bluuebunny/crossref_metadata_2025 huggingface dataset:
Phosphorus sorption - desorption by purple soils of China in relation to their properties
Authors: Li M. , Hou Y. L. , Zhu B.
Published: May 2007

The understanding of phosphorus (P) sorption and desorption by soil is important for better managing soil P source and relieving water eutrophication. In this study, sorption–desorption behaviour of P was investigated in purple soils, collected from 3 kinds of purple parent materials with different kinds of land cover, in the upper reaches of Yangtze River, China, using a batch equilibrium technique. Results showed that most of the farmed purple soils had P sorption capacity (PSC) values ranging from 476 to 685 mg P/kg, while higher PSC values were observed in the soils from forestland and paddy field. A single-point P sorption index (PSI) was found to be significantly correlated with PSC (R2 = 0.94, P < 0.001), suggesting its use in estimating PSC across different types of purple soils. The PSC of purple soils was positively and strongly related to the contents of amorphous Fe and Al oxides (r = 0.73, P < 0.001), clay (r = 0.55, P < 0.01), and organic matter (r = 0.50, P < 0.05). Furthermore, the constant relating to binding strength was positively correlated with the content of amorphous Fe and Al oxides (r = 0.66, P < 0.01), but negatively correlated with labile Ca (r = –0.43, P < 0.05) and soil pH (r = –0.53, P < 0.01). Some acidic purple soils with high binding energy featured a power desorption curve, suggesting that P release risk can be accelerated once the P sorbed exceeds a certain threshold. Other soils with low binding energy demonstrated a linear desorption curve. The P desorption percentage was significantly correlated with soil test P (r = 0.78, P < 0.01) and the degree of P saturation (r = 0.82, P < 0.01), but negatively correlated with PSC (r = –0.66, P < 0.01).
Interaction between innate immune cells and a bacterial type III secretion system in mutualistic and pathogenic associations
Authors: Silver Adam C. , Kikuchi Yoshitomo , Fadl Amin A. , Sha Jian , Chopra Ashok K. , Graf Joerg
Published: May 2007

Animals house a community of bacterial symbionts in their digestive tracts that contribute to their well being. The medicinal leech,
Hirudo verbana
, has a remarkably simple gut population carrying two extracellular microbes in the crop where the ingested blood is stored. This simplicity renders it attractive for studying colonization factors.
Aeromonas veronii
, one of the leech symbionts, can be genetically manipulated and is a pathogen of mammals. Screening transposon mutants of
A. veronii
for colonization defects in the leech, we found one mutant, JG752, with a transposon insertion in an
ascU
homolog, encoding an essential component of type III secretion systems (T3SS). Competing JG752 against the wild type revealed that JG752 was increasingly attenuated over time (10-fold at 18 h and >10,000-fold at 96 h). This colonization defect was linked to
ascU
by complementing JG752 with the operon containing
ascU
. Fluorescence
in situ
hybridization analysis revealed that at 42 h 38% of JG752 cells were phagocytosed by leech macrophage-like cells compared with <0.1% of the parental strain. Using mammalian macrophages, a lactate dehydrogenase release assay revealed that cytotoxicity was significantly reduced in macrophages exposed to JG752. In a mouse septicemia model, JG752 killed only 30% of mice, whereas the parent strain killed 100%, showing the importance of T3SS for both pathogenesis and mutualism. Phagocytic immune cells are important not only in defending against pathogens but also in maintaining the mutualistic symbiont community inside the leech, demonstrating that animals use similar, conserved mechanisms to control bacterial populations, even when the outcomes differ dramatically.
Functional identification of the hematopoietic stem cell niche in the ventral domain of the embryonic dorsal aorta
Authors: Taoudi Samir , Medvinsky Alexander
Published: May 2007

The first definitive/adult-type hematopoietic stem cells (HSCs) in the mouse aorta–gonad–mesonephros region emerge between embryonic days 10.5 and 11.5. The discovery of clusters of hematopoietic cells on the ventral luminal surface of the dorsal aorta in various vertebrate species has led to speculation that the floor of the dorsal aorta may play an essential role for the development of the definitive hematopoietic system. Here, we functionally show affiliation of definitive HSCs with the ventral floor of the dorsal aorta, whereas colony-forming hematopoietic activity is associated with both ventral and dorsal domains. We show that a rare population of PECAM1
high
CD45
+
cells, within which definitive HSCs reside, is predominantly localized to intraaortic clusters. Furthermore, using
ex vivo
culture analysis, we demonstrate that the ventral domain of the dorsal aorta has an exclusive functional capacity of inducing and expanding definitive HSCs.
Broadly neutralizing anti-hepatitis B virus antibody reveals a complementarity determining region H3 lid-opening mechanism
Authors: Chi Seung-Wook , Maeng Cheol-Young , Kim Seung Jun , Oh Mee Sook , Ryu Chun Jeih , Kim Sang Jick , Han Kyou-Hoon , Hong Hyo Jeong , Ryu Seong Eon
Published: May 2007

The humanized monoclonal antibody HzKR127 recognizes the preS1 domain of the human hepatitis B virus surface proteins with a broadly neutralizing activityin vivo. We present the crystal structures of HzKR127 Fab and its complex with a major epitope peptide. In the complex structure, the bound peptide forms a type IV β-turn followed by 310helical turn, the looped-out conformation of which provides a structural basis for broad neutralization. Upon peptide binding, the antibody undergoes a dramatic complementarity determining region H3 lid opening. To understand the structural implication of the virus neutralization, we carried out comprehensive alanine-scanning mutagenesis of all complementarity determining region residues in HzKR127 Fab. The functional mapping of the antigen-combining site demonstrates the specific roles of major binding determinants in antigen binding, contributing to the rational design for maximal humanization and affinity maturation of the antibody.
Multigene amplification and massively parallel sequencing for cancer mutation discovery
Authors: Dahl Fredrik , Stenberg Johan , Fredriksson Simon , Welch Katrina , Zhang Michael , Nilsson Mats , Bicknell David , Bodmer Walter F. , Davis Ronald W. , Ji Hanlee
Published: May 2007

We have developed a procedure for massively parallel resequencing of multiple human genes by combining a highly multiplexed and target-specific amplification process with a high-throughput parallel sequencing technology. The amplification process is based on oligonucleotide constructs, called selectors, that guide the circularization of specific DNA target regions. Subsequently, the circularized target sequences are amplified in multiplex and analyzed by using a highly parallel sequencing-by-synthesis technology. As a proof-of-concept study, we demonstrate parallel resequencing of 10 cancer genes covering 177 exons with average sequence coverage per sample of 93%. Seven cancer cell lines and one normal genomic DNA sample were studied with multiple mutations and polymorphisms identified among the 10 genes. Mutations and polymorphisms in the
TP53
gene were confirmed by traditional sequencing.
Loss of Nocturnin, a circadian deadenylase, confers resistance to hepatic steatosis and diet-induced obesity
Authors: Green Carla B. , Douris Nicholas , Kojima Shihoko , Strayer Carl A. , Fogerty Joseph , Lourim David , Keller Susanna R. , Besharse Joseph C.
Published: May 2007

The mammalian circadian system consists of a central oscillator in the suprachiasmatic nucleus of the hypothalamus, which coordinates peripheral clocks in organs throughout the body. Although circadian clocks control the rhythmic expression of a large number of genes involved in metabolism and other aspects of circadian physiology, the consequences of genetic disruption of circadian-controlled pathways remain poorly defined. Here we report that the targeted disruption of
Nocturnin
(
Ccrn4l
) in mice, a gene that encodes a circadian deadenylase, confers resistance to diet-induced obesity. Mice lacking Nocturnin remain lean on high-fat diets, with lower body weight and reduced visceral fat. However, unlike lean lipodystrophic mouse models, these mice do not have fatty livers and do not exhibit increased activity or reduced food intake. Gene expression data suggest that
Nocturnin
knockout mice have deficits in lipid metabolism or uptake, in addition to changes in glucose and insulin sensitivity. Our data support a pivotal role for Nocturnin downstream of the circadian clockwork in the posttranscriptional regulation of genes necessary for nutrient uptake, metabolism, and storage.
Vitamin D receptor is essential for normal keratinocyte stem cell function
Authors: Cianferotti Luisella , Cox Megan , Skorija Kristi , Demay Marie B.
Published: May 2007

The major physiological role of the vitamin D receptor (VDR) is the maintenance of mineral ion homeostasis. Mutation of the VDR, in humans and mice, results in alopecia. Unlike the effects of the VDR on mineral ion homeostasis, the actions of the VDR that prevent alopecia are ligand-independent. Although absence of the VDR does not prevent the development of a keratinocyte stem cell niche in the bulge region of the hair follicle, it results in an inability of these stem cells to regenerate the lower portion of the hair follicle
in vivo
and impairs keratinocyte stem cell colony formation
in vitro
. VDR ablation is associated with a gradual decrease in keratinocyte stem cells, accompanied by an increase in sebaceous activity, a phenotype analogous to that seen with impaired canonical Wnt signaling. Transient gene expression assays demonstrate that the cooperative transcriptional effects of β-catenin and Lef1 are abolished in keratinocytes isolated from VDR-null mice, revealing a role for the unliganded VDR in canonical Wnt signaling. Thus, absence of the VDR impairs canonical Wnt signaling in keratinocytes and leads to the development of alopecia due to a defect in keratinocyte stem cells.
Polarity reveals intrinsic cell chirality
Authors: Xu Jingsong , Van Keymeulen Alexandra , Wakida Nicole M. , Carlton Pete , Berns Michael W. , Bourne Henry R.
Published: May 2007

Like blood neutrophils, dHL60 cells respond to a uniform concentration of attractant by polarizing in apparently random directions. How each cell chooses its own direction is unknown. We now find that an arrow drawn from the center of the nucleus of an unpolarized cell to its centrosome strongly predicts the subsequent direction of attractant-induced polarity: Of 60 cells that polarized in response to uniform f-Met-Leu-Phe (fMLP), 42 polarized to the left of this arrow, 6 polarized to the right, and 12 polarized directly toward or away from the centrosome. To investigate this directional bias we perturbed a regulatory pathway, downstream of Cdc42 and partitioning-defective 6 (Par6), which controls centrosome orientation relative to polarity of other cells. Dominant negative Par6 mutants block polarity altogether, as previously shown for disrupting Cdc42 activity. Cells remain able to polarize, but without directional bias, if their microtubules are disrupted with nocodazole, or they express mutant proteins that interfere with activities of PKCζ or dynein. Expressing constitutively active glycogen synthase kinase 3β (GSK3β) causes cells to polarize preferentially to the right. Distributions of most of these polarity regulators localize to the centrosome but show no left–right asymmetry before polarization. Together, these findings suggest that an intrinsically chiral structure, perhaps the centrosome, serves as a template for directing polarity in the absence of spatial cues. Such a template could help to determine left–right asymmetry and planar polarity in development.
Age-related changes in adaptation to severe anemia in childhood in developing countries
Authors: O'Donnell Angela , Premawardhena A. , Arambepola M. , Allen S. J. , Peto T. E. A. , Fisher C. A. , Rees D. C. , Olivieri Nancy F. , Weatherall D. J.
Published: May 2007

Severe forms of anemia in children in the developing countries may be characterized by different clinical manifestations at particular stages of development. Whether this reflects developmental changes in adaptation to anemia or other mechanisms is not clear. The pattern of adaptation to anemia has been assessed in 110 individuals with hemoglobin (Hb) E β-thalassemia, one of the commonest forms of inherited anemia in Asia. It has been found that age and Hb levels are independent variables with respect to erythropoietin response and that there is a decline in the latter at a similar degree of anemia during development. To determine whether this finding is applicable to anemia due to other causes, a similar study has been carried out on 279 children with severe anemia due to
Plasmodium falciparum
malaria; the results were similar to those in the patients with thalassemia. These observations may have important implications both for the better understanding of the pathophysiology of profound anemia in early life and for its more logical and cost-effective management.
Acquisition of Methicillin-Resistant Staphylococcus aureus in the Acute Care Setting: Incidence and Risk Factors
Authors: Rioux Christophe , Armand-Lefevre Laurence , Guerinot Wafaa , Andremont Antoine , Lucet Jean-Christophe
Published: May 2007

Our objective was to assess the incidence of and risk factors for methicillin-resistant Staphylococcus aureus (MRSA) acquisition among patients in acute care wards. For 5 months, patients were screened for MRSA colonization at admission and at discharge. At admission, 6.6% of patients had cultures positive for MRSA, and 3.1% of patients who had tested negative for MRSA on admission had cultures positive for MRSA at discharge. Only the presence of chronic skin breaks at admission was independently associated with MRSA acquisition.
Pseudo-outbreak ofBordetella bronchisepticaInfection Associated With Contaminated Rabbit Blood Used as a Broth Culture Supplement
Authors: Calfee David P. , Kornblum John , Jenkins Stephen G.
Published: May 2007

A cluster of clinical isolates ofBordetella bronchisepticawas identified by microbiology laboratory personnel. A clinical and molecular epidemiologic study determined that this cluster represented a pseudo-outbreak due to bacterial contamination of rabbit blood used as a broth culture supplement. This pseudo-outbreak highlights the importance of quality assurance programs in the laboratory.
Impact of Different Methods for Describing the Extent of Prior Antibiotic Exposure on the Association Between Antibiotic Use and Antibiotic-Resistant Infection
Authors: Hyle Emily P. , Bilker Warren B. , Gasink Leanne B. , Lautenbach Ebbing
Published: May 2007

Objective.

Many studies have investigated the association between prior antibiotic use and antibiotic resistance. However, methods used in past studies to describe the extent of prior antibiotic use (eg, use of the 2 categories exposure versus no exposure and measurement of duration of exposure) have not been reviewed. The impact of the use of different methods for quantifying the use of antibiotics is unknown. The objectives of this study were to characterize past approaches to describing the extent of antibiotic use and to identify the impact of the use of different methods on associations between use of specific antibiotics and infection with an antibiotic-resistant-organism.

Methods.

We conducted a systematic review of studies that investigated risk factors for extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella species to identify variability in past approaches to describing the extent of antibiotic use. We then reanalyzed a data set from a prior study of risk factors for infection with ESBL-producing E. coli and Klebsiella species. We developed 2 separate multivariable models: 1 in which prior antibiotic use was described as a categorical variable (eg, exposure or no exposure) and 1 in which antibiotic use was described as a continuous variable (eg, measured in antibiotic-days). These models were compared qualitatively.

Setting.

Large academic medical center.

Results.

The 25 articles included in the systematic review revealed a variety of methods used to describe the extent of prior antibiotic exposure. Only 1 study justified its approach. Results from the 2 multivariable models that used different methodologic approaches differed substantially. Specifically, use of third-generation cephalosporins was a risk factor for infection with ESBL-producing E. coli and Klebsiella species when antibiotic use was described as a continuous variable but not when antibiotic use was described as a categorical variable.

Conclusions.

There has been no consistent method for assessing the extent of prior antibiotic exposure. The use of different methods may substantially alter the identified antimicrobial risk factors, which has important implications for the resultant interventions regarding antimicrobial use.
Epidemiology and Genetic Diversity of Methicillin-ResistantStaphylococcus aureusStrains in Residential Care Homes for Elderly Persons in Hong Kong
Authors: Ho Pak-Leung , Wang Teresa K. F. , Ching Patricia , Mak Gannon C. , Lai Eileen , Yam Wing-Cheong , Seto Wing-Hong
Published: May 2007

Objective.

To determine the prevalence and molecular epidemiology of methicillin-resistantStaphylococcus aureus(MRSA) strains among residents in residential care homes for the elderly in Hong Kong.

Design.

Cross-sectional and descriptive study.

Participants.

A total of 949 residents in 13 residential care homes for elderly persons in Hong Kong in January 2005.

Methods.

MRSA colonization was assessed by culture of swab specimens from anterior nares and active skin lesions. Characteristics of residents were obtained by a standard questionnaire. All MRSA isolates were analyzed by polymerase chain reaction for their staphylococcal cassette chromosome (SCC)meccontent and were typed by pulsed-field gel electrophoresis (PFGE) and multilocus sequencing.

Results.

MRSA colonization was detected in 27 residents (2.8%). No MRSA was found in 2 facilities. The rate of MRSA carriage in the other 11 facilities ranged from 1.9% to 4.2%. In univariate analysis, functional immobility (odds ratio [OR], 1.4), history of hospital admission (OR, 2.3), and the use of nebulized medication (OR, 5.4) were significantly associated with MRSA colonization. The isolates had 11 unique antibiograms, with 14 isolates susceptible to all but 1 or 2 of the non-β-lactam antimicrobial agents tested. The isolates exhibited SCCmectypes I (1 isolate), II (2 isolates), III (1 isolate), IV/IVA (10 isolates), and V (13 isolates). No isolates had the Panton-Valentine leukocidin genes. PFGE analysis clustered all except 1 isolate into 7 PFGE types, designated HKU10 to HKU70. Between 1 and 4 unique PFGE types were found in the individual residential care facilities.

Conclusion.

This study documented the emergence of SCCmec types IV and V among genetically diverse MRSA strains in residential care homes for elderly persons in Hong Kong.
Risk of Transmission Associated With Live Attenuated Vaccines Given to Healthy Persons Caring for or Residing With an Immunocompromised Patient
Authors: Kamboj Mini , Sepkowitz Kent A.
Published: May 2007

Objective.

Persons who receive live attenuated vaccine may occasionally transmit the vaccine strain to others. The risk of such transmission is a concern, especially for persons who provide care to immunocompromised patients (ie, family and healthcare workers [HCWs]). Since the Advisory Committee on Immunization Practices released guidelines 10 years ago, several new live attenuated products have been introduced, and additional information on older vaccines has become available. To better define the risk of transmission associated with live vaccines, we reviewed the currently available literature.

Results.

A review of the medical literature revealed no major risk of transmission associated with any live attenuated vaccine. A theoretical risk continues to exist for the live attenuated intranasal influenza vaccine and the smallpox vaccine.

Conclusions.

The available data support routine vaccination with live attenuated vaccines for all household contacts of immunocompromised patients and for HCWs caring for such Patients. The benefit for immunocompromised patients of providing herd immunity against this group of potentially devastating pathogens outweighs the risk, if any, of secondary transmission.
Hand Rub–Associated Fire Incidents During 25,038 Hospital-Years in Germany
Authors: Kramer Axel , Kampf Günter
Published: May 2007

Fire incidents in German hospitals related to the use of alcohol-based hand rubs were analyzed. Seven nonsevere fire incidents were identified, occurring during 25,038 hospital-years, which were caused by individual human actions and not by technical failure. The results underline the safety of using alcohol-based hand rubs in hospitals.
Exposure to Pulmonary Tuberculosis in a Neonatal Intensive Care Unit: Unique Aspects of Contact Investigation and Management of Hospitalized Neonates
Authors: Nania Joseph Jacob , Skinner Jena , Wilkerson Kathie , Warkentin Jon V. , Thayer Valerie , Swift Melanie , Schaffner William , Talbot Thomas R.
Published: May 2007

Objective.

We describe the investigation of a tuberculosis (TB) exposure in which a neonatal intensive care unit (NICU) respiratory therapist was the index patient, as well as the rationale by which exposed infants were managed and possible explanations for the lack of transmission to these patients.

Design.

Description of an exposure investigation.

Setting.

Academic, level IV NICU of a tertiary care children's hospital.

Participants.

Contacts of a respiratory therapist with pulmonary TB disease, including household members, healthcare coworkers, and infant patients.

Results.

In addition to 5 household contacts, 248 healthcare coworkers and 180 infant patients were identified as possibly exposed during the 24 days that the index patient worked between December 3, 2004, and January 30, 2005. Tuberculin skin tests (TSTs) were performed for 233 of the 235 contacts with the greatest degree of exposure (household and coworker contacts) who had a previously documented negative TST result or whose TST status was unknown prior to the investigation. No cases of latent tuberculosis infection or TB disease were identified. Because of characteristics of the index case, the exposure duration and setting, the infants' small lung volumes, and lack of evidence of transmission to higher-risk contacts, infants were not clinically evaluated or empirically treated for TB disease. Surveillance for subsequent illness was carried out by primary healthcare providers and parents. No TB disease or unexplained illness in these infants was reported in the 20 months following the exposure.

Conclusion.

After limited hospital exposure to a healthcare worker with pulmonary TB disease who is not highly contagious, neonates can be safely managed without specific evaluation for TB disease or empirical treatment.
A Cluster of Hemodialysis-Related Bacteremia Linked to Artificial Fingernails
Authors: Gordin Fred M. , Schultz Maureen E. , Huber Ruth , Zubairi Sabiha , Stock Frida , Kariyil Joseph
Published: May 2007

We examined a cluster of 5 hemodialysis patients who contracted gram-negative bacteremia. A nurse who used an artificial fingernail to open a vial of heparin that was mixed to make a flush solution had a culture of an artificial fingernail specimen positive for Serratia marcescens. The typing of the S. marcescens strains isolated from the 5 patients and the nurse showed them to be identical. This finding provides strong support for policies prohibiting artificial nails for healthcare workers in all hemodialysis units.
Nurses' Intentions to Wear Gloves During Venipuncture Procedures: A Behavioral Psychology Perspective
Authors: Doi Suhail A. R. , Amigó María Florencia
Published: May 2007

Registered nurses working at a teaching hospital in Kuwait were surveyed to assess the psychosocial variables associated with their intention to comply with glove-wearing recommendations. Perceived consequences and normative beliefs, as well as sex and years of nursing experience, significantly influenced their behavioral intentions, suggesting that improvements in intention to comply are more likely to come from practical demonstrations that show nurses the potential outcomes of both using and not using gloves.
Impact of Different Methods of Feedback to Clinicians After Postprescription Antimicrobial Review Based on the Centers for Disease Control and Prevention's 12 Steps to Prevent Antimicrobial Resistance Among Hospitalized Adults
Authors: Cosgrove Sara E. , Patel Alpa , Song Xiaoyan , Miller Robert E. , Speck Kathleen , Banowetz Amy , Hadler Rachel , Sinkowitz-Cochran Ronda L. , Cardo Denise M. , Srinivasan Arjun
Published: May 2007

Objectives.

To evaluate (1) the framework of the 12 Steps to Prevent Antimicrobial Resistance Among Hospitalized Adults that is part of the Centers for Disease Control and Prevention (CDC) Campaign to Prevent Antimicrobial Resistance in Healthcare Settings, with regard to steps addressing antimicrobial use; and (2) methods of feedback to clinicians regarding antimicrobial use after postprescription review.

Design.

Prospective intervention to identify and modify inappropriate antimicrobial therapy.

Setting.

A 1,000-bed, tertiary care teaching hospital.

Patients.

Inpatients in selected medicine and surgery units receiving broad-spectrum antimicrobials for 48-72 hours.

Interventions.

We created a computer-based clinical-event detection system that automatically identified inpatients taking broad-spectrum and “reserve” antimicrobials for 48-72 hours. Although prior approval was required for initial administration of broad-spectrum and reserve antimicrobials, once approval was obtained, therapy with the antimicrobials could be continued indefinitely at the discretion of the treating clinician. Therapy that was ongoing at 48-72 hours was reviewed by an infectious diseases pharmacist or physician, and when indicated feedback was provided to clinicians to modify or discontinue therapy. Feedback was provided via a direct telephone call, a note on the front of the medical record, or text message sent to the clinician's pager. The acceptance rate of feedback was recorded and recommendations were categorized according to the 12 steps recommended by the CDC.

Results.

Interventions were recommended for 334 (30%) of 1,104 courses of antimicrobial therapy reviewed. A total of 87% of interventions fit into one of the CDC's 12 steps of prevention: 39% into step 3 (“target the pathogen”), 1% into step 4 (“access experts”), 3% into steps 7 and 8 (“treat infection, not colonization or contamination”), 18% into step 9 (“say ‘no’ to vancomycin”), and 26% into step 10 (“stop treatment when no infection”). The rate of compliance with recommendations to improve antimicrobial use was 72%. No differences in compliance were seen with the different methods of feedback.

Conclusions.

Nearly one-third of antimicrobial courses did not follow the CDC's recommended 12 steps for prevention of antimicrobial resistance. Clinicians demonstrated high compliance with following suggestions made after postprescription review, suggesting that it is a useful approach to decreasing and improving antimicrobial use among inpatients.
Increase in the Rate of Sternal Surgical Site Infection After Coronary Artery Bypass Graft: A Marker of Higher Severity of Illness
Authors: Fakih Mohamad G. , Sharma Mamta , Khatib Riad , Berriel-Cass Dorine , Meisner Susan , Harrington Steven , Saravolatz Louis
Published: May 2007

Objective.

To evaluate factors related to a gradual rise in sternal surgical site infection (SSI) rates.

Design.

Retrospective cohort study.

Setting.

A 608-bed, tertiary care teaching hospital.

Patients.

All patients who underwent coronary artery bypass graft (CABG) from January 2000 through September 2004.

Results.

Of 3,578 patients who underwent CABG, 144 (4%) had sternal SSI. There was an increase in infection rate, with a marked reduction in the number of operations per year. The percentage of patients with peripheral vascular disease increased from 12% to 24.3% (P < .001), and the percentage with congestive heart failure increased from 17% to 22% (P < .001). Between 2002 and 2004, the mean duration of surgery increased from 233 to 290 minutes (P < .001), the percentage of patients with a National Nosocomial Infections Surveillance System (NNIS) risk index of 2 increased from 14.3% to 38% (P < .001), and the percentage of patients with a postoperative stay in the intensive care unit of greater than 72 hours increased from 29% to 40.6% (P < .001). Multivariate analysis showed diabetes mellitus, peripheral vascular disease, obesity, duration of surgery, and postoperative stay in the intensive care unit of greater than 72 hours to be independently associated with infection.

Conclusions.

An increase in infection in the CABG population not associated with an outbreak may be a reflection of a change in the severity of illness. Preoperative, intraoperative, and postoperative markers for increased infection risk may be used, in addition to the NNIS risk index, to assess the patient population risk.
AcinetobacterSkin Carriage Among US Army Soldiers Deployed in Iraq
Authors: Griffith Matthew E. , Lazarus Donald R. , Mann Paul B. , Boger John A. , Hospenthal Duane R. , Murray Clinton K.
Published: May 2007

Skin carriage ofAcinetobacter calcoaceticus-baumanniicomplex was not detected among a representative sample of 102 US Army soldiers stationed in Iraq. This observation refutes the hypothesis that preinjury skin carriage serves as the reservoir for theAcinetobacterinfections seen in US military combat casualties.
T-Pile—a package for thermodynamic calculations for biomolecules
Authors: Gront Dominik , Kolinski Andrzej
Published: May 2007

Summary: Molecular dynamics and Monte Carlo, usually conducted in canonical ensemble, deliver a plethora of biomolecular conformations. Proper analysis of the simulation data is a crucial part of biophysical and bioinformatics studies. Sequence alignment problem can be also formulated in terms of Boltzmann distribution. Therefore tools for efficient analysis of canonical ensemble data become extremely valuable. T-Pile package, presented here provides a user-friendly implementation of most important algorithms such as multihistogram analysis and reweighting technique. The package can be used in studies of virtually any system governed by Boltzmann distribution.

Availability: T-Pile can be downloaded from: http://biocomp.chem.uw.edu.pl/services/tpile. These pages provide a comprehensive tutorial and documentation with illustrative examples of applications.

Contact:  dgront@chem.uw.edu.pl

Supplementary information: Supplementary data are available at Bioinformatics online.
Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations
Authors: Toleno Donna M. , Morrell Peter L. , Clegg Michael T.
Published: May 2007

Motivation: Errors in nucleotide sequence and SNP genotyping data are problematic when inferring haplotypes. Previously published methods for error detection in haplotype data make use of pedigree information; however, for many samples, individuals are not related by pedigree. This article describes a method for detecting errors in haplotypes by considering the recombinational history implied by the patterns of variation, three SNPs at a time.

Results: Coalescent simulations provide evidence that the method is robust to high levels of recombination as well as homologous gene conversion, indicating that patterns produced by both proximate and distant SNPs may be useful for detecting unlikely three-site haplotypes.

Availability: The perl script implementing the described method is called EDUT (Error Detection Using Triplets) and is available on request from the authors.

Contact:  mclegg@uci.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
An evaluation of automated homology modelling methods at low target–template sequence similarity
Authors: Dalton James A. R. , Jackson Richard M.
Published: May 2007

Motivation: There are two main areas of difficulty in homology modelling that are particularly important when sequence identity between target and template falls below 50%: sequence alignment and loop building. These problems become magnified with automatic modelling processes, as there is no human input to correct mistakes. As such we have benchmarked several stand-alone strategies that could be implemented in a workflow for automated high-throughput homology modelling. These include three new sequence-structure alignment programs: 3D-Coffee, Staccato and SAlign, plus five homology modelling programs and their respective loop building methods: Builder, Nest, Modeller, SegMod/ENCAD and Swiss-Model. The SABmark database provided 123 targets with at least five templates from the same SCOP family and sequence identities ≤50%.

Results: When using Modeller as the common modelling program, 3D-Coffee outperforms Staccato and SAlign using both multiple templates and the best single template, and across the sequence identity range 20–50%. The mean model RMSD generated from 3D-Coffee using multiple templates is 15 and 28% (or using single templates, 3 and 13%) better than those generated by Staccato and Salign, respectively. 3D-Coffee gives equivalent modelling accuracy from multiple and single templates, but Staccato and SAlign are more successful with single templates, their quality deteriorating as additional lower sequence identity templates are added. Evaluating the different homology modelling programs, on average Modeller performs marginally better in overall modelling than the others tested. However, on average Nest produces the best loops with an 8% improvement by mean RMSD compared to the loops generated by Builder.

Contact:  r.m.jackson@leeds.ac.uk.

Supplementary information: Supplementary data are available at Bioinformatics online.
Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays
Authors: Laakso Marko , Tuupanen Sari , Karhu Auli , Lehtonen Rainer , Aaltonen Lauri A. , Hautaniemi Sampsa
Published: May 2007

Motivation: Single nucleic polymorphisms (SNPs) are one of the most abundant genetic variations in the human genome. Recently, several platforms for high-throughput SNP analysis have become available, capable of measuring thousands of SNPs across the genome. Tools for analysing and visualizing these large genetic data sets in biologically relevant manner are rare. This hinders effective use of the SNP-array data in research on complex diseases, such as cancer.

Results: We describe a computational framework to analyse and visualize SNP-array data, and link the results in relevant databases. Our major objective is to develop methods for identifying DNA regions that likely harbour recessive mutations. Thus, the algorithms are designed to have high sensitivity and the identified regions are ranked using a scoring algorithm. We have also developed annotation tools that automatically query gene IDs, exon counts, microarray probe IDs, etc. In our case study, we apply the methods for identifying candidate regions for recessively inherited colorectal cancer predisposition and suggest directions for wet-lab experiments.

Availability: R-package implementation is available at http://www.ltdk.helsinki.fi/sysbio/csb/downloads/CohortComparator/

Contact:  sampsa.hautaniemi@helsinki.fi

Supplementary information: Supplementary data are available at Bioinformatics online.
Statistical prediction of protein–chemical interactions based on chemical structure and mass spectrometry data
Authors: Nagamine Nobuyoshi , Sakakibara Yasubumi
Published: May 2007

Motivation: Prediction of interactions between proteins and chemical compounds is of great benefit in drug discovery processes. In this field, 3D structure-based methods such as docking analysis have been developed. However, the genomewide application of these methods is not really feasible as 3D structural information is limited in availability.

Results: We describe a novel method for predicting protein–chemical interaction using SVM. We utilize very general protein data, i.e. amino acid sequences, and combine these with chemical structures and mass spectrometry (MS) data. MS data can be of great use in finding new chemical compounds in the future. We assessed the validity of our method in the dataset of the binding of existing drugs and found that more than 80% accuracy could be obtained. Furthermore, we conducted comprehensive target protein predictions for MDMA, and validated the biological significance of our method by successfully finding proteins relevant to its known functions.

Availability: Available on request from the authors.

Contact:  yasu@bio.keio.ac.jp

Supplementary information: Appendix–technical details of method, Supplementary Table 1–7 and Supplementary Figure 1.
Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies
Authors: Feng Jian , Naiman Daniel Q. , Cooper Bret
Published: May 2007

Motivation: In proteomics, reverse database searching is used to control the false match frequency for tandem mass spectrum/peptide sequence matches, but reversal creates sequences devoid of patterns that usually challenge database-search software.

Results: We designed an unsupervised pattern recognition algorithm for detecting patterns with various lengths from large sequence datasets. The patterns found in a protein sequence database were used to create decoy databases using a Monte Carlo sampling algorithm. Searching these decoy databases led to the prediction of false positive rates for spectrum/peptide sequence matches. We show examples where this method, independent of instrumentation, database-search software and samples, provides better estimation of false positive identification rates than a prevailing reverse database searching method. The pattern detection algorithm can also be used to analyze sequences for other purposes in biology or cryptology.

Availability: On request from the authors.

Contact:  Bret.Cooper@ars.usda.gov

Supplementary information:  http://bioinformatics.psb.ugent.be/
The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family
Authors: Fischer Markus , Knoll Michael , Sirim Demet , Wagner Florian , Funke Sonja , Pleiss Juergen
Published: May 2007

Summary: The Cytochrome P450 Engineering Database (CYPED) has been designed to serve as a tool for a comprehensive and systematic comparison of protein sequences and structures within the vast and diverse family of cytochrome P450 monooxygenases (CYPs). The CYPED currently integrates sequence and structure data of 3911 and 25 proteins, respectively. Proteins are grouped into homologous families and superfamilies according to Nelson's classification. Nonclassified CYP sequences are assigned by similarity. Functionally relevant residues are annotated. The web accessible version contains multisequence alignments, phylogenetic trees and HMM profiles. The CYPED is regularly updated and supplies all data for download. Thus, it provides a valuable data source for phylogenetic analysis, investigation of sequence–function relationships and the design of CYPs with improved biochemical properties.

Abbreviations: Cytochrome P450 Engineering Database, CYPED; cytochrome P450 monooxygenase, CYP; Hidden Markov Model, HMM.

Availability:  www.cyped.uni-stuttgart.de

Contact:  Juergen.Pleiss@itb.uni-stuttgart.de
A Randomized Pilot Study of Atractylenolide I on Gastric Cancer Cachexia Patients
Authors: Liu Yi , Jia Zhongwu , Dong Lei , Wang Rui , Qiu Genquan
Published: May 2007

We determined the therapeutic efficacy of atractylenolide I (ATR), extracted from largehead atractylodes rhizome, in managing gastric cancer cachexia (GCC), and interpreted its probable pharmacological mechanism via investigating tumor necrosis factor alpha (TNF‐α), interleukin‐1 (IL‐1), interleukin‐6 (IL‐6) and proteolysis‐inducing factor (PIF). This was a randomized but not‐blinded pilot. The study group (n = 11) received 1.32 g per day of atractylenolide I (ATR) and the control group (n = 11) received 3.6 g per day of fish‐oil‐enriched nutritional supplementation (FOE) for 7 weeks. Conservative therapy was similar in both groups. Clinical [appetite, body weight, mid‐arm muscle circumference (MAMC), Karnofsky performance status (KPS) status], biomarker (TNF‐α, IL‐1, IL‐6 and PIF) were evaluated in the basal state, at the third and seventh weeks. To analyze changes of cytokines, an immumohistochemistry technique was adopted. Base line characteristics were similar in both groups. Effects on MAMC and body weight increase, TNF‐α increase and IL‐1 decreases of serum level were significant in both groups (P < 0.05). ATR was significantly more effective than FOE in improving appetite and KPS status, and decreasing PIF positive rate (P < 0.05). Slight nausea (3/11) and dry mouth (1/11) were shown in intervention groups but did not interrupt treatment. These preliminary findings suggest that ATR might be beneficial in alleviating symptoms, in modulating cytokine and in inhibiting PIF proteolysis of gastric cancer cachexia. Further research using a randomized controlled design is necessary to confirm these pilot study findings.
The Life Threatened Child and the Life Enhancing Clown: Towards a Model of Therapeutic Clowning
Authors: Koller Donna , Gryski Camilla
Published: May 2007

In the last decade, there has been a rapid growth in the presence of clowns in hospitals, particularly in pediatric settings. The proliferation of clowns in health care settings has resulted in varying levels of professionalism and accountability. For this reason, there is a need to examine various forms of clowning, in particular therapeutic clowning in pediatric settings. The purpose of this article is to address what therapeutic clowning is and to describe the extent to which it can provide a complementary form of health care. In an attempt to apply theory to practice, the article will draw upon the experiences of a therapeutic clown within a pediatric setting while providing a historical and theoretical account of how clowns came to be in hospitals. Toward this end, a proposed model of therapeutic clowning will be offered which can be adapted for a variety of settings where children require specialized forms of play in order to enhance their coping, development and adjustment to life changes. Finally, current research on clowning in children′s hospitals will be reviewed including a summary of findings from surveys administered at the Hospital for Sick Children.
Estrogenic Activities of Fatty Acids and a Sterol Isolated from Royal Jelly
Authors: Suzuki Kazu-Michi , Isohama Yoichiro , Maruyama Hiroe , Yamada Yayoi , Narita Yukio , Ohta Shozo , Araki Yoko , Miyata Takeshi , Mishima Satoshi
Published: May 2007

We have previously reported that royal jelly (RJ) from honeybees (Apis mellifera) has weak estrogenic activity mediated by interaction with estrogen receptors that leads to changes in gene expression and cell proliferation. In this study, we isolated four compounds from RJ that exhibit estrogenic activity as evaluated by a ligand‐binding assay for the estrogen receptor (ER) β. These compounds were identified as 10‐hydroxy‐trans‐2‐decenoic acid, 10‐hydroxydecanoic acid, trans‐2‐decenoic acid and 24‐methylenecholesterol. All these compounds inhibited binding of 17β‐estradiol to ERβ, although more weakly than diethylstilbestrol or phytoestrogens. However, these compounds had little or no effect on the binding of 17β‐estradiol to ERα. Expression assays suggested that these compounds activated ER, as evidenced by enhanced transcription of a reporter gene containing an estrogen‐responsive element. Treatment of MCF‐7 cells with these compounds enhanced their proliferation, but concomitant treatment with tamoxifen blocked this effect. Exposure of immature rats to these compounds by subcutaneous injection induced mild hypertrophy of the luminal epithelium of the uterus, but was not associated with an increase in uterine weight. These findings provide evidence that these compounds contribute to the estrogenic effect of RJ.
First International Conference between West and East—Leonardo and Lao‐Tze. Western Science Meets Eastern Wisdom. Experiences of Scientists and Intellectuals for the Creation of a New Paradigm of Modern Science
Authors: Daniele Flavio
Published: May 2007

The Conference was organized and supported by: Nei Dan School (European School of Internal Martial Arts), NIB (Laboratory of Molecular Biology and Stem Cell Bioengineering, National Institute of Biostructures and Biosystems, Institute of Cardiology, S.Orsola‐Malpighi Hospital, Bologna), WACIMA (Worldwide Association Chinese Internal Martial Arts), Arti D’Oriente (Magazine of Eastern culture and traditions), Nuovo Orizzonte (Taiji Quan School in Florence), Samurai (Journal on Martial Arts), and Pinus (First National Institute for the Unification of Medical Strategies). Nei Dan School (www.taichineidan.com, neidan@libero.it) was in charge of the organization. Future meetings of the Centro studi ‘Tao and Science’ will take place in spring 2007 in Firenze and in October 2007 in Bologna. For information: E‐mail: neidan@libero.it; web site: www.taichineidan.com, www.taoandscience.com.
The Treatment of Pulmonary Diseases and Respiratory‐Related Conditions with Inhaled (Nebulized or Aerosolized) Glutathione
Authors: Prousky Jonathan
Published: May 2007

Reduced glutathione or simply glutathione (γ‐glutamylcysteinylglycine; GSH) is found in the cytosol of most cells of the body. GSH in the epithelial lining fluid (ELF) of the lower respiratory tract is thought to be the first line of defense against oxidative stress. Inhalation (nebulized or aerosolized) is the only known method that increases GSH′s levels in the ELF. A review of the literature was conducted to examine the clinical effectiveness of inhaled GSH as a treatment for various pulmonary diseases and respiratory‐related conditions. This report also discusses clinical and theoretical indications for GSH inhalation, potential concerns with this treatment, its presumed mechanisms of action, optimal doses to be administered and other important details. Reasons for inhaled GSH′s effectiveness include its role as a potent antioxidant, and possibly improved oxygenation and host defenses. Theoretical uses of this treatment include Farmer′s lung, pre‐ and postexercise, multiple chemical sensitivity disorder and cigarette smoking. GSH inhalation should not be used as a treatment for primary lung cancer. Testing for sulfites in the urine is recommended prior to GSH inhalation. Minor side effects such as transient coughing and an unpleasant odor are common with this treatment. Major side effects such as bronchoconstriction have only occurred among asthma patients presumed to be sulfite‐sensitive. The potential applications of inhaled GSH are numerous when one considers just how many pulmonary diseases and respiratory‐related conditions are affected by deficient antioxidant status or an over production of oxidants, poor oxygenation and/or impaired host defenses. More studies are clearly warranted.
Humor and Laughter May Influence Health: III. Laughter and Health Outcomes
Authors: Bennett Mary Payne , Lengacher Cecile
Published: May 2007

This is part three of a four‐part series reviewing the evidence on how humor influences physiological and psychological well‐being. The first article included basic background information, definitions and a review of the theoretical underpinnings for this area of research. The second article discussed use of humor as a complementary therapy within various clinical samples, as well as evidence concerning how a sense of humor influences physiological and psychological wellbeing. This third article examines how laughter influences health outcomes; including muscle tension, cardio‐respiratory functioning and various stress physiology measures.