bluuebunny/crossref_metadata_2025 huggingface dataset:
A Prospective Study of Outcomes, Healthcare Resource Utilization, and Costs Associated With Postoperative Nosocomial Infections
Authors: Herwaldt Loreen A. , Cullen Joseph J. , Scholz David , French Pamela , Zimmerman M. Bridget , Pfaller Michael A. , Wenzel Richard P. , Perl Trish M
Published: November 2006

Objective.

We evaluated 4 important outcomes associated with postoperative nosocomial infection: costs, mortality, excess length of stay, and utilization of healthcare resources.

Design.

The outcomes for patients who underwent general, cardiothoracic, and neurosurgical operations were recorded during a previous clinical trial. Multivariable analyses including significant covariates were conducted to determine whether nosocomial infection significantly affected the outcomes.

Setting.

A large tertiary care medical center and an affiliated Veterans Affairs Medical Center.

Patients.

A total of 3,864 surgical patients.

Results.

The overall nosocomial infection rate was 11.3%. Important covariates included age, Karnofsky score, McCabe and Jackson classification of the severity of underlying disease, National Nosocomial Infection Surveillance system risk index, and number of comorbidities. After accounting for covariates, nosocomial infection was associated with increased postoperative length of stay, increased costs, increased hospital readmission rate, and increased use of antimicrobial agents in the outpatient setting. Nosocomial infection was not associated independently with a significantly increased risk of death in this surgical population.

Conclusion.

Postoperative nosocomial infection was associated with increased costs of care and with increased utilization of medical resources. To accurately assess the effects of nosocomial infections, one must take into account important covariates. Surgeons seeking to decrease the cost of care and resource utilization must identify ways to decrease the rate of postoperative nosocomial infection.
Excess Length of Stay Attributable to Surgical Site Infection Following Hip Replacement: A Nested Case-Control Study
Authors: Jodra Vicente Monge , Soler Lourdes Sainz de los Terreros , Pérez Cristina Díaz-Agero , Requejo Carmen María Saa , Farrás Nieves Plana
Published: November 2006

Objective.

We estimated the impact of hip replacement-associated surgical site infection (SSI) on morbidity and length of stay.

Methods.

This was a pairwise matched (1 : 1) case-control study nested in a cohort. All patients who underwent hip replacement from January 1, 2000, to June 30, 2004, were prospectively enrolled for the nested case-control design analysis and were monitored from the time of surgery until hospital discharge, including any patients readmitted because of infection.

Results.

Among the 1,260 hip replacements performed, 28 SSIs were detected, yielding a crude SSI rate of 2.2%. The median excess length of stay attributable to SSI was 32.5 days (P< .001), whereas the median prolonged postoperative stay due to SSI was 31 days (P< .001). Deep-wound SSI was the type that prolonged hospital stay the most (up to 49 days). Of the patients who developed an SSI, 4 required revision surgery, for an SSI-related morbidity rate of 14.3%.

Conclusion.

SSI prolongs hospital stay; however, although hospital stay is a rough indicator of the cost of this complication, to accurately estimate the costs of SSI, we would need to consider individual costs in a linear regression model adjusted for all possible confounding factors.
Impact of Postdischarge Surveillance on the Rate of Surgical Site Infection After Orthopedic Surgery
Authors: Huotari Kaisa , Lyytikäinen Outi ,   Hospital Infection Surveillance Team
Published: November 2006

Objective.

To evaluate the impact of postdischarge surveillance on surgical site infection (SSI) rates after orthopedic surgery.

Setting.

Nine hospitals participating in the Finnish Hospital Infection Program.

Patients.

All patients who underwent hip or knee arthroplasty or open reduction of a femur fracture during 1999-2002.

Results.

The date of discharge was available for 11,812 procedures (90%). The median length of hospital stay was 8 days (range per hospital, 6-9 days). The overall SSI rate was 3.3% (range, 0.8%-6.4%). Of 384 SSIs detected, 216 (56%; range, 28%-90%) were detected after discharge: 93 (43%) were detected on readmission to the hospital, 73 (34%) at completion of a postdischarge questionnaire, and 23 (11%) at a follow-up visit. For 27 postdischarge SSIs (13%), the location of detection was unknown. Altogether, 32 (86%) of 37 of organ/space SSIs, 57 (80%) of 71 deep incisional SSIs, and 127 (46%) of 276 superficial incisional SSIs were detected after discharge. Most SSIs (70%) detected on readmission were severe (organ/space or deep incisional), whereas most SSIs (86%) detected at follow-up visits or at completion of a postdischarge questionnaire were superficial. Of all SSIs, 78% (range, 48%-100%) were microbiologically confirmed. Microbiologic confirmation was less common after discharge than during postoperative hospital stay (66% vs 93%; P< .001).

Conclusions.

Postdischarge surveillance had a large impact on the rate of SSI detected after orthopedic surgery. However, postdischarge surveillance conducted by means of a questionnaire detected only a minority of deep incisional and organ/space SSIs.
Improved Risk Adjustment for Comparison of Surgical Site Infection Rates
Authors: Geubbels Eveline L. P. E. , Grobbee Diederick E. , Vandenbroucke-Grauls Christina M. J. E. , Wille Jan C. , Boer Annette S. de
Published: November 2006

Objective.

To develop prognostic models for improved risk adjustment in surgical site infection surveillance for 5 surgical procedures and to compare these models with the National Nosocomial Infection Surveillance system (NNIS) risk index.

Design.

In a multicenter cohort study, prospective assessment of surgical site infection and risk factors was performed from 1996 to 2000. In addition, risk factors abstracted from patient files, available in a national medical register, were used. The c-index was used to measure the ability of procedure-specific logistic regression models to predict surgical site infection and to compare these models with models based on the NNIS risk index. A c-index of 0.5 indicates no predictive power, and 1.0 indicates perfect predictive power.

Setting.

Sixty-two acute care hospitals in the Dutch national surveillance network for nosocomial infections.

Participants.

Patients who underwent 1 of 5 procedures for which the predictive ability of the NNIS risk index was moderate: reconstruction of the aorta (n= 875), femoropopliteal or femorotibial bypass (n= 641), colectomy (n= 1,142), primarytotal hip prosthesis (n= 13,770), and cesarean section (n= 2,962).

Results.

The predictive power of the new model versus the NNIS index was 0.75 versus 0.62 for reconstruction of the aorta (P< .01), 0.78 versus 0.58 for femoropopliteal or femorotibial bypass (P< .001), 0.69 versus 0.62 for colectomy (P< .001), 0.64 versus 0.56 for primary total hip prosthesis arthroplasty (P< .001), and 0.70 versus 0.54 for cesarean section (P< .001).

Conclusion.

Data available from hospital information systems can be used to develop models that are better at predicting the risk of surgical site infection than the NNIS risk index. Additional data collection may be indicated for certain procedures–for example, total hip prosthesis arthroplasty.
Risk Factors for Surgical Site Infection in a Tanzanian District Hospital: A Challenge for the Traditional National Nosocomial Infections Surveillance System Index
Authors: Fehr Jan , Hatz Christoph , Soka Isaac , Kibatala Patience , Urassa Honorathy , Smith Thomas , Mshinda Hassan , Frei Reno , Widmer Andreas
Published: November 2006

The incidence of surgical site infections (SSIs) was 24% in a district hospital in Tanzania. Wound classification was not an independent risk factor for SSI, indicating that risk scores developed in industrialized countries may require adjustments for nonindustrialized countries. The National Nosocomial Infections Surveillance system score required adjustments to reliably predict SSI, probably to account for improper hygiene and the lack of adjustment for the duration of surgery (defined as the 75th percentile of the duration for each type of operative procedure) to reflect local circumstances. Multidrug-resistant pathogens, such as methicillin-resistant Staphylococcus aureus and gram-negative pathogens expressing broad-spectrum β-lactamases, have already emerged.
A Chemoattractant-mediated Gi-coupled Pathway Activates Adenylyl Cyclase in Human Neutrophils
Authors: Mahadeo Dana C. , Janka-Junttila Mirkka , Smoot Rory L. , Roselova Pavla , Parent Carole A.
Published: November 2006

Neutrophils and Dictyostelium use conserved signal transduction pathways to decipher chemoattractant gradients and migrate directionally. In both cell types, addition of chemoattractants stimulates the production of cAMP, which has been suggested to regulate chemotaxis. We set out to define the mechanism by which chemoattractants increase cAMP levels in human neutrophils. We show that chemoattractants elicit a rapid and transient activation of adenylyl cyclase (AC). This activation is sensitive to pertussis toxin treatment but independent of phosphoinositide-3 kinase activity and an intact cytoskeleton. Remarkably, and in sharp contrast to Gαs-mediated activation, chemoattractant-induced AC activation is lost in cell lysates. Of the nine, differentially regulated transmembrane AC isoforms in the human genome, we find that isoforms III, IV, VII, and IX are expressed in human neutrophils. We conclude that the signal transduction cascade used by chemoattractants to activate AC is conserved in Dictyostelium and human neutrophils and is markedly different from the canonical Gαs-meditated pathway.
Atg27 Is Required for Autophagy-dependent Cycling of Atg9
Authors: Yen Wei-Lien , Legakis Julie E. , Nair Usha , Klionsky Daniel J.
Published: November 2006

Autophagy is a catabolic pathway for the degradation of cytosolic proteins or organelles and is conserved among all eukaryotic cells. The hallmark of autophagy is the formation of double-membrane cytosolic vesicles, termed autophagosomes, which sequester cytoplasm; however, the mechanism of vesicle formation and the membrane source remain unclear. In the yeast Saccharomyces cerevisiae, selective autophagy mediates the delivery of specific cargos to the vacuole, the analog of the mammalian lysosome. The transmembrane protein Atg9 cycles between the mitochondria and the pre-autophagosomal structure, which is the site of autophagosome biogenesis. Atg9 is thought to mediate the delivery of membrane to the forming autophagosome. Here, we characterize a second transmembrane protein Atg27 that is required for specific autophagy in yeast. Atg27 is required for Atg9 cycling and shuttles between the pre-autophagosomal structure, mitochondria, and the Golgi complex. These data support a hypothesis that multiple membrane sources supply the lipids needed for autophagosome formation.
Aberrant Translation of CytochromecOxidase Subunit 1 mRNA Species in the Absence of Mss51p in the YeastSaccharomyces cerevisiae
Authors: Zambrano Andrea , Fontanesi Flavia , Solans Asun , de Oliveira Rodrigo Leite , Fox Thomas D. , Tzagoloff Alexander , Barrientos Antoni
Published: November 2006

Expression of yeast mitochondrial genes depends on specific translational activators acting on the 5′-untranslated region of their target mRNAs. Mss51p is a translational factor for cytochrome c oxidase subunit 1 (COX1) mRNA and a key player in down-regulating Cox1p expression when subunits with which it normally interacts are not available. Mss51p probably acts on the 5′-untranslated region of COX1 mRNA to initiate translation and on the coding sequence itself to facilitate elongation. Mss51p binds newly synthesized Cox1p, an interaction that could be necessary for translation. To gain insight into the different roles of Mss51p on Cox1p biogenesis, we have analyzed the properties of a new mitochondrial protein, mp15, which is synthesized in mss51 mutants and in cytochrome oxidase mutants in which Cox1p translation is suppressed. The mp15 polypeptide is not detected in cox14 mutants that express Cox1p normally. We show that mp15 is a truncated translation product of COX1 mRNA whose synthesis requires the COX1 mRNA-specific translational activator Pet309p. These results support a key role for Mss51p in translationally regulating Cox1p synthesis by the status of cytochrome oxidase assembly.
Prohibitins Interact Genetically with Atp23, a Novel Processing Peptidase and Chaperone for the F1FO-ATP Synthase
Authors: Osman Christof , Wilmes Claudia , Tatsuta Takashi , Langer Thomas
Published: November 2006

The generation of cellular energy depends on the coordinated assembly of nuclear and mitochondrial-encoded proteins into multisubunit respiratory chain complexes in the inner membrane of mitochondria. Here, we describe the identification of a conserved metallopeptidase present in the intermembrane space, termed Atp23, which exerts dual activities during the biogenesis of the F1FO-ATP synthase. On one hand, Atp23 serves as a processing peptidase and mediates the maturation of the mitochondrial-encoded FO-subunit Atp6 after its insertion into the inner membrane. On the other hand and independent of its proteolytic activity, Atp23 promotes the association of mature Atp6 with Atp9 oligomers. This assembly step is thus under the control of two substrate-specific chaperones, Atp10 and Atp23, which act on opposite sides of the inner membrane. Strikingly, both ATP10 and ATP23 were found to genetically interact with prohibitins, which build up large, ring-like assemblies with a proposed scaffolding function in the inner membrane. Our results therefore characterize not only a novel processing peptidase with chaperone activity in the mitochondrial intermembrane space but also link the function of prohibitins to the F1FO-ATP synthase complex.
QSCOP—SCOP quantified by structural relationships
Authors: Suhrer Stefan J. , Wiederstein Markus , Sippl Manfred J.
Published: November 2006

Summary: The database SCOP (Structural Classification Of Proteins) has become a major resource in bioinformatics and protein science. A particular strength of SCOP is the flexibility of its rules enabling the preservation of the many details spotted by experts in the classification process. Here we endow classic SCOP Families with quantified structural information and comment on the structural diversity found in the SCOP hierarchy.

Availability: Quantified SCOP (QSCOP) is available as a public WEB service.

Contact:  sippl@came.sbg.ac.at
Integrating transcription factor binding site information with gene expression datasets
Authors: Jeffery Ian B. , Madden Stephen F. , McGettigan Paul A. , Perrière Guy , Culhane Aedín C. , Higgins Desmond G.
Published: November 2006

Motivation: Microarrays are widely used to measure gene expression differences between sets of biological samples. Many of these differences will be due to differences in the activities of transcription factors. In principle, these differences can be detected by associating motifs in promoters with differences in gene expression levels between the groups. In practice, this is hard to do.

Results: We combine correspondence analysis, between group analysis and co-inertia analysis to determine which motifs, from a database of promoter motifs, are strongly associated with differences in gene expression levels. Given a database of motifs and gene expression levels from a set of arrays, the method produces a ranked list of motifs associated with any specified split in the arrays. We give an example using the Gene Atlas compendium of gene expression levels for human tissues where we search for motifs that are associated with expression in central nervous system (CNS) or muscle tissues. Most of the motifs that we find are known from previous work to be strongly associated with expression in CNS or muscle. We give a second example using a published prostate cancer dataset where we can simply and clearly find which transcriptional pathways are associated with differences between benign and metastatic samples.

Availability: The source code is freely available upon request from the authors.

Contact:  Ian.Jeffery@ucd.ie
Extensions to gene set enrichment
Authors: Jiang Zhen , Gentleman Robert
Published: November 2006

Motivation: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture changes in the expression of pre-defined sets of genes. We propose number of extensions to GSEA, including the use of different statistics to describe the association between genes and phenotypes of interest. We make use of dimension reduction procedures, such as principle component analysis, to identify gene sets with correlated expression. We also address issues that arise when gene sets overlap.

Results: Our proposals extend the range of applicability of GSEA and allow for adjustments based on other covariates. We have provided a well-defined procedure to address interpretation issues that can raise when gene sets have substantial overlap. We have shown how standard dimension reduction methods, such as PCA, can be used to help further interpret GSEA.

Contact:  zjiang@fhcrc.org

Supplementary information: Supplementary data are available at Bioinformatics online.
Mosclust: a software library for discovering significant structures in bio-molecular data
Authors: Valentini Giorgio
Published: November 2006

Summary: The R package mosclust (model order selection for clustering problems) implements algorithms based on the concept of stability for discovering significant structures in bio-molecular data. The software library provides stability indices obtained through different data perturbations methods (resampling, random projections, noise injection), as well as statistical tests to assess the significance of multi-level structures singled out from the data.

Availability:  

Contact:  valentini@dsi.unimi.it

Supplementary information:
Mclip: motif detection based on cliques of gapped local profile-to-profile alignments
Authors: Frickey Tancred , Weiller Georg
Published: November 2006

Summary: A multitude of motif-finding tools have been published, which can generally be assigned to one of three classes: expectation-maximization, Gibbs-sampling or enumeration. Irrespective of this grouping, most motif detection tools only take into account similarities across ungapped sequence regions, possibly causing short motifs located peripherally and in varying distance to a ‘core’ motif to be missed. We present a new method, adding to the set of expectation-maximization approaches, that permits the use of gapped alignments for motif elucidation.

Availability: The program is available for download from:

Contact:  Georp.Weiller@anu.edu.au

Supplementary information:
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring
Authors: Garcia Olivier , Saveanu Cosmin , Cline Melissa , Fromont-Racine Micheline , Jacquier Alain , Schwikowski Benno , Aittokallio Tero
Published: November 2006

Summary: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds the GO categories over-represented in a given network. Our plug-in, named GOlorize, first highlights the class members with category-specific color-coding and then constructs an enhanced visualization of the network using a class-directed layout algorithm

Availability:

Contact:  teanai@pasteur.fr

Supplementary information: Installation instructions and tutorial at
Efficacy of Sanfujiu to Treat Allergies: Patient Outcomes at 1 Year after Treatment
Authors: Tai Chen-Jei , Chang Chia-Pei , Huang Chung-Yu , Chien Li-Yin
Published: November 2006

Sanfujiu is a treatment method of applying herbal paste onto the acupoints Fengmen and Feishu during the three hottest days of summer to treat patients with allergies. The objectives of this study were to determine the treatment efficacy at 1 year after the Sanfujiu treatment, and examine variations in the perceived efficacy of Sanfujiu among different subgroups, based on the patients′ ages, diagnoses and number of reactive symptoms immediately after the treatment. We enrolled 105 patients who completed Sanfujiu treatment at a medical university hospital in Taipei as the subjects. One year after treatment, trained interviewers conducted telephone interviews with the patients. Approximately 60% of them perceived the treatment as being effective at 1 year later, which was higher than that at 1 week after treatment (45.7%). Younger subjects (<19 years of age) and patients with asthma were more likely to report the treatment as being effective. Patients who had more reactive symptoms after the third Sanfujiu treatment were more likely to report the treatment as being effective. The results demonstrated that Sanfujiu was moderately effective, as perceived by patients in Taiwan, in treating their allergic symptoms.
Treatment Preferences for CAM in Children with Chronic Pain
Authors: Tsao Jennie C. I. , Meldrum Marcia , Kim Su C. , Jacob Margaret C. , Zeltzer Lonnie K.
Published: November 2006

CAM therapies have become increasingly popular in pediatric populations. Yet, little is known about children′s preferences for CAM. This study examined treatment preferences in chronic pediatric pain patients offered a choice of CAM therapies for their pain. Participants were 129 children (94 girls) (mean age = 14.5 years ± 2.4; range = 8–18 years) presenting at a multidisciplinary, tertiary clinic specializing in pediatric chronic pain. Bivariate and multivariate analyses were used to examine the relationships between CAM treatment preferences and patient′s sociodemographic and clinical characteristics, as well as their self‐reported level of functioning. Over 60% of patients elected to try at least one CAM approach for pain. The most popular CAM therapies were biofeedback, yoga and hypnosis; the least popular were art therapy and energy healing, with craniosacral, acupuncture and massage being intermediate. Patients with a diagnosis of fibromyalgia (80%) were the most likely to try CAM versus those with other pain diagnoses. In multivariate analyses, pain duration emerged as a significant predictor of CAM preferences. For mind‐based approaches (i.e. hypnosis, biofeedback and art therapy), pain duration and limitations in family activities were both significant predictors. When given a choice of CAM therapies, this sample of children with chronic pain, irrespective of pain diagnosis, preferred non‐invasive approaches that enhanced relaxation and increased somatic control. Longer duration of pain and greater impairment in functioning, particularly during family activities increased the likelihood that such patients agreed to engage in CAM treatments, especially those that were categorized as mind‐based modalities.
Nourishing Yin and Promoting Blood Circulation of TCM to Treat Hemorheologic Disorder Induced by Diabetes Mellitus in Rats
Authors: Xia Rong , Huang Ping , Shao Guo-ming
Published: November 2006

Diabetes mellitus, DM, is commonly accompanied with various stages of hemorheologic disturbances that are the main causes of the development of chronic DM. In this study, simple Chinese material medica [yang‐yin jiang‐tang preparation (YYJT)] was given to alloxan‐induced DM rats and analyzed to compare the changes of fasting blood glucose (FBG), fasting insulin (FINS), hemorheologic parameters and insulin‐like growth factor II (IGF‐II) before and after administration. The results suggested that YYJT can significantly downregulate FBG (P < 0.005), improve insulin resistance and beta‐cell secretion (P < 0.05), decrease whole blood viscosity at low and high shear rates, gathering of blood index test (GIT) and fibrinogen (FIB) (P < 0.05), and enlarge the function of IGF‐II (P < 0.05). We concluded that YYJT could prevent and treat hemorheologic disorder in DM rats by means of reducing glucose, improving insulin resistance and elevating IGF‐II.
Standardization of Nomenclature in Acupuncture Research (SoNAR)
Authors: White Peter , Golianu Brenda , Zaslawski Chris , Seung-Hoon Choi
Published: November 2006

As more clinical acupuncture trials for pain are published, it becomes increasingly difficult to compare and evaluate the merits and shortcomings of such studies. A major contributory factor to this centers on the description of, and the assumptions made about, the control intervention used. In considering an acupuncture control, it is important to evaluate its physiological activity and thus far, this has not been done. A variety of different and sometimes very novel controls have been tried and used in the research setting and the inevitable consequence of this is confusion, particularly when attempting to interpret the results of trials. Researchers and other interested parties such as patients, primary care practitioners, funding agencies etc., searching for evidence in the literature are likely to be misled or confused by such variability. There is therefore a need to define and standardize many of these terms, to clarify reporting and to convey the correct information in a way that it is not misleading. This paper details the background and need for this and is primarily intended to assist those who intend to publish primary and secondary acupuncture research. However, standardization of reporting will be of benefit to anybody who will need to examine the literature for evidence. This article proposes and recommends a nomenclature when reporting future acupuncture clinical research. This nomenclature arose through discussion at a meeting convened by the World Health Organisation (Western Pacific Regional Office) and will be incorporated into their policy document later this year.
Cochlear Implantation in a Patient With Bilateral Deep Brain Stimulators
Authors: St. Martin Michele B. , Hirsch Barry E.
Published: November 2006

Objective: We report the case of a patient successfully implanted with a Nucleus Contour cochlear implant after placement of a deep brain stimulator for Parkinson disease.

Methods: The authors conducted a case report and literature review.

Results: Successful hookup and mapping of the device was performed 1 month after implantation without evidence of aberrant activity of the deep brain stimulators.

Conclusions: To our knowledge, this is the first reported case of successful implantation of both a cochlear implant and a deep brain stimulator in the same patient. We have outlined one approach to avoiding detrimental interactions between cochlear implant and deep brain stimulator devices.
Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines
Authors: Khattra Jaswinder , Delaney Allen D. , Zhao Yongjun , Siddiqui Asim , Asano Jennifer , McDonald Helen , Pandoh Pawan , Dhalla Noreen , Prabhu Anna-liisa , Ma Kevin , Lee Stephanie , Ally Adrian , Tam Angela , Sa Danne , Rogers Sean , Charest David , Stott Jeff , Zuyderduyn Scott , Varhol Richard , Eaves Connie , Jones Steven , Holt Robert , Hirst Martin , Hoodless Pamela A. , Marra Marco A.
Published: November 2006

We describe the details of a serial analysis of gene expression (SAGE) library construction and analysis platform that has enabled the generation of >298 high-quality SAGE libraries and >30 million SAGE tags primarily from sub-microgram amounts of total RNA purified from samples acquired by microdissection. Several RNA isolation methods were used to handle the diversity of samples processed, and various measures were applied to minimize ditag PCR carryover contamination. Modifications in the SAGE protocol resulted in improved cloning and DNA sequencing efficiencies. Bioinformatic measures to automatically assess DNA sequencing results were implemented to analyze the integrity of ditag structure, linker or cross-species ditag contamination, and yield of high-quality tags per sequence read. Our analysis of singleton tag errors resulted in a method for correcting such errors to statistically determine tag accuracy. From the libraries generated, we produced an essentially complete mapping of reliable 21-base-pair tags to the mouse reference genome sequence for a meta-library of ∼5 million tags. Our analyses led us to reject the commonly held notion that duplicate ditags are artifacts. Rather than the usual practice of discarding such tags, we conclude that they should be retained to avoid introducing bias into the results and thereby maintain the quantitative nature of the data, which is a major theoretical advantage of SAGE as a tool for global transcriptional profiling.
Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns
Authors: Roh Tae-young , Wei Gang , Farrell Catherine M. , Zhao Keji
Published: November 2006

Comparative genomic studies have been useful in identifying transcriptional regulatory elements in higher eukaryotic genomes, but many important regulatory elements cannot be detected by such analyses due to evolutionary variations and alignment tool limitations. Therefore, in this study we exploit the highly conserved nature of epigenetic modifications to identify potential transcriptional enhancers. By using a high-resolution genome-wide mapping technique, which combines the chromatin immunoprecipitation and serial analysis of gene expression assays, we have recently determined the distribution of lysine 9/14-diacetylated histone H3 in human T cells. We showed the existence of 46,813 regions with clusters of histone acetylation, termed histone acetylation islands, some of which correspond to known transcriptional regulatory elements. In the present study, we find that 4679 sequences conserved between human and pufferfish coincide with histone acetylation islands, and random sampling shows that 33% (13/39) of these can function as transcriptional enhancers in human Jurkat T cells. In addition, by comparing the human histone acetylation island sequences with mouse genome sequences, we find that despite the conservation of many of these regions between these species, 21,855 of these sequences are not conserved. Furthermore, we demonstrate that about 50% (26/51) of these nonconserved sequences have enhancer activity in Jurkat cells, and that many of the orthologous mouse sequences also have enhancer activity in addition to conserved epigenetic modification patterns in mouse T-cell chromatin. Therefore, by combining epigenetic modification and sequence data, we have established a novel genome-wide method for identifying regulatory elements not discernable by comparative genomics alone.
To be named or not to be named—Heteropodarke pleijeli sp. n. (Annelida, Polychaeta)
Authors: Muona Jyrki
Published: November 2006

Heteropodarke pleijeli n. sp. (Annelida, Polychaeta, Hesionidae) is described from Papua New Guinea. This taxon was characterized in a PhyloCode context by Pleijel in 1999 and again in 2000. The valid name for this annelid will be decided by the zoological community in the future, but the description provided here is regarded as the only available and thus valid one.

© The Willi Hennig Society 2006.
High‐level serum B‐cell activating factor and promoter polymorphisms in patients with idiopathic thrombocytopenic purpura
Authors: Emmerich Florian , Bal Gürkan , Barakat Alaa , Milz Julian , Mühle Caroline , Martinez‐Gamboa Lorena , Dörner Thomas , Salama Abdulgabar
Published: November 2006

Idiopathic thrombocytopenic purpura (ITP) is an autoimmune disorder in which platelets are opsonised by autoantibodies and destroyed by macrophages. Therefore, ITP represents a prototype of a B‐cell‐mediated autoimmune disorder. B‐cell activating factor (BAFF) is a member of the tumour necrosis factor family and an important regulator of B‐cell development. BAFF levels were determined in serum samples from 53 patients with ITP. Serum BAFF levels in patients with an active ITP were increased when compared with the healthy control group (median 1620 pg/ml vs. 977 pg/ml; P < 0·001). Moreover, immunosuppressive treatment was associated with strongly suppressed BAFF levels (median 629 pg/ml; P < 0·01). In addition, a polymorphic site was detected in the BAFF promoter region (−871) that appeared to occur more frequently in ITP patients than in healthy persons. This promoter variant was associated with very high BAFF levels in ITP patients. Our data suggest that BAFF is an important pathogenetic factor in the development of ITP.
Haematopoietic progenitor cells utilise conventional PKC to suppress PKB/Akt activity in response to c‐Kit stimulation
Authors: Edling Charlotte E. , Pedersen Malin , Carlsson Leif , Rönnstrand Lars , Palmer Ruth H. , Hallberg Bengt
Published: November 2006

Receptor tyrosine kinase (RTK) c‐Kit signalling is crucial for the proliferation, survival and differentiation of haematopoietic stem cells (HSCs). To further understand the mechanisms underlying these events we explored how the downstream mediators interact. The present study investigated the function of conventional protein kinase Cs (c‐PKC) in c‐Kit mediated signalling pathways in HSC‐like cell lines. This analysis supported earlier findings, that steel factor (SF) activates c‐PKC, extracellular signal‐regulated kinase (Erk) and protein kinase B (PKB). The present results were consistent with an important role of c‐PKC in the positive activation of Erk and for proliferation. Further, it was observed that c‐PKC negatively regulated PKB activity upon SF stimulation, indicating that c‐PKC acts as a suppressor of c‐Kit signalling. Finally, these observations were extended to show that c‐PKC mediated the phosphorylation of the endogenous c‐Kit receptor on serine 746, resulting in decreased overall tyrosine phosphorylation of c‐Kit upon SF stimulation. This report showed that this specific feedback mechanism of c‐PKC mediated phosphorylation of the c‐Kit receptor has consequences for both proliferation and survival of HSC‐like cell lines.
A comparison of the binding of secretory component to immunoglobulin A (IgA) in human colostral S‐IgA1 and S‐IgA2
Authors: Almogren Adel , Senior Bernard W. , Kerr Michael A.
Published: November 2006

A detailed investigation of the binding of secretory component to immunoglobulin A (IgA) in human secretory IgA2 (S‐IgA2) was made possible by the development of a new method of purifying S‐IgA1, S‐IgA2 and free secretory component from human colostrum using thiophilic gel chromatography and chromatography on Jacalin‐agarose. Sodium dodecyl sulphate–polyacrylamide gel electrophoresis of unreduced pure S‐IgA2 revealed that, unlike in S‐IgA1, a significant proportion of the secretory component was bound non‐covalently in S‐IgA2. When S‐IgA1 was incubated with a protease purified from Proteus mirabilis the secretory component, but not the α‐chain, was cleaved. This is in contrast to serum IgA1, in which the α‐chain was cleaved under the same conditions – direct evidence that secretory component does protect the α‐chain from proteolytic cleavage in S‐IgA. Comparisons between the products of cleavage with P. mirabilis protease of free secretory component and bound secretory component in S‐IgA1 and S‐IgA2 also indicated that, contrary to the general assumption, the binding of secretory component to IgA is different in S‐IgA2 from that in S‐IgA1.
Effects of wounding, fruit age and wetness duration on the development of cherry brown rot in the UK
Authors: Xu X.‐M. , Bertone C. , Berrie A.
Published: November 2006

This research investigated the effects of wounding, fruit age and wetness duration on the development of cherry brown rot. Both Monilinia laxa and M. fructigena infected wounded detached cherry fruits, but M. laxa caused more infections than M. fructigena and only M. laxa efficiently infected intact detached fruits. Results from field monitoring and controlled inoculation in a polyethylene tunnel showed that the susceptibility of fruits to infection by M. laxa increased with fruit maturity. Infection of attached intact fruits by M. laxa was not affected by the length (3–24 h) of the wet period tested.
Efficacy and safety of preemptive anti‐CMV therapy with valganciclovir after kidney transplantation
Authors: Lopau Kai , Greser Alexandra , Wanner Christoph
Published: November 2006

Abstract: Background: CMV infections still pose a potentially serious threat to kidney transplant recipients and have a significant impact on graft as well as patient survival. The antiviral agent valganciclovir (VGCV) has a greater bioavailability after oral administration than oral ganciclovir (GCV) and can be considered a substitute for GCV. The substance is approved in North America and Europe for anti‐CMV prophylaxis after organ transplantation. In this pilot study, we examined if VGCV could also be administered in preemptive treatment of CMV infections.

Methods: Twenty‐eight renal transplant recipients suffering from 32 asymptomatic episodes of CMV infection were treated with VGCV and followed up. CMV infection was diagnosed by routine controls of pp65‐antigenemia in pre‐defined intervals. All patients received sequential quadruple immunosuppression. VGCV was given for up to 12 wk in a dosage adapted to renal graft function. Efficacy and safety parameters were monitored for 16 wk.

Results: Twenty‐seven episodes of CMV antigenemia, two patients progressing to CMV syndrome and three patients progressing to CMV disease were treated. Primary efficiency was 79%, Four patients relapsed and were treated with a second course resulting in serological recovery. Two patients did not respond to oral VCGV and were switched to another antiviral agent. Graft function remained stable during and after treatment. Serious side effects were seen in seven patients, four patients complained of diarrhea and gastrointestinal pain, three patients suffered from leucopenia, in one of these treatment had to be temporary paused. Fifty‐nine percent of all episodes were treated in a completely ambulatory setting.

Conclusions: VGCV can be considered as an option also for preemptive treatment of CMV infections after renal transplantation. The antiviral potency seems to be adequate, potential side effects are comparable with IV GCV. Because of the improved pharmacokinetics of VGCV the substance can be used to abbreviate or even completely avoid in‐hospital care of CMV infections.
Changes in Hospitalisation Rates and Costs in New South Wales, 1996–97 and 2000–01
Authors: Walker Agnes , Thurecht Linc , Harding Ann
Published: November 2006

Changes in hospital admission rates and costs in New South Wales (NSW) between 1996‐97 and 2000–01 were examined by age, hospital type and socioeconomic status. A novel method led to a more accurate assessment of hospital patients' socio‐economic status than was previously possible. Use of unit record hospitals data and full population Census data allowed very high levels of disaggregation. Considerable increases in the baby boomer and frail aged populations led to higher hospital admission rates over the period. This was driven by the private sector, which saw its admission rates increase by 20 per cent (with the public sector rate declining by 6per cent). Public hospital admission rates by age were found to be up to 40 per cent greater for the poorest 20 per cent of the population than for the richest 20 per cent‐with a reversal of the pattern for private hospitals (up to 45 per cent greater for the richest 20 per cent than for the poorest 20 per cent). In a period when total NSW hospital expenditures increased by 21 per cent, we found that ‘per admission costs’ in the inpatient non‐psychiatric sub‐sector changed little.
Modes of Entrance by Gender and Wage Differential in the French Labour Market
Authors: Moulin Stéphane
Published: November 2006

Abstract.  This paper explores the gender wage differential after the exit from school in France. Using survey longitudinal data on young men and women leaving the French school system in 1998, we show that the residual entrance‐level wage differential by gender may be explained by the expected gender differential of access to job opportunities. A hierarchical classification is used to estimate the probability to obtain easy access to non‐subsidized jobs. After control for hours worked and hierarchical levels, and for the predicted values of this previous estimation, we find no significant impact of gender on entrance‐level wages.
Modelling Labour Demand Dynamics beyond the Frictionless Environment
Authors: Drakos Konstantinos , Kallandranis Christos
Published: November 2006

Abstract. In this study we develop a simple econometric model for labour demand dynamics by explicitly considering deviations from the standard frictionless economic environment. In particular, we explore the potential effect on labour demand of capital market imperfections, labour market institutional rigidities in the form of union power, and the impact of uncertainty. In addition, in the presence of uncertainty, adjustment costs and irreversibility emerge as an important factor that introduces an option value of waiting. According to our results, leverage exerts a direct negative impact on employment dynamics indicating that capital market imperfections are indeed present. Moreover, leverage is found to also affect the adjustment process of employment. Finally, we document asymmetric effects of frictions on labour demand across different size groups that imply a higher vulnerability of small and medium sectors with respect to debt levels. Uncertainty exerts a significantly negative impact on labour demand, which is compatible with presence of partial irreversibility of employment decisions. Finally, unions over and above their effect via higher wages are positively related to employment, a finding that is indicative of their pursue for job security.
Earnings‐related Severance Pay
Authors: Goerke Laszlo
Published: November 2006

Abstract.  In an efficiency wage economy, lump‐sum severance pay from which shirkers can be excluded raises employment. However, severance payments are usually related to wages. It is shown that earnings‐related, mandated severance pay will have ambiguous employment effects if effort can be varied continuously. A substitution of the earnings‐related for the lump‐sum component reduces employment. Thus, the prevalent form of severance payments in OECD countries might have less advantageous employment effects than previously conjectured.
Strike Outcomes and Wage Settlements in Spain
Authors: Jiménez‐Martin Sergi
Published: November 2006

Abstract.  This paper analyses collective bargaining using Spanish firm‐level data. Central to the analysis are the joint determination of wage and strike outcomes in a dynamic framework and the possibility of separate wage equation for strike and non‐strike outcomes. Conditional to strikes taking place, we confirm a negative relationship between strike duration and wage changes in a dynamic context. In this sense, the joint effect of the strike variables is positive for short strikes and negative for long ones (above 20 days). Furthermore, we find selection in wage equations induced by the strike outcome. In this sense, the possibility of wage determination processes being different in strike and non‐strike samples is not rejected by the data. In particular, wage dynamics are of opposite sign in both strike and non‐strike equations. Finally, we find evidence of a 0.33 percentage points wage change strike premium.
HETEROGENEOUS SPACE IN REGIONAL ECONOMICS AND BEYOND
Authors: Greenhut John G. , Howard Smith Dean
Published: November 2006

Abstract.  This paper points to the multiple forces which establish differential prices and outputs over heterogeneous space. Such space clearly applies to a regional economy where costly distance provides opportunities for sellers to discriminate in price among customers. Similar discriminatory opportunities may be created in a spaceless world through, for example, product differentiation and the passage of time. It is in this broad perspective that a generalized theory of discriminatory spatial pricing is formulated. Simulations reveal a remarkable panoply of cost, price, and output relationships, highlighting the criticality of variations in elasticity in determining macro, micro, and regional economic behaviour.
SPECIALIZATION AND TRADE: A GAME THEORETICAL APPROACH
Authors: Yao Shuntian , Li Ke
Published: November 2006

Abstract.  In this paper we consider the problem of specialization and trade for large economies with a continuum of ex ante identical individuals and with a finite number of goods. Different from the classical treatment, we adopt a game theoretical approach. Therefore in our models the prices of traded goods are endogenously formulated according to the bidding strategies of the producer‐consumers. Furthermore, we assume that in the beginning individuals randomly choose their professions. As a result, with a short‐run Nash equilibrium different types of professionals may have different utility levels; while through a dynamic process, a long‐run Nash equilibrium with utility equalization is reached. Besides, we also attempt to provide a new algorithm for the computation of general equilibrium models in the Yang‐Ng framework.
THE DEVELOPMENT OF INITIAL PUBLIC OFFERING MARKETS FOR EMERGING COMPANIES IN JAPAN
Authors: Mizuno Mitsuru
Published: November 2006

Abstract.  This paper reviews the development of IPO markets for emerging companies in Japan, especially after an entry of NASDAQ in Japan in 2000 with a view to assess whether they have provided markets for the growth firms and whether venture capital investments have shown an increase. Using the publicly available data, it examines the features of the three IPO markets and confirmed that JASDAQ is a market for traditional industries with relatively large size of emerging companies, whereas both Mothers and Hercules offer markets for new industries with young companies. It also discusses possible measures to further enhance market development.
A NOTE ON ‘AN INFRAMARGINAL ANALYSIS OF THE RICARDIAN MODEL’
Authors: Zhang Dingsheng , Shi Heling
Published: November 2006

Abstract.  This is a note about Cheng et al.'s paper, in which we consider a dual structure of division of labour and trade that is missed in the model of Cheng et al. Though the inclusion of the dual structure will not change the main results in the paper by Cheng et al., it explores an interesting way to use a general equilibrium model to describe a dual structure with underemployment in a transitional period of economic development.
JAPAN: THE CASE FOR A TAYLOR RULE? A SIMPLE APPROACH
Authors: Depalo Domenico
Published: November 2006

Abstract.  In this article I propose two different models for analyzing the conduct of monetary policy, facing certain expectations. The first is a autoregressive model, which implicitly accounts for adaptive expectations, while the second accounts for the rational expectations. I used these models to judge whether or not the Taylor rule can be a good benchmark for the conduct of monetary policy in Japan. The conclusion is that a simple AR model fits the data better than the Taylor rule, and that assuming rational expectations in Japan could be highly misleading, at least since the mid‐1990s.
EAST ASIAN REGIONAL TRADE AGREEMENTS: DO THEY PROMOTE GLOBAL FREE TRADE?
Authors: Park Innwon
Published: November 2006

Abstract.  We quantitatively evaluate the effects different paths have on East Asian Regional Trade Agreements (RTA), which include expansionary, duplicate and overlapping RTAs. By applying a computable general equilibrium model analysis, we find that the static effect of existing, proposed and negotiating East Asian RTAs on world and members’ welfare is sufficiently positive. It will lead to non‐discriminatory global free trade, by triggering the domino effect of regionalism if the RTAs take an expansionary path by cooperating with each other, in contrast to competing to achieve the first mover advantage, or hub self‐interest.