bluuebunny/crossref_metadata_2025 huggingface dataset:
Building and analysing genome-wide gene disruption networks
Authors: Rung J. , Schlitt T. , Brazma A. , Freivalds K. , Vilo J.
Published: May 2011

Motivation: Microarray experiments comparing expression levels of all genes in yeast for hundreds of mutants allow us to examine properties of gene regulatory networks on a genomic scale. We can investigate questions such as network modularity, connectivity, and look for genes with particular roles in the network structure.

Results: We have built genome-wide disruption networks for yeast, using a representation of gene expression data as directed labelled graphs. Nodes represent genes and arcs connect nodes if the disruption of the source gene significantly alters the expression of the target gene. We are interested in features of the resulting disruption networks that are robust over a range of significance cutoffs. The networks show a significant overlap with analogous networks constructed from scientific literature. In disruption networks the number of arcs adjacent to different nodes are distributed roughly according to a power-law, like in many complex systems where the robustness against perturbations is important. The networks are dominated by a single large component and do not have an obvious modular structure. Genes with the highest outdegrees often encode proteins with regulatory functions, whereas genes with the highest indegrees are predominantly involved in metabolism. The local structure of the networks is meaningful, genes involved in the same cellular processes are close together in the network.

Keywords: gene networks, microarrays, yeast, graph visualisation

Availability: http://www.ebi.ac.uk/microarray/networks

Contact: schlitt@ebi.ac.ukjohan@ebi.ac.uk

These authors contributed equally to this paper.
BioMiner—modeling, analyzing, and visualizing biochemical pathways and networks
Authors: Šırava M. , Schäfer T. , Eiglsperger M. , Kaufmann M. , Kohlbacher O. , Bornberg-Bauer E. , Lenhof H. P.
Published: May 2011

Motivation: Understanding the biochemistry of a newly sequenced organism is an essential task for post-genomic analysis. Since, however, genome and array data grow much faster than biochemical information, it is necessary to infer reactions by comparative analysis. No integrated and easy to use software tool for this purpose exists as yet.

Results: We present a new software system—BioMiner—for analyzing and visualizing biochemical pathways and networks. BioMiner is based on a new comprehensive, extensible and reusable data model—BioCore—which can be used to model biochemical pathways and networks. As a first application we present PathFinder, a new tool predicting biochemical pathways by comparing groups of related organisms based on sequence similarity. We successfully tested PathFinder with a number of experiments, e.g. the well studied glycolysis in bacteria. Additionally, an application called PathViewer for the visualization of metabolic networks is presented. PathViewer is the first application we are aware of which supports the graphical comparison of metabolic networks of different organisms.

Availability: http://www.zbi.uni-saarland.de/chair/projects/BioMiner

Contact: schaefer@bioinf.uni-sb.de

Supplementary Information: Additional information on experimental results can be found on our web site.

Keywords: Biochemical data model, metabolic and regulatory pathways, visualization, Java, XML.
Principles of protein-protein interactions
Authors: Teichmann Sarah A.
Published: May 2011

In the postgenomic era, one of the most interesting and important challenges is to understand protein interactions on a large scale. The physical interactions between protein domains are fundamental to the workings of a cell: in multi-domain polypeptide chains, in multi-subunit proteins and in transient complexes between proteins that also exist independently. Thus experimental investigation of protein-protein interactions has been extensive, including recent large-scale screens using mass spectrometry. The role of computational research on protein-protein interactions encompasses not only prediction, but also understanding the nature of the interactions and their three-dimensional structures. I will discuss properties such as sequence conservation and co-regulation of genes and proteins involved in different types of physical interactions. Given that all proteins consist of their evolutionary units, the domains, all interactions occur between these domains. The interactions between domains belonging to different protein families will be the second topic of my talk.
Automated annotation of keywords for proteins related to
mycoplasmataceae using machine learning techniques
Authors: Bazzan Ana L.C. , Engel Paulo M. , Schroeder Luciana F. , da Silva Sérgio C.
Published: May 2011

Motivation: With the increase in submission of sequences to public databases, the curators of these are not able to cope with the amount of information. The motivation of this work is to generate a system for automated annotation of data we are particularly interested in, namely proteins related to the Mycoplasmataceae family. Following previous works on automatic annotation using symbolic machine learning techniques, the present work proposes a method of automatic annotation of keywords (a part of the SWISS–PROT annotation procedure), and the validation, by an expert, of the annotation rules generated. The aim of this procedure is twofold: to complete the annotation of keywords of those proteins which is far from adequate, and to produce a prototype of the validation environment, which is aimed at an expert who does not have a deep knowledge of the structure of the current databases containing the necessary information s/he needs.

Results: As for the first objective, a rate of correct keywords annotation of 60% is reported in the literature. Our preliminary results show that with a slightly different method, applied this method to data related to Mycoplasmataceae only, we are able to increase that rate of correct annotation.

Contact: bazzan@inf.ufrgs.br

*Corresponding author; supported by CNPq
Multiple sequence alignment with arbitrary gap costs:
Computing an optimal solution using polyhedral combinatorics
Authors: Althaus Ernst , Caprara Alberto , Lenhof Hans-Peter , Reinert Knut
Published: May 2011

Multiple sequence alignment is one of the dominant problems in computational molecular biology. Numerous scoring functions and methods have been proposed, most of which result in NP-hard problems. In this paper we propose for the first time a general formulation for multiple alignment with arbitrary gap-costs based on an integer linear program (ILP). In addition we describe a branch-and-cut algorithm to effectively solve the ILP to optimality. We evaluate the performances of our approach in terms of running time and quality of the alignments using the BAliBase database of reference alignments. The results show that our implementation ranks amongst the best programs developed so far.

Contact: althaus@icsi.berkeley.edu
An efficient and accurate distance based algorithm to
reconstruct tandem duplication trees
Authors: Elemento Olivier , Gascuel Olivier
Published: May 2011

The problem of reconstructing the duplication tree of a set of tandemly repeated sequences which are supposed to have arisen through unequal recombination, was first introduced by Fitch (1977, Genetics, 86, 93–104), and has recently received a lot of attention. In this paper, we describe DTSCORE, a fast distance based algorithm to reconstruct tandem duplication trees, which is statistically consistent. As a cousin of the ADDTREE algorithm (Sattath and Tversky, 1977, Psychometrika, 42, 319–345), the raw DTSCORE has a time complexity in O(n5), where n is the number of observed repeated sequences. Through a series of algorithmic refinements, we improve its complexity to O(n4) in the worst case, but stress that the refined DTSCORE algorithm should perform faster with real data. We assess the topological accuracy of DTSCORE using simulated data sets, and compare it to existing reconstruction methods. The results clearly show that DTSCORE is more accurate than all the other methods we studied. Finally, we report the results of DTSCORE on a real dataset.

Supplementary information: http://www.lirmm.fr/w3ifa/MAAS/

Contact: gascuel@lirmm.fr
Grid computing for improving conformational sampling in NMR structure
calculation
Authors: Mareuil Fabien , Blanchet Christophe , Malliavin Thérèse E. , Nilges Michael
Published: May 2011

Motivation: Methods for automatic nuclear magnetic resonance (NMR) structure determination need to face a high level of ambiguity encountered in NMR spectra recorded by solid-state NMR and by solution NMR of partially unfolded proteins, leading to time-consuming calculations. The software package Ambiguous Restraints for Iterative Assignment (ARIA) allows for straightforward parallelization of the calculation, as the conformers can be generated in parallel on many nodes.

Results: Due to its architecture, the adaptation of ARIA to grid computing can be easily achieved by using the middleware glite and JDL (Job Description Language) scripts. This adaptation makes it possible to address highly ambiguous datasets, because of the much larger conformational sampling that can be generated by use of the grid computational power.

Availability: The version 2.3.1 of ARIA implemented on the grid is freely available from the ARIA web site: aria.pasteur.fr/downloads.

Contact:  nilges@pasteur.fr; tere@pasteur.fr
PLIO: an ontology for formal description of protein–ligand interactions
Authors: Ivchenko Olga , Younesi Erfan , Shahid Mohammad , Wolf Antje , Müller Bernd , Hofmann-Apitius Martin
Published: May 2011

Motivation: Biomedical ontologies have proved to be valuable tools for data analysis and data interoperability. Protein–ligand interactions are key players in drug discovery and development; however, existing public ontologies that describe the knowledge space of biomolecular interactions do not cover all aspects relevant to pharmaceutical modelling and simulation.

Results: The protein–ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references. The quality of the ontology was assessed based on structural, functional and usability features. Validation of the lexicalized ontology by means of natural language processing (NLP)-based methods showed a satisfactory performance (F-score = 81%). Through integration into our information retrieval environment we can demonstrate that PLIO supports lexical search in PubMed abstracts. The usefulness of PLIO is demonstrated by two use-case scenarios and it is shown that PLIO is able to capture both confirmatory and new knowledge from simulation and empirical studies.

Availability: The PLIO ontology is made freely available to the public at http://www.scai.fraunhofer.de/bioinformatics/downloads.html.

Contact:  martin.hofmann-apitius@scai.fraunhofer.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic
profiles
Authors: Ostrovnaya Irina , Seshan Venkatraman E. , Olshen Adam B. , Begg Colin B.
Published: May 2011

Summary: If a cancer patient develops multiple tumors, it is sometimes impossible to determine whether these tumors are independent or clonal based solely on pathological characteristics. Investigators have studied how to improve this diagnostic challenge by comparing the presence of loss of heterozygosity (LOH) at selected genetic locations of tumor samples, or by comparing genomewide copy number array profiles. We have previously developed statistical methodology to compare such genomic profiles for an evidence of clonality. We assembled the software for these tests in a new R package called ‘Clonality’. For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results.

Availability: Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html) and http://www.mskcc.org/mskcc/html/13287.cfm.

Contact:  ostrovni@mskcc.org
The new patient with renal failure
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses incidence and prevalence of kidney disease, definition and prevalence of chronic kidney disease, causes of end-stage kidney disease (ESKD) and acute kidney injury, modality of renal replacement therapy worldwide, patient survival with ESKD, presentation of renal disease, presenting clinical features of ESKD, examination findings in ESKD, investigations for patients with ESKD, assessment of renal function at/near end stage, complications of renal failure, management of renal failure, assessment of patients for dialysis, supportive care in ESKD, assessment of patients for dialysis, checklist for assessing patients in a low clearance clinic, haemodialysis vs peritoneal dialysis, choosing which dialysis modality, concept of integrated care, education for dialysis, choice of dialysis modality, when to start dialysis in ESKD, how to persuade the patient to start dialysis, clinical indications for starting dialysis in ESKD, the acutely presenting patient or ‘crashlander’, and psychosocial effects of starting dialysis in ESKD.
Nursing a patient on haemodialysis
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter explores nursing a patient on haemodialysis, including nursing care of vascular access, pre- and post-operative care of access, cannulation of fistulae, complications of fistulae and their management, grafts, percutaneous tunnelled and temporary vascular catheters, complications of vascular catheters and their management, strategy for improving vascular access, preparation for haemodialysis, initiation of treatment, intradialytic monitoring, discontinuing haemodialysis, post-dialysis evaluation, dialysis machine alarms, psychological care of haemodialysis patients, the dialysis unit, infection on the dialysis unit, and infection control policies.
Standards documents: the UK Renal Association, the US K/DOQI guidelines, and the European Best Practice guidelines
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses standards documents in dialysis, including the UK Renal Association clinical practice guidelines, American K/DOQI guidelines, and European Best Practice guidelines.
Psychiatric assessment
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Organic illness
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Legal issues
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
ICD-10/DSM-IV index
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
A Description of Intraoperative Ventilator Management in Patients with Acute Lung Injury and the Use of Lung Protective Ventilation Strategies
Authors: Blum James M. , Maile Michael , Park Pauline K. , Morris Michelle , Jewell Elizabeth , Dechert Ronald , Rosenberg Andrew L.
Published: May 2011

Background

The incidence of acute lung injury (ALI) in hypoxic patients undergoing surgery is currently unknown. Previous studies have identified lung protective ventilation strategies that are beneficial in the treatment of ALI. The authors sought to determine the incidence and examine the use of lung protective ventilation strategies in patients receiving anesthetics with a known history of ALI.

Methods

The ventilation parameters that were used in all patients were reviewed, with an average preoperative PaO₂/Fio₂ [corrected] ratio of ≤ 300 between January 1, 2005 and July 1, 2009. This dataset was then merged with a dataset of patients screened for ALI. The median tidal volume, positive end-expiratory pressure, peak inspiratory pressures, fraction inhaled oxygen, oxygen saturation, and tidal volumes were compared between groups.

Results

A total of 1,286 patients met criteria for inclusion; 242 had a diagnosis of ALI preoperatively. Comparison of patients with ALI versus those without ALI found statistically yet clinically insignificant differences between the ventilation strategies between the groups in peak inspiratory pressures and positive end-expiratory pressure but no other category. The tidal volumes in cc/kg predicted body weight were approximately 8.7 in both groups. Peak inspiratory pressures were found to be 27.87 cm H₂O on average in the non-ALI group and 29.2 in the ALI group.

Conclusion

Similar ventilation strategies are used between patients with ALI and those without ALI. These findings suggest that anesthesiologists are not using lung protective ventilation strategies when ventilating patients with low PaO₂/Fio₂ [corrected] ratios and ALI, and instead are treating hypoxia and ALI with higher concentrations of oxygen and peak pressures.
Role of Mycoplasma pneumoniae glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in mediating interactions with the human extracellular matrix
Authors: Dumke Roger , Hausner Marius , Jacobs Enno
Published: May 2011

In different, phylogenetically unrelated micro-organisms, glycolytic enzymes play a dual role. In the cytosol they are involved in metabolic reactions whereas the surface-localized fraction of the enzymes contributes to adhesion and virulence. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a typical member of this group of multifunctional proteins. In this study, we characterized the GAPDH of Mycoplasma pneumoniae, a common pathogen of the human respiratory mucosa. Full-length GAPDH of M. pneumoniae was successfully expressed and used to produce a polyclonal antiserum. By immunofluorescence, colony blot and ELISA experiments with different fractions of the M. pneumoniae proteins, GAPDH was demonstrated to be present in the cytosol and at even higher concentrations at the surface of mycoplasmas. Nevertheless, antibodies against recombinant GAPDH were not detected in sera of immunized animals or of patients with confirmed M. pneumoniae infection. Recombinant GAPDH bound to different human cell lines in a concentration-dependent manner, and binding was inhibited by specific anti-GAPDH serum. In contrast, this antiserum did not significantly influence the adherence of M. pneumoniae to HeLa cells. When different human extracellular matrix proteins were tested in Western blot assays, GAPDH bound to fibrinogen. The results showed that the GAPDH of M. pneumoniae is a member of the family of cytosol-localized glycolytic enzymes, which also occur at the surface of the bacterium, and mediates interactions with the extracellular matrix proteins of the human host. Thus, the surface-exposed fraction of GAPDH may be a factor that contributes to the successful colonization of the human respiratory tract by M. pneumoniae.
Residency time, migration route and survival of Atlantic salmon Salmo salar smolts in a Canadian fjord
Authors: Dempson J. B. , Robertson M. J. , Pennell C. J. , Furey G. , Bloom M. , Shears M. , Ollerhead L. M. N. , Clarke K. D. , Hinks R. , Robertson G. J.
Published: May 2011

Atlantic salmon Salmo salar smolts (n = 181) from two rivers were surgically implanted with acoustic transmitters and released to determine migration route, residency time and survival in a 50 km long estuarine fjord located on the south coast of Newfoundland, Canada. Data obtained from automated receivers placed throughout the Bay d’Espoir fjord indicated that migrating smolts used different routes to reach the outer areas of the fjord. The duration of time that smolts spent in the immediate estuary zone also differed between the two localities (7 and 17 days) although the total time smolts were resident in the fjord was similar and extensive (40 days). Many smolts were resident for periods of 4–8 weeks moving back and forth in the outer part of the fjord where maximum water depths range from 300 to 700 m. Survival in the estuary zone was greater for smolts with prolonged residency in estuarine habitat. Overall smolt survival to the fjord exit was moderately high (54–85%), indicating that the initial phase of migration did not coincide with a period of unusually high mortality.
Recent status scores for version 6 of the Addiction Severity Index (ASI‐6)
Authors: Cacciola John S. , Alterman Arthur I. , Habing Brian , McLellan A. Thomas
Published: May 2011

Aims  To describe the derivation of recent status scores (RSSs) for version 6 of the Addiction Severity Index (ASI‐6).

Design  118 ASI‐6 recent status items were subjected to nonparametric item response theory (NIRT) analyses followed by confirmatory factor analysis (CFA). Generalizability and concurrent validity of the derived scores were determined.

Setting and participants  A total of 607 recent admissions to variety of substance abuse treatment programs constituted the derivation sample; a subset (n = 252) comprised the validity sample.

Measurements  The ASI‐6 interview and a validity battery of primarily self‐report questionnaires that included at least one measure corresponding to each of the seven ASI domains were administered.

Findings  Nine summary scales describing recent status that achieved or approached both high scalability and reliability were derived; one scale for each of six areas (medical, employment/finances, alcohol, drug, legal, psychiatric) and three scales for the family/social area. Intercorrelations among the RSSs also supported the multi‐dimensionality of the ASI‐6. Concurrent validity analyses yielded strong evidence supporting the validity of six of the RSSs (medical, alcohol, drug, employment, family/social problems, psychiatric). Evidence was weaker for the legal, family/social support and child problems RSSs. Generalizability analyses of the scales to males versus females and whites versus blacks supported the comparability of the findings, with slight exceptions.

Conclusions  The psychometric analyses to derive Addiction Severity Index version 6 recent status scores support the multi‐dimensionality of the Addiction Severity Index version 6 (i.e. the relative independence of different life functioning areas), consistent with research on earlier editions of the instrument. In general, the Addiction Severity Index version 6 scales demonstrate acceptable scalability, reliability and concurrent validity. While questions remain about the generalizability of some scales to population subgroups, the overall findings coupled with updated and more extensive content in the Addiction Severity Index version 6 support its use in clinical practice and research.
Novel major histocompatibility complex class II alleles in a group of Chinese rhesus macaques (Macaca mulatta)
Authors: Yang G.‐B. , Zong C.‐M. , Lei N. , Qiu C.‐L. , Duan J.‐Z. , Xing H. , Shao Y.
Published: May 2011

Seven novel MhcMamu‐DQB1 alleles were observed in a population of rhesus macaques of Chinese origin.
A Phylogeny‐Based Comparison of Tarantula Spider Anti‐Predator Behavior Reveals Correlation of Morphology and Behavior
Authors: Blatchford Richard , Walker Sean , Marshall Samuel
Published: May 2011

We studied anti‐predator strategies in nine species of tarantulas from Asia, Africa, and the Americas. Tarantulas in the New World possess urticating hairs which induce inflammation when in contact with vertebrate mucus membranes and skin. In contrast, tarantulas from the Old World lack this defense but are observed to exhibit a much greater willingness to escalate to an active defense when provoked. We had three goals: (1) describe the behaviors exhibited by each taxon in response to two levels of provocation, (2) look for the presence of alternative classes of anti‐predator strategy as predicted by the Old World–New World dichotomy in aggressive defense, and (3) examine the evolution of these behaviors in the context of the phylogeny of the group. We compared the response of nine different mygalomorph spider genera to two levels of aversive stimuli: puffs of air and prodding. We found that the overall structure of the defensive behavior was similar between the different taxa, consisting of fleeing, rearing, striking, and biting. Some genera did exhibit unique behaviors such as stridulating (Hysterocrates) or rocking (Haplopelma and Selenocosmia). We found that the genera from the New World exhibited low levels of escalation in their defense behaviors, while those from the Old World readily escalated to striking and biting. Our findings are consistent with the hypothesis that the possession of urticating hairs is associated with very low levels of active defense behaviors such as striking and biting. The phylogenetic analysis indicates that both the notable levels of aggression displayed by the African taxa tested and the relative passivity of the New World tarantulas each represents a synapomorphy.
The long‐term survival of Phytophthora cinnamomi in mature Banksia grandis killed by the pathogen
Authors: Collins S. , McComb J. A. , Howard K. , Shearer B. L. , Colquhoun I. J. , Hardy G. E. St. J.
Published: May 2011

The ability of Phytophthora cinnamomi to survive long dry periods is the key to its persistence in the south‐west of Western Australia. It has been proposed that dead Banksia grandis are a significant long‐term reservoir for P. cinnamomi inoculum. To test this, 36 healthy B. grandis trees were inoculated in April 1999, and the presence of viable propagules in planta was determined between 2 and 34 months after tree death. By 10 months after inoculation, 75% of the trees had died, with the remaining seven trees dying by 22 months. The pathogen was more commonly recovered from bark than from wood, except from those trees that died at 22 months, and more commonly from above‐ground trunks than below‐ground trunks and roots until 8 months after plant death. In trees that died 12 months after inoculation, P. cinnamomi was recovered from 60% of trunk and root core samples at 3 months, declining to 33% at 10 months, 5.5% at 12 months and 0.1% at 34 months after tree death. In trees that died at 22 months, P. cinnamomi was recovered from 87% of trunk and root samples 2 months after tree death, decreasing to 0.5% by 33 months. This study suggests that the pathogen does not have a saprotrophic phase within dead B. grandis tissue, and B. grandis is unlikely to be a long‐term reservoir for P. cinnamomi. However, the manipulation of the density of B. grandis and the use of fire to facilitate the breakdown of dead Banksia trunks in the Eucalyptus marginata (jarrah) forest may reduce the spread and impact of P. cinnamomi.
Effect of β‐glucosidase on the meat quality and digestibility in broilers
Authors: Qian L. C. , Sun J. Y. , Fu S. J.
Published: May 2011

This study investigated the effects of supplementary β‐glucosidase on the carcass composition, meat quality, weight of digestive organ and apparent digestibility in male broilers. Two hundred and forty male, 1‐day avine broiler chicks were randomly allocated into four treatment groups and fed with corn–soya bean meal supplemented with 0 (control), 0.6, 1.2 and 1.8 U/g of β‐glucosidase respectively. The results showed that there were no significant differences (p > 0.05) among groups in carcass composition (percentages of eviscerated yield, half‐eviscerated yield, muscle yield of breast and leg). However, adding 0.6 U/g β‐glucosidase to the diet not only altered the meat quality by decreasing the drip loss ratio (p < 0.05) and relative lightness (L*) value (p < 0.01), increasing relative redness (a*) value (p < 0.01), but also significantly decreased the pancreas to body weight ratio (p < 0.05), however, with little effect on liver, proventriculus and gizzard to body weight ratio (p > 0.05). The length and width of duodenum villus were not affected by the addition of β‐glucosidase, but the coefficients of total tract apparent digestibility of protein and fat increased by 9.02% (p < 0.05) and 7.40% (p < 0.01) respectively; the parameters of ash were not affected by β‐glucosidase addition (p < 0.05). This study provided valuable information for evaluation of the effect of supplementary β‐glucosidase on the meat quality and digestibility of broilers.
Mortality 6 years after inpatient treatment of female Japanese patients with eating disorders associated with alcoholism
Authors: Suzuki Kenji , Takeda Aya , Yoshino Aihide
Published: May 2011

Aims:  This study was conducted to clarify the mortality of patients with eating disorders associated with alcoholism. We focused on the mortality rate 6 years after inpatient treatment of patients with eating disorders associated with alcoholism compared with eating disorder patients without alcoholism and alcoholic patients without eating disorders.

Methods:  The subjects were 164 female Japanese patients 30 years of age or younger with eating disorders or alcoholism who were inpatients at some time during the period from 1990 to 1998 at the Japanese National Hospital Organization, Kurihama Alcoholism Center. A semi‐structured interview concerning alcohol problems, eating problems, psychiatric disorders and other clinical characteristics was conducted at the time of the first admission. A survey concerning survival was conducted in October 2001, and 100% of the patients were followed up.

Results:  The mortality of the 47 eating disorder patients with alcoholism, 86 eating disorder patients without alcoholism, and 31 alcoholics without eating disorders was 27.7%, 3.5%, and 19.4%, respectively, at 6 years after inpatient treatment, showing significant differences. On the Kaplan–Meier survival curves, the mortality of the eating disorder patients with alcoholism was significantly higher than that of the patients without alcoholism, but not significantly higher than that of young female alcoholics without eating disorders. The 13 eating disorder patients with alcoholism who had died were five anorexia nervosa and seven bulimia nervosa patients.

Conclusion:  The results of the study suggest that comorbid alcoholism is a major factor in the death of anorexia nervosa and bulimia nervosa patients.
Targeted mutation of the calbindin D28k gene selectively alters nonvisual photosensitivity
Authors: Butler Matthew P. , LeSauter Joseph , Sichel Amarynth N. , Silver Rae
Published: May 2011

Light intensity is an important determinant of diverse physiological and behavioral responses within the non‐image‐forming visual system. Thresholds differ among various photic responses, namely control of circadian rhythms, vigilance state, activity level and pupil constriction, but the mechanisms that regulate photosensitivity are not known. Calbindin D28k (CalB) is a calcium‐binding protein associated with light processing in the mammalian circadian clock. Loss‐of‐function studies indicate that CalB‐deficient mice (CalB−/−) have deficits in their ability to entrain to light–dark cycles. To explore the role of CalB in modulating photosensitivity, thresholds for three behaviors mediated by the non‐image‐forming visual system (entrainment, masking and pupillary light reflex; PLR) were compared in CalB−/− and wildtype mice, and the localization of CalB protein in these circuits was examined in adult and juvenile mice. The results reveal a divergence in how CalB affects thresholds to photic cues among these responses. Entrainment and masking were 40‐ to 60‐fold less sensitive in CalB−/− than in wildtype mice. On the other hand, the PLR in CalB−/− mice was 80‐ to 200‐fold more sensitive. Though CalB is expressed in the retina and in brain circuits regulating entrainment we found no CalB expression in any component of the PLR pathway, namely the olivary pretectal nucleus, Edinger–Westphal nucleus and ciliary ganglion. The behavioral and anatomical data together suggest that, in normal animals, the retinal response to light is blunted in the presence of CalB, but responsiveness of the higher order processes that transduce afferent retinal input is enhanced.
Independent directors and firm performance in family controlled firms: evidence from Indonesia
Authors: Prabowo Muhammad , Simpson John
Published: May 2011

We analyse the relationship between board structure and firm performance in family‐controlled firms using a sample of Indonesian non‐financial companies. We find that the share of independent directors on the board has an insignificant relationship with firm performance. We suspect that the result is driven by the lack of institutional reforms in relation to the appointment of independent directors. Our analysis shows strong empirical support for the proposition that family control (family ownership and family involvement on the board) is negatively related to firm performance. However, the significant effect of family ownership disappears when family involvement on the board is taken into the model. This result indicates that family ownership is more detrimental to firm performance whenever the family is highly involved in control decisions. Our results suggest that Indonesia needs to implement governance reforms that prevent majority owners from exercising excessive control over firms.
Assessing the performance of inflation targeting in East Asian economies
Authors: Taguchi Hiroyuki , Kato Chizuru
Published: May 2011

This paper examines the implementation and performance of inflation targeting (IT) in four East Asian emerging market economies: Indonesia, Korea, the Philippines, and Thailand. It also examines monetary policy in Malaysia, a country that has not adopted IT. The study estimates policy reaction functions to test the links between the adoption of IT and use of a monetary policy rule. The impulse responses of prices to a monetary policy shock are also estimated to identify monetary policy impacts on prices. The findings on the monetary policies of the five economies can be summarised as follows. Korea has taken an inflation‐responsive and forward‐looking policy stance under inflation targeting, which has had an effect on the stability of prices. Indonesia and Thailand have conducted inflation‐responsive but backward‐looking policy stances, which have had no impact in terms of price stabilisation. The Philippines (which adopted IT but under a pegged exchange rate regime) and Malaysia have neither followed inflation‐responsive rules nor had policy impacts in terms of controlling inflation.
Biofuels and the policy implications for China
Authors: Wang Qi , Tian Zhihong
Published: May 2011

The paper explores China's biofuel policy and compares biofuel development in China and the rest of the world. It is argued that biofuel development depends on financial support, price intervention, and trade barriers, which all call for government support. China's biofuel industry is developing fast but under strict control. China should refer to other countries' experiences and make policy decisions according to national strategies and local conditions.
Central bank losses: causes and consequences
Authors: Sweidan Osama D.
Published: May 2011

This paper seeks to understand the causes and consequences of central banks' losses. Ignorance of this vital issue over a sustained period has led to negative impacts on economies and on central banking and monetary policy effectiveness. Data from developing countries and economies in transition show that central bank losses have reached significant magnitudes. Engaging in quasi‐fiscal activities is responsible for most such losses because it increases central banks' expenditures. The main features of these fiscal activities are their large size and riskiness, and they are difficult to control. Central bank revenues can also be negatively affected because of declines in inflation rates and in the demand for money.
GOD, VALUE, AND NATURALISM
Authors: Ellis Fiona
Published: May 2011

I consider whether there are philosophical developments which can deepen our understanding of God. I focus upon the relation between experience and physical things and the nature of value. I reject the narrow limits of experience presupposed by the verificationist, and the related monopoly of science on reality. I recommend a conception of reality which is rich enough to accommodate physical things and also the intertwining of value in the natural world. I detect structural similarities between these two problems and the problem of God, and consider how they might be related at the level of content.
REFLECTIONS ON THE DISTINCTNESS OF JUDAISM AND THE SCIENCES
Authors: Samuelson Norbert M.
Published: May 2011

Abstract.  The object of this essay is to explain what there is about discussions of Judaism and the sciences that is distinctive from discussions about religion in general and the sciences. The description draws primarily but not exclusively from recent meetings of the Judaism, Medicine, and Science Group in Tempe, Arizona. The author's Jewish Faith and Modern Science, together with a selective bibliography of writings in this subfield, are used to generate a list of science issues—focused around the religious doctrines of creation, revelation, and redemption in Judaism—that raise specific challenges to Jewish faith. Special attention is given to Leon Kass's The Hungry Soul as an example of a distinctive way to integration knowledge of both science and rabbinic Judaism on a philosophical issue.
SELF‐CONTROL FAILURE IN CATHOLICISM, ISLAM, AND COGNITIVE PSYCHOLOGY
Authors: Cottam Steven
Published: May 2011

Abstract.  Our human condition is often defined in terms of human fallibility; we are human specifically because we fail to live up to our own expectations. This paper explores various conceptions of one form of human fallibility: self‐control failure. Self‐control failure is examined through two conceptualizations, with each conceptualization observed through a corresponding theological and psychological lens: first, as the result of a divided, conflicted humanity, as understood by the Catholic Doctrine of Original Sin and psychological Dual‐Process Theories of Cognition; and second, as the result of limited goal perception, as understood by Islamic conceptions of human memory and psychological Construal Level Theory. A concluding discussion considers two broader implications of the preceding analysis: first, that an appropriate understanding of human fallibility can help us to mitigate its effects, and second, that a conversation regarding overlapping concepts across academic disciplines and religious traditions can enrich understanding of said concepts.
MATERIALIST SPIRITUALITY?
Authors: Voelker Paul
Published: May 2011

Abstract. Contrary to proposals that seek a harmonious integration of “science and religion” or “science and spirituality,” I argue that contemporary scientific and philosophical work at the mind‐brain interface gives us reason to be skeptical of many of the claims found within religious spiritualities. Religious spiritualities typically presume commitment to strong versions of metaphysical dualism, while contemporary mind science gives us every reason to think that the mind is the brain. If materialism is true, what becomes of spirituality? Materialism or naturalism is widely understood to be an anti‐religious position with corrosive effects on morality. I correct this impression, arguing that materialism offers a compelling account of moral objectivity and is fully compatible with an appreciation for many aspects of religion. I further suggest that nothing precludes dialogue and conversation between naturalists and religious believers.
EXPLORING HUMANITY AND OUR RELATIONS
Authors: Hogue Michael , Schweitz Lea F.
Published: May 2011

Abstract.  This brief article introduces a symposium series on science and spirituality. Articles by Paul Voelker, Andrea Hollingsworth, Jason P. Roberts, Stephen McMillin, and Steven Cottam represent the prize‐winning papers from the first two symposia.
RE‐READING GENESIS, JOHN, AND JOB: A CHRISTIAN RESPONSE TO DARWINISM
Authors: Southgate Christopher
Published: May 2011

Abstract.  This article offers one response from within Christianity to the theological challenges of Darwinism. It identifies evolutionary theory as a key aspect of the context of contemporary Christian hermeneutics. Examples of the need for re‐reading of scripture, and reassessment of key doctrines, in the light of Darwinism include the reading of the creation and fall accounts of Genesis 1–3, the reformulation of the Christian doctrine of humanity as created in the image of God, and the possibility of a new approach to the Incarnation in the light of evolution and semiotics. Finally, a theodicy in respect of evolutionary suffering is outlined, in dialogue with recent writings attributing such suffering to a force in opposition to God. The latter move is rejected on both theological and scientific grounds. Further work on evolutionary theodicy is proposed, in relation in particular to the doctrine of creatio ex nihilo.
Nesting success of the Mauritius Fody Foudia rubra in relation to its use of exotic trees as nest sites
Authors: SAFFORD R. J.
Published: May 2011

Nest site choice and nesting success were studied in the Mauritius Fody Foudia rubra, a rare, island‐endemic bird. Most pairs whose nests were found nested only in exotic plantation trees (Cryptomeria, Eucalyptus and Pinus) although native trees were available; around half of the total population nested in exotics. Most nesting failure resulted from nest predation, apparently by exotic Black Rats Rattus rattus and Crab‐eating Macaques Macaca fascicularis. Nesting success was much higher in Cryptomeria (46%) than in other tree species (6%), and I conclude that this fact explains why fodies selected Cryptomeria for nesting. The same seems certain to be true for the Pink Pigeon Columba mayeri, which nested only in Cryptomeria. Larger samples of nests might reveal that Pinus and Eucalyptus support a nesting success intermediate between native trees and Cryptomeria, thereby explaining their use for nesting.
MEASURING THE UNORGANIZED SECTOR IN INDIA
Authors: KULSHRESHTHA A. C.
Published: May 2011

Small, informal enterprises play an important role in shaping the growth of a developing economy undergoing a process of structural reforms. The informal sector as defined in the resolution of the 15th International Conference of Labour Statisticians (ICLS), January 1993, consists of unincorporated household enterprises which differ from formal enterprises in terms of technology, economies of scale, use of labor intensive processes, and virtual absence of well maintained accounts. Although the informal sector has been characterized as above, no clear‐cut operational definition of informal sector is available for the purpose of data collection. In India and in other developing countries in Asia and the Pacific, however, the “unorganized” segment of the economy closely approximates the ICLS concept of the informal sector. The unorganized segment is labor intensive and provides employment to a sizable section of the population. This paper examines the problems of measuring the unorganized sector and explains the approach taken by the Indian Central Statistical Office. The size of the informal sector is examined in terms of the employment it generates and its contribution to value added.
BARRIERS TO ENTRY AND RETURNS TO CAPITAL IN INFORMAL ACTIVITIES: EVIDENCE FROM SUB‐SAHARAN AFRICA
Authors: GRIMM MICHAEL , KRÜGER JENS , LAY JANN
Published: May 2011

This paper investigates the patterns of capital entry barriers and capital returns in informal micro and small enterprises (MSEs) using a unique micro dataset for seven West African countries. Our findings support the view of a heterogeneous informal sector that is not primarily host to subsistence activities. While an assessment of initial investment identifies some informal activities with negligible entry barriers, a notable cost of entry is associated with most activities. We find very heterogeneous patterns of capital returns in informal MSEs. At very low levels of capital, marginal returns are extremely high—often exceeding 70 percent per month. Above a capital stock of 150 International Dollars, marginal returns are found to be relatively low at around 4–7 percent monthly. We provide some evidence that the high returns at low capital stocks reflect high risks. At the same time, most MSEs appear to be severely capital constrained.
Relaxin promotes growth and maturation of mouse neonatal cardiomyocytes in vitro: clues for cardiac regeneration
Authors: Nistri Silvia , Pini Alessandro , Sassoli Chiara , Squecco Roberta , Francini Fabio , Formigli Lucia , Bani Daniele
Published: May 2011

The demonstration that the adult heart contains myocardial progenitor cells which can be recruited in an attempt to replace the injured myocardium has sparkled interest towards novel molecules capable of improving the differentiation of these cells. In this context, the peptide hormone relaxin (RLX), recently validated as a cardiovascular hormone, is a promising candidate. This study was designed to test the hypothesis that RLX may promote the growth and maturation of mouse neonatal immature cardiomyocytes in primary culture. The cultures were studied at 2, 12, 24 and 48 hrs after the addition of human recombinant H2 RLX (100 ng/ml), the main circulating form of the hormone, or plain medium by combining molecular biology, morphology and electrophysiology. RLX modulated cell proliferation, promoting it at 2 and 12 hrs and inhibiting it at 24 hrs; RLX also induced the expression of both cardiac‐specific transcription factors (GATA‐4 and Nkx2‐5) and cardiac‐specific structural genes (connexin 43, troponin T and HCN4 ion channel) at both the mRNA and protein level. Consistently, RLX induced the appearance of ultrastructural and electrophysiological signs of functionally competent, mature cardiomyocytes. In conclusion, this study provides novel circumstantial evidence that RLX specifically acts on immature cardiomyocytes by promoting their proliferation and maturation. This notion suggests that RLX, for which the heart is both a source and target organ, may be an endogenous regulator of cardiac morphogenesis during pre‐natal life and could participate in heart regeneration and repair, both as endogenous myocardium‐derived factor and exogenous cardiotropic drug, during adult life.
Detection of nine microorganisms from the initial carious root lesions using a TaqMan‐based real‐time PCR
Authors: Bizhang M , Ellerbrock BI , Preza D , Raab WHM , Singh P , Beikler T , Henrich B , Zimmer S
Published: May 2011

Oral Diseases (2011) 17, 642–652

Objective:  The purpose of this study was to quantify nine selected cariogenic bacteria in plaque from sound root surfaces and initial carious root lesions using TaqMan PCR and to analyse a putative dependence on the kind of initial periodontal treatment.

Material and Methods:  Fifty‐four subjects with generalized chronic periodontitis were randomly allocated to one of the following initial periodontal therapies: full‐mouth disinfection, full‐mouth scaling and root planing or scaling and root planing within 7 days. Plaque samples were taken before and after periodontal treatment and analysed by TaqMan PCR.

Results:  The quantity of the cariogenic bacteria Actinomyces spp., Streptococcus mutans, Streptococcus sobrinus, Lactobacilllus spp., Rothia dentocariosa, Parvimonas micra, Propionibacterium acnes and Neisseria mucosa were significantly higher, while the quantity of Veillonella parvula was significantly lower on initial carious lesions than on the sound surfaces both before and after periodontal therapy. No significant differences could be found in any of the tested bacteria except P. micra on initial carious lesions and sound surfaces for both examinations between the groups.

Conclusion:  All the nine species analysed were found to be present in initial carious root lesions as well as sound root surfaces but in different quantities, independent of the different periodontal therapies.