bluuebunny/crossref_metadata_2025 huggingface dataset:
Beyond ‘Dull and Sterile Routines’?: Dalits Organizing for Social Change in Tamil Nadu
Authors: Gorringe Hugo
Published: October 2010

Drawing on fieldwork with Dalit movements in Tamil Nadu, this article focuses on often neglected aspects of activism. A pervasive lack of resources has rendered Tamil Dalit movements overly incident-sensitive: reacting to caste atrocities rather than pursuing a positive agenda. Movement leaders thus concentrate on community-building by means of exclusive rhetoric that is, at times, divorced from the day-to-day concerns of their constituents. High-profile events and fiery speeches attract attention and foster collective identity, but are only part of a wider struggle in which the more mundane and everyday aspects of struggle—establishing strong networks, chasing up officials, seeking alternate sources of employment and so on—may be most effective. Changing caste relations, it is argued, requires continual commitment rather than episodic protest. This challenges what we mean by ‘movement success’ and ‘activism’.
New Beginnings between Public and Private: Arendt and Ethnographies of Activism
Authors: Day Sophie , Goddard Victoria
Published: October 2010

We explore Arendt’s idiom of ‘new beginnings’ which, for her, constitute the very heart of the political in the light of two case studies. Drawing on examples of political action in the human rights organization of the Mothers of Plaza de Mayo in Buenos Aires, Argentina, and among sex workers in London, this article engages with the complex and productive interface of what Arendt calls praxis and poiesis. We suggest that it is precisely through this interface that these women activists have articulated ‘a new beginning’. Their actions call into question the distinctions that Arendt also makes between private and public insofar as these are given beforehand or assumed independently of such action. They also, we hope, contribute to a broader consideration of activism and ethnography.
Conceptualizing lesbian sexual identity development: Narrative accounts of socializing structures and individual decisions and actions
Authors: Shapiro Danielle N , Rios Desdamona , Stewart Abigail J
Published: October 2010

Many theories have aimed to chart lesbian, gay and bisexual identity development. These include traditional developmental models as well as newer approaches designed to capture a more fluid, multidimensional trajectory, both of which have tended to neglect the role of intersectional identities, context and individual variation in lesbian identity development. This study used inductive research methods, informed by grounded theory, to examine lesbian identity development in life narrative interviews with four lesbian scholar-activists from different national and racial backgrounds. The women’s narratives suggest that a dynamic, non-linear, and contextualized representation of sexual identity development may more accurately describe lesbian identity development in terms of intersecting identities, national and local contexts, and personal and professional relationships.
‘What you look like is such a big factor’: Girls’ own reflections about the appearance culture in an all-girls’ school
Authors: Carey Renee N , Donaghue Ngaire , Broderick Pia
Published: October 2010

High school is a key venue for the development and expression of body image concerns in adolescent girls. Researchers have begun to investigate the role of school-based ‘appearance cultures’ in magnifying the body image concerns of students. To date, however, no research has examined girls’ experience as participants within these cultures, and thus the opportunity to learn how girls account for the development and maintenance of these cultures has been missed. In interviews with nine girls attending an all-girls’ school, the existence of a strong ‘appearance culture’ in the school was identified as a major influence on the body image concerns of students. Girls talked about the ways in which appearance-focused conversations, dieting, and weight monitoring occurred as part of the everyday interaction with friends and peers at school. They also identified many ways in which their school attempted to address body image concerns, although these attempts were often portrayed as ineffective, if not counter-productive. These findings suggest that attempts to address the body image concerns of students will need to be sensitive to the lived reality of appearance cultures within schools.
Protective effects of Chinese and Brazilian propolis treatment against hepatorenal lesion in diabetic rats
Authors: Zhu Wei , Li Ying-Hua , Chen Min-Li , Hu Fu-Liang
Published: October 2010

Diabetes mellitus promoted an overproduction of free radicals and an increased incidence of both diabetic nephropathy and liver disease. In this report, we evaluated the effects of Chinese and Brazilian propolis on streptozotocin-induced hepatorenal injury in rats. The results demonstrated that Chinese propolis-treated rats had a 7.4% reduction in the glycated hemoglobin (HbAlc) level compared with untreated diabetic rats. Additionally, Chinese propolis induced an increase in the serum superoxide dismutase (SOD) level significantly while Brazilian propolis raised serum SOD and reduced level of malonaldehyde (MDA) and nitric synthetase (NOS). Of the measurable decrease in serum alanine transaminase (ALT), aspartate transaminase (AST) and microalbuminuria demonstrated the propolis-mediated improvement of hepatorenal function, which was further confirmed by histological examination. We also observed that Chinese and Brazilian propolis increased hepatorenal glutathione peroxidase (GSH-px) level and inhibited MDA production significantly. These results suggested that propolis may prevent hepatorenal injury by inhibiting lipid peroxidation and enhancing the activities of antioxidant enzymes.
Village Water Tanks In Gujarat’s Desert Region
Authors: Das Keshab
Published: October 2010

Recognizing the dearth of detailed analyses of the economic and environmental performance of such systems meant exclusively for domestic uses, this article enquires into the relevance and explores possible modernization/revival of talavs (tanks) in two villages of Gujarat’s Kutch district in the Thar deserts, India’s driest region. It analyzes the pattern of water use, dependence on alternative sources and households’ willingness to pay for reviving/modernizing talavs. Cost estimates between reviving talavs and piped system have been compared. The findings suggest that talavs remain important sources of domestic water and if modernized/revived and, importantly, the ownership is vested in the local community, these can be of substantive use, especially, during summer. Hydrogeology-specific technological strategies to harness rainwater and modernize talavs need to be explored as enhanced supply per se can reduce costs significantly. In such ventures, whether and how state can intervene or shall seek private participation, both for financing and providing technical and management support, need to be explored. In case of talavs, the trickier issue has been management with community participation. Emphasizing scientific intervention in the traditional water harvesting systems, to enhance the supply, the article argues for community management as a useful strategy to protect and improvise the systems.
Carnage in Paradise
Authors: Kisekka-Ntale Fredrick
Published: October 2010

Different perceptions and claims lead to conflicts over environmental outcomes. By elucidating the role of the state and its relationship to local institutions, one can better understand contemporary institutional conflict and the need to create mechanisms for inter-institutional cooperation in environmental decision making, particularly in the realm of protected area management. The article is based on findings from one of the remaining few Afro-tropical rainforests. Located in western Kenya, Kakamega forest is under immense threat of survival. The forest is located in a densely populated area and inhabited by poor farming communities, largely of Luhya descent. The study analyses varied notions related to local people’s perception of institutional regimes. The aim of the article is to shed more light on what is meant by institutions, institutionalism and point to some common misleading notions associated with the terms; explain the institutional dimensions of environmental decision making in the context of shifting discourses in protected area management; explain the most common basis of institutional conflict over the environment and summarize by drawing emphasis on how comanagement in protected reserves requires the recognition of local institutional rights and how this can both reduce institutional conflict to achieve a sustainable relationship between societies and the environment.
Business Support for Farmers
Authors: McElwee Gerard , Annibal Ivan
Published: October 2010

The article presents an account of a Farm Support Project in Cornwall which provides support, advice and an outreach facility for farmers in the Penwith district of Cornwall, UK. It discusses how effective such schemes are, particularly in an external environment, which poses threats to the farm sector in the UK. Three kinds of questions about the nature of farming and the status of farmers are posed. The first set of questions includes polarizations about the hegemonic position of farmers. Second, macro-economic, and thus policy, questions concerning the economic ‘footprint’ of the farmer and the farm’s relationship with the economy are posed in Cornwall. The third set of questions concerns the economic role and entrepreneurial capability of the farmer in Cornwall. The Penwith Scheme encompasses an integrated approach to providing business support to farmers including signposting specialist advisers, the facilitation of training assistance with major grant applications, the development of ‘social capital’ through to help in accessing sources of social support. Farm Cornwall is a unique example of support to farmers. Replication of such a scheme across other rural regions and indeed other business sectors is possible and desirable but would require a full appraisal of the efficacy of regional and local business support to rural business.
Growth-Inequality-Poverty (GIP) Hypothesis in Rural Pakistan (1964–2006)
Authors: Zaman Khalid , Ikram Waseem , Ahmad Mehboob
Published: October 2010

This article attempts an assessment of the legitimacy of the Growth–Inequality–Poverty (GIP) hypothesis in the rural Pakistan using a recent technique, that is, the bounds testing approach. Based on this model, income distribution has stimulated positive adjustment to rural poverty, whereas economic growth and the steady period are found to influence rural poverty negatively. Additionally, a co-integrated relationship between poverty, in-equality and growth was noticed in both the long and short runs. Further analysis showed that rural poverty Granger-caused economic growth in the period of study. Thus, this study provides substantiation to support the GIP hypothesis in the Pakistan economy.
Teaching Labor Relations With Norma Rae
Authors: Taylor Vicki Fairbanks , Provitera Michael J.
Published: October 2010

Undergraduate business students in North America are often unfamiliar with the labor organizing process and frequently fail to identify with the reasons why workers join unions. This article suggests a discussion exercise based on the 1979 film, Norma Rae, by 20th Century Fox, as an effective tool for familiarizing students with fundamental topics in labor relations such as the union organizing process, union avoidance strategies, and unfair labor practices. In addition, the film and the discussion-based exercise can be used to help students further explore the sources of individual attitudes toward unions, union instrumentality perceptions, union voting intentions, and contemporary issues in private sector labor relations. Collected data show positive responses from students who viewed the movie and participated in the discussion-based exercise. Suggestions are offered for using the film and the discussion-based exercise in the classroom to engage students in the study of labor relations.
Differentiation of Farmed and Wild Turbot (Psetta maxima): Proximate Chemical Composition, Fatty Acid Profile, Trace Minerals and Antimicrobial Resistance of Contaminant Bacteria
Authors: Martínez B. , Miranda J.M. , Nebot C. , Rodriguez J.L. , Cepeda A. , Franco C.M.
Published: October 2010

The proximate, cholesterol, fatty acid and trace mineral compositions in the flesh of farmed and wild turbot (Psetta maxima) were evaluated. Additionally, the potential influence of the use of antimicrobial agents in the bacteria carried by farmed turbot was investigated. For this purpose, a total of 144 Pseudomonas spp. and 127 Aeromonas spp. were isolated and tested for their susceptibility to 12 antimicrobials by a disk diffusion method. Farmed turbot contained higher fat, cholesterol and calories as well as lower moisture content than its wild counterpart. The fatty acid profile of farmed turbot included higher levels of myristic, pentadecanoic, palmitoleic, gadoleic, cetoleic, linoleic, linolenic, stearidonic, eicosadienoic and eicosapentaenoic acids, and lower levels of stearic, arachidonic, docosapentaenoic and docosahexaenoic acids than its wild counterpart. The proportions of polyunsaturated fatty acids and n-3/n-6 ratios were higher in wild turbot than in farmed turbot. With respect to trace minerals, no toxic levels were found, and higher amounts of Cd, Co, Cu, Fe, Mn, Pb and Zn, as well as lower amounts of Cr, were found in farmed turbot relative to wild turbot. The antimicrobial resistance of Pseudomonas spp. and Aeromonas spp. were quite similar, with only the trimethoprim-sulfamethoxazole resistance of Aeromonas spp. isolated from farmed turbot being higher than those isolated from wild turbot. In the case of ampicillin, Pseudomonas spp. isolated from wild turbot showed higher resistance levels than those of their counterparts isolated from farmed turbot. In conclusion, the nutritional parameters of wild turbot are more adequate with respect to nutritional recommendations, while no differences were observed in food safety derived from trace mineral concentrations or the antimicrobial resistance of bacteria isolated from wild and farmed turbot.
Cognitive impairment in relation to MRI metrics in patients with clinically isolated syndrome
Authors: Khalil M , Enzinger C , Langkammer C , Petrovic K , Loitfelder M , Tscherner M , Jehna M , Bachmaier G , Wallner-Blazek M , Ropele S , Schmidt R , Fuchs S , Fazekas F
Published: October 2010

Background: Cognitive deficits are frequent in multiple sclerosis (MS) and have been associated with morphologic brain changes. Less information exists on their extent and relation to MRI findings in clinically isolated syndrome (CIS). It is also unclear if structural changes as detected by magnetization transfer (MT) imaging may provide an additional explanation for cognitive dysfunction.

Objective: To analyse the extent of cognitive deficits and their relation to MRI metrics including MT imaging in CIS compared to relapsing-remitting MS (RRMS).

Methods: Forty-four CIS and 80 RRMS patients underwent the Brief Repeatable Battery of Neuropsychological Tests (BRB-N) and a 3 T MRI scan.

Results: BRB-N subtests revealed similar results in CIS and RRMS. Impaired mental processing speed was most prevalent in both groups (CIS 13.6%; RRMS 16.3%) and thus served for correlation with MRI metrics. Using stepwise linear regression analyses, the strongest predictor for decreased mental processing speed was normalized cortex volume ( p < 0.001) followed by T2-lesion load ( p < 0.05) in RRMS, whereas cortical MT ratio was the only MRI parameter associated with decreased mental processing speed in CIS ( p < 0.005).

Conclusion: Cognitive dysfunction occurs in CIS in a pattern similar to RRMS, with impaired mental processing speed being most prevalent. Cortical MT-ratio changes may be an early sign for tissue changes related to impaired mental processing speed in CIS while this association shifts to increased signs of cortical atrophy and lesion load in RRMS.
Multiple modernities and multiple proximities: McDonald’s and Kentucky Fried Chicken in Chinese television commercials
Authors: Jia Lu
Published: October 2010

Homogenization and diversification are major themes in studies of globalization and culture. McDonald’s and Kentucky Fried Chicken (KFC) are often used as evidence to describe these two themes. The aim of this study is to examine the extent to which homogenization and diversification occur in the television commercials for McDonald’s and KFC in China as well as the strategic models they adopt to manipulate the tension between homogenization and diversification. La Pastina and Straubhaar’s theory is used to map out two different strategic models: genre proximity and cultural proximity. The study finds that homogenization exceeds diversification in the commercials of McDonald’s and KFC as a whole. Comparatively, McDonald’s adopts genre proximity and KFC adopts cultural proximity. The adoption of different models offers a cultural explanation for KFC’s triumph in the competition with McDonald’s in the Chinese fast food market.
Voices in the hills of Rwanda: African press accountability of the 1994 pogrom
Authors: Alozie Emmanuel C.
Published: October 2010

This study attempts to discern the frames that dominated the coverage of the 1994 Rwandan crisis and genocide in Kenya’s Daily Nation and Nigeria’s Guardian, two leading African dailies. The study found that there was a great deal of overlap between the two newspapers with regard to the major frames: bane of a nation, Rwandan national introspection, an(other) African cataclysm, together with world inaction and indifference emerged as the dominant themes. However, there were also differences in coverage. The national/regional interest emerged as a theme in the Daily Nation but did not develop in the coverage by The Guardian. Both papers also went to considerable lengths to explore the background to the crisis and its wider implications.
The Impact of Illusory Fatigue on Executive Control
Authors: Clarkson Joshua J. , Hirt Edward R. , Austin Chapman D. , Jia Lile
Published: October 2010

The human mind is quite adept at modifying and regulating thoughts, judgments, and behaviors. Recent research has demonstrated that depletion of self-regulatory resources can impair executive function through restriction of working memory capacity. The current work explored whether the mere perception of resource depletion (i.e., illusory fatigue) is sufficient to directly produce these deficits in executive control. To manipulate illusory fatigue, participants were exposed to a depleting or nondepleting task before being presented with false feedback about the effects of the initial task on their state of resource depletion. Participants then completed a well-established index of working memory capacity. Findings revealed that individuals provided with feedback that led to perceptions of low depletion exhibited greater working memory capacity. This effect was independent of individuals' actual state of depletion and was furthermore mediated by their perceived level of depletion. Implications for spontaneous resource replenishment are discussed.
Failure mode transition and mechanical properties of similar and dissimilar resistance spot welds of DP600 and low carbon steels
Authors: Pouranvari M. , Marashi S. P. H. , Mousavizadeh S. M.
Published: October 2010

The present work addresses the microstructure and mechanical properties of similar and dissimilar resistance spot welds of low carbon steel (LCS) and dual phase steel (DP600). Correlations between the critical fusion zone size required to ensure pullout failure mode, the weld microstructure and the weld hardness characteristics were developed. Dissimilar DP600/LCS spot welds exhibit the lowest tendency to fail in interfacial failure mode. Effects of weld physical attributes and weld microstructure on the peak load and energy absorption of similar and dissimilar DP600/LCS resistance spot welds are analysed.
Effect of post-weld heat treatment on joint properties of friction welded joint between brass and low carbon steel
Authors: Kimura M. , Kusaka M. , Kaizu K. , Fuji A.
Published: October 2010

This paper describes the effect of post-weld heat treatment (PWHT) on joint properties of copper–zinc alloy (brass) and low carbon steel friction welded joints. The as-welded joint obtained 100% joint efficiency and the brass base metal fracture without cracking at the weld interface, and had no intermetallic compound layer. The joint efficiency with PWHT decreased with increasing heating temperature and its holding time, and its scatter increased with those increasing parameters. When the joint was heat treated at 823 K for 360 ks, it did not achieve 100% joint efficiency and fractured between the weld interface and the brass base metal although it had no intermetallic compound. The cracking at the peripheral portion of the weld interface was generated through PWHT. The cracking was due to the dezincification and the embrittlement of the brass side during PWHT.
Modelling microstructural evolution during multiple pass friction stir welding
Authors: Robson J. D. , Upadhyay P. , Reynolds A. P.
Published: October 2010

The effect of multiple weld passes on the microstructure and properties of friction stir welds in aerospace aluminium alloy AA 7050 has been investigated with the aid of a microstructure model. Each weld pass leads to a reduction in minimum strength in the heat affected zone, the decrease being greatest after the first pass. The model predicts that this is due to partial dissolution and coarsening of the strengthening precipitatates, which up to weld pass 3 is dominated by dissolution, and beyond weld pass 3 by coarsening. Microstructural evolution in the nugget is predicted to involve complete precipitate dissolution during each pass, followed by reprecipitation on the refined grain boundaries. A post-weld aging treatment after multiple passes is predicted not to be effective in improving minimum strength since precipitation occurs via growth and coarsening of existing particles, not nucleation of new precipitates.
Bortezomib resistance in mantle cell lymphoma is associated with plasmacytic differentiation
Authors: Pérez-Galán Patricia , Mora-Jensen Helena , Weniger Marc A. , Shaffer Arthur L. , Rizzatti Edgar G. , Chapman Colby M. , Mo Clifton C. , Stennett Lawrence S. , Rader Christoph , Liu Poching , Raghavachari Nalini , Stetler-Stevenson Maryalice , Yuan Constance , Pittaluga Stefania , Maric Irina , Dunleavy Kieron M. , Wilson Wyndham H. , Staudt Louis M. , Wiestner Adrian
Published: October 2010

Bortezomib induces remissions in 30%-50% of patients with relapsed mantle cell lymphoma (MCL). Conversely, more than half of patients' tumors are intrinsically resistant to bortezomib. The molecular mechanism of resistance has not been defined. We generated a model of bortezomib-adapted subclones of the MCL cell lines JEKO and HBL2 that were 40- to 80-fold less sensitive to bortezomib than the parental cells. Acquisition of bortezomib resistance was gradual and reversible. Bortezomib-adapted subclones showed increased proteasome activity and tolerated lower proteasome capacity than the parental lines. Using gene expression profiling, we discovered that bortezomib resistance was associated with plasmacytic differentiation, including up-regulation of IRF4 and CD38 and expression of CD138. In contrast to plasma cells, plasmacytic MCL cells did not increase immunoglobulin secretion. Intrinsically bortezomib-resistant MCL cell lines and primary tumor cells from MCL patients with inferior clinical response to bortezomib also expressed plasmacytic features. Knockdown of IRF4 was toxic for the subset of MCL cells with plasmacytic differentiation, but only slightly sensitized cells to bortezomib. We conclude that plasmacytic differentiation in the absence of an increased secretory load can enable cells to withstand the stress of proteasome inhibition. Expression of CD38 and IRF4 could serve as markers of bortezomib resistance in MCL. This study has been registered at http://clinicaltrials.gov as NCT00131976.
Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks
Authors: Li Yong , Liu Lili , Bai Xi , Cai Hua , Ji Wei , Guo Dianjing , Zhu Yanming
Published: October 2010

Background

Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discretization has been conducted, in the context of gene regulatory network inference from time series gene expression data.

Results

In this study, we propose a new discretization method "bikmeans", and compare its performance with four other widely-used discretization methods using different datasets, modeling algorithms and number of intervals. Sensitivities, specificities and total accuracies were calculated and statistical analysis was carried out. Bikmeans method always gave high total accuracies.

Conclusions

Our results indicate that proper discretization methods can consistently improve gene regulatory network inference independent of network modeling algorithms and datasets. Our new method, bikmeans, resulted in significant better total accuracies than other methods.
zTrap: zebrafish gene trap and enhancer trap database
Authors: Kawakami Koichi , Abe Gembu , Asada Tokuko , Asakawa Kazuhide , Fukuda Ryuichi , Ito Aki , Lal Pradeep , Mouri Naoko , Muto Akira , Suster Maximilliano L , Takakubo Hitomi , Urasaki Akihiro , Wada Hironori , Yoshida Mikio
Published: October 2010

Background

We have developed genetic methods in zebrafish by using the Tol2 transposable element; namely, transgenesis, gene trapping, enhancer trapping and the Gal4FF-UAS system. Gene trap constructs contain a splice acceptor and the GFP or Gal4FF (a modified version of the yeast Gal4 transcription activator) gene, and enhancer trap constructs contain the zebrafish hsp70l promoter and the GFP or Gal4FF gene. By performing genetic screens using these constructs, we have generated transgenic zebrafish that express GFP and Gal4FF in specific cells, tissues and organs. Gal4FF expression is visualized by creating double transgenic fish carrying a Gal4FF transgene and the GFP reporter gene placed downstream of the Gal4-recognition sequence (UAS). Further, the Gal4FF-expressing cells can be manipulated by mating with UAS effector fish. For instance, when fish expressing Gal4FF in specific neurons are crossed with the UAS:TeTxLC fish carrying the tetanus neurotoxin gene downstream of UAS, the neuronal activities are inhibited in the double transgenic fish. Thus, these transgenic fish are useful to study developmental biology and neurobiology.

Description

To increase the usefulness of the transgenic fish resource, we developed a web-based database named zTrap http://kawakami.lab.nig.ac.jp/ztrap/. The zTrap database contains images of GFP and Gal4FF expression patterns, and genomic DNA sequences surrounding the integration sites of the gene trap and enhancer trap constructs. The integration sites are mapped onto the Ensembl zebrafish genome by in-house Blat analysis and can be viewed on the zTrap and Ensembl genome browsers. Furthermore, zTrap is equipped with the functionality to search these data for expression patterns and genomic loci of interest. zTrap contains the information about transgenic fish including UAS reporter and effector fish.

Conclusion

zTrap is a useful resource to find gene trap and enhancer trap fish lines that express GFP and Gal4FF in desired patterns, and to find insertions of the gene trap and enhancer trap constructs that are located within or near genes of interest. These transgenic fish can be utilized to observe specific cell types during embryogenesis, to manipulate their functions, and to discover novel genes and cis-regulatory elements. Therefore, zTrap should facilitate studies on genomics, developmental biology and neurobiology utilizing the transgenic zebrafish resource.
ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome
Authors: Ling Yi , Du Zhou , Zhang Zhenhai , Su Zhen
Published: October 2010

Background

Maize (Zea mays ssp. mays L.) is an important model for plant basic and applied research. In 2009, the B73 maize genome sequencing made a great step forward, using clone by clone strategy; however, functional annotation and gene classification of the maize genome are still limited. Thus, a well-annotated datasets and informative database will be important for further research discoveries. Signal transduction is a fundamental biological process in living cells, and many protein families participate in this process in sensing, amplifying and responding to various extracellular or internal stimuli. Therefore, it is a good starting point to integrate information on the maize functional genes involved in signal transduction.

Results

Here we introduce a comprehensive database 'ProFITS' (Protein Families Involved in the Transduction of Signalling), which endeavours to identify and classify protein kinases/phosphatases, transcription factors and ubiquitin-proteasome-system related genes in the B73 maize genome. Users can explore gene models, corresponding transcripts and FLcDNAs using the three abovementioned protein hierarchical categories, and visualize them using an AJAX-based genome browser (JBrowse) or Generic Genome Browser (GBrowse). Functional annotations such as GO annotation, protein signatures, protein best-hits in the Arabidopsis and rice genome are provided. In addition, pre-calculated transcription factor binding sites of each gene are generated and mutant information is incorporated into ProFITS. In short, ProFITS provides a user-friendly web interface for studies in signal transduction process in maize.

Conclusion

ProFITS, which utilizes both the B73 maize genome and full length cDNA (FLcDNA) datasets, provides users a comprehensive platform of maize annotation with specific focus on the categorization of families involved in the signal transduction process. ProFITS is designed as a user-friendly web interface and it is valuable for experimental researchers. It is freely available now to all users at http://bioinfo.cau.edu.cn/ProFITS.
Toxicogenomic analysis of exposure to TCDD, PCB126 and PCB153: identification of genomic biomarkers of exposure to AhR ligands
Authors: Ovando Bladimir J , Ellison Corie A , Vezina Chad M , Olson James R
Published: October 2010

Background

Two year cancer bioassays conducted by the National Toxicology Program have shown chronic exposure to dioxin-like compounds (DLCs) to lead to the development of both neoplastic and non-neoplastic lesions in the hepatic tissue of female Sprague Dawley rats. Most, if not all, of the hepatotoxic effects induced by DLC's are believed to involve the binding and activation of the transcription factor, the aryl hydrocarbon receptor (AhR). Toxicogenomics was implemented to identify genomic responses that may be contributing to the development of hepatotoxicity in rats.

Results

Through comparative analysis of time-course microarray data, unique hepatic gene expression signatures were identified for the DLCs, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) (100 ng/kg/day) and 3,3',4,4',5-pentachlorobiphenyl (PCB126) (1000 ng/kg/day) and the non-DLC 2,2',4,4',5,5',-hexachlorobiphenyl (PCB153) (1000 μg/kg/day). A common time independent signature of 41 AhR genomic biomarkers was identified which exhibited at least a 2-fold change in expression following subchronic (13-wk) and chronic (52-wk) p.o. exposure to TCDD and PCB126, but not the non DLC, PCB153. Real time qPCR analysis validated that 30 of these genes also exhibited at least a 2-fold change in hepatic expression at 24 hr following a single exposure to TCDD (5 μg/kg, po). Phenotypic anchoring was conducted which identified forty-six genes that were differently expressed both following chronic p.o. exposure to DLCs and in previously reported studies of cholangiocarcinoma or hepatocellular adenoma.

Conclusions

Together these analyses provide a comprehensive description of the genomic responses which occur in rat hepatic tissue with exposure to AhR ligands and will help to isolate those genomic responses which are contributing to the hepatotoxicity observed with exposure to DLCs. In addition, the time independent gene expression signature of the AhR ligands may assist in identifying other agents with the potential to elicit dioxin-like hepatotoxic responses.
The role of sigma factor RpoH1 in the pH stress response of Sinorhizobium meliloti
Authors: de Lucena Daniella KC , Pühler Alfred , Weidner Stefan
Published: October 2010

Background

Environmental pH stress constitutes a limiting factor for S. meliloti survival and development. The response to acidic pH stress in S. meliloti is versatile and characterized by the differential expression of genes associated with various cellular functions. The purpose of this study was to gain detailed insight into the participation of sigma factors in the complex stress response system of S. meliloti 1021 using pH stress as an effector.

Results

In vitro assessment of S meliloti wild type and sigma factor mutants provided first evidence that the sigma factor RpoH1 plays a major role in the pH stress response. Differential expression of genes related to rhizobactin biosynthesis was observed in microarray analyses performed with the rpoH1 mutant at pH 7.0. The involvement of the sigma factor RpoH1 in the regulation of S. meliloti genes upon pH stress was analyzed by comparing time-course experiments of the wild type and the rpoH1 mutant. Three classes of S. meliloti genes could be identified, which were transcriptionally regulated in an RpoH1-independent, an RpoH1-dependent or in a complex manner. The first class of S. meliloti genes, regulated in an RpoH1-independent manner, comprises the group of the exopolysaccharide I biosynthesis genes and also the group of genes involved in motility and flagellar biosynthesis. The second class of S. meliloti genes, regulated in an RpoH1-dependent manner, is composed of genes known from heat shock studies, like ibpA, grpE and groEL5, as well as genes involved in translation like tufA and rplC. Finally, the third class of S. meliloti genes was regulated in a complex manner, which indicates that besides sigma factor RpoH1, further regulation takes place. This was found to be the case for the genes dctA, ndvA and smc01505.

Conclusions

Clustering of time-course microarray data of S. meliloti wild type and sigma factor rpoH1 mutant allowed for the identification of gene clusters, each with a unique time-dependent expression pattern, as well as for the classification of genes according to their dependence on RpoH1 expression and regulation. This study provided clear evidence that the sigma factor RpoH1 plays a major role in pH stress response.
Evaluation of the endoplasmic reticulum-stress response in eIF2B-mutated lymphocytes and lymphoblasts from CACH/VWM patients
Authors: Horzinski Laetitia , Kantor Liraz , Huyghe Aurélia , Schiffmann Raphael , Elroy-Stein Orna , Boespflug-Tanguy Odile , Fogli Anne
Published: October 2010

Background

Eukaryotic translation initiation factor 2B (eIF2B), a guanine nucleotide exchange factor (GEF) and a key regulator of translation initiation under normal and stress conditions, causes an autosomal recessive leukodystrophy of a wide clinical spectrum. EBV-immortalised lymphocytes (EIL) from eIF2B-mutated patients exhibit a decrease in eIF2B GEF activity. eIF2B-mutated primary fibroblasts have a hyper-induction of activating transcription factor 4 (ATF4) which is involved in the protective unfolded protein response (UPR), also known as the ER-stress response. We tested the hypothesis that EIL from eIF2B-mutated patients also exhibit a heightened ER-stress response.

Methods

We used thapsigargin as an ER-stress agent and looked at polysomal profiles, rate of protein synthesis, translational activation of ATF4, and transcriptional induction of stress-specific mRNAs (ATF4, CHOP, ASNS, GRP78) in normal and eIF2B-mutated EIL. We also compared the level of stress-specific mRNAs between EIL and primary lymphocytes (PL).

Results

Despite the low eIF2B GEF activity in the 12 eIF2B-mutated EIL cell lines tested (range 40-70% of normal), these cell lines did not differ from normal EIL in their ATF4-mediated ER-stress response. The absence of hyper-induction of ATF4-mediated ER-stress response in eIF2B-mutated EIL in contrast to primary fibroblasts is not related to their transformation by EBV. Indeed, PL exhibited a higher induction of the stress-specific mRNAs in comparison to EIL, but no hyper-induction of the UPR was noticed in the eIF2B-mutated cell lines in comparison to controls.

Conclusions

Taken together with work of others, our results demonstrate the absence of a major difference in ER-stress response between controls and eIF2B-mutated cells. Therefore, components of the ER-stress response cannot be used as discriminantory markers in eIF2B-related disorders.
Oxidative stress in skin fibroblasts cultures from patients with Parkinson's disease
Authors: del Hoyo Pilar , García-Redondo Alberto , de Bustos Fernando , Molina José Antonio , Sayed Youssef , Alonso-Navarro Hortensia , Caballero Luis , Arenas Joaquín , Agúndez José AG , Jiménez-Jiménez Félix Javier
Published: October 2010

Background

In the substantia nigra of Parkinson's disease (PD) patients, increased lipid peroxidation, decreased activities of the mitochondrial complex I of the respiratory chain, catalase and glutathione-peroxidase, and decreased levels of reduced glutathione have been reported. These observations suggest that oxidative stress and mitochondrial dysfunction play a role in the neurodegeneration in PD. We assessed enzymatic activities of respiratory chain and other enzymes involved in oxidative processes in skin fibroblasts cultures of patients with PD.

Methods

We studied respiratory chain enzyme activities, activities of total, Cu/Zn- and Mn-superoxide-dismutase, gluthatione-peroxidase and catalase, and coenzyme Q10 levels in skin fibroblasts cultures from 20 Parkinson's disease (PD) patients and 19 age- and sex- matched healthy controls.

Results

When compared with controls, PD patients showed significantly lower specific activities for complex V (both corrected by citrate synthase activity and protein concentrations). Oxidized, reduced and total coenzyme Q10 levels (both corrected by citrate synthase and protein concentrations), and activities of total, Cu/Zn- and Mn-superoxide-dismutase, gluthatione-peroxidase and catalase, did not differ significantly between PD-patients and control groups. Values for enzyme activities in the PD group did not correlate with age at onset, duration, scores of the Unified Parkinson's Disease Rating scales and Hoehn-Yahr staging.

Conclusions

The main result of this study was the decreased activity of complex V in PD patients. This complex synthesizes ATP from ADP using an electrochemical gradient generated by complexes I-IV. These results suggest decreased energetic metabolism in fibroblasts of patients with PD.
Comparison of thymidine phosphorylase expression and prognostic factors in gallbladder and bile duct cancer
Authors: Won Hye Sung , Lee Myung Ah , Chung Eun-Seon , Kim Dong-Goo , You Young Kyoung , Hong Tae Ho , Lee In-Seok
Published: October 2010

Background

Biliary tract cancers have limitations in information about different location-related pathogenesis and clinico-pathological characteristics. The goal of this study was to investigate anatomical site-related similarities and differences in biliary tract cancers and to assess the expression and clinical significance of functional proteins such as p53, cyclin D1, survivin, thymidine phosphorylase, and ERCC1.

Methods

One hundred and sixty-one patients with biliary tract adenocarcinomas, who underwent curative or palliative surgery in a single institution between October 1994 and December 2003 were evaluated, retrospectively. The level of protein expression of p53, cyclin D1, survivin, thymidine phosphorylase, and ERCC1 was assessed by immunohistochemistry.

Results

With respect to clinico-pathological characteristics, gallbladder cancer was more frequent in women, and bile duct cancer was more common in men. Perineural invasion was more common in bile duct cancer. Recurrence as a distant metastasis was more common in gallbladder cancer. Immunohistochemical analysis revealed that thymidine phosphorylase expression was significantly higher in gallbladder cancer than in bile duct cancer. Positive thymidine phosphorylase and p53 staining were associated with an advanced stage. Differentiation, vascular invasion, perineural invasion, lymphatic invasion, lymph node metastasis, and TNM stage independently predicted poor prognosis in biliary tract cancer. These correlations were seen more clearly in gallbladder cancer. The immunohistochemical staining patterns of p53, cyclin D1, survivin, thymidine phosphorylase, and ERCC1 showed no prognostic significance in biliary tract cancers.

Conclusions

We concluded that gallbladder and bile duct cancers are considered to be separate diseases with different clinico-pathological characteristics and prognostic factors. In addition, we hypothesize that high expression of thymidine phosphorylase by gallbladder cancer results in a higher response rate to capecitabine by gallbladder cancer than bile duct cancer.
Use of complementary and alternative medicine by those with a chronic disease and the general population - results of a national population based survey
Authors: Metcalfe Amy , Williams Jeanne , McChesney Jane , Patten Scott B , Jetté Nathalie
Published: October 2010

Background

The use of complementary and alternative medicine (CAM) is becoming more common, but population-based descriptions of its patterns of use are lacking. This study aimed to determine the prevalence of CAM use in the general population and for those with asthma, diabetes, epilepsy and migraine.

Methods

Data from cycles 1.1, 2.1 and 3.1 of the Canadian Community Health Survey (CCHS) were used for the study. The CCHS is a national cross-sectional survey administered to 400,055 Canadians aged ≥12 between 2001-2005. Self-reported information about professionally diagnosed health conditions was elicited. CCHS surveys use a multistage stratified cluster design to randomly select a representative sample of Canadian household residents. Descriptive data on the utilization of CAM services was calculated and logistic regression was used to determine what sociodemographic factors predict CAM use.

Results

Weighted estimates show that 12.4% (95% Confidence Interval (CI): 12.2-12.5) of Canadians visited a CAM practitioner in the year they were surveyed; this rate was significantly higher for those with asthma 15.1% (95% CI: 14.5-15.7) and migraine 19.0% (95% CI: 18.4-19.6), and significantly lower for those with diabetes 8.0% (95% CI: 7.4-8.6) while the rate in those with epilepsy (10.3%, 95% CI: 8.4-12.2) was not significantly different from the general population.

Conclusion

A large proportion of Canadians use CAM services. Physicians should be aware that their patients may be accessing other services and should be prepared to ask and answer questions about the risks and benefits of CAM services in conjunction with standard medical care.
PPARgamma activation attenuates T-lymphocyte-dependent inflammation of adipose tissue and development of insulin resistance in obese mice
Authors: Foryst-Ludwig Anna , Hartge Martin , Clemenz Markus , Sprang Christiane , Heß Katharina , Marx Nikolaus , Unger Thomas , Kintscher Ulrich
Published: October 2010

Background

Inflammation of adipose tissue (AT) has been recently accepted as a first step towards obesity-mediated insulin resistance. We could previously show that mice fed with high fat diet (HFD) develop systemic insulin resistance (IR) and glucose intolerance (GI) associated with CD4-positive T-lymphocyte infiltration into visceral AT. These T-lymphocytes, when enriched in AT, participate in the development of fat tissue inflammation and subsequent recruitment of proinflammatory macrophages. The aim of this work was to elucidate the action of the insulin sensitizing PPARgamma on T-lymphocyte infiltration during development of IR, and comparison of the PPARgamma-mediated anti-inflammatory effects of rosiglitazone and telmisartan in diet-induced obesity model (DIO-model) in mice.

Methods

In order to investigate the molecular mechanisms underlying early development of systemic insulin resistance and glucose intolerance male C57BL/6J mice were fed with high fat diet (HFD) for 10-weeks in parallel to the pharmacological intervention with rosiglitazone, telmisartan, or vehicle.

Results

Both rosiglitazone and telmisartan were able to reduce T-lymphocyte infiltration into AT analyzed by quantitative analysis of the T-cell marker CD3gamma and the chemokine SDF1alpha. Subsequently, both PPARgamma agonists were able to attenuate macrophage infiltration into AT, measured by the reduction of MCP1 and F4/80 expression. In parallel to the reduction of AT-inflammation, ligand-activated PPARgamma improved diet-induced IR and GI.

Conclusion

Together the present study demonstrates a close connection between PPARgamma-mediated anti-inflammation in AT and systemic improvement of glucose metabolism identifying T-lymphocytes as one cellular mediator of PPARgamma´s action.
Urine alkalization facilitates uric acid excretion
Authors: Kanbara Aya , Hakoda Masayuki , Seyama Issei
Published: October 2010

Background

Increase in the incidence of hyperuricemia associated with gout as well as hypertension, renal diseases and cardiovascular diseases has been a public health concern. We examined the possibility of facilitated excretion of uric acid by change in urine pH by managing food materials.

Methods

Within the framework of the Japanese government's health promotion program, we made recipes which consist of protein-rich and less vegetable-fruit food materials for H+-load (acid diet) and others composed of less protein but vegetable-fruit rich food materials (alkali diet). Healthy female students were enrolled in this consecutive 5-day study for each test. From whole-day collected urine, total volume, pH, organic acid, creatinine, uric acid and all cations (Na+,K+,Ca2+,Mg2+,NH4
+) and anions (Cl-,SO4
2-,PO4
-) necessary for the estimation of acid-base balance were measured.

Results

Urine pH reached a steady state 3 days after switching from ordinary daily diets to specified regimens. The amount of acid generated ([SO4
2-] +organic acid-gut alkai) were linearly related with those of the excretion of acid (titratable acidity+ [NH4
+] - [HCO3
-]), indicating that H+ in urine is generated by the metabolic degradation of food materials. Uric acid and excreted urine pH retained a linear relationship, where uric acid excretion increased from 302 mg/day at pH 5.9 to 413 mg/day at pH 6.5, despite the fact that the alkali diet contained a smaller purine load than the acid diet.

Conclusion

We conclude that alkalization of urine by eating nutritionally well-designed food is effective for removing uric acid from the body.