bluuebunny/crossref_metadata_2025_split huggingface dataset:
Workers’ Participation in Management, Workers’ Control of Production
Authors: Gunn Christopher 
Published: May 2011

For several decades workers’ participation in management was a persistent demand of the left. In the neoliberal era it became, in a twisted way, a reality for some workers. Team organization of production, reduction of supervisory staffing, and a constant drive for productivity improvement became the norm, requiring broader managerial involvement by workers in their activities. Workers’ control of production remains on the radical agenda, but with broader implications. Workers’ control of production implies dramatic changes in the relationship between capital and labor, and with them development of alternative forms of production and distribution. JEL classification: J54, B51, L23
The Role of Workers in Management
Authors: Campbell Al 
Published: May 2011

Independent of whatever other advantages it might have for the workers, worker ownership has repeatedly demonstrated in the real world that it is no guarantee for worker participation in management. The participation of workers in management as a first step toward worker self-management requires institutions and practices that will both allow such participation and promote it. This paper considers, in the frame of four standard issues in worker self-management, six specific institutions and practices common to the collection of co-ops that constitute the Mondragón complex that have generated meaningful worker participation in management in this large corporation. JEL classification: J54, L29, M19
Global Restructuring, Social Distancing, and a Community-Based Worker’s Center Response
Authors: Ji Minsun 
Published: May 2011

This paper addresses the impacts of global “social distancing” on employers and workers and examines community-based worker center strategies to mitigate those impacts. Through a case study of El Centro Humanitario, Denver’s human rights center for immigrant day laborers, the paper addresses how community organizations can respond to social distancing by “organizing the unorganized,” and crafting strategies such as worker-owned cooperatives to promote workers’ rights while reconnecting workers to their work and to each other. JEL classification: L31, L33, P32
Race in Early Tobacco Advertising
Authors: Goldstein Jonathan P. 
Published: May 2011

This paper analyzes the inclusion/exclusion and portrayal of minorities (African and Native American) in one early form of tobacco advertising: American tobacco cards from 1880-1911. I test hypotheses related to: 1) attempts to hide the accomplishments/lifestyle of minorities; 2) the inclusion of minorities for exploitative purposes; 3) the role of competition on discrimination; and 4) the existence of progressive undercurrents in this form of advertising. My econometric analysis shows that American tobacco cards contributed via exclusion to the hidden from view treatment of minority lifestyles. The majority of minority inclusions was exploitative in nature promoting racial stereotyping and niche audience marketing, yet a limited progressive undercurrent of treatment, particularly for Native Americans, did emerge. JEL classification: B500, J150, N310
Metabolic syndrome and exaggerated blood pressure response to exercise in newly diagnosed hypertensive patients
Authors: Tsioufis Costas , Kasiakogias Alexandros , Tsiachris Dimitris , Kordalis Athanasios , Thomopoulos Costas , Giakoumis Michalis , Bounas Pavlos , Pittaras Andreas , Michaelides Andreas , Stefanadis Christodoulos 
Published: May 2011

Background: Running evidence supports a prognostic value of an exaggerated blood pressure response to exercise (EBPR). The impact of the metabolic syndrome (MS) on EBPR in hypertensive patients has not been investigated. Design: A cross-sectional study in the setting of an outpatient hypertension clinic. Methods: In total, 325 non-diabetic patients with newly diagnosed hypertension were divided into two groups based on the presence ( n = 95) or absence ( n = 230) of the MS as defined with NCEP-ATP III criteria. All subjects underwent ambulatory blood pressure monitoring, echocardiography and exercise treadmill testing. Results: Hypertensive patients with MS exhibited higher prevalence of EBPR (by 17%, p = 0.002) and peak exercise systolic BP (by 10.4 mmHg, p = 0.001) irrespectively of confounders. Metabolic equivalents were higher in hypertensives with MS (by 0.6 ml/kg/min, p = 0.048), but the difference lost significance after adjusting for confounders, including body mass index. Logistic regression analysis identified the MS as an independent predictor of an EBPR ( p = 0.016). Hypertensive patients with MS had a 2.3-fold risk of exhibiting EBPR compared to those without MS. However, individual components of MS altogether as well as each one separately failed to predict EBPR. Conclusions: Presence of MS in newly diagnosed hypertensive patients is associated with increased peak exercise BP and a higher frequency of EBPR over and above its separate elements.
Distribution of short and lifetime risks for cardiovascular disease in Italians
Authors: Di Castelnuovo Augusto , Costanzo Simona , Persichillo Mariarosaria , Olivieri Marco , de Curtis Amalia , Zito Francesco , Donati Maria Benedetta , de Gaetano Giovanni , Iacoviello Licia 
Published: May 2011

Background: Guidelines for primary prevention recommend calculation of lifetime risk for cardiovascular disease (CVD) in addition to short-time risk. We aimed at evaluating the distribution of CVD lifetime risk and the percentage of Italians having low short-term, but high lifetime, risk. Design: Cross-sectional general population-based cohort study. Methods: We included 8,403 (46% men) cardiovascular disease-free individuals aged 35–50 years, among those randomly recruited in the framework of the MOLI-SANI cohort. Participants were stratified into three groups: low short-time (10-year) (≤3% and non diabetic)/low lifetime, low short-time/high lifetime, and high short-time risk. Short-time risk was evaluated by the equation provided by the Italian CUORE project. Lifetime risk was evaluated using the algorithm derived from the Framingham cohort. Results: High short-time risk was prevalent in 16% population (32% of men and 2% of women). Among individuals with low short-time risk, 80% had high lifetime risk (82% men and 78% women). The proportion of individuals with very low lifetime risk due to all optimal risk factors was 4.1% only (1.5% men and 6.3% women). Conclusions: A large proportion of Italian adults not qualified for CVD primary prevention because of their very low short-time predicted CVD risk, are in fact at high risk to develop a CVD event in their lifetime; therefore population-based approaches should be sought to modify the overall distribution of individual risk factors. These findings offer helpful information for policy makers involved in contrasting the burden of CVD, especially in women and young men.
Discrimination of approved drugs from experimental drugs by learning methods
Authors: Tang Kailin , Zhu Ruixin , Li Yixue , Cao Zhiwei 
Published: May 2011

AbstractBackgroundTo assess whether a compound is druglike or not as early as possible is always critical in drug discovery process. There have been many efforts made to create sets of 'rules' or 'filters' which, it is hoped, will help chemists to identify 'drug-like' molecules from 'non-drug' molecules. However, among the chemical space of the druglike molecules, the minority will be approved drugs. Classifying approved drugs from experimental drugs may be more helpful to obtain future approved drugs. Therefore, discrimination of approved drugs from experimental ones has been done in this paper by analyzing the compounds in terms of existing drugs features and machine learning methods.ResultsFour methodologies were compared by their performance to classify approved drugs from experimental ones. The best results were obtained by SVM, in which the accuracy is 0.7911, the sensitivity is 0.5929, and the specificity is 0.8743. Based on the results, consensus model was developed to effectively discriminate drugs, which further pushed the correct classification rate up to 0.8517, sensitivity up to 0.7242, specificity up to 0.9352. The applications on the Traditional Chinese Medicine Ingredients Database (TCM-ID) tested the methods. Therefore this model has been proven to be a potent tool for identifying drug molecules.ConclusionThe studies would have potential applications in the research of combinatorial library design and virtual high throughput screening for drug discovery.
Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps
Authors: Fraccalvieri Domenico , Pandini Alessandro , Stella Fabio , Bonati Laura 
Published: May 2011

Abstract

Background
Molecular dynamics (MD) simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs) were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering.

Results
The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions.

Conclusions
The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to conformational ensembles from other sources.
Detection of QTL with effects on osmoregulation capacities in the rainbow trout (Oncorhynchus mykiss)
Authors: Le Bras Yvan , Dechamp Nicolas , Krieg Francine , Filangi Olivier , Guyomard René , Boussaha Mekki , Bovenhuis Henk , Pottinger Thomas G , Prunet Patrick , Le Roy Pascale , Quillet Edwige 
Published: May 2011

AbstractBackgroundThere is increasing evidence that the ability to adapt to seawater in teleost fish is modulated by genetic factors. Most studies have involved the comparison of species or strains and little is known about the genetic architecture of the trait. To address this question, we searched for QTL affecting osmoregulation capacities after transfer to saline water in a nonmigratory captive-bred population of rainbow trout.ResultsA QTL design (5 full-sib families, about 200 F2 progeny each) was produced from a cross between F0 grand-parents previously selected during two generations for a high or a low cortisol response after a standardized confinement stress. When fish were about 18 months old (near 204 g body weight), individual progeny were submitted to two successive hyper-osmotic challenges (30 ppt salinity) 14 days apart. Plasma chloride and sodium concentrations were recorded 24 h after each transfer. After the second challenge, fish were sacrificed and a gill index (weight of total gill arches corrected for body weight) was recorded. The genome scan was performed with 196 microsatellites and 85 SNP markers. Unitrait and multiple-trait QTL analyses were carried out on the whole dataset (5 families) through interval mapping methods with the QTLMap software. For post-challenge plasma ion concentrations, significant QTL (P < 0.05) were found on six different linkage groups and highly suggestive ones (P < 0.10) on two additional linkage groups. Most QTL affected concentrations of both chloride and sodium during both challenges, but some were specific to either chloride (2 QTL) or sodium (1 QTL) concentrations. Six QTL (4 significant, 2 suggestive) affecting gill index were discovered. Two were specific to the trait, while the others were also identified as QTL for post-challenge ion concentrations. Altogether, allelic effects were consistent for QTL affecting chloride and sodium concentrations but inconsistent for QTL affecting ion concentrations and gill morphology. There was no systematic lineage effect (grand-parental origin of QTL alleles) on the recorded traits.ConclusionsFor the first time, genomic loci associated with effects on major physiological components of osmotic adaptation to seawater in a nonmigratory fish were revealed. The results pave the way for further deciphering of the complex regulatory mechanisms underlying seawater adaptation and genes involved in osmoregulatory physiology in rainbow trout and other euryhaline fishes.
A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly
Authors: Wang Yan , Sun Silong , Liu Bo , Wang Hui , Deng Jie , Liao Yongcui , Wang Qian , Cheng Feng , Wang Xiaowu , Wu Jian 
Published: May 2011

Abstract

Background

Brassica rapa is an economically important crop and a model plant for studies concerning polyploidization and the evolution of extreme morphology. The multinational B. rapa Genome Sequencing Project (BrGSP) was launched in 2003. In 2008, next generation sequencing technology was used to sequence the B. rapa genome. Several maps concerning B. rapa pseudochromosome assembly have been published but their coverage of the genome is incomplete, anchoring approximately 73.6% of the scaffolds on to chromosomes. Therefore, a new genetic map to aid pseudochromosome assembly is required.

Results
This study concerns the construction of a reference genetic linkage map for Brassica rapa, forming the backbone for anchoring sequence scaffolds of the B. rapa genome resulting from recent sequencing efforts. One hundred and nineteen doubled haploid (DH) lines derived from microspore cultures of an F1 cross between a Chinese cabbage (B. rapa ssp. pekinensis) DH line (Z16) and a rapid cycling inbred line (L144) were used to construct the linkage map. PCR-based insertion/deletion (InDel) markers were developed by re-sequencing the two parental lines. The map comprises a total of 507 markers including 415 InDels and 92 SSRs. Alignment and orientation using SSR markers in common with existing B. rapa linkage maps allowed ten linkage groups to be identified, designated A01-A10. The total length of the linkage map was 1234.2 cM, with an average distance of 2.43 cM between adjacent marker loci. The lengths of linkage groups ranged from 71.5 cM to 188.5 cM for A08 and A09, respectively. Using the developed linkage map, 152 scaffolds were anchored on to the chromosomes, encompassing more than 82.9% of the B. rapa genome. Taken together with the previously available linkage maps, 183 scaffolds were anchored on to the chromosomes and the total coverage of the genome was 88.9%.

Conclusions
The development of this linkage map is vital for the integration of genome sequences and genetic information, and provides a useful resource for the international Brassica research community.
PNA-FISH as a new diagnostic method for the determination of clarithromycin resistance of Helicobacter pylori
Authors: Cerqueira Laura , Fernandes Ricardo M , Ferreira Rui M , Carneiro Fátima , Dinis-Ribeiro Mário , Figueiredo Céu , Keevil Charles W , Azevedo Nuno F , Vieira Maria J 
Published: May 2011

Abstract

Background
Triple therapy is the gold standard treatment for Helicobacter pylori eradication from the human stomach, but increased resistance to clarithromycin became the main factor of treatment failure. Until now, fastidious culturing methods are generally the method of choice to assess resistance status. In this study, a new genotypic method to detect clarithromycin resistance in clinical samples, based on fluorescent in situ hybridization (FISH) using a set of peptide nucleic acid probes (PNA), is proposed.

Results
The set of probes targeting the point mutations responsible for clarithromycin resistance was applied to H. pylori suspensions and showed 100% sensitivity and specificity (95% CI, 79.9-100 and 95% CI, 71.6-100 respectively). This method can also be amenable for application to gastric biopsy samples, as resistance to clarithromycin was also detected when histological slides were tested.

Conclusions
The optimized PNA-FISH based diagnostic method to detect H. pylori clarithromycin resistance shown to be a very sensitive and specific method for the detection of clarithromycin resistance in the H. pylori smears and also proved to be a reliable method for the diagnosis of this pathogen in clinical samples and an alternative to existing plating methods.
Sequencing and Characterization of Pseudomonas aeruginosa phage JG004
Authors: Garbe Julia , Bunk Boyke , Rohde Manfred , Schobert Max 
Published: May 2011

Abstract

Background
Phages could be an important alternative to antibiotics, especially for treatment of multiresistant bacteria as e.g. Pseudomonas aeruginosa. For an effective use of bacteriophages as antimicrobial agents, it is important to understand phage biology but also genes of the bacterial host essential for phage infection.

Results
We isolated and characterized a lytic Pseudomonas aeruginosa phage, named JG004, and sequenced its genome. Phage JG004 is a lipopolysaccharide specific broad-host-range phage of the Myoviridae phage family. The genome of phage JG004 encodes twelve tRNAs and is highly related to the PAK-P1 phage genome. To investigate phage biology and phage-host interactions, we used transposon mutagenesis of the P. aeruginosa host and identified P. aeruginosa genes, which are essential for phage infection. Analysis of the respective P. aeruginosa mutants revealed several characteristics, such as host receptor and possible spermidine-dependance of phage JG004.

Conclusions
Whole genome sequencing of phage JG004 in combination with identification of P. aeruginosa host genes essential for infection, allowed insights into JG004 biology, revealed possible resistance mechanisms of the host bacterium such as mutations in LPS and spermidine biosynthesis and can also be used to characterize unknown gene products in P. aeruginosa.
Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter
Authors: Smolander Olli-Pekka , Kandhavelu Meenakshisundaram , Mannerström Henrik , Lihavainen Eero , Kalaichelvan Shanmugapriya , Healy Shannon , Yli-Harja Olli , Karp Matti , Ribeiro Andre S 
Published: May 2011

Abstract

Background
Gene expression in Escherichia coli is regulated by several mechanisms. We measured in single cells the expression level of a single copy gene coding for green fluorescent protein (GFP), integrated into the genome and driven by a tetracycline inducible promoter, for varying induction strengths. Also, we measured the transcriptional activity of a tetracycline inducible promoter controlling the transcription of a RNA with 96 binding sites for MS2-GFP.

Results
The distribution of GFP levels in single cells is found to change significantly as induction reaches high levels, causing the Fano factor of the cells' protein levels to increase with mean level, beyond what would be expected from a Poisson-like process of RNA transcription. In agreement, the Fano factor of the cells' number of RNA molecules target for MS2-GFP follows a similar trend. The results provide evidence that the dynamics of the promoter complex formation, namely, the variability in its duration from one transcription event to the next, explains the change in the distribution of expression levels in the cell population with induction strength.

Conclusions
The results suggest that the open complex formation of the tetracycline inducible promoter, in the regime of strong induction, affects significantly the dynamics of RNA production due to the variability of its duration from one event to the next.
Bayesian adjustment for measurement error in continuous exposures in an individually matched case-control study
Authors: Espino-Hernandez Gabriela , Gustafson Paul , Burstyn Igor 
Published: May 2011

Abstract

Background
In epidemiological studies explanatory variables are frequently subject to measurement error. The aim of this paper is to develop a Bayesian method to correct for measurement error in multiple continuous exposures in individually matched case-control studies. This is a topic that has not been widely investigated. The new method is illustrated using data from an individually matched case-control study of the association between thyroid hormone levels during pregnancy and exposure to perfluorinated acids. The objective of the motivating study was to examine the risk of maternal hypothyroxinemia due to exposure to three perfluorinated acids measured on a continuous scale. Results from the proposed method are compared with those obtained from a naive analysis.

Methods
Using a Bayesian approach, the developed method considers a classical measurement error model for the exposures, as well as the conditional logistic regression likelihood as the disease model, together with a random-effect exposure model. Proper and diffuse prior distributions are assigned, and results from a quality control experiment are used to estimate the perfluorinated acids' measurement error variability. As a result, posterior distributions and 95% credible intervals of the odds ratios are computed. A sensitivity analysis of method's performance in this particular application with different measurement error variability was performed.

Results
The proposed Bayesian method to correct for measurement error is feasible and can be implemented using statistical software. For the study on perfluorinated acids, a comparison of the inferences which are corrected for measurement error to those which ignore it indicates that little adjustment is manifested for the level of measurement error actually exhibited in the exposures. Nevertheless, a sensitivity analysis shows that more substantial adjustments arise if larger measurement errors are assumed.

Conclusions
In individually matched case-control studies, the use of conditional logistic regression likelihood as a disease model in the presence of measurement error in multiple continuous exposures can be justified by having a random-effect exposure model. The proposed method can be successfully implemented in WinBUGS to correct individually matched case-control studies for several mismeasured continuous exposures under a classical measurement error model.