bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel software package for cross-platform transcriptome analysis (CPTRA)
Authors: Zhou Xin , Su Zhen , Sammons R Douglas , Peng Yanhui , Tranel Patrick J , Stewart C Neal , Yuan Joshua S
Published: October 2009

Background

Next-generation sequencing techniques enable several novel transcriptome profiling approaches. Recent studies indicated that digital gene expression profiling based on short sequence tags has superior performance as compared to other transcriptome analysis platforms including microarrays. However, the transcriptomic analysis with tag-based methods often depends on available genome sequence. The use of tag-based methods in species without genome sequence should be complemented by other methods such as cDNA library sequencing. The combination of different next generation sequencing techniques like 454 pyrosequencing and Illumina Genome Analyzer (Solexa) will enable high-throughput and accurate global gene expression profiling in species with limited genome information. The combination of transcriptome data acquisition methods requires cross-platform transcriptome data analysis platforms, including a new software package for data processing.

Results

Here we presented a software package, CPTRA: C ross-P latform TR anscriptome A nalysis, to analyze transcriptome profiling data from separate methods. The software package is available at http://people.tamu.edu/~syuan/cptra/cptra.html. It was applied to the case study of non-target site glyphosate resistance in horseweed; and the data was mined to discover resistance target gene(s). For the software, the input data included a long-read sequence dataset with proper annotation, and a short-read sequence tag dataset for the quantification of transcripts. By combining the two datasets, the software carries out the unique sequence tag identification, tag counting for transcript quantification, and cross-platform sequence matching functions, whereby the short sequence tags can be annotated with a function, level of expression, and Gene Ontology (GO) classification. Multiple sequence search algorithms were implemented and compared. The analysis highlighted the importance of transport genes in glyphosate resistance and identified several candidate genes for down-stream analysis.

Conclusion

CPTRA is a powerful software package for next generation sequencing-based transcriptome profiling in species with limited genome information. According to our case study, the strategy can greatly broaden the application of the next generation sequencing for transcriptome analysis in species without reference genome sequence.
An automated proteomic data analysis workflow for mass spectrometry
Authors: Pendarvis Ken , Kumar Ranjit , Burgess Shane C , Nanduri Bindu
Published: October 2009

Background

Mass spectrometry-based protein identification methods are fundamental to proteomics. Biological experiments are usually performed in replicates and proteomic analyses generate huge datasets which need to be integrated and quantitatively analyzed. The Sequest™ search algorithm is a commonly used algorithm for identifying peptides and proteins from two dimensional liquid chromatography electrospray ionization tandem mass spectrometry (2-D LC ESI MS2) data. A number of proteomic pipelines that facilitate high throughput 'post data acquisition analysis' are described in the literature. However, these pipelines need to be updated to accommodate the rapidly evolving data analysis methods. Here, we describe a proteomic data analysis pipeline that specifically addresses two main issues pertinent to protein identification and differential expression analysis: 1) estimation of the probability of peptide and protein identifications and 2) non-parametric statistics for protein differential expression analysis. Our proteomic analysis workflow analyzes replicate datasets from a single experimental paradigm to generate a list of identified proteins with their probabilities and significant changes in protein expression using parametric and non-parametric statistics.

Results

The input for our workflow is Bioworks™ 3.2 Sequest (or a later version, including cluster) output in XML format. We use a decoy database approach to assign probability to peptide identifications. The user has the option to select "quality thresholds" on peptide identifications based on the P value. We also estimate probability for protein identification. Proteins identified with peptides at a user-specified threshold value from biological experiments are grouped as either control or treatment for further analysis in ProtQuant. ProtQuant utilizes a parametric (ANOVA) method, for calculating differences in protein expression based on the quantitative measure ΣXcorr. Alternatively ProtQuant output can be further processed using non-parametric Monte-Carlo resampling statistics to calculate P values for differential expression. Correction for multiple testing of ANOVA and resampling P values is done using Benjamini and Hochberg's method. The results of these statistical analyses are then combined into a single output file containing a comprehensive protein list with probabilities and differential expression analysis, associated P values, and resampling statistics.

Conclusion

For biologists carrying out proteomics by mass spectrometry, our workflow facilitates automated, easy to use analyses of Bioworks (3.2 or later versions) data. All the methods used in the workflow are peer-reviewed and as such the results of our workflow are compliant with proteomic data submission guidelines to public proteomic data repositories including PRIDE. Our workflow is a necessary intermediate step that is required to link proteomics data to biological knowledge for generating testable hypotheses.
Graph ranking for exploratory gene data analysis
Authors: Gao Cuilan , Dang Xin , Chen Yixin , Wilkins Dawn
Published: October 2009

Background

Microarray technology has made it possible to simultaneously monitor the expression levels of thousands of genes in a single experiment. However, the large number of genes greatly increases the challenges of analyzing, comprehending and interpreting the resulting mass of data. Selecting a subset of important genes is inevitable to address the challenge. Gene selection has been investigated extensively over the last decade. Most selection procedures, however, are not sufficient for accurate inference of underlying biology, because biological significance does not necessarily have to be statistically significant. Additional biological knowledge needs to be integrated into the gene selection procedure.

Results

We propose a general framework for gene ranking. We construct a bipartite graph from the Gene Ontology (GO) and gene expression data. The graph describes the relationship between genes and their associated molecular functions. Under a species condition, edge weights of the graph are assigned to be gene expression level. Such a graph provides a mathematical means to represent both species-independent and species-dependent biological information. We also develop a new ranking algorithm to analyze the weighted graph via a kernelized spatial depth (KSD) approach. Consequently, the importance of gene and molecular function can be simultaneously ranked by a real-valued measure, KSD, which incorporates the global and local structure of the graph. Over-expressed and under-regulated genes also can be separately ranked.

Conclusion

The gene-function bigraph integrates molecular function annotations into gene expression data. The relevance of genes is described in the graph (through a common function). The proposed method provides an exploratory framework for gene data analysis.
Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom
Authors: Xu Zhanyou , Zhang Dandan , Hu Jun , Zhou Xin , Ye Xia , Reichel Kristen L , Stewart Nathan R , Syrenne Ryan D , Yang Xiaohan , Gao Peng , Shi Weibing , Doeppke Crissa , Sykes Robert W , Burris Jason N , Bozell Joseph J , Cheng Max Zong-Ming , Hayes Douglas G , Labbe Nicole , Davis Mark , Stewart C Neal , Yuan Joshua S
Published: October 2009

Background

As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modification has been a major task for bioenergy feedstock improvement. The study of the evolution and function of lignin biosynthesis genes thus has two-fold implications. First, the lignin biosynthesis pathway provides an excellent model to study the coordinative evolution of a biochemical pathway in plants. Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement.

Results

We analyzed lignin biosynthesis genes from fourteen plant species and one symbiotic fungal species. Comprehensive comparative genome analysis was carried out to study the distribution, relatedness, and family expansion of the lignin biosynthesis genes across the plant kingdom. In addition, we also analyzed the comparative synteny map between rice and sorghum to study the evolution of lignin biosynthesis genes within the Poaceae family and the chromosome evolution between the two species. Comprehensive lignin biosynthesis gene expression analysis was performed in rice, poplar and Arabidopsis. The representative data from rice indicates that different fates of gene duplications exist for lignin biosynthesis genes. In addition, we also carried out the biomass composition analysis of nine Arabidopsis mutants with both MBMS analysis and traditional wet chemistry methods. The results were analyzed together with the genomics analysis.

Conclusion

The research revealed that, among the species analyzed, the complete lignin biosynthesis pathway first appeared in moss; the pathway is absent in green algae. The expansion of lignin biosynthesis gene families correlates with substrate diversity. In addition, we found that the expansion of the gene families mostly occurred after the divergence of monocots and dicots, with the exception of the C4H gene family. Gene expression analysis revealed different fates of gene duplications, largely confirming plants are tolerant to gene dosage effects. The rapid expansion of lignin biosynthesis genes indicated that the translation of transgenic lignin modification strategies from model species to bioenergy feedstock might only be successful between the closely relevant species within the same family.
Structural and functional-annotation of an equine whole genome oligoarray
Authors: Bright Lauren A , Burgess Shane C , Chowdhary Bhanu , Swiderski Cyprianna E , McCarthy Fiona M
Published: October 2009

Background

The horse genome is sequenced, allowing equine researchers to use high-throughput functional genomics platforms such as microarrays; next-generation sequencing for gene expression and proteomics. However, for researchers to derive value from these functional genomics datasets, they must be able to model this data in biologically relevant ways; to do so requires that the equine genome be more fully annotated. There are two interrelated types of genomic annotation: structural and functional. Structural annotation is delineating and demarcating the genomic elements (such as genes, promoters, and regulatory elements). Functional annotation is assigning function to structural elements. The Gene Ontology (GO) is the de facto standard for functional annotation, and is routinely used as a basis for modelling and hypothesis testing, large functional genomics datasets.

Results

An Equine Whole Genome Oligonucleotide (EWGO) array with 21,351 elements was developed at Texas A&M University. This 70-mer oligoarray was designed using the approximately 7× assembled and annotated sequence of the equine genome to be one of the most comprehensive arrays available for expressed equine sequences. To assist researchers in determining the biological meaning of data derived from this array, we have structurally annotated it by mapping the elements to multiple database accessions, including UniProtKB, Entrez Gene, NRPD (Non-Redundant Protein Database) and UniGene. We next provided GO functional annotations for the gene transcripts represented on this array. Overall, we GO annotated 14,531 gene products (68.1% of the gene products represented on the EWGO array) with 57,912 annotations. GAQ (GO Annotation Quality) scores were calculated for this array both before and after we added GO annotation. The additional annotations improved the meanGAQ score 16-fold. This data is publicly available at AgBase
http://www.agbase.msstate.edu/.

Conclusion

Providing additional information about the public databases which link to the gene products represented on the array allows users more flexibility when using gene expression modelling and hypothesis-testing computational tools. Moreover, since different databases provide different types of information, users have access to multiple data sources. In addition, our GO annotation underpins functional modelling for most gene expression analysis tools and enables equine researchers to model large lists of differentially expressed transcripts in biologically relevant ways.
Phylogeny and evolutionary history of Leymus(Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase
Authors: Fan Xing , Sha Li-Na , Yang Rui-Wu , Zhang Hai-Qin , Kang Hou-Yang , Ding Cun-Bang , Zhang Li , Zheng You-Liang , Zhou Yong-Hong
Published: October 2009

Background

Single- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa.Leymusis a polyploid genus with a diverse array of morphology, ecology and distribution in Triticeae. The genomic constitution ofLeymuswas assigned as NsXm, where Ns was presumed to be originated fromPsathyrostachys, while Xm represented a genome of unknown origin. In addition, little is known about the evolutionary history ofLeymus. Here, we investigate the phylogenetic relationship, genome donor, and evolutionary history ofLeymusbased on a single-copy nuclearAcc1gene.

Results

Two homoeologues of theAcc1gene were isolated from nearly all the sampledLeymusspecies using allele-specific primer and were analyzed with those from 35 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1)Leymusis closely related toPsathyrostachys,Agropyron, andEremopyrum; (2)Psathyrostachys junceais an ancestral Ns-genome donor ofLeymusspecies; (3) the Xm genome inLeymusmay be originated from an ancestral lineage ofAgropyronandEremopyrum triticeum; (4) theAcc1sequences ofLeymusspecies from the Qinghai-Tibetan plateau are evolutionarily distinct; (5) North AmericaLeymusspecies might originate from colonization via the Bering land bridge; (6)Leymusoriginated about 11-12MYA in Eurasia, and adaptive radiation might have occurred inLeymusduring the period of 3.7-4.3 MYA and 1.7-2.1 MYA.

Conclusion

Leymusspecies have allopolyploid origin. It is hypothesized that the adaptive radiation ofLeymusspecies might have been triggered by the recent upliftings of the Qinghai-Tibetan plateau and subsequent climatic oscillations. Adaptive radiation may have promoted the rapid speciation, as well as the fixation of unique morphological characters inLeymus. Our results shed new light on our understanding of the origin of Xm genome, the polyploidization events and evolutionary history ofLeymusthat could account for the rich diversity and ecological adaptation ofLeymusspecies.
AI-2 does not function as a quorum sensing molecule in Campylobacter jejuni during exponential growth in vitro
Authors: Holmes Kathryn , Tavender Tim J , Winzer Klaus , Wells Jerry M , Hardie Kim R
Published: October 2009

Background

Campylobacter jejuni contains a homologue of the luxS gene shown to be responsible for the production of the signalling molecule autoinducer-2 (AI-2) in Vibrio harveyi and Vibrio cholerae. The aim of this study was to determine whether AI-2 acted as a diffusible quorum sensing signal controlling C. jejuni gene expression when it is produced at high levels during mid exponential growth phase.

Results

AI-2 activity was produced by the parental strain NCTC 11168 when grown in rich Mueller-Hinton broth (MHB) as expected, but interestingly was not present in defined Modified Eagles Medium (MEM-α). Consistent with previous studies, the luxS mutant showed comparable growth rates to the parental strain and exhibited decreased motility halos in both MEM-α and MHB. Microarray analysis of genes differentially expressed in wild type and luxS mutant strains showed that many effects on mRNA transcript abundance were dependent on the growth medium and linked to metabolic functions including methionine metabolism. Addition of exogenously produced AI-2 to the wild type and the luxS mutant, growing exponentially in either MHB or MEM-α did not induce any transcriptional changes as analysed by microarray.

Conclusion

Taken together these results led us to conclude that there is no evidence for the role of AI-2 in cell-to-cell communication in C. jejuni strain NCTC 11168 under the growth conditions used, and that the effects of the luxS mutation on the transcriptome are related to the consequential loss of function in the activated methyl cycle.
Vitamin C supplement use may protect against gallstones: an observational study on a randomly selected population
Authors: Walcher Thomas , Haenle Mark M , Kron Martina , Hay Birgit , Mason Richard A , Walcher Daniel , Steinbach Gerald , Kern Peter , Piechotowski Isolde , Adler Guido , Boehm Bernhard O , Koenig Wolfgang , Kratzer Wolfgang ,   the EMIL study group
Published: October 2009

Background

Animal experiments have shown a protective effect of vitamin C on the formation of gallstones. Few data in humans suggest an association between reduced vitamin C intake and increased prevalence of gallstone disease. The aim of this study was to assess the possible association of regular vitamin C supplementation with gallstone prevalence.

Methods

An observational, population-based study of 2129 subjects aged 18-65 years randomly selected from the general population in southern Germany was conducted. Abdominal ultrasound examination, completion of a standardized questionnaire, compilation of anthropometric data and blood tests were used. Data were collected in November and December 2002. Data analysis was conducted between December 2005 and January 2006.

Results

Prevalence of gallstones in the study population was 7.8% (167/2129). Subjects reporting vitamin C supplementation showed a prevalence of 4.7% (11/232), whereas in subjects not reporting regular vitamin C supplementation, the prevalence was 8.2% (156/1897). Female gender, hereditary predisposition, increasing age and body-mass index (BMI) were associated with increased prevalence of gallstones. Logistic regression with backward elimination adjusted for these factors showed reduced gallstone prevalence for vitamin C supplementation (odds ratio, OR 0.34; 95% confidence interval, CI 0.14 to 0.81; P = 0.01), increased physical activity (OR 0.62; 95% CI, 0.42 to 0.94; P = 0.02), and higher total cholesterol (OR 0.65; 95% CI, 0.52 to 0.79; P < 0.001).

Conclusion

Regular vitamin C supplementation and, to a lesser extent, increased physical activity and total cholesterol levels are associated with a reduced prevalence of gallstones. Regular vitamin C supplementation might exert a protective effect on the development of gallstones.
Influence of the RNase H domain of retroviral reverse transcriptases on the metal specificity and substrate selection of their polymerase domains
Authors: Talele Tanaji T , Upadhyay Alok , Pandey Virendra N
Published: October 2009

Reverse transcriptases from HIV-1 and MuLV respectively prefer Mg2+ and Mn2+ for their polymerase activity, with variable fidelity, on both RNA and DNA templates. The function of the RNase H domain with respect to these parameters is not yet understood. To evaluate this function, two chimeric enzymes were constructed by swapping the RNase H domains between HIV-1 RT and MuLV RT. Chimeric HIV-1 RT, having the RNase H domain of MuLV RT, inherited the divalent cation preference characteristic of MuLV RT on the DNA template with no significant change on the RNA template. Chimeric MuLV RT, likewise partially inherited the metal ion preference of HIV-1 RT. Unlike the wild-type MuLV RT, chimeric MuLV RT is able to use both Mn.dNTP and Mg.dNTP on the RNA template with similar efficiency, while a 30-fold higher preference for Mn.dNTP was seen on the DNA template. The metal preferences for the RNase H activity of chimeric HIV-1 RT and chimeric MuLV RT were, respectively, Mn2+ and Mg2+, a property acquired through their swapped RNase H domains. Chimeric HIV-1 RT displayed higher fidelity and discrimination against rNTPs than against dNTPs substrates, a property inherited from MuLV RT. The overall fidelity of the chimeric MuLV RT was decreased in comparison to the parental MuLV RT, suggesting that the RNase H domain profoundly influences the function of the polymerase domain.
Human stool contains a previously unrecognized diversity of novel astroviruses
Authors: Finkbeiner Stacy R , Holtz Lori R , Jiang Yanfang , Rajendran Priya , Franz Carl J , Zhao Guoyan , Kang Gagandeep , Wang David
Published: October 2009

Human astroviruses are a leading cause of gastrointestinal disease. Since their discovery in 1975, 8 closely related serotypes have been described in humans, and more recently, two new astrovirus species, astrovirus MLB1 and astrovirus VA1, were identified in diarrhea patients. In this study, we used consensus astrovirus primers targeting the RNA polymerase to define the diversity of astroviruses present in pediatric patients with diarrhea on two continents. From 416 stool specimens comprising two different cohorts from Vellore, India, 35 samples were positive. These positive samples were analyzed further by either sequencing of the ~400 bp amplicon generated by the consensus PCR or by performing additional RT-PCR specific for individual astroviruses. 19 samples contained the classic human astrovirus serotypes 1-8 while 7 samples were positive for the recently described astrovirus MLB1. Strikingly, from samples that were positive in the consensus PCR screen but negative in the specific PCR assays, five samples contained sequences that were highly divergent from all previously described astroviruses. Sequence analysis suggested that three novel astroviruses, tentatively named astroviruses VA2, MLB2 and VA3, were present in these five patient specimens (AstV-VA2 in 2 patients, AstV-MLB2 in 2 patients and AstV-VA3 in one patient). Using the same RT-PCR screening strategy, 13 samples out of 466 tested stool specimens collected in St. Louis, USA were positive. Nine samples were positive for the classic human astroviruses. One sample was positive for AstV-VA2, and 3 samples were positive for AstV-MLB2 demonstrating that these two viruses are globally widespread. Collectively, these findings underscore the tremendous diversity of astroviruses present in fecal specimens from diarrhea patients. Given that a significant fraction of diarrhea etiologies is currently unknown, it is plausible that these or other yet unrecognized astroviruses may be responsible for at least part of the undiagnosed cases.
Antiretroviral treatment outcomes from a nurse‐driven, community‐supported HIV/AIDS treatment programme in rural Lesotho: observational cohort assessment at two years
Authors: Cohen Rachel , Lynch Sharonann , Bygrave Helen , Eggers Evi , Vlahakis Natalie , Hilderbrand Katherine , Knight Louise , Pillay Prinitha , Saranchuk Peter , Goemaere Eric , Makakole Lipontso , Ford Nathan
Published: October 2009

Introduction

Lesotho has the third highest HIV prevalence in the world (an adult prevalence of 23.2%). Despite a lack of resources for health, the country has implemented state‐of‐the‐art antiretroviral treatment guidelines, including early initiation of treatment (<350 cells/mm3), tenofovir in first line, and nurse‐initiated and managed HIV care, including antiretroviral therapy (ART), at primary health care level.

Programme approach

We describe two‐year outcomes of a decentralized HIV/AIDS care programme run by Doctors Without Borders/Médecins Sans Frontières, the Ministry of Health and Social Welfare, and the Christian Health Association of Lesotho in Scott catchment area, a rural health zone covering 14 clinics and one district hospital. Outcome data are described through a retrospective cohort analysis of adults and children initiated on ART between 2006 and 2008.

Discussion and Evaluation

Overall, 13,243 people have been enrolled in HIV care (5% children), and 5376 initiated on ART (6.5% children), 80% at primary care level. Between 2006 and 2008, annual enrolment more than doubled for adults and children, with no major external increase in human resources. The proportion of adults arriving sick (CD4 <50 cells/mm3) decreased from 22.2% in 2006 to 11.9% in 2008. Twelve‐month outcomes are satisfactory in terms of mortality (11% for adults; 9% for children) and loss to follow up (8.8%). At 12 months, 80% of adults and 89% of children were alive and in care, meaning they were still taking their treatment; at 24 months, 77% of adults remained in care.

Conclusion

Despite major resource constraints, Lesotho is comparing favourably with its better resourced neighbour, using the latest international ART recommendations. The successful two‐year outcomes are further evidence that HIV/AIDS care and treatment can be provided effectively at the primary care level. The programme highlights how improving HIV care strengthened the primary health care system, and validates several critical areas for task shifting that are being considered by other countries in the region, including nurse‐driven ART for adults and children, and lay counsellor‐supported testing and counselling, adherence and case management.
Melanocortin peptides inhibit urate crystal-induced activation of phagocytic cells
Authors: Capsoni Franco , Ongari Anna Maria , Reali Eva , Catania Anna
Published: October 2009

Introduction

The melanocortin peptides have marked anti-inflammatory potential, primarily through inhibition of proinflammatory cytokine production and action on phagocytic cell functions. Gout is an acute form of arthritis caused by the deposition of urate crystals, in which phagocytic cells and cytokines play a major pathogenic role. We examined whether alpha-melanocyte-stimulating hormone (α-MSH) and its synthetic derivative (CKPV)2 influence urate crystal-induced monocyte (Mo) activation and neutrophil responses in vitro.

Methods

Purified Mos were stimulated with monosodium urate (MSU) crystals in the presence or absence of melanocortin peptides. The supernatants were tested for their ability to induce neutrophil activation in terms of chemotaxis, production of reactive oxygen intermediates (ROIs), and membrane expression of CD11b, Toll-like receptor-2 (TLR2) and TLR4. The proinflammatory cytokines interleukin (IL)-1β, IL-8, and tumor necrosis factor-alpha (TNF-α) and caspase-1 were determined in the cell-free supernatants. In parallel experiments, purified neutrophils were preincubated overnight with or without melanocortin peptides before the functional assays.

Results

The supernatants from MSU crystal-stimulated Mos exerted chemoattractant and priming activity on neutrophils, estimated as ROI production and CD11b membrane expression. The supernatants of Mos stimulated with MSU in the presence of melanocortin peptides had less chemoattractant activity for neutrophils and less ability to prime neutrophils for CD11b membrane expression and oxidative burst. MSU crystal-stimulated Mos produced significant levels of IL-1β, IL-8, TNF-α, and caspase-1. The concentrations of proinflammatory cytokines, but not of caspase-1, were reduced in the supernatants from Mos stimulated by MSU crystals in the presence of melanocortin peptides. Overnight incubation of neutrophils with the peptides significantly inhibited their ability to migrate toward chemotactic supernatants and their capacity to be primed in terms of ROI production.

Conclusions

α-MSH and (CKPV)2 have a dual effect on MSU crystal-induced inflammation, inhibiting the Mos' ability to produce neutrophil chemoattractants and activating compounds and preventing the neutrophil responses to these proinflammatory substances. These findings reinforce previous observations on the potential role of α-MSH and related peptides as a new class of drugs for treatment of inflammatory arthritis.
Electrical muscle stimulation preserves the muscle mass of critically ill patients: a randomized study
Authors: Gerovasili Vasiliki , Stefanidis Konstantinos , Vitzilaios Konstantinos , Karatzanos Eleftherios , Politis Panagiotis , Koroneos Apostolos , Chatzimichail Aikaterini , Routsi Christina , Roussos Charis , Nanas Serafim
Published: October 2009

Introduction

Critically ill patients are characterized by increased loss of muscle mass, partially attributed to sepsis and multiple organ failure, as well as immobilization. Recent studies have shown that electrical muscle stimulation (EMS) may be an alternative to active exercise in chronic obstructive pulmonary disease (COPD) and chronic heart failure (CHF) patients with myopathy. The aim of our study was to investigate the EMS effects on muscle mass preservation of critically ill patients with the use of ultrasonography (US).

Methods

Forty-nine critically ill patients (age: 59 ± 21 years) with an APACHE II admission score ≥13 were randomly assigned after stratification upon admission to receive daily EMS sessions of both lower extremities (EMS-group) or to the control group (control group). Muscle mass was evaluated with US, by measuring the cross sectional diameter (CSD) of the vastus intermedius and the rectus femoris of the quadriceps muscle.

Results

Twenty-six patients were finally evaluated. Right rectus femoris and right vastus intermedius CSD decreased in both groups (EMS group: from 1.42 ± 0.48 to 1.31 ± 0.45 cm, P = 0.001 control group: from 1.59 ± 0.53 to 1.37 ± 0.5 cm, P = 0.002; EMS group: from 0.91 ± 0.39 to 0.81 ± 0.38 cm, P = 0.001 control group: from 1.40 ± 0.64 to 1.11 ± 0.56 cm, P = 0.004, respectively). However, the CSD of the right rectus femoris decreased significantly less in the EMS group (-0.11 ± 0.06 cm, -8 ± 3.9%) as compared to the control group (-0.21 ± 0.10 cm, -13.9 ± 6.4%; P < 0.05) and the CSD of the right vastus intermedius decreased significantly less in the EMS group (-0.10 ± 0.05 cm, -12.5 ± 7.4%) as compared to the control group (-0.29 ± 0.28 cm, -21.5 ± 15.3%; P < 0.05).

Conclusions

EMS is well tolerated and seems to preserve the muscle mass of critically ill patients. The potential use of EMS as a preventive and rehabilitation tool in ICU patients with polyneuromyopathy needs to be further investigated.

Trial Registration

clinicaltrials.gov: NCT00882830
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genomes
Authors: Jiang Cizhong , Pugh B Franklin
Published: October 2009

Nucleosomes have position-specific functions in controlling gene expression. A complete systematic genome-wide reference map of absolute and relative nucleosome positions is needed to minimize potential confusion when referring to the function of individual nucleosomes (or nucleosome-free regions) across datasets. We compiled six high-resolution genome-wide maps of Saccharomyces cerevisiae nucleosome positions from multiple labs and detection platforms, and report new insights. Data downloads, reference position assignment software, queries, and a visualization browser are available online http://atlas.bx.psu.edu/.
A randomized double-blind comparison of moxifloxacin and doxycycline/metronidazole/ciprofloxacin in the treatment of acute, uncomplicated pelvic inflammatory disease
Authors: Heystek M , Ross J D C
Published: October 2009

This multicentre, double-blind study was undertaken to demonstrate non-inferiority of once-daily oral moxifloxacin compared with combination therapy in the management of acute, uncomplicated pelvic inflammatory disease (PID). Women aged ≥18 years with PID were randomized to receive moxifloxacin (400 mg once daily) for 14 days or comparator treatment (doxycycline [100 mg twice daily] plus metronidazole [400 mg three times daily] for 14 days, plus one single 500-mg ciprofloxacin dose). Of the 434 valid per protocol (PP) patients, the overall clinical success rates at 2–14 days post-therapy were 96.6% (moxifloxacin) and 98.0% (comparator); moxifloxacin was non-inferior to the comparator regimen both in the PP (95% confidence interval [CI]: −4.5, 1.6) and intent-to-treat (95% CI: −5.8, 6.9) populations. Clinical success rates at 21–35 days post-therapy were 93.8% (166/177; data missing for 47 patients) for moxifloxacin and 91.3% (147/161; data missing for 37 patients) for the comparator. Bacteriological success rates at 2–14 days post-therapy were 92.5% (moxifloxacin) and 88.2% (comparator). Once-daily dosing and proven efficacy suggest that moxifloxacin may be of value in acute, uncomplicated PID.
Preliminary HIV test result disclosure: lessons we can learn
Authors: Tayal S , Chawla G
Published: October 2009

Result disclosure following routine HIV testing can be challenging. We present an interesting real life scenario regarding a young heterosexual Caucasian male patient, who was diagnosed as having a positive HIV antibody result following a routine HIV screening test, his confirmatory test result was HIV negative. This article covers important lessons learnt from the case.
Successful treatment of a large Buschke–Lowenstein tumour with chemo-radiotherapy
Authors: Armstrong N , Foley G , Wilson J , Finan P , Sebag-Montefiore D
Published: October 2009

We report the case of a patient with a large Buschke–Lowenstein tumour which had previously recurred following local excision. A preferred treatment modality for this rare variant of human papillomavirus has not been clearly defined. Treatment with chemo-radiotherapy in this case resulted in complete resolution of the disease without the need for further surgical intervention.
What service users want: a new clinic results service. Can we satisfy both patients' needs and wants?
Authors: Challenor R , Deegan S
Published: October 2009

Many clinics still have a ‘no news is good news’ (NNIGN) policy for clinic results. We asked our service users their preferences for obtaining results. We also designed a new clinic results service. Patients were invited to complete a service evaluation questionnaire. They were given nine options for obtaining results and asked to rate acceptability on a 1–9 scale (unacceptable to acceptable). Completed questionnaires were compared with the actual method they chose to obtain results for that visit. In all, 1000 questionnaires (561 females, 439 males) were completed. Average acceptability score was highest for mobile phone (7.7), followed by text (5.8) and letter (5.7). NNIGN (3.7) and returning for results (3.6) received the least popular ratings. When compared with the actual method chosen, mobile phone was the most popular (62%) followed by letter (17%). Only 10% of patients found NNIGN acceptable. Following the evaluation we purchased texting software and redesigned our results service. There are now four options for receiving results – texting, letter, patient telephones us and NNIGN. We believe we have been able to satisfy both patients' needs and their wishes by redesigning our service around their views.
Locating Objects in the Plane Using Global Optimization Techniques
Authors: Blanquero Rafael , Carrizosa Emilio , Hansen Pierre
Published: October 2009

We address the problem of locating objects in the plane such as segments, arcs of circumferences, arbitrary convex sets, their complements or their boundaries. Given a set of points, we seek the rotation and translation for such an object optimizing a very general performance measure, which includes as a particular case the classical objectives in semi-obnoxious facility location. In general, the above-mentioned model yields a global optimization problem, whose resolution is dealt with using difference of convex (DC) techniques such as outer approximation or branch and bound.
Bid-Price Controls for Network Revenue Management: Martingale Characterization of Optimal Bid Prices
Authors: Akan Mustafa , Ata Barış
Published: October 2009

We consider a continuous-time, rate-based model of network revenue management. Under mild assumptions, we construct a simple ε-optimal bid-price control, which can be viewed as a perturbation of a bid-price control in the classical sense [Williamson, E. L. 1992. Airline network seat control. Ph.D. thesis, MIT, Cambridge, MA]. We show that the associated bid-price process forms a martingale and the corresponding booking controls converge in an appropriate sense to an optimal control as ε tends to 0. Moreover, we show that there exists an optimal generalized bid-price control, where the bid-price process forms a martingale and is used in conjunction with a capacity usage limit process. We also discuss its connection to the bid-price controls in the classical sense and sufficient conditions for the (near) optimality of the latter.
Equilibrium Capacity Expansion Under Stochastic Demand Growth
Authors: Garcia Alfredo , Shen Zhijiang
Published: October 2009

In critical energy infrastructure sectors (e.g., electric power generation, natural gas transportation, oil-refining capacity), maintaining a certain level of excess capacity is socially valuable (because it serves to protect against unexpected market conditions) but not necessarily compatible with the incentives for individual firms in the market. In this paper, we develop a dynamic oligopoly model with a stochastically growing demand to analyze the inherent tension in market-based incentives for capacity expansion where capacity additions take place over long time lags. Our results indicate that the market fails to induce the socially optimal level of capacity. However, the magnitude of this failure varies greatly as a function of entry costs and the relative profitability of investments in the market (as measured by the ratio of maximum markup over production costs and investment costs). In general, the likelihood of insufficient capacity in equilibrium increases with decreasing probability of demand growth, increasing discount and depreciation rates, and/or increasing investment and/or production costs. We discuss the public policy implications of our results.
Bounds and Heuristics for Optimal Bayesian Inventory Control with Unobserved Lost Sales
Authors: Chen Li
Published: October 2009

In most retail environments, when inventory runs out, the unmet demand is lost and not observed. The sales data are effectively censored by the inventory level. Factoring this censored data effect into demand estimation and inventory control decision makes the problem difficult to solve. In this paper, we focus on developing bounds and heuristics for this problem. Specifically, we consider a finite-horizon inventory control problem for a nonperishable product with unobserved lost sales and a demand distribution having an unknown parameter. The parameter is estimated sequentially by the Bayesian updating method. We first derive a set of solution upper bounds that work for all prior and demand distributions. For a fairly general monotone likelihood-ratio distribution family, we derive relaxed but easily computable lower and upper bounds along an arbitrary sample path. We then propose two heuristics. The first heuristic is derived from the solution bound results. Computing this heuristic solution only requires the evaluation of the objective function in the observed lost-sales case. The second heuristic is based on the approximation of the first-order condition. We combine the first-order derivatives of the simpler observed lost-sales and perishable-inventory models to obtain the approximation. For the latter case, we obtain a recursive formula that simplifies the computation. Finally, we conduct an extensive numerical study to evaluate and compare the bounds and heuristics. The numerical results indicate that both heuristics perform very well. They outperform the myopic policies by a wide margin.
Balancing Exploration and Exploitation Through Structural Design: The Isolation of Subgroups and Organizational Learning
Authors: Fang Christina , Lee Jeho , Schilling Melissa A.
Published: October 2009

The classic trade-off between exploration and exploitation in organizational learning has attracted vigorous attention by researchers over the last two decades. Despite this attention, however, the question of how firms can better maintain the balance of exploration and exploitation remains unresolved. Drawing on a wide range of research on population and organization structure, we argue that an organization divided into semi-isolated subgroups may help strike this balance. We simulate such an organization, systematically varying the interaction pattern between individuals to explore how the degree of subgroup isolation and intergroup connectivity influences organizational learning. We also test this model with a range of contingency variables highlighted in the management research. We find that moderate levels of cross-group linking lead to the highest equilibrium performance by enabling superior ideas to diffuse across groups without reducing organizational diversity too quickly. This finding is remarkably resilient to a wide range of variance in factors such as problem complexity, environmental dynamism, and personnel turnover.
Business Group Affiliation and Firm Search Behavior in India: Responsiveness and Focus of Attention
Authors: Vissa Balagopal , Greve Henrich R. , Chen Wei-Ru
Published: October 2009

This paper investigates the effects of organizational form on problemistic search. We contrast how Indian firms affiliated with business groups and unaffiliated firms evaluate performance and react by adjusting their internal technology search and external market search. We propose that, compared with unaffiliated firms, business group–affiliated (BG-affiliated) firms are more externally oriented in setting aspiration levels and more likely to respond to low performance in the market domain. We find support for an external orientation of BG-affiliated firms and find that group affiliation determines the responsiveness to performance feedback in different search domains. The findings suggest a need to add considerations of organizational form and governance to the theory of organizational search.
How Much to Copy? Determinants of Effective Imitation Breadth
Authors: Csaszar Felipe A. , Siggelkow Nicolaj
Published: October 2009

It is a common and frequently implicit assumption in the literature on knowledge transfer and organizational learning that imitating practices from high-performing firms has a positive impact on the imitating firm. Although a large body of research has identified obstacles to successful imitation, not much is known about what breadth of imitation is most effective. In this paper, we use a simulation model to explore how context and firm similarity, interdependence among practices, context and firm similarity, and time horizon interact in nontrivial ways to determine the payoffs that arise from different breadths of imitation. The results of the model allow us to qualify and refine predictions of the extant literature on imitation. In particular, the results shed light on the conditions under which increases in imitation breadth, and hence investments that facilitate the faithful copying of more practices, are valuable. In addition, the results of the model highlight that imitation can serve two different functions—mimicking high performers, and generating search by dislodging a firm from its current set of practices—each requiring different organizational routines for its successful implementation.
A Good Riddance? Spin-Offs and the Technological Performance of Parent Firms
Authors: McKendrick David G. , Wade James B. , Jaffee Jonathan
Published: October 2009

How do spin-offs—new ventures created by former employees of an incumbent firm—affect the technological performance of their parents? Conventional wisdom holds that spin-offs hurt parent firms: the parent loses key staff, routines are disrupted, and performance declines. Although having some basis in fact, we think the negative effects are overstated. We argue that spin-offs can enable parent firms to realign with their environment, thereby avoiding the oncoming obsolescence arising from the combination of organizational inertia and environmental drift. Using data from the hard disk drive industry, we find evidence that although the main effect of having a spin-off on a parent firm's technological performance is positive, the overall impact of a spin-off depends upon the technological sophistication of the spin-off and the time since the spin-off occurred. Indeed, parent firms of technologically sophisticated (successful) spin-offs initially suffer poorer technological performance, but over time they outperform firms that had no spin-offs. Both effects are amplified to the extent that the spin-off is more successful, which we attribute to both increased environmental realignment and the positive signal that successful spin-offs transmit to the broader labor market about the parent organization's reputation as an incubator of entrepreneurs and a desirable place to work.
Does In-Store Marketing Work? Effects of the Number and Position of Shelf Facings on Brand Attention and Evaluation at the Point of Purchase
Authors: Chandon Pierre , Hutchinson J. Wesley , Bradlow Eric T. , Young Scott H.
Published: October 2009

Recent trends in marketing have demonstrated an increased focus on in-store expenditures with the hope of “grabbing consumers” at the point of purchase, but does this make sense? To help answer this question, the authors examine the interplay between in-store and out-of-store factors on consumer attention to and evaluation of brands displayed on supermarket shelves. Using an eye-tracking experiment, they find that the number of facings has a strong impact on evaluation that is entirely mediated by its effect on visual attention and works particularly well for frequent users of the brand, for low-market-share brands, and for young and highly educated consumers who are willing to trade off brand and price. They also find that gaining in-store attention is not always sufficient to drive sales. For example, top- and middle-shelf positions gain more attention than low-shelf positions; however, only top-shelf positions carry through to brand evaluation. The results underscore the importance of combining eye-tracking and purchase data to obtain a full picture of the effects of in-store and out-of-store marketing at the point of purchase.