bluuebunny/crossref_metadata_2025 huggingface dataset:
Toxicity of sodium tungstate to earthworm, oat, radish, and lettuce
Authors: Bamford Josie E , Butler Alicia D , Heim Katherine E , Pittinger Charles A , Lemus Ranulfo , Staveley Jane P , Lee K. Brian , Venezia Carmen , Pardus Michael J
Published: July 2011

Due to unknown effects of the potential exposure of the terrestrial environment to tungsten substances, a series of toxicity studies of sodium tungstate (Na2WO4) was conducted. The effect on earthworm (Eisenia fetida) survival and reproduction was examined using Organisation for Economic Co-operation and Development (OECD) Guideline 222. No effect on either endpoint was seen at the highest concentration tested, resulting in a 56-d no-observed-effect concentration (NOEC) of ≥586 mg tungsten/kg dry soil (nominal concentrations). The effect of sodium tungstate on emergence and growth of plant species was examined according to OECD Guideline 208: oat (Avena sativa), radish (Raphanus sativus), and lettuce (Lactuca sativa). No effects on emergence, shoot height, and dry shoot weight were observed in oats exposed to the highest concentration, resulting in a 21-d NOEC of ≥586 mg tungsten/kg dry soil. The NOECs for radish and lettuce were 65 and 21.7 mg tungsten/kg dry soil (nominal concentrations), respectively. Respective 21-d median effective concentration values (EC50) for radish and lettuce were >586 and 313 mg tungsten/kg dry soil (based on shoot height) (confidence level [CL] −8.5–615); EC25 values were 152 (CL 0–331) and 55 (CL 0–114) mg tungsten/kg dry soil. Results are consistent with the few other tungsten substance terrestrial toxicity studies in the literature. Environ. Toxicol. Chem. 2011;30:2312–2318. © 2011 SETAC
An approach for developing simple generic models for ecological risk assessments of fish populations
Authors: Hanson Niklas , Stark John D
Published: July 2011

It has been argued that current approaches for ecological risk assessment (ERA) do not provide value relevance for risk managers and that the uncertainty in the predictions is large. One important reason for this is that current approaches are based on individual-level endpoints, but the environmental protection goals are defined on the population level. Population models may be useful tools to link the individual to the population and thus increase value relevance and reduce uncertainty. However, this requires that simple models and guidance on how to use them are made available for risk assessors. In the present study, an approach for developing simple generic models for the ERA of fish populations is presented. Fish have high ecological and economic value and are frequently used in ERA. It is, therefore, highly desirable to develop better methods for ERA of fish populations. The models were based on five types of life histories, and they were set up to be useful in a number of different management scenarios based on different environmental protection goals. A decision framework was set up for three levels of models (continuous, time limited, and varying exposure) and three levels of environmental protection. Data from previously published studies were tested for two of the environmental protection levels. The models provided maximum acceptable concentrations (MAC) that fell between the MACs of traditional ERA based on acute or chronic data, respectively. Environ. Toxicol. Chem. 2011;30:2372–2383. © 2011 SETAC
Toxicokinetic-toxicodynamic modeling of quantal and graded sublethal endpoints: A brief discussion of concepts
Authors: Ashauer Roman , Agatz Annika , Albert Carlo , Ducrot Virginie , Galic Nika , Hendriks Jan , Jager Tjalling , Kretschmann Andreas , O'Connor Isabel , Rubach Mascha Nadine , Nyman Anna-Maija , Schmitt Walter , Stadnicka Julita , van den Brink Paul J , Preuss Thomas G
Published: July 2011

We report on the advantages and problems of using toxicokinetic-toxicodynamic (TKTD) models for the analysis, understanding, and simulation of sublethal effects. Only a few toxicodynamic approaches for sublethal effects are available. These differ in their effect mechanism and emphasis on linkages between endpoints. We discuss how the distinction between quantal and graded endpoints and the type of linkage between endpoints can guide model design and selection. Strengths and limitations of two main approaches and possible ways forward are outlined. Environ. Toxicol. Chem. 2011;30:2519–2524. © 2011 SETAC
Therapeutic response in musculoskeletal soft tissue sarcomas: evaluation by MRI
Authors: Wang Xin , Jacobs Michael A. , Fayad Laura
Published: July 2011

This article provides a literature review of the use of MRI in monitoring the treatment response of soft tissue sarcomas. The basic classification and physiology of soft tissue tumors are introduced. Then, the major treatment options for soft tissue sarcomas are summarized with brief coverage of possible responses and grading systems. Four major branches of MRI techniques are covered, including conventional T1‐ and T2‐weighted imaging, contrast‐enhanced MRI, MR diffusion and perfusion imaging, and MRS, with a focus on the tumor microenvironment. Although this literature survey focuses on recent clinical developments using these MRI techniques, research venues in preclinical studies, as well as in potential applications other than soft tissue sarcomas, are also included when comparable and/or mutually supporting. Examples from other less‐discussed MRI modalities are also briefly covered, not only to complement, but also to expand, the scope and depth of information for various kinds of lesions. Copyright © 2011 John Wiley & Sons, Ltd.
Correlation of phospholipid metabolites with prostate cancer pathologic grade, proliferative status and surgical stage – impact of tissue environment
Authors: Keshari K. R. , Tsachres H. , Iman R. , Delos Santos L. , Tabatabai Z. L. , Shinohara K. , Vigneron D. B. , Kurhanewicz J.
Published: July 2011

This study investigates the relationship between phospholipid metabolite concentrations, Gleason score, rate of cellular proliferation and surgical stage in malignant prostatectomy samples by performing one‐ and two‐dimensional, high‐resolution magic angle spinning, total correlation spectroscopy, pathology and Ki‐67 staining on the same surgical samples. At radical prostatectomy, surgical samples were obtained from 49 patients [41 with localized TNM stage T1 and T2, and eight with local cancer spread (TNM stage T3)]. Thirteen of the tissue samples were high‐grade prostate cancer [Gleason score: 4 + 3 (n = 7); 4 + 4 (n = 6)], 22 low‐grade prostate cancer [Gleason score: 3 + 3 (n = 17); 3 + 4 (n = 5)] and 14 benign prostate tissues. This study demonstrates that high‐grade prostate cancer shows significantly higher Ki‐67 staining and concentrations of phosphocholine (PC) and glycerophosphocholine (GPC) than does low‐grade prostate cancer (2.4 ± 2.8% versus 7.6 ± 3.5%, p < 0.005, and 0.671 ± 0.461 versus 1.87 ± 2.15 mmolal, p < 0.005, respectively). In patients with local cancer spread, increases in [PC + GPC + PE + GPE] (PE, phosphoethanolamine; GPE, glycerophosphoethanolamine] and Ki‐67 index approached significance (4.2 ± 2.5 versus 2.7 ± 2.4 mmolal, p = 0.07, and 5.3 ± 3.8% versus 2.9 ± 3.8%, p = 0.07, respectively). PC and Ki‐67 were significantly lower and GPC higher in prostate tissues when compared with cell cultures, presumably because of a lack of important stromal–epithelial interactions in cell cultures. The findings of this study will need to be validated in a larger cohort of surgical patients with clinical outcome data, but support the role of in vivo 1H MRSI in discriminating between low‐ and high‐grade prostate cancer based on the magnitude of elevation of the in vivo total choline resonance. Copyright © 2011 John Wiley & Sons, Ltd.
Probucol Suppresses Enterocytic Accumulation of Amyloid‐β Induced by Saturated Fat and Cholesterol Feeding
Authors: Pallebage‐Gamarallage Menuka M. , Galloway Susan , Takechi Ryusuke , Dhaliwal Satvinder , Mamo John C. L.
Published: July 2011

Amyloid‐β (Aβ) is secreted from lipogenic organs such as intestine and liver as an apolipoprotein of nascent triacylglycerol rich lipoproteins. Chronically elevated plasma Aβ may compromise cerebrovascular integrity and exacerbate amyloidosis—a hallmark feature of Alzheimer's disease (AD). Probucol is a hypocholesterolemic agent that reduces amyloid burden in transgenic amyloid mice, but the mechanisms for this effect are presently unclear. In this study, the effect of Probucol on intestinal lipoprotein‐Aβ homeostasis was explored. Wild‐type mice were fed a control low‐fat diet and enterocytic Aβ was stimulated by high‐fat (HF) diet enriched in 10% (w/w) saturated fat and 1% (w/w) cholesterol for the duration of 1 month. Mice treated with Probucol had the drug incorporated into the chow at 1% (w/w). Quantitative immunofluorescence was utilised to determine intestinal apolipoprotein B (apo B) and Aβ abundance. We found apo B in both the perinuclear region of the enterocytes and the lacteals in all groups. However, HF feeding and Probucol treatment increased secretion of apo B into the lacteals without any change in net villi abundance. On the other hand, HF‐induced enterocytic perinuclear Aβ was significantly attenuated by Probucol. No significant changes in Aβ were observed within the lacteals. The findings of this study support the notion that Probucol suppresses dietary fat induced stimulation of Aβ biosynthesis and attenuate availability of apo B lipoprotein‐Aβ for secretion.
The radiation burden from increasingly complex endovascular aortic aneurysm repair
Authors: Thakor Avnesh S. , Winterbottom Andrew , Mercuri Mathew , Cousins Claire , Gaunt Michael E.
Published: July 2011

Objectives

With increasing experience, endovascular aortic aneurysm repair (EVAR) has been extended to patients with less suitable aorto-iliac anatomy in an attempt to reduce peri-operative mortality. However, more complex EVAR procedures may take longer and can result in higher rates of complications, additional interventional procedures and more frequent radiological imaging, which may offset some of the benefit. This study determined the radiation burden for standard EVAR, as determined by the EVAR-1 trial criteria, and more complex EVAR.

Methods

A total of 123 elective patients aged >60, with aneurysms >5.5 cm who received a bifurcated stent-graft were allocated into a group based on whether or not they fulfilled strict EVAR-1 trial criteria. The mean radiation dose was calculated for each group, together with the additional radiation burden from routine pre- and post-EVAR CT examinations and pre-EVAR iliac artery embolisation.

Results

Patients not meeting the EVAR-1 trial criteria had significantly longer fluoroscopic screening times and higher radiation doses. The radiation burden in all patients was higher following exposure from routine CT examinations and following pre-EVAR iliac artery embolisation.

Conclusion

Whilst the radiation from standard EVAR is acceptable, more complicated and challenging EVARs, accompanied with additional radiological investigations and procedures, can significantly increase the radiation burden.
Electrical synapses formed by connexin36 regulate inhibition- and experience-dependent plasticity
Authors: Postma Friso , Liu Cheng-Hang , Dietsche Caitlin , Khan Mariam , Lee Hey-Kyoung , Paul David , Kanold Patrick O.
Published: July 2011

The mammalian brain constantly adapts to new experiences of the environment, and inhibitory circuits play a crucial role in this experience-dependent plasticity. A characteristic feature of inhibitory neurons is the establishment of electrical synapses, but the function of electrical coupling in plasticity is unclear. Here we show that elimination of electrical synapses formed by connexin36 altered inhibitory efficacy and caused frequency facilitation of inhibition consistent with a decreased GABA release in the inhibitory network. The altered inhibitory efficacy was paralleled by a failure of theta-burst long-term potentiation induction and by impaired ocular dominance plasticity in the visual cortex. Together, these data suggest a unique mechanism for regulating plasticity in the visual cortex involving synchronization of inhibitory networks via electrical synapses.
VEGF modulates NMDA receptors activity in cerebellar granule cells through Src-family kinases before synapse formation
Authors: Meissirel Claire , Ruiz de Almodovar Carmen , Knevels Ellen , Coulon Cathy , Chounlamountri Naura , Segura Inmaculada , de Rossi Pierre , Vinckier Stefan , Anthonis Kristof , Deléglise Bérangère , de Mol Maria , Ali Carine , Dassonville Karel , Loyens Ellen , Honnorat Jérôme , Michotte Yvette , Rogemond Véronique , Smolders Ilse , Voets Thomas , Vivien Denis , Vanden Berghe Pieter , Van Den Bosch Ludo , Robberecht Wim , Chédotal Alain , Oliviero Salvatore , Dewerchin Mieke , Schmucker Dietmar , Thomasset Nicole , Salin Paul , Carmeliet Peter
Published: July 2011

NMDA type glutamate receptors (NMDARs) are best known for their role in synaptogenesis and synaptic plasticity. Much less is known about their developmental role before neurons form synapses. We report here that VEGF, which promotes migration of granule cells (GCs) during postnatal cerebellar development, enhances NMDAR-mediated currents and Ca2+influx in immature GCs before synapse formation. The VEGF receptor Flk1 forms a complex with the NMDAR subunits NR1 and NR2B. In response to VEGF, the number of Flk1/NR2B coclusters on the cell surface increases. Stimulation of Flk1 by VEGF activates Src-family kinases, which increases tyrosine phosphorylation of NR2B. Inhibition of Src-family kinases abolishes the VEGF-dependent NR2B phosphorylation and amplification of NMDAR-mediated currents and Ca2+influx in GCs. These findings identify VEGF as a modulator of NMDARs before synapse formation and highlight a link between an activity-independent neurovascular guidance cue (VEGF) and an activity-regulated neurotransmitter receptor (NMDAR).
Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase
Authors: Liu Zheyun , Tan Chuang , Guo Xunmin , Kao Ya-Ting , Li Jiang , Wang Lijuan , Sancar Aziz , Zhong Dongping
Published: July 2011

Photolyase uses blue light to restore the major ultraviolet (UV)-induced DNA damage, the cyclobutane pyrimidine dimer (CPD), to two normal bases by splitting the cyclobutane ring. Our earlier studies showed that the overall repair is completed in 700 ps through a cyclic electron-transfer radical mechanism. However, the two fundamental processes, electron-tunneling pathways and cyclobutane ring splitting, were not resolved. Here, we use ultrafast UV absorption spectroscopy to show that the CPD splits in two sequential steps within 90 ps and the electron tunnels between the cofactor and substrate through a remarkable route with an intervening adenine. Site-directed mutagenesis reveals that the active-site residues are critical to achieving high repair efficiency, a unique electrostatic environment to optimize the redox potentials and local flexibility, and thus balance all catalytic reactions to maximize enzyme activity. These key findings reveal the complete spatio-temporal molecular picture of CPD repair by photolyase and elucidate the underlying molecular mechanism of the enzyme’s high repair efficiency.
Effects of Size‐Based Environmental Regulations: Evidence of Regulatory Avoidance
Authors: Sneeringer Stacy , Key Nigel
Published: July 2011

United States environmental regulations often vary by operation size, with larger facilities facing more regulatory stringency. However, such legislative structure may have unintended consequences if operations downsize, slow their growth, or enter at a smaller scale in order to avoid regulation. In this study we use a regression‐discontinuity framework and exploit the size threshold of federal and state rules targeting large‐scale livestock operations to examine whether facilities adjust size to avoid regulation. We find statistical evidence of avoidance, primarily by operations entering at sizes just below the threshold.
Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data
Authors: Ramirez-Gonzalez Ricardo , Caccamo Mario , MacLean Daniel
Published: July 2011

Summary: Scientists now use high-throughput sequencing technologies and short-read assembly methods to create draft genome assemblies in just days. Tools and pipelines like the assembler, and the workflow management environments make it easy for a non-specialist to implement complicated pipelines to produce genome assemblies and annotations very quickly. Such accessibility results in a proliferation of assemblies and associated files, often for many organisms. These assemblies get used as a working reference by lots of different workers, from a bioinformatician doing gene prediction or a bench scientist designing primers for PCR. Here we describe Gee Fu, a database tool for genomic assembly and feature data, including next-generation sequence alignments. Gee Fu is an instance of a Ruby-On-Rails web application on a feature database that provides web and console interfaces for input, visualization of feature data via AnnoJ, access to data through a web-service interface, an API for direct data access by Ruby scripts and access to feature data stored in BAM files. Gee Fu provides a platform for storing and sharing different versions of an assembly and associated features that can be accessed and updated by bench biologists and bioinformaticians in ways that are easy and useful for each.

Availability:  http://tinyurl.com/geefu

Contact:  dan.maclean@tsl.ac.uk
Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context
Authors: Xiong Hui Yuan , Barash Yoseph , Frey Brendan J.
Published: July 2011

Motivation: Alternative splicing is a major contributor to cellular diversity in mammalian tissues and relates to many human diseases. An important goal in understanding this phenomenon is to infer a ‘splicing code’ that predicts how splicing is regulated in different cell types by features derived from RNA, DNA and epigenetic modifiers.

Methods: We formulate the assembly of a splicing code as a problem of statistical inference and introduce a Bayesian method that uses an adaptively selected number of hidden variables to combine subgroups of features into a network, allows different tissues to share feature subgroups and uses a Gibbs sampler to hedge predictions and ascertain the statistical significance of identified features.

Results: Using data for 3665 cassette exons, 1014 RNA features and 4 tissue types derived from 27 mouse tissues (http://genes.toronto.edu/wasp), we benchmarked several methods. Our method outperforms all others, and achieves relative improvements of 52% in splicing code quality and up to 22% in classification error, compared with the state of the art. Novel combinations of regulatory features and novel combinations of tissues that share feature subgroups were identified using our method.

Contact:  frey@psi.toronto.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
ContEst: estimating cross-contamination of human samples in next-generation sequencing data
Authors: Cibulskis Kristian , McKenna Aaron , Fennell Tim , Banks Eric , DePristo Mark , Getz Gad
Published: July 2011

Summary: Here, we present ContEst, a tool for estimating the level of cross-individual contamination in next-generation sequencing data. We demonstrate the accuracy of ContEst across a range of contamination levels, sources and read depths using sequencing data mixed in silico at known concentrations. We applied our tool to published cancer sequencing datasets and report their estimated contamination levels.

Availability and Implementation: ContEst is a GATK module, and distributed under a BSD style license at http://www.broadinstitute.org/cancer/cga/contest

Contact:  kcibul@broadinstitute.org; gadgetz@broadinstitute.org

Supplementary information:  Supplementary data is available at Bioinformatics online.
Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer
Authors: Yuan Yinyin , Rueda Oscar M. , Curtis Christina , Markowetz Florian
Published: July 2011

Motivation: Copy number alterations (CNAs) associated with cancer are known to contribute to genomic instability and gene deregulation. Integrating CNAs with gene expression helps to elucidate the mechanisms by which CNAs act and to identify the transcriptional downstream targets of CNAs. Such analyses can help to sort functional driver events from the many accompanying passenger alterations. However, the way CNAs affect gene expression can vary in different cellular contexts, for example between different subtypes of the same cancer. Thus, it is important to develop computational approaches capable of inferring differential connectivity of regulatory networks in different cellular contexts.

Results: We propose a statistical deregulation model that integrates copy number and expression data of different disease subtypes to jointly model common and differential regulatory relationships. Our model not only identifies CNAs driving gene expression changes, but at the same time also predicts differences in regulation that distinguish one cancer subtype from the other. We implement our model in a penalized regression framework and demonstrate in a simulation study the feasibility and accuracy of our approach. Subsequently, we show that this model can identify both known and novel aspects of cross-talk between the ER and NOTCH pathways in ER-negative-specific deregulations, when compared with ER-positive breast cancer. This flexible model can be applied on other modalities such as methylation or microRNA and expression to disentangle cancer signaling pathways.

Availability: The Bioconductor-compliant R package DANCE is available from www.markowetzlab.org/software/

Contact:  yinyin.yuan@cancer.org.uk; florian.markowetz@cancer.org.uk
The Science of Difference: Developing Tools for Discrimination in the American Life Insurance Industry, 1830–1930
Authors: Bouk Dan
Published: July 2011

The Science of Difference examines life insurance companies' significant impact on the development of systems of human classification and discrimination in modern America. It pays closest attention to the tools employed by life insurance companies to enable and justify their discriminatory practices, tracing their evolution over the course of the nineteenth and early twentieth centuries. Companies used life tables to think about sectional difference prior to the civil war; they collected statistics to defend the propriety of racial discrimination; and they revolutionized risk by inventing the medical “impairment.” Drawing on company archives and personal papers, as well as a wide range of publications, the dissertation describes corporate research in the financial industry, argues for the importance of cultural factors in tracing business history, and shows how the industry built a national statistical community with tools designed to measure and price human difference.
Exposure to sennoside–digoxin interaction and risk of digoxin toxicity: a population‐based nested case–control study†
Authors: Wang Meng‐Ting , Li I‐Hsun , Lee Wan‐Ju , Huang Tien‐Yu , Leu Hsin‐Bang , Chan Agnes L.F.
Published: July 2011

Aims

Digoxin is an important medication for heart failure (HF) patients and sennosides are widely used to treat constipation. Recently, safety concerns have been raised about a possible interaction between sennosides and digoxin, an issue that has not been studied empirically. This study therefore aimed to evaluate whether exposure to sennoside–digoxin interaction is associated with an increased risk of digoxin toxicity.

Methods and results

This was a population‐based nested case–control study that analysed data obtained from the Taiwan National Health Insurance Research Database between 1 January 2001 and 31 December 2004. All HF patients treated with digoxin for the first time were included as the study cohort. Of these, cases were identified as subjects hospitalized for digoxin toxicity (International Classification of Diseases, Ninth Revision, Clinical Modification,ICD‐9‐CM 972.1), and matched to randomly selected controls. Use of sennosides was compared between the two groups. Odds ratios (ORs) were employed to quantify the risk associated with exposure to sennoside–digoxin interaction by conditional logistic regression. The study cohort comprised 222 527 HF patients, of whom 524 were identified as cases and 2 502 as matched controls. Use of sennosides during the 14 days preceding the index date was found to be associated with a 1.61‐fold increased risk of digoxin toxicity [95% confidence interval (CI) = 1.15, 2.25]. Additionally, a greater risk was observed for sennosides prescribed at an average daily dose ≥24 mg (adjusted OR = 1.93; 95% CI = 1.27, 2.94).

Conclusion

The combined use of sennosides and digoxin was found to be associated with a modest increased risk of digoxin toxicity in HF patients.
Norepinephrine Infusion into Nucleus Basalis Elicits Microarousal in Desflurane-anesthetized Rats
Authors: Pillay Siveshigan , Vizuete Jeannette A. , McCallum J. Bruce , Hudetz Anthony G.
Published: July 2011

Background

The nucleus basalis of Meynert of the basal forebrain has been implicated in the regulation of the state of consciousness across normal sleep-wake cycles. Its role in the modulation of general anesthesia was investigated.

Methods

Rats were chronically implanted with bilateral infusion cannulae in the nucleus basalis of Meynert and epidural electrodes to record the electroencephalogram in frontal and visual cortices. Animals were anesthetized with desflurane at a concentration required for the loss of righting reflex (4.6 ± 0.5%). Norepinephrine (17.8 nmol) or artificial cerebrospinal fluid was infused at 0.2 μl/min (1 μl total). Behavioral response to infusion was measured by scoring the orofacial, limb, and head movements, and postural changes.

Results

Behavioral responses were higher after norepinephrine (2.1 ± 1) than artificial cerebrospinal fluid (0.63 ± 0.8) infusion (P < 0.01, Student t test). Responses were brief (1-2 min), repetitive, and more frequent after norepinephrine infusion (P < 0.0001, chi-square test). Electroencephalogram delta power decreased after norepinephrine in frontal (70 ± 7%) but not in visual cortex (P < 0.05, Student t test). Simultaneously, electroencephalogram cross-approximate entropy between frontal and visual cortices increased from 3.17 ± 0.56 to 3.85 ± 0.29 after norepinephrine infusion (P < 0.01, Student t test). Behavioral activation was predictable by the decrease in frontal delta power (logistic regression, P < 0.05).

Conclusions

Norepinephrine infusion into the nucleus basalis of Meynert can modulate anesthetic depth presumably by ascending activation of the cortex. The transient nature of the responses suggests a similarity with microarousals normally observed during natural sleep, and may imply a mechanism for transient awareness under light anesthesia.
Mycoplasma neophronis sp. nov., isolated from the upper respiratory tract of Canarian Egyptian vultures (Neophron percnopterus majorensis)
Authors: Suárez-Pérez A. , Ramírez A. S. , Rosales R. S. , Calabuig P. , Poveda C. , Rosselló-Móra R. , Nicholas R. A. J. , Poveda J. B.
Published: July 2011

Six strains with the typical characteristics of mycoplasmas were isolated from the tracheae of six Canarian Egyptian vultures (Neophron percnopterus majorensis). The results of biochemical, serological and molecular genetic studies showed that the isolates were nearly identical and that they could be considered as representing a novel species of the genus

Mycoplasma

. Colonies possessed the typical fried-egg appearance and electron micrographs revealed a pleomorphic cellular morphology with the lack of a cell wall. The isolates hydrolysed arginine and required sterol for growth but did not ferment glucose or hydrolyse urea. We propose that the isolates be assigned to a novel species,Mycoplasma neophronis sp. nov. The type strain is G.A.T ( = DSM 24097T = ATCC BAA-2157T). The antiserum of strain G.A.T has been deposited in the

Mollicutes

collection at Purdue University (Indiana, USA).
True single-molecule DNA sequencing of a pleistocene horse bone
Authors: Orlando Ludovic , Ginolhac Aurelien , Raghavan Maanasa , Vilstrup Julia , Rasmussen Morten , Magnussen Kim , Steinmann Kathleen E. , Kapranov Philipp , Thompson John F. , Zazula Grant , Froese Duane , Moltke Ida , Shapiro Beth , Hofreiter Michael , Al-Rasheid Khaled A.S. , Gilbert M. Thomas P. , Willerslev Eske
Published: July 2011

Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first “true single molecule sequencing” of ancient DNA. We generated 115.9 Mb and 76.9 Mb of DNA sequences from a permafrost-preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing libraries of ancient DNA molecules, as required for second-generation sequencing, introduce biases into the data that reduce the efficiency of the sequencing process and limit our ability to fully explore the molecular complexity of ancient DNA extracts. We demonstrate that simple modifications to the standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by threefold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3′ ends of ancient templates, indicating the presence of 3′-sequence overhangs. Our results suggest that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third-generation sequencing approaches.
Arabidopsis MPK3 and MPK6 Play Different Roles in Basal and Oligogalacturonide- or Flagellin-Induced Resistance against Botrytis cinerea
Authors: Galletti Roberta , Ferrari Simone , De Lorenzo Giulia
Published: July 2011

Mitogen-activated protein kinases (MAPKs) are fundamental components of the plant innate immune system. MPK3 and MPK6 are Arabidopsis (Arabidopsis thaliana) MAPKs activated by pathogens and elicitors such as oligogalacturonides (OGs), which function as damage-associated molecular patterns, and flg22, a well-known microbe-associated molecular pattern. However, the specific contribution of MPK3 and MPK6 to the regulation of elicitor-induced defense responses is not completely defined. In this work we have investigated the roles played by these MAPKs in elicitor-induced resistance against the fungal pathogen Botrytis cinerea. Analysis of single mapk mutants revealed that lack of MPK3 increases basal susceptibility to the fungus, as previously reported, but does not significantly affect elicitor-induced resistance. Instead, lack of MPK6 has no effect on basal resistance but suppresses OG- and flg22-induced resistance to B. cinerea. Overexpression of the AP2C1 phosphatase leads to impaired OG- and flg22-induced phosphorylation of both MPK3 and MPK6, and to phenotypes that recapitulate those of the single mapk mutants. These data indicate that OG- and flg22-induced defense responses effective against B. cinerea are mainly dependent on MAPKs, with a greater contribution of MPK6.
Zinc Finger Protein5Is Required for the Control of Trichome Initiation by Acting Upstream ofZinc Finger Protein8in Arabidopsis
Authors: Zhou Zhongjing , An Lijun , Sun Lili , Zhu Shuijin , Xi Wanyan , Broun Pierre , Yu Hao , Gan Yinbo
Published: July 2011

Arabidopsis (Arabidopsis thaliana) trichome development is a model system for studying cell development, cell differentiation, and the cell cycle. Our previous studies have shown that the GLABROUS INFLORESCENCE STEMS (GIS) family genes, GIS, GIS2, and ZINC FINGER PROTEIN8 (ZFP8), control shoot maturation and epidermal cell fate by integrating gibberellins (GAs) and cytokinin signaling in Arabidopsis. Here, we show that a new C2H2 zinc finger protein, ZFP5, plays an important role in controlling trichome cell development through GA signaling. Overexpression of ZFP5 results in the formation of ectopic trichomes on carpels and other inflorescence organs. zfp5 loss-of-function mutants exhibit a reduced number of trichomes on sepals, cauline leaves, paraclades, and main inflorescence stems in comparison with wild-type plants. More importantly, it is found that ZFP5 mediates the regulation of trichome initiation by GAs. These results are consistent with ZFP5 expression patterns and the regional influence of GA on trichome initiation. The molecular analyses suggest that ZFP5 functions upstream of GIS, GIS2, ZFP8, and the key trichome initiation regulators GLABROUS1 (GL1) and GL3. Using a steroid-inducible activation of ZFP5 and chromatin immunoprecipitation experiments, we further demonstrate that ZFP8 is the direct target of ZFP5 in controlling epidermal cell differentiation.
Linkages and technology spillovers in the presence of foreign firms
Authors: Samirana Pattnayak Sanja , Thangavelu Shandre M.
Published: July 2011

Purpose

This paper aims to examine production linkage and technology spillovers due to the presence of foreign firms in the Indian pharmaceutical industry.

Design/methodology/approach

This study employs the semi‐parametric estimation method suggested by Olley and Pakes to control for unobserved firm heterogeneity that accounts for the endogeneity of input selection with respect to productivity.

Findings

The results suggest that R&D activities of foreign firms lead to positive technology spillover to local firms. However, we also found negative linkage from the activities of foreign firms. The negative linkage could be explained by the large reverse engineering activities that occur on existing drugs in the Indian pharmaceutical industry, where the enclave activities of foreign firms might be a preemptive strategy to reduce the flow of technologies to downstream local firms and to protect their firm‐specific (product) technology.

Originality/value

The results provide support for strong institutional arrangements such as giving protection for Intellectual Property Rights, which might be important for attracting and creating linkages with activities of foreign firms in the host country.
Fragmentation in the automobile manufacturing industry: evidence from Portugal
Authors: Faustino Horácio C. , Carlos Leitão Nuno
Published: July 2011

Purpose

This paper aims to examine the determinants of vertical intra‐industry trade (VIIT) in the automobile components industry between Portugal and the European Union 27 (EU‐27) and the BRIC countries (Brazil, Russia, India and China) during the period 1995‐2006.

Design/methodology/approach

The paper formulates some theoretical hypotheses that may explain the fragmentation of the production in the automobile industry. These hypotheses are tested using a dynamic panel data analysis. The estimates are more reliable because the instruments used control for the potential endogeneity of the explanatory variables.

Findings

The results indicate that VIIT is a positive function of the difference in per‐capita GDP between Portugal and its trading partners, confirming the Linder hypothesis. Moreover, there is statistical evidence that geographical distance influences negatively this type of VIIT between Portugal and the EU‐27 only. The results do not confirm the hypothesis that there is a positive correlation between differences in endowments and VIIT in the automobile components sector.

Originality/value

This paper confirms some relevant theoretical hypotheses on the causes of the fragmentation/outsourcing. The good results obtained with the Arellano and Bond GMM system estimator suggest that the building of dynamic theoretical models will be of interest to academic researchers in fragmentation theory.
Foreign direct investment and employment in manufacturing and services sectors
Authors: Nyen Wong Koi , Cheong Tang Tuck
Published: July 2011

Purpose

This paper aims to examine both the cointegrating and causal relationships among inward FDI and the host country's employment in manufacturing and services sectors.

Design/methodology/approach

This paper applies autoregressive distributed lag (ARDL) framework to test the cointegration and causality patterns using Singapore as a case.

Findings

Apart from the presence of a unique long‐run relationship, the findings also show evidence of long‐run causality, running from employment in manufacturing and services to FDI inflows, and from FDI inflows and services employment to manufacturing employment. Furthermore, there is evidence of short‐run causality showing strong FDI‐employment and employment linkages, predominantly from the manufacturing to services.

Research limitations/implications

One likely area of future research is to extend this paper by using disaggregated data, e.g. FDI inflows by sector (manufacturing and services), and employment by the respective sectors.

Practical implications

Manufacturing and services have been regarded as the “twin engines” of growth for the Singapore economy. As the economy is moving up the value chain from downstream to upstream activities, a significant proportion of foreign direct investment (FDI) has been attracted to the manufacturing and services sectors. The present study provides useful policy implications towards promoting foreign investment in emerging areas of and manpower development in both sectors of the economy.

Originality/value

This paper explores the possible interactions between FDI inflows and employment in manufacturing and services sectors as well as the employment linkages between manufacturing and services in Singapore.
Financial structure and economic growth link in African countries: a panel cointegration analysis
Authors: Ahmed Abdullahi D. , Wahid Abu N.M.
Published: July 2011

Purpose

This paper aims to use the newly developed panel data cointegration analysis and the dynamic time series modeling approach to examine the linkages between financial structure (market‐based vs bank‐based) and economic growth in African economies.

Design/methodology/approach

The research investigates the dynamic relationship between financial structure and economic growth in a panel of a group of seven African developing countries over the period of 1986‐2007. The paper uses various indicators/measures of financial structure and financial system, and employs the traditional time‐series analysis for causality as well as the newly developed panel unit root and cointegration techniques and estimated finance‐growth relationship using FMOLS for heterogeneous panel.

Findings

From the dynamic heterogeneous panel approach, the paper firstly finds that market‐based financial system is important for explaining output growth through enhancing efficiency and productivity. Second, the authors' empirical evidence supports the view that higher levels of banking system development are positively associated with capital accumulation growth and lead to faster rates of economic growth.

Originality/value

Panel cointegration, group mean panel FMOLS and country‐by‐country time series investigations indicate that the market‐based financial system is important for explaining output growth through enhancing efficiency and productivity, whereas the development of banking system is significantly associated with capital accumulation growth. Further results from the time‐series approach show evidence of unidirectional causality running from market‐oriented as well as bank‐oriented financial systems to economic growth.
Practical wisdom for management from the Chinese classical traditions
Authors: de Bettignies Henri‐Claude , Keung Ip Po , Bai Xuezhu , Habisch André , Lenssen Gilbert
Published: July 2011

Purpose

This paper aims to provide an overview of this special issue.

Design/methodology/approach

The guest editorial introduces the papers in this special issue, focusing on practical wisdom for management from the Chinese classical traditions.

Findings

Chinese culture increasingly will permeate international culture and move from peripheral to mainstream status. To ignore this in management education would be a grave oversight.

Originality/value

The issue offers insights into the value of practical wisdom from Confucianism, the origins of Chinese classical trditions and Daoism, and the various streams of thought within the classical Chinese traditions and their contemporary relevance.
Confucian global leadership in Chinese tradition: classical and contemporary
Authors: Cheng Chung‐ying
Published: July 2011

Purpose

This paper aims to inquire and argue for a renovated model of Confucian political leadership as a way of political governance rooted in a philosophy of humanity and its potential for development.

Design/methodology/approach

The paper is primarily critical and constructive through philosophical analysis and synthesis of ideas and insights into nature of man and political leadership in light of Confucian texts and practices.

Findings

Based on reflection and analysis, the classical model of political leadership is shown to consist of core values of virtues and visions in classical Confucianism. By conceptual reconstruction a new Confucian model is formulated in such a way in which ethics of utilities and ethics of justice and righteousness are incorporated. The author further shows how it can be realized in different functions of modernized political and economic leadership. The author finds that this move resulted in achieving an essential transformation toward a more realistic application and practice in a global world.

Practical implications

In so far as the new model deals with a process of normative harmonization in which it can be further enhanced by comprehensive considerations of intrinsic human values and future development of humanity as a whole, this model provides a practical method for meeting the urgent needs on different levels of leadership and management for creative and world‐oriented attitude‐building, policy‐making and strategic seminar‐course designing for graduate and executive training in contemporary business schools.

Originality/value

The author has innovatively constructed the new Confucian model and show how political leadership in this model has the capability and ability to persevere in seeking harmony and harmonization among traditions and nations in the global world. The author has also explained how and why morality when properly supported can be a global leading power for bringing harmony and harmonization to the world. The author has formed a new concept of political leadership force and named it the moral power in addition to but not separated in its persuasion from hard power, soft power and smart power of Joseph Nye. The author's formulation and argument for the new model with its moral power constitute a highly significant contribution to the understanding of Confucian political leadership in contemporary global contexts.
Rethinking ethical leadership, social capital and customer relationship
Authors: Zheng Qinqin , Wang Miao , Li Zhiqiang
Published: July 2011

Purpose

Practical wisdom from Chinese classical traditions is still an enlightening resource for contemporary management. Based in traditional Chinese perspectives, this paper aims to explore the influence of ethical leadership and social capital on customer relationship.

Design/methodology/approach

The authors conduct a survey of senior executives in 215 Chinese companies. Structural model testing and hierarchical regressions are used to analyze the data.

Findings

The empirical analysis affirms the authors' hypotheses that both ethical leadership and social capital have significant influence on customer relationship.

Research limitations/implications

The results imply that traditional Chinese perspectives on contemporary management research have a potentially important impact.

Practical implications

It may also be valuable for Chinese firms to incorporate classical traditions into their daily practice: to enhance ethical leadership and obtain more social capital.

Originality/value

This study is a modest step towards an integration of traditional perspectives into research on the role of ethical leadership, and social capital, in maintaining good customer relationship in China.
Leadership and organizational patterns in the Daodejing
Authors: Gerstner Ansgar
Published: July 2011

Purpose

Although the Daodejing is a text that is more than 2,400 years old, its concepts regarding leadership nevertheless fit well into current discussions on sustainability and responsibility. This paper aims to explore these concepts.

Design/methodology/approach

The paper focuses on the strategic aspects that can be found in the Daodejing's approach to leadership.

Findings

The Daodejing offers interesting perspectives on the relationship between personal development and sustainability. Because of their topicality these concepts are moreover particularly interesting within the context of corporate culture and glocalization for multinational companies operating in China.

Originality/value

The paper explores aspects of the philosophy of the Daodejing that often get neglected, but which offer interesting perspectives on current issues in management.
Chinese wisdom, management practices and the humanities
Authors: Vermander Benoit
Published: July 2011

Purpose

This article aims at showing that the relationship between Chinese classical wisdoms and managerial practices should not be reduced to the establishment of an “art of war” applicable to management practices, but should rather be understood as an ever‐evolving work of critical reinterpretation, so as to liberate the creative and strategic potential that this tradition embodies.

Design/methodology/approach

It does so by critically deconstructing the question of the “relevance” of Chinese wisdom for managerial practices, by assessing the way contemporary Sinology understands and interprets the concept of “Chinese wisdom”, and by designing a strategy for applying these insights to managerial education.

Findings

It thus shows that only historical contextualization and textual studies can ground an understanding of Chinese tradition applicable to managerial education.

Practical implications

By doing so, it helps educators to re‐anchor managerial education into the field and methodologies of humanities studies.

Originality/value

It thus goes against the utilitarian and over‐simplified syntheses of Chinese thought that are currently dominant in the managerial literature about China, and proposes new ways for making the study of China a channel through which to develop in our students a sense of relativity, complexity and empathy applicable to an array of cultural contexts.