
Authors: Jacewicz Ewa , Fox Robert Allen , Salmons Joseph
Published: October 2010

Purpose

To investigate regional dialect variation in the vowel systems of typically developing 8- to 12-year-old children.

Method

Thirteen vowels in isolatedh_dwords were produced by 94 children and 93 adults (males and females). All participants spoke American English and were born and raised in 1 of 3 distinct dialect regions in the United States: western North Carolina (Southern dialect), central Ohio (Midland dialect), and southeastern Wisconsin (Northern Midwestern dialect). Acoustic analysis included formant frequencies (F1 and F2) measured at 5 equidistant time points in a vowel and formant movement (trajectory length).

Results

Children’s productions showed many dialect-specific features comparable to those in adult speakers, both in terms of vowel dispersion patterns and formant movement. Different features were also found, including systemic vowel changes, significant monophthongization of selected vowels, and greater formant movement in diphthongs.

Conclusions

The acoustic results provide evidence for regional distinctiveness in children’s vowel systems. Children acquire not only the systemic relations among vowels but also their dialect-specific patterns of formant dynamics. Directing attention to the regional variation in the production of American English vowels, this work may prove helpful in better understanding and interpreting the development of vowel categories and vowel systems in children.
Definition of new alleles of MIC‐A using sequencing‐based typing
Authors: Yao Z. , Volgger A. , Helmberg W. , Keller E. , Fan L. A. , Chandanayingyong D. , Albert E. D.
Published: October 2010

We have sequenced exons 2, 3 and 4 of MIC‐A in 23 homozygous cell lines, 22 families and 54 unrelated individuals. This has led to the definition of seven polymorphic positions in exon 2, 13 in exon 3 and 12 in exon 4, yielding a total of 33 different MIC‐A allelic specificities, of which 16 have not been described before. The newly defined sequences and those of the alleles defined before were entered into a database of the SCORE program (Helmberg et al., 1998, Tissue Antigens, 51, 587) for comprehensive genotyping analysis. In the tested sample, only one genotype present in two individuals gave rise to an ambiguous genotype. If all possible combinations of the 33 alleles are considered, 10 of 636 combinations are ambiguous. The MIC‐A exon 2, 3 and 4 polymorphism is characterized by diallelic single base exchanges and by a considerable degree of exon shuffling. The majority of heterozygote positions identified are non‐synonymous, i.e. five of seven in exon 2, 13 of 13 in exon 3 and eight of 12 in exon 4, suggesting an important function for the MIC‐A polymorphism.
Negative association between type 1 diabetes and HLA DQB1*0602‐DQA1*0102 is attenuated with age at onset
Authors: Graham Jinko , Kockum Ingrid , Sanjeevi Carani B. , Landin‐Olsson Mona , Nyström Lennarth , Sundkvist Göran , Arnqvist Hans , Blohmé Göran , Lithner Folke , Littorin Bengt , Scherstén Bengt , Wibell Lars , Östman Jan , Lernmark Åke , Breslow Norman , Gisela Dahlquist
Published: October 2010

HLA‐associated relative risks of type 1 (insulin‐dependent) diabetes mellitus were analysed in population‐based Swedish patients and controls aged 0–34 years. The age dependence of HLA‐associated relative risks was assessed by likelihood ratio tests of regression parameters in separate logistic regression models for each HLA category. The analyses demonstrated an attenuation with increasing age at onset in the relative risk for the positively associated DQB1*0201‐A1*0502/B1*0302‐A1*0301 (DQ2/8) genotype (P=0.02) and the negatively associated DQB1*0602‐A1*0102 (DQ6.2) haplotype (P=0.004). At birth, DQ6.2‐positive individuals had an estimated relative risk of 0.03, but this increased to 1.1 at age 35 years. Relative risks for individuals with DQ genotype 8/8 or 8/X or DQ genotype 2/2 or 2/X, where X is any DQ haplotype other than 2, 8 or 6.2, were not significantly age‐dependent. An exploratory analysis of DQ haplotypes other than 2, 8 and 6.2 suggested that the risk of type 1 diabetes increases with age for DQB1*0604‐A1*0102 (DQ6.4) and that the peak risk for the negatively associated DQB1*0301‐A1*0501 haplotype is at age 18 years. There was also weak evidence that the risk for DQB1*0303‐A1*0301 (DQ9), which has a positive association in the Japanese population, may decrease with age. We speculate that HLA‐DQ alleles have a significant effect on the rate of beta cell destruction, which is accelerated in DQ2/8‐positive individuals and inhibited, but not completely blocked, in DQ6.2‐positive individuals.
Allochronic differentiation among Daphnia species, hybrids and backcrosses: the importance of sexual reproduction for population dynamics and genetic architecture
Authors: Jankowski T. , Straile D.
Published: October 2010

Seasonal dynamics of the abundance, sexual reproduction and genetic architecture in a Daphnia hyalina-galeata hybrid complex were studied in the large and deep Lake Constance. We found evidence for the occurrence of first and second order hybridization. Our study revealed strong differences between the parental species not only regarding their seasonal dynamics, genetic architecture and diversity, but also their sexual reproductive behaviour. The overwintering D. hyalina showed low genetic diversity, no genetic differentiation during the season, and reproduced sexually in autumn, whereas D. galeata reached higher levels of genetic diversity, reproduced sexually in early summer, and exhibited changes in genetic structure during the season, but was only present from spring to autumn. However, in both species sexual reproduction was a rare event, and daphnids, including hybrids, reproduced predominantly asexually. This allows long-term persistence of hybrids as well without continuing hybridization events. Within all variables studied, F1 and F2 hybrids showed an intermediate pattern, whereas proposed backcross hybrids were more similar to their respective parentals. These differences in phenotype as well as significant differences in pairwise Fst values between parentals suggest that gene flow seems to be relatively low in the Lake Constance hybrid system. We found evidence for unidirectional introgression by backcrossing from D. galeata to D. hyalina and found a decrease in at least one of the proposed introgressed alleles in the hyalina-backcross while the season progressed. Our findings suggest allochronic differentiation within this hybrid population and different microevolutionary trajectories of the parental species, which will be discussed in the light of the ongoing reoligotrophication process of Lake Constance.
Liquid to quasicrystal transition in bilayer water
Authors: Johnston Jessica C. , Kastelowitz Noah , Molinero Valeria
Published: October 2010

The phase behavior of confined water is a topic of intense and current interest due to its relevance in biology, geology, and materials science. Nevertheless, little is known about the phases that water forms even when confined in the simplest geometries, such as water confined between parallel surfaces. Here we use molecular dynamics simulations to compute the phase diagram of two layers of water confined between parallel non hydrogen bonding walls. This study shows that the water bilayer forms a dodecagonal quasicrystal, as well as two previously unreported bilayer crystals, one tiled exclusively by pentagonal rings. Quasicrystals, structures with long-range order but without periodicity, have never before been reported for water. The dodecagonal quasicrystal is obtained from the bilayer liquid through a reversible first-order phase transition and has diffusivity intermediate between that of the bilayer liquid and ice phases. The water quasicrystal and the ice polymorphs based on pentagons are stabilized by compression of the bilayer and are not templated by the confining surfaces, which are smooth. This demonstrates that these novel phases are intrinsically favored in bilayer water and suggests that these structures could be relevant not only for confined water but also for the wetting and properties of water at interfaces.
First-principles study of hydrogen adsorption in metal-doped COF-10
Authors: Wu Miao Miao , Wang Qian , Sun Qiang , Jena Puru , Kawazoe Yoshiyuki
Published: October 2010

Covalent organic frameworks (COFs), due to their low-density, high-porosity, and high-stability, have promising applications in gas storage. In this study we have explored the potential of COFs doped with Li and Ca metal atoms for storing hydrogen under ambient thermodynamic conditions. Using density functional theory we have performed detailed calculations of the sites Li and Ca atoms occupy in COF-10 and their interaction with hydrogen molecules. The binding energy of Li atom on COF-10 substrate is found to be about 1.0 eV and each Li atom can adsorb up to three H2 molecules. However, at high concentration, Li atoms cluster and, consequently, their hydrogen storage capacity is reduced due to steric hindrance between H2 molecules. On the other hand, due to charge transfer from Li to the substrate, O sites provide additional enhancement for hydrogen adsorption. With increasing concentration of doped metal atoms, the COF-10 substrate provides an additional platform for storing hydrogen. Similar conclusions are reached for Ca doped COF-10.
Structure and dynamics of liquid methanol confined within functionalized silica nanopores
Authors: Elola M. Dolores , Rodriguez Javier , Laria Daniel
Published: October 2010

Molecular dynamics simulations have been carried out to investigate the structure and dynamics of liquid methanol confined in 3.3 nm diameter cylindrical silica pores. Three cavities differing in the characteristics of the functional groups at their walls have been examined: (i) smooth hydrophobic pores in which dispersive forces prevail, (ii) hydrophilic cavities with surfaces covered by polar silanol groups, and (iii) a much more rugged pore in which 60% of the previous interfacial hydroxyl groups were replaced by the bulkier trimethylsilyl ones. Confinement promotes a considerable structure at the vicinity of the pore walls which is enhanced in the case of hydroxylated surfaces. Moreover, in the presence of the trimethylsilyl groups, the propagation of this interface-induced spatial ordering extends down to the central region of the pore. Concerning the dynamical modes, we observed an overall slowdown in both the translational and rotational motions. An analysis of these mobilities from a local perspective shows that the largest retardations operate at the vicinity of the interfaces. The gross features of the rotational dynamics were analyzed in terms of contributions arising from bulk and surface states. Compared to the bulk dynamical behavior, the characteristic timescales associated with the rotational motions show the most dramatic increments. A dynamical analysis of hydrogen bond formation and breaking processes is also included.
The Seasonal Variability of Population in Estonian Municipalities
Authors: Silm Siiri , Ahas Rein
Published: October 2010

The authors study the seasonal variability of population in Estonia, and develop a methodology for the monitoring of the short-term mobility of population with mobile-positioning data. The locations of calculated home anchor points of telephone users were analysed by use of the dataset of EMT, Estonia's biggest mobile operator, over a period of 2 years. The results showed that approximately 5% of the population of Estonia change their place of residence seasonally. The number of residents rises during the summer months in coastal areas, the surroundings of cities, and in specific ‘dacha’ areas. Most of these seasonal migrants originated from cities and towns. The timing and geography of the seasonal migration patterns studied showed the different directions and causes of seasonal moves. The methodology developed for the monitoring of short-term migration is suitable for the monitoring of movements over more extensive territory. In order to determine the causes and composition of these migrations, however, one must use additional survey studies or observations.
Distribution of thermogenic activity in floral tissues of Nelumbo nucifera
Authors: Grant Nicole M. , Miller Rebecca A. , Watling Jennifer R. , Robinson Sharon A.
Published: October 2010

Thermogenesis in Nelumbo nucifera (Gaertn.) has been known to scientists for many years; however, the extent of heating by different floral parts remains unclear. We present evidence that the receptacle, stamens and petals produce heat independently, and that the source of heating in these tissues is most likely the alternative oxidase (AOX). The temperatures of the receptacle, petals and stamens were significantly higher than non-thermogenic leaf tissue. After removal from the pedicel, the receptacle retained the most heat (8.1 ± 1.9°C above non-thermogenic tissue temperature) and the petals the least (2.8 ± 4.2°C), with the stamens intermediate. High AOX protein levels and flux through the AOX pathway (in all tissues) during the thermogenic period are consistent with AOX being the mechanism used for thermogenesis. Lipids and carbohydrates were investigated as possible substrates for thermogenesis. There was little change in total lipids during floral development; however, soluble carbohydrate levels decreased by 70% with the onset of thermogenesis. These sugars may fuel thermogenesis in the stamens. The localisation of AOX protein in the various floral parts and the evolutionary significance of its heating role are discussed.
Systematic Review and Cost Analysis Comparing Use of chlorhexidine with Use of Iodine for Preoperative Skin Antisepsis to Prevent Surgical Site Infection
Authors: Lee Ingi , Agarwal Rajender K. , Lee Bruce Y. , Fishman Neil O. , Umscheid Craig A.
Published: October 2010

Objective.

To compare use of chlorhexidine with use of iodine for preoperative skin antisepsis with respect to effectiveness in preventing surgical site infections (SSIs) and cost.

Methods.

We searched the Agency for Healthcare Research and Quality website, the Cochrane Library, Medline, and EMBASE up to January 2010 for eligible studies. Included studies were systematic reviews, meta-analyses, or randomized controlled trials (RCTs) comparing preoperative skin antisepsis with chlorhexidine and with iodine and assessing for the outcomes of SSI or positive skin culture result after application. One reviewer extracted data and assessed individual study quality, quality of evidence for each outcome, and publication bias. Meta-analyses were performed using a fixed-effects model. Using results from the meta-analysis and cost data from the Hospital of the University of Pennsylvania, we developed a decision analytic cost-benefit model to compare the economic value, from the hospital perspective, of antisepsis with iodine versus antisepsis with 2 preparations of chlorhexidine (ie, 4% chlorhexidine bottle and single-use applicators of a 2% chlorhexidine gluconate [CHG] and 70% isopropyl alcohol [IPA] solution), and also performed sensitivity analyses.

Results.

Nine RCTs with a total of 3,614 patients were included in the meta-analysis. Meta-analysis revealed that chlorhexidine antisepsis was associated with significantly fewer SSIs (adjusted risk ratio, 0.64 [95% confidence interval, [0.51–0.80]) and positive skin culture results (adjusted risk ratio, 0.44 [95% confidence interval, 0.35–0.56]) than was iodine antisepsis. In the cost-benefit model baseline scenario, switching from iodine to chlorhexidine resulted in a net cost savings of $16-$26 per surgical case and $349,904–$568,594 per year for the Hospital of the University of Pennsylvania. Sensitivity analyses showed that net cost savings persisted under most circumstances.

Conclusions.

Preoperative skin antisepsis with chlorhexidine is more effective than preoperative skin antisepsis with iodine for preventing SSI and results in cost savings.
Ex situ Sn diffusion: a well-suited technique for enhancing the photovoltaic properties of a SnS absorber layer
Authors: Sajeesh T H , Kartha C Sudha , Sanjeeviraja C , Abe T , Kashiwaba Y , Vijayakumar K P
Published: October 2010

Sn atoms were thermally diffused into tin (II) sulfide (SnS) films prepared using chemical spray pyrolysis. This was achieved by depositing a layer of Sn metal over SnS films followed by annealing of the Sn/SnS bilayer films at 100 °C in high vacuum for 30 min. There was no contamination due to the formation of additional phases of Sn compounds up to a very high percentage of Sn diffusion. Contamination due to Sn–O–S phase was removed by Sn diffusion. The samples were optimized to achieve higher photosensitivity and low resistivity. All these enhanced properties were obtained without altering the optimum band gap of the SnS film which is suitable for maximum photovoltaic conversion efficiency.
One-dimensional modelling of DBDs in Ne–Xe mixtures for excimer lamps
Authors: Belasri A , Khodja K , Bendella S , Harrache Z
Published: October 2010

Dielectric barrier discharges (DBDs) are a promising technology for high-intensity sources of specific ultraviolet (UV) and vacuum ultraviolet (VUV) radiation. In this work, the microdischarge dynamics in DBDs for Ne–Xe mixtures under the close conditions of excimer lamp working has been investigated. The computer model including the cathode fall, the positive column and the dielectric is composed of two coupled sub-models. The first submodel describes the electrical properties of the discharge and is based on a fluid, two-moments description of electron and ion transport coupled with Poisson's equation during the discharge pulse. The second submodel, based on three main modules: a plasma chemistry module, a circuit module and a Boltzmann equation module, with source terms deduced from the electric model, describes the time variations of charged and excited species concentrations and the UV photon emission. The use of the present description allows a good resolution near the sheath at high pressure and it predicts correctly the waveform of the discharge behaviour. The effects of operation voltage, dielectric capacitance, gas mixture composition, gas pressure, as well as the secondary electron emission by ion at the cathode on the discharge characteristics and the 173 nm photon generation have been investigated and discussed.
Evolution of optical constants of silicon dioxide on silicon from ultrathin films to thick films
Authors: Cai Qing-Yuan , Zheng Yu-Xiang , Mao Peng-Hui , Zhang Rong-Jun , Zhang Dong-Xu , Liu Ming-Hui , Chen Liang-Yao
Published: October 2010

A series of SiO2 films with thickness range 1–600 nm have been deposited on crystal silicon (c-Si) substrates by electron beam evaporation (EBE) method. Variable-angle spectroscopic ellipsometry (VASE) in combination with a two-film model (ambient-oxide-interlayer substrate) was used to determine the optical constants and thicknesses of the investigated films. The refractive indices of SiO2 films thicker than 60 nm are close to those of bulk SiO2. For the thin films deposited at the rate of ∼1.0 nm s−1, the refractive indices increase with decreasing thickness from ∼60 to ∼10 nm and then drop sharply with decreasing thickness below ∼10 nm. However, for thin films deposited at the rates of ∼0.4 and ∼0.2 nm s−1, the refractive indices monotonically increase with decreasing thickness below 60 nm. The optical constants of the ultrathin film depend on the morphology of the film, the stress exerted on the film, as well as the stoichiometry of the oxide film.
Low-temperature transport properties of TaxN thin films (0.72 ⩽ x ⩽ 0.83)
Authors: Očko Miroslav , Žonja Sanja , Nelson G L , Freericks J K , Yu Lei , Newman N
Published: October 2010

We report on low-temperature (4–320 K) transport properties of Ta
x
N thin films deposited on an amorphous SiO2 substrate. In this work, Ta
x
N thin films were restricted to a narrow range of x: 0.72 ⩽ x ⩽ 0.83 yet show considerable and nonmonotonic variation of their transport properties with Ta concentration. This behaviour is consistent with a local minimum in the density of electronic states at the Fermi level, as calculated for the rock salt intermetallic Ta4N5, and a rigid band model for describing the transport. The temperature dependence of the resistivity is best fit to the unusual form exp(−T/T
0). Interestingly enough, the fit parameter T
0 correlates well with the temperature of the maximum of the corresponding thermopower. Both of these characteristics, the fit and the correlation with the thermopower, are consistent with the Jonson–Mahan many-body formalism for charge and thermal transport when one has a nontrivial temperature dependence of the chemical potential. At the lowest temperatures measured, we have also found that the resistivity and thermopower show signatures of electron–electron interactions. We discuss also our results in the light of some theories usually used for describing transport of thin films and to other experimental investigations that have been performed on Ta
x
N.
Enhanced near-field noise absorption of transparent ZnO nanofilms by Al substitution
Authors: Tong Shi-Yuan , Wu Jenn-Ming , Huang Yu-Ting , Yang Min-Da , Tung Mean-Jue
Published: October 2010

Transparent Al-doped ZnO (AZO) conductive films were prepared by confocal dc-reactive magnetron sputtering using Zn and Al targets in an Ar/O2 reactive atmosphere. The effect of Al substitution on the near-field radio-frequency (RF) noise absorption of the AZO films was investigated. After a standard short–open–load–through calibration, the near-field RF noise attenuation was measured using a RF microstrip test fixture suitable for quasi-transverse electromagnetic wave propagation. The RF noise absorption capability of the AZO films is enhanced from essentially zero to 26% (4–6 GHz) by doping with 5.9% Al. Surface proximity-induced loss is considered the dominating mechanism in the RF noise absorption of AZO films. The crystal quality and morphology are affected significantly by the substitution of Al in AZO films. Dc conductivities, dielectric properties and optical characterizations are also discussed.
Facile and solvent-free routes for the synthesis of size-controllable Fe
3
O
4 nanoparticles
Authors: Ngo Thanh Hieu , Tran Dai Lam , Do Hung Manh , Tran Vinh Hoang , Le Van Hong , Nguyen Xuan Phuc
Published: October 2010

Magnetite nanoparticles are one of the most important materials that are widely used in both medically diagnostic and therapeutic research. In this paper, we present some facile and non-toxic synthetic approaches for size-controllable preparations of magnetite nanoparticles, which are appropriate for biomedical applications, namely (i) co-precipitation; (ii) reduction–precipitation and (iii) oxidation–precipitation. Magnetic characterizations of the obtained nanoparticles have been studied and discussed. The oxidation precipitation route was chosen for investigation of the dependence of kinetic driven activation energy and that of coercive force on particle size (and temperature) during the course of the reaction. The structural–magnetic behavior was also correlated. Being solvent and surfactant-free, these methods are advantageous for synthesis and further functionalization towards biomedical applications.
Investigation of rectenna for microwave power conversion
Authors: Karimov Kh S , Saleem M , Shah M , Shafique S
Published: October 2010

This paper presents the fabrication of organic semiconductor (OS) rectifiers and an investigation of rectifying antenna (rectenna) under the effect of microwave power. As a source of microwaves, a patch antenna fed by a generator was used. The rectenna contains a built-in rectifier. The surface-type Ag/NiPc/Au cell, with organic semiconductor nickel phthalocyanine (NiPc) as the active material, was used as a rectenna. The rectifier was fabricated by thermal deposition of Ag, Au and NiPc thin films on thoroughly cleaned glass substrate. The measured I–V characteristics of the cell showed rectifying behavior. The rectenna was tested at frequency ranges of 8–16 GHz at different intensities of radiation and vertical and horizontal positions of the rectenna's axes. Under the effect of microwave power at the output of the rectenna, the output dc voltage and current were detected.
Discovering homotypic binding events at high spatial resolution
Authors: Guo Yuchun , Papachristoudis Georgios , Altshuler Robert C. , Gerber Georg K. , Jaakkola Tommi S. , Gifford David K. , Mahony Shaun
Published: October 2010

Motivation: Clusters of protein–DNA interaction events involving the same transcription factor are known to act as key components of invertebrate and mammalian promoters and enhancers. However, detecting closely spaced homotypic events from ChIP-Seq data is challenging because random variation in the ChIP fragmentation process obscures event locations.

Results: The Genome Positioning System (GPS) can predict protein–DNA interaction events at high spatial resolution from ChIP-Seq data, while retaining the ability to resolve closely spaced events that appear as a single cluster of reads. GPS models observed reads using a complexity penalized mixture model and efficiently predicts event locations with a segmented EM algorithm. An optional mode permits GPS to align common events across distinct experiments. GPS detects more joint events in synthetic and actual ChIP-Seq data and has superior spatial resolution when compared with other methods. In addition, the specificity and sensitivity of GPS are superior to or comparable with other methods.

Availability:  http://cgs.csail.mit.edu/gps

Contact:  gifford@mit.edu; mahony@mit.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Observations on Copy Number Variations in a Kidney‐yang Deficiency Syndrome Family
Authors: Liu Wei Wei , Gao Yong Xiang , Zhou Li Ping , Duan Azure , Tan Ling Ling , Li Wan Zhen , Yan Min , Yang Hong Ya , Yan Shi Lin , Wang Mi Qu , Ding Wei Jun
Published: October 2010

We have performed an analysis of a family with kidney‐yang deficiency syndrome (KDS) in order to determine the structural genomic variations through a novel approach designated as “copy number variants” (CNVs). Twelve KDS subjects and three healthy spouses from this family were included in this study. Genomic DNA samples were genotyped utilizing an Affymetrix 100 K single nucleotide polymorphism array, and CNVs were identified by Copy Number Algorithm (CNAT4.0, Affymetrix). Our results demonstrate that 447 deleted and 476 duplicated CNVs are shared among KDS subjects within the family. The homologus ratio of deleted CNVs was as high as 99.78%. One‐copy‐duplicated CNVs display mid‐range homology. For two copies of duplicated CNVs (CNV4), a markedly heterologous ratio was observed. Therefore, with the important exception of CNV4, our data shows that CNVs shared among KDS subjects display typical Mendelian inheritance. A total of 113 genes with established functions were identified from the CNV flanks; significantly enriched genes surrounding CNVs may contribute to certain adaptive benefit. These genes could be classified into categories including: binding and transporter, cell cycle, signal transduction, biogenesis, nerve development, metabolism regulation and immune response. They can also be included into three pathways, that is, signal transduction, metabolic processes and immunological networks. Particularly, the results reported here are consistent with the extensive impairments observed in KDS patients, involving the mass‐energy‐information‐carrying network. In conclusion, this article provides the first set of CNVs from KDS patients that will facilitate our further understanding of the genetic basis of KDS and will allow novel strategies for a rational therapy of this disease.
The Impact of Group Drumming on Social‐Emotional Behavior in Low‐Income Children
Authors: Ho Ping , Tsao Jennie C. I. , Bloch Lian , Zeltzer Lonnie K.
Published: October 2010

Low‐income youth experience social‐emotional problems linked to chronic stress that are exacerbated by lack of access to care. Drumming is a non‐verbal, universal activity that builds upon a collectivistic aspect of diverse cultures and does not bear the stigma of therapy. A pretest‐post‐test non‐equivalent control group design was used to assess the effects of 12 weeks of school counselor‐led drumming on social‐emotional behavior in two fifth‐grade intervention classrooms versus two standard education control classrooms. The weekly intervention integrated rhythmic and group counseling activities to build skills, such as emotion management, focus and listening. The Teacher’s Report Form was used to assess each of 101 participants (n= 54 experimental,n= 47 control, 90% Latino, 53.5% female, mean age 10.5 years, range 10–12 years). There was 100% retention. ANOVA testing showed that intervention classrooms improved significantly compared to the control group in broad‐band scales (total problems (P< .01), internalizing problems (P< .02)), narrow‐band syndrome scales (withdrawn/depression (P< .02), attention problems (P< .01), inattention subscale (P< .001)), Diagnostic and Statistical Manual of Mental Disorders‐oriented scales (anxiety problems (P< .01), attention deficit/hyperactivity problems (P< .01), inattention subscale (P< .001), oppositional defiant problems (P< .03)), and other scales (post‐traumatic stress problems (P< .01), sluggish cognitive tempo (P< .001)). Participation in group drumming led to significant improvements in multiple domains of social‐emotional behavior. This sustainable intervention can foster positive youth development and increase student‐counselor interaction. These findings underscore the potential value of the arts as a therapeutic tool.
Pharmacodynamic and Pharmacokinetic Interactions of Propranolol with Garlic (Allium sativum) in Rats
Authors: Asdaq Syed Mohammed Basheeruddin , Inamdar Mohammed Naseeruddin
Published: October 2010

Garlic preparations and propranolol (PRO) are agents recognized as cardioprotective and potent antihypertensive agents when they are used individually. However, there is no report available to explain the role of combined therapy during simultaneous hypertension and myocardial damage in rats. We aimed to determine the pharmacokinetic and pharmacodynamic interaction of PRO with garlic homogenate (GH), in rats. The influence of garlic on pharmacokinetics of PRO was determined by HPLC method; while pharmacodynamic interaction was studied in animals with hypertension (10% fructose) and myocardial damage (isoproterenol, 175 mg kg−1, s.c. 2 days). PRO was given orally at 10 mg kg−1for 1 week, whereas, GH was administered at three different doses of 125, 250 and 500 mg kg−1, p.o. in their respective groups during fourth to sixth week of high fructose (HF) period, once daily. Systolic blood pressure (SBP), heart rate, cholesterol, triglycerides, glucose, creatine phosphokinase‐MB, lactate dehydrogenase, superoxide dismutase and catalase were measured and histopathological studies were carried out. The bioavailability and half life of PRO were significantly enhanced by 2‐ and 3‐fold, respectively, in animals pretreated with garlic (250 mg kg−1). Administration of PRO and low to moderate doses of GH (125, 250 mg kg−1), either alone or together showed fall in fluid intake and body weight. The combined therapy of GH 250 mg kg−1and PRO was found to be most effective in reducing SBP, cholesterol, triglycerides and glucose. These observations suggest that careful addition of garlic in moderate doses in PRO regimen might result in beneficial effect during treatment of hypertensive animals with myocardial damage.
Can information from marine protected areas be used to inform control-rule-based management of small-scale, data-poor stocks?
Authors: McGilliard Carey R. , Hilborn Ray , MacCall Alec , Punt André E. , Field John C.
Published: October 2010

McGilliard, C. R., Hilborn, R. MacCall, A., Punt, A. E., and Field, J. C. 2011. Can information from marine protected areas be used to inform control-rule-based management of small-scale, data-poor stocks? – ICES Journal of Marine Science, 68: 201–211. Many small-scale, nearshore fisheries lack the historical catch and survey information needed for conventional stock-assessment-based management. The potential use of the ratio of the density of fish outside a marine protected area to that inside it each year (the density ratio, DR) in a control rule is evaluated to determine the direction and magnitude of change in fishing effort in the next year. Management strategy evaluation was used to evaluate the performance of this DR control rule (DRCR) for a range of movement rates of larvae and adults and other biological scenarios, and the parameters of the control rule that maximized cumulative catch (over 95 years) for each scenario were found. The cumulative catch under the optimal DRCR was 90% of the cumulative catch from an optimal constant effort rule (CER). A small range of parameter values for the DRCR produced 75% or more of the cumulative catch produced from optimal CERs for a variety of assumptions about biology and initial stock status. The optimal DRCR was most sensitive to the movement patterns of larvae and adults and survey variability.
Adult Foot and Ankle Problems
Authors: Bowyer Gavin W.
Published: October 2010

Adults with foot and ankle problems often present to the GP complaining of pain and impaired function, including difficulties with work, social and domestic activities. The aim of this article is to provide GPs with a knowledge base on the orthopaedic problems affecting the adult foot and ankle, so that the doctor can manage this sizeable part of the workload, with treatment and appropriate referral to allied health care professionals and to secondary care.
Vertigo
Authors: Rigg Carolyn , Anderson Ross
Published: October 2010

Dizziness is a common complaint in general practice and is used by patients to describe many different sensations. The key to making the diagnosis is to qualify exactly what the patient means by ‘dizzy’ in order to establish whether this represents true vertigo. This article aims to provide an overview of common causes of vertigo encountered in general practice.
Physician Attitudes and Practices of Enteral Nutrition as Primary Treatment of Paediatric Crohn Disease in North America
Authors: Stewart Michael , Day Andrew S , Otley Anthony
Published: October 2010

Background:

The use of exclusive enteral nutrition (EEN) in children with Crohn disease has not been universally adopted by North American paediatric gastroenterologists. This is in stark contrast to their European counterparts. The present study aimed to define attitudes and practice patterns of EEN use by members of the North American Society for Paediatric Gastroenterology, Hepatology, and Nutrition.

Methods:

Members were contacted by e‐mail and provided with access to a Web‐based survey.

Results:

Surveys were completed by 326 of 1162 (30.7%) eligible North American Society for Paediatric Gastroenterology, Hepatology, and Nutrition members from North America (86% United States, 14% Canada). Thirty‐one percent of respondents reported never using EEN, 55% reported sparse use, and 12% reported regular use. Physicians in Canada reported significantly more use than those in United States (P < 0.001). Currently working and previously working in a centre where EEN was used were highly correlated with both the perceived appropriateness of EEN and the regularity of its use (P < 0.01). More American physicians than Canadian physicians reported that concurrent medical therapy was necessary to induce remission (P < 0.001). Canadian respondents were more likely to use maintenance therapy than American respondents (P = 0.02). Compliance issues were seen as the main disadvantages of EEN and as the major barrier to increased use by nonregular users.

Conclusions:

There are significant variations in the patterns of use and the acceptance of EEN between Canada and the United States, with Canadian physicians showing a greater use of EEN. The use of EEN appears influenced by the extent to which physicians are exposed to its use both in their training and in their current practice setting.
Human infection with Delftia tsuruhatensis isolated from a central venous catheter
Authors: Preiswerk Benjamin , Ullrich Silvia , Speich Rudolf , Bloemberg Guido V. , Hombach Michael
Published: October 2010

We present the case of a patient with catheter-related infection caused by Delftia tsuruhatensis, a newly described species closely related to Delftia acidovorans (formerly Comamonas acidovorans). To date, D. tsuruhatensis has not been described as a pathogen. To the best of our knowledge, this is the first report describing D. tsuruhatensis as the causative agent of a human infection.
Evaluation of a liquid bead array system for high-risk human papillomavirus detection and genotyping in comparison with Hybrid Capture II, DNA chip and sequencing methods
Authors: Cho Eun Jung , Do Jin Hwan , Kim Yoon Sun , Bae Sumi , Ahn Woong Shick
Published: October 2010

Since persistent infection with high-risk human papillomavirus (HPV) is a known cause of high-grade cervical intraepithelial neoplasia and cervical cancer, several HPV DNA detection methods have been developed during the last decade. The Hybrid Capture II (HCII) assay, which allows detection of 13 high-risk HPVs, has been well validated; however, it does not provide any genotype-specific information. The oncogenic activity of HPV is dependent on its genotype. The prophylactic effects of HPV vaccines are based on L1 virus-like particles and are limited mainly to infections corresponding to the HPV type used to develop the immunogen. Therefore, accurate detection and genotyping are important for treatment as well as screening. A newly developed HPV genotyping system using a liquid bead array was evaluated with 286 cervical samples and the results were compared to two commercially available methods, i.e. the HCII and HPV DNA chip assays, and sequencing. The sensitivity for detection of high-risk HPV was 85.3 % (HCII), 94.7 % (DNA chip) and 99.0 % (liquid bead array). The liquid bead array showed almost perfect agreement (κ=0.95) with genotype information confirmed by sequencing, while substantial agreement (κ=0.8) was observed between DNA chip and sequencing. Furthermore, the liquid bead array had superior detection of 26 HPVs (16 high-risk and 10 low-risk types) and has proven to be as accurate as sequencing in identifying individual HPV types, even in cases with multiple HPV infections.
Corynebacterium jeikeium pacemaker infection associated with antineutrophil cytoplasmic antibodies: a single positive blood culture could be sufficient for diagnosis
Authors: Bechara C. , Gousseff M. , Passeron A. , Podglajen I. , Day N. , Pouchot J. , Lavergne T. , Mainardi J.-L.
Published: October 2010

Corynebacterium jeikeium, a member of the non-diphtheria corynebacteria, has been rarely reported as being responsible for cardiovascular-device infection. Here, we report what is believed to be the first case of C. jeikeium pacemaker infection associated with the presence of proteinase-3 antineutrophil cytoplasmic antibodies. The diagnosis was established based on the positivity of a single positive blood culture and led to pacemaker extraction. This observation highlights the difficulty in the diagnosis of cardiac-device infection in the presence of a single positive blood culture with a fastidious microorganism that could be considered as a contaminant. It also underscores the need for device extraction to ensure healing.
Polyamine biosynthesis and transport mechanisms are crucial for fitness and pathogenesis of Streptococcus pneumoniae
Authors: Shah Pratik , Nanduri Bindu , Swiatlo Edwin , Ma Yinfa , Pendarvis Ken
Published: October 2010

Polyamines such as cadaverine, putrescine and spermidine are polycationic molecules that have pleiotropic effects on cells via their interaction with nucleic acids.Streptococcus pneumoniae(the pneumococcus) is a Gram-positive pathogen capable of causing pneumonia, septicaemia, otitis media and meningitis. Pneumococci have a polyamine transport operon (potABCD) responsible for the binding and transport of putrescine and spermidine, and can synthesize cadaverine and spermidine using their lysine decarboxylase (cad) and spermidine synthase (speE) enzymes. Previous studies from our laboratory have shown that an increase in PotD expression is seen following exposure to various stresses, while during infection,potDinactivation significantly attenuates pneumococcal virulence, and anti-PotD immune responses are protective in mice. In spite of their relative importance, not much is known about the global contribution of polyamine biosynthesis and transport pathways to pneumococcal disease. Mutants deficient in polyamine biosynthesis (ΔspeEor Δcad) or transport genes (ΔpotABCD) were constructed and were found to be attenuated in murine models of pneumococcal colonization and pneumonia, either alone or in competition with the wild-type strain. The ΔspeEmutant was also attenuated during invasive disease, while thepotABCDandcadgenes seemed to be dispensable. HPLC analyses showed reduced intracellular polyamine levels in all mutant strains compared with wild-type bacteria. High-throughput proteomic analyses indicated reduced expression of growth, replication and virulence factors in mutant strains. Thus, polyamine biosynthesis and transport mechanisms are intricately linked to the fitness, survival and pathogenesis of the pneumococcus in host microenvironments, and may represent important targets for prophylactic and therapeutic interventions.
Glutathione biosynthesis in the yeast pathogens Candida glabrata and Candida albicans: essential in C. glabrata, and essential for virulence in C. albicans
Authors: Yadav Amit Kumar , Desai Prashant Ramesh , Rai Maruti Nandan , Kaur Rupinder , Ganesan Kaliannan , Bachhawat Anand Kumar
Published: October 2010

Redox pathways play a key role in pathogenesis. Glutathione, a central molecule in redox homeostasis in yeasts, is an essential metabolite, but its requirements can be met either from endogenous biosynthesis or from the extracellular milieu. In this report we have examined the importance of glutathione biosynthesis in two major human opportunistic fungal pathogens, Candida albicans and Candida glabrata. As the genome sequence of C. glabrata had suggested the absence of glutathione transporters, we initially investigated exogenous glutathione utilization in C. glabrata by disruption of the MET15 gene, involved in methionine biosynthesis. We observed an organic sulphur auxotrophy in a C. glabrata met15Δ strain; however, unlike its Saccharomyces cerevisiae counterpart, the C. glabrata met15Δ strain was unable to grow on exogenous glutathione. This inability to grow on exogenous glutathione was demonstrated to be due to the lack of a functional glutathione transporter, despite the presence of a functional glutathione degradation machinery (the Dug pathway). In the absence of the ability to obtain glutathione from the extracellular medium, we examined and could demonstrate that γ-glutamyl cysteine synthase, the first enzyme of glutathione biosynthesis, was essential in C. glabrata. Further, although γ-glutamyl cysteine synthase has been reported to be non-essential in C. albicans, we report here for what is believed to be the first time that the enzyme is required for survival in human macrophages in vitro, as well as for virulence in a murine model of disseminated candidiasis. The essentiality of γ-glutamyl cysteine synthase in C. glabrata, and its essentiality for virulence in C. albicans, make the enzyme a strong candidate for antifungal development.
Probing the initiation and effector phases of the somatic piRNA pathway inDrosophila
Authors: Haase Astrid D. , Fenoglio Silvia , Muerdter Felix , Guzzardo Paloma M. , Czech Benjamin , Pappin Darryl J. , Chen Caifu , Gordon Assaf , Hannon Gregory J.
Published: October 2010

Combining RNAi in cultured cells and analysis of mutant animals, we probed the roles of known Piwi-interacting RNA (piRNA) pathway components in the initiation and effector phases of transposon silencing. Squash associated physically with Piwi, and reductions in its expression led to modest transposon derepression without effects on piRNAs, consistent with an effector role. Alterations in Zucchini or Armitage reduced both Piwi protein and piRNAs, indicating functions in the formation of a stable Piwi RISC (RNA-induced silencing complex). Notably, loss of Zucchini or mutations within its catalytic domain led to accumulation of unprocessed precursor transcripts fromflamenco, consistent with a role for this putative nuclease in piRNA biogenesis.