bluuebunny/crossref_metadata_2025 huggingface dataset:
A horizontal crack in a layered structure satisfies deformation for the 2004–2006 uplift of Campi Flegrei
Authors: Amoruso A. , Crescentini L. , Linde A. T. , Sacks I. S. , Scarpa R. , Romano P.
Published: November 2007

Sources responsible for volcanic unrest produce characteristic surface deformation. Given a sufficient number of distributed observation points, inversion is the preferred procedure for retrieving the source parameters of location and volume or pressure change. Most often the solutions have been for point sources embedded in a homogeneous half‐space. Recent work indicates that layered structures, particularly those with soft superficial layers, significantly perturb the deformation pattern compared with that for the homogeneous medium. We apply the methods of L. Crescentini and A. Amoruso to data for the most recent mini‐uplift in the Campi Flegrei caldera and show that models using a homogeneous medium cannot adequately fit all the data. Incorporating a layered structure appropriate for Campi Flegrei allows a significantly better fit, avoiding characteristic discrepancies which are revealed by a synthetic test. Failure to use such structure results in incorrect source parameters, possibly leading to misleading geophysical interpretations.
Causes of sudden, short‐term changes in ice‐stream surface elevation
Authors: Sergienko O. V. , MacAyeal D. R. , Bindschadler R. A.
Published: November 2007

Recent satellite‐borne observations of Antarctica's ice streams show sudden, spatially confined surface‐elevation changes that are interpreted as caused by subglacial water movement. Using a numerical model of idealized ice‐stream flow coupled to various simple treatments of subglacial bed conditions, we demonstrate that ice‐stream flow dynamics significantly modulates the surface‐elevation expression of processes taking place at the ice‐stream bed. This modulation means that observed surface‐elevation changes do not directly translate to basal‐elevation changes, e.g. inflation or deflation of subglacial water pockets, of equal magnitude and shape. Thus, subglacial water volume change is not directly proportional to the area integral of surface‐elevation changes. Model results show that ambiguities in interpretation of surface elevation changes can be overcome with additional measurements, such as of surface velocity change, and through development of methodology designed to understand transfer of basal change to surface change.
Evidence for a modest undercount bias in early historical Atlantic tropical cyclone counts
Authors: Mann Michael E. , Sabbatelli Thomas A. , Neu Urs
Published: November 2007

We obtain new insights into the reliability of long‐term historical Atlantic tropical cyclone (‘TC’) counts through the use of a statistical model that relates variations in annual Atlantic TC counts to climate state variables. We find that the existence of a substantial undercount bias in late 19th through mid 20th century TC counts is inconsistent with the statistical relationship between TC counts and climate.
Total Electron Content Estimation with Reg‐Est
Authors: Nayir H. , Arikan F. , Arikan O. , Erol C. B.
Published: November 2007

Total Electron Content (TEC) constitutes one of the key elements for observing the variable structure of the ionosphere. GPS provides a cost‐effective alternative in TEC estimation through earth‐based receivers. In this paper, one of the TEC estimation methods, namely Reg‐Est, is investigated in detail in terms of its parameters and developed further to include improvements. Reg‐Est estimates robust TEC using GPS measurements of 30 s time resolution. The method combines the vertical TEC computed from all the satellites in view over 10° horizon limit in the least squares sense through the minimization of a cost function which also includes a high pass penalty filter. Optional weighting functions and sliding window median filters are added to enrich the processing and smoothing of the data. In this study, the input to the Reg‐Est is enlarged to include phase‐corrected TEC. The best way of including the instrumental biases is investigated and the algorithm is updated to include the biases in the slant TEC computation. The effect of the thin shell height of the ionosphere in Reg‐Est estimates is studied. It is concluded that the Reg‐Est algorithm is very robust to the choice of thin shell height. The best weighting function to reduce the multipath effects and to minimize the non‐ionospheric noise is selected. The improved Reg‐Est algorithm can be used for all latitudes and for both quite and disturbed days of the ionosphere. The Reg‐Est TEC are in excellent accordance with the estimates from IGS analysis centers.
Interference of organic signals in highly time resolved nitrate measurements by low mass resolution aerosol mass spectrometry
Authors: Bae Min‐Suk , Schwab James J. , Zhang Qi , Hogrefe Olga , Demerjian Kenneth L. , Weimer Silke , Rhoads Kevin , Orsini Doug , Venkatachari Prasanna , Hopke Philip K.
Published: November 2007

Highly time resolved measurements of nitrate in ambient aerosols were conducted by an Aerodyne Quadrupole Aerosol Mass Spectrometer (Q‐AMS or simply AMS) and a particle‐into‐liquid sampler (PILS) coupled to ion chromatography from field intensives at two sites: an urban site in New York City (Queens College; QC) for wintertime (22 January to 5 February 2004) and a rural site in southwestern New York state (Pinnacle State Park; PSP) for summertime (18 July to 6 August 2004). In this study, we report that in rural atmospheres the inorganic nitrate signal from Q‐AMS may contain significant interferences from organic signals. Analysis of the QC data indicates a good agreement between the PILS‐nitrate and AMS‐nitrate measurements (R2 = 0.94; linear regression slope = 1.05). In addition, the m/z 30 and m/z 46 (two dominant ion fragments in nitrate mass spectrum) signals tightly correlate at QC (R2 = 0.98) and have an average ratio similar to that determined in the laboratory for NH4NO3 (m/z 30/m/z 46 = 2.4). In contrast, at the PSP site the correlation between PILS‐ and AMS‐nitrate was poor (R2 = 0.34), the AMS reported nitrate values were substantially higher, and the m/z 30 to m/z 46 ratios were generally much larger than 2.4. These observations, together with evaluations by aerosol phase ion balance, indicate that the AMS m/z 30 signals at PSP have been strongly influenced by organic compounds that also produce signals at m/z 30, e.g., organic nitrates (NO+), oxygenated organics (CH2O+), hydrocarbon‐like organics (C2H6+), and nitrogen‐containing organic compounds (CH4N+).
Sodium lidar–observed strong inertia‐gravity wave activities in the mesopause region over Fort Collins, Colorado (41°N, 105°W)
Authors: Li Tao , She C.‐Y. , Liu Han‐Li , Leblanc Thierry , McDermid I. Stuart
Published: November 2007

In December 2004, the Colorado State University sodium lidar system at Fort Collins, Colorado (41°N, 105°W), conducted an ∼80‐hour continuous campaign for the simultaneous observations of mesopause region sodium density, temperature, and zonal and meridional winds. This data set reveals the significant inertia‐gravity wave activities with a period of ∼18 hours, which are strong in both wind components since UT day 338 (second day of the campaign), and weak in temperature and sodium density. The considerable variability of wave activities was observed with both wind amplitudes growing up to ∼40 m/s at 95–100 km in day 339 and then decreasing dramatically in day 340. We also found that the sodium density wave perturbation is correlated in phase with temperature perturbation below 90 km, and ∼180° out of phase above. Applying the linear wave theory, we estimated the wave horizontal propagation direction, horizontal wavelength, and apparent horizontal phase speed to be ∼25° south of west, ∼1800 ± 150 km, and ∼28 ± 2 m/s, respectively. The vertical profiles of wave intrinsic period, intrinsic phase speed, and vertical wavelength were also estimated. While the onset of enhanced inertia‐gravity wave amplitude in the night of 338 was observed to be in coincidence with short‐period gravity wave breaking via convective instability, the decrease of inertia‐gravity wave amplitude after noon of day 339 was also observed to coincide with the development of atmospheric dynamical instability layers with downward phase progression clearly correlated with the 18‐hour inertia‐gravity wave, suggesting likely breaking of this inertia‐gravity wave via dynamical (shear) instability.
A two‐parameter climate elasticity of streamflow index to assess climate change effects on annual streamflow
Authors: Fu Guobin , Charles Stephen P. , Chiew Francis H. S.
Published: November 2007

This study extends the single parameter precipitation elasticity of streamflow index into a two parameter climate elasticity index, as a function of both precipitation and temperature, in order to assess climatic effects on annual streamflow. Application of the proposed index to two basins indicates that the single parameter precipitation elasticity index may give a general relationship between precipitation and streamflow in some cases, but that it cannot reflect the complicated non‐linear relationship among streamflow, precipitation and temperature. For example, for the Spokane River basin the climate elasticity of streamflow index varies from 2.4 to 0.2, for a precipitation increase of 20%, as temperature varies from 1°C lower to 1.8°C higher than the long term mean. Thus a 20% precipitation increase may result in a streamflow increase of 48% if the temperature is 1°C lower but only a 4% increase if the temperature is 1.8°C higher than the long‐term mean. The proposed method can be applied to other basins to assess potential climate change effects on annual streamflow. The results of the two case studies can inform planning of long‐term basin water management strategies taking into account global change scenarios.
Probabilistic structure of the distance between tributaries of given size in river networks
Authors: Convertino Matteo , Rigon Riccardo , Maritan Amos , Rodriguez‐Iturbe Ignacio , Rinaldo Andrea
Published: November 2007

We analyze the distribution of the distances between tributaries of a given size (or of sizes larger than a given area) draining along either an open boundary or the mainstream of a river network. By proposing a description of the distance separating prescribed merging contributing areas, we also address related variables, like mean (or bankfull) flow rates and channel and riparian area widths, which are derived under a set of reasonable hydrologic assumptions. The importance of such distributions lies in their ecological, hydrologic, and geomorphic implications on the spreading of species along the ecological corridor defined by the river network and on the propagation of infections due to water‐borne diseases, particularly in view of exact theoretical predictions explicitly using the alongstream distribution of confluences carrying a given flow. Use is made here of real river networks, suitably extracted from digital elevation models, optimal channel networks, and exactly solved tree‐like constructs like the Peano and the Scheidegger networks. The results obtained redefine theoretically in a coherent and general manner and verify observationally the distribution function of the above distances and thus provide the general probabilistic structure of tributaries in river networks. Specifically, we find that the probability of exceedence of the alongstream distancedof tributaries of size larger thanahas the explicit formP(≥d) = exp (−Cd/aH/(1+H)), whereCis a constant that depends on the choice of boundary conditions andH≤ 1 is the Hurst exponent.
Modernization of Passenger Reservation System: Indian Railways’ Dilemma
Authors: Srivastava Shirish C , Mathur Sharat S , Teo Thompson SH
Published: November 2007

This teaching case discusses the challenges being faced by the technology managers at Indian Railways (IR) in the current scenario of a resurgent national economy coupled with increasing customer expectations. In the face of growing competition from road and low-cost airlines, to retain its customers, IR has responded by changing its business rules. The Railway Ministry expects a rapid response from Centre for Railway Information Systems (CRIS) to incorporate all these changes in the passenger reservation system (PRS). The old PRS, which is time-tested and reliable, and has been serving the customers’ needs for nearly two decades, is now proving to be relatively inflexible to match the rapidly changing business requirements. Although the current scenario of a constant need to change the programming logic of PRS has been making maintenance tougher for CRIS officials, they have realized that PRS is a time-tested, proven, and reliable technology. Though they would be happy to replace the old PRS with a new state-of-art system that would provide them greater maintenance flexibility, the repercussions associated with possible failure of the new system are far too serious. The case exhibits the current dilemma being faced by the head of CRIS, the umbrella agency for information technology (IT) implementation in IR: whether IR should continue using the old PRS technology with its inherent shortcomings, or should it take the risk and go in for a wholesale replacement with a new state-of-art technology which would provide greater maintenance flexibility?
Newspaper coverage of drug policy: an analysis of pre‐election reporting of the Greens' drug policy in Australia
Authors: JONES SANDRA C. , HALL DANIKA , COWLIN FIONA
Published: November 2007

Introduction and Aims. With the headline ‘Ecstasy Over The Counter’ in a popular daily newspaper, the debate on drug policy officially entered the arena of the 2003 New South Wales (Australia) State Election. The debate resurfaced in the lead‐up to the 2004 Australian Federal Election. This paper analyses the pre‐election coverage of drug policy issues in four Australian newspapers. Design and Methods. Four high‐circulation daily newspapers were monitored for a one‐month period prior to both elections and analysed for their coverage of drug policy, particularly with respect to the policy of the Greens. Results. The newspapers took different perspectives on drug policy issues, with two framing it in emotive terms as a moral debate and two framing it as political manoeuvring. Discussion and Conclusion. The newspapers focused upon emotive and sensationalist factors. They did not provide their readers with information or a rationale for the formulation of drug policy, be this from a harm minimisation or zero tolerance perspective.
The role of drug and alcohol policy in reducing Indigenous over‐representation in prison*
Authors: WEATHERBURN D. J.
Published: November 2007

Australian Indigenous imprisonment rates are higher now than they were at the time of the Royal Commission into Aboriginal Deaths in Custody. The Commission attributed Indigenous imprisonment to Indigenous cultural, economic and social disadvantage. Noel Pearson has argued that Indigenous drug and alcohol use is a more important cause of Indigenous contact with the justice system than Indigenous disadvantage. In this paper I argue that the available evidence provides strong support for Pearson's view and for the proposition that future efforts to reduce Indigenous imprisonment should place more emphasis on supply‐side strategies for reducing Indigenous drug and alcohol abuse.
The influence of alcohol and tobacco use in orthopaedic inpatients on complications of surgery
Authors: WILLIAMS GERARD , DALY MICHELLE , PROUDE ELIZABETH M. , KERMODE STEVEN , DAVIS MICHELLE , BARLING JAN , HABER PAUL S.
Published: November 2007

Introduction and Aims. Tobacco use and heavy alcohol consumption are associated with increased morbidity and mortality. There is limited research on the correlation between tobacco and risky levels of alcohol use and the possible complications associated with a hospital admission. The underestimation of problem drinking, in particular, has obvious repercussions for the management of patients in hospital. If alcohol‐related problems go undetected or unrecorded, treatment may be inadequate or inappropriate. The aims of the project were to assess the prevalence of high‐risk alcohol and tobacco use in orthopaedic in‐patients and to examine any relationship between alcohol and tobacco use and the number and type of complications, management and length of stay. Design and Method. One hundred and fifty‐three consecutive orthopaedic admissions to the Orthopaedic Ward at Lismore Base Hospital were screened using the Drinkcheck questionnaire, which is based on the Alcohol Use Disorders Identification Test (AUDIT), but which also screens for tobacco use. Nursing staff on the ward completed a Complications Evaluation Questionnaire (CEQ). The risk status of the subjects was compared to the number and type of complications, to assess any effects of alcohol and tobacco on post‐surgical complications. Results. Significant correlations were found between tobacco use, hazardous and harmful alcohol use and numerous medical complications and behavioural problems. Behavioural problems associated with risky alcohol use included verbal abuse, agitation and sleep disturbances, particularly in men; problems associated with tobacco use included agitation and non‐compliance. Discussion and Conclusions. Orthopaedic patients who smoke and/or drink heavily prior to surgery may have more non‐medical complications than non‐smokers and light or non‐drinkers. All surgery patients should thus be screened for alcohol and tobacco use and alcohol withdrawal, which may cause other symptoms such as behavioural problems, non‐compliance and verbal abuse post‐surgery.
An outcome evaluation of the New South Wales Sober Driver Programme: a remedial programme for recidivist drink drivers
Authors: MILLS KATHERINE L. , HODGE WENDY , JOHANSSON KLAS , CONIGRAVE KATHERINE M.
Published: November 2007

Introduction and Aims. Recidivist drink drivers pose a considerable threat to public safety. The present study evaluates the effectiveness of a remedial programme for recidivist drink drivers, the New South Wales Sober Driver Programme (SDP). SDP combines educational components and elements of group cognitive behavioural therapy in relation to drink driving behaviour. It is delivered in conjunction with punitive sanctions. Design and Methods. The evaluation design included a comparison of recidivism rates over 2 years for SDP participants and a community control group of convicted drink drivers who received legal sanctions alone. Quantitative and qualitative surveys of SDP participants were also conducted before, immediately after and 4 months after the programme. Outcome measures included recidivism, change in participant knowledge and attitudes, self‐reported behavioural intentions and skill development. Results. SDP participants were 43% less likely to re‐offend over 2 years compared with community controls who had received sanctions alone. Survey respondents demonstrated improved knowledge, attitudes and skills regarding drink driving. Discussion and Conclusions. SDP appears to be an effective intervention, demonstrating greater reductions in recidivism when compared with legal sanctions alone.
Quality of life, depression and anxiety in alcohol dependence
Authors: SAATCIOGLU OMER , YAPICI ASLIHAN , CAKMAK DURAN
Published: November 2007

Introduction and Aims. Quality of life is recognised increasingly as an important component in the evaluation of disease processes. Comorbid psychiatric diagnoses accompanying alcohol addiction, especially severe cases of anxiety or depression, may have a negative impact on quality of life. This study focused on the impact of severity of anxiety and depression on quality of life of 150 alcohol‐dependent patients treated in hospital. Design and Methods. Consecutive patients were evaluated using relevant quality of life scales at the study's onset and 3 and 6 weeks after the complete disappearance of withdrawal symptoms. Patients were classified into three groups: patients with alcohol dependence only, patients with depression and patients with anxiety. Results. The level of anxiety and depression decreased from the initial evaluation to week 3 in patients with a high level of anxiety and depression, whereas the level of anxiety increased in the alcohol only‐dependent patients. Initial evaluation conducted using the quality of life scales indicated significant differences between the three patient groups: physical health (F = 7.92, p = 0.001); psychological (F = 32.21, p = 0.001); social relationship (F = 3.45, p = 0.03); and environment (F = 7.79, p = 0.001). At weeks 3 and 6, quality of life for physical health, psychological and environment areas differed significantly between patient groups, but social relationships did not. At weeks 3 and 6, quality of life was lowest in patients with depression and highest in alcohol only‐dependent patients with a low severity of depression or anxiety. Discussion and Conclusions. Symptoms of anxiety and depression accompanying alcohol addiction lead to an increase in severity of the problems associated with the addiction and have a negative effect on quality of life. Measurement of quality of life within the scope of treatment programmes would help to identify treatment requirements in addicted patients.
Harm reduction programmes in the Asia–Pacific Region
Authors: REID GARY , DEVANEY MADONNA L. , BALDWIN SIMON
Published: November 2007

Introduction and Aims. This paper reports on the public health intervention of harm reduction to address drug use issues in the Asia – Pacific region. Design and Methods. It is based on the report ‘Situational analysis of illicit drug issues and responses in Asia and the Pacific’, commissioned by the Australian National Council on Drugs Asia Pacific Drug Issues Committee. A comprehensive desk‐based review based on published and unpublished literature and key informant data. Results. Drug use in the Asia – Pacific region is widespread, resulting in serious adverse health consequences. Needle and syringe programmes are found in some parts of Asia, but not in the six Pacific Island countries reviewed. Outreach and peer education programmes are implemented, but overall appear minor in size and scope. Substitution therapy programmes appear to be entering a new era of acceptance in some parts of Asia. Primary health care specifically for drug users overall is limited. Discussion and Conclusions. Harm reduction programmes in the Asia – Pacific region are either small in scale or do not exist. Most programmes lack the technical capacity, human resources and a limited scope of operations to respond effectively to the needs of drug users. Governments in this region should be encouraged to endorse evidence‐based harm reduction programmes.
Client satisfaction and risk behaviours of the users of syringe dispensing machines: a pilot study
Authors: ISLAM MD MOFIZUL , STERN TIM , CONIGRAVE KATHERINE M. , WODAK ALEX
Published: November 2007

Introduction and Aims. The study examines risk behaviours of the users of syringe dispensing machines (SDMs) and evaluates the usefulness of these machines in providing injecting drug users (IDUs) with sterile injecting equipment. Design and Methods. Self‐administered questionnaires were used among users of SDMs in an Area Health Service of Sydney. Results. The majority of the 167 participants reported being happy with the quality of the SDM services. Problems identified with machines were that they were often broken or jammed (32.8% respondents), not in the right place (21.9%) or require money (16.7%). Just over half (50.9%) of the IDUs use SDMs only from 5 p.m. to 9 a.m., the time when almost all other outlets for accessing sterile injecting equipment remain closed. Relatively young IDUs (age ≤ 30 years) were more likely to prefer SDMs over staffed needle syringe programmes (NSPs) compared with older users (age > 30) and to identify stigma (a desire to hide their identity or not liking the way people treat them at staffed NSPs or chemists) as a main reason for using these machines. Primary users of SDMs do not differ from primary users of NSP/chemists in terms of sharing of needles. Those users who had shared in the last month were nearly four times as likely to have never used condoms in sexual encounters over that period (95% confidence interval: 1.2–14.5). Discussion and Conclusion. SDMs appear to complement other outlets of NSPs. Providing free‐of‐cost equipment from SDMs should be considered carefully, as needing money to buy equipment was a reason given for sharing of needles by 35% of those who shared.
The detection of illicit drugs in oral fluid: another potential strategy to reduce illicit drug‐related harm
Authors: DYER KYLE R. , WILKINSON CATHERINE
Published: November 2007

As many of the harms associated with drug use may be due to intoxication, particularly where the individual is driving, operating machinery or involved in other tasks requiring high level psycho‐motor functioning, it follows that having a valid, reliable convenient measure of recent drug use and, if possible, intoxication, will be important in reducing drug‐related harm. Oral fluid testing is the latest technology offering promise in this area. As with any such technology, it has advantages and disadvantages. In this Harm Reduction Digest, Dyer and Wilkinson describe the technology, its strengths and limitations and provide examples of where it is currently being employed in practice. This is a must read paper for those of us interested in reducing drug‐related harm.
Fast and accurate identification of semi-tryptic peptides in shotgun proteomics
Authors: Alves Pedro , Arnold Randy J. , Clemmer David E. , Li Yixue , Reilly James P. , Sheng Quanhu , Tang Haixu , Xun Zhiyin , Zeng Rong , Radivojac Predrag
Published: November 2007

Motivation: One of the major problems in shotgun proteomics is the low peptide coverage when analyzing complex protein samples. Identifying more peptides, e.g. non-tryptic peptides, may increase the peptide coverage and improve protein identification and/or quantification that are based on the peptide identification results. Searching for all potential non-tryptic peptides is, however, time consuming for shotgun proteomics data from complex samples, and poses a challenge for a routine data analysis.

Results: We hypothesize that non-tryptic peptides are mainly created from the truncation of regular tryptic peptides before separation. We introduce the notion of truncatability of a tryptic peptide, i.e. the probability of the peptide to be identified in its truncated form, and build a predictor to estimate a peptide's truncatability from its sequence. We show that our predictions achieve useful accuracy, with the area under the ROC curve from 76% to 87%, and can be used to filter the sequence database for identifying truncated peptides. After filtering, only a limited number of tryptic peptides with the highest truncatability are retained for non-tryptic peptide searching. By applying this method to identification of semi-tryptic peptides, we show that a significant number of such peptides can be identified within a searching time comparable to that of tryptic peptide identification.

Contact:  predrag@indiana.edu; rarnold@indiana.edu; hatang@indiana.edu
Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways
Authors: Hardy Simon , Robillard Pierre N.
Published: November 2007

Motivation: Cellular signaling networks are dynamic systems that propagate and process information, and, ultimately, cause phenotypical responses. Understanding the circuitry of the information flow in cells is one of the keys to understanding complex cellular processes. The development of computational quantitative models is a promising avenue for attaining this goal. Not only does the analysis of the simulation data based on the concentration variations of biological compounds yields information about systemic state changes, but it is also very helpful for obtaining information about the dynamics of signal propagation.

Results: This article introduces a new method for analyzing the dynamics of signal propagation in signaling pathways using Petri net theory. The method is demonstrated with the Ca2+/calmodulin-dependent protein kinase II (CaMKII) regulation network. The results constitute temporal information about signal propagation in the network, a simplified graphical representation of the network and of the signal propagation dynamics and a characterization of some signaling routes as regulation motifs.

Contact:  simon.hardy@polymtl.ca

Supplementary information: Complete data of the Petri net model of the CaMKII regulation pathway available at http://www.polymtl.ca/rgl/Downloads.php
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models
Authors: Qian Yuntao , Murphy Robert F.
Published: November 2007

Motivation: There is extensive interest in automating the collection, organization and analysis of biological data. Data in the form of images in online literature present special challenges for such efforts. The first steps in understanding the contents of a figure are decomposing it into panels and determining the type of each panel. In biological literature, panel types include many kinds of images collected by different techniques, such as photographs of gels or images from microscopes. We have previously described the SLIF system (http://slif.cbi.cmu.edu) that identifies panels containing fluorescence microscope images among figures in online journal articles as a prelude to further analysis of the subcellular patterns in such images. This system contains a pretrained classifier that uses image features to assign a type (class) to each separate panel. However, the types of panels in a figure are often correlated, so that we can consider the class of a panel to be dependent not only on its own features but also on the types of the other panels in a figure.

Results: In this article, we introduce the use of a type of probabilistic graphical model, a factor graph, to represent the structured information about the images in a figure, and permit more robust and accurate inference about their types. We obtain significant improvement over results for considering panels separately.

Availability: The code and data used for the experiments described here are available from http://murphylab.web.cmu.edu/software

Contact:  murphy@cmu.edu
Analysis of a Gibbs sampler method for model-based clustering of gene expression data
Authors: Joshi Anagha , Van de Peer Yves , Michoel Tom
Published: November 2007

Motivation: Over the last decade, a large variety of clustering algorithms have been developed to detect coregulatory relationships among genes from microarray gene expression data. Model-based clustering approaches have emerged as statistically well-grounded methods, but the properties of these algorithms when applied to large-scale data sets are not always well understood. An in-depth analysis can reveal important insights about the performance of the algorithm, the expected quality of the output clusters, and the possibilities for extracting more relevant information out of a particular data set.

Results: We have extended an existing algorithm for model-based clustering of genes to simultaneously cluster genes and conditions, and used three large compendia of gene expression data for Saccharomyces cerevisiae to analyze its properties. The algorithm uses a Bayesian approach and a Gibbs sampling procedure to iteratively update the cluster assignment of each gene and condition. For large-scale data sets, the posterior distribution is strongly peaked on a limited number of equiprobable clusterings. A GO annotation analysis shows that these local maxima are all biologically equally significant, and that simultaneously clustering genes and conditions performs better than only clustering genes and assuming independent conditions. A collection of distinct equivalent clusterings can be summarized as a weighted graph on the set of genes, from which we extract fuzzy, overlapping clusters using a graph spectral method. The cores of these fuzzy clusters contain tight sets of strongly coexpressed genes, while the overlaps exhibit relations between genes showing only partial coexpression.

Availability: GaneSh, a Java package for coclustering, is available under the terms of the GNU General Public License from our website at http://bioinformatics.psb.ugent.be/software

Contact:  yves.vandepeer@psb.ugent.be

Supplementary information: Supplementary data are available on our website at http://bioinformatics.psb.ugent.be/supplementary_data/anjos/gibbs
NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks
Authors: Kachalo Sema , Zhang Ranran , Sontag Eduardo , Albert Réka , DasGupta Bhaskar
Published: November 2007

Summary: We present a software for combined synthesis, inference and simplification of signal transduction networks. The main idea of our method lies in representing observed indirect causal relationships as network paths and using techniques from combinatorial optimization to find the sparsest graph consistent with all experimental observations. We illustrate the biological usability of our software by applying it to a previously published signal transduction network and by using it to synthesize and simplify a novel network corresponding to activation-induced cell death in large granular lymphocyte leukemia.

Availability: NET-SYNTHESIS is freely downloadable from http://www.cs.uic.edu/~dasgupta/network-synthesis/

Contact:  dasgupta@cs.uic.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees
Authors: Fuchsberger Christian , Falchi Mario , Forer Lukas , Pramstaller Peter P.
Published: November 2007

Summary: PedVizApi is a Java API (application program interface) for the visual analysis of large and complex pedigrees. It provides all the necessary functionality for the interactive exploration of extended genealogies. While available packages are mostly focused on a static representation or cannot be added to an existing application, PedVizApi is a highly flexible open source library for the efficient construction of visual-based applications for the analysis of family data. An extensive demo application and a R interface is provided.

Availability:  http://www.pedvizapi.org

Contact:  christian.fuchsberger@eurac.edu
Reforming Johannes: Brahms, Kreisler Junior and the Piano Trio in B, Op. 8
Authors: Moseley Roger
Published: November 2007

A comparison of the 1854 and 1891 versions of the Piano Trio in B, op. 8, explores how musical allusion can be interpreted to convey Johannes Brahms's attitudes to critics, friends, other composers and his own past. The young Brahms's attachment to E. T. A. Hoffmann's literary alter ego Johannes Kreisler helps explain the extent to which the music of others makes itself heard in the first version of the trio. Changing standards of criticism affected the nature and scope of Brahms's revision, which expunged perceived allusions; the older Brahms's more detached compositional approach shared elements with Heinrich Schenker's analytical perspective. There are also parallels between Brahms's excisions and the surgical innovations of his friend and musical ally Theodor Billroth. Both Brahms and Billroth were engaged with the removal of foreign bodies in order to preserve organic integrity, but traces of others – and of the past – persist throughout the revised trio.
Reflective process in action: the uncovering of the ritual of washing in clinical nursing practice
Authors: JONES ADRIAN
Published: November 2007

Reflection can be utilized to reveal aspects of clinical practice which remain shrouded in ritualistic origin.

The underlying themes surrounding the action of washing patients can be traced to Victorian legacies and the nurse education process.

The nurse‐patient relationship serves as a template for the deliverance of nursing interventions.

An incomplete awareness of the nurse‐patient relationship persists as to its initiation, continuation and usefulness in clinical nursing.

Following reflection, there has been an increased awareness of feelings and attitudes surrounding the activity of washing a patient.
Nurse involvement in cardiac rehabilitation prior to hospital discharge
Authors: NEWENS ANDREW J. , BOND SENGA , PRIEST JONATHAN , McCOLL ELAINE
Published: November 2007

Summary

Interviews were undertaken with 202 men admitted to five hospitals in northeast England following an uncomplicated first myocardial infarction. The likelihood of patients speaking to a nurse about recovery or seeing a physiotherapist, dietician or specialist rehabilitation nurse, varied considerably between hospitals.

Whilst virtually all patients received written information concerning some aspect of life‐style change or cardiac rehabilitation, the quality and range of information, particularly with regard to information about stress or anxiety, was frequently limited.

Instructions about seeing a general practitioner following discharge were often vague; formal rehabilitation programmes, where they existed, excluded some patients.

The study suggests that much patient education is dependent on the provision of written information alone, and that further evaluation of the effectiveness of self‐help material supported by nursing input is desirable.
Minimum requirements for new dental materials*
Authors: MJÖR I. A.
Published: November 2007

Summary  A brief review of the development of standards for testing and certification of dental materials is presented. The tests employed in the standards are not correlated for the clinical use of the materials, nor to the reasons for failures of the materials. They are, therefore, of limited value for the selection of materials to be used in practice but they are important for quality control of the manufacture of the materials. Previous certification programmes are being discontinued. The responsibility for selecting safe and efficient materials is transferred to the clinicians whereas making safe and efficient materials still is the responsibility of the manufacturers.
Advanced Heart Failure: Prognosis, Uncertainty, and Decision Making
Authors: Zapka Jane G. , Moran William P. , Goodlin Sarah J. , Knott Kelly
Published: November 2007

Heart failure is a serious clinical management challenge for both patients and primary care physicians. The authors studied the perceptions and practices of internal medicine residents and faculty at an academic medical center in the Southeast to guide design of strategies to improve heart failure care. Data were collected via a self‐administered survey. Eighty‐nine faculty and resident physicians in general internal medicine and geriatrics participated (74% response rate). Items measured perceived skills and barriers, adherence to guidelines, and physician understanding of patient prognosis. Case studies explored practice approaches. Clinical knowledge and related scales were generally good and comparable between physician groups. Palliative care and prognostic skills were self‐rated with wide variance. Physicians rated patient noncompliance and low lifestyle change motivation as major barriers. Given the complexities of caring for elderly persons with heart failure and comorbid conditions, there are significant opportunities for improving physician skills in decision making, patient‐centered counseling, and palliative care.
Immediate Functional Loading of Single‐Tooth TiO2 Grit‐Blasted Implant Restoration. A Controlled Prospective Study in a Porcine Model. Part II: Histology and Histomorphometry
Authors: Bousdras Vasilios A. , Walboomers Frank , Jansen John A. , Cunningham James L. , Blunn Gordon , Petrie Aviva , Jaecques Siegfried , Naert Ignace E. , Sindet‐Pedersen Steen , Goodship Allen E.
Published: November 2007

Background:  Evidently, there is a fast‐moving shift from delayed to immediate implant loading. The hypothesis to be tested was that bone reactions adjacent to single TiO2‐microthreaded implants exposed to immediate masticatory loading for 10 weeks after placement would modulate osseointegration.

Materials and Methods:  Cylindrical‐ and tapered‐designed implants (Astra Tech AB, Mölndal, Sweden) replaced first and third mandibular premolars respectively in 12 pigs. The animals were allocated into two groups based on soft and hard diet feeding. Each animal received, at random positions, four different masticatory loading conditions: implant with either (1) a cover screw only, (2) a healing abutment, (3) an implant with a crown without occlusal contact, or (4) an implant with a crown in contact with the antagonistic teeth.

Results:  Histomorphometry showed that there were no statistically significant differences in bone‐implant contact (BIC), bone mass inside/outside of the threads and soft tissue ingrowth ratio for all the implants at 10 weeks after placement irrespective of masticatory loading condition. Bone loss showed a trend of progressive increase for implants with a healing abutment toward implants with occlusal contact.

Conclusions:  The results of this study rejected the hypothesis and could be explained by the fact that grit‐blasted acid‐etched implants were already placed in dense bone.
DETECTION OF MULTIDRUG‐RESISTANT SALMONELLA TYPHIMURIUM DT104 IN POULTRY BY SELECTIVE ENRICHMENT AND CLOTH‐BASED HYBRIDIZATION ARRAY SYSTEM
Authors: BLAIS BURTON W. , MARTINEZ‐PEREZ AMALIA , LEGGATE JOHANNA , GAUTHIER MARTINE
Published: November 2007

A rapid method was devised for the selective enrichment and detection of multi‐antibiotic‐resistant Salmonella enterica subsp. enterica serotype Typhimurium (S. Typhimurium) DT104 in poultry. The target organism was pre‐enriched in trypticase soy broth supplemented with chloramphenicol, followed by plating on modified semisolid Rappaport Vassiliadis medium and sampling a portion of the swarming growth. The presence of S. Typhimurium DT104 was determined by testing the growth using a cloth‐based hybridization array system (CHAS) targeting antibiotic resistance and other marker genes associated with this organism. In this CHAS, a multiplex polymerase chain reaction incorporating digoxigenin–dUTP was used to simultaneously amplify seven target gene sequences, with subsequent rapid detection of the amplicons by hybridization with an array of probes immobilized on polyester cloth and immunoenzymatic assay of the bound label. This procedure permitted the rapid determination of S. Typhimurium DT104 in chicken carcass rinse, powdered egg and feed samples inoculated with different levels of the target organism.

PRACTICAL APPLICATIONS

The combined selective enrichment and CHAS procedure will enable the rapid screening of poultry and related products for the presence of multidrug resistant Salmonella Typhimurium DT104. The convenience of this approach lies in the fact that samples containing salmonellae requiring more comprehensive analysis can be rapidly identified on the basis of a simple preliminary enrichment procedure involving examination of MSRV plating media for characteristic swarming growth. The swarming growth is readily sampled and analyzed by the DT104 CHAS to determine the presence of key marker genes associated with the multidrug resistant pathogen, obviating the need for time‐ and labor‐consuming conventional purification and antimicrobial susceptibility testing procedures.
AUTOMATIC AND RAPID MEASUREMENT OF MICROBIAL SUSPENSION GROWTH PARAMETERS: APPLICATION TO THE EVALUATION OF EFFECTOR AGENTS
Authors: ELLISON W.J. , PEDARROS‐CAUBET F. , CAUBET R.
Published: November 2007

Traditional methods of assessing antimicrobial agents give little information about the quantitative effect of an inhibitor or stimulator (effector) upon the growth parameters of microbial suspension. Current methods using conductance and light absorption data have lightened the workload, but they do not go beyond determining the exponential growth rate. We have developed mathematical models which, when combined with data provided by these rapid methods, measure the quantitative effect of an antimicrobial agent upon five characteristic growth parameters of a suspension: adaptation time, specific reduction rate during the adaptation phase, exponential growth rate, maximum cell concentration and specific reduction rate during the stationary phase. In addition, our methods can measure the instantaneous growth rate. This allows real‐time studies of the effect of chemical or physical stresses upon subsequent microbial growth. We illustrate some of the applications with examples taken from studies of the antimicrobial effects of certain essential oils and spices upon bacterial suspensions.
MEASUREMENT OF MECHANICAL PROPERTIES OF COEXTRUDED DUAL‐PHASE PRODUCTS
Authors: SAMUEL LALITHA , DOGAN HULYA , MCGRANE SCOTT , KOKINI JOZEF L.
Published: November 2007

This study focused on developing and validating a comprehensive, objective and robust methodology for the textural characterization of coextruded dual‐phase products. Uniaxial compression and penetration tests were done to measure the mechanical properties of the different phases, the shell and the filler on whole dual‐phase products. The resulting force deformation curves were used to derive quantitative measures for the textural properties of the shell and the filler phases of the products. Among the techniques used for textural characterization, penetration tests with a punch probe gave the most reliable, reproducible and comprehensive mechanical characterization of the dual‐phase products. Textural parameters corresponding to the shell and filler were hardness, energy required to shear through the individual phases (toughness) and the elasticity of the shell. The developed methodology was first tested with model materials, whose mechanical properties are well known, and then validated using dual‐phase products available commercially for human and pet consumption.

PRACTICAL APPLICATIONS

Dual‐texture products utilizing extrusion are commercially available with a crunchy exterior shell and a soft viscous filler inside the shell. A method was developed in this study using a penetration probe to assess the quality of dual‐texture extruded products. The developed method works on model systems and commercially available samples.
Differential expression of ionic conductances in interstitial cells of Cajal in the murine gastric antrum
Authors: Takeda Yukari , Koh Sang Don , Sanders Kenton M. , Ward Sean M.
Published: November 2007

Two distinct populations of interstitial cells of Cajal (ICC) exist within the tunica muscularis of the gastric antrum, and these cells serve different physiological functions. One population of ICC generates and actively propagates electrical slow waves, and the other population of ICC is innervated by excitatory and inhibitory motor neurons and mediates enteric motor neurotransmission. In spite of the key role of ICC in gastric excitability, little is known about the ionic conductances that underlie the functional diversity of these cells. In the present study we isolated ICC from the murine gastric antrum and investigated the Ca2+‐dependent ionic conductances expressed by these cells using the patch clamp technique. Conductances in ICC were compared with those expressed in smooth muscle cells. The cells studied were identified by RT‐PCR using cell‐specific primers that included Myh11 (smooth muscle cells), Kit (ICC) and Uchl1 (enteric neurons) following electrophysiolgical recordings. Distinct ionic conductances were observed in Kit‐positive cells. One group of ICC expressed a basal non‐selective cation conductance (NSCC) that was inhibited by an increase in [Ca2+]i in a calmodulin (CaM)‐dependent manner. A second population of ICC generated spontaneous transient inward currents (STICs) and expressed a basal noisy NSCC that was facilitated by an increase in [Ca2+]i in a CaM‐dependent manner. The [Ca2+]i‐facilitated NSCC in ICC was blocked by the Cl− channel antagonists 4,4′‐diisothiocyanatostilbene‐2,2′‐disulphonic acid (DIDS), anthracene‐9‐carboxylate (9‐AC) and niflumic acid. These data suggest that distinct NSCC are expressed in subpopulations of ICC and these conductances may underlie the functional differences of these cells within the gastric antrum.